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b/_sources/collaboration.md.txt @@ -0,0 +1,13 @@ +(collaboration)= + +# Collaborative version control and code review + +```{toctree} +:maxdepth: 1 + +collaboration/concepts.md +collaboration/same-repository.md +collaboration/code-review.md +collaboration/forking-workflow.md +collaboration/demo-discussion.md +``` diff --git a/_sources/collaboration/code-review.md.txt b/_sources/collaboration/code-review.md.txt new file mode 100644 index 0000000..4a55b03 --- /dev/null +++ b/_sources/collaboration/code-review.md.txt @@ -0,0 +1,144 @@ +(code-review)= + +# Practicing code review + +In this episode we will practice the code review process. We will learn how to +ask for changes in a pull request, how to suggest a change in a pull request, +and how to modify a pull request. + +This will enable research groups to work more collaboratively and to not only +improve the code quality but also to learn from each other. + + +## Exercise + +:::{prereq} Exercise preparation +We can continue in the same exercise repository which we have used in the +previous episode. +::: + +:::{exercise} Exercise: Practicing code review (25 min) + +**Technical requirements**: +- If you create the commits locally: [Being able to authenticate to GitHub](https://coderefinery.github.io/installation/ssh/) + +**What is familiar** from previous lessons: +- Creating a branch. +- Committing a change on the new branch. +- Opening and merging pull requests. + +**What will be new** in this exercise: +- As a reviewer, we will learn how to ask for changes in a pull request. +- As a reviewer, we will learn how to suggest a change in a pull request. +- As a submitter, we will learn how to modify a pull request without closing + the incomplete one and opening a new one. + +**Exercise tasks**: +1. Create a new branch and one or few commits: in these improve something but also + deliberately introduce a typo and also a larger mistake which we will want to fix during the code review. +1. Open a pull request towards the main branch. +1. As a reviewer to somebody else's pull request, ask for an improvement and + also directly suggest a change for the small typo. (Hint: + suggestions are possible through the GitHub web interface, view of + a pull request, "Files changed" view, after selecting some lines. + Look for the "±" button.) +1. As the submitter, learn how to accept the suggested change. (Hint: + GitHub web interface, "Files Changed" view.) +1. As the submitter, improve the pull request without having to close and open + a new one: by adding a new commit to the same branch. (Hint: push + to the branch again.) +1. Once the changes are addressed, merge the pull request. +::: + + +## Help and discussion + +From here on out, we don't give detailed steps to the solution. You +need to combine what you know, and the extra info below, in order to +solve the above. + +### How to ask for changes in a pull request + +Technically, there are at least two common ways to ask for changes in a pull +request. + +Either in the comment field of the pull request: +:::{figure} img/code-review/comment.png +:width: 60% +:class: with-border +:alt: Screenshot of a pull request comment field +:::: + +Or by using the "Review changes": +:::{figure} img/code-review/files-changed.png +:width: 100% +:class: with-border +:alt: Screenshot of a pull request navigating to the "Review changes" tab +:::: + +And always please be kind and constructive in your comments. Remember that the +goal is not gate-keeping but **collaborative learning**. + + +### How to suggest a change in a pull request as a reviewer + +If you see a very small problem that is easy to fix, you can suggest a change +as a reviewer. + +Instead of asking the submitter to tiny problem, you can suggest a change by +clicking on the plus sign next to the line number in the "Files changed" tab: +:::{figure} img/code-review/leave-comment.png +:width: 100% +:class: with-border +:alt: Screenshot of leaving a comment to a line in a pull request +:::: + +Here you can comment on specific lines or even line ranges. + +But now the interesting part is to click on the "Add a suggestion" symbol (the +one that looks like plus and minus). Now you can fix the tiny problem (in this +case a typo) and then click on the "Add single comment" button: +:::{figure} img/code-review/add-suggestion.png +:width: 60% +:class: with-border +:alt: Sequence of clicks to add a suggestion to a line in a pull request +:::: + +The result is this and the submitter can accept the change with a single click: +:::{figure} img/code-review/commit-suggestion.png +:width: 60% +:class: with-border +:alt: Screenshot of a pull request with a suggested change +:::: + +After accepting with "Commit suggestion", the improvement gets added to the +pull request. + + +### How to modify a pull request to address the review comments + +If the reviewer asks for changes, it is not necessary to close the pull request +and later open a new one. It can even be counter-productive to do so: This can +fragment the discussion and the history of the pull request and can make it +harder to understand the context of the changes. + +A much better mechanism to recognize that pull requests are not implemented +from a specific commit to a specific branch, but **always from a branch to a +branch**. + +This means that you can make amendments to the pull request by adding new +commits to the same source branch. This way the pull request will be updated +automatically and the reviewer can see the new changes and comment on them. + +The fact that pull requests are from branch to branch also strongly suggests +that it is a good practice to create a new branch for each pull request. +Otherwise you could accidentally modify an open pull request by adding new +commits to the source branch. + + +## Summary + +- Our process isn't just about code now. It's about discussion and + working together to make the whole process better. +- GitHub discussions and reviewing are quite powerful and can make + small changes easy. diff --git a/_sources/collaboration/concepts.md.txt b/_sources/collaboration/concepts.md.txt new file mode 100644 index 0000000..c0a7d27 --- /dev/null +++ b/_sources/collaboration/concepts.md.txt @@ -0,0 +1,69 @@ +(concepts)= + +# Concepts around collaboration + +```{objectives} +- Be able to decide whether to divide work at the branch level or at the repository level. +``` + + +## Commits, branches, repositories, forks, clones + +- **repository**: The project, contains all data and history (commits, branches, tags). +- **commit**: Snapshot of the project, gets a unique identifier (e.g. `c7f0e8bfc718be04525847fc7ac237f470add76e`). +- **branch**: Independent development line. The main development line is often called `main`. +- **tag**: A pointer to one commit, to be able to refer to it later. Like a [commemorative plaque](https://en.wikipedia.org/wiki/Commemorative_plaque) + that you attach to a particular commit (e.g. `phd-printed` or `paper-submitted`). +- **cloning**: Copying the whole repository to your laptop - the first time. It is not necessary to download each file one by one. +- **forking**: Taking a copy of a repository (which is typically not yours) - your + copy (fork) stays on GitHub/GitLab and you can make changes to your copy. + + +## Cloning a repository + +In order to make a complete copy a whole repository, the `git clone` command +can be used. When cloning, all the files, of all or selected branches, of a +repository are copied in one operation. Cloning of a repository is of relevance +in a few different situations: +* Working on your own, cloning is the operation that you can use to create + multiple instances of a repository on, for instance, a personal computer, a + server, and a supercomputer. +* The parent repository could be a repository that you or your colleague own. A + common use case for cloning is when working together within a smaller team + where everyone has read and write access to the same git repository. +* Alternatively, cloning can be made from a public repository of a code that + you would like to use. Perhaps you have no intention to work on the code, but + would like to stay in tune with the latest developments, also in-between + releases of new versions of the code. + + +```{figure} img/overview/forkandclone.png +:alt: Forking and cloning +:width: 100% +:class: with-border + +Forking and cloning +``` + + +## Forking a repository + +When a fork is made on GitHub/GitLab a complete copy, of all or selected +branches, of the repository is made. The copy will reside under a different +account on GitHub/GitLab. Forking of a repository is of high relevance when +working with a git repository to which you do not have write access. +* In the fork repository commits can be made to the base branch (`main` or + `master`), and to other branches. +* The commits that are made within the branches of the fork repository can be + contributed back to the parent repository by means of pull or merge requests. + + +## Synchronizing changes between repositories + +- We need a mechanism to communicate changes between the repositories. +- We will **pull** or **fetch** updates **from** remote repositories (we will soon discuss the difference between pull and fetch). +- We will **push** updates **to** remote repositories. +- We will learn how to suggest changes within repositories on GitHub and across repositories (**pull request**). +- Repositories that are forked or cloned do not automatically synchronize themselves: + We will learn how to update forks (by pulling from the "central" repository). +- A main difference between cloning a repository and forking a repository is that the former is a general operation for generating copies of a repository to different computers, whereas forking is a particular operation implemented on GitHub/GitLab. diff --git a/_sources/collaboration/demo-discussion.md.txt b/_sources/collaboration/demo-discussion.md.txt new file mode 100644 index 0000000..d6b4f28 --- /dev/null +++ b/_sources/collaboration/demo-discussion.md.txt @@ -0,0 +1,5 @@ +(collaboration-demo-discussion)= + +# Conclict resolution, rebasing, and organizational strategies + +(40 min demo and discussion) diff --git a/_sources/collaboration/forking-workflow.md.txt b/_sources/collaboration/forking-workflow.md.txt new file mode 100644 index 0000000..f8c254d --- /dev/null +++ b/_sources/collaboration/forking-workflow.md.txt @@ -0,0 +1,223 @@ +(forking-workflow)= + +# How to contribute changes to repositories that belong to others + +In this episode we prepare you to suggest and contribute changes to +repositories that belong to others. These might be open source projects that +you use in your work. + +We will see how Git and services like GitHub or GitLab can be used to suggest +modification without having to ask for write access to the repository and +accept modifications without having to grant write access to others. + + +## Exercise + +:::{prereq} Exercise preparation +- The exercise repository is now different: + (note the `-forking-exercise`). +- First **fork** the exercise repository to your GitHub account. +- Then **clone your fork** to your computer (if you wish to work locally). +- Double-check that you have forked the correct repository. +::: + +:::{exercise} Exercise: Collaborating within the same repository (25 min) + +**Technical requirements**: +- If you create the commits locally: [Being able to authenticate to GitHub](https://coderefinery.github.io/installation/ssh/) + +**What is familiar** from previous lessons: +- Forking a repository. +- Creating a branch. +- Committing a change on the new branch. +- Opening and merging pull requests. + +**What will be new** in this exercise: +- Opening a pull request towards the upstream repository. +- Pull requests can be coupled with automated testing. +- Learning that your fork can get out of date. +- After the pull requests are merged, updating your fork with the changes. +- Learn how to approach other people's repositories with ideas, changes, and requests. + +**Exercise tasks**: +1. Open an issue in the upstream exercise repository where you describe the + change you want to make. Take note of the issue number. +1. Create a new branch in your fork of the repository. +1. Make a change to the recipe book on the new branch and in the commit cross-reference the issue you opened. + See the walk-through below for how to do this. +1. Open a pull request towards the upstream repository. +1. The instructor will review and merge the pull requests. + During the review, pay attention to the automated test step (here for + demonstration purposes, we test whether the recipe contains an ingredients + and an instructions sections). +1. After few pull requests are merged, update your fork with the changes. +1. Check that in your fork you can see changes from other people's pull requests. +::: + + +## Help and discussion + + +### Help! I don't have permissions to push my local changes + +Maybe you see an error like this one: +```text +Please make sure you have the correct access rights +and the repository exists. +``` + +Or like this one: +```text +failed to push some refs to workshop-material/recipe-book-forking-exercise.git +``` + +In this case you probably try to push the changes not to your fork but to the original repository +and in this exercise you do not have write access to the original repository. + +The simpler solution is to clone again but this time your fork. + +:::{solution} Recovery + +But if you want to keep your local changes, you can change the remote URL to point to your fork. +Check where your remote points to with `git remote --verbose`. + +It should look like this (replace `USER` with your GitHub username): +```console +$ git remote --verbose + +origin git@github.com:USER/recipe-book-forking-exercise.git (fetch) +origin git@github.com:USER/recipe-book-forking-exercise.git (push) +``` + +It should **not** look like this: +```console +$ git remote --verbose + +origin git@github.com:workshop-material/recipe-book-forking-exercise.git (fetch) +origin git@github.com:workshop-material/recipe-book-forking-exercise.git (push) +``` + +In this case you can adjust "origin" to point to your fork with: +```console +$ git remote set-url origin git@github.com:USER/recipe-book-forking-exercise.git +``` +::: + + +### Opening a pull request towards the upstream repository + +We have learned in the previous episode that pull requests are always from +branch to branch. But the branch can be in a different repository. + +When you open a pull request in a fork, by default GitHub will suggest to +direct it towards the default branch of the upstream repository. + +This can be changed and it should always be verified, but in this case this is +exactly what we want to do, from fork towards upstream: +:::{figure} img/forking-workflow/pull-request-form.png +:width: 100% +:class: with-border +:alt: Screenshot of a pull request from fork towards upstream +:::: + + +### Pull requests can be coupled with automated testing + +We added an automated test here just for fun and so that you see that this is +possible to do. + +In this exercise, the test is silly. It will check whether the recipe contains +both an ingredients and an instructions section. + +In this example the test failed: +:::{figure} img/forking-workflow/all-checks-failed.png +:width: 60% +:class: with-border +:alt: Screenshot of a failed test in a pull request +:::: + +Click on the "Details" link to see the details of the failed test: +:::{figure} img/forking-workflow/check-details.png +:width: 60% +:class: with-border +:alt: Screenshot of details why the test failed +:::: + +**How can this be useful?** +- The project can define what kind of tests are expected to pass before a pull + request can be merged. +- The reviewer can see the results of the tests, without having to run them + locally. + +**How does it work?** +- We added a GitHub Actions workflow + to automatically run on each push or pull request towards the `main` branch. + +What tests or steps can you image for your project to run automatically with +each pull request? + + +### How to update your fork with changes from upstream + +This used to be difficult but now it is two mouse clicks. + +Navigate to your fork and notice how GitHub tells you that your fork is behind. +In my case, it is 9 commits behind upstream. To fix this, click on "Sync fork" +and then "Update branch": +:::{figure} img/forking-workflow/sync-fork.png +:width: 80% +:class: with-border +:alt: Screenshot on GitHub fork page showing that the fork is behind +:::: + +After the update my "branch is up to date" with the upstream repository: +:::{figure} img/forking-workflow/fork-after-update.png +:width: 80% +:class: with-border +:alt: Screenshot on GitHub after fork has been updated +:::: + + +### How to approach other people’s repositories with ideas, changes, and requests + +**Contributing very minor changes** +- Clone or fork+clone repository +- Create a branch +- Commit and push change +- Open a pull request or merge request + +**If you observe an issue and have an idea how to fix it** +- Open an issue in the repository you wish to contribute to +- Describe the problem +- If you have a suggestion on how to fix it, describe your suggestion +- Possibly **discuss and get feedback** +- If you are working on the fix, indicate it in the issue so that others know that somebody is working on it and who is working on it +- Submit your fix as pull request or merge request which references/closes the issue + +:::{admonition} Motivation +- **Inform others about an observed problem** +- Make it clear whether this issue is up for grabs or already being worked on +::: + +**If you have an idea for a new feature** +- Open an issue in the repository you wish to contribute to +- In the issue, write a short proposal for your suggested change or new feature +- Motivate why and how you wish to do this +- Also indicate where you are unsure and where you would like feedback +- **Discuss and get feedback before you code** +- Once you start coding, indicate that you are working on it +- Once you are done, submit your new feature as pull request or merge request which references/closes the issue/proposal + +:::{admonition} Motivation +- **Get agreement and feedback before writing 5000 lines of code** which might be rejected +- If we later wonder why something was done, we have the issue/proposal as + reference and can read up on the reasoning behind a code change +::: + + +## Summary + +- This forking workflow lets you propose changes to repositories for + which **you have no write access**. +- This is the way that much modern open-source software works. +- You can now contribute to any project you can view. diff --git a/_sources/collaboration/same-repository.md.txt b/_sources/collaboration/same-repository.md.txt new file mode 100644 index 0000000..1a69d1d --- /dev/null +++ b/_sources/collaboration/same-repository.md.txt @@ -0,0 +1,280 @@ +(same-repository)= + +# Collaborating within the same repository + +In this episode, we will learn how to collaborate within the same repository. +We will learn how to cross-reference issues and pull requests, how to review +pull requests, and how to use draft pull requests. + +This exercise will form a good basis for collaboration that is suitable for +most research groups. + +:::{note} +When you read or hear **pull request**, please think of a **change proposal**. +::: + + +## Exercise + +In this exercise, we will contribute to a repository via a **pull request**. +This means that you propose some change, and then it is accepted (or not). + +::::::{prereq} Exercise preparation + +- **First we need to get access** to the [exercise repository](https://github.com/workshop-material/recipe-book) to which we will + contribute. + - Instructor collects GitHub usernames from learners and adds them as collaborators to the exercise repository + (Settings -> Collaborators and teams -> Manage access -> Add people). + +- **Don't forget to accept the invitation** + - Check + - Alternatively check the inbox for the email account you registered with + GitHub. GitHub emails you an invitation link, but if you don't receive it + you can go to your GitHub notifications in the top right corner. The + maintainer can also "copy invite link" and share it within the group. + +- **Watching and unwatching repositories** + - Now that you are a collaborator, you get notified about new issues and pull + requests via email. + - If you do not wish this, you can "unwatch" a repository (top of + the project page). + - However, we recommend watching repositories you are interested + in. You can learn things from experts just by watching the + activity that come through a popular project. + :::{figure} img/unwatch.png + :alt: Unwatching a repository + + Unwatch a repository by clicking "Unwatch" in the repository view, + then "Participating and @mentions" - this way, you will get + notifications about your own interactions. + ::: +:::::: + +:::{exercise} Exercise: Collaborating within the same repository (25 min) + +**Technical requirements** (from installation instructions): +- If you create the commits locally: [Being able to authenticate to GitHub](https://coderefinery.github.io/installation/ssh/) + +**What is familiar** from the previous workshop day (not repeated here): +- Cloning a repository. +- Creating a branch. +- Committing a change on the new branch. +- Submit a pull request towards the main branch. + +**What will be new** in this exercise: +- If you create the changes locally, you will need to **push** them to the remote repository. +- Learning what a protected branch is and how to modify a protected branch: using a pull request. +- Cross-referencing issues and pull requests. +- Practice to review a pull request. +- Learn about the value of draft pull requests. + +**Exercise tasks**: +1. Start in the [exercise + repository](https://github.com/workshop-material/recipe-book) and open an + issue where you describe the change you want to make. Note down the issue + number since you will need it later. +1. Create a new branch. +1. Make a change to the recipe book on the new branch and in the commit + cross-reference the issue you opened (see the walk-through below + for how to do that). +1. Push your new branch (with the new commit) to the repository you + are working on. +1. Open a pull request towards the main branch. +1. Review somebody else's pull request and give constructive feedback. Merge their pull request. +1. Try to create a new branch with some half-finished work and open a draft + pull request. Verify that the draft pull request cannot be merged since it + is not meant to be merged yet. +::: + + +## Solution and hints + +### (1) Opening an issue + +This is done through the GitHub web interface. For example, you could +give the name of the recipe you want to add (so that others don't add +the same one). It is the "Issues" tab. + + +### (2) Create a new branch. + +If on GitHub, you can make the branch in the web interface. + + +### (3) Make a change adding the recipe + +Add a new file with the recipe in it. Commit the file. In the commit +message, include the note about the issue number, saying that this +will close that issue. + + +#### Cross-referencing issues and pull requests + +Each issue and each pull request gets a number and you can cross-reference them. + +When you open an issue, note down the issue number (in this case it is `#2`): +:::{figure} img/same-repository/issue-number.png +:width: 60% +:class: with-border +:alt: Each issue gets a number +::: + +You can reference this issue number in a commit message or in a pull request, like in this +commit message: +```text +this is the new recipe; fixes #2 +``` + +If you forget to do that in your commit message, you can also reference the issue +in the pull request description. And instead of `fixes` you can also use `closes` or `resolves` +or `fix` or `close` or `resolve` (case insensitive). + +Here are all the keywords that GitHub recognizes: + + +Then observe what happens in the issue once your commit gets merged: it will +automatically close the issue and create a link between the issue and the +commit. This is very useful for tracking what changes were made in response to +which issue and to know from when until when precisely the issue was open. + + +### (4) Push to GitHub as a new branch + +Push the branch to the repository. You should end up with a branch +visible in the GitHub web view. + +This is only necessary if you created the changes locally. If you created the +changes directly on GitHub, you can skip this step. + +:::::{tabs} +::::{group-tab} VS Code +In VS Code, you can "publish the branch" to the remote repository by clicking +the cloud icon in the bottom left corner of the window: +:::{figure} img/same-repository/vscode-publish-branch.png +:width: 60% +:class: with-border +:alt: Publishing a branch in VS Code +::: +:::: + +::::{group-tab} Command line +If you have a local branch `my-branch` and you want to push it to the remote +and make it visible there, first verify what your remote is: +```console +$ git remote --verbose + +origin git@github.com:USER/recipe-book.git (fetch) +origin git@github.com:USER/recipe-book.git (push) +``` + +In this case the remote is called `origin` and refers to the address +git@github.com:USER/recipe-book.git. Both can be used +interchangeably. Make sure it points to the right repository, ideally a +repository that you can write to. + +Now that you have a remote, you can push your branch to it: +```console +$ git push origin my-branch +``` +This will create a new branch on the remote repository with the same name as +your local branch. + +You can also do this: +```console +$ git push --set-upstream origin my-branch +``` +This will connect the local branch and the remote branch so that in the future +you can just type `git push` and `git pull` without specifying the branch name +(but this depends on your Git configuration). + + +**Troubleshooting** + +If you don't have a remote yet, you can add it with (adjust `ADDRESS` to your repository address): +```console +$ git remote add origin ADDRESS +``` + +ADDRESS is the part that you copy from here: +:::{figure} img/same-repository/clone-address.png +:width: 60% +:class: with-border +:alt: Copying the clone address from GitHub +::: + +If the remote points to the wrong place, you can change it with: +```console +$ git remote set-url origin NEWADDRESS +``` +:::: +::::: + + +### (5) Open a pull request towards the main branch + +This is done through the GitHub web interface. + + +### (6) Reviewing pull requests + +You review through the GitHub web interface. + +Checklist for reviewing a pull request: +- Be kind, on the other side is a human who has put effort into this. +- Be constructive: if you see a problem, suggest a solution. +- Towards which branch is this directed? +- Is the title descriptive? +- Is the description informative? +- Scroll down to see commits. +- Scroll down to see the changes. +- If you get incredibly many changes, also consider the license or copyright + and ask where all that code is coming from. +- Again, be kind and constructive. +- Later we will learn how to suggest changes directly in the pull request. + +If someone is new, it's often nice to say something encouraging in the +comments before merging (even if it's just "thanks"). If all is good +and there's not much else to say, you could merge directly. + + +### (7) Draft pull requests + +Try to create a draft pull request: +:::{figure} img/same-repository/draft-pr.png +:width: 60% +:class: with-border +:alt: Creating a draft pull request +:::: + +Verify that the draft pull request cannot be merged until it is marked as ready +for review: +:::{figure} img/same-repository/draft-pr-wip.png +:width: 60% +:class: with-border +:alt: Draft pull request cannot be merged +:::: + +Draft pull requests can be useful for: +- **Feedback**: You can open a pull request early to get feedback on your work without + signaling that it is ready to merge. +- **Information**: They can help communicating to others that a change is coming up and in + progress. + + +### What is a protected branch? And how to modify it? + +A protected branch on GitHub or GitLab is a branch that cannot (accidentally) +deleted or force-pushed to. It is also possible to require that a branch cannot +be directly pushed to or modified, but that changes must be submitted via a +pull request. + +To protect a branch in your own repository, go to "Settings" -> "Branches". + + + +### Summary + +- We used all the same pieces that we've learned previously. +- But we successfully contributed to a collaborative project! +- The pull request allowed us to contribute without changing directly: + this is very good when it's not mainly our project. diff --git a/_sources/credit.md.txt b/_sources/credit.md.txt new file mode 100644 index 0000000..9639997 --- /dev/null +++ b/_sources/credit.md.txt @@ -0,0 +1,10 @@ +# Credit + +The following material (all CC-BY) was reused to create this workshop material: +- +- +- +- +- + +(I will also summarize what changes have been made to the original material) diff --git a/_sources/documentation.md.txt b/_sources/documentation.md.txt new file mode 100644 index 0000000..571c5c3 --- /dev/null +++ b/_sources/documentation.md.txt @@ -0,0 +1,384 @@ +(documentation)= + +# Code documentation + +:::{objectives} +- Discuss what makes good documentation. +- Improve the README of your project or our example project. +- Explore Sphinx which is a popular tool to build documentation websites. +- Learn how to leverage GitHub Actions and GitHub Pages to build and deploy documentation. +::: + +:::{instructor-note} +- (30 min) Discussion +- (30 min) Exercise: Set up a Sphinx documentation and add API documentation +- (15 min) Demo: Building documentation with GitHub Actions +::: + + +## Why? 💗✉️ to your future self + +- You will probably use your code in the future and may forget details. +- You may want others to use your code or contribute + (almost impossible without documentation). + + +## In-code documentation + +Not very useful (more commentary than comment): +```python +# now we check if temperature is below -50 +if temperature < -50: + print("ERROR: temperature is too low") +``` + +More useful (explaining **why**): +```python +# we regard temperatures below -50 degrees as measurement errors +if temperature < -50: + print("ERROR: temperature is too low") +``` + +Keeping zombie code "just in case" (rather use version control): +```python +# do not run this code! +# if temperature > 0: +# print("It is warm") +``` + +Emulating version control: +```python +# John Doe: threshold changed from 0 to 15 on August 5, 2013 +if temperature > 15: + print("It is warm") +``` + + +## Many languages allow "docstrings" + +Example (Python): +```python +def kelvin_to_celsius(temp_k: float) -> float: + """ + Converts temperature in Kelvin to Celsius. + + Parameters + ---------- + temp_k : float + temperature in Kelvin + + Returns + ------- + temp_c : float + temperature in Celsius + """ + assert temp_k >= 0.0, "ERROR: negative T_K" + + temp_c = temp_k - 273.15 + + return temp_c +``` + +:::{keypoints} +- Documentation which is only in the source code is not enough. +- Often a README is enough. +- Documentation needs to be kept + **in the same Git repository** as the code since we want it to evolve with + the code. +::: + + +## Often a README is enough - checklist + +- **Purpose** +- Requirements +- Installation instructions +- **Copy-paste-able example to get started** +- Tutorials covering key functionality +- Reference documentation (e.g. API) covering all functionality +- Authors and **recommended citation** +- License +- Contribution guide + +See also the +[JOSS review checklist](https://joss.readthedocs.io/en/latest/review_checklist.html). + + +## What if you need more than a README? + +- Write documentation in + [Markdown (.md)](https://en.wikipedia.org/wiki/Markdown) + or + [reStructuredText (.rst)](https://en.wikipedia.org/wiki/ReStructuredText) + or + [R Markdown (.Rmd)](https://rmarkdown.rstudio.com/) + +- In the **same repository** as the code -> version control and **reproducibility** + +- Use one of many tools to build HTML out of md/rst/Rmd: + [Sphinx](https://sphinx-doc.org), + [MkDocs](https://www.mkdocs.org/), + [Zola](https://www.getzola.org/), [Jekyll](https://jekyllrb.com/), + [Hugo](https://gohugo.io/), RStudio, [knitr](https://yihui.org/knitr/), + [bookdown](https://bookdown.org/), + [blogdown](https://bookdown.org/yihui/blogdown/), ... + +- Deploy the generated HTML to [GitHub Pages](https://pages.github.com/) or + [GitLab Pages](https://docs.gitlab.com/ee/user/project/pages/) + + +## Diátaxis + +Diátaxis is a systematic approach to technical documentation authoring. + +- Overview: +- How to use Diátaxis **as a guide** to work: + + +## Exercise: Set up a Sphinx documentation + +:::{prereq} Preparation +In this episode we will use the following 5 packages which we installed +previously as part of the {ref}`conda` or {ref}`venv`: +``` +myst-parser +sphinx +sphinx-rtd-theme +sphinx-autoapi +sphinx-autobuild +``` + +Which repository to use? You have 3 options: +- Clone **your fork** of the planets example repository. +- If you don't have that, you can clone the original repository itself: + +- You can try this with **your own project** and the project does not have to + be a Python project. +::: + +There are at least two ways to get started with Sphinx: +1. Use `sphinx-quickstart` to create a new Sphinx project. +1. **This is what we will do**: Create three files (`doc/conf.py`, `doc/index.md`, and `doc/about.md`) + as starting point and improve from there. + +::::{exercise} Exercise: Set up a Sphinx documentation +1. Create the following three files in your project: + ``` + planets/ + ├── doc/ + │ ├── conf.py + │ ├── index.md + │ └── about.md + └── ... + ``` + + This is `conf.py`: + ```python + project = "planets" + copyright = "2024, Authors" + author = "Authors" + release = "0.1" + + exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] + + extensions = [ + "myst_parser", # in order to use markdown + ] + + myst_enable_extensions = [ + "colon_fence", # ::: can be used instead of ``` for better rendering + ] + + html_theme = "sphinx_rtd_theme" + ``` + + This is `index.md` (feel free to adjust): + ```markdown + # Our code documentation + + Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor + incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis + nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. + Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu + fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in + culpa qui officia deserunt mollit anim id est laborum. + + :::{toctree} + :maxdepth: 2 + :caption: Some caption + + about.md + ::: + ``` + + This is `about.md` (feel free to adjust): + ```markdown + # About this code + + Work in progress ... + ``` + +1. Run `sphinx-build` to build the HTML documentation: + ```console + $ sphinx-build doc _build + + ... lots of output ... + The HTML pages are in _build. + ``` + +1. Try to open `_build/index.html` in your browser. + +1. Experiment with adding more content, images, equations, code blocks, ... + - [typography](https://myst-parser.readthedocs.io/en/latest/syntax/typography.html) + - [images](https://myst-parser.readthedocs.io/en/latest/syntax/images_and_figures.html) + - [math and equations](https://myst-parser.readthedocs.io/en/latest/syntax/math.html) + - [code blocks](https://myst-parser.readthedocs.io/en/latest/syntax/code_and_apis.html) +:::: + +There is a lot more you can do: +- This is useful if you want to check the integrity of all internal and external links: + ```console + $ sphinx-build doc -W -b linkcheck _build + ``` +- [sphinx-autobuild](https://pypi.org/project/sphinx-autobuild/) + provides a local web server that will automatically refresh your view + every time you save a file - which makes writing and testing much easier. + + +## Demo: Building documentation with GitHub Actions + +First we need to extend the `environment.yml` file to include the necessary packages: +```{code-block} yaml +--- +emphasize-lines: 9-12 +--- +name: planets +channels: + - conda-forge +dependencies: + - python=3.12 + - numpy + - click + - matplotlib + - myst-parser + - sphinx + - sphinx-rtd-theme + - sphinx-autoapi +``` + +Then we add a GitHub Actions workflow `.github/workflow/sphinx.yml` to build the documentation: +```{code-block} yaml +--- +emphasize-lines: 31 +--- +name: Build documentation + +on: + push: + branches: [ main ] + pull_request: + branches: [ main ] + +permissions: + contents: write + +jobs: + docs: + runs-on: ubuntu-latest + + steps: + - name: Checkout + uses: actions/checkout@v4 + + - uses: mamba-org/setup-micromamba@v1 + with: + micromamba-version: '1.5.8-0' # any version from https://github.com/mamba-org/micromamba-releases + environment-file: environment.yml + init-shell: bash + cache-environment: true + post-cleanup: 'all' + generate-run-shell: false + + - name: Sphinx build + run: | + sphinx-build doc _build + shell: bash -el {0} + + - name: Deploy to GitHub Pages + uses: peaceiris/actions-gh-pages@v4 + if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }} + with: + publish_branch: gh-pages + github_token: ${{ secrets.GITHUB_TOKEN }} + publish_dir: _build/ + force_orphan: true +``` + +Now: +- Add these two changes to the GitHub repository. +- Go to "Settings" -> "Pages" -> "Branch" -> `gh-pages` -> "Save". +- Look at "Actions" tab and observe the workflow running and hopefully + deploying the website. +- Finally visit the generated site. You find it by clicking the About wheel + icon on top right of your repository. There, select "Use your GitHub Pages + website". +- **This is how we build almost all of our lesson websites** (including this one). +- Another popular place to deploy Sphinx documentation is [ReadTheDocs](https://readthedocs.org/). + + +## Optional: How to auto-generate API documentation in Python + +Add three tiny modifications (highlighted) to `doc/conf.py` to auto-generate API documentation +(this requires the `sphinx-autoapi` package): +```{code-block} python +--- +emphasize-lines: 10, 14, 17 +--- +project = "planets" +copyright = "2024, Authors" +author = "Authors" +release = "0.1" + +exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] + +extensions = [ + "myst_parser", # in order to use markdown + "autoapi.extension", # in order to use markdown +] + +# search this directory for Python files +autoapi_dirs = [".."] + +# ignore this file when generating API documentation +autoapi_ignore = ["*/conf.py"] + +myst_enable_extensions = [ + "colon_fence", # ::: can be used instead of ``` for better rendering +] + +html_theme = "sphinx_rtd_theme" +``` + +Then rebuild the documentation (or push the changes and let GitHub rebuild it) +and you should see a new section "API Reference". + + +## Confused about reStructuredText vs. Markdown vs. MyST? + +- At the beginning there was reStructuredText and Sphinx was built for reStructuredText. +- Independently, Markdown was invented and evolved into a couple of flavors. +- Markdown became more and more popular but was limited compared to reStructuredText. +- Later, [MyST](https://myst-parser.readthedocs.io/en/latest/syntax/typography.html) + was invented to be able to write + something that looks like Markdown but in addition can do everything that + reStructuredText can do with extra directives. + + +## Where to read more + +- [CodeRefinery documentation lesson](https://coderefinery.github.io/documentation/) +- [Sphinx documentation](https://www.sphinx-doc.org/) +- [Sphinx + ReadTheDocs guide](https://sphinx-rtd-tutorial.readthedocs.io/en/latest/index.html) +- For more Markdown functionality, see the [Markdown guide](https://www.markdownguide.org/basic-syntax/). +- For Sphinx additions, see [Sphinx Markup Constructs](https://www.sphinx-doc.org/en/master/markup/index.html). +- [An opinionated guide on documentation in Python](https://docs.python-guide.org/writing/documentation/) diff --git a/_sources/example.md.txt b/_sources/example.md.txt new file mode 100644 index 0000000..9805632 --- /dev/null +++ b/_sources/example.md.txt @@ -0,0 +1,95 @@ +(example-project)= + +# Example project: Simulating the motion of planets + +The [example code](https://github.com/workshop-material/planets) that we will study +is a hopefully simple N-body simulation written in Python. It is not important +or expected that we understand the code in any detail. + +:::{video} video/animation.mp4 +:width: 600 +::: + +The **big picture** is that the code simulates the motion of a number of +planets: +- We can choose the number of planets. +- Each planet starts with a random position, velocity, and mass. +- At each time step, the code calculates the gravitational force between each + pair of planets. +- The forces accelerate each planet, the acceleration modifies the velocity, + the velocity modifies the position of each planet. +- We can choose the number of time steps. +- The units were chosen to make numbers easy to read. + + +## Example run + +:::{instructor-note} +The instructor demonstrates running the code on their computer. +::: + +The code is written to accept **command-line arguments** to specify the number +of planets and the number of time steps. + +We first generate starting data: +```console +$ python generate-data.py --num-planets 10 --output-file initial.csv +``` + +The generated file (initial.csv) could look like this: +``` +px,py,pz,vx,vy,vz,mass +-46.88,-42.51,88.33,-0.86,-0.18,0.55,6.70 +-5.29,17.09,-96.13,0.66,0.45,-0.17,3.51 +83.53,-92.83,-68.77,-0.26,-0.48,0.24,6.84 +-36.31,25.48,64.16,0.85,0.75,-0.56,1.53 +-68.38,-17.21,-97.07,0.60,0.26,0.69,6.63 +-48.37,-48.74,3.92,-0.92,-0.33,-0.93,8.60 +40.53,-75.50,44.18,-0.62,-0.31,-0.53,8.04 +-27.21,10.78,-78.82,-0.09,-0.55,-0.03,5.35 +88.42,-74.95,-45.85,0.81,0.68,0.56,5.36 +39.09,53.12,-59.54,-0.54,0.56,0.07,8.98 +``` + +Then we can simulate their motion (in this case for 20 steps): +```console +$ python simulate.py --num-steps 20 \ + --input-file initial.csv \ + --output-file final.csv +``` + +The `--output-file` (final.csv) is again a CSV file (comma-separated values) +and contains the final positions of all planets. + +It is possible to run on **multiple cores** and to **animate** the result. +Here is an example with 100 planets: +```{code-block} console +--- +emphasize-lines: 7,11 +--- +$ python generate-data.py --num-planets 100 --output-file initial.csv + +$ python simulate.py --num-steps 50 \ + --input-file initial.csv \ + --output-file final.csv \ + --trajectories-file trajectories.npz \ + --num-cores 8 + +$ python animate.py --initial-file initial.csv \ + --trajectories-file trajectories.npz \ + --output-file animation.mp4 +``` + +:::{admonition} Learning goals +- What are the most important steps to make this code **reusable by others** + and **our future selves**? +- Be able to apply these techniques to your own code/script. +::: + +:::{admonition} We will not focus on ... +- ... how the code works internally in detail. +- ... whether this is the most efficient algorithm. +- ... whether the code is numerically stable. +- ... how to code scales with the number of cores. +- ... whether it is portable to other operating systems (we will discuss this later). +::: diff --git a/_sources/index.md.txt b/_sources/index.md.txt new file mode 100644 index 0000000..647b711 --- /dev/null +++ b/_sources/index.md.txt @@ -0,0 +1,142 @@ +# Reproducible research software development using Python + + +## Big-picture goal + +This is a **hands-on course on research software engineering**. In this +workshop we assume that most workshop participants use Python in their work or +a leading a group which uses Python. Therefore, some of the examples will use +Python as the example language. + +We will work with an example project and go through all the steps of a typical +software project. Once we have seen the building blocks, we will try to apply +them to own projects. Workshop participants will receive and also learn to give +constructive code feedback. + + +## Prerequisites + +:::{prereq} Preparation +1. Get a **GitHub account** following [these instructions](https://coderefinery.github.io/installation/github/). +1. You will need a **text editor**. If you don't have a favorite one, we recommend + [VS Code](https://coderefinery.github.io/installation/vscode/). +1. **If you prefer to work in the terminal** and not in VS Code, set up these two (skip this if you use VS Code): + - [Git in the terminal](https://coderefinery.github.io/installation/git-in-terminal/) + - [SSH or HTTPS connection to GitHub from terminal](https://coderefinery.github.io/installation/ssh/) +1. **One of these two software environments** (if you are not sure which one to + choose or have no preference, choose Conda): + - {ref}`conda` + - {ref}`venv` (Snakemake is not available in this environment) +1. **Optional** and only on Linux: [Apptainer](https://apptainer.org/) following + [these instructions](https://apptainer.org/docs/admin/1.3/installation.html#install-from-pre-built-packages). +::: + + +## Schedule + +### Day 1 + +- 13:00-13:30 - **Welcome and introduction** + - Practical information (tools, communication, breaks, etc.) + - Motivation (reproducibility, robustness, distribution, improvement, trust, etc.) + - What will learn and achieve from this course? + - {ref}`example-project` + +- 13:30-14:45 - {ref}`version-control` (1/2) + - {ref}`version-control-motivation` (15 min) + - {ref}`browsing` (30 min) + - {ref}`branching-and-committing` (30 min) + +- 15:00-16:30 - {ref}`version-control` (2/2) + - Merging (40 min) + - Conflict resolution (30 min) + - {ref}`practical-advice` (20 min) + - {ref}`sharing-repositories` (30 min) + +- 16:45-18:00 - {ref}`documentation` + + +### Day 2 + +- 09:00-10:30 - {ref}`collaboration` (1/2) + - {ref}`concepts` (10 min) + - {ref}`same-repository` (40 min) + - {ref}`code-review` (40 min) + +- 10:45-12:15 - {ref}`collaboration` (2/2) + - {ref}`forking-workflow` (50 min) + - {ref}`collaboration-demo-discussion` (40 min) + +- 16:45-18:00 - **Debriefing and Q&A** + - Participants work on their projects + - Together we study actual codes that participants wrote or work on + - Constructively we discuss possible improvements + - Give individual feedback on code projects + + +### Day 3 + +- 09:00-10:30 - {ref}`testing` + +- 10:45-12:15 - {ref}`reusable` + - Tracking dependencies with requirements.txt and environment.yml + - Recording environments in containers + +- 13:00-14:45 - Code quality and good practices + - {ref}`refactoring-demo` (90 min) + - {ref}`refactoring-concepts` (15 min) + +- 15:00-16:30 - {ref}`publishing` + - Licenses + - Publishing the code via Zenodo + - Packaging the code + - Sharing the code via PyPI + +- 16:45-18:00 - **Debriefing and Q&A** + - Participants work on their projects + - Together we study actual codes that participants wrote or work on + - Constructively we discuss possible improvements + - Give individual feedback on code projects + + +### If we have time left + +- {ref}`profiling` + + +```{toctree} +:maxdepth: 1 +:caption: Software environment +:hidden: + +installation/conda +installation/virtual-environment +``` + +```{toctree} +:maxdepth: 1 +:caption: Episodes +:hidden: + +example +version-control +documentation +collaboration +testing +reusable +refactoring-demo +refactoring-concepts +publishing +profiling +``` + +```{toctree} +:maxdepth: 1 +:caption: Reference +:hidden: + +credit +All lessons +CodeRefinery +Reusing +``` diff --git a/_sources/installation/conda.md.txt b/_sources/installation/conda.md.txt new file mode 100644 index 0000000..830161f --- /dev/null +++ b/_sources/installation/conda.md.txt @@ -0,0 +1,82 @@ +(conda)= + +# Conda environment + +A Conda environment is an isolated software environment that is used to manage dependencies for a project +and you decide where it is located. + +You will need a `environment.yml` file that documents the dependencies: +```yaml +name: coderefinery +channels: + - conda-forge + - bioconda +dependencies: + - python >= 3.10 + - black + - click + - flit + - ipywidgets + - isort + - jupyterlab + - jupyterlab_code_formatter + - jupyterlab-git + - matplotlib + - myst-parser + - nbdime + - numpy + - pandas + - pytest + - pytest-cov + - scalene + - seaborn + - snakemake-minimal + - sphinx + - sphinx-autoapi + - sphinx-autobuild + - sphinx_rtd_theme >= 2.0 + - vulture + - scikit-image +``` + + +## Before you create a virtual environment + +1. Create a new directory for this course. +1. In this directory, create an `environment.yml` file and copy-paste the dependencies above into it. + + +## Choose the tool to manage the environment + +If you are already using one of these tools, please continue using the tool that you like and know. +If you are new to this, **we recommend using Miniconda or Miniforge**. + +- [Anaconda](https://docs.anaconda.com/anaconda/install/) + - Advantages: easy to install, easy to use, good for beginners + - Disadvantages: large download, installs more than we will need, license restrictions +- [Miniconda](https://docs.anaconda.com/miniconda/) + - Advantages: small size, installs only what you need + - Disadvantages: no graphical interface, license restrictions +- [Miniforge](https://github.com/conda-forge/miniforge) + - Advantages: small size, no license restrictions + - Disadvantages: no graphical interface +- [Micromamba](https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html) + - Advantages: fast, small size + - Disadvantages: no graphical interface +- [Pixi](https://pixi.sh/latest/) + - Advantages: fast and new + - Disadvantages: new and less tested and not documented here + + +## Creating the virtual environment + +1. Open your terminal shell (e.g. Bash or Zsh). +2. Activate `conda` using `conda activate` or `source ~/miniconda3/bin/activate`. +3. Run the following command: + ```console + $ conda env create --file environment.yml + ``` +4. Make sure that you see "coderefinery" in the output when you ask for a list of all available environments: + ```console + $ conda env list + ``` diff --git a/_sources/installation/virtual-environment.md.txt b/_sources/installation/virtual-environment.md.txt new file mode 100644 index 0000000..69b3231 --- /dev/null +++ b/_sources/installation/virtual-environment.md.txt @@ -0,0 +1,77 @@ +(venv)= + +# Virtual environment + +A virtual environment is an isolated software environment that is used to manage dependencies for a project +and you decide where it is located. + +You will need a `requirements.txt` file that documents the dependencies: +``` +black +click +flit +ipywidgets +isort +jupyterlab +jupyterlab-code-formatter +jupyterlab-git +matplotlib +myst-parser +nbdime +numpy +pandas +pytest +pytest-cov +scalene +seaborn +sphinx +sphinx-autoapi +sphinx-autobuild +sphinx_rtd_theme >= 2.0 +vulture +scikit-image +``` + + +## Before you create a virtual environment + +1. Create a new directory for this course. +1. In this directory, create a `requirements.txt` file and copy-paste the dependencies above into it. + + +## Creating the virtual environment + +Now create a virtual environment in this directory either using [pip and +venv](https://packaging.python.org/en/latest/guides/installing-using-pip-and-virtual-environments/) +(more traditional and safer) or using [uv](https://docs.astral.sh/uv/) (more modern but also less tested): + +:::::{tabs} + +::::{group-tab} pip and venv +Create a new virtual environment and activate it: +```console +$ python3 -m venv coderefinery-environment +$ source coderefinery-environment/bin/activate +``` + +Install the dependencies into the environment: +```console +$ python3 -m pip install -r requirements.txt +``` +:::: + + +::::{group-tab} uv +Create a new virtual environment and activate it: +```console +$ uv venv coderefinery-environment +$ source coderefinery-environment/bin/activate +``` + +Install the dependencies into the environment: +```console +$ uv pip install -r requirements.txt +``` +:::: + +::::: diff --git a/_sources/profiling.md.txt b/_sources/profiling.md.txt new file mode 100644 index 0000000..0683e06 --- /dev/null +++ b/_sources/profiling.md.txt @@ -0,0 +1,16 @@ +(profiling)= + +# Profiling memory and CPU usage + +Profilers: +- cProfile or profile +- line_profiler +- viztracer +- scalene +- Intel VTune +- PyInstrument +- py-spy +- Pyflame +- timeit + +(here I will add some examples that we can profile together) diff --git a/_sources/publishing.md.txt b/_sources/publishing.md.txt new file mode 100644 index 0000000..bc3a12e --- /dev/null +++ b/_sources/publishing.md.txt @@ -0,0 +1,11 @@ +(publishing)= + +# How to release and publish your code + +Part 1: +- 30 min: Overview over software licenses and code publishing +- 15 min: We add a license, CFF file, and publish to Zenodo (sandbox) + +Part 2: +- 30 min: Creating a Python package with the help of flit +- 15 min: Deploy the package to test-PyPI using GitHub Actions diff --git a/_sources/refactoring-concepts.md.txt b/_sources/refactoring-concepts.md.txt new file mode 100644 index 0000000..78039ad --- /dev/null +++ b/_sources/refactoring-concepts.md.txt @@ -0,0 +1,8 @@ +(refactoring-concepts)= + +# Concepts in refactoring and modular code design + +Topics: +- Pure functions +- Design patterns: functional design vs. object-oriented design +- How to design your code before writing it: document-driven development diff --git a/_sources/refactoring-demo.md.txt b/_sources/refactoring-demo.md.txt new file mode 100644 index 0000000..e7266bf --- /dev/null +++ b/_sources/refactoring-demo.md.txt @@ -0,0 +1,115 @@ +(refactoring-demo)= + +# Demo: From a script towards a workflow + +In this episode we will explore code quality and good practices in Python using +a hands-on approach. We will together build up a small project and improve it +step by step. + +We will start from a relatively simple image processing script which can read a +telescope image of stars and our goal is to **count the number of stars** in +the image. Later we will want to be able to process many such images. + +The (fictional) telescope images look like the one below here ([in this +repository](https://github.com/workshop-material/random-star-images) we can find more): +:::{figure} refactoring/stars.png +:alt: Generated image representing a telescope image of stars +:width: 60% + +Generated image representing a telescope image of stars. +::: + +:::{admonition} Rough plan for this demo +- (15 min) Discuss how we would solve the problem, run example code, and make it work (as part of a Jupyter notebook)? +- (15 min) Refactor the positioning code into a function and a module +- (15 min) Now we wish to process many images - discuss how we would approach this +- (15 min) Introduce CLI and discuss the benefits +- (30 min) From a script to a workflow (using Snakemake) +::: + +:::{solution} Starting point (spoiler alert) + +We can imagine that we pieced together the following code +based on some examples we found online: +```python +import matplotlib.pyplot as plt +from skimage import io, filters, color +from skimage.measure import label, regionprops + + +image = io.imread("stars.png") +sigma = 0.5 + +# if there is a fourth channel (alpha channel), ignore it +rgb_image = image[:, :, :3] +gray_image = color.rgb2gray(rgb_image) + +# apply a gaussian filter to reduce noise +image_smooth = filters.gaussian(gray_image, sigma) + +# threshold the image to create a binary image (bright stars will be white, background black) +thresh = filters.threshold_otsu(image_smooth) +binary_image = image_smooth > thresh + +# label connected regions (stars) in the binary image +labeled_image = label(binary_image) + +# get properties of labeled regions +regions = regionprops(labeled_image) + +# extract star positions (centroids) +star_positions = [region.centroid for region in regions] + +# plot the original image +plt.figure(figsize=(8, 8)) +plt.imshow(image, cmap="gray") + +# overlay star positions with crosses +for star in star_positions: + plt.plot(star[1], star[0], "rx", markersize=5, markeredgewidth=0.1) + +plt.savefig("detected-stars.png", dpi=300) + +print(f"number of stars detected: {len(star_positions)}") +``` +::: + + +## Plan + +Topics we wish to show and discuss: +- Naming (and other) conventions, project organization, modularity +- The value of pure functions and immutability +- Refactoring (explained through examples) +- Auto-formatting and linting with tools like black, vulture, ruff +- Moving a project under Git +- How to document dependencies +- Structuring larger software projects in a modular way +- Command-line interfaces +- Workflows with Snakemake + +We will work together on the code on the big screen, and participants will be +encouraged to give suggestions and ask questions. We will **end up with a Git +repository** which will be shared with workshop participants. + + +## Possible solutions + +:::{solution} Script after some work, with command-line interface (spoiler alert) +This is one possible solution (`count-stars.py`): +```{literalinclude} refactoring/count-stars.py +:language: python +``` +::: + +:::{solution} Snakemake rules which define a workflow (spoiler alert) +This is one possible solution (`snakefile`): +```{literalinclude} refactoring/snakefile +:language: python +``` + +We can process as many images as we like by running: +```console +$ snakemake --cores 4 # adjust to the number of available cores +``` +::: diff --git a/_sources/reusable.md.txt b/_sources/reusable.md.txt new file mode 100644 index 0000000..c86455a --- /dev/null +++ b/_sources/reusable.md.txt @@ -0,0 +1,13 @@ +(reusable)= + +# How to make the project more reusable + +Part 1: +- 15 min: Motivation +- 15 min: Best practices for managing dependencies in Python +- 20 min: Exercise + +Part 2: +- 10 min: Introduction to containers +- 20 min: Demonstration +- 10 min: Discussion diff --git a/_sources/testing.md.txt b/_sources/testing.md.txt new file mode 100644 index 0000000..da43e9f --- /dev/null +++ b/_sources/testing.md.txt @@ -0,0 +1,222 @@ +(testing)= + +# Automated testing + +:::{objectives} +- Know **where to start** in your own project. +- Have an example for how to make the **testing part of code review**. +::: + +:::{instructor-note} +- (15 min) Motivation +- (15 min) End-to-end tests +- (15 min) Pytest +- (15 min) Adding the unit test to GitHub Actions +- (10 min) What else is possible +- (20 min) Exercise +::: + + +## Motivation + +Testing is a way to check that the code does what it is expected to. + +- **Less scary to change code**: tests will tell you whether something broke. +- **Easier for new people** to join. +- Easier for somebody to **revive an old code**. +- **End-to-end test**: run the whole code and compare result to a reference. +- **Unit tests**: test one unit (function or module). Can guide towards better + structured code: complicated code is more difficult to test. + + +## How testing is often taught + +```python +def add(a, b): + return a + b + + +def test_add(): + assert add(1, 2) == 3 +``` + +How this feels: +:::{figure} img/owl.png +:alt: Instruction on how to draw an owl +:width: 50% +:class: with-border + +[Citation needed] +::: + +Instead, we will look at and **discuss a real example** where we test components +from our example project. + + +## Where to start + +Short answer: **Start with an end-to-end test**. + +:::{solution} Longer answer +- A simple script or notebook probably does not need an automated test. + +**If you have nothing yet**: +- Start with an end-to-end test. +- Describe in words how *you* check whether the code still works. +- Translate the words into a script (any language). +- Run the script automatically on every code change. + +**If you want to start with unit-testing**: +- You want to rewrite a function? Start adding a unit test right there first. +::: + + +## End-to-end tests + +- This is our end-to-end test: +- Note how we can run it [on GitHub automatically](https://github.com/workshop-material/planets/blob/813d49a247f36e9c1e10cbe78ecf1ae4b6e971c3/.github/workflows/test.yml#L28). +- Also browse . +- If we have time, we can try to create a pull request which would break the + code and see how the test fails. + +:::{discussion} +Is the [end-to-end test](https://github.com/workshop-material/planets/blob/main/test.sh) +perfect? No. But it's a good starting point. Discuss its limitations. +::: + + +## Pytest + +First we need to add a test function, for instance +for [this function](https://github.com/workshop-material/planets/blob/813d49a247f36e9c1e10cbe78ecf1ae4b6e971c3/simulate.py#L31-L39): +```{code-block} python +--- +emphasize-lines: 12-20 +--- +def force_between_planets(position1, mass1, position2, mass2): + G = 1.0 # gravitational constant + + r = position2 - position1 + distance = (r[0] ** 2 + r[1] ** 2 + r[2] ** 2) ** 0.5 + force_magnitude = G * mass1 * mass2 / distance**2 + force = (r / distance) * force_magnitude + + return force + + +def test_force_between_planets(): + position1 = np.array([0.0, 0.0, 0.0]) + mass1 = 1.0 + position2 = np.array([1.0, 0.0, 0.0]) + mass2 = 2.0 + + force = force_between_planets(position1, mass1, position2, mass2) + + assert np.allclose(force, [2.0, 0.0, 0.0]) +``` + +Let us run the test with: +```console +$ pytest simulate.py +``` + +Explanation: `pytest` will look for functions starting with `test_` in files +and directories given as arguments. It will run them and report the results. + +Now let us try this: +- Commit the test. +- Break the function on purpose and run the test. +- Does the test fail as expected? + + +## Adding the unit test to GitHub Actions + +Our next goal is that we want GitHub to run the unit test +automatically on every change. + +First we need to extend our +[environment.yml](https://github.com/workshop-material/planets/blob/main/environment.yml): +```{code-block} yaml +--- +emphasize-lines: 9 +--- +name: planets +channels: + - conda-forge +dependencies: + - python=3.12 + - numpy + - click + - matplotlib + - pytest +``` + +We also need to extend `.github/workflows/test.yml` (highlighted line): +```{code-block} yaml +--- +emphasize-lines: 29 +--- +name: Test + +on: + push: + branches: [ main ] + pull_request: + branches: [ main ] + +jobs: + build: + runs-on: ubuntu-latest + + steps: + - name: Checkout + uses: actions/checkout@v4 + + - uses: mamba-org/setup-micromamba@v1 + with: + micromamba-version: '1.5.8-0' # any version from https://github.com/mamba-org/micromamba-releases + environment-file: environment.yml + init-shell: bash + cache-environment: true + post-cleanup: 'all' + generate-run-shell: false + + - name: Run tests + run: | + ./test.sh + pytest simulate.py + shell: bash -el {0} +``` + +If we have time, we can try to create a pull request which would break the +code and see how the test fails. + + +## What else is possible + +- The testing above used **example-based** testing. + +- **Test coverage**: how much of the code is traversed by tests? + - Python: [pytest-cov](https://pytest-cov.readthedocs.io/) + - Result can be deployed to services like [Codecov](https://about.codecov.io/) or [Coveralls](https://coveralls.io/). + +- **Property-based** testing: generates arbitrary data matching your specification and checks that your guarantee still holds in that case. + - Python: [hypothesis](https://hypothesis.readthedocs.io/) + +- **Snapshot-based** testing: makes it easier to generate snapshots for regression tests. + - Python: [syrupy](https://syrupy-project.github.io/syrupy/) + +- **Mutation testing**: tests pass -> change a line of code (make a mutant) -> test again and check whether all mutants get "killed". + - Python: [mutmut](https://mutmut.readthedocs.io/) + + +## Exercises + +Experiment with the example project and what we learned above or try it on your +own project: +- Add a unit test. +- Try to run it locally. +- Check whether it fails when you break the corresponding function. +- Try to run it on GitHub Actions. +- Create a pull request which would break the code and see whether the automatic test would catch it. +- Try to design an end-to-end test for your project. diff --git a/_sources/version-control.md.txt b/_sources/version-control.md.txt new file mode 100644 index 0000000..efcfece --- /dev/null +++ b/_sources/version-control.md.txt @@ -0,0 +1,13 @@ +(version-control)= + +# Introduction to version control with Git and GitHub + +```{toctree} +:maxdepth: 1 + +version-control/motivation.md +version-control/browsing.md +version-control/branching-and-committing.md +version-control/practical-advice.md +version-control/sharing.md +``` diff --git a/_sources/version-control/branching-and-committing.md.txt b/_sources/version-control/branching-and-committing.md.txt new file mode 100644 index 0000000..702e712 --- /dev/null +++ b/_sources/version-control/branching-and-committing.md.txt @@ -0,0 +1,339 @@ +(branching-and-committing)= + +# Creating branches and commits + +The first and most basic task to do in Git is **record changes** using +commits. In this part, we will record changes in two +ways: on a **new branch** (which supports multiple lines of work at once), and directly +on the "main" branch (which happens to be the default branch here). + +:::{objectives} +- Record new changes to our own copy of the project. +- Understand adding changes in two separate branches. +- See how to compare different versions. +::: + + +## Background + +- In the previous episode we have browsed an existing **repository** and saw **commits** + and **branches**. +- Each **commit** is a snapshot of the entire project at a certain + point in time and has a unique identifier (**hash**) . +- A **branch** is a line of development, and the `main` branch or `master` branch + are often the default branch in Git. +- A branch in Git is like a **sticky note that is attached to a commit**. When we add + new commits to a branch, the sticky note moves to the new commit. +- **Tags** are a way to mark a specific commit as important, for example a release + version. They are also like a sticky note, but they don't move when new + commits are added. + +:::{figure} img/gophers.png +:alt: Branching explained with a gopher +:width: 100% + +What if two people, at the same time, make two different changes? Git +can merge them together easily. Image created using +([inspiration](https://twitter.com/jay_gee/status/703360688618536960)). +::: + + +## Exercise: Creating branches and commits + +:::{figure} img/illustrations/branches.png +:alt: Illustration of what we want to achieve in this exercise +:width: 60% + +Illustration of what we want to achieve in this exercise. +::: + +:::{exercise} Exercise: Practice creating commits and branches (20 min) +1. First create a new branch and then either add a new file or modify an + existing file and commit the change. Make sure that you now work **on your + copy** of the example repository. In your commit you can share a Git or + programming trick you like. +1. In a new commit, modify the file again. +1. Switch to the `main` branch and create a commit there. +1. Browse the network and locate the commits that you just created ("Insights" -> "Network"). +1. Compare the branch that you created with the `main` branch. Can you find an easy way to see the differences? +1. Can you find a way to compare versions between two arbitrary commits in the repository? +1. Try to rename the branch that you created and then browse the network again. +1. Try to create a tag for one of the commits that you created (on GitHub, + create a "release"). +::: + +The solution below goes over most of the answers, and you are +encouraged to use it when the hints aren't enough - this is by +design. + + +## Solution and walk-through + + +### (1) Create a new branch and a new commit + +:::::{tabs} +::::{group-tab} GitHub +1. Where it says "main" at the top left, click, enter a new branch + name `new-tutorial`, click on the offer to create the new branch + ("Create branch new-tutorial from main"). +1. Make sure you are still on the `new-tutorial` branch (it should say + it at the top), and click "Add file" → "Create new file" from the + upper right. +1. Enter a filename where it says "Name your file...". +1. Share some Git or programming trick you like. +1. Click "Commit changes" +1. Enter a commit message. Then click "Commit + changes". + +You should appear back at the file browser view, and see your +modification there. +:::: + +::::{group-tab} VS Code +1. Make sure that you are on the main branch. +1. Version control button on left sidebar → Three dots in upper right of source control → Branch → Create branch. +1. VS Code automatically switches to the new branch. +4. Create a new file. +4. In the version control sidebar, click the `+` sign to add the file for the next commit. +4. Enter a brief message and click "Commit". +:::: + +::::{group-tab} Command line +Create a new branch called `new-tutorial` from `main` and switch to it: +```console +$ git switch --create new-tutorial main +``` + +Then create the new file. Finally add and commit the file: +```console +$ git add tutorial.md # or a different file name +$ git commit -m "sharing a programming trick" +``` +:::: +::::: + + +### (2) Modify the file again with a new commit + +:::::{tabs} +::::{group-tab} GitHub +This is similar to before, but we click on the existing file to +modify. + +1. Click on the file you added or modified previously. +2. Click the edit button, the pencil icon at top-right. +3. Follow the "Commit changes" instructions as in the previous step. +:::: + +::::{group-tab} VS Code +Repeat as in the previous step. +:::: + +::::{group-tab} Command line +Modify the file. Then commit the new change: +```console +$ git add tutorial.md +$ git commit -m "short summary of the change" +``` + +Make sure to replace "short summary of the change" with a meaningful commit +message. +:::: +::::: + + +### (3) Switch to the main branch and create a commit there + +:::::{tabs} +::::{group-tab} GitHub +1. Go back to the main repository page (your user's page). +1. In the branch switch view (top left above the file view), switch to + `main`. +1. Modify another file that already exists, following the pattern + from above. +:::: + +::::{group-tab} VS Code +Use the branch selector at the bottom to switch back to the main branch. Repeat the same steps as above, +but this time modify a different file. +:::: + +::::{group-tab} Command line +First switch to the `main` branch: +```console +$ git switch main +``` + +Then modify a file. Finally `git add` and then commit the change: +```console +$ git commit -m "short summary of the change" +``` +:::: +::::: + + +### (4) Browse the commits you just made + +Let's look at what we did. Now, the `main` and `new-tutorial` branches +have diverged: both have some modifications. Try to find the commits +you created. + +:::::{tabs} +::::{group-tab} GitHub +Insights tab → Network view (just like we have done before). +:::: + +::::{group-tab} VS Code +This requires an extension. Opening the VS Code terminal lets you use the +command line method (View → Terminal will open a terminal at bottom). This is +a normal command line interface and very useful for work. +:::: + +::::{group-tab} Command line +```console +$ git graph +$ git log --graph --oneline --decorate --all # if you didn't define git graph yet. +``` +:::: +::::: + + +### (5) Compare the branches + +Comparing changes is an important thing we need to do. When using the +GitHub view only, this may not be so common, but we'll show it so that +it makes sense later on. + +:::::{tabs} + +::::{group-tab} GitHub +A nice way to compare branches is to add `/compare` to the URL of the repository, +for example (replace USER): +`https://github.com/USER/planets/compare` +:::: + +::::{group-tab} VS Code +This seems to require an extension. We recommend you use the command line method. +:::: + +::::{group-tab} Command line +```console +$ git diff main new-tutorial +``` + +Try also the other way around: +```console +$ git diff new-tutorial main +``` + +Try also this if you only want to see the file names that are different: +```console +$ git diff --name-only main new-tutorial +``` +:::: +::::: + + +### (6) Compare two arbitrary commits + +This is similar to above, but not only between branches. + +:::::{tabs} +::::{group-tab} GitHub +Following the `/compare`-trick above, one can compare commits on GitHub by +adjusting the following URL: +`https://github.com/USER/planets/compare/VERSION1..VERSION2` + +Replace `USER` with your username and `VERSION1` and `VERSION2` with a commit hash or branch name. +Please try it out. +:::: + +::::{group-tab} VS Code +Again, we recommend using the Command Line method. +:::: + +::::{group-tab} Command line +First try this to get a short overview of the commits: +```console +$ git log --oneline +``` + +Then try to compare any two commit identifiers with `git diff`. +:::: +::::: + + +### (7) Renaming a branch + +:::::{tabs} +::::{group-tab} GitHub + +Branch button → View all branches → three dots at right side → Rename branch. + +:::: +::::{group-tab} VS Code +Version control sidebar → Three dots (same as in step 2) → Branch → Rename branch. Make sure you are on the right branch before you start. +:::: + +::::{group-tab} Command line +Renaming the current branch: +```console +$ git branch -m new-branch-name +``` + +Renaming a different branch: +```console +$ git branch -m different-branch new-branch-name +``` +:::: +::::: + + +### (8) Creating a tag + +Tags are a way to mark a specific commit as important, for example a release +version. They are also like a sticky note, but they don't move when new +commits are added. + +:::::{tabs} +::::{group-tab} GitHub +On the right side, below "Releases", click on "Create a new release". + +What GitHub calls releases are actually tags in Git with additional metadata. +For the purpose of this exercise we can use them interchangeably. +:::: + +::::{group-tab} VS Code +Version control sidebar → Three dots (same as in step 2) → Tags → Create tag. Make sure you are on the expected commit before you do this. +:::: + +::::{group-tab} Command line +Creating a tag: +```console +$ git tag -a v1.0 -m "New manuscript version for the pre-print" +``` +:::: +::::: + + +## Summary + +In this part, we saw how we can make changes to our files. With branches, we +can track several lines of work at once, and can compare their differences. + +- You could commit directly to `main` if there is only one single line + of work and it's only you. +- You could commit to branches if there are multiple lines of work at + once, and you don't want them to interfere with each other. +- Tags are useful to mark a specific commit as important, for example a + release version. +- In Git, commits form a so-called "graph". Branches are tags in Git function + like sticky notes that stick to specific commits. What this means for us is + that it does not cost any significant disk space to create new branches. +- Not all files should be added to Git. For example, temporary files or + files with sensitive information or files which are generated as part of + the build process should not be added to Git. For this we use + `.gitignore` (more about this later: {ref}`practical-advice`). +- Unsure on which branch you are or what state the repository is in? + On the command line, use `git status` frequently to get a quick overview. diff --git a/_sources/version-control/browsing.md.txt b/_sources/version-control/browsing.md.txt new file mode 100644 index 0000000..d3c3dc0 --- /dev/null +++ b/_sources/version-control/browsing.md.txt @@ -0,0 +1,374 @@ +(browsing)= + +# Forking, cloning, and browsing + +In this episode, we will look at an **existing repository** to understand how +all the pieces work together. Along the way, we will make a copy (by +**forking** and/or **cloning**) of the repository for us, which will be used +for our own changes. + +:::{objectives} +- See a real Git repository and understand what is inside of it. +- Understand how version control allows advanced inspection of a + repository. +- See how Git allows multiple people to work on the same project at the same time. +- **See the big picture** instead of remembering a bunch of commands. +::: + + +## GitHub, VS Code, or command line + +We offer **three different paths** for this exercise: +- **GitHub** (this is the one we will demonstrate) +- **VS Code** (if you prefer to follow along using an editor) +- **Command line** (for people comfortable with the command line) + + +## Creating a copy of the repository by "forking" or "cloning" + +A **repository** is a collection of files in one directory tracked by Git. A +GitHub repository is GitHub's copy, which adds things like access control, +issue tracking, and discussions. Each GitHub repository is owned by a user or +organization, who controls access. + +First, we need to make **our own copy** of the exercise repository. This will +become important later, when we make our own changes. + +:::{figure} img/illustrations/fork.png +:alt: Illustration of forking a repository on GitHub +:width: 50% + +Illustration of forking a repository on GitHub. +::: + +:::{figure} img/illustrations/clone.png +:alt: Illustration of cloning a repository to your computer +:width: 50% + +Illustration of cloning a repository to your computer. +::: + +:::{figure} img/illustrations/clone-of-fork.png +:alt: Illustration of cloning a forked repository to your computer +:width: 60% + +It is also possible to do this: to clone a forked repository to your computer. +::: + +At all times you should be aware of if you are looking at **your repository** +or the **upstream repository** (original repository): +- Your repository: https://github.com/**USER**/planets +- Upstream repository: https://github.com/**workshop-material**/planets + +:::{admonition} How to create a fork +1. Go to the repository view on GitHub: +1. First, on GitHub, click the button that says "Fork". It is towards + the top-right of the screen. +1. You should shortly be redirected to your copy of the repository + **USER/planets**. +::: + +:::{instructor-note} +Before starting the exercise session show +how to fork the repository to own account +(above). +::: + + + +## Exercise: Copy and browse an existing project + +Work on this by yourself or in pairs. + + + + + + + + + + + + +::::::{prereq} Exercise preparation +:::::{tabs} +::::{group-tab} GitHub +In this case you will work on a fork. + +You only need to open your own view, as described above. The browser +URL should look like `https://github.com/USER/planets`, where +`USER` is your GitHub username. +:::: + +::::{group-tab} VS Code +You need to have forked the repository as described above. + +We need to start by making a clone of this repository so that you can work +locally. + +1. Start VS Code. +1. If you don't have the default view (you already have a project +open), go to File → New Window. +1. Under "Start" on the screen, select "Clone Git Repository...". Alternatively + navigate to the "Source Control" tab on the left sidebar and click on the "Clone Repository" button. +1. Paste in this URL: `https://github.com/USER/planets`, where + `USER` is your username. You can copy this from the browser. +1. Browse and select the folder in which you want to clone the + repository. +1. Say yes, you want to open this repository. +1. Select "Yes, I trust the authors" (the other option works too). +:::: + +::::{group-tab} Command line +**This path is advanced and we do not include all command line +information: you need to be somewhat +comfortable with the command line already.** + +You need to have forked the repository as described above. + +We need to start by making a clone of this repository so that you can work +locally. + +1. Start the terminal in which you use Git (terminal application, or + Git Bash). +1. Change to the directory where you would want the repository to be + (`cd ~/code` for example, if the `~/code` directory is where you + store your files). +1. Run the following command: `git clone + https://github.com/USER/planets`, where `USER` is your + username. You might need to use a SSH clone command instead of + HTTPS, depending on your setup. +1. Change to that directory: `cd planets` +:::: +::::: +:::::: + + +:::{exercise} Exercise: Browsing an existing project (20 min) + +Browse the [example project](https://github.com/workshop-material/planets) and +explore commits and branches, either on a fork or on a clone. Take notes and +prepare questions. The hints are for the GitHub path in the browser. + +1. Browse the **commit history**: Are commit messages understandable? + (Hint: "Commit history", the timeline symbol, above the file list) +1. Compare the commit history with the **network graph** ("Insights" -> "Network"). Can you find the branches? +1. Try to find the **history of commits for a single file**, e.g. `simulate.py`. + (Hint: "History" button in the file view) +1. **Which files include the word "position"**? + (Hint: the GitHub search on top of the repository view) +1. In the `simulate.py` file, find out **who modified each line last and when** + (click on file, then click "Blame" button). Find out who modified the gravitational constant + last and in which commit. + (Hint: "Blame" view in the file view) +1. Can you use this code yourself? **Are you allowed to share + modifications**? + (Hint: look for a license file) +::: + +The solution below goes over most of the answers, and you are +encouraged to use it when the hints aren't enough - this is by +design. + + +## Solution and walk-through + +### (1) Basic browsing + +The most basic thing to look at is the history of commits. + +* This is visible from a button in the repository view. We see every + change, when, and who has committed. +* Every change has a unique identifier, such as `244c993`. This can + be used to identify both this change, and the whole project's + version as of that change. +* Clicking on a change in the view shows more. + +:::::{tabs} + +::::{group-tab} GitHub +Click on the timeline symbol in the repository view: + :::{figure} img/browsing/history.png + :alt: Screenshot on GitHub of where to find the commit history + :width: 100% + :class: with-border + ::: +:::: + +::::{group-tab} VS Code +This can be done from "Timeline", in the bottom of explorer, but only +for a single file. +:::: + +::::{group-tab} Command line +Run: +```console +$ git log +``` + +Try also: +```console +$ git log --oneline +``` +:::: + +::::: + + +### (2) Compare commit history with network graph + +The commit history we saw above looks linear: one commit after +another. But if we look at the network view, we see some branches and +merges. We'll see how to do these later. This is another one of the +basic Git views. + +:::::{tabs} +::::{group-tab} GitHub +In a new browser tab, open the "Insights" tab, and click on "Network". +You can hover over the commit dots to see the person who committed and +how they correspond with the commits in the other view: + :::{figure} img/browsing/network.png + :alt: Screenshot on GitHub of the network graph + :width: 100% + :class: with-border + ::: +:::: + +::::{group-tab} VS Code +We don't know how to do this without an extension. Try starting a terminal and using the +"Command line" option. +:::: + +::::{group-tab} Command line +This is a useful command to browse the network of commits locally: +```console +$ git log --graph --oneline --decorate --all +``` + +To avoid having to type this long command every time, you can define an alias (shortcut): +```console +$ git config --global alias.graph "log --graph --oneline --decorate --all" +``` + +From then on, you can use `git graph` to see the network graph. +:::: + +::::: + + +### (3) How can you browse the history of a single file? + +We see the history for the whole repository, but we can also see it +for a single file. + +:::::{tabs} + +::::{group-tab} GitHub +Navigate to the file view: Main page → simulate.py. +Click the "History" button near the top right. +:::: + +::::{group-tab} VS Code +Open simulate.py file in the editor. Under the file browser, +we see a "Timeline" view there. +:::: + +::::{group-tab} Command line +The `git log` command can take a filename and provide the log of only +a single file: + +``` +$ git log simulate.py +``` +:::: + +::::: + + +### (4) Which files include the word "position"? + +Version control makes it very easy to find all occurrences of a single +word. This is useful for things like finding where functions or +variables are defined or used. + +:::::{tabs} +::::{group-tab} GitHub +We go to the main file view. We click the Search magnifying +class at the very top, type "position", and click enter. We see every +instance, including the context. + +:::{admonition} Searching in a forked repository will not work instantaneously! + +It usually takes a few minutes before one can search for keywords in a forked repository +since it first needs to build the search index the very first time we search. +Start it, continue with other steps, then come back to this. +::: +:::: + +::::{group-tab} VS Code +If you use the "Search" magnifying class on the left sidebar, and +search for "position" it shows the occurrences in every file. You can +click to see the usage in context. +:::: + +::::{group-tab} Command line +`grep` is the command line tool that searches for lines matching a term +```console +$ git grep position # only the lines +$ git grep -C 3 position # three lines of context +$ git grep -i position # case insensitive +``` +:::: + +::::: + + +### (5) Who modified each line last and when? + +This is called the "annotate" or "blame" view. The name "blame" +is very unfortunate, but it is the standard term for historical reasons +for this functionality and it is not meant to blame anyone. + +:::::{tabs} + +::::{group-tab} GitHub +From a file view, change preview to "Blame" towards the top-left. +To get the actual commit, click on the commit message. +:::: + +::::{group-tab} VS Code +This requires an extension. We recommend for now you use the command +line version, after opening a terminal. +:::: + +::::{group-tab} Command line +These two commands are similar but have slightly different output. +```console +$ git annotate simulate.py +$ git blame simulate.py +``` +:::: + +::::: + + +### (6) Can you use this code yourself? Are you allowed to share modifications? + +- Look at the file `LICENSE`. +- On GitHub, click on the file to see a nice summary of what we can do with this: + :::{figure} img/browsing/license.png + :alt: Screenshot on GitHub summarizing license terms + :width: 100% + :class: with-border + ::: + + +### Summary + +- Git allowed us to understand this simple project much better than we + could, if it was just a few files on our own computer. +- It was easy to share the project with the course. +- By forking the repository, we created our own copy. This is + important for the following, where we will make changes to + our copy. diff --git a/_sources/version-control/motivation.md.txt b/_sources/version-control/motivation.md.txt new file mode 100644 index 0000000..25ab06f --- /dev/null +++ b/_sources/version-control/motivation.md.txt @@ -0,0 +1,118 @@ +(version-control-motivation)= + +# Motivation + +:::{objectives} +- Browse **commits** and **branches** of a Git repository. +- Remember that commits are like **snapshots** of the repository at a certain + point in time. +- Know the difference between **Git** (something that tracks changes) and + **GitHub/GitLab** (a platform to host Git repositories). +::: + + +## Why do we need to keep track of versions? + +Version control is an answer to the following questions (do you recognize some +of them?): + +- "It broke ... hopefully I have a working version somewhere?" + +- "Can you please send me the latest version?" + +- "Where is the latest version?" + +- "Which version are you using?" + +- "Which version have the authors used in the paper I am trying to reproduce?" + +- "Found a bug! Since when was it there?" + +- "I am sure it used to work. When did it change?" + +- "My laptop is gone. Is my thesis now gone?" + + +## Demonstration + +- Example repository: +- Commits are like **snapshots** and if we break something we can go back to a + previous snapshot. +- Commits carry **metadata** about changes: author, date, commit message, and + a checksum. +- **Branches** are like parallel universes where you can experiment with + changes without affecting the default branch: + + ("Insights" -> "Network") +- With version control we can **annotate code** + ([example](https://github.com/workshop-material/planets/blame/main/animate.py)). +- **Collaboration**: We can fork (make a copy on GitHub), clone (make a copy + to our computer), review, compare, share, and discuss. +- **Code review**: Others can suggest changes using pull requests or merge + requests. These can be reviewed and discussed before they are merged. + Conceptually, they are similar to "suggesting changes" in Google Docs. + + +## Features: roll-back, branching, merging, collaboration + +- **Roll-back**: you can always go back to a previous version and compare + +- **Branching and merging**: + - Work on different ideas at the same time + - Different people can work on the same code/project without interfering + - You can experiment with an idea and discard it if it turns out to be a bad idea + +:::{figure} img/gophers.png +:alt: Branching explained with a gopher +:width: 100% + +Image created using +([inspiration](https://twitter.com/jay_gee/status/703360688618536960)). +::: + +- **Collaboration**: review, compare, share, discuss + +- [Example network graph](https://github.com/workshop-material/planets/network) + + +## Talking about code + +Which of these two is more practical? +1. "Clone the code, go to the file 'simulate.py', and search for 'force_between_planets'. + Oh! But make sure you use the version from September 2024." +1. Or I can send you a permalink: + + +## What we typically like to snapshot + +- Software (this is how it started but Git/GitHub can track a lot more) +- Scripts +- Documents (plain text files much better suitable than Word documents) +- Manuscripts (Git is great for collaborating/sharing LaTeX or [Quarto](https://quarto.org/) manuscripts) +- Configuration files +- Website sources +- Data + +::::{discussion} + In this example somebody tried to keep track of versions without a version + control system tool like Git. Discuss the following directory listing. What + possible problems do you anticipate with this kind of "version control": + ```text + myproject-2019.zip + myproject-2020-february.zip + myproject-2021-august.zip + myproject-2023-09-19-working.zip + myproject-2023-09-21.zip + myproject-2023-09-21-test.zip + myproject-2023-09-21-myversion.zip + myproject-2023-09-21-newfeature.zip + ... + (100 more files like these) + ``` + + :::{solution} + - Giving a version to a collaborator and merging changes later with own + changes sounds like lots of work. + - What if you discover a bug and want to know since when the bug existed? + ::: +:::: diff --git a/_sources/version-control/practical-advice.md.txt b/_sources/version-control/practical-advice.md.txt new file mode 100644 index 0000000..5e4c460 --- /dev/null +++ b/_sources/version-control/practical-advice.md.txt @@ -0,0 +1,136 @@ +(practical-advice)= + +# Practical advice: How much Git is necessary? + + +## Writing useful commit messages + +Useful commit messages **summarize the change and provide context**. + +If you need a commit message that is longer than one line, +then the convention is: **one line summarizing the commit, then one empty line, +then paragraph(s) with more details in free form, if necessary**. + +Good example: +```{code-block} text +--- +emphasize-lines: 1 +--- +increase alpha to 2.0 for faster convergence + +the motivation for this change is +to enable ... +... +(more context) +... +this is based on a discussion in #123 +``` + +- **Why something was changed is more important than what has changed.** +- Cross-reference to issues and discussions if possible/relevant. +- Bad commit messages: "fix", "oops", "save work" +- Bad examples: [http://whatthecommit.com](http://whatthecommit.com) +- Write commit messages that will be understood + 15 years from now by someone else than you. Or by your future you. +- Many projects start out as projects "just for me" and end up to be successful projects + that are developed by 50 people over decades. +- [Commits with multiple authors](https://help.github.com/articles/creating-a-commit-with-multiple-authors/) are possible. + +Good references: + +- ["My favourite Git commit"](https://fatbusinessman.com/2019/my-favourite-git-commit) +- ["On commit messages"](https://who-t.blogspot.com/2009/12/on-commit-messages.html) +- ["How to Write a Git Commit Message"](https://chris.beams.io/posts/git-commit/) + +```{note} +A great way to learn how to write commit messages and to get inspired by their +style choices: **browse repositories of codes that you use/like**: + +Some examples (but there are so many good examples): +- [SciPy](https://github.com/scipy/scipy/commits/main) +- [NumPy](https://github.com/numpy/numpy/commits/main) +- [Pandas](https://github.com/pandas-dev/pandas/commits/main) +- [Julia](https://github.com/JuliaLang/julia/commits/master) +- [ggplot2](https://github.com/tidyverse/ggplot2/commits/main), + compare with their [release + notes](https://github.com/tidyverse/ggplot2/releases) +- [Flask](https://github.com/pallets/flask/commits/main), + compare with their [release + notes](https://github.com/pallets/flask/blob/main/CHANGES.rst) + +When designing commit message styles consider also these: +- How will you easily generate a changelog or release notes? +- During code review, you can help each other improving commit messages. +``` + +But remember: it is better to make any commit, than no commit. Especially in small projects. +**Let not the perfect be the enemy of the good enough**. + + +## What level of branching complexity is necessary for each project? + +**Simple personal projects**: +- Typically start with just the `main` branch. +- Use branches for unfinished/untested ideas. +- Use branches when you are not sure about a change. +- Use tags to mark important milestones. +- If you are unsure what to do with unfinished and not working code, commit it + to a branch. + +**Projects with few persons: you accept things breaking sometimes** +- It might be reasonable to commit to the `main` branch and feature branches. + +**Projects with few persons: changes are reviewed by others** +- You create new feature branches for changes. +- Changes are reviewed before they are merged to the `main` branch. +- Consider to write-protect the `main` branch so that it can only be changed + with pull requests or merge requests. + + +## How large should a commit be? + +- Better too small than too large (easier to combine than to split). +- Often I make a commit at the end of the day (this is a unit I would not like to lose). +- Smaller sized commits may be easier to review for others than huge commits. +- Imperfect commits are better than no commits. +- A commit should not contain unrelated changes to simplify review and possible + repair/adjustments/undo later (but again: imperfect commits are better than no commits). + + +## Working on the command line? Use "git status" all the time + +The `git status` command is one of the most useful commands in Git +to inform about which branch we are on, what we are about to commit, +which files might not be tracked, etc. + + +## How about staging and committing? + +- Commit early and often: rather create too many commits than too few. + You can always combine commits later. +- Once you commit, it is very, very hard to really lose your code. +- Always fully commit (or stash) before you do dangerous things, so that you know you are safe. + Otherwise it can be hard to recover. +- Later you can start using the staging area (where you first stage and then commit in a second step). +- Later start using `git add -p` and/or `git commit -p`. + + +## What to avoid + +- Committing **generated files/directories** (example: `__pycache__`, `*.pyc`) -> + use [.gitignore + files](https://docs.github.com/en/get-started/getting-started-with-git/ignoring-files) + ([collection of .gitignore templates](https://github.com/github/gitignore)). + +- Committing **huge files** -> use code review to detect this. + +- Committing **unrelated changes** together. + +- Postponing commits because the changes are "unfinished"/"ugly" -> better ugly + commits than no commits. + +- When working with branches: + - Not updating your branch before starting new work. + - Too ambitious branch which risks to never get completed. + - Over-engineering the branch layout and safeguards in small projects. + - Working on unrelated things on the same branch. diff --git a/_sources/version-control/sharing.md.txt b/_sources/version-control/sharing.md.txt new file mode 100644 index 0000000..6fb6401 --- /dev/null +++ b/_sources/version-control/sharing.md.txt @@ -0,0 +1,301 @@ +(sharing-repositories)= + +# Optional: How to turn your project to a Git repo and share it + +:::{objectives} +- Turn our own coding project (small or large, finished or unfinished) into a + Git repository. +- Be able to share a repository on the web to have a backup or so that others + can reuse and collaborate or even just find it. +::: + + +## Exercise + +:::{figure} img/illustrations/sharing.png +:alt: Illustration of how we turn a project into a Git repository and share it +:width: 100% + +From a bunch of files to a local repository which we then share on GitHub. +::: + + +:::::{exercise} Exercise: Turn your project to a Git repo and share it (20 min) + +1. Create a new directory called **myproject** with one or few files in it. + This represents our own project. It is not yet a Git repository. You can try + that with your own project or use a simple placeholder example. +2. Turn this new directory into a Git repository. +3. Share this repository on GitHub (or GitLab, since it really works the same). + +We offer **three different paths** of how to do this exercise. +* Via **GitHub web interface**: easy and can be a good starting point if you are completely + new to Git. +* **VS Code** is quite easy, since VS Code can offer to create the + GitHub repositories for you. +* **Command line**: you need to create the + repository on GitHub and link it yourself. + +::::{tabs} + +:::{group-tab} Only using GitHub +### Create an repository on GitHub + +First log into GitHub, then follow the screenshots and descriptions below. +```{figure} img/sharing/new-repository.png +:alt: Screenshot on GitHub before a new repository form is opened +:width: 60% +:class: with-border + +Click on the "plus" symbol on top right, then on "New repository". +``` + +Then: +```{figure} img/sharing/create-repository-with-readme.png +:alt: Screenshot on GitHub just before a new repository is created +:width: 100% +:class: with-border + +Choose a repository name, add a short description, and in this case **make sure to check** "Add a +README file". Finally "Create repository". +``` + + +### Upload your files + +Now that the repository is created, you can upload your files: +```{figure} img/sharing/upload-files.png +:alt: Screenshot on GitHub just before uploading files +:width: 100% +:class: with-border + +Click on the "+" symbol and then on "Upload files". +``` +::: + +:::{group-tab} VS Code +In VS Code it only takes few clicks. + +First, open the folder in VS Code. My example project here contains two files. +Then click on the source control icon: +```{figure} img/sharing/vscode-start.png +:alt: Screenshot of VS Code before clicking on the source control icon +:width: 100% +:class: with-border + +Open the folder in VS Code. Then click on the source control icon. +``` + +```{figure} img/sharing/vscode-publish-to-github1.png +:alt: Screenshot of VS Code before publishing to GitHub +:width: 100% +:class: with-border + +Choose "Publish to GitHub". In this case I never even clicked on "Initialize Repository". +``` + +```{figure} img/sharing/vscode-publish-to-github2.png +:alt: Screenshot of VS Code before publishing to GitHub +:width: 100% +:class: with-border + +In my case I chose to "Publish to GitHub public repository". Here you can also rename +the repository if needed. +``` + +```{figure} img/sharing/vscode-authorize.png +:alt: Screenshot of VS Code asking for authorization +:width: 50% +:class: with-border + +First time you do this you might need to authorize VS Code to access your +GitHub account by redirecting you to https://github.com/login/oauth/authorize. +``` + +```{figure} img/sharing/vscode-publish-to-github3.png +:alt: Screenshot of VS Code after publishing to GitHub +:width: 100% +:class: with-border + +After it is published, click on "Open on GitHub". +``` +::: + +:::{group-tab} Command line +### Put your project under version control + +My example project here consists of two files. Replace this with your own +example files: +```console +$ ls -l + +.rw------- 19k user 7 Mar 17:36 LICENSE +.rw------- 21 user 7 Mar 17:36 myscript.py +``` + +I will first initialize a Git repository in this directory. +If you get an error, try without the `-b main` (and your default branch will +then be called `master`, this will happen for Git versions older than +2.28): +```console +$ git init -b main +``` + +Now add and commit the two files to the Git repository: +```console +$ git add LICENSE myscript.py +$ git commit -m "putting my project under version control" +``` + +If you want to add all files in one go, you can use `git +add .` instead of `git add LICENSE myscript.py`. + +Now you have a Git repository with one commit. Verify this with `git log`. +But it's still only on your computer. Let's put it on GitHub next. + + +### Create an empty repository on GitHub + +First log into GitHub, then follow the screenshots and descriptions below. +```{figure} img/sharing/new-repository.png +:alt: Screenshot on GitHub before a new repository form is opened +:width: 60% +:class: with-border + +Click on the "plus" symbol on top right, then on "New repository". +``` + +Then create an empty repository without any files and without any commits: +```{figure} img/sharing/create-repository.png +:alt: Screenshot on GitHub just before a new repository is created +:width: 100% +:class: with-border + +Choose a repository name, add a short description, but please **do not check** "Add a +README file". For "Add .gitignore" and "Choose a license" also leave as "None". Finally "Create repository". +``` + +Once you click the green "Create repository", you will see a page similar to: +```{figure} img/sharing/bare-repository.png +:alt: Screenshot on GitHub after a bare repository was created +:width: 100% +:class: with-border +``` + +What this means is that we have now an empty project with either an HTTPS or an +SSH address: click on the HTTPS and SSH buttons to see what happens. + + +### Push an existing repository from your computer to GitHub + +We now want to follow the "**... or push an existing repository from the command line**": + +1. In your terminal make sure you are still in your myproject directory. +2. Copy paste the three lines below the red arrow to the terminal and execute + those, in my case (**you need to replace the "USER" part and possibly also + the repository name**): + +`````{tabs} + ````{group-tab} SSH + ```console + $ git remote add origin git@github.com:USER/myproject.git + ``` + ```` + ````{group-tab} HTTPS + ```console + $ git remote add origin https://github.com/USER/myproject.git + ``` + ```` +````` + +Then: +```console +$ git branch -M main +$ git push -u origin main +``` + +The meaning of the above lines: +- Add a remote reference with the name "origin" +- Rename current branch to "main" +- Push branch "main" to "origin" + +You should now see: + +```text +Enumerating objects: 4, done. +Counting objects: 100% (4/4), done. +Delta compression using up to 12 threads +Compressing objects: 100% (3/3), done. +Writing objects: 100% (4/4), 6.08 KiB | 6.08 MiB/s, done. +Total 4 (delta 0), reused 0 (delta 0), pack-reused 0 +To github.com:USER/myproject.git + * [new branch] main -> main +branch 'main' set up to track 'origin/main'. +``` + +Reload your GitHub project website and your commits should now be +online! + + +### Troubleshooting + +**error: remote origin already exists** +- Explanation: You probably ran a `git remote add origin ...` command, then changed your + mind about HTTPS or SSH and then tried to run the other `git remote add + origin ...` command but "origin" then already exists. +- Recovery: + - First remove "origin" with `git remote remove origin` + - Then run the correct `git remote add origin ...` command + +**remote contains work that you do not have** +- Explanation: You probably clicked on "Add a README file" and now the + repository on GitHub is not empty but contains one commit and locally you + have a different history. Git now prevents you from accidentally overwriting + the history on GitHub. +- Recovery: + - Use `git push --force` instead of `git push`, which will force Git to overwrite the history on GitHub + - Note that this is a powerful but also possibly dangerous option but here it + helps us. If it's a brand new repo, it probably is fine to do this. For real + repositories, don't do this unless you are very sure what is happening. +::: + +:::{group-tab} RStudio + +This is not fully explained, because a lot of it is similar to the "Command +line" method (and an RStudio expert could help us some). The main differences +are: + +### Put your project under version control + +1. Tools → Version control → Project setup → Version control system = Git. +1. Select "Yes" for "do you want to initialize a new git repository for this project. +1. Select yes to restart the project with RStudio. +1. Switch to branch `main` to have you branch named that. + +### Create an empty repository on GitHub + +Same as command line + +### Push an existing repository from your computer to GitHub + +1. Under the "Create new branch" button → "Add Remote" +1. Remote name: `origin` +1. Remote URL: as in command line (remember to select SSH or HTTPS as you have configured your RStudio) +1. The "Push" (up arrow) button will send changes on your current branch to the remote. The "Pull" (down arrow) will get changes from the remote. + +### Troubleshooting + +Same as command line + +::: +:::: +::::: + + +## Is putting software on GitHub/GitLab/... publishing? + +It is a good first step but to make your code truly **findable and +accessible**, consider making your code **citable and persistent**: Get a +persistent identifier (PID) such as DOI in addition to sharing the code +publicly, by using services like [Zenodo](https://zenodo.org) or similar +services. diff --git a/_static/_sphinx_javascript_frameworks_compat.js b/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 0000000..8141580 --- /dev/null +++ b/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. Multiple values per key are supported, + * it will always return arrays of strings for the value parts. + */ +jQuery.getQueryParameters = function(s) { + if (typeof s === 'undefined') + s = document.location.search; + var parts = s.substr(s.indexOf('?') + 1).split('&'); + var result = {}; + for (var i = 0; i < parts.length; i++) { + var tmp = parts[i].split('=', 2); + var key = jQuery.urldecode(tmp[0]); + var value = jQuery.urldecode(tmp[1]); + if (key in result) + result[key].push(value); + else + result[key] = [value]; + } + return result; +}; + +/** + * highlight a given string on a jquery object by wrapping it in + * span elements with the given class name. + */ +jQuery.fn.highlightText = function(text, className) { + function highlight(node, addItems) { + if (node.nodeType === 3) { + var val = node.nodeValue; + var pos = val.toLowerCase().indexOf(text); + if (pos >= 0 && + !jQuery(node.parentNode).hasClass(className) && + !jQuery(node.parentNode).hasClass("nohighlight")) { + var span; + var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.className = className; + } + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + node.parentNode.insertBefore(span, node.parentNode.insertBefore( + document.createTextNode(val.substr(pos + text.length)), + node.nextSibling)); + node.nodeValue = val.substr(0, pos); + if (isInSVG) { + var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); + var bbox = node.parentElement.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute('class', className); + addItems.push({ + "parent": node.parentNode, + "target": rect}); + } + } + } + else if (!jQuery(node).is("button, select, textarea")) { + jQuery.each(node.childNodes, function() { + highlight(this, addItems); + }); + } + } + var addItems = []; + var result = this.each(function() { + highlight(this, addItems); + }); + for (var i = 0; i < addItems.length; ++i) { + jQuery(addItems[i].parent).before(addItems[i].target); + } + return result; +}; + +/* + * backward compatibility for jQuery.browser + * This will be supported until firefox bug is fixed. + */ +if (!jQuery.browser) { + jQuery.uaMatch = function(ua) { + ua = ua.toLowerCase(); + + var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || + /(webkit)[ \/]([\w.]+)/.exec(ua) || + /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || + /(msie) ([\w.]+)/.exec(ua) || + ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || + []; + + return { + browser: match[ 1 ] || "", + version: match[ 2 ] || "0" + }; + }; + jQuery.browser = {}; + jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; +} diff --git a/_static/basic.css b/_static/basic.css new file mode 100644 index 0000000..f316efc --- /dev/null +++ b/_static/basic.css @@ -0,0 +1,925 @@ +/* + * basic.css + * ~~~~~~~~~ + * + * Sphinx stylesheet -- basic theme. + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; +} + +div.section::after { + display: block; + content: ''; + clear: left; +} + +/* -- relbar ---------------------------------------------------------------- */ + +div.related { + width: 100%; + font-size: 90%; +} + +div.related h3 { + display: none; +} + +div.related ul { + margin: 0; + padding: 0 0 0 10px; + list-style: none; +} + +div.related li { + display: inline; +} + +div.related li.right { + float: right; + margin-right: 5px; +} + +/* -- sidebar --------------------------------------------------------------- */ + +div.sphinxsidebarwrapper { + padding: 10px 5px 0 10px; +} + +div.sphinxsidebar { + float: left; + width: 230px; + margin-left: -100%; + font-size: 90%; + word-wrap: break-word; + overflow-wrap : break-word; +} + +div.sphinxsidebar ul { + list-style: none; +} + +div.sphinxsidebar ul ul, +div.sphinxsidebar ul.want-points { + margin-left: 20px; + list-style: square; +} + +div.sphinxsidebar ul ul { + margin-top: 0; + margin-bottom: 0; +} + +div.sphinxsidebar form { + margin-top: 10px; +} + +div.sphinxsidebar input { + border: 1px solid #98dbcc; + font-family: sans-serif; + font-size: 1em; +} + +div.sphinxsidebar #searchbox form.search { + overflow: hidden; +} + +div.sphinxsidebar #searchbox input[type="text"] { + float: left; + width: 80%; + padding: 0.25em; + box-sizing: border-box; +} + +div.sphinxsidebar #searchbox input[type="submit"] { + float: left; + width: 20%; + border-left: none; + padding: 0.25em; + box-sizing: border-box; +} + + +img { + border: 0; + max-width: 100%; +} + +/* -- search page ----------------------------------------------------------- */ + +ul.search { + margin: 10px 0 0 20px; + padding: 0; +} + +ul.search li { + padding: 5px 0 5px 20px; + background-image: url(file.png); + background-repeat: no-repeat; + background-position: 0 7px; +} + +ul.search li a { + font-weight: bold; +} + +ul.search li p.context { + color: #888; + margin: 2px 0 0 30px; + text-align: left; +} + +ul.keywordmatches li.goodmatch a { + font-weight: bold; +} + +/* -- index page ------------------------------------------------------------ */ + +table.contentstable { + width: 90%; + margin-left: auto; + margin-right: auto; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable ul { + margin-top: 0; + margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: 360px; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, figure.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, figure.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, figure.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-default, figure.align-default, .figure.align-default { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-default { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar, +aside.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px; + background-color: #ffe; + width: 40%; + float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; +} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} + +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +.translated { + background-color: rgba(207, 255, 207, 0.2) +} + +.untranslated { + background-color: rgba(255, 207, 207, 0.2) +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + +td.linenos pre { + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; +} + +table.highlighttable td { + margin: 0; + padding: 0; +} + +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; +} + +div.code-block-caption code { + background-color: transparent; +} + +table.highlighttable td.linenos, +span.linenos, +div.highlight span.gp { /* gp: Generic.Prompt */ + user-select: none; + -webkit-user-select: text; /* Safari fallback only */ + -webkit-user-select: none; /* Chrome/Safari */ + -moz-user-select: none; /* Firefox */ + -ms-user-select: none; /* IE10+ */ +} + +div.code-block-caption span.caption-number { + padding: 0.1em 0.3em; + font-style: italic; +} + +div.code-block-caption span.caption-text { +} + +div.literal-block-wrapper { + margin: 1em 0; +} + +code.xref, a code { + background-color: transparent; + font-weight: bold; +} + +h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { + background-color: transparent; +} + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family: sans-serif; +} + +div.viewcode-block:target { + margin: -1px -10px; + padding: 0 10px; +} + +/* -- math display ---------------------------------------------------------- */ + +img.math { + vertical-align: middle; +} + +div.body div.math p { + text-align: center; +} + +span.eqno { + float: right; +} + +span.eqno a.headerlink { + position: absolute; + z-index: 1; +} + +div.math:hover a.headerlink { + visibility: visible; +} + +/* -- printout stylesheet --------------------------------------------------- */ + +@media print { + div.document, + div.documentwrapper, + div.bodywrapper { + margin: 0 !important; + width: 100%; + } + + div.sphinxsidebar, + div.related, + div.footer, + #top-link { + display: none; + } +} \ No newline at end of file diff --git a/_static/check-solid.svg b/_static/check-solid.svg new file mode 100644 index 0000000..92fad4b --- /dev/null +++ b/_static/check-solid.svg @@ -0,0 +1,4 @@ + + + + diff --git a/_static/clipboard.min.js b/_static/clipboard.min.js new file mode 100644 index 0000000..54b3c46 --- /dev/null +++ b/_static/clipboard.min.js @@ -0,0 +1,7 @@ +/*! + * clipboard.js v2.0.8 + * https://clipboardjs.com/ + * + * Licensed MIT © Zeno Rocha + */ +!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return o}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),c=n.n(e);function a(t){try{return document.execCommand(t)}catch(t){return}}var f=function(t){t=c()(t);return a("cut"),t};var l=function(t){var e,n,o,r=1 + + + + diff --git a/_static/copybutton.css b/_static/copybutton.css new file mode 100644 index 0000000..40eafe5 --- /dev/null +++ b/_static/copybutton.css @@ -0,0 +1,93 @@ +/* Copy buttons */ +button.copybtn { + position: absolute; + display: flex; + top: .3em; + right: .3em; + width: 1.7em; + height: 1.7em; + opacity: 0; + transition: opacity 0.3s, border .3s, background-color .3s; + user-select: none; + padding: 0; + border: none; + outline: none; + border-radius: 0.4em; + /* The colors that GitHub uses */ + border: #1b1f2426 1px solid; + background-color: #f6f8fa; + color: #57606a; +} + +button.copybtn.success { + border-color: #22863a; + color: #22863a; +} + +button.copybtn svg { + stroke: currentColor; + width: 1.5em; + height: 1.5em; + padding: 0.1em; +} + +div.highlight { + position: relative; +} + +.highlight:hover button.copybtn { + opacity: 1; +} + +.highlight button.copybtn:hover { + background-color: rgb(235, 235, 235); +} + +.highlight button.copybtn:active { + background-color: rgb(187, 187, 187); +} + +/** + * A minimal CSS-only tooltip copied from: + * https://codepen.io/mildrenben/pen/rVBrpK + * + * To use, write HTML like the following: + * + *

Short

+ */ + .o-tooltip--left { + position: relative; + } + + .o-tooltip--left:after { + opacity: 0; + visibility: hidden; + position: absolute; + content: attr(data-tooltip); + padding: .2em; + font-size: .8em; + left: -.2em; + background: grey; + color: white; + white-space: nowrap; + z-index: 2; + border-radius: 2px; + transform: translateX(-102%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); +} + +.o-tooltip--left:hover:after { + display: block; + opacity: 1; + visibility: visible; + transform: translateX(-100%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); + transition-delay: .5s; +} + +/* By default the copy button shouldn't show up when printing a page */ +@media print { + button.copybtn { + display: none; + } +} diff --git a/_static/copybutton.js b/_static/copybutton.js new file mode 100644 index 0000000..f3ecd03 --- /dev/null +++ b/_static/copybutton.js @@ -0,0 +1,241 @@ +// Localization support +const messages = { + 'en': { + 'copy': 'Copy', + 'copy_to_clipboard': 'Copy to clipboard', + 'copy_success': 'Copied!', + 'copy_failure': 'Failed to copy', + }, + 'es' : { + 'copy': 'Copiar', + 'copy_to_clipboard': 'Copiar al portapapeles', + 'copy_success': '¡Copiado!', + 'copy_failure': 'Error al copiar', + }, + 'de' : { + 'copy': 'Kopieren', + 'copy_to_clipboard': 'In die Zwischenablage kopieren', + 'copy_success': 'Kopiert!', + 'copy_failure': 'Fehler beim Kopieren', + }, + 'fr' : { + 'copy': 'Copier', + 'copy_to_clipboard': 'Copié dans le presse-papier', + 'copy_success': 'Copié !', + 'copy_failure': 'Échec de la copie', + }, + 'ru': { + 'copy': 'Скопировать', + 'copy_to_clipboard': 'Скопировать в буфер', + 'copy_success': 'Скопировано!', + 'copy_failure': 'Не удалось скопировать', + }, + 'zh-CN': { + 'copy': '复制', + 'copy_to_clipboard': '复制到剪贴板', + 'copy_success': '复制成功!', + 'copy_failure': '复制失败', + }, + 'it' : { + 'copy': 'Copiare', + 'copy_to_clipboard': 'Copiato negli appunti', + 'copy_success': 'Copiato!', + 'copy_failure': 'Errore durante la copia', + } +} + +let locale = 'en' +if( document.documentElement.lang !== undefined + && messages[document.documentElement.lang] !== undefined ) { + locale = document.documentElement.lang +} + +let doc_url_root = DOCUMENTATION_OPTIONS.URL_ROOT; +if (doc_url_root == '#') { + doc_url_root = ''; +} + +/** + * SVG files for our copy buttons + */ +let iconCheck = ` + ${messages[locale]['copy_success']} + + +` + +// If the user specified their own SVG use that, otherwise use the default +let iconCopy = ``; +if (!iconCopy) { + iconCopy = ` + ${messages[locale]['copy_to_clipboard']} + + + +` +} + +/** + * Set up copy/paste for code blocks + */ + +const runWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} + +const codeCellId = index => `codecell${index}` + +// Clears selected text since ClipboardJS will select the text when copying +const clearSelection = () => { + if (window.getSelection) { + window.getSelection().removeAllRanges() + } else if (document.selection) { + document.selection.empty() + } +} + +// Changes tooltip text for two seconds, then changes it back +const temporarilyChangeTooltip = (el, oldText, newText) => { + el.setAttribute('data-tooltip', newText) + el.classList.add('success') + setTimeout(() => el.setAttribute('data-tooltip', oldText), 2000) + setTimeout(() => el.classList.remove('success'), 2000) +} + +// Changes the copy button icon for two seconds, then changes it back +const temporarilyChangeIcon = (el) => { + el.innerHTML = iconCheck; + setTimeout(() => {el.innerHTML = iconCopy}, 2000) +} + +const addCopyButtonToCodeCells = () => { + // If ClipboardJS hasn't loaded, wait a bit and try again. This + // happens because we load ClipboardJS asynchronously. + if (window.ClipboardJS === undefined) { + setTimeout(addCopyButtonToCodeCells, 250) + return + } + + // Add copybuttons to all of our code cells + const COPYBUTTON_SELECTOR = 'div.highlight pre'; + const codeCells = document.querySelectorAll(COPYBUTTON_SELECTOR) + codeCells.forEach((codeCell, index) => { + const id = codeCellId(index) + codeCell.setAttribute('id', id) + + const clipboardButton = id => + `` + codeCell.insertAdjacentHTML('afterend', clipboardButton(id)) + }) + +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} + + +var copyTargetText = (trigger) => { + var target = document.querySelector(trigger.attributes['data-clipboard-target'].value); + + // get filtered text + let exclude = '.linenos, .gp'; + + let text = filterText(target, exclude); + return formatCopyText(text, '', false, true, true, true, '', '') +} + + // Initialize with a callback so we can modify the text before copy + const clipboard = new ClipboardJS('.copybtn', {text: copyTargetText}) + + // Update UI with error/success messages + clipboard.on('success', event => { + clearSelection() + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_success']) + temporarilyChangeIcon(event.trigger) + }) + + clipboard.on('error', event => { + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_failure']) + }) +} + +runWhenDOMLoaded(addCopyButtonToCodeCells) \ No newline at end of file diff --git a/_static/copybutton_funcs.js b/_static/copybutton_funcs.js new file mode 100644 index 0000000..dbe1aaa --- /dev/null +++ b/_static/copybutton_funcs.js @@ -0,0 +1,73 @@ +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +export function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +export function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} diff --git a/_static/css/badge_only.css b/_static/css/badge_only.css new file mode 100644 index 0000000..c718cee --- /dev/null +++ b/_static/css/badge_only.css @@ -0,0 +1 @@ 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+ return this; // for chaining... + } +})(jQuery); + +// NO good way to do this!. Copy a hack from here +// https://stackoverflow.com/questions/901115/how-can-i-get-query-string-values-in-javascript +// https://stackoverflow.com/a/2880929 +var urlParams; +(window.onpopstate = function () { + var match, + pl = /\+/g, // Regex for replacing addition symbol with a space + search = /([^&=]+)=?([^&]*)/g, + decode = function (s) { return decodeURIComponent(s.replace(pl, " ")); }, + query = window.location.search.substring(1); + urlParams = {}; + while (match = search.exec(query)) + urlParams[decode(match[1])] = decode(match[2]); +})(); + +// Select heading levels +var maxHeading = urlParams['h'] +if (maxHeading === undefined) maxHeading = 2 +var headingLevels = []; +for (h=2 ; h (sections.length-1) ) { + // if we would scroll past bottom, or above top, do nothing + return; + } + + console.log('xxxxxx'); + var targetSection = sections[targetPos]; + console.log(targetSection, typeof(targetSection)); + + // Return targetSection top and height + var secProperties = section_top_and_height(targetSection); 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background-color: #E75C58 +} + +div.highlight .-Color[class*=-BGGreen] { + background-color: #00A250 +} + +div.highlight .-Color[class*=-BGYellow] { + background-color: #DDB62B +} + +div.highlight .-Color[class*=-BGBlue] { + background-color: #208FFB +} + +div.highlight .-Color[class*=-BGMagenta] { + background-color: #D160C4 +} + +div.highlight .-Color[class*=-BGCyan] { + background-color: #60C6C8 +} + +div.highlight .-Color[class*=-BGWhite] { + background-color: #C5C1B4 +} + +/* Font colors for 8-bit ANSI */ + +div.highlight .-Color[class*=-C0] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC0] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C1] { + color: #800000 +} + +div.highlight .-Color[class*=-BGC1] { + background-color: #800000 +} + +div.highlight .-Color[class*=-C2] { + color: #008000 +} + +div.highlight .-Color[class*=-BGC2] { + background-color: #008000 +} + +div.highlight .-Color[class*=-C3] { + color: #808000 +} + +div.highlight .-Color[class*=-BGC3] { + background-color: #808000 +} + +div.highlight .-Color[class*=-C4] { + color: #000080 +} + +div.highlight .-Color[class*=-BGC4] { + background-color: #000080 +} + +div.highlight .-Color[class*=-C5] { + color: #800080 +} + +div.highlight .-Color[class*=-BGC5] { + background-color: #800080 +} + +div.highlight .-Color[class*=-C6] { + color: #008080 +} + +div.highlight .-Color[class*=-BGC6] { + background-color: #008080 +} + +div.highlight .-Color[class*=-C7] { + color: #C0C0C0 +} + +div.highlight .-Color[class*=-BGC7] { + background-color: #C0C0C0 +} + +div.highlight .-Color[class*=-C8] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC8] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C9] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC9] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C10] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC10] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C11] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC11] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C12] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC12] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C13] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC13] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C14] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC14] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C15] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC15] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C16] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC16] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C17] { + color: #00005F +} + +div.highlight .-Color[class*=-BGC17] { + background-color: #00005F +} + +div.highlight .-Color[class*=-C18] { + color: #000087 +} + +div.highlight .-Color[class*=-BGC18] { + background-color: #000087 +} + +div.highlight .-Color[class*=-C19] { + color: #0000AF +} + +div.highlight .-Color[class*=-BGC19] { + background-color: #0000AF +} + +div.highlight .-Color[class*=-C20] { + color: #0000D7 +} + +div.highlight .-Color[class*=-BGC20] { + background-color: #0000D7 +} + +div.highlight .-Color[class*=-C21] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC21] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C22] { + color: #005F00 +} + +div.highlight .-Color[class*=-BGC22] { + background-color: #005F00 +} + +div.highlight .-Color[class*=-C23] { + color: #005F5F +} + +div.highlight .-Color[class*=-BGC23] { + background-color: #005F5F +} + +div.highlight .-Color[class*=-C24] { + color: #005F87 +} + +div.highlight .-Color[class*=-BGC24] { + background-color: #005F87 +} + +div.highlight .-Color[class*=-C25] { + color: #005FAF +} + +div.highlight .-Color[class*=-BGC25] { + background-color: #005FAF +} + +div.highlight .-Color[class*=-C26] { + color: #005FD7 +} + +div.highlight .-Color[class*=-BGC26] { + background-color: #005FD7 +} + +div.highlight .-Color[class*=-C27] { + color: #005FFF +} + +div.highlight .-Color[class*=-BGC27] { + background-color: #005FFF +} + +div.highlight .-Color[class*=-C28] { + color: #008700 +} + +div.highlight .-Color[class*=-BGC28] { + background-color: #008700 +} + +div.highlight .-Color[class*=-C29] { + color: #00875F +} + +div.highlight .-Color[class*=-BGC29] { + background-color: #00875F +} + +div.highlight .-Color[class*=-C30] { + color: #008787 +} + +div.highlight .-Color[class*=-BGC30] { + background-color: #008787 +} + +div.highlight .-Color[class*=-C31] { + color: #0087AF +} + +div.highlight .-Color[class*=-BGC31] { + background-color: #0087AF +} + +div.highlight .-Color[class*=-C32] { + color: #0087D7 +} + +div.highlight .-Color[class*=-BGC32] { + background-color: #0087D7 +} + +div.highlight .-Color[class*=-C33] { + color: #0087FF +} + +div.highlight .-Color[class*=-BGC33] { + background-color: #0087FF +} + +div.highlight .-Color[class*=-C34] { + color: #00AF00 +} + +div.highlight .-Color[class*=-BGC34] { + background-color: #00AF00 +} + +div.highlight .-Color[class*=-C35] { + color: #00AF5F +} + +div.highlight .-Color[class*=-BGC35] { + background-color: #00AF5F +} + +div.highlight .-Color[class*=-C36] { + color: #00AF87 +} + +div.highlight .-Color[class*=-BGC36] { + background-color: #00AF87 +} + +div.highlight .-Color[class*=-C37] { + color: #00AFAF +} + +div.highlight .-Color[class*=-BGC37] { + background-color: #00AFAF +} + +div.highlight .-Color[class*=-C38] { + color: #00AFD7 +} + +div.highlight .-Color[class*=-BGC38] { + background-color: #00AFD7 +} + +div.highlight .-Color[class*=-C39] { + color: #00AFFF +} + +div.highlight .-Color[class*=-BGC39] { + background-color: #00AFFF +} + +div.highlight .-Color[class*=-C40] { + color: #00D700 +} + +div.highlight .-Color[class*=-BGC40] { + background-color: #00D700 +} + +div.highlight .-Color[class*=-C41] { + color: #00D75F +} + +div.highlight .-Color[class*=-BGC41] { + background-color: #00D75F +} + +div.highlight .-Color[class*=-C42] { + color: #00D787 +} + +div.highlight .-Color[class*=-BGC42] { + background-color: #00D787 +} + +div.highlight .-Color[class*=-C43] { + color: #00D7AF +} + +div.highlight .-Color[class*=-BGC43] { + background-color: #00D7AF +} + +div.highlight .-Color[class*=-C44] { + color: #00D7D7 +} + +div.highlight .-Color[class*=-BGC44] { + background-color: #00D7D7 +} + +div.highlight .-Color[class*=-C45] { + color: #00D7FF +} + +div.highlight .-Color[class*=-BGC45] { + background-color: #00D7FF +} + +div.highlight .-Color[class*=-C46] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC46] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C47] { + color: #00FF5F +} + +div.highlight .-Color[class*=-BGC47] { + background-color: #00FF5F +} + +div.highlight .-Color[class*=-C48] { + color: #00FF87 +} + +div.highlight .-Color[class*=-BGC48] { + background-color: #00FF87 +} + +div.highlight .-Color[class*=-C49] { + color: #00FFAF +} + +div.highlight .-Color[class*=-BGC49] { + background-color: #00FFAF +} + +div.highlight .-Color[class*=-C50] { + color: #00FFD7 +} + +div.highlight .-Color[class*=-BGC50] { + background-color: #00FFD7 +} + +div.highlight .-Color[class*=-C51] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC51] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C52] { + color: #5F0000 +} + +div.highlight .-Color[class*=-BGC52] { + background-color: #5F0000 +} + +div.highlight .-Color[class*=-C53] { + color: #5F005F +} + +div.highlight .-Color[class*=-BGC53] { + background-color: #5F005F +} + +div.highlight .-Color[class*=-C54] { + color: #5F0087 +} + +div.highlight .-Color[class*=-BGC54] { + background-color: #5F0087 +} + +div.highlight .-Color[class*=-C55] { + color: #5F00AF +} + +div.highlight .-Color[class*=-BGC55] { + background-color: #5F00AF +} + +div.highlight .-Color[class*=-C56] { + color: #5F00D7 +} + +div.highlight .-Color[class*=-BGC56] { + background-color: #5F00D7 +} + +div.highlight .-Color[class*=-C57] { + color: #5F00FF +} + +div.highlight .-Color[class*=-BGC57] { + background-color: #5F00FF +} + +div.highlight .-Color[class*=-C58] { + color: #5F5F00 +} + +div.highlight .-Color[class*=-BGC58] { + background-color: #5F5F00 +} + +div.highlight .-Color[class*=-C59] { + color: #5F5F5F +} + +div.highlight .-Color[class*=-BGC59] { + background-color: #5F5F5F +} + +div.highlight .-Color[class*=-C60] { + color: #5F5F87 +} + +div.highlight .-Color[class*=-BGC60] { + background-color: #5F5F87 +} + +div.highlight .-Color[class*=-C61] { + color: #5F5FAF +} + +div.highlight .-Color[class*=-BGC61] { + background-color: #5F5FAF +} + +div.highlight .-Color[class*=-C62] { + color: #5F5FD7 +} + +div.highlight .-Color[class*=-BGC62] { + background-color: #5F5FD7 +} + +div.highlight .-Color[class*=-C63] { + color: #5F5FFF +} + +div.highlight .-Color[class*=-BGC63] { + background-color: #5F5FFF +} + +div.highlight .-Color[class*=-C64] { + color: #5F8700 +} + +div.highlight .-Color[class*=-BGC64] { + background-color: #5F8700 +} + +div.highlight .-Color[class*=-C65] { + color: #5F875F +} + +div.highlight .-Color[class*=-BGC65] { + background-color: #5F875F +} + +div.highlight .-Color[class*=-C66] { + color: #5F8787 +} + +div.highlight .-Color[class*=-BGC66] { + background-color: #5F8787 +} + +div.highlight .-Color[class*=-C67] { + color: #5F87AF +} + +div.highlight .-Color[class*=-BGC67] { + background-color: #5F87AF +} + +div.highlight .-Color[class*=-C68] { + color: #5F87D7 +} + +div.highlight .-Color[class*=-BGC68] { + background-color: #5F87D7 +} + +div.highlight .-Color[class*=-C69] { + color: #5F87FF +} + +div.highlight .-Color[class*=-BGC69] { + background-color: #5F87FF +} + +div.highlight .-Color[class*=-C70] { + color: #5FAF00 +} + +div.highlight .-Color[class*=-BGC70] { + background-color: #5FAF00 +} + +div.highlight .-Color[class*=-C71] { + color: #5FAF5F +} + +div.highlight .-Color[class*=-BGC71] { + background-color: #5FAF5F +} + +div.highlight .-Color[class*=-C72] { + color: #5FAF87 +} + +div.highlight .-Color[class*=-BGC72] { + background-color: #5FAF87 +} + +div.highlight .-Color[class*=-C73] { + color: #5FAFAF +} + +div.highlight .-Color[class*=-BGC73] { + background-color: #5FAFAF +} + +div.highlight .-Color[class*=-C74] { + color: #5FAFD7 +} + +div.highlight .-Color[class*=-BGC74] { + background-color: #5FAFD7 +} + +div.highlight .-Color[class*=-C75] { + color: #5FAFFF +} + +div.highlight .-Color[class*=-BGC75] { + background-color: #5FAFFF +} + +div.highlight .-Color[class*=-C76] { + color: #5FD700 +} + +div.highlight .-Color[class*=-BGC76] { + background-color: #5FD700 +} + +div.highlight .-Color[class*=-C77] { + color: #5FD75F +} + +div.highlight .-Color[class*=-BGC77] { + background-color: #5FD75F +} + +div.highlight .-Color[class*=-C78] { + color: #5FD787 +} + +div.highlight .-Color[class*=-BGC78] { + background-color: #5FD787 +} + +div.highlight .-Color[class*=-C79] { + color: #5FD7AF +} + +div.highlight .-Color[class*=-BGC79] { + background-color: #5FD7AF +} + +div.highlight .-Color[class*=-C80] { + color: #5FD7D7 +} + +div.highlight .-Color[class*=-BGC80] { + background-color: #5FD7D7 +} + +div.highlight .-Color[class*=-C81] { + color: #5FD7FF +} + +div.highlight .-Color[class*=-BGC81] { + background-color: #5FD7FF +} + +div.highlight .-Color[class*=-C82] { + color: #5FFF00 +} + +div.highlight .-Color[class*=-BGC82] { + background-color: #5FFF00 +} + +div.highlight .-Color[class*=-C83] { + color: #5FFF5F +} + +div.highlight .-Color[class*=-BGC83] { + background-color: #5FFF5F +} + +div.highlight .-Color[class*=-C84] { + color: #5FFF87 +} + +div.highlight .-Color[class*=-BGC84] { + background-color: #5FFF87 +} + +div.highlight .-Color[class*=-C85] { + color: #5FFFAF +} + +div.highlight .-Color[class*=-BGC85] { + background-color: #5FFFAF +} + +div.highlight .-Color[class*=-C86] { + color: #5FFFD7 +} + +div.highlight .-Color[class*=-BGC86] { + background-color: #5FFFD7 +} + +div.highlight .-Color[class*=-C87] { + color: #5FFFFF +} + +div.highlight .-Color[class*=-BGC87] { + background-color: #5FFFFF +} + +div.highlight .-Color[class*=-C88] { + color: #870000 +} + +div.highlight .-Color[class*=-BGC88] { + background-color: #870000 +} + +div.highlight .-Color[class*=-C89] { + color: #87005F +} + +div.highlight .-Color[class*=-BGC89] { + background-color: #87005F +} + +div.highlight .-Color[class*=-C90] { + color: #870087 +} + +div.highlight .-Color[class*=-BGC90] { + background-color: #870087 +} + +div.highlight .-Color[class*=-C91] { + color: #8700AF +} + +div.highlight .-Color[class*=-BGC91] { + background-color: #8700AF +} + +div.highlight .-Color[class*=-C92] { + color: #8700D7 +} + +div.highlight .-Color[class*=-BGC92] { + background-color: #8700D7 +} + +div.highlight .-Color[class*=-C93] { + color: #8700FF +} + +div.highlight .-Color[class*=-BGC93] { + background-color: #8700FF +} + +div.highlight .-Color[class*=-C94] { + color: #875F00 +} + +div.highlight .-Color[class*=-BGC94] { + background-color: #875F00 +} + +div.highlight .-Color[class*=-C95] { + color: #875F5F +} + +div.highlight .-Color[class*=-BGC95] { + background-color: #875F5F +} + +div.highlight .-Color[class*=-C96] { + color: #875F87 +} + +div.highlight .-Color[class*=-BGC96] { + background-color: #875F87 +} + +div.highlight .-Color[class*=-C97] { + color: #875FAF +} + +div.highlight .-Color[class*=-BGC97] { + background-color: #875FAF +} + +div.highlight .-Color[class*=-C98] { + color: #875FD7 +} + +div.highlight .-Color[class*=-BGC98] { + background-color: #875FD7 +} + +div.highlight .-Color[class*=-C99] { + color: #875FFF +} + +div.highlight .-Color[class*=-BGC99] { + background-color: #875FFF +} + +div.highlight .-Color[class*=-C100] { + color: #878700 +} + +div.highlight .-Color[class*=-BGC100] { + background-color: #878700 +} + +div.highlight .-Color[class*=-C101] { + color: #87875F +} + +div.highlight .-Color[class*=-BGC101] { + background-color: #87875F +} + +div.highlight .-Color[class*=-C102] { + color: #878787 +} + +div.highlight .-Color[class*=-BGC102] { + background-color: #878787 +} + +div.highlight .-Color[class*=-C103] { + color: #8787AF +} + +div.highlight .-Color[class*=-BGC103] { + background-color: #8787AF +} + +div.highlight .-Color[class*=-C104] { + color: #8787D7 +} + +div.highlight .-Color[class*=-BGC104] { + background-color: #8787D7 +} + +div.highlight .-Color[class*=-C105] { + color: #8787FF +} + +div.highlight .-Color[class*=-BGC105] { + background-color: #8787FF +} + +div.highlight .-Color[class*=-C106] { + color: #87AF00 +} + +div.highlight .-Color[class*=-BGC106] { + background-color: #87AF00 +} + +div.highlight .-Color[class*=-C107] { + color: #87AF5F +} + +div.highlight .-Color[class*=-BGC107] { + background-color: #87AF5F +} + +div.highlight .-Color[class*=-C108] { + color: #87AF87 +} + +div.highlight .-Color[class*=-BGC108] { + background-color: #87AF87 +} + +div.highlight .-Color[class*=-C109] { + color: #87AFAF +} + +div.highlight .-Color[class*=-BGC109] { + background-color: #87AFAF +} + +div.highlight .-Color[class*=-C110] { + color: #87AFD7 +} + +div.highlight .-Color[class*=-BGC110] { + background-color: #87AFD7 +} + +div.highlight .-Color[class*=-C111] { + color: #87AFFF +} + +div.highlight .-Color[class*=-BGC111] { + background-color: #87AFFF +} + +div.highlight .-Color[class*=-C112] { + color: #87D700 +} + +div.highlight .-Color[class*=-BGC112] { + background-color: #87D700 +} + +div.highlight .-Color[class*=-C113] { + color: #87D75F +} + +div.highlight .-Color[class*=-BGC113] { + background-color: #87D75F +} + +div.highlight .-Color[class*=-C114] { + color: #87D787 +} + +div.highlight .-Color[class*=-BGC114] { + background-color: #87D787 +} + +div.highlight .-Color[class*=-C115] { + color: #87D7AF +} + +div.highlight .-Color[class*=-BGC115] { + background-color: #87D7AF +} + +div.highlight .-Color[class*=-C116] { + color: #87D7D7 +} + +div.highlight .-Color[class*=-BGC116] { + background-color: #87D7D7 +} + +div.highlight .-Color[class*=-C117] { + color: #87D7FF +} + +div.highlight .-Color[class*=-BGC117] { + background-color: #87D7FF +} + +div.highlight .-Color[class*=-C118] { + color: #87FF00 +} + +div.highlight .-Color[class*=-BGC118] { + background-color: #87FF00 +} + +div.highlight .-Color[class*=-C119] { + color: #87FF5F +} + +div.highlight .-Color[class*=-BGC119] { + background-color: #87FF5F +} + +div.highlight .-Color[class*=-C120] { + color: #87FF87 +} + +div.highlight .-Color[class*=-BGC120] { + background-color: #87FF87 +} + +div.highlight .-Color[class*=-C121] { + color: #87FFAF +} + +div.highlight .-Color[class*=-BGC121] { + background-color: #87FFAF +} + +div.highlight .-Color[class*=-C122] { + color: #87FFD7 +} + +div.highlight .-Color[class*=-BGC122] { + background-color: #87FFD7 +} + +div.highlight .-Color[class*=-C123] { + color: #87FFFF +} + +div.highlight .-Color[class*=-BGC123] { + background-color: #87FFFF +} + +div.highlight .-Color[class*=-C124] { + color: #AF0000 +} + +div.highlight .-Color[class*=-BGC124] { + background-color: #AF0000 +} + +div.highlight .-Color[class*=-C125] { + color: #AF005F +} + +div.highlight .-Color[class*=-BGC125] { + background-color: #AF005F +} + +div.highlight .-Color[class*=-C126] { + color: #AF0087 +} + +div.highlight .-Color[class*=-BGC126] { + background-color: #AF0087 +} + +div.highlight .-Color[class*=-C127] { + color: #AF00AF +} + +div.highlight .-Color[class*=-BGC127] { + background-color: #AF00AF +} + +div.highlight .-Color[class*=-C128] { + color: #AF00D7 +} + +div.highlight .-Color[class*=-BGC128] { + background-color: #AF00D7 +} + +div.highlight .-Color[class*=-C129] { + color: #AF00FF +} + +div.highlight .-Color[class*=-BGC129] { + background-color: #AF00FF +} + +div.highlight .-Color[class*=-C130] { + color: #AF5F00 +} + +div.highlight .-Color[class*=-BGC130] { + background-color: #AF5F00 +} + +div.highlight .-Color[class*=-C131] { + color: #AF5F5F +} + +div.highlight .-Color[class*=-BGC131] { + background-color: #AF5F5F +} + +div.highlight .-Color[class*=-C132] { + color: #AF5F87 +} + +div.highlight .-Color[class*=-BGC132] { + background-color: #AF5F87 +} + +div.highlight .-Color[class*=-C133] { + color: #AF5FAF +} + +div.highlight .-Color[class*=-BGC133] { + background-color: #AF5FAF +} + +div.highlight .-Color[class*=-C134] { + color: #AF5FD7 +} + +div.highlight .-Color[class*=-BGC134] { + background-color: #AF5FD7 +} + +div.highlight .-Color[class*=-C135] { + color: #AF5FFF +} + +div.highlight .-Color[class*=-BGC135] { + background-color: #AF5FFF +} + +div.highlight .-Color[class*=-C136] { + color: #AF8700 +} + +div.highlight .-Color[class*=-BGC136] { + background-color: #AF8700 +} + +div.highlight .-Color[class*=-C137] { + color: #AF875F +} + +div.highlight .-Color[class*=-BGC137] { + background-color: #AF875F +} + +div.highlight .-Color[class*=-C138] { + color: #AF8787 +} + +div.highlight .-Color[class*=-BGC138] { + background-color: #AF8787 +} + +div.highlight .-Color[class*=-C139] { + color: #AF87AF +} + +div.highlight .-Color[class*=-BGC139] { + background-color: #AF87AF +} + +div.highlight .-Color[class*=-C140] { + color: #AF87D7 +} + +div.highlight .-Color[class*=-BGC140] { + background-color: #AF87D7 +} + +div.highlight .-Color[class*=-C141] { + color: #AF87FF +} + +div.highlight .-Color[class*=-BGC141] { + background-color: #AF87FF +} + +div.highlight .-Color[class*=-C142] { + color: #AFAF00 +} + +div.highlight .-Color[class*=-BGC142] { + background-color: #AFAF00 +} + +div.highlight .-Color[class*=-C143] { + color: #AFAF5F +} + +div.highlight .-Color[class*=-BGC143] { + background-color: #AFAF5F +} + +div.highlight .-Color[class*=-C144] { + color: #AFAF87 +} + +div.highlight .-Color[class*=-BGC144] { + background-color: #AFAF87 +} + +div.highlight 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score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms, anchor) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + "Search finished, found ${resultCount} page(s) matching the search query." + ).replace('${resultCount}', resultCount); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString, anchor) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + for (const removalQuery of [".headerlink", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent) return docContent.textContent; + + console.warn( + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + _parseQuery: (query) => { + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename]. + const normalResults = []; + const nonMainIndexResults = []; + + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase().trim(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + const score = Math.round(Scorer.title * queryLower.length / title.length); + const boost = titles[file] === title ? 1 : 0; // add a boost for document titles + normalResults.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score + boost, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } + } + } + } + + // lookup as object + objectTerms.forEach((term) => + normalResults.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/_static/sphinx_highlight.js b/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/_static/sphinx_lesson.css b/_static/sphinx_lesson.css new file mode 100644 index 0000000..14b20c6 --- /dev/null +++ b/_static/sphinx_lesson.css @@ -0,0 +1,51 @@ +/* sphinx_lesson.css */ + +body.wy-body-for-nav img.with-border { + border: 2px solid; +} + +.rst-content .admonition-no-content { + padding-bottom: 0px; +} + +.rst-content .demo > .admonition-title::before { + content: "\01F440"; /* Eyes */ } +.rst-content .type-along > .admonition-title::before { + content: "\02328\0FE0F"; /* Keyboard */ } +.rst-content .exercise > .admonition-title::before { + content: "\0270D\0FE0F"; /* Hand */ } +.rst-content .solution > .admonition-title::before { + content: "\02714\0FE0E"; /* Check mark */ } +.rst-content .homework > .admonition-title::before { + content: "\01F4DD"; /* Memo */ } +.rst-content .discussion > .admonition-title::before { + content: "\01F4AC"; /* Speech balloon */ } +.rst-content .questions > .admonition-title::before { + content: "\02753\0FE0E"; /* Question mark */ } +.rst-content .prerequisites > .admonition-title::before { + content: "\02699"; /* Gear */ } +.rst-content .seealso > .admonition-title::before { + content: "\027A1\0FE0E"; /* Question mark */ } + + +/* instructor-note */ +.rst-content .instructor-note { + background: #e7e7e7; +} +.rst-content .instructor-note > .admonition-title { + background: #6a6a6a; +} +.rst-content .instructor-note > .admonition-title::before { + content: ""; +} + + +/* sphinx_toggle_button, make the font white */ +.rst-content .toggle.admonition button.toggle-button { + color: white; +} + +/* sphinx-togglebutton, remove underflow when toggled to hidden mode */ +.rst-content .admonition.toggle-hidden { + padding-bottom: 0px; +} diff --git a/_static/sphinx_rtd_theme_ext_color_contrast.css b/_static/sphinx_rtd_theme_ext_color_contrast.css new file mode 100644 index 0000000..e68feb8 --- /dev/null +++ b/_static/sphinx_rtd_theme_ext_color_contrast.css @@ -0,0 +1,47 @@ +/* The following are for web accessibility of sphinx_rtd_theme: they + * solve some of the most frequent contrast issues. Remove when this + * solved: + * https://github.com/readthedocs/sphinx_rtd_theme/issues/971 + */ +/* background: #fcfcfc, note boxes #E7F2FA */ +a { color: #2573A7; } /* original #2980B9, #1F5C84; */ +body { color: #242424; } /* original #404040, #383838 */ +.wy-side-nav-search>a, .wy-side-nav-search .wy-dropdown>a { + color: #ffffff; +} /* original #fcfcfc */ +footer { color: #737373; } /* original gray=#808080*/ +footer span.commit code, footer span.commit .rst-content tt, .rst-content footer span.commit tt { + color: #737373; +} /* original gray=#808080*/ +.rst-content tt.literal, .rst-content tt.literal, .rst-content code.literal { + color: #AB2314; +} +/* Sidebar background */ +.wy-side-nav-search { background-color: #277CB4;} + +/* Same, but for pygments */ +.highlight .ch { color: #3E7A89; } /* #! line */ +.highlight .c1 { color: #3E7A89; } /* also comments */ +.highlight .nv { color: #AD3ECC; } /* variable */ +.highlight .gp { color: #B45608; } /* prompt character, $*/ +.highlight .si { color: #3975B1; } /* ${} variable text */ +.highlight .nc { color: #0C78A7; } + +/* Sphinx admonitions */ +/* warning */ +.wy-alert.wy-alert-warning .wy-alert-title, .rst-content .wy-alert-warning.note .wy-alert-title, .rst-content .attention .wy-alert-title, .rst-content .caution .wy-alert-title, .rst-content .wy-alert-warning.danger .wy-alert-title, .rst-content .wy-alert-warning.error .wy-alert-title, .rst-content .wy-alert-warning.hint .wy-alert-title, .rst-content .wy-alert-warning.important .wy-alert-title, .rst-content .wy-alert-warning.tip .wy-alert-title, .rst-content .warning .wy-alert-title, .rst-content .wy-alert-warning.seealso .wy-alert-title, .rst-content .admonition-todo .wy-alert-title, .rst-content .wy-alert-warning.admonition .wy-alert-title, .wy-alert.wy-alert-warning .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-warning .admonition-title, .rst-content .wy-alert-warning.note .admonition-title, .rst-content .attention .admonition-title, .rst-content .caution .admonition-title, .rst-content .wy-alert-warning.danger .admonition-title, .rst-content .wy-alert-warning.error .admonition-title, .rst-content .wy-alert-warning.hint .admonition-title, .rst-content .wy-alert-warning.important .admonition-title, .rst-content .wy-alert-warning.tip .admonition-title, .rst-content .warning .admonition-title, .rst-content .wy-alert-warning.seealso .admonition-title, .rst-content .admonition-todo .admonition-title, .rst-content .wy-alert-warning.admonition .admonition-title { + background: #B15E16; } +/* important */ +.wy-alert.wy-alert-success .wy-alert-title, .rst-content .wy-alert-success.note .wy-alert-title, .rst-content .wy-alert-success.attention .wy-alert-title, .rst-content .wy-alert-success.caution .wy-alert-title, .rst-content .wy-alert-success.danger .wy-alert-title, .rst-content .wy-alert-success.error .wy-alert-title, .rst-content .hint .wy-alert-title, .rst-content .important .wy-alert-title, .rst-content .tip .wy-alert-title, .rst-content .wy-alert-success.warning .wy-alert-title, .rst-content .wy-alert-success.seealso .wy-alert-title, .rst-content .wy-alert-success.admonition-todo .wy-alert-title, .rst-content .wy-alert-success.admonition .wy-alert-title, .wy-alert.wy-alert-success .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-success .admonition-title, .rst-content .wy-alert-success.note .admonition-title, .rst-content .wy-alert-success.attention .admonition-title, .rst-content .wy-alert-success.caution .admonition-title, .rst-content .wy-alert-success.danger .admonition-title, .rst-content .wy-alert-success.error .admonition-title, .rst-content .hint .admonition-title, .rst-content .important .admonition-title, .rst-content .tip .admonition-title, .rst-content .wy-alert-success.warning .admonition-title, .rst-content .wy-alert-success.seealso .admonition-title, .rst-content .wy-alert-success.admonition-todo .admonition-title, .rst-content .wy-alert-success.admonition .admonition-title { + background: #12826C; } +/* seealso, note, etc */ +.wy-alert.wy-alert-info .wy-alert-title, .rst-content .note .wy-alert-title, .rst-content .wy-alert-info.attention .wy-alert-title, .rst-content .wy-alert-info.caution .wy-alert-title, .rst-content .wy-alert-info.danger .wy-alert-title, .rst-content .wy-alert-info.error .wy-alert-title, .rst-content .wy-alert-info.hint .wy-alert-title, .rst-content .wy-alert-info.important .wy-alert-title, .rst-content .wy-alert-info.tip .wy-alert-title, .rst-content .wy-alert-info.warning .wy-alert-title, .rst-content .seealso .wy-alert-title, .rst-content .wy-alert-info.admonition-todo .wy-alert-title, .rst-content .wy-alert-info.admonition .wy-alert-title, .wy-alert.wy-alert-info .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-info .admonition-title, .rst-content .note .admonition-title, .rst-content .wy-alert-info.attention .admonition-title, .rst-content .wy-alert-info.caution .admonition-title, .rst-content .wy-alert-info.danger .admonition-title, .rst-content .wy-alert-info.error .admonition-title, .rst-content .wy-alert-info.hint .admonition-title, .rst-content .wy-alert-info.important .admonition-title, .rst-content .wy-alert-info.tip .admonition-title, .rst-content .wy-alert-info.warning .admonition-title, .rst-content .seealso .admonition-title, .rst-content .wy-alert-info.admonition-todo .admonition-title, .rst-content .wy-alert-info.admonition .admonition-title { + background: #277CB4; } +/* error, danger */ +.rst-content .danger .admonition-title, .rst-content .danger .wy-alert-title, .rst-content .error .admonition-title, .rst-content .error .wy-alert-title, .rst-content .wy-alert-danger.admonition-todo .admonition-title, .rst-content .wy-alert-danger.admonition-todo .wy-alert-title, .rst-content .wy-alert-danger.admonition .admonition-title, .rst-content .wy-alert-danger.admonition .wy-alert-title, .rst-content .wy-alert-danger.attention .admonition-title, .rst-content .wy-alert-danger.attention .wy-alert-title, .rst-content .wy-alert-danger.caution .admonition-title, .rst-content .wy-alert-danger.caution .wy-alert-title, .rst-content .wy-alert-danger.hint .admonition-title, .rst-content .wy-alert-danger.hint .wy-alert-title, .rst-content .wy-alert-danger.important .admonition-title, .rst-content .wy-alert-danger.important .wy-alert-title, .rst-content .wy-alert-danger.note .admonition-title, .rst-content .wy-alert-danger.note .wy-alert-title, .rst-content .wy-alert-danger.seealso .admonition-title, .rst-content .wy-alert-danger.seealso .wy-alert-title, .rst-content .wy-alert-danger.tip .admonition-title, .rst-content .wy-alert-danger.tip .wy-alert-title, .rst-content .wy-alert-danger.warning .admonition-title, .rst-content .wy-alert-danger.warning .wy-alert-title, .rst-content .wy-alert.wy-alert-danger .admonition-title, .wy-alert.wy-alert-danger .rst-content .admonition-title, .wy-alert.wy-alert-danger .wy-alert-title { + background: #e31704; +} + +/* Generic admonition titles */ +.wy-alert-title, .rst-content .admonition-title { + background: #277CB4; } diff --git a/_static/style.css b/_static/style.css new file mode 100644 index 0000000..59e60ee --- /dev/null +++ b/_static/style.css @@ -0,0 +1,6 @@ +.rst-content .objectives { + background: #fee0d2; +} +.rst-content .objectives > .admonition-title { + background: #fc9272; +} diff --git a/_static/tabs.css b/_static/tabs.css new file mode 100644 index 0000000..957ba60 --- /dev/null +++ b/_static/tabs.css @@ -0,0 +1,89 @@ +.sphinx-tabs { + margin-bottom: 1rem; +} + +[role="tablist"] { + border-bottom: 1px solid #a0b3bf; +} + +.sphinx-tabs-tab { + position: relative; + font-family: Lato,'Helvetica Neue',Arial,Helvetica,sans-serif; + color: #1D5C87; + line-height: 24px; + margin: 0; + font-size: 16px; + font-weight: 400; + background-color: rgba(255, 255, 255, 0); + border-radius: 5px 5px 0 0; + border: 0; + padding: 1rem 1.5rem; + margin-bottom: 0; +} + +.sphinx-tabs-tab[aria-selected="true"] { + font-weight: 700; + border: 1px solid #a0b3bf; + border-bottom: 1px solid white; + margin: -1px; + background-color: white; +} + +.sphinx-tabs-tab:focus { + z-index: 1; + outline-offset: 1px; +} + +.sphinx-tabs-panel { + position: relative; + padding: 1rem; + border: 1px solid #a0b3bf; + margin: 0px -1px -1px -1px; + border-radius: 0 0 5px 5px; + border-top: 0; + background: white; +} + +.sphinx-tabs-panel.code-tab { + padding: 0.4rem; +} + +.sphinx-tab img { + margin-bottom: 24 px; +} + +/* Dark theme preference styling */ + +@media (prefers-color-scheme: dark) { + body[data-theme="auto"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); + } + + body[data-theme="auto"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); + } + + body[data-theme="auto"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 1px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); + } +} + +/* Explicit dark theme styling */ + +body[data-theme="dark"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); +} + +body[data-theme="dark"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); +} + +body[data-theme="dark"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 2px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); +} diff --git a/_static/tabs.js b/_static/tabs.js new file mode 100644 index 0000000..48dc303 --- /dev/null +++ b/_static/tabs.js @@ -0,0 +1,145 @@ +try { + var session = window.sessionStorage || {}; +} catch (e) { + var session = {}; +} + +window.addEventListener("DOMContentLoaded", () => { + const allTabs = document.querySelectorAll('.sphinx-tabs-tab'); + const tabLists = document.querySelectorAll('[role="tablist"]'); + + allTabs.forEach(tab => { + tab.addEventListener("click", changeTabs); + }); + + tabLists.forEach(tabList => { + tabList.addEventListener("keydown", keyTabs); + }); + + // Restore group tab selection from session + const lastSelected = session.getItem('sphinx-tabs-last-selected'); + if (lastSelected != null) selectNamedTabs(lastSelected); +}); + +/** + * Key focus left and right between sibling elements using arrows + * @param {Node} e the element in focus when key was pressed + */ +function keyTabs(e) { + const tab = e.target; + let nextTab = null; + if (e.keyCode === 39 || e.keyCode === 37) { + tab.setAttribute("tabindex", -1); + // Move right + if (e.keyCode === 39) { + nextTab = tab.nextElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.firstElementChild; + } + // Move left + } else if (e.keyCode === 37) { + nextTab = tab.previousElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.lastElementChild; + } + } + } + + if (nextTab !== null) { + nextTab.setAttribute("tabindex", 0); + nextTab.focus(); + } +} + +/** + * Select or deselect clicked tab. If a group tab + * is selected, also select tab in other tabLists. + * @param {Node} e the element that was clicked + */ +function changeTabs(e) { + // Use this instead of the element that was clicked, in case it's a child + const notSelected = this.getAttribute("aria-selected") === "false"; + const positionBefore = this.parentNode.getBoundingClientRect().top; + const notClosable = !this.parentNode.classList.contains("closeable"); + + deselectTabList(this); + + if (notSelected || notClosable) { + selectTab(this); + const name = this.getAttribute("name"); + selectNamedTabs(name, this.id); + + if (this.classList.contains("group-tab")) { + // Persist during session + session.setItem('sphinx-tabs-last-selected', name); + } + } + + const positionAfter = this.parentNode.getBoundingClientRect().top; + const positionDelta = positionAfter - positionBefore; + // Scroll to offset content resizing + window.scrollTo(0, window.scrollY + positionDelta); +} + +/** + * Select tab and show associated panel. + * @param {Node} tab tab to select + */ +function selectTab(tab) { + tab.setAttribute("aria-selected", true); + + // Show the associated panel + document + .getElementById(tab.getAttribute("aria-controls")) + .removeAttribute("hidden"); +} + +/** + * Hide the panels associated with all tabs within the + * tablist containing this tab. + * @param {Node} tab a tab within the tablist to deselect + */ +function deselectTabList(tab) { + const parent = tab.parentNode; + const grandparent = parent.parentNode; + + Array.from(parent.children) + .forEach(t => t.setAttribute("aria-selected", false)); + + Array.from(grandparent.children) + .slice(1) // Skip tablist + .forEach(panel => panel.setAttribute("hidden", true)); +} + +/** + * Select grouped tabs with the same name, but no the tab + * with the given id. + * @param {Node} name name of grouped tab to be selected + * @param {Node} clickedId id of clicked tab + */ +function selectNamedTabs(name, clickedId=null) { + const groupedTabs = document.querySelectorAll(`.sphinx-tabs-tab[name="${name}"]`); + const tabLists = Array.from(groupedTabs).map(tab => tab.parentNode); + + tabLists + .forEach(tabList => { + // Don't want to change the tabList containing the clicked tab + const clickedTab = tabList.querySelector(`[id="${clickedId}"]`); + if (clickedTab === null ) { + // Select first tab with matching name + const tab = tabList.querySelector(`.sphinx-tabs-tab[name="${name}"]`); + deselectTabList(tab); + selectTab(tab); + } + }) +} + +if (typeof exports === 'undefined') { + exports = {}; +} + +exports.keyTabs = keyTabs; +exports.changeTabs = changeTabs; +exports.selectTab = selectTab; +exports.deselectTabList = deselectTabList; +exports.selectNamedTabs = selectNamedTabs; diff --git a/_static/term_role_formatting.css b/_static/term_role_formatting.css new file mode 100644 index 0000000..0b66095 --- /dev/null +++ b/_static/term_role_formatting.css @@ -0,0 +1,4 @@ +/* Make terms bold */ +a.reference span.std-term { + font-weight: bold; +} diff --git a/_static/togglebutton.css b/_static/togglebutton.css new file mode 100644 index 0000000..54a6787 --- /dev/null +++ b/_static/togglebutton.css @@ -0,0 +1,160 @@ +/** + * Admonition-based toggles + */ + +/* Visibility of the target */ +.admonition.toggle .admonition-title ~ * { + transition: opacity .3s, height .3s; +} + +/* Toggle buttons inside admonitions so we see the title */ +.admonition.toggle { + position: relative; +} + +/* Titles should cut off earlier to avoid overlapping w/ button */ +.admonition.toggle .admonition-title { + padding-right: 25%; + cursor: pointer; +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:hover { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 1%); +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:active { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 3%); +} + +/* Remove extra whitespace below the admonition title when hidden */ +.admonition.toggle-hidden { + padding-bottom: 0; +} + +.admonition.toggle-hidden .admonition-title { + margin-bottom: 0; +} + +/* hides all the content of a page until de-toggled */ +.admonition.toggle-hidden .admonition-title ~ * { + height: 0; + margin: 0; + opacity: 0; + visibility: hidden; +} + +/* General button style and position*/ +button.toggle-button { + /** + * Background and shape. By default there's no background + * but users can style as they wish + */ + background: none; + border: none; + outline: none; + + /* Positioning just inside the admonition title */ + position: absolute; + right: 0.5em; + padding: 0px; + border: none; + outline: none; +} + +/* Display the toggle hint on wide screens */ +@media (min-width: 768px) { + button.toggle-button.toggle-button-hidden:before { + content: attr(data-toggle-hint); /* This will be filled in by JS */ + font-size: .8em; + align-self: center; + } +} + +/* Icon behavior */ +.tb-icon { + transition: transform .2s ease-out; + height: 1.5em; + width: 1.5em; + stroke: currentColor; /* So that we inherit the color of other text */ +} + +/* The icon should point right when closed, down when open. */ +/* Open */ +.admonition.toggle button .tb-icon { + transform: rotate(90deg); +} + +/* Closed */ +.admonition.toggle button.toggle-button-hidden .tb-icon { + transform: rotate(0deg); +} + +/* With details toggles, we don't rotate the icon so it points right */ +details.toggle-details .tb-icon { + height: 1.4em; + width: 1.4em; + margin-top: 0.1em; /* To center the button vertically */ +} + + +/** + * Details-based toggles. + * In this case, we wrap elements with `.toggle` in a details block. + */ + +/* Details blocks */ +details.toggle-details { + margin: 1em 0; +} + + +details.toggle-details summary { + display: flex; + align-items: center; + cursor: pointer; + list-style: none; + border-radius: .2em; + border-left: 3px solid #1976d2; + background-color: rgb(204 204 204 / 10%); + padding: 0.2em 0.7em 0.3em 0.5em; /* Less padding on left because the SVG has left margin */ + font-size: 0.9em; +} + +details.toggle-details summary:hover { + background-color: rgb(204 204 204 / 20%); +} + +details.toggle-details summary:active { + background: rgb(204 204 204 / 28%); +} + +.toggle-details__summary-text { + margin-left: 0.2em; +} + +details.toggle-details[open] summary { + margin-bottom: .5em; +} + +details.toggle-details[open] summary .tb-icon { + transform: rotate(90deg); +} + +details.toggle-details[open] summary ~ * { + animation: toggle-fade-in .3s ease-out; +} + +@keyframes toggle-fade-in { + from {opacity: 0%;} + to {opacity: 100%;} +} + +/* Print rules - we hide all toggle button elements at print */ +@media print { + /* Always hide the summary so the button doesn't show up */ + details.toggle-details summary { + display: none; + } +} \ No newline at end of file diff --git a/_static/togglebutton.js b/_static/togglebutton.js new file mode 100644 index 0000000..215a7ee --- /dev/null +++ b/_static/togglebutton.js @@ -0,0 +1,187 @@ +/** + * Add Toggle Buttons to elements + */ + +let toggleChevron = ` + + + +`; + +var initToggleItems = () => { + var itemsToToggle = document.querySelectorAll(togglebuttonSelector); + console.log(`[togglebutton]: Adding toggle buttons to ${itemsToToggle.length} items`) + // Add the button to each admonition and hook up a callback to toggle visibility + itemsToToggle.forEach((item, index) => { + if (item.classList.contains("admonition")) { + // If it's an admonition block, then we'll add a button inside + // Generate unique IDs for this item + var toggleID = `toggle-${index}`; + var buttonID = `button-${toggleID}`; + + item.setAttribute('id', toggleID); + if (!item.classList.contains("toggle")){ + item.classList.add("toggle"); + } + // This is the button that will be added to each item to trigger the toggle + var collapseButton = ` + `; + + title = item.querySelector(".admonition-title") + title.insertAdjacentHTML("beforeend", collapseButton); + thisButton = document.getElementById(buttonID); + + // Add click handlers for the button + admonition title (if admonition) + admonitionTitle = document.querySelector(`#${toggleID} > .admonition-title`) + if (admonitionTitle) { + // If an admonition, then make the whole title block clickable + admonitionTitle.addEventListener('click', toggleClickHandler); + admonitionTitle.dataset.target = toggleID + admonitionTitle.dataset.button = buttonID + } else { + // If not an admonition then we'll listen for the button click + thisButton.addEventListener('click', toggleClickHandler); + } + + // Now hide the item for this toggle button unless explicitly noted to show + if (!item.classList.contains("toggle-shown")) { + toggleHidden(thisButton); + } + } else { + // If not an admonition, wrap the block in a
block + // Define the structure of the details block and insert it as a sibling + var detailsBlock = ` +
+ + ${toggleChevron} + ${toggleHintShow} + +
`; + item.insertAdjacentHTML("beforebegin", detailsBlock); + + // Now move the toggle-able content inside of the details block + details = item.previousElementSibling + details.appendChild(item) + item.classList.add("toggle-details__container") + + // Set up a click trigger to change the text as needed + details.addEventListener('click', (click) => { + let parent = click.target.parentElement; + if (parent.tagName.toLowerCase() == "details") { + summary = parent.querySelector("summary"); + details = parent; + } else { + summary = parent; + details = parent.parentElement; + } + // Update the inner text for the proper hint + if (details.open) { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintShow; + } else { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintHide; + } + + }); + + // If we have a toggle-shown class, open details block should be open + if (item.classList.contains("toggle-shown")) { + details.click(); + } + } + }) +}; + +// This should simply add / remove the collapsed class and change the button text +var toggleHidden = (button) => { + target = button.dataset['target'] + var itemToToggle = document.getElementById(target); + if (itemToToggle.classList.contains("toggle-hidden")) { + itemToToggle.classList.remove("toggle-hidden"); + button.classList.remove("toggle-button-hidden"); + } else { + itemToToggle.classList.add("toggle-hidden"); + button.classList.add("toggle-button-hidden"); + } +} + +var toggleClickHandler = (click) => { + // Be cause the admonition title is clickable and extends to the whole admonition + // We only look for a click event on this title to trigger the toggle. + + if (click.target.classList.contains("admonition-title")) { + button = click.target.querySelector(".toggle-button"); + } else if (click.target.classList.contains("tb-icon")) { + // We've clicked the icon and need to search up one parent for the button + button = click.target.parentElement; + } else if (click.target.tagName == "polyline") { + // We've clicked the SVG elements inside the button, need to up 2 layers + button = click.target.parentElement.parentElement; + } else if (click.target.classList.contains("toggle-button")) { + // We've clicked the button itself and so don't need to do anything + button = click.target; + } else { + console.log(`[togglebutton]: Couldn't find button for ${click.target}`) + } + target = document.getElementById(button.dataset['button']); + toggleHidden(target); +} + +// If we want to blanket-add toggle classes to certain cells +var addToggleToSelector = () => { + const selector = ""; + if (selector.length > 0) { + document.querySelectorAll(selector).forEach((item) => { + item.classList.add("toggle"); + }) + } +} + +// Helper function to run when the DOM is finished +const sphinxToggleRunWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} +sphinxToggleRunWhenDOMLoaded(addToggleToSelector) +sphinxToggleRunWhenDOMLoaded(initToggleItems) + +/** Toggle details blocks to be open when printing */ +if (toggleOpenOnPrint == "true") { + window.addEventListener("beforeprint", () => { + // Open the details + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.dataset["togglestatus"] = el.open; + el.open = true; + }); + + // Open the admonitions + document.querySelectorAll(".admonition.toggle.toggle-hidden").forEach((el) => { + console.log(el); + el.querySelector("button.toggle-button").click(); + el.dataset["toggle_after_print"] = "true"; + }); + }); + window.addEventListener("afterprint", () => { + // Re-close the details that were closed + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.open = el.dataset["togglestatus"] == "true"; + delete el.dataset["togglestatus"]; + }); + + // Re-close the admonition toggle buttons + document.querySelectorAll(".admonition.toggle").forEach((el) => { + if (el.dataset["toggle_after_print"] == "true") { + el.querySelector("button.toggle-button").click(); + delete el.dataset["toggle_after_print"]; + } + }); + }); +} diff --git a/branch/main/_images/add-suggestion.png b/branch/main/_images/add-suggestion.png new file mode 100644 index 0000000..0a28544 Binary files /dev/null and b/branch/main/_images/add-suggestion.png differ diff --git a/branch/main/_images/all-checks-failed.png b/branch/main/_images/all-checks-failed.png new file mode 100644 index 0000000..5175684 Binary files /dev/null and b/branch/main/_images/all-checks-failed.png differ diff --git a/branch/main/_images/animation.mp4 b/branch/main/_images/animation.mp4 new file mode 100644 index 0000000..f037fd4 Binary files /dev/null and b/branch/main/_images/animation.mp4 differ diff --git a/branch/main/_images/bare-repository.png 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a/branch/main/_sources/collaboration/code-review.md.txt b/branch/main/_sources/collaboration/code-review.md.txt new file mode 100644 index 0000000..4a55b03 --- /dev/null +++ b/branch/main/_sources/collaboration/code-review.md.txt @@ -0,0 +1,144 @@ +(code-review)= + +# Practicing code review + +In this episode we will practice the code review process. We will learn how to +ask for changes in a pull request, how to suggest a change in a pull request, +and how to modify a pull request. + +This will enable research groups to work more collaboratively and to not only +improve the code quality but also to learn from each other. + + +## Exercise + +:::{prereq} Exercise preparation +We can continue in the same exercise repository which we have used in the +previous episode. +::: + +:::{exercise} Exercise: Practicing code review (25 min) + +**Technical requirements**: +- If you create the commits locally: [Being able to authenticate to GitHub](https://coderefinery.github.io/installation/ssh/) + +**What is familiar** from previous lessons: +- Creating a branch. +- Committing a change on the new branch. +- Opening and merging pull requests. + +**What will be new** in this exercise: +- As a reviewer, we will learn how to ask for changes in a pull request. +- As a reviewer, we will learn how to suggest a change in a pull request. +- As a submitter, we will learn how to modify a pull request without closing + the incomplete one and opening a new one. + +**Exercise tasks**: +1. Create a new branch and one or few commits: in these improve something but also + deliberately introduce a typo and also a larger mistake which we will want to fix during the code review. +1. Open a pull request towards the main branch. +1. As a reviewer to somebody else's pull request, ask for an improvement and + also directly suggest a change for the small typo. (Hint: + suggestions are possible through the GitHub web interface, view of + a pull request, "Files changed" view, after selecting some lines. + Look for the "±" button.) +1. As the submitter, learn how to accept the suggested change. (Hint: + GitHub web interface, "Files Changed" view.) +1. As the submitter, improve the pull request without having to close and open + a new one: by adding a new commit to the same branch. (Hint: push + to the branch again.) +1. Once the changes are addressed, merge the pull request. +::: + + +## Help and discussion + +From here on out, we don't give detailed steps to the solution. You +need to combine what you know, and the extra info below, in order to +solve the above. + +### How to ask for changes in a pull request + +Technically, there are at least two common ways to ask for changes in a pull +request. + +Either in the comment field of the pull request: +:::{figure} img/code-review/comment.png +:width: 60% +:class: with-border +:alt: Screenshot of a pull request comment field +:::: + +Or by using the "Review changes": +:::{figure} img/code-review/files-changed.png +:width: 100% +:class: with-border +:alt: Screenshot of a pull request navigating to the "Review changes" tab +:::: + +And always please be kind and constructive in your comments. Remember that the +goal is not gate-keeping but **collaborative learning**. + + +### How to suggest a change in a pull request as a reviewer + +If you see a very small problem that is easy to fix, you can suggest a change +as a reviewer. + +Instead of asking the submitter to tiny problem, you can suggest a change by +clicking on the plus sign next to the line number in the "Files changed" tab: +:::{figure} img/code-review/leave-comment.png +:width: 100% +:class: with-border +:alt: Screenshot of leaving a comment to a line in a pull request +:::: + +Here you can comment on specific lines or even line ranges. + +But now the interesting part is to click on the "Add a suggestion" symbol (the +one that looks like plus and minus). Now you can fix the tiny problem (in this +case a typo) and then click on the "Add single comment" button: +:::{figure} img/code-review/add-suggestion.png +:width: 60% +:class: with-border +:alt: Sequence of clicks to add a suggestion to a line in a pull request +:::: + +The result is this and the submitter can accept the change with a single click: +:::{figure} img/code-review/commit-suggestion.png +:width: 60% +:class: with-border +:alt: Screenshot of a pull request with a suggested change +:::: + +After accepting with "Commit suggestion", the improvement gets added to the +pull request. + + +### How to modify a pull request to address the review comments + +If the reviewer asks for changes, it is not necessary to close the pull request +and later open a new one. It can even be counter-productive to do so: This can +fragment the discussion and the history of the pull request and can make it +harder to understand the context of the changes. + +A much better mechanism to recognize that pull requests are not implemented +from a specific commit to a specific branch, but **always from a branch to a +branch**. + +This means that you can make amendments to the pull request by adding new +commits to the same source branch. This way the pull request will be updated +automatically and the reviewer can see the new changes and comment on them. + +The fact that pull requests are from branch to branch also strongly suggests +that it is a good practice to create a new branch for each pull request. +Otherwise you could accidentally modify an open pull request by adding new +commits to the source branch. + + +## Summary + +- Our process isn't just about code now. It's about discussion and + working together to make the whole process better. +- GitHub discussions and reviewing are quite powerful and can make + small changes easy. diff --git a/branch/main/_sources/collaboration/concepts.md.txt b/branch/main/_sources/collaboration/concepts.md.txt new file mode 100644 index 0000000..c0a7d27 --- /dev/null +++ b/branch/main/_sources/collaboration/concepts.md.txt @@ -0,0 +1,69 @@ +(concepts)= + +# Concepts around collaboration + +```{objectives} +- Be able to decide whether to divide work at the branch level or at the repository level. +``` + + +## Commits, branches, repositories, forks, clones + +- **repository**: The project, contains all data and history (commits, branches, tags). +- **commit**: Snapshot of the project, gets a unique identifier (e.g. `c7f0e8bfc718be04525847fc7ac237f470add76e`). +- **branch**: Independent development line. The main development line is often called `main`. +- **tag**: A pointer to one commit, to be able to refer to it later. Like a [commemorative plaque](https://en.wikipedia.org/wiki/Commemorative_plaque) + that you attach to a particular commit (e.g. `phd-printed` or `paper-submitted`). +- **cloning**: Copying the whole repository to your laptop - the first time. It is not necessary to download each file one by one. +- **forking**: Taking a copy of a repository (which is typically not yours) - your + copy (fork) stays on GitHub/GitLab and you can make changes to your copy. + + +## Cloning a repository + +In order to make a complete copy a whole repository, the `git clone` command +can be used. When cloning, all the files, of all or selected branches, of a +repository are copied in one operation. Cloning of a repository is of relevance +in a few different situations: +* Working on your own, cloning is the operation that you can use to create + multiple instances of a repository on, for instance, a personal computer, a + server, and a supercomputer. +* The parent repository could be a repository that you or your colleague own. A + common use case for cloning is when working together within a smaller team + where everyone has read and write access to the same git repository. +* Alternatively, cloning can be made from a public repository of a code that + you would like to use. Perhaps you have no intention to work on the code, but + would like to stay in tune with the latest developments, also in-between + releases of new versions of the code. + + +```{figure} img/overview/forkandclone.png +:alt: Forking and cloning +:width: 100% +:class: with-border + +Forking and cloning +``` + + +## Forking a repository + +When a fork is made on GitHub/GitLab a complete copy, of all or selected +branches, of the repository is made. The copy will reside under a different +account on GitHub/GitLab. Forking of a repository is of high relevance when +working with a git repository to which you do not have write access. +* In the fork repository commits can be made to the base branch (`main` or + `master`), and to other branches. +* The commits that are made within the branches of the fork repository can be + contributed back to the parent repository by means of pull or merge requests. + + +## Synchronizing changes between repositories + +- We need a mechanism to communicate changes between the repositories. +- We will **pull** or **fetch** updates **from** remote repositories (we will soon discuss the difference between pull and fetch). +- We will **push** updates **to** remote repositories. +- We will learn how to suggest changes within repositories on GitHub and across repositories (**pull request**). +- Repositories that are forked or cloned do not automatically synchronize themselves: + We will learn how to update forks (by pulling from the "central" repository). +- A main difference between cloning a repository and forking a repository is that the former is a general operation for generating copies of a repository to different computers, whereas forking is a particular operation implemented on GitHub/GitLab. diff --git a/branch/main/_sources/collaboration/demo-discussion.md.txt b/branch/main/_sources/collaboration/demo-discussion.md.txt new file mode 100644 index 0000000..d6b4f28 --- /dev/null +++ b/branch/main/_sources/collaboration/demo-discussion.md.txt @@ -0,0 +1,5 @@ +(collaboration-demo-discussion)= + +# Conclict resolution, rebasing, and organizational strategies + +(40 min demo and discussion) diff --git a/branch/main/_sources/collaboration/forking-workflow.md.txt b/branch/main/_sources/collaboration/forking-workflow.md.txt new file mode 100644 index 0000000..f8c254d --- /dev/null +++ b/branch/main/_sources/collaboration/forking-workflow.md.txt @@ -0,0 +1,223 @@ +(forking-workflow)= + +# How to contribute changes to repositories that belong to others + +In this episode we prepare you to suggest and contribute changes to +repositories that belong to others. These might be open source projects that +you use in your work. + +We will see how Git and services like GitHub or GitLab can be used to suggest +modification without having to ask for write access to the repository and +accept modifications without having to grant write access to others. + + +## Exercise + +:::{prereq} Exercise preparation +- The exercise repository is now different: + (note the `-forking-exercise`). +- First **fork** the exercise repository to your GitHub account. +- Then **clone your fork** to your computer (if you wish to work locally). +- Double-check that you have forked the correct repository. +::: + +:::{exercise} Exercise: Collaborating within the same repository (25 min) + +**Technical requirements**: +- If you create the commits locally: [Being able to authenticate to GitHub](https://coderefinery.github.io/installation/ssh/) + +**What is familiar** from previous lessons: +- Forking a repository. +- Creating a branch. +- Committing a change on the new branch. +- Opening and merging pull requests. + +**What will be new** in this exercise: +- Opening a pull request towards the upstream repository. +- Pull requests can be coupled with automated testing. +- Learning that your fork can get out of date. +- After the pull requests are merged, updating your fork with the changes. +- Learn how to approach other people's repositories with ideas, changes, and requests. + +**Exercise tasks**: +1. Open an issue in the upstream exercise repository where you describe the + change you want to make. Take note of the issue number. +1. Create a new branch in your fork of the repository. +1. Make a change to the recipe book on the new branch and in the commit cross-reference the issue you opened. + See the walk-through below for how to do this. +1. Open a pull request towards the upstream repository. +1. The instructor will review and merge the pull requests. + During the review, pay attention to the automated test step (here for + demonstration purposes, we test whether the recipe contains an ingredients + and an instructions sections). +1. After few pull requests are merged, update your fork with the changes. +1. Check that in your fork you can see changes from other people's pull requests. +::: + + +## Help and discussion + + +### Help! I don't have permissions to push my local changes + +Maybe you see an error like this one: +```text +Please make sure you have the correct access rights +and the repository exists. +``` + +Or like this one: +```text +failed to push some refs to workshop-material/recipe-book-forking-exercise.git +``` + +In this case you probably try to push the changes not to your fork but to the original repository +and in this exercise you do not have write access to the original repository. + +The simpler solution is to clone again but this time your fork. + +:::{solution} Recovery + +But if you want to keep your local changes, you can change the remote URL to point to your fork. +Check where your remote points to with `git remote --verbose`. + +It should look like this (replace `USER` with your GitHub username): +```console +$ git remote --verbose + +origin git@github.com:USER/recipe-book-forking-exercise.git (fetch) +origin git@github.com:USER/recipe-book-forking-exercise.git (push) +``` + +It should **not** look like this: +```console +$ git remote --verbose + +origin git@github.com:workshop-material/recipe-book-forking-exercise.git (fetch) +origin git@github.com:workshop-material/recipe-book-forking-exercise.git (push) +``` + +In this case you can adjust "origin" to point to your fork with: +```console +$ git remote set-url origin git@github.com:USER/recipe-book-forking-exercise.git +``` +::: + + +### Opening a pull request towards the upstream repository + +We have learned in the previous episode that pull requests are always from +branch to branch. But the branch can be in a different repository. + +When you open a pull request in a fork, by default GitHub will suggest to +direct it towards the default branch of the upstream repository. + +This can be changed and it should always be verified, but in this case this is +exactly what we want to do, from fork towards upstream: +:::{figure} img/forking-workflow/pull-request-form.png +:width: 100% +:class: with-border +:alt: Screenshot of a pull request from fork towards upstream +:::: + + +### Pull requests can be coupled with automated testing + +We added an automated test here just for fun and so that you see that this is +possible to do. + +In this exercise, the test is silly. It will check whether the recipe contains +both an ingredients and an instructions section. + +In this example the test failed: +:::{figure} img/forking-workflow/all-checks-failed.png +:width: 60% +:class: with-border +:alt: Screenshot of a failed test in a pull request +:::: + +Click on the "Details" link to see the details of the failed test: +:::{figure} img/forking-workflow/check-details.png +:width: 60% +:class: with-border +:alt: Screenshot of details why the test failed +:::: + +**How can this be useful?** +- The project can define what kind of tests are expected to pass before a pull + request can be merged. +- The reviewer can see the results of the tests, without having to run them + locally. + +**How does it work?** +- We added a GitHub Actions workflow + to automatically run on each push or pull request towards the `main` branch. + +What tests or steps can you image for your project to run automatically with +each pull request? + + +### How to update your fork with changes from upstream + +This used to be difficult but now it is two mouse clicks. + +Navigate to your fork and notice how GitHub tells you that your fork is behind. +In my case, it is 9 commits behind upstream. To fix this, click on "Sync fork" +and then "Update branch": +:::{figure} img/forking-workflow/sync-fork.png +:width: 80% +:class: with-border +:alt: Screenshot on GitHub fork page showing that the fork is behind +:::: + +After the update my "branch is up to date" with the upstream repository: +:::{figure} img/forking-workflow/fork-after-update.png +:width: 80% +:class: with-border +:alt: Screenshot on GitHub after fork has been updated +:::: + + +### How to approach other people’s repositories with ideas, changes, and requests + +**Contributing very minor changes** +- Clone or fork+clone repository +- Create a branch +- Commit and push change +- Open a pull request or merge request + +**If you observe an issue and have an idea how to fix it** +- Open an issue in the repository you wish to contribute to +- Describe the problem +- If you have a suggestion on how to fix it, describe your suggestion +- Possibly **discuss and get feedback** +- If you are working on the fix, indicate it in the issue so that others know that somebody is working on it and who is working on it +- Submit your fix as pull request or merge request which references/closes the issue + +:::{admonition} Motivation +- **Inform others about an observed problem** +- Make it clear whether this issue is up for grabs or already being worked on +::: + +**If you have an idea for a new feature** +- Open an issue in the repository you wish to contribute to +- In the issue, write a short proposal for your suggested change or new feature +- Motivate why and how you wish to do this +- Also indicate where you are unsure and where you would like feedback +- **Discuss and get feedback before you code** +- Once you start coding, indicate that you are working on it +- Once you are done, submit your new feature as pull request or merge request which references/closes the issue/proposal + +:::{admonition} Motivation +- **Get agreement and feedback before writing 5000 lines of code** which might be rejected +- If we later wonder why something was done, we have the issue/proposal as + reference and can read up on the reasoning behind a code change +::: + + +## Summary + +- This forking workflow lets you propose changes to repositories for + which **you have no write access**. +- This is the way that much modern open-source software works. +- You can now contribute to any project you can view. diff --git a/branch/main/_sources/collaboration/same-repository.md.txt b/branch/main/_sources/collaboration/same-repository.md.txt new file mode 100644 index 0000000..1a69d1d --- /dev/null +++ b/branch/main/_sources/collaboration/same-repository.md.txt @@ -0,0 +1,280 @@ +(same-repository)= + +# Collaborating within the same repository + +In this episode, we will learn how to collaborate within the same repository. +We will learn how to cross-reference issues and pull requests, how to review +pull requests, and how to use draft pull requests. + +This exercise will form a good basis for collaboration that is suitable for +most research groups. + +:::{note} +When you read or hear **pull request**, please think of a **change proposal**. +::: + + +## Exercise + +In this exercise, we will contribute to a repository via a **pull request**. +This means that you propose some change, and then it is accepted (or not). + +::::::{prereq} Exercise preparation + +- **First we need to get access** to the [exercise repository](https://github.com/workshop-material/recipe-book) to which we will + contribute. + - Instructor collects GitHub usernames from learners and adds them as collaborators to the exercise repository + (Settings -> Collaborators and teams -> Manage access -> Add people). + +- **Don't forget to accept the invitation** + - Check + - Alternatively check the inbox for the email account you registered with + GitHub. GitHub emails you an invitation link, but if you don't receive it + you can go to your GitHub notifications in the top right corner. The + maintainer can also "copy invite link" and share it within the group. + +- **Watching and unwatching repositories** + - Now that you are a collaborator, you get notified about new issues and pull + requests via email. + - If you do not wish this, you can "unwatch" a repository (top of + the project page). + - However, we recommend watching repositories you are interested + in. You can learn things from experts just by watching the + activity that come through a popular project. + :::{figure} img/unwatch.png + :alt: Unwatching a repository + + Unwatch a repository by clicking "Unwatch" in the repository view, + then "Participating and @mentions" - this way, you will get + notifications about your own interactions. + ::: +:::::: + +:::{exercise} Exercise: Collaborating within the same repository (25 min) + +**Technical requirements** (from installation instructions): +- If you create the commits locally: [Being able to authenticate to GitHub](https://coderefinery.github.io/installation/ssh/) + +**What is familiar** from the previous workshop day (not repeated here): +- Cloning a repository. +- Creating a branch. +- Committing a change on the new branch. +- Submit a pull request towards the main branch. + +**What will be new** in this exercise: +- If you create the changes locally, you will need to **push** them to the remote repository. +- Learning what a protected branch is and how to modify a protected branch: using a pull request. +- Cross-referencing issues and pull requests. +- Practice to review a pull request. +- Learn about the value of draft pull requests. + +**Exercise tasks**: +1. Start in the [exercise + repository](https://github.com/workshop-material/recipe-book) and open an + issue where you describe the change you want to make. Note down the issue + number since you will need it later. +1. Create a new branch. +1. Make a change to the recipe book on the new branch and in the commit + cross-reference the issue you opened (see the walk-through below + for how to do that). +1. Push your new branch (with the new commit) to the repository you + are working on. +1. Open a pull request towards the main branch. +1. Review somebody else's pull request and give constructive feedback. Merge their pull request. +1. Try to create a new branch with some half-finished work and open a draft + pull request. Verify that the draft pull request cannot be merged since it + is not meant to be merged yet. +::: + + +## Solution and hints + +### (1) Opening an issue + +This is done through the GitHub web interface. For example, you could +give the name of the recipe you want to add (so that others don't add +the same one). It is the "Issues" tab. + + +### (2) Create a new branch. + +If on GitHub, you can make the branch in the web interface. + + +### (3) Make a change adding the recipe + +Add a new file with the recipe in it. Commit the file. In the commit +message, include the note about the issue number, saying that this +will close that issue. + + +#### Cross-referencing issues and pull requests + +Each issue and each pull request gets a number and you can cross-reference them. + +When you open an issue, note down the issue number (in this case it is `#2`): +:::{figure} img/same-repository/issue-number.png +:width: 60% +:class: with-border +:alt: Each issue gets a number +::: + +You can reference this issue number in a commit message or in a pull request, like in this +commit message: +```text +this is the new recipe; fixes #2 +``` + +If you forget to do that in your commit message, you can also reference the issue +in the pull request description. And instead of `fixes` you can also use `closes` or `resolves` +or `fix` or `close` or `resolve` (case insensitive). + +Here are all the keywords that GitHub recognizes: + + +Then observe what happens in the issue once your commit gets merged: it will +automatically close the issue and create a link between the issue and the +commit. This is very useful for tracking what changes were made in response to +which issue and to know from when until when precisely the issue was open. + + +### (4) Push to GitHub as a new branch + +Push the branch to the repository. You should end up with a branch +visible in the GitHub web view. + +This is only necessary if you created the changes locally. If you created the +changes directly on GitHub, you can skip this step. + +:::::{tabs} +::::{group-tab} VS Code +In VS Code, you can "publish the branch" to the remote repository by clicking +the cloud icon in the bottom left corner of the window: +:::{figure} img/same-repository/vscode-publish-branch.png +:width: 60% +:class: with-border +:alt: Publishing a branch in VS Code +::: +:::: + +::::{group-tab} Command line +If you have a local branch `my-branch` and you want to push it to the remote +and make it visible there, first verify what your remote is: +```console +$ git remote --verbose + +origin git@github.com:USER/recipe-book.git (fetch) +origin git@github.com:USER/recipe-book.git (push) +``` + +In this case the remote is called `origin` and refers to the address +git@github.com:USER/recipe-book.git. Both can be used +interchangeably. Make sure it points to the right repository, ideally a +repository that you can write to. + +Now that you have a remote, you can push your branch to it: +```console +$ git push origin my-branch +``` +This will create a new branch on the remote repository with the same name as +your local branch. + +You can also do this: +```console +$ git push --set-upstream origin my-branch +``` +This will connect the local branch and the remote branch so that in the future +you can just type `git push` and `git pull` without specifying the branch name +(but this depends on your Git configuration). + + +**Troubleshooting** + +If you don't have a remote yet, you can add it with (adjust `ADDRESS` to your repository address): +```console +$ git remote add origin ADDRESS +``` + +ADDRESS is the part that you copy from here: +:::{figure} img/same-repository/clone-address.png +:width: 60% +:class: with-border +:alt: Copying the clone address from GitHub +::: + +If the remote points to the wrong place, you can change it with: +```console +$ git remote set-url origin NEWADDRESS +``` +:::: +::::: + + +### (5) Open a pull request towards the main branch + +This is done through the GitHub web interface. + + +### (6) Reviewing pull requests + +You review through the GitHub web interface. + +Checklist for reviewing a pull request: +- Be kind, on the other side is a human who has put effort into this. +- Be constructive: if you see a problem, suggest a solution. +- Towards which branch is this directed? +- Is the title descriptive? +- Is the description informative? +- Scroll down to see commits. +- Scroll down to see the changes. +- If you get incredibly many changes, also consider the license or copyright + and ask where all that code is coming from. +- Again, be kind and constructive. +- Later we will learn how to suggest changes directly in the pull request. + +If someone is new, it's often nice to say something encouraging in the +comments before merging (even if it's just "thanks"). If all is good +and there's not much else to say, you could merge directly. + + +### (7) Draft pull requests + +Try to create a draft pull request: +:::{figure} img/same-repository/draft-pr.png +:width: 60% +:class: with-border +:alt: Creating a draft pull request +:::: + +Verify that the draft pull request cannot be merged until it is marked as ready +for review: +:::{figure} img/same-repository/draft-pr-wip.png +:width: 60% +:class: with-border +:alt: Draft pull request cannot be merged +:::: + +Draft pull requests can be useful for: +- **Feedback**: You can open a pull request early to get feedback on your work without + signaling that it is ready to merge. +- **Information**: They can help communicating to others that a change is coming up and in + progress. + + +### What is a protected branch? And how to modify it? + +A protected branch on GitHub or GitLab is a branch that cannot (accidentally) +deleted or force-pushed to. It is also possible to require that a branch cannot +be directly pushed to or modified, but that changes must be submitted via a +pull request. + +To protect a branch in your own repository, go to "Settings" -> "Branches". + + + +### Summary + +- We used all the same pieces that we've learned previously. +- But we successfully contributed to a collaborative project! +- The pull request allowed us to contribute without changing directly: + this is very good when it's not mainly our project. diff --git a/branch/main/_sources/credit.md.txt b/branch/main/_sources/credit.md.txt new file mode 100644 index 0000000..9639997 --- /dev/null +++ b/branch/main/_sources/credit.md.txt @@ -0,0 +1,10 @@ +# Credit + +The following material (all CC-BY) was reused to create this workshop material: +- +- +- +- +- + +(I will also summarize what changes have been made to the original material) diff --git a/branch/main/_sources/documentation.md.txt b/branch/main/_sources/documentation.md.txt new file mode 100644 index 0000000..571c5c3 --- /dev/null +++ b/branch/main/_sources/documentation.md.txt @@ -0,0 +1,384 @@ +(documentation)= + +# Code documentation + +:::{objectives} +- Discuss what makes good documentation. +- Improve the README of your project or our example project. +- Explore Sphinx which is a popular tool to build documentation websites. +- Learn how to leverage GitHub Actions and GitHub Pages to build and deploy documentation. +::: + +:::{instructor-note} +- (30 min) Discussion +- (30 min) Exercise: Set up a Sphinx documentation and add API documentation +- (15 min) Demo: Building documentation with GitHub Actions +::: + + +## Why? 💗✉️ to your future self + +- You will probably use your code in the future and may forget details. +- You may want others to use your code or contribute + (almost impossible without documentation). + + +## In-code documentation + +Not very useful (more commentary than comment): +```python +# now we check if temperature is below -50 +if temperature < -50: + print("ERROR: temperature is too low") +``` + +More useful (explaining **why**): +```python +# we regard temperatures below -50 degrees as measurement errors +if temperature < -50: + print("ERROR: temperature is too low") +``` + +Keeping zombie code "just in case" (rather use version control): +```python +# do not run this code! +# if temperature > 0: +# print("It is warm") +``` + +Emulating version control: +```python +# John Doe: threshold changed from 0 to 15 on August 5, 2013 +if temperature > 15: + print("It is warm") +``` + + +## Many languages allow "docstrings" + +Example (Python): +```python +def kelvin_to_celsius(temp_k: float) -> float: + """ + Converts temperature in Kelvin to Celsius. + + Parameters + ---------- + temp_k : float + temperature in Kelvin + + Returns + ------- + temp_c : float + temperature in Celsius + """ + assert temp_k >= 0.0, "ERROR: negative T_K" + + temp_c = temp_k - 273.15 + + return temp_c +``` + +:::{keypoints} +- Documentation which is only in the source code is not enough. +- Often a README is enough. +- Documentation needs to be kept + **in the same Git repository** as the code since we want it to evolve with + the code. +::: + + +## Often a README is enough - checklist + +- **Purpose** +- Requirements +- Installation instructions +- **Copy-paste-able example to get started** +- Tutorials covering key functionality +- Reference documentation (e.g. API) covering all functionality +- Authors and **recommended citation** +- License +- Contribution guide + +See also the +[JOSS review checklist](https://joss.readthedocs.io/en/latest/review_checklist.html). + + +## What if you need more than a README? + +- Write documentation in + [Markdown (.md)](https://en.wikipedia.org/wiki/Markdown) + or + [reStructuredText (.rst)](https://en.wikipedia.org/wiki/ReStructuredText) + or + [R Markdown (.Rmd)](https://rmarkdown.rstudio.com/) + +- In the **same repository** as the code -> version control and **reproducibility** + +- Use one of many tools to build HTML out of md/rst/Rmd: + [Sphinx](https://sphinx-doc.org), + [MkDocs](https://www.mkdocs.org/), + [Zola](https://www.getzola.org/), [Jekyll](https://jekyllrb.com/), + [Hugo](https://gohugo.io/), RStudio, [knitr](https://yihui.org/knitr/), + [bookdown](https://bookdown.org/), + [blogdown](https://bookdown.org/yihui/blogdown/), ... + +- Deploy the generated HTML to [GitHub Pages](https://pages.github.com/) or + [GitLab Pages](https://docs.gitlab.com/ee/user/project/pages/) + + +## Diátaxis + +Diátaxis is a systematic approach to technical documentation authoring. + +- Overview: +- How to use Diátaxis **as a guide** to work: + + +## Exercise: Set up a Sphinx documentation + +:::{prereq} Preparation +In this episode we will use the following 5 packages which we installed +previously as part of the {ref}`conda` or {ref}`venv`: +``` +myst-parser +sphinx +sphinx-rtd-theme +sphinx-autoapi +sphinx-autobuild +``` + +Which repository to use? You have 3 options: +- Clone **your fork** of the planets example repository. +- If you don't have that, you can clone the original repository itself: + +- You can try this with **your own project** and the project does not have to + be a Python project. +::: + +There are at least two ways to get started with Sphinx: +1. Use `sphinx-quickstart` to create a new Sphinx project. +1. **This is what we will do**: Create three files (`doc/conf.py`, `doc/index.md`, and `doc/about.md`) + as starting point and improve from there. + +::::{exercise} Exercise: Set up a Sphinx documentation +1. Create the following three files in your project: + ``` + planets/ + ├── doc/ + │ ├── conf.py + │ ├── index.md + │ └── about.md + └── ... + ``` + + This is `conf.py`: + ```python + project = "planets" + copyright = "2024, Authors" + author = "Authors" + release = "0.1" + + exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] + + extensions = [ + "myst_parser", # in order to use markdown + ] + + myst_enable_extensions = [ + "colon_fence", # ::: can be used instead of ``` for better rendering + ] + + html_theme = "sphinx_rtd_theme" + ``` + + This is `index.md` (feel free to adjust): + ```markdown + # Our code documentation + + Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor + incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis + nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. + Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu + fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in + culpa qui officia deserunt mollit anim id est laborum. + + :::{toctree} + :maxdepth: 2 + :caption: Some caption + + about.md + ::: + ``` + + This is `about.md` (feel free to adjust): + ```markdown + # About this code + + Work in progress ... + ``` + +1. Run `sphinx-build` to build the HTML documentation: + ```console + $ sphinx-build doc _build + + ... lots of output ... + The HTML pages are in _build. + ``` + +1. Try to open `_build/index.html` in your browser. + +1. Experiment with adding more content, images, equations, code blocks, ... + - [typography](https://myst-parser.readthedocs.io/en/latest/syntax/typography.html) + - [images](https://myst-parser.readthedocs.io/en/latest/syntax/images_and_figures.html) + - [math and equations](https://myst-parser.readthedocs.io/en/latest/syntax/math.html) + - [code blocks](https://myst-parser.readthedocs.io/en/latest/syntax/code_and_apis.html) +:::: + +There is a lot more you can do: +- This is useful if you want to check the integrity of all internal and external links: + ```console + $ sphinx-build doc -W -b linkcheck _build + ``` +- [sphinx-autobuild](https://pypi.org/project/sphinx-autobuild/) + provides a local web server that will automatically refresh your view + every time you save a file - which makes writing and testing much easier. + + +## Demo: Building documentation with GitHub Actions + +First we need to extend the `environment.yml` file to include the necessary packages: +```{code-block} yaml +--- +emphasize-lines: 9-12 +--- +name: planets +channels: + - conda-forge +dependencies: + - python=3.12 + - numpy + - click + - matplotlib + - myst-parser + - sphinx + - sphinx-rtd-theme + - sphinx-autoapi +``` + +Then we add a GitHub Actions workflow `.github/workflow/sphinx.yml` to build the documentation: +```{code-block} yaml +--- +emphasize-lines: 31 +--- +name: Build documentation + +on: + push: + branches: [ main ] + pull_request: + branches: [ main ] + +permissions: + contents: write + +jobs: + docs: + runs-on: ubuntu-latest + + steps: + - name: Checkout + uses: actions/checkout@v4 + + - uses: mamba-org/setup-micromamba@v1 + with: + micromamba-version: '1.5.8-0' # any version from https://github.com/mamba-org/micromamba-releases + environment-file: environment.yml + init-shell: bash + cache-environment: true + post-cleanup: 'all' + generate-run-shell: false + + - name: Sphinx build + run: | + sphinx-build doc _build + shell: bash -el {0} + + - name: Deploy to GitHub Pages + uses: peaceiris/actions-gh-pages@v4 + if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }} + with: + publish_branch: gh-pages + github_token: ${{ secrets.GITHUB_TOKEN }} + publish_dir: _build/ + force_orphan: true +``` + +Now: +- Add these two changes to the GitHub repository. +- Go to "Settings" -> "Pages" -> "Branch" -> `gh-pages` -> "Save". +- Look at "Actions" tab and observe the workflow running and hopefully + deploying the website. +- Finally visit the generated site. You find it by clicking the About wheel + icon on top right of your repository. There, select "Use your GitHub Pages + website". +- **This is how we build almost all of our lesson websites** (including this one). +- Another popular place to deploy Sphinx documentation is [ReadTheDocs](https://readthedocs.org/). + + +## Optional: How to auto-generate API documentation in Python + +Add three tiny modifications (highlighted) to `doc/conf.py` to auto-generate API documentation +(this requires the `sphinx-autoapi` package): +```{code-block} python +--- +emphasize-lines: 10, 14, 17 +--- +project = "planets" +copyright = "2024, Authors" +author = "Authors" +release = "0.1" + +exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] + +extensions = [ + "myst_parser", # in order to use markdown + "autoapi.extension", # in order to use markdown +] + +# search this directory for Python files +autoapi_dirs = [".."] + +# ignore this file when generating API documentation +autoapi_ignore = ["*/conf.py"] + +myst_enable_extensions = [ + "colon_fence", # ::: can be used instead of ``` for better rendering +] + +html_theme = "sphinx_rtd_theme" +``` + +Then rebuild the documentation (or push the changes and let GitHub rebuild it) +and you should see a new section "API Reference". + + +## Confused about reStructuredText vs. Markdown vs. MyST? + +- At the beginning there was reStructuredText and Sphinx was built for reStructuredText. +- Independently, Markdown was invented and evolved into a couple of flavors. +- Markdown became more and more popular but was limited compared to reStructuredText. +- Later, [MyST](https://myst-parser.readthedocs.io/en/latest/syntax/typography.html) + was invented to be able to write + something that looks like Markdown but in addition can do everything that + reStructuredText can do with extra directives. + + +## Where to read more + +- [CodeRefinery documentation lesson](https://coderefinery.github.io/documentation/) +- [Sphinx documentation](https://www.sphinx-doc.org/) +- [Sphinx + ReadTheDocs guide](https://sphinx-rtd-tutorial.readthedocs.io/en/latest/index.html) +- For more Markdown functionality, see the [Markdown guide](https://www.markdownguide.org/basic-syntax/). +- For Sphinx additions, see [Sphinx Markup Constructs](https://www.sphinx-doc.org/en/master/markup/index.html). +- [An opinionated guide on documentation in Python](https://docs.python-guide.org/writing/documentation/) diff --git a/branch/main/_sources/example.md.txt b/branch/main/_sources/example.md.txt new file mode 100644 index 0000000..9805632 --- /dev/null +++ b/branch/main/_sources/example.md.txt @@ -0,0 +1,95 @@ +(example-project)= + +# Example project: Simulating the motion of planets + +The [example code](https://github.com/workshop-material/planets) that we will study +is a hopefully simple N-body simulation written in Python. It is not important +or expected that we understand the code in any detail. + +:::{video} video/animation.mp4 +:width: 600 +::: + +The **big picture** is that the code simulates the motion of a number of +planets: +- We can choose the number of planets. +- Each planet starts with a random position, velocity, and mass. +- At each time step, the code calculates the gravitational force between each + pair of planets. +- The forces accelerate each planet, the acceleration modifies the velocity, + the velocity modifies the position of each planet. +- We can choose the number of time steps. +- The units were chosen to make numbers easy to read. + + +## Example run + +:::{instructor-note} +The instructor demonstrates running the code on their computer. +::: + +The code is written to accept **command-line arguments** to specify the number +of planets and the number of time steps. + +We first generate starting data: +```console +$ python generate-data.py --num-planets 10 --output-file initial.csv +``` + +The generated file (initial.csv) could look like this: +``` +px,py,pz,vx,vy,vz,mass +-46.88,-42.51,88.33,-0.86,-0.18,0.55,6.70 +-5.29,17.09,-96.13,0.66,0.45,-0.17,3.51 +83.53,-92.83,-68.77,-0.26,-0.48,0.24,6.84 +-36.31,25.48,64.16,0.85,0.75,-0.56,1.53 +-68.38,-17.21,-97.07,0.60,0.26,0.69,6.63 +-48.37,-48.74,3.92,-0.92,-0.33,-0.93,8.60 +40.53,-75.50,44.18,-0.62,-0.31,-0.53,8.04 +-27.21,10.78,-78.82,-0.09,-0.55,-0.03,5.35 +88.42,-74.95,-45.85,0.81,0.68,0.56,5.36 +39.09,53.12,-59.54,-0.54,0.56,0.07,8.98 +``` + +Then we can simulate their motion (in this case for 20 steps): +```console +$ python simulate.py --num-steps 20 \ + --input-file initial.csv \ + --output-file final.csv +``` + +The `--output-file` (final.csv) is again a CSV file (comma-separated values) +and contains the final positions of all planets. + +It is possible to run on **multiple cores** and to **animate** the result. +Here is an example with 100 planets: +```{code-block} console +--- +emphasize-lines: 7,11 +--- +$ python generate-data.py --num-planets 100 --output-file initial.csv + +$ python simulate.py --num-steps 50 \ + --input-file initial.csv \ + --output-file final.csv \ + --trajectories-file trajectories.npz \ + --num-cores 8 + +$ python animate.py --initial-file initial.csv \ + --trajectories-file trajectories.npz \ + --output-file animation.mp4 +``` + +:::{admonition} Learning goals +- What are the most important steps to make this code **reusable by others** + and **our future selves**? +- Be able to apply these techniques to your own code/script. +::: + +:::{admonition} We will not focus on ... +- ... how the code works internally in detail. +- ... whether this is the most efficient algorithm. +- ... whether the code is numerically stable. +- ... how to code scales with the number of cores. +- ... whether it is portable to other operating systems (we will discuss this later). +::: diff --git a/branch/main/_sources/index.md.txt b/branch/main/_sources/index.md.txt new file mode 100644 index 0000000..647b711 --- /dev/null +++ b/branch/main/_sources/index.md.txt @@ -0,0 +1,142 @@ +# Reproducible research software development using Python + + +## Big-picture goal + +This is a **hands-on course on research software engineering**. In this +workshop we assume that most workshop participants use Python in their work or +a leading a group which uses Python. Therefore, some of the examples will use +Python as the example language. + +We will work with an example project and go through all the steps of a typical +software project. Once we have seen the building blocks, we will try to apply +them to own projects. Workshop participants will receive and also learn to give +constructive code feedback. + + +## Prerequisites + +:::{prereq} Preparation +1. Get a **GitHub account** following [these instructions](https://coderefinery.github.io/installation/github/). +1. You will need a **text editor**. If you don't have a favorite one, we recommend + [VS Code](https://coderefinery.github.io/installation/vscode/). +1. **If you prefer to work in the terminal** and not in VS Code, set up these two (skip this if you use VS Code): + - [Git in the terminal](https://coderefinery.github.io/installation/git-in-terminal/) + - [SSH or HTTPS connection to GitHub from terminal](https://coderefinery.github.io/installation/ssh/) +1. **One of these two software environments** (if you are not sure which one to + choose or have no preference, choose Conda): + - {ref}`conda` + - {ref}`venv` (Snakemake is not available in this environment) +1. **Optional** and only on Linux: [Apptainer](https://apptainer.org/) following + [these instructions](https://apptainer.org/docs/admin/1.3/installation.html#install-from-pre-built-packages). +::: + + +## Schedule + +### Day 1 + +- 13:00-13:30 - **Welcome and introduction** + - Practical information (tools, communication, breaks, etc.) + - Motivation (reproducibility, robustness, distribution, improvement, trust, etc.) + - What will learn and achieve from this course? + - {ref}`example-project` + +- 13:30-14:45 - {ref}`version-control` (1/2) + - {ref}`version-control-motivation` (15 min) + - {ref}`browsing` (30 min) + - {ref}`branching-and-committing` (30 min) + +- 15:00-16:30 - {ref}`version-control` (2/2) + - Merging (40 min) + - Conflict resolution (30 min) + - {ref}`practical-advice` (20 min) + - {ref}`sharing-repositories` (30 min) + +- 16:45-18:00 - {ref}`documentation` + + +### Day 2 + +- 09:00-10:30 - {ref}`collaboration` (1/2) + - {ref}`concepts` (10 min) + - {ref}`same-repository` (40 min) + - {ref}`code-review` (40 min) + +- 10:45-12:15 - {ref}`collaboration` (2/2) + - {ref}`forking-workflow` (50 min) + - {ref}`collaboration-demo-discussion` (40 min) + +- 16:45-18:00 - **Debriefing and Q&A** + - Participants work on their projects + - Together we study actual codes that participants wrote or work on + - Constructively we discuss possible improvements + - Give individual feedback on code projects + + +### Day 3 + +- 09:00-10:30 - {ref}`testing` + +- 10:45-12:15 - {ref}`reusable` + - Tracking dependencies with requirements.txt and environment.yml + - Recording environments in containers + +- 13:00-14:45 - Code quality and good practices + - {ref}`refactoring-demo` (90 min) + - {ref}`refactoring-concepts` (15 min) + +- 15:00-16:30 - {ref}`publishing` + - Licenses + - Publishing the code via Zenodo + - Packaging the code + - Sharing the code via PyPI + +- 16:45-18:00 - **Debriefing and Q&A** + - Participants work on their projects + - Together we study actual codes that participants wrote or work on + - Constructively we discuss possible improvements + - Give individual feedback on code projects + + +### If we have time left + +- {ref}`profiling` + + +```{toctree} +:maxdepth: 1 +:caption: Software environment +:hidden: + +installation/conda +installation/virtual-environment +``` + +```{toctree} +:maxdepth: 1 +:caption: Episodes +:hidden: + +example +version-control +documentation +collaboration +testing +reusable +refactoring-demo +refactoring-concepts +publishing +profiling +``` + +```{toctree} +:maxdepth: 1 +:caption: Reference +:hidden: + +credit +All lessons +CodeRefinery +Reusing +``` diff --git a/branch/main/_sources/installation/conda.md.txt b/branch/main/_sources/installation/conda.md.txt new file mode 100644 index 0000000..830161f --- /dev/null +++ b/branch/main/_sources/installation/conda.md.txt @@ -0,0 +1,82 @@ +(conda)= + +# Conda environment + +A Conda environment is an isolated software environment that is used to manage dependencies for a project +and you decide where it is located. + +You will need a `environment.yml` file that documents the dependencies: +```yaml +name: coderefinery +channels: + - conda-forge + - bioconda +dependencies: + - python >= 3.10 + - black + - click + - flit + - ipywidgets + - isort + - jupyterlab + - jupyterlab_code_formatter + - jupyterlab-git + - matplotlib + - myst-parser + - nbdime + - numpy + - pandas + - pytest + - pytest-cov + - scalene + - seaborn + - snakemake-minimal + - sphinx + - sphinx-autoapi + - sphinx-autobuild + - sphinx_rtd_theme >= 2.0 + - vulture + - scikit-image +``` + + +## Before you create a virtual environment + +1. Create a new directory for this course. +1. In this directory, create an `environment.yml` file and copy-paste the dependencies above into it. + + +## Choose the tool to manage the environment + +If you are already using one of these tools, please continue using the tool that you like and know. +If you are new to this, **we recommend using Miniconda or Miniforge**. + +- [Anaconda](https://docs.anaconda.com/anaconda/install/) + - Advantages: easy to install, easy to use, good for beginners + - Disadvantages: large download, installs more than we will need, license restrictions +- [Miniconda](https://docs.anaconda.com/miniconda/) + - Advantages: small size, installs only what you need + - Disadvantages: no graphical interface, license restrictions +- [Miniforge](https://github.com/conda-forge/miniforge) + - Advantages: small size, no license restrictions + - Disadvantages: no graphical interface +- [Micromamba](https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html) + - Advantages: fast, small size + - Disadvantages: no graphical interface +- [Pixi](https://pixi.sh/latest/) + - Advantages: fast and new + - Disadvantages: new and less tested and not documented here + + +## Creating the virtual environment + +1. Open your terminal shell (e.g. Bash or Zsh). +2. Activate `conda` using `conda activate` or `source ~/miniconda3/bin/activate`. +3. Run the following command: + ```console + $ conda env create --file environment.yml + ``` +4. Make sure that you see "coderefinery" in the output when you ask for a list of all available environments: + ```console + $ conda env list + ``` diff --git a/branch/main/_sources/installation/virtual-environment.md.txt b/branch/main/_sources/installation/virtual-environment.md.txt new file mode 100644 index 0000000..69b3231 --- /dev/null +++ b/branch/main/_sources/installation/virtual-environment.md.txt @@ -0,0 +1,77 @@ +(venv)= + +# Virtual environment + +A virtual environment is an isolated software environment that is used to manage dependencies for a project +and you decide where it is located. + +You will need a `requirements.txt` file that documents the dependencies: +``` +black +click +flit +ipywidgets +isort +jupyterlab +jupyterlab-code-formatter +jupyterlab-git +matplotlib +myst-parser +nbdime +numpy +pandas +pytest +pytest-cov +scalene +seaborn +sphinx +sphinx-autoapi +sphinx-autobuild +sphinx_rtd_theme >= 2.0 +vulture +scikit-image +``` + + +## Before you create a virtual environment + +1. Create a new directory for this course. +1. In this directory, create a `requirements.txt` file and copy-paste the dependencies above into it. + + +## Creating the virtual environment + +Now create a virtual environment in this directory either using [pip and +venv](https://packaging.python.org/en/latest/guides/installing-using-pip-and-virtual-environments/) +(more traditional and safer) or using [uv](https://docs.astral.sh/uv/) (more modern but also less tested): + +:::::{tabs} + +::::{group-tab} pip and venv +Create a new virtual environment and activate it: +```console +$ python3 -m venv coderefinery-environment +$ source coderefinery-environment/bin/activate +``` + +Install the dependencies into the environment: +```console +$ python3 -m pip install -r requirements.txt +``` +:::: + + +::::{group-tab} uv +Create a new virtual environment and activate it: +```console +$ uv venv coderefinery-environment +$ source coderefinery-environment/bin/activate +``` + +Install the dependencies into the environment: +```console +$ uv pip install -r requirements.txt +``` +:::: + +::::: diff --git a/branch/main/_sources/profiling.md.txt b/branch/main/_sources/profiling.md.txt new file mode 100644 index 0000000..0683e06 --- /dev/null +++ b/branch/main/_sources/profiling.md.txt @@ -0,0 +1,16 @@ +(profiling)= + +# Profiling memory and CPU usage + +Profilers: +- cProfile or profile +- line_profiler +- viztracer +- scalene +- Intel VTune +- PyInstrument +- py-spy +- Pyflame +- timeit + +(here I will add some examples that we can profile together) diff --git a/branch/main/_sources/publishing.md.txt b/branch/main/_sources/publishing.md.txt new file mode 100644 index 0000000..bc3a12e --- /dev/null +++ b/branch/main/_sources/publishing.md.txt @@ -0,0 +1,11 @@ +(publishing)= + +# How to release and publish your code + +Part 1: +- 30 min: Overview over software licenses and code publishing +- 15 min: We add a license, CFF file, and publish to Zenodo (sandbox) + +Part 2: +- 30 min: Creating a Python package with the help of flit +- 15 min: Deploy the package to test-PyPI using GitHub Actions diff --git a/branch/main/_sources/refactoring-concepts.md.txt b/branch/main/_sources/refactoring-concepts.md.txt new file mode 100644 index 0000000..78039ad --- /dev/null +++ b/branch/main/_sources/refactoring-concepts.md.txt @@ -0,0 +1,8 @@ +(refactoring-concepts)= + +# Concepts in refactoring and modular code design + +Topics: +- Pure functions +- Design patterns: functional design vs. object-oriented design +- How to design your code before writing it: document-driven development diff --git a/branch/main/_sources/refactoring-demo.md.txt b/branch/main/_sources/refactoring-demo.md.txt new file mode 100644 index 0000000..e7266bf --- /dev/null +++ b/branch/main/_sources/refactoring-demo.md.txt @@ -0,0 +1,115 @@ +(refactoring-demo)= + +# Demo: From a script towards a workflow + +In this episode we will explore code quality and good practices in Python using +a hands-on approach. We will together build up a small project and improve it +step by step. + +We will start from a relatively simple image processing script which can read a +telescope image of stars and our goal is to **count the number of stars** in +the image. Later we will want to be able to process many such images. + +The (fictional) telescope images look like the one below here ([in this +repository](https://github.com/workshop-material/random-star-images) we can find more): +:::{figure} refactoring/stars.png +:alt: Generated image representing a telescope image of stars +:width: 60% + +Generated image representing a telescope image of stars. +::: + +:::{admonition} Rough plan for this demo +- (15 min) Discuss how we would solve the problem, run example code, and make it work (as part of a Jupyter notebook)? +- (15 min) Refactor the positioning code into a function and a module +- (15 min) Now we wish to process many images - discuss how we would approach this +- (15 min) Introduce CLI and discuss the benefits +- (30 min) From a script to a workflow (using Snakemake) +::: + +:::{solution} Starting point (spoiler alert) + +We can imagine that we pieced together the following code +based on some examples we found online: +```python +import matplotlib.pyplot as plt +from skimage import io, filters, color +from skimage.measure import label, regionprops + + +image = io.imread("stars.png") +sigma = 0.5 + +# if there is a fourth channel (alpha channel), ignore it +rgb_image = image[:, :, :3] +gray_image = color.rgb2gray(rgb_image) + +# apply a gaussian filter to reduce noise +image_smooth = filters.gaussian(gray_image, sigma) + +# threshold the image to create a binary image (bright stars will be white, background black) +thresh = filters.threshold_otsu(image_smooth) +binary_image = image_smooth > thresh + +# label connected regions (stars) in the binary image +labeled_image = label(binary_image) + +# get properties of labeled regions +regions = regionprops(labeled_image) + +# extract star positions (centroids) +star_positions = [region.centroid for region in regions] + +# plot the original image +plt.figure(figsize=(8, 8)) +plt.imshow(image, cmap="gray") + +# overlay star positions with crosses +for star in star_positions: + plt.plot(star[1], star[0], "rx", markersize=5, markeredgewidth=0.1) + +plt.savefig("detected-stars.png", dpi=300) + +print(f"number of stars detected: {len(star_positions)}") +``` +::: + + +## Plan + +Topics we wish to show and discuss: +- Naming (and other) conventions, project organization, modularity +- The value of pure functions and immutability +- Refactoring (explained through examples) +- Auto-formatting and linting with tools like black, vulture, ruff +- Moving a project under Git +- How to document dependencies +- Structuring larger software projects in a modular way +- Command-line interfaces +- Workflows with Snakemake + +We will work together on the code on the big screen, and participants will be +encouraged to give suggestions and ask questions. We will **end up with a Git +repository** which will be shared with workshop participants. + + +## Possible solutions + +:::{solution} Script after some work, with command-line interface (spoiler alert) +This is one possible solution (`count-stars.py`): +```{literalinclude} refactoring/count-stars.py +:language: python +``` +::: + +:::{solution} Snakemake rules which define a workflow (spoiler alert) +This is one possible solution (`snakefile`): +```{literalinclude} refactoring/snakefile +:language: python +``` + +We can process as many images as we like by running: +```console +$ snakemake --cores 4 # adjust to the number of available cores +``` +::: diff --git a/branch/main/_sources/reusable.md.txt b/branch/main/_sources/reusable.md.txt new file mode 100644 index 0000000..c86455a --- /dev/null +++ b/branch/main/_sources/reusable.md.txt @@ -0,0 +1,13 @@ +(reusable)= + +# How to make the project more reusable + +Part 1: +- 15 min: Motivation +- 15 min: Best practices for managing dependencies in Python +- 20 min: Exercise + +Part 2: +- 10 min: Introduction to containers +- 20 min: Demonstration +- 10 min: Discussion diff --git a/branch/main/_sources/testing.md.txt b/branch/main/_sources/testing.md.txt new file mode 100644 index 0000000..da43e9f --- /dev/null +++ b/branch/main/_sources/testing.md.txt @@ -0,0 +1,222 @@ +(testing)= + +# Automated testing + +:::{objectives} +- Know **where to start** in your own project. +- Have an example for how to make the **testing part of code review**. +::: + +:::{instructor-note} +- (15 min) Motivation +- (15 min) End-to-end tests +- (15 min) Pytest +- (15 min) Adding the unit test to GitHub Actions +- (10 min) What else is possible +- (20 min) Exercise +::: + + +## Motivation + +Testing is a way to check that the code does what it is expected to. + +- **Less scary to change code**: tests will tell you whether something broke. +- **Easier for new people** to join. +- Easier for somebody to **revive an old code**. +- **End-to-end test**: run the whole code and compare result to a reference. +- **Unit tests**: test one unit (function or module). Can guide towards better + structured code: complicated code is more difficult to test. + + +## How testing is often taught + +```python +def add(a, b): + return a + b + + +def test_add(): + assert add(1, 2) == 3 +``` + +How this feels: +:::{figure} img/owl.png +:alt: Instruction on how to draw an owl +:width: 50% +:class: with-border + +[Citation needed] +::: + +Instead, we will look at and **discuss a real example** where we test components +from our example project. + + +## Where to start + +Short answer: **Start with an end-to-end test**. + +:::{solution} Longer answer +- A simple script or notebook probably does not need an automated test. + +**If you have nothing yet**: +- Start with an end-to-end test. +- Describe in words how *you* check whether the code still works. +- Translate the words into a script (any language). +- Run the script automatically on every code change. + +**If you want to start with unit-testing**: +- You want to rewrite a function? Start adding a unit test right there first. +::: + + +## End-to-end tests + +- This is our end-to-end test: +- Note how we can run it [on GitHub automatically](https://github.com/workshop-material/planets/blob/813d49a247f36e9c1e10cbe78ecf1ae4b6e971c3/.github/workflows/test.yml#L28). +- Also browse . +- If we have time, we can try to create a pull request which would break the + code and see how the test fails. + +:::{discussion} +Is the [end-to-end test](https://github.com/workshop-material/planets/blob/main/test.sh) +perfect? No. But it's a good starting point. Discuss its limitations. +::: + + +## Pytest + +First we need to add a test function, for instance +for [this function](https://github.com/workshop-material/planets/blob/813d49a247f36e9c1e10cbe78ecf1ae4b6e971c3/simulate.py#L31-L39): +```{code-block} python +--- +emphasize-lines: 12-20 +--- +def force_between_planets(position1, mass1, position2, mass2): + G = 1.0 # gravitational constant + + r = position2 - position1 + distance = (r[0] ** 2 + r[1] ** 2 + r[2] ** 2) ** 0.5 + force_magnitude = G * mass1 * mass2 / distance**2 + force = (r / distance) * force_magnitude + + return force + + +def test_force_between_planets(): + position1 = np.array([0.0, 0.0, 0.0]) + mass1 = 1.0 + position2 = np.array([1.0, 0.0, 0.0]) + mass2 = 2.0 + + force = force_between_planets(position1, mass1, position2, mass2) + + assert np.allclose(force, [2.0, 0.0, 0.0]) +``` + +Let us run the test with: +```console +$ pytest simulate.py +``` + +Explanation: `pytest` will look for functions starting with `test_` in files +and directories given as arguments. It will run them and report the results. + +Now let us try this: +- Commit the test. +- Break the function on purpose and run the test. +- Does the test fail as expected? + + +## Adding the unit test to GitHub Actions + +Our next goal is that we want GitHub to run the unit test +automatically on every change. + +First we need to extend our +[environment.yml](https://github.com/workshop-material/planets/blob/main/environment.yml): +```{code-block} yaml +--- +emphasize-lines: 9 +--- +name: planets +channels: + - conda-forge +dependencies: + - python=3.12 + - numpy + - click + - matplotlib + - pytest +``` + +We also need to extend `.github/workflows/test.yml` (highlighted line): +```{code-block} yaml +--- +emphasize-lines: 29 +--- +name: Test + +on: + push: + branches: [ main ] + pull_request: + branches: [ main ] + +jobs: + build: + runs-on: ubuntu-latest + + steps: + - name: Checkout + uses: actions/checkout@v4 + + - uses: mamba-org/setup-micromamba@v1 + with: + micromamba-version: '1.5.8-0' # any version from https://github.com/mamba-org/micromamba-releases + environment-file: environment.yml + init-shell: bash + cache-environment: true + post-cleanup: 'all' + generate-run-shell: false + + - name: Run tests + run: | + ./test.sh + pytest simulate.py + shell: bash -el {0} +``` + +If we have time, we can try to create a pull request which would break the +code and see how the test fails. + + +## What else is possible + +- The testing above used **example-based** testing. + +- **Test coverage**: how much of the code is traversed by tests? + - Python: [pytest-cov](https://pytest-cov.readthedocs.io/) + - Result can be deployed to services like [Codecov](https://about.codecov.io/) or [Coveralls](https://coveralls.io/). + +- **Property-based** testing: generates arbitrary data matching your specification and checks that your guarantee still holds in that case. + - Python: [hypothesis](https://hypothesis.readthedocs.io/) + +- **Snapshot-based** testing: makes it easier to generate snapshots for regression tests. + - Python: [syrupy](https://syrupy-project.github.io/syrupy/) + +- **Mutation testing**: tests pass -> change a line of code (make a mutant) -> test again and check whether all mutants get "killed". + - Python: [mutmut](https://mutmut.readthedocs.io/) + + +## Exercises + +Experiment with the example project and what we learned above or try it on your +own project: +- Add a unit test. +- Try to run it locally. +- Check whether it fails when you break the corresponding function. +- Try to run it on GitHub Actions. +- Create a pull request which would break the code and see whether the automatic test would catch it. +- Try to design an end-to-end test for your project. diff --git a/branch/main/_sources/version-control.md.txt b/branch/main/_sources/version-control.md.txt new file mode 100644 index 0000000..efcfece --- /dev/null +++ b/branch/main/_sources/version-control.md.txt @@ -0,0 +1,13 @@ +(version-control)= + +# Introduction to version control with Git and GitHub + +```{toctree} +:maxdepth: 1 + +version-control/motivation.md +version-control/browsing.md +version-control/branching-and-committing.md +version-control/practical-advice.md +version-control/sharing.md +``` diff --git a/branch/main/_sources/version-control/branching-and-committing.md.txt b/branch/main/_sources/version-control/branching-and-committing.md.txt new file mode 100644 index 0000000..702e712 --- /dev/null +++ b/branch/main/_sources/version-control/branching-and-committing.md.txt @@ -0,0 +1,339 @@ +(branching-and-committing)= + +# Creating branches and commits + +The first and most basic task to do in Git is **record changes** using +commits. In this part, we will record changes in two +ways: on a **new branch** (which supports multiple lines of work at once), and directly +on the "main" branch (which happens to be the default branch here). + +:::{objectives} +- Record new changes to our own copy of the project. +- Understand adding changes in two separate branches. +- See how to compare different versions. +::: + + +## Background + +- In the previous episode we have browsed an existing **repository** and saw **commits** + and **branches**. +- Each **commit** is a snapshot of the entire project at a certain + point in time and has a unique identifier (**hash**) . +- A **branch** is a line of development, and the `main` branch or `master` branch + are often the default branch in Git. +- A branch in Git is like a **sticky note that is attached to a commit**. When we add + new commits to a branch, the sticky note moves to the new commit. +- **Tags** are a way to mark a specific commit as important, for example a release + version. They are also like a sticky note, but they don't move when new + commits are added. + +:::{figure} img/gophers.png +:alt: Branching explained with a gopher +:width: 100% + +What if two people, at the same time, make two different changes? Git +can merge them together easily. Image created using +([inspiration](https://twitter.com/jay_gee/status/703360688618536960)). +::: + + +## Exercise: Creating branches and commits + +:::{figure} img/illustrations/branches.png +:alt: Illustration of what we want to achieve in this exercise +:width: 60% + +Illustration of what we want to achieve in this exercise. +::: + +:::{exercise} Exercise: Practice creating commits and branches (20 min) +1. First create a new branch and then either add a new file or modify an + existing file and commit the change. Make sure that you now work **on your + copy** of the example repository. In your commit you can share a Git or + programming trick you like. +1. In a new commit, modify the file again. +1. Switch to the `main` branch and create a commit there. +1. Browse the network and locate the commits that you just created ("Insights" -> "Network"). +1. Compare the branch that you created with the `main` branch. Can you find an easy way to see the differences? +1. Can you find a way to compare versions between two arbitrary commits in the repository? +1. Try to rename the branch that you created and then browse the network again. +1. Try to create a tag for one of the commits that you created (on GitHub, + create a "release"). +::: + +The solution below goes over most of the answers, and you are +encouraged to use it when the hints aren't enough - this is by +design. + + +## Solution and walk-through + + +### (1) Create a new branch and a new commit + +:::::{tabs} +::::{group-tab} GitHub +1. Where it says "main" at the top left, click, enter a new branch + name `new-tutorial`, click on the offer to create the new branch + ("Create branch new-tutorial from main"). +1. Make sure you are still on the `new-tutorial` branch (it should say + it at the top), and click "Add file" → "Create new file" from the + upper right. +1. Enter a filename where it says "Name your file...". +1. Share some Git or programming trick you like. +1. Click "Commit changes" +1. Enter a commit message. Then click "Commit + changes". + +You should appear back at the file browser view, and see your +modification there. +:::: + +::::{group-tab} VS Code +1. Make sure that you are on the main branch. +1. Version control button on left sidebar → Three dots in upper right of source control → Branch → Create branch. +1. VS Code automatically switches to the new branch. +4. Create a new file. +4. In the version control sidebar, click the `+` sign to add the file for the next commit. +4. Enter a brief message and click "Commit". +:::: + +::::{group-tab} Command line +Create a new branch called `new-tutorial` from `main` and switch to it: +```console +$ git switch --create new-tutorial main +``` + +Then create the new file. Finally add and commit the file: +```console +$ git add tutorial.md # or a different file name +$ git commit -m "sharing a programming trick" +``` +:::: +::::: + + +### (2) Modify the file again with a new commit + +:::::{tabs} +::::{group-tab} GitHub +This is similar to before, but we click on the existing file to +modify. + +1. Click on the file you added or modified previously. +2. Click the edit button, the pencil icon at top-right. +3. Follow the "Commit changes" instructions as in the previous step. +:::: + +::::{group-tab} VS Code +Repeat as in the previous step. +:::: + +::::{group-tab} Command line +Modify the file. Then commit the new change: +```console +$ git add tutorial.md +$ git commit -m "short summary of the change" +``` + +Make sure to replace "short summary of the change" with a meaningful commit +message. +:::: +::::: + + +### (3) Switch to the main branch and create a commit there + +:::::{tabs} +::::{group-tab} GitHub +1. Go back to the main repository page (your user's page). +1. In the branch switch view (top left above the file view), switch to + `main`. +1. Modify another file that already exists, following the pattern + from above. +:::: + +::::{group-tab} VS Code +Use the branch selector at the bottom to switch back to the main branch. Repeat the same steps as above, +but this time modify a different file. +:::: + +::::{group-tab} Command line +First switch to the `main` branch: +```console +$ git switch main +``` + +Then modify a file. Finally `git add` and then commit the change: +```console +$ git commit -m "short summary of the change" +``` +:::: +::::: + + +### (4) Browse the commits you just made + +Let's look at what we did. Now, the `main` and `new-tutorial` branches +have diverged: both have some modifications. Try to find the commits +you created. + +:::::{tabs} +::::{group-tab} GitHub +Insights tab → Network view (just like we have done before). +:::: + +::::{group-tab} VS Code +This requires an extension. Opening the VS Code terminal lets you use the +command line method (View → Terminal will open a terminal at bottom). This is +a normal command line interface and very useful for work. +:::: + +::::{group-tab} Command line +```console +$ git graph +$ git log --graph --oneline --decorate --all # if you didn't define git graph yet. +``` +:::: +::::: + + +### (5) Compare the branches + +Comparing changes is an important thing we need to do. When using the +GitHub view only, this may not be so common, but we'll show it so that +it makes sense later on. + +:::::{tabs} + +::::{group-tab} GitHub +A nice way to compare branches is to add `/compare` to the URL of the repository, +for example (replace USER): +`https://github.com/USER/planets/compare` +:::: + +::::{group-tab} VS Code +This seems to require an extension. We recommend you use the command line method. +:::: + +::::{group-tab} Command line +```console +$ git diff main new-tutorial +``` + +Try also the other way around: +```console +$ git diff new-tutorial main +``` + +Try also this if you only want to see the file names that are different: +```console +$ git diff --name-only main new-tutorial +``` +:::: +::::: + + +### (6) Compare two arbitrary commits + +This is similar to above, but not only between branches. + +:::::{tabs} +::::{group-tab} GitHub +Following the `/compare`-trick above, one can compare commits on GitHub by +adjusting the following URL: +`https://github.com/USER/planets/compare/VERSION1..VERSION2` + +Replace `USER` with your username and `VERSION1` and `VERSION2` with a commit hash or branch name. +Please try it out. +:::: + +::::{group-tab} VS Code +Again, we recommend using the Command Line method. +:::: + +::::{group-tab} Command line +First try this to get a short overview of the commits: +```console +$ git log --oneline +``` + +Then try to compare any two commit identifiers with `git diff`. +:::: +::::: + + +### (7) Renaming a branch + +:::::{tabs} +::::{group-tab} GitHub + +Branch button → View all branches → three dots at right side → Rename branch. + +:::: +::::{group-tab} VS Code +Version control sidebar → Three dots (same as in step 2) → Branch → Rename branch. Make sure you are on the right branch before you start. +:::: + +::::{group-tab} Command line +Renaming the current branch: +```console +$ git branch -m new-branch-name +``` + +Renaming a different branch: +```console +$ git branch -m different-branch new-branch-name +``` +:::: +::::: + + +### (8) Creating a tag + +Tags are a way to mark a specific commit as important, for example a release +version. They are also like a sticky note, but they don't move when new +commits are added. + +:::::{tabs} +::::{group-tab} GitHub +On the right side, below "Releases", click on "Create a new release". + +What GitHub calls releases are actually tags in Git with additional metadata. +For the purpose of this exercise we can use them interchangeably. +:::: + +::::{group-tab} VS Code +Version control sidebar → Three dots (same as in step 2) → Tags → Create tag. Make sure you are on the expected commit before you do this. +:::: + +::::{group-tab} Command line +Creating a tag: +```console +$ git tag -a v1.0 -m "New manuscript version for the pre-print" +``` +:::: +::::: + + +## Summary + +In this part, we saw how we can make changes to our files. With branches, we +can track several lines of work at once, and can compare their differences. + +- You could commit directly to `main` if there is only one single line + of work and it's only you. +- You could commit to branches if there are multiple lines of work at + once, and you don't want them to interfere with each other. +- Tags are useful to mark a specific commit as important, for example a + release version. +- In Git, commits form a so-called "graph". Branches are tags in Git function + like sticky notes that stick to specific commits. What this means for us is + that it does not cost any significant disk space to create new branches. +- Not all files should be added to Git. For example, temporary files or + files with sensitive information or files which are generated as part of + the build process should not be added to Git. For this we use + `.gitignore` (more about this later: {ref}`practical-advice`). +- Unsure on which branch you are or what state the repository is in? + On the command line, use `git status` frequently to get a quick overview. diff --git a/branch/main/_sources/version-control/browsing.md.txt b/branch/main/_sources/version-control/browsing.md.txt new file mode 100644 index 0000000..d3c3dc0 --- /dev/null +++ b/branch/main/_sources/version-control/browsing.md.txt @@ -0,0 +1,374 @@ +(browsing)= + +# Forking, cloning, and browsing + +In this episode, we will look at an **existing repository** to understand how +all the pieces work together. Along the way, we will make a copy (by +**forking** and/or **cloning**) of the repository for us, which will be used +for our own changes. + +:::{objectives} +- See a real Git repository and understand what is inside of it. +- Understand how version control allows advanced inspection of a + repository. +- See how Git allows multiple people to work on the same project at the same time. +- **See the big picture** instead of remembering a bunch of commands. +::: + + +## GitHub, VS Code, or command line + +We offer **three different paths** for this exercise: +- **GitHub** (this is the one we will demonstrate) +- **VS Code** (if you prefer to follow along using an editor) +- **Command line** (for people comfortable with the command line) + + +## Creating a copy of the repository by "forking" or "cloning" + +A **repository** is a collection of files in one directory tracked by Git. A +GitHub repository is GitHub's copy, which adds things like access control, +issue tracking, and discussions. Each GitHub repository is owned by a user or +organization, who controls access. + +First, we need to make **our own copy** of the exercise repository. This will +become important later, when we make our own changes. + +:::{figure} img/illustrations/fork.png +:alt: Illustration of forking a repository on GitHub +:width: 50% + +Illustration of forking a repository on GitHub. +::: + +:::{figure} img/illustrations/clone.png +:alt: Illustration of cloning a repository to your computer +:width: 50% + +Illustration of cloning a repository to your computer. +::: + +:::{figure} img/illustrations/clone-of-fork.png +:alt: Illustration of cloning a forked repository to your computer +:width: 60% + +It is also possible to do this: to clone a forked repository to your computer. +::: + +At all times you should be aware of if you are looking at **your repository** +or the **upstream repository** (original repository): +- Your repository: https://github.com/**USER**/planets +- Upstream repository: https://github.com/**workshop-material**/planets + +:::{admonition} How to create a fork +1. Go to the repository view on GitHub: +1. First, on GitHub, click the button that says "Fork". It is towards + the top-right of the screen. +1. You should shortly be redirected to your copy of the repository + **USER/planets**. +::: + +:::{instructor-note} +Before starting the exercise session show +how to fork the repository to own account +(above). +::: + + + +## Exercise: Copy and browse an existing project + +Work on this by yourself or in pairs. + + + + + + + + + + + + +::::::{prereq} Exercise preparation +:::::{tabs} +::::{group-tab} GitHub +In this case you will work on a fork. + +You only need to open your own view, as described above. The browser +URL should look like `https://github.com/USER/planets`, where +`USER` is your GitHub username. +:::: + +::::{group-tab} VS Code +You need to have forked the repository as described above. + +We need to start by making a clone of this repository so that you can work +locally. + +1. Start VS Code. +1. If you don't have the default view (you already have a project +open), go to File → New Window. +1. Under "Start" on the screen, select "Clone Git Repository...". Alternatively + navigate to the "Source Control" tab on the left sidebar and click on the "Clone Repository" button. +1. Paste in this URL: `https://github.com/USER/planets`, where + `USER` is your username. You can copy this from the browser. +1. Browse and select the folder in which you want to clone the + repository. +1. Say yes, you want to open this repository. +1. Select "Yes, I trust the authors" (the other option works too). +:::: + +::::{group-tab} Command line +**This path is advanced and we do not include all command line +information: you need to be somewhat +comfortable with the command line already.** + +You need to have forked the repository as described above. + +We need to start by making a clone of this repository so that you can work +locally. + +1. Start the terminal in which you use Git (terminal application, or + Git Bash). +1. Change to the directory where you would want the repository to be + (`cd ~/code` for example, if the `~/code` directory is where you + store your files). +1. Run the following command: `git clone + https://github.com/USER/planets`, where `USER` is your + username. You might need to use a SSH clone command instead of + HTTPS, depending on your setup. +1. Change to that directory: `cd planets` +:::: +::::: +:::::: + + +:::{exercise} Exercise: Browsing an existing project (20 min) + +Browse the [example project](https://github.com/workshop-material/planets) and +explore commits and branches, either on a fork or on a clone. Take notes and +prepare questions. The hints are for the GitHub path in the browser. + +1. Browse the **commit history**: Are commit messages understandable? + (Hint: "Commit history", the timeline symbol, above the file list) +1. Compare the commit history with the **network graph** ("Insights" -> "Network"). Can you find the branches? +1. Try to find the **history of commits for a single file**, e.g. `simulate.py`. + (Hint: "History" button in the file view) +1. **Which files include the word "position"**? + (Hint: the GitHub search on top of the repository view) +1. In the `simulate.py` file, find out **who modified each line last and when** + (click on file, then click "Blame" button). Find out who modified the gravitational constant + last and in which commit. + (Hint: "Blame" view in the file view) +1. Can you use this code yourself? **Are you allowed to share + modifications**? + (Hint: look for a license file) +::: + +The solution below goes over most of the answers, and you are +encouraged to use it when the hints aren't enough - this is by +design. + + +## Solution and walk-through + +### (1) Basic browsing + +The most basic thing to look at is the history of commits. + +* This is visible from a button in the repository view. We see every + change, when, and who has committed. +* Every change has a unique identifier, such as `244c993`. This can + be used to identify both this change, and the whole project's + version as of that change. +* Clicking on a change in the view shows more. + +:::::{tabs} + +::::{group-tab} GitHub +Click on the timeline symbol in the repository view: + :::{figure} img/browsing/history.png + :alt: Screenshot on GitHub of where to find the commit history + :width: 100% + :class: with-border + ::: +:::: + +::::{group-tab} VS Code +This can be done from "Timeline", in the bottom of explorer, but only +for a single file. +:::: + +::::{group-tab} Command line +Run: +```console +$ git log +``` + +Try also: +```console +$ git log --oneline +``` +:::: + +::::: + + +### (2) Compare commit history with network graph + +The commit history we saw above looks linear: one commit after +another. But if we look at the network view, we see some branches and +merges. We'll see how to do these later. This is another one of the +basic Git views. + +:::::{tabs} +::::{group-tab} GitHub +In a new browser tab, open the "Insights" tab, and click on "Network". +You can hover over the commit dots to see the person who committed and +how they correspond with the commits in the other view: + :::{figure} img/browsing/network.png + :alt: Screenshot on GitHub of the network graph + :width: 100% + :class: with-border + ::: +:::: + +::::{group-tab} VS Code +We don't know how to do this without an extension. Try starting a terminal and using the +"Command line" option. +:::: + +::::{group-tab} Command line +This is a useful command to browse the network of commits locally: +```console +$ git log --graph --oneline --decorate --all +``` + +To avoid having to type this long command every time, you can define an alias (shortcut): +```console +$ git config --global alias.graph "log --graph --oneline --decorate --all" +``` + +From then on, you can use `git graph` to see the network graph. +:::: + +::::: + + +### (3) How can you browse the history of a single file? + +We see the history for the whole repository, but we can also see it +for a single file. + +:::::{tabs} + +::::{group-tab} GitHub +Navigate to the file view: Main page → simulate.py. +Click the "History" button near the top right. +:::: + +::::{group-tab} VS Code +Open simulate.py file in the editor. Under the file browser, +we see a "Timeline" view there. +:::: + +::::{group-tab} Command line +The `git log` command can take a filename and provide the log of only +a single file: + +``` +$ git log simulate.py +``` +:::: + +::::: + + +### (4) Which files include the word "position"? + +Version control makes it very easy to find all occurrences of a single +word. This is useful for things like finding where functions or +variables are defined or used. + +:::::{tabs} +::::{group-tab} GitHub +We go to the main file view. We click the Search magnifying +class at the very top, type "position", and click enter. We see every +instance, including the context. + +:::{admonition} Searching in a forked repository will not work instantaneously! + +It usually takes a few minutes before one can search for keywords in a forked repository +since it first needs to build the search index the very first time we search. +Start it, continue with other steps, then come back to this. +::: +:::: + +::::{group-tab} VS Code +If you use the "Search" magnifying class on the left sidebar, and +search for "position" it shows the occurrences in every file. You can +click to see the usage in context. +:::: + +::::{group-tab} Command line +`grep` is the command line tool that searches for lines matching a term +```console +$ git grep position # only the lines +$ git grep -C 3 position # three lines of context +$ git grep -i position # case insensitive +``` +:::: + +::::: + + +### (5) Who modified each line last and when? + +This is called the "annotate" or "blame" view. The name "blame" +is very unfortunate, but it is the standard term for historical reasons +for this functionality and it is not meant to blame anyone. + +:::::{tabs} + +::::{group-tab} GitHub +From a file view, change preview to "Blame" towards the top-left. +To get the actual commit, click on the commit message. +:::: + +::::{group-tab} VS Code +This requires an extension. We recommend for now you use the command +line version, after opening a terminal. +:::: + +::::{group-tab} Command line +These two commands are similar but have slightly different output. +```console +$ git annotate simulate.py +$ git blame simulate.py +``` +:::: + +::::: + + +### (6) Can you use this code yourself? Are you allowed to share modifications? + +- Look at the file `LICENSE`. +- On GitHub, click on the file to see a nice summary of what we can do with this: + :::{figure} img/browsing/license.png + :alt: Screenshot on GitHub summarizing license terms + :width: 100% + :class: with-border + ::: + + +### Summary + +- Git allowed us to understand this simple project much better than we + could, if it was just a few files on our own computer. +- It was easy to share the project with the course. +- By forking the repository, we created our own copy. This is + important for the following, where we will make changes to + our copy. diff --git a/branch/main/_sources/version-control/motivation.md.txt b/branch/main/_sources/version-control/motivation.md.txt new file mode 100644 index 0000000..25ab06f --- /dev/null +++ b/branch/main/_sources/version-control/motivation.md.txt @@ -0,0 +1,118 @@ +(version-control-motivation)= + +# Motivation + +:::{objectives} +- Browse **commits** and **branches** of a Git repository. +- Remember that commits are like **snapshots** of the repository at a certain + point in time. +- Know the difference between **Git** (something that tracks changes) and + **GitHub/GitLab** (a platform to host Git repositories). +::: + + +## Why do we need to keep track of versions? + +Version control is an answer to the following questions (do you recognize some +of them?): + +- "It broke ... hopefully I have a working version somewhere?" + +- "Can you please send me the latest version?" + +- "Where is the latest version?" + +- "Which version are you using?" + +- "Which version have the authors used in the paper I am trying to reproduce?" + +- "Found a bug! Since when was it there?" + +- "I am sure it used to work. When did it change?" + +- "My laptop is gone. Is my thesis now gone?" + + +## Demonstration + +- Example repository: +- Commits are like **snapshots** and if we break something we can go back to a + previous snapshot. +- Commits carry **metadata** about changes: author, date, commit message, and + a checksum. +- **Branches** are like parallel universes where you can experiment with + changes without affecting the default branch: + + ("Insights" -> "Network") +- With version control we can **annotate code** + ([example](https://github.com/workshop-material/planets/blame/main/animate.py)). +- **Collaboration**: We can fork (make a copy on GitHub), clone (make a copy + to our computer), review, compare, share, and discuss. +- **Code review**: Others can suggest changes using pull requests or merge + requests. These can be reviewed and discussed before they are merged. + Conceptually, they are similar to "suggesting changes" in Google Docs. + + +## Features: roll-back, branching, merging, collaboration + +- **Roll-back**: you can always go back to a previous version and compare + +- **Branching and merging**: + - Work on different ideas at the same time + - Different people can work on the same code/project without interfering + - You can experiment with an idea and discard it if it turns out to be a bad idea + +:::{figure} img/gophers.png +:alt: Branching explained with a gopher +:width: 100% + +Image created using +([inspiration](https://twitter.com/jay_gee/status/703360688618536960)). +::: + +- **Collaboration**: review, compare, share, discuss + +- [Example network graph](https://github.com/workshop-material/planets/network) + + +## Talking about code + +Which of these two is more practical? +1. "Clone the code, go to the file 'simulate.py', and search for 'force_between_planets'. + Oh! But make sure you use the version from September 2024." +1. Or I can send you a permalink: + + +## What we typically like to snapshot + +- Software (this is how it started but Git/GitHub can track a lot more) +- Scripts +- Documents (plain text files much better suitable than Word documents) +- Manuscripts (Git is great for collaborating/sharing LaTeX or [Quarto](https://quarto.org/) manuscripts) +- Configuration files +- Website sources +- Data + +::::{discussion} + In this example somebody tried to keep track of versions without a version + control system tool like Git. Discuss the following directory listing. What + possible problems do you anticipate with this kind of "version control": + ```text + myproject-2019.zip + myproject-2020-february.zip + myproject-2021-august.zip + myproject-2023-09-19-working.zip + myproject-2023-09-21.zip + myproject-2023-09-21-test.zip + myproject-2023-09-21-myversion.zip + myproject-2023-09-21-newfeature.zip + ... + (100 more files like these) + ``` + + :::{solution} + - Giving a version to a collaborator and merging changes later with own + changes sounds like lots of work. + - What if you discover a bug and want to know since when the bug existed? + ::: +:::: diff --git a/branch/main/_sources/version-control/practical-advice.md.txt b/branch/main/_sources/version-control/practical-advice.md.txt new file mode 100644 index 0000000..5e4c460 --- /dev/null +++ b/branch/main/_sources/version-control/practical-advice.md.txt @@ -0,0 +1,136 @@ +(practical-advice)= + +# Practical advice: How much Git is necessary? + + +## Writing useful commit messages + +Useful commit messages **summarize the change and provide context**. + +If you need a commit message that is longer than one line, +then the convention is: **one line summarizing the commit, then one empty line, +then paragraph(s) with more details in free form, if necessary**. + +Good example: +```{code-block} text +--- +emphasize-lines: 1 +--- +increase alpha to 2.0 for faster convergence + +the motivation for this change is +to enable ... +... +(more context) +... +this is based on a discussion in #123 +``` + +- **Why something was changed is more important than what has changed.** +- Cross-reference to issues and discussions if possible/relevant. +- Bad commit messages: "fix", "oops", "save work" +- Bad examples: [http://whatthecommit.com](http://whatthecommit.com) +- Write commit messages that will be understood + 15 years from now by someone else than you. Or by your future you. +- Many projects start out as projects "just for me" and end up to be successful projects + that are developed by 50 people over decades. +- [Commits with multiple authors](https://help.github.com/articles/creating-a-commit-with-multiple-authors/) are possible. + +Good references: + +- ["My favourite Git commit"](https://fatbusinessman.com/2019/my-favourite-git-commit) +- ["On commit messages"](https://who-t.blogspot.com/2009/12/on-commit-messages.html) +- ["How to Write a Git Commit Message"](https://chris.beams.io/posts/git-commit/) + +```{note} +A great way to learn how to write commit messages and to get inspired by their +style choices: **browse repositories of codes that you use/like**: + +Some examples (but there are so many good examples): +- [SciPy](https://github.com/scipy/scipy/commits/main) +- [NumPy](https://github.com/numpy/numpy/commits/main) +- [Pandas](https://github.com/pandas-dev/pandas/commits/main) +- [Julia](https://github.com/JuliaLang/julia/commits/master) +- [ggplot2](https://github.com/tidyverse/ggplot2/commits/main), + compare with their [release + notes](https://github.com/tidyverse/ggplot2/releases) +- [Flask](https://github.com/pallets/flask/commits/main), + compare with their [release + notes](https://github.com/pallets/flask/blob/main/CHANGES.rst) + +When designing commit message styles consider also these: +- How will you easily generate a changelog or release notes? +- During code review, you can help each other improving commit messages. +``` + +But remember: it is better to make any commit, than no commit. Especially in small projects. +**Let not the perfect be the enemy of the good enough**. + + +## What level of branching complexity is necessary for each project? + +**Simple personal projects**: +- Typically start with just the `main` branch. +- Use branches for unfinished/untested ideas. +- Use branches when you are not sure about a change. +- Use tags to mark important milestones. +- If you are unsure what to do with unfinished and not working code, commit it + to a branch. + +**Projects with few persons: you accept things breaking sometimes** +- It might be reasonable to commit to the `main` branch and feature branches. + +**Projects with few persons: changes are reviewed by others** +- You create new feature branches for changes. +- Changes are reviewed before they are merged to the `main` branch. +- Consider to write-protect the `main` branch so that it can only be changed + with pull requests or merge requests. + + +## How large should a commit be? + +- Better too small than too large (easier to combine than to split). +- Often I make a commit at the end of the day (this is a unit I would not like to lose). +- Smaller sized commits may be easier to review for others than huge commits. +- Imperfect commits are better than no commits. +- A commit should not contain unrelated changes to simplify review and possible + repair/adjustments/undo later (but again: imperfect commits are better than no commits). + + +## Working on the command line? Use "git status" all the time + +The `git status` command is one of the most useful commands in Git +to inform about which branch we are on, what we are about to commit, +which files might not be tracked, etc. + + +## How about staging and committing? + +- Commit early and often: rather create too many commits than too few. + You can always combine commits later. +- Once you commit, it is very, very hard to really lose your code. +- Always fully commit (or stash) before you do dangerous things, so that you know you are safe. + Otherwise it can be hard to recover. +- Later you can start using the staging area (where you first stage and then commit in a second step). +- Later start using `git add -p` and/or `git commit -p`. + + +## What to avoid + +- Committing **generated files/directories** (example: `__pycache__`, `*.pyc`) -> + use [.gitignore + files](https://docs.github.com/en/get-started/getting-started-with-git/ignoring-files) + ([collection of .gitignore templates](https://github.com/github/gitignore)). + +- Committing **huge files** -> use code review to detect this. + +- Committing **unrelated changes** together. + +- Postponing commits because the changes are "unfinished"/"ugly" -> better ugly + commits than no commits. + +- When working with branches: + - Not updating your branch before starting new work. + - Too ambitious branch which risks to never get completed. + - Over-engineering the branch layout and safeguards in small projects. + - Working on unrelated things on the same branch. diff --git a/branch/main/_sources/version-control/sharing.md.txt b/branch/main/_sources/version-control/sharing.md.txt new file mode 100644 index 0000000..6fb6401 --- /dev/null +++ b/branch/main/_sources/version-control/sharing.md.txt @@ -0,0 +1,301 @@ +(sharing-repositories)= + +# Optional: How to turn your project to a Git repo and share it + +:::{objectives} +- Turn our own coding project (small or large, finished or unfinished) into a + Git repository. +- Be able to share a repository on the web to have a backup or so that others + can reuse and collaborate or even just find it. +::: + + +## Exercise + +:::{figure} img/illustrations/sharing.png +:alt: Illustration of how we turn a project into a Git repository and share it +:width: 100% + +From a bunch of files to a local repository which we then share on GitHub. +::: + + +:::::{exercise} Exercise: Turn your project to a Git repo and share it (20 min) + +1. Create a new directory called **myproject** with one or few files in it. + This represents our own project. It is not yet a Git repository. You can try + that with your own project or use a simple placeholder example. +2. Turn this new directory into a Git repository. +3. Share this repository on GitHub (or GitLab, since it really works the same). + +We offer **three different paths** of how to do this exercise. +* Via **GitHub web interface**: easy and can be a good starting point if you are completely + new to Git. +* **VS Code** is quite easy, since VS Code can offer to create the + GitHub repositories for you. +* **Command line**: you need to create the + repository on GitHub and link it yourself. + +::::{tabs} + +:::{group-tab} Only using GitHub +### Create an repository on GitHub + +First log into GitHub, then follow the screenshots and descriptions below. +```{figure} img/sharing/new-repository.png +:alt: Screenshot on GitHub before a new repository form is opened +:width: 60% +:class: with-border + +Click on the "plus" symbol on top right, then on "New repository". +``` + +Then: +```{figure} img/sharing/create-repository-with-readme.png +:alt: Screenshot on GitHub just before a new repository is created +:width: 100% +:class: with-border + +Choose a repository name, add a short description, and in this case **make sure to check** "Add a +README file". Finally "Create repository". +``` + + +### Upload your files + +Now that the repository is created, you can upload your files: +```{figure} img/sharing/upload-files.png +:alt: Screenshot on GitHub just before uploading files +:width: 100% +:class: with-border + +Click on the "+" symbol and then on "Upload files". +``` +::: + +:::{group-tab} VS Code +In VS Code it only takes few clicks. + +First, open the folder in VS Code. My example project here contains two files. +Then click on the source control icon: +```{figure} img/sharing/vscode-start.png +:alt: Screenshot of VS Code before clicking on the source control icon +:width: 100% +:class: with-border + +Open the folder in VS Code. Then click on the source control icon. +``` + +```{figure} img/sharing/vscode-publish-to-github1.png +:alt: Screenshot of VS Code before publishing to GitHub +:width: 100% +:class: with-border + +Choose "Publish to GitHub". In this case I never even clicked on "Initialize Repository". +``` + +```{figure} img/sharing/vscode-publish-to-github2.png +:alt: Screenshot of VS Code before publishing to GitHub +:width: 100% +:class: with-border + +In my case I chose to "Publish to GitHub public repository". Here you can also rename +the repository if needed. +``` + +```{figure} img/sharing/vscode-authorize.png +:alt: Screenshot of VS Code asking for authorization +:width: 50% +:class: with-border + +First time you do this you might need to authorize VS Code to access your +GitHub account by redirecting you to https://github.com/login/oauth/authorize. +``` + +```{figure} img/sharing/vscode-publish-to-github3.png +:alt: Screenshot of VS Code after publishing to GitHub +:width: 100% +:class: with-border + +After it is published, click on "Open on GitHub". +``` +::: + +:::{group-tab} Command line +### Put your project under version control + +My example project here consists of two files. Replace this with your own +example files: +```console +$ ls -l + +.rw------- 19k user 7 Mar 17:36 LICENSE +.rw------- 21 user 7 Mar 17:36 myscript.py +``` + +I will first initialize a Git repository in this directory. +If you get an error, try without the `-b main` (and your default branch will +then be called `master`, this will happen for Git versions older than +2.28): +```console +$ git init -b main +``` + +Now add and commit the two files to the Git repository: +```console +$ git add LICENSE myscript.py +$ git commit -m "putting my project under version control" +``` + +If you want to add all files in one go, you can use `git +add .` instead of `git add LICENSE myscript.py`. + +Now you have a Git repository with one commit. Verify this with `git log`. +But it's still only on your computer. Let's put it on GitHub next. + + +### Create an empty repository on GitHub + +First log into GitHub, then follow the screenshots and descriptions below. +```{figure} img/sharing/new-repository.png +:alt: Screenshot on GitHub before a new repository form is opened +:width: 60% +:class: with-border + +Click on the "plus" symbol on top right, then on "New repository". +``` + +Then create an empty repository without any files and without any commits: +```{figure} img/sharing/create-repository.png +:alt: Screenshot on GitHub just before a new repository is created +:width: 100% +:class: with-border + +Choose a repository name, add a short description, but please **do not check** "Add a +README file". For "Add .gitignore" and "Choose a license" also leave as "None". Finally "Create repository". +``` + +Once you click the green "Create repository", you will see a page similar to: +```{figure} img/sharing/bare-repository.png +:alt: Screenshot on GitHub after a bare repository was created +:width: 100% +:class: with-border +``` + +What this means is that we have now an empty project with either an HTTPS or an +SSH address: click on the HTTPS and SSH buttons to see what happens. + + +### Push an existing repository from your computer to GitHub + +We now want to follow the "**... or push an existing repository from the command line**": + +1. In your terminal make sure you are still in your myproject directory. +2. Copy paste the three lines below the red arrow to the terminal and execute + those, in my case (**you need to replace the "USER" part and possibly also + the repository name**): + +`````{tabs} + ````{group-tab} SSH + ```console + $ git remote add origin git@github.com:USER/myproject.git + ``` + ```` + ````{group-tab} HTTPS + ```console + $ git remote add origin https://github.com/USER/myproject.git + ``` + ```` +````` + +Then: +```console +$ git branch -M main +$ git push -u origin main +``` + +The meaning of the above lines: +- Add a remote reference with the name "origin" +- Rename current branch to "main" +- Push branch "main" to "origin" + +You should now see: + +```text +Enumerating objects: 4, done. +Counting objects: 100% (4/4), done. +Delta compression using up to 12 threads +Compressing objects: 100% (3/3), done. +Writing objects: 100% (4/4), 6.08 KiB | 6.08 MiB/s, done. +Total 4 (delta 0), reused 0 (delta 0), pack-reused 0 +To github.com:USER/myproject.git + * [new branch] main -> main +branch 'main' set up to track 'origin/main'. +``` + +Reload your GitHub project website and your commits should now be +online! + + +### Troubleshooting + +**error: remote origin already exists** +- Explanation: You probably ran a `git remote add origin ...` command, then changed your + mind about HTTPS or SSH and then tried to run the other `git remote add + origin ...` command but "origin" then already exists. +- Recovery: + - First remove "origin" with `git remote remove origin` + - Then run the correct `git remote add origin ...` command + +**remote contains work that you do not have** +- Explanation: You probably clicked on "Add a README file" and now the + repository on GitHub is not empty but contains one commit and locally you + have a different history. Git now prevents you from accidentally overwriting + the history on GitHub. +- Recovery: + - Use `git push --force` instead of `git push`, which will force Git to overwrite the history on GitHub + - Note that this is a powerful but also possibly dangerous option but here it + helps us. If it's a brand new repo, it probably is fine to do this. For real + repositories, don't do this unless you are very sure what is happening. +::: + +:::{group-tab} RStudio + +This is not fully explained, because a lot of it is similar to the "Command +line" method (and an RStudio expert could help us some). The main differences +are: + +### Put your project under version control + +1. Tools → Version control → Project setup → Version control system = Git. +1. Select "Yes" for "do you want to initialize a new git repository for this project. +1. Select yes to restart the project with RStudio. +1. Switch to branch `main` to have you branch named that. + +### Create an empty repository on GitHub + +Same as command line + +### Push an existing repository from your computer to GitHub + +1. Under the "Create new branch" button → "Add Remote" +1. Remote name: `origin` +1. Remote URL: as in command line (remember to select SSH or HTTPS as you have configured your RStudio) +1. The "Push" (up arrow) button will send changes on your current branch to the remote. The "Pull" (down arrow) will get changes from the remote. + +### Troubleshooting + +Same as command line + +::: +:::: +::::: + + +## Is putting software on GitHub/GitLab/... publishing? + +It is a good first step but to make your code truly **findable and +accessible**, consider making your code **citable and persistent**: Get a +persistent identifier (PID) such as DOI in addition to sharing the code +publicly, by using services like [Zenodo](https://zenodo.org) or similar +services. diff --git a/branch/main/_static/_sphinx_javascript_frameworks_compat.js b/branch/main/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 0000000..8141580 --- /dev/null +++ b/branch/main/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. Multiple values per key are supported, + * it will always return arrays of strings for the value parts. + */ +jQuery.getQueryParameters = function(s) { + if (typeof s === 'undefined') + s = document.location.search; + var parts = s.substr(s.indexOf('?') + 1).split('&'); + var result = {}; + for (var i = 0; i < parts.length; i++) { + var tmp = parts[i].split('=', 2); + var key = jQuery.urldecode(tmp[0]); + var value = jQuery.urldecode(tmp[1]); + if (key in result) + result[key].push(value); + else + result[key] = [value]; + } + return result; +}; + +/** + * highlight a given string on a jquery object by wrapping it in + * span elements with the given class name. + */ +jQuery.fn.highlightText = function(text, className) { + function highlight(node, addItems) { + if (node.nodeType === 3) { + var val = node.nodeValue; + var pos = val.toLowerCase().indexOf(text); + if (pos >= 0 && + !jQuery(node.parentNode).hasClass(className) && + !jQuery(node.parentNode).hasClass("nohighlight")) { + var span; + var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.className = className; + } + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + node.parentNode.insertBefore(span, node.parentNode.insertBefore( + document.createTextNode(val.substr(pos + text.length)), + node.nextSibling)); + node.nodeValue = val.substr(0, pos); + if (isInSVG) { + var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); + var bbox = node.parentElement.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute('class', className); + addItems.push({ + "parent": node.parentNode, + "target": rect}); + } + } + } + else if (!jQuery(node).is("button, select, textarea")) { + jQuery.each(node.childNodes, function() { + highlight(this, addItems); + }); + } + } + var addItems = []; + var result = this.each(function() { + highlight(this, addItems); + }); + for (var i = 0; i < addItems.length; ++i) { + jQuery(addItems[i].parent).before(addItems[i].target); + } + return result; +}; + +/* + * backward compatibility for jQuery.browser + * This will be supported until firefox bug is fixed. + */ +if (!jQuery.browser) { + jQuery.uaMatch = function(ua) { + ua = ua.toLowerCase(); + + var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || + /(webkit)[ \/]([\w.]+)/.exec(ua) || + /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || + /(msie) ([\w.]+)/.exec(ua) || + ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || + []; + + return { + browser: match[ 1 ] || "", + version: match[ 2 ] || "0" + }; + }; + jQuery.browser = {}; + jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; +} diff --git a/branch/main/_static/basic.css b/branch/main/_static/basic.css new file mode 100644 index 0000000..f316efc --- /dev/null +++ b/branch/main/_static/basic.css @@ -0,0 +1,925 @@ +/* + * basic.css + * ~~~~~~~~~ + * + * Sphinx stylesheet -- basic theme. + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; +} + +div.section::after { + display: block; + content: ''; + clear: left; +} + +/* -- relbar ---------------------------------------------------------------- */ + +div.related { + width: 100%; + font-size: 90%; +} + +div.related h3 { + display: none; +} + +div.related ul { + margin: 0; + padding: 0 0 0 10px; + list-style: none; +} + +div.related li { + display: inline; +} + +div.related li.right { + float: right; + margin-right: 5px; +} + +/* -- sidebar --------------------------------------------------------------- */ + +div.sphinxsidebarwrapper { + padding: 10px 5px 0 10px; +} + +div.sphinxsidebar { + float: left; + width: 230px; + margin-left: -100%; + font-size: 90%; + word-wrap: break-word; + overflow-wrap : break-word; +} + +div.sphinxsidebar ul { + list-style: none; +} + +div.sphinxsidebar ul ul, +div.sphinxsidebar ul.want-points { + margin-left: 20px; + list-style: square; +} + +div.sphinxsidebar ul ul { + margin-top: 0; + margin-bottom: 0; +} + +div.sphinxsidebar form { + margin-top: 10px; +} + +div.sphinxsidebar input { + border: 1px solid #98dbcc; + font-family: sans-serif; + font-size: 1em; +} + +div.sphinxsidebar #searchbox form.search { + overflow: hidden; +} + +div.sphinxsidebar #searchbox input[type="text"] { + float: left; + width: 80%; + padding: 0.25em; + box-sizing: border-box; +} + +div.sphinxsidebar #searchbox input[type="submit"] { + float: left; + width: 20%; + border-left: none; + padding: 0.25em; + box-sizing: border-box; +} + + +img { + border: 0; + max-width: 100%; +} + +/* -- search page ----------------------------------------------------------- */ + +ul.search { + margin: 10px 0 0 20px; + padding: 0; +} + +ul.search li { + padding: 5px 0 5px 20px; + background-image: url(file.png); + background-repeat: no-repeat; + background-position: 0 7px; +} + +ul.search li a { + font-weight: bold; +} + +ul.search li p.context { + color: #888; + margin: 2px 0 0 30px; + text-align: left; +} + +ul.keywordmatches li.goodmatch a { + font-weight: bold; +} + +/* -- index page ------------------------------------------------------------ */ + +table.contentstable { + width: 90%; + margin-left: auto; + margin-right: auto; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable ul { + margin-top: 0; + margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: 360px; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, figure.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, figure.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, figure.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-default, figure.align-default, .figure.align-default { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-default { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar, +aside.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px; + background-color: #ffe; + width: 40%; + float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; +} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} + +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +.translated { + background-color: rgba(207, 255, 207, 0.2) +} + +.untranslated { + background-color: rgba(255, 207, 207, 0.2) +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + +td.linenos pre { + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; +} + +table.highlighttable td { + margin: 0; + padding: 0; +} + +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; +} + +div.code-block-caption code { + background-color: transparent; +} + +table.highlighttable td.linenos, +span.linenos, +div.highlight span.gp { /* gp: Generic.Prompt */ + user-select: none; + -webkit-user-select: text; /* Safari fallback only */ + -webkit-user-select: none; /* Chrome/Safari */ + -moz-user-select: none; /* Firefox */ + -ms-user-select: none; /* IE10+ */ +} + +div.code-block-caption span.caption-number { + padding: 0.1em 0.3em; + font-style: italic; +} + +div.code-block-caption span.caption-text { +} + +div.literal-block-wrapper { + margin: 1em 0; +} + +code.xref, a code { + background-color: transparent; + font-weight: bold; +} + +h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { + background-color: transparent; +} + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family: sans-serif; +} + +div.viewcode-block:target { + margin: -1px -10px; + padding: 0 10px; +} + +/* -- math display ---------------------------------------------------------- */ + +img.math { + vertical-align: middle; +} + +div.body div.math p { + text-align: center; +} + +span.eqno { + float: right; +} + +span.eqno a.headerlink { + position: absolute; + z-index: 1; +} + +div.math:hover a.headerlink { + visibility: visible; +} + +/* -- printout stylesheet --------------------------------------------------- */ + +@media print { + div.document, + div.documentwrapper, + div.bodywrapper { + margin: 0 !important; + width: 100%; + } + + div.sphinxsidebar, + div.related, + div.footer, + #top-link { + display: none; + } +} \ No newline at end of file diff --git a/branch/main/_static/check-solid.svg b/branch/main/_static/check-solid.svg new file mode 100644 index 0000000..92fad4b --- /dev/null +++ b/branch/main/_static/check-solid.svg @@ -0,0 +1,4 @@ + + + + diff --git a/branch/main/_static/clipboard.min.js b/branch/main/_static/clipboard.min.js new file mode 100644 index 0000000..54b3c46 --- /dev/null +++ b/branch/main/_static/clipboard.min.js @@ -0,0 +1,7 @@ +/*! + * clipboard.js v2.0.8 + * https://clipboardjs.com/ + * + * Licensed MIT © Zeno Rocha + */ +!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return o}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),c=n.n(e);function a(t){try{return document.execCommand(t)}catch(t){return}}var f=function(t){t=c()(t);return a("cut"),t};var l=function(t){var e,n,o,r=1 + + + + diff --git a/branch/main/_static/copybutton.css b/branch/main/_static/copybutton.css new file mode 100644 index 0000000..40eafe5 --- /dev/null +++ b/branch/main/_static/copybutton.css @@ -0,0 +1,93 @@ +/* Copy buttons */ +button.copybtn { + position: absolute; + display: flex; + top: .3em; + right: .3em; + width: 1.7em; + height: 1.7em; + opacity: 0; + transition: opacity 0.3s, border .3s, background-color .3s; + user-select: none; + padding: 0; + border: none; + outline: none; + border-radius: 0.4em; + /* The colors that GitHub uses */ + border: #1b1f2426 1px solid; + background-color: #f6f8fa; + color: #57606a; +} + +button.copybtn.success { + border-color: #22863a; + color: #22863a; +} + +button.copybtn svg { + stroke: currentColor; + width: 1.5em; + height: 1.5em; + padding: 0.1em; +} + +div.highlight { + position: relative; +} + +.highlight:hover button.copybtn { + opacity: 1; +} + +.highlight button.copybtn:hover { + background-color: rgb(235, 235, 235); +} + +.highlight button.copybtn:active { + background-color: rgb(187, 187, 187); +} + +/** + * A minimal CSS-only tooltip copied from: + * https://codepen.io/mildrenben/pen/rVBrpK + * + * To use, write HTML like the following: + * + *

Short

+ */ + .o-tooltip--left { + position: relative; + } + + .o-tooltip--left:after { + opacity: 0; + visibility: hidden; + position: absolute; + content: attr(data-tooltip); + padding: .2em; + font-size: .8em; + left: -.2em; + background: grey; + color: white; + white-space: nowrap; + z-index: 2; + border-radius: 2px; + transform: translateX(-102%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); +} + +.o-tooltip--left:hover:after { + display: block; + opacity: 1; + visibility: visible; + transform: translateX(-100%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); + transition-delay: .5s; +} + +/* By default the copy button shouldn't show up when printing a page */ +@media print { + button.copybtn { + display: none; + } +} diff --git a/branch/main/_static/copybutton.js b/branch/main/_static/copybutton.js new file mode 100644 index 0000000..f3ecd03 --- /dev/null +++ b/branch/main/_static/copybutton.js @@ -0,0 +1,241 @@ +// Localization support +const messages = { + 'en': { + 'copy': 'Copy', + 'copy_to_clipboard': 'Copy to clipboard', + 'copy_success': 'Copied!', + 'copy_failure': 'Failed to copy', + }, + 'es' : { + 'copy': 'Copiar', + 'copy_to_clipboard': 'Copiar al portapapeles', + 'copy_success': '¡Copiado!', + 'copy_failure': 'Error al copiar', + }, + 'de' : { + 'copy': 'Kopieren', + 'copy_to_clipboard': 'In die Zwischenablage kopieren', + 'copy_success': 'Kopiert!', + 'copy_failure': 'Fehler beim Kopieren', + }, + 'fr' : { + 'copy': 'Copier', + 'copy_to_clipboard': 'Copié dans le presse-papier', + 'copy_success': 'Copié !', + 'copy_failure': 'Échec de la copie', + }, + 'ru': { + 'copy': 'Скопировать', + 'copy_to_clipboard': 'Скопировать в буфер', + 'copy_success': 'Скопировано!', + 'copy_failure': 'Не удалось скопировать', + }, + 'zh-CN': { + 'copy': '复制', + 'copy_to_clipboard': '复制到剪贴板', + 'copy_success': '复制成功!', + 'copy_failure': '复制失败', + }, + 'it' : { + 'copy': 'Copiare', + 'copy_to_clipboard': 'Copiato negli appunti', + 'copy_success': 'Copiato!', + 'copy_failure': 'Errore durante la copia', + } +} + +let locale = 'en' +if( document.documentElement.lang !== undefined + && messages[document.documentElement.lang] !== undefined ) { + locale = document.documentElement.lang +} + +let doc_url_root = DOCUMENTATION_OPTIONS.URL_ROOT; +if (doc_url_root == '#') { + doc_url_root = ''; +} + +/** + * SVG files for our copy buttons + */ +let iconCheck = ` + ${messages[locale]['copy_success']} + + +` + +// If the user specified their own SVG use that, otherwise use the default +let iconCopy = ``; +if (!iconCopy) { + iconCopy = ` + ${messages[locale]['copy_to_clipboard']} + + + +` +} + +/** + * Set up copy/paste for code blocks + */ + +const runWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} + +const codeCellId = index => `codecell${index}` + +// Clears selected text since ClipboardJS will select the text when copying +const clearSelection = () => { + if (window.getSelection) { + window.getSelection().removeAllRanges() + } else if (document.selection) { + document.selection.empty() + } +} + +// Changes tooltip text for two seconds, then changes it back +const temporarilyChangeTooltip = (el, oldText, newText) => { + el.setAttribute('data-tooltip', newText) + el.classList.add('success') + setTimeout(() => el.setAttribute('data-tooltip', oldText), 2000) + setTimeout(() => el.classList.remove('success'), 2000) +} + +// Changes the copy button icon for two seconds, then changes it back +const temporarilyChangeIcon = (el) => { + el.innerHTML = iconCheck; + setTimeout(() => {el.innerHTML = iconCopy}, 2000) +} + +const addCopyButtonToCodeCells = () => { + // If ClipboardJS hasn't loaded, wait a bit and try again. This + // happens because we load ClipboardJS asynchronously. + if (window.ClipboardJS === undefined) { + setTimeout(addCopyButtonToCodeCells, 250) + return + } + + // Add copybuttons to all of our code cells + const COPYBUTTON_SELECTOR = 'div.highlight pre'; + const codeCells = document.querySelectorAll(COPYBUTTON_SELECTOR) + codeCells.forEach((codeCell, index) => { + const id = codeCellId(index) + codeCell.setAttribute('id', id) + + const clipboardButton = id => + `` + codeCell.insertAdjacentHTML('afterend', clipboardButton(id)) + }) + +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} + + +var copyTargetText = (trigger) => { + var target = document.querySelector(trigger.attributes['data-clipboard-target'].value); + + // get filtered text + let exclude = '.linenos, .gp'; + + let text = filterText(target, exclude); + return formatCopyText(text, '', false, true, true, true, '', '') +} + + // Initialize with a callback so we can modify the text before copy + const clipboard = new ClipboardJS('.copybtn', {text: copyTargetText}) + + // Update UI with error/success messages + clipboard.on('success', event => { + clearSelection() + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_success']) + temporarilyChangeIcon(event.trigger) + }) + + clipboard.on('error', event => { + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_failure']) + }) +} + +runWhenDOMLoaded(addCopyButtonToCodeCells) \ No newline at end of file diff --git a/branch/main/_static/copybutton_funcs.js b/branch/main/_static/copybutton_funcs.js new file mode 100644 index 0000000..dbe1aaa --- /dev/null +++ b/branch/main/_static/copybutton_funcs.js @@ -0,0 +1,73 @@ +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +export function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +export function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} diff --git a/branch/main/_static/css/badge_only.css b/branch/main/_static/css/badge_only.css new file mode 100644 index 0000000..c718cee --- /dev/null +++ b/branch/main/_static/css/badge_only.css @@ 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+ return this; // for chaining... + } +})(jQuery); + +// NO good way to do this!. Copy a hack from here +// https://stackoverflow.com/questions/901115/how-can-i-get-query-string-values-in-javascript +// https://stackoverflow.com/a/2880929 +var urlParams; +(window.onpopstate = function () { + var match, + pl = /\+/g, // Regex for replacing addition symbol with a space + search = /([^&=]+)=?([^&]*)/g, + decode = function (s) { return decodeURIComponent(s.replace(pl, " ")); }, + query = window.location.search.substring(1); + urlParams = {}; + while (match = search.exec(query)) + urlParams[decode(match[1])] = decode(match[2]); +})(); + +// Select heading levels +var maxHeading = urlParams['h'] +if (maxHeading === undefined) maxHeading = 2 +var headingLevels = []; +for (h=2 ; h (sections.length-1) ) { + // if we would scroll past bottom, or above top, do nothing + return; + } + + console.log('xxxxxx'); + var targetSection = sections[targetPos]; + console.log(targetSection, typeof(targetSection)); + + // Return targetSection top and height + var secProperties = section_top_and_height(targetSection); + var top = secProperties['top']; + var height = secProperties['height'] + var win_height = window.innerHeight; + //console.info(top, height, win_height) + + var scroll_to = 0; + if (height >= win_height || height == 0) { + scroll_to = top; + } else { + scroll_to = top - (win_height-height)/3.; + } + //console.info(top, height, win_height, scroll_to) + + $('html, body').animate({ + scrollTop: scroll_to //+ 'px' + }, 'fast'); + +} + + +function minipres() { + /* Enable the minipres mode: + - call the hide() function + - set up the scrolling listener + */ + document.addEventListener('keydown', function (event) { + switch(event.which) { + case 37: // left + switch_slide(-1); + event.preventDefault(); + return false; + break; + //case 38: // up + case 39: // right + switch_slide(+1); + event.preventDefault(); + return false; + break; + //case 40: // down + default: + return; // exit this handler for other keys + } + }, true) + + hide() + + // Increase space between sections + //$("div .section").css('margin-bottom', '50%'); 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+} + +/* Pandas tables. Pulled from the Jupyter / nbsphinx CSS */ +div.cell_output table { + border: none; + border-collapse: collapse; + border-spacing: 0; + color: black; + font-size: 1em; + table-layout: fixed; +} + +div.cell_output thead { + border-bottom: 1px solid black; + vertical-align: bottom; +} + +div.cell_output tr, +div.cell_output th, +div.cell_output td { + text-align: right; + vertical-align: middle; + padding: 0.5em 0.5em; + line-height: normal; + white-space: normal; + max-width: none; + border: none; +} + +div.cell_output th { + font-weight: bold; +} + +div.cell_output tbody tr:nth-child(odd) { + background: #f5f5f5; +} + +div.cell_output tbody tr:hover { + background: rgba(66, 165, 245, 0.2); +} + +/** source code line numbers **/ +span.linenos { + opacity: 0.5; +} + +/* Inline text from `paste` operation */ + +span.pasted-text { + font-weight: bold; +} + +span.pasted-inline img { + max-height: 2em; +} + +tbody span.pasted-inline img { + max-height: none; +} + +/* Font colors for 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background-color: #E75C58 +} + +div.highlight .-Color[class*=-BGGreen] { + background-color: #00A250 +} + +div.highlight .-Color[class*=-BGYellow] { + background-color: #DDB62B +} + +div.highlight .-Color[class*=-BGBlue] { + background-color: #208FFB +} + +div.highlight .-Color[class*=-BGMagenta] { + background-color: #D160C4 +} + +div.highlight .-Color[class*=-BGCyan] { + background-color: #60C6C8 +} + +div.highlight .-Color[class*=-BGWhite] { + background-color: #C5C1B4 +} + +/* Font colors for 8-bit ANSI */ + +div.highlight .-Color[class*=-C0] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC0] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C1] { + color: #800000 +} + +div.highlight .-Color[class*=-BGC1] { + background-color: #800000 +} + +div.highlight .-Color[class*=-C2] { + color: #008000 +} + +div.highlight .-Color[class*=-BGC2] { + background-color: #008000 +} + +div.highlight .-Color[class*=-C3] { + color: #808000 +} + +div.highlight .-Color[class*=-BGC3] { + background-color: #808000 +} + +div.highlight .-Color[class*=-C4] { + color: #000080 +} + +div.highlight .-Color[class*=-BGC4] { + background-color: #000080 +} + +div.highlight .-Color[class*=-C5] { + color: #800080 +} + +div.highlight .-Color[class*=-BGC5] { + background-color: #800080 +} + +div.highlight .-Color[class*=-C6] { + color: #008080 +} + +div.highlight .-Color[class*=-BGC6] { + background-color: #008080 +} + +div.highlight .-Color[class*=-C7] { + color: #C0C0C0 +} + +div.highlight .-Color[class*=-BGC7] { + background-color: #C0C0C0 +} + +div.highlight .-Color[class*=-C8] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC8] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C9] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC9] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C10] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC10] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C11] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC11] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C12] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC12] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C13] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC13] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C14] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC14] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C15] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC15] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C16] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC16] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C17] { + color: #00005F +} + +div.highlight .-Color[class*=-BGC17] { + background-color: #00005F +} + +div.highlight .-Color[class*=-C18] { + color: #000087 +} + +div.highlight .-Color[class*=-BGC18] { + background-color: #000087 +} + +div.highlight .-Color[class*=-C19] { + color: #0000AF +} + +div.highlight .-Color[class*=-BGC19] { + background-color: #0000AF +} + +div.highlight .-Color[class*=-C20] { + color: #0000D7 +} + +div.highlight .-Color[class*=-BGC20] { + background-color: #0000D7 +} + +div.highlight .-Color[class*=-C21] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC21] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C22] { + color: #005F00 +} + +div.highlight .-Color[class*=-BGC22] { + background-color: #005F00 +} + +div.highlight .-Color[class*=-C23] { + color: #005F5F +} + +div.highlight .-Color[class*=-BGC23] { + background-color: #005F5F +} + +div.highlight .-Color[class*=-C24] { + color: #005F87 +} + +div.highlight .-Color[class*=-BGC24] { + background-color: #005F87 +} + +div.highlight .-Color[class*=-C25] { + color: #005FAF +} + +div.highlight .-Color[class*=-BGC25] { + background-color: #005FAF +} + +div.highlight .-Color[class*=-C26] { + color: #005FD7 +} + +div.highlight .-Color[class*=-BGC26] { + background-color: #005FD7 +} + +div.highlight .-Color[class*=-C27] { + color: #005FFF +} + +div.highlight .-Color[class*=-BGC27] { + background-color: #005FFF +} + +div.highlight .-Color[class*=-C28] { + color: #008700 +} + +div.highlight .-Color[class*=-BGC28] { + background-color: #008700 +} + +div.highlight .-Color[class*=-C29] { + color: #00875F +} + +div.highlight .-Color[class*=-BGC29] { + background-color: #00875F +} + +div.highlight .-Color[class*=-C30] { + color: #008787 +} + +div.highlight .-Color[class*=-BGC30] { + background-color: #008787 +} + +div.highlight .-Color[class*=-C31] { + color: #0087AF +} + +div.highlight .-Color[class*=-BGC31] { + background-color: #0087AF +} + +div.highlight .-Color[class*=-C32] { + color: #0087D7 +} + +div.highlight .-Color[class*=-BGC32] { + background-color: #0087D7 +} + +div.highlight .-Color[class*=-C33] { + color: #0087FF +} + +div.highlight .-Color[class*=-BGC33] { + background-color: #0087FF +} + +div.highlight .-Color[class*=-C34] { + color: #00AF00 +} + +div.highlight .-Color[class*=-BGC34] { + background-color: #00AF00 +} + +div.highlight .-Color[class*=-C35] { + color: #00AF5F +} + +div.highlight .-Color[class*=-BGC35] { + background-color: #00AF5F +} + +div.highlight .-Color[class*=-C36] { + color: #00AF87 +} + +div.highlight .-Color[class*=-BGC36] { + background-color: #00AF87 +} + +div.highlight .-Color[class*=-C37] { + color: #00AFAF +} + +div.highlight .-Color[class*=-BGC37] { + background-color: #00AFAF +} + +div.highlight .-Color[class*=-C38] { + color: #00AFD7 +} + +div.highlight .-Color[class*=-BGC38] { + background-color: #00AFD7 +} + +div.highlight .-Color[class*=-C39] { + color: #00AFFF +} + +div.highlight .-Color[class*=-BGC39] { + background-color: #00AFFF +} + +div.highlight .-Color[class*=-C40] { + color: #00D700 +} + +div.highlight .-Color[class*=-BGC40] { + background-color: #00D700 +} + +div.highlight .-Color[class*=-C41] { + color: #00D75F +} + +div.highlight .-Color[class*=-BGC41] { + background-color: #00D75F +} + +div.highlight .-Color[class*=-C42] { + color: #00D787 +} + +div.highlight .-Color[class*=-BGC42] { + background-color: #00D787 +} + +div.highlight .-Color[class*=-C43] { + color: #00D7AF +} + +div.highlight .-Color[class*=-BGC43] { + background-color: #00D7AF +} + +div.highlight .-Color[class*=-C44] { + color: #00D7D7 +} + +div.highlight .-Color[class*=-BGC44] { + background-color: #00D7D7 +} + +div.highlight .-Color[class*=-C45] { + color: #00D7FF +} + +div.highlight .-Color[class*=-BGC45] { + background-color: #00D7FF +} + +div.highlight .-Color[class*=-C46] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC46] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C47] { + color: #00FF5F +} + +div.highlight .-Color[class*=-BGC47] { + background-color: #00FF5F +} + +div.highlight .-Color[class*=-C48] { + color: #00FF87 +} + +div.highlight .-Color[class*=-BGC48] { + background-color: #00FF87 +} + +div.highlight .-Color[class*=-C49] { + color: #00FFAF +} + +div.highlight .-Color[class*=-BGC49] { + background-color: #00FFAF +} + +div.highlight .-Color[class*=-C50] { + color: #00FFD7 +} + +div.highlight .-Color[class*=-BGC50] { + background-color: #00FFD7 +} + +div.highlight .-Color[class*=-C51] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC51] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C52] { + color: #5F0000 +} + +div.highlight .-Color[class*=-BGC52] { + background-color: #5F0000 +} + +div.highlight .-Color[class*=-C53] { + color: #5F005F +} + +div.highlight .-Color[class*=-BGC53] { + background-color: #5F005F +} + +div.highlight .-Color[class*=-C54] { + color: #5F0087 +} + +div.highlight .-Color[class*=-BGC54] { + background-color: #5F0087 +} + +div.highlight .-Color[class*=-C55] { + color: #5F00AF +} + +div.highlight .-Color[class*=-BGC55] { + background-color: #5F00AF +} + +div.highlight .-Color[class*=-C56] { + color: #5F00D7 +} + +div.highlight .-Color[class*=-BGC56] { + background-color: #5F00D7 +} + +div.highlight .-Color[class*=-C57] { + color: #5F00FF +} + +div.highlight .-Color[class*=-BGC57] { + background-color: #5F00FF +} + +div.highlight .-Color[class*=-C58] { + color: #5F5F00 +} + +div.highlight .-Color[class*=-BGC58] { + background-color: #5F5F00 +} + +div.highlight .-Color[class*=-C59] { + color: #5F5F5F +} + +div.highlight .-Color[class*=-BGC59] { + background-color: #5F5F5F +} + +div.highlight .-Color[class*=-C60] { + color: #5F5F87 +} + +div.highlight .-Color[class*=-BGC60] { + background-color: #5F5F87 +} + +div.highlight .-Color[class*=-C61] { + color: #5F5FAF +} + +div.highlight .-Color[class*=-BGC61] { + background-color: #5F5FAF +} + +div.highlight .-Color[class*=-C62] { + color: #5F5FD7 +} + +div.highlight .-Color[class*=-BGC62] { + background-color: #5F5FD7 +} + +div.highlight .-Color[class*=-C63] { + color: #5F5FFF +} + +div.highlight .-Color[class*=-BGC63] { + background-color: #5F5FFF +} + +div.highlight .-Color[class*=-C64] { + color: #5F8700 +} + +div.highlight .-Color[class*=-BGC64] { + background-color: #5F8700 +} + +div.highlight .-Color[class*=-C65] { + color: #5F875F +} + +div.highlight .-Color[class*=-BGC65] { + background-color: #5F875F +} + +div.highlight .-Color[class*=-C66] { + color: #5F8787 +} + +div.highlight .-Color[class*=-BGC66] { + background-color: #5F8787 +} + +div.highlight .-Color[class*=-C67] { + color: #5F87AF +} + +div.highlight .-Color[class*=-BGC67] { + background-color: #5F87AF +} + +div.highlight .-Color[class*=-C68] { + color: #5F87D7 +} + +div.highlight .-Color[class*=-BGC68] { + background-color: #5F87D7 +} + +div.highlight .-Color[class*=-C69] { + color: #5F87FF +} + +div.highlight .-Color[class*=-BGC69] { + background-color: #5F87FF +} + +div.highlight .-Color[class*=-C70] { + color: #5FAF00 +} + +div.highlight .-Color[class*=-BGC70] { + background-color: #5FAF00 +} + +div.highlight .-Color[class*=-C71] { + color: #5FAF5F +} + +div.highlight .-Color[class*=-BGC71] { + background-color: #5FAF5F +} + +div.highlight .-Color[class*=-C72] { + color: #5FAF87 +} + +div.highlight .-Color[class*=-BGC72] { + background-color: #5FAF87 +} + +div.highlight .-Color[class*=-C73] { + color: #5FAFAF +} + +div.highlight .-Color[class*=-BGC73] { + background-color: #5FAFAF +} + +div.highlight .-Color[class*=-C74] { + color: #5FAFD7 +} + +div.highlight .-Color[class*=-BGC74] { + background-color: #5FAFD7 +} + +div.highlight .-Color[class*=-C75] { + color: #5FAFFF +} + +div.highlight .-Color[class*=-BGC75] { + background-color: #5FAFFF +} + +div.highlight .-Color[class*=-C76] { + color: #5FD700 +} + +div.highlight .-Color[class*=-BGC76] { + background-color: #5FD700 +} + +div.highlight .-Color[class*=-C77] { + color: #5FD75F +} + +div.highlight .-Color[class*=-BGC77] { + background-color: #5FD75F +} + +div.highlight .-Color[class*=-C78] { + color: #5FD787 +} + +div.highlight .-Color[class*=-BGC78] { + background-color: #5FD787 +} + +div.highlight .-Color[class*=-C79] { + color: #5FD7AF +} + +div.highlight .-Color[class*=-BGC79] { + background-color: #5FD7AF +} + +div.highlight .-Color[class*=-C80] { + color: #5FD7D7 +} + +div.highlight .-Color[class*=-BGC80] { + background-color: #5FD7D7 +} + +div.highlight .-Color[class*=-C81] { + color: #5FD7FF +} + +div.highlight .-Color[class*=-BGC81] { + background-color: #5FD7FF +} + +div.highlight .-Color[class*=-C82] { + color: #5FFF00 +} + +div.highlight .-Color[class*=-BGC82] { + background-color: #5FFF00 +} + +div.highlight .-Color[class*=-C83] { + color: #5FFF5F +} + +div.highlight .-Color[class*=-BGC83] { + background-color: #5FFF5F +} + +div.highlight .-Color[class*=-C84] { + color: #5FFF87 +} + +div.highlight .-Color[class*=-BGC84] { + background-color: #5FFF87 +} + +div.highlight .-Color[class*=-C85] { + color: #5FFFAF +} + +div.highlight .-Color[class*=-BGC85] { + background-color: #5FFFAF +} + +div.highlight .-Color[class*=-C86] { + color: #5FFFD7 +} + +div.highlight .-Color[class*=-BGC86] { + background-color: #5FFFD7 +} + +div.highlight .-Color[class*=-C87] { + color: #5FFFFF +} + +div.highlight .-Color[class*=-BGC87] { + background-color: #5FFFFF +} + +div.highlight .-Color[class*=-C88] { + color: #870000 +} + +div.highlight .-Color[class*=-BGC88] { + background-color: #870000 +} + +div.highlight .-Color[class*=-C89] { + color: #87005F +} + +div.highlight .-Color[class*=-BGC89] { + background-color: #87005F +} + +div.highlight .-Color[class*=-C90] { + color: #870087 +} + +div.highlight .-Color[class*=-BGC90] { + background-color: #870087 +} + +div.highlight .-Color[class*=-C91] { + color: #8700AF +} + +div.highlight .-Color[class*=-BGC91] { + background-color: #8700AF +} + +div.highlight .-Color[class*=-C92] { + color: #8700D7 +} + +div.highlight .-Color[class*=-BGC92] { + background-color: #8700D7 +} + +div.highlight .-Color[class*=-C93] { + color: #8700FF +} + +div.highlight .-Color[class*=-BGC93] { + background-color: #8700FF +} + +div.highlight .-Color[class*=-C94] { + color: #875F00 +} + +div.highlight .-Color[class*=-BGC94] { + background-color: #875F00 +} + +div.highlight .-Color[class*=-C95] { + color: #875F5F +} + +div.highlight .-Color[class*=-BGC95] { + background-color: #875F5F +} + +div.highlight .-Color[class*=-C96] { + color: #875F87 +} + +div.highlight .-Color[class*=-BGC96] { + background-color: #875F87 +} + +div.highlight .-Color[class*=-C97] { + color: #875FAF +} + +div.highlight .-Color[class*=-BGC97] { + background-color: #875FAF +} + +div.highlight .-Color[class*=-C98] { + color: #875FD7 +} + +div.highlight .-Color[class*=-BGC98] { + background-color: #875FD7 +} + +div.highlight .-Color[class*=-C99] { + color: #875FFF +} + +div.highlight .-Color[class*=-BGC99] { + background-color: #875FFF +} + +div.highlight .-Color[class*=-C100] { + color: #878700 +} + +div.highlight .-Color[class*=-BGC100] { + background-color: #878700 +} + +div.highlight .-Color[class*=-C101] { + color: #87875F +} + +div.highlight .-Color[class*=-BGC101] { + background-color: #87875F +} + +div.highlight .-Color[class*=-C102] { + color: #878787 +} + +div.highlight .-Color[class*=-BGC102] { + background-color: #878787 +} + +div.highlight .-Color[class*=-C103] { + color: #8787AF +} + +div.highlight .-Color[class*=-BGC103] { + background-color: #8787AF +} + +div.highlight .-Color[class*=-C104] { + color: #8787D7 +} + +div.highlight .-Color[class*=-BGC104] { + background-color: #8787D7 +} + +div.highlight .-Color[class*=-C105] { + color: #8787FF +} + +div.highlight .-Color[class*=-BGC105] { + background-color: #8787FF +} + +div.highlight .-Color[class*=-C106] { + color: #87AF00 +} + +div.highlight .-Color[class*=-BGC106] { + background-color: #87AF00 +} + +div.highlight .-Color[class*=-C107] { + color: #87AF5F +} + +div.highlight .-Color[class*=-BGC107] { + background-color: #87AF5F +} + +div.highlight .-Color[class*=-C108] { + color: #87AF87 +} + +div.highlight .-Color[class*=-BGC108] { + background-color: #87AF87 +} + +div.highlight .-Color[class*=-C109] { + color: #87AFAF +} + +div.highlight .-Color[class*=-BGC109] { + background-color: #87AFAF +} + +div.highlight .-Color[class*=-C110] { + color: #87AFD7 +} + +div.highlight .-Color[class*=-BGC110] { + background-color: #87AFD7 +} + +div.highlight .-Color[class*=-C111] { + color: #87AFFF +} + +div.highlight .-Color[class*=-BGC111] { + background-color: #87AFFF +} + +div.highlight .-Color[class*=-C112] { + color: #87D700 +} + +div.highlight .-Color[class*=-BGC112] { + background-color: #87D700 +} + +div.highlight .-Color[class*=-C113] { + color: #87D75F +} + +div.highlight .-Color[class*=-BGC113] { + background-color: #87D75F +} + +div.highlight .-Color[class*=-C114] { + color: #87D787 +} + +div.highlight .-Color[class*=-BGC114] { + background-color: #87D787 +} + +div.highlight .-Color[class*=-C115] { + color: #87D7AF +} + +div.highlight .-Color[class*=-BGC115] { + background-color: #87D7AF +} + +div.highlight .-Color[class*=-C116] { + color: #87D7D7 +} + +div.highlight .-Color[class*=-BGC116] { + background-color: #87D7D7 +} + +div.highlight .-Color[class*=-C117] { + color: #87D7FF +} + +div.highlight .-Color[class*=-BGC117] { + background-color: #87D7FF +} + +div.highlight .-Color[class*=-C118] { + color: #87FF00 +} + +div.highlight .-Color[class*=-BGC118] { + background-color: #87FF00 +} + +div.highlight .-Color[class*=-C119] { + color: #87FF5F +} + +div.highlight .-Color[class*=-BGC119] { + background-color: #87FF5F +} + +div.highlight .-Color[class*=-C120] { + color: #87FF87 +} + +div.highlight .-Color[class*=-BGC120] { + background-color: #87FF87 +} + +div.highlight .-Color[class*=-C121] { + color: #87FFAF +} + +div.highlight .-Color[class*=-BGC121] { + background-color: #87FFAF +} + +div.highlight .-Color[class*=-C122] { + color: #87FFD7 +} + +div.highlight .-Color[class*=-BGC122] { + background-color: #87FFD7 +} + +div.highlight .-Color[class*=-C123] { + color: #87FFFF +} + +div.highlight .-Color[class*=-BGC123] { + background-color: #87FFFF +} + +div.highlight .-Color[class*=-C124] { + color: #AF0000 +} + +div.highlight .-Color[class*=-BGC124] { + background-color: #AF0000 +} + +div.highlight .-Color[class*=-C125] { + color: #AF005F +} + +div.highlight .-Color[class*=-BGC125] { + background-color: #AF005F +} + +div.highlight .-Color[class*=-C126] { + color: #AF0087 +} + +div.highlight .-Color[class*=-BGC126] { + background-color: #AF0087 +} + +div.highlight .-Color[class*=-C127] { + color: #AF00AF +} + +div.highlight .-Color[class*=-BGC127] { + background-color: #AF00AF +} + +div.highlight .-Color[class*=-C128] { + color: #AF00D7 +} + +div.highlight .-Color[class*=-BGC128] { + background-color: #AF00D7 +} + +div.highlight .-Color[class*=-C129] { + color: #AF00FF +} + +div.highlight .-Color[class*=-BGC129] { + background-color: #AF00FF +} + +div.highlight .-Color[class*=-C130] { + color: #AF5F00 +} + +div.highlight .-Color[class*=-BGC130] { + background-color: #AF5F00 +} + +div.highlight .-Color[class*=-C131] { + color: #AF5F5F +} + +div.highlight .-Color[class*=-BGC131] { + background-color: #AF5F5F +} + +div.highlight .-Color[class*=-C132] { + color: #AF5F87 +} + +div.highlight .-Color[class*=-BGC132] { + background-color: #AF5F87 +} + +div.highlight .-Color[class*=-C133] { + color: #AF5FAF +} + +div.highlight .-Color[class*=-BGC133] { + background-color: #AF5FAF +} + +div.highlight .-Color[class*=-C134] { + color: #AF5FD7 +} + +div.highlight .-Color[class*=-BGC134] { + background-color: #AF5FD7 +} + +div.highlight .-Color[class*=-C135] { + color: #AF5FFF +} + +div.highlight .-Color[class*=-BGC135] { + background-color: #AF5FFF +} + +div.highlight .-Color[class*=-C136] { + color: #AF8700 +} + +div.highlight .-Color[class*=-BGC136] { + background-color: #AF8700 +} + +div.highlight .-Color[class*=-C137] { + color: #AF875F +} + +div.highlight .-Color[class*=-BGC137] { + background-color: #AF875F +} + +div.highlight .-Color[class*=-C138] { + color: #AF8787 +} + +div.highlight .-Color[class*=-BGC138] { + background-color: #AF8787 +} + +div.highlight .-Color[class*=-C139] { + color: #AF87AF +} + +div.highlight .-Color[class*=-BGC139] { + background-color: #AF87AF +} + +div.highlight .-Color[class*=-C140] { + color: #AF87D7 +} + +div.highlight .-Color[class*=-BGC140] { + background-color: #AF87D7 +} + +div.highlight .-Color[class*=-C141] { + color: #AF87FF +} + +div.highlight .-Color[class*=-BGC141] { + background-color: #AF87FF +} + +div.highlight .-Color[class*=-C142] { + color: #AFAF00 +} + +div.highlight .-Color[class*=-BGC142] { + background-color: #AFAF00 +} + +div.highlight .-Color[class*=-C143] { + color: #AFAF5F +} + +div.highlight .-Color[class*=-BGC143] { + background-color: #AFAF5F +} + +div.highlight .-Color[class*=-C144] { + color: #AFAF87 +} + +div.highlight .-Color[class*=-BGC144] { + background-color: #AFAF87 +} + +div.highlight .-Color[class*=-C145] { + color: #AFAFAF +} + +div.highlight .-Color[class*=-BGC145] { + background-color: #AFAFAF +} + +div.highlight .-Color[class*=-C146] { + color: #AFAFD7 +} + +div.highlight .-Color[class*=-BGC146] { + background-color: #AFAFD7 +} + +div.highlight .-Color[class*=-C147] { + color: #AFAFFF +} + +div.highlight .-Color[class*=-BGC147] { + background-color: #AFAFFF +} + +div.highlight .-Color[class*=-C148] { + color: #AFD700 +} + +div.highlight .-Color[class*=-BGC148] { + background-color: #AFD700 +} + +div.highlight .-Color[class*=-C149] { + color: #AFD75F +} + +div.highlight .-Color[class*=-BGC149] { + background-color: #AFD75F +} + +div.highlight .-Color[class*=-C150] { + color: #AFD787 +} + +div.highlight .-Color[class*=-BGC150] { + background-color: #AFD787 +} + +div.highlight .-Color[class*=-C151] { + color: #AFD7AF +} + +div.highlight .-Color[class*=-BGC151] { + background-color: #AFD7AF +} + +div.highlight .-Color[class*=-C152] { + color: #AFD7D7 +} + +div.highlight .-Color[class*=-BGC152] { + background-color: #AFD7D7 +} + +div.highlight .-Color[class*=-C153] { + color: #AFD7FF +} + +div.highlight .-Color[class*=-BGC153] { + background-color: #AFD7FF +} + +div.highlight .-Color[class*=-C154] { + color: #AFFF00 +} + +div.highlight .-Color[class*=-BGC154] { + background-color: #AFFF00 +} + +div.highlight .-Color[class*=-C155] { + color: #AFFF5F +} + +div.highlight .-Color[class*=-BGC155] { + background-color: #AFFF5F +} + +div.highlight .-Color[class*=-C156] { + color: #AFFF87 +} + +div.highlight .-Color[class*=-BGC156] { + background-color: #AFFF87 +} + +div.highlight .-Color[class*=-C157] { + color: #AFFFAF +} + +div.highlight .-Color[class*=-BGC157] { + background-color: #AFFFAF +} + +div.highlight .-Color[class*=-C158] { + color: #AFFFD7 +} + +div.highlight .-Color[class*=-BGC158] { + background-color: #AFFFD7 +} + +div.highlight .-Color[class*=-C159] { + color: #AFFFFF +} + +div.highlight .-Color[class*=-BGC159] { + background-color: #AFFFFF +} + +div.highlight .-Color[class*=-C160] { + color: #D70000 +} + +div.highlight .-Color[class*=-BGC160] { + background-color: #D70000 +} + +div.highlight .-Color[class*=-C161] { + color: #D7005F +} + +div.highlight .-Color[class*=-BGC161] { + background-color: #D7005F +} + +div.highlight .-Color[class*=-C162] { + color: #D70087 +} + +div.highlight .-Color[class*=-BGC162] { + background-color: #D70087 +} + +div.highlight .-Color[class*=-C163] { + color: #D700AF +} + +div.highlight .-Color[class*=-BGC163] { + background-color: #D700AF +} + +div.highlight .-Color[class*=-C164] { + color: #D700D7 +} + +div.highlight .-Color[class*=-BGC164] { + background-color: #D700D7 +} + +div.highlight .-Color[class*=-C165] { + color: #D700FF +} + +div.highlight .-Color[class*=-BGC165] { + background-color: #D700FF +} + +div.highlight .-Color[class*=-C166] { + color: #D75F00 +} + +div.highlight .-Color[class*=-BGC166] { + background-color: #D75F00 +} + +div.highlight .-Color[class*=-C167] { + color: #D75F5F +} + +div.highlight .-Color[class*=-BGC167] { + background-color: #D75F5F +} + +div.highlight .-Color[class*=-C168] { + color: #D75F87 +} + +div.highlight .-Color[class*=-BGC168] { + background-color: #D75F87 +} + +div.highlight .-Color[class*=-C169] { + color: #D75FAF +} + +div.highlight .-Color[class*=-BGC169] { + background-color: #D75FAF +} + +div.highlight .-Color[class*=-C170] { + color: #D75FD7 +} + +div.highlight .-Color[class*=-BGC170] { + background-color: #D75FD7 +} + +div.highlight .-Color[class*=-C171] { + color: #D75FFF +} + +div.highlight .-Color[class*=-BGC171] { + background-color: #D75FFF +} + +div.highlight .-Color[class*=-C172] { + color: #D78700 +} + +div.highlight .-Color[class*=-BGC172] { + background-color: #D78700 +} + +div.highlight .-Color[class*=-C173] { + color: #D7875F +} + +div.highlight .-Color[class*=-BGC173] { + background-color: #D7875F +} + +div.highlight .-Color[class*=-C174] { + color: #D78787 +} + +div.highlight .-Color[class*=-BGC174] { + background-color: #D78787 +} + +div.highlight .-Color[class*=-C175] { + color: #D787AF +} + +div.highlight .-Color[class*=-BGC175] { + background-color: #D787AF +} + +div.highlight .-Color[class*=-C176] { + color: #D787D7 +} + +div.highlight .-Color[class*=-BGC176] { + background-color: #D787D7 +} + +div.highlight .-Color[class*=-C177] { + color: #D787FF +} + +div.highlight .-Color[class*=-BGC177] { + background-color: #D787FF +} + +div.highlight .-Color[class*=-C178] { + color: #D7AF00 +} + +div.highlight .-Color[class*=-BGC178] { + background-color: #D7AF00 +} + +div.highlight .-Color[class*=-C179] { + color: #D7AF5F +} + +div.highlight .-Color[class*=-BGC179] { + background-color: #D7AF5F +} + +div.highlight .-Color[class*=-C180] { + color: #D7AF87 +} + +div.highlight .-Color[class*=-BGC180] { + background-color: #D7AF87 +} + +div.highlight .-Color[class*=-C181] { + color: #D7AFAF +} + +div.highlight .-Color[class*=-BGC181] { + background-color: #D7AFAF +} + +div.highlight .-Color[class*=-C182] { + color: #D7AFD7 +} + +div.highlight .-Color[class*=-BGC182] { + background-color: #D7AFD7 +} + +div.highlight .-Color[class*=-C183] { + color: #D7AFFF +} + +div.highlight .-Color[class*=-BGC183] { + background-color: #D7AFFF +} + +div.highlight .-Color[class*=-C184] { + color: #D7D700 +} + +div.highlight .-Color[class*=-BGC184] { + background-color: #D7D700 +} + +div.highlight .-Color[class*=-C185] { + color: #D7D75F +} + +div.highlight .-Color[class*=-BGC185] { + background-color: #D7D75F +} + +div.highlight .-Color[class*=-C186] { + color: #D7D787 +} + +div.highlight .-Color[class*=-BGC186] { + background-color: #D7D787 +} + +div.highlight .-Color[class*=-C187] { + color: #D7D7AF +} + +div.highlight .-Color[class*=-BGC187] { + background-color: #D7D7AF +} + +div.highlight .-Color[class*=-C188] { + color: #D7D7D7 +} + +div.highlight .-Color[class*=-BGC188] { + background-color: #D7D7D7 +} + +div.highlight .-Color[class*=-C189] { + color: #D7D7FF +} + +div.highlight .-Color[class*=-BGC189] { + background-color: #D7D7FF +} + +div.highlight .-Color[class*=-C190] { + color: #D7FF00 +} + +div.highlight .-Color[class*=-BGC190] { + background-color: #D7FF00 +} + +div.highlight .-Color[class*=-C191] { + color: #D7FF5F +} + +div.highlight .-Color[class*=-BGC191] { + background-color: #D7FF5F +} + +div.highlight .-Color[class*=-C192] { + color: #D7FF87 +} + +div.highlight .-Color[class*=-BGC192] { + background-color: #D7FF87 +} + +div.highlight .-Color[class*=-C193] { + color: #D7FFAF +} + +div.highlight .-Color[class*=-BGC193] { + background-color: #D7FFAF +} + +div.highlight .-Color[class*=-C194] { + color: #D7FFD7 +} + +div.highlight .-Color[class*=-BGC194] { + background-color: #D7FFD7 +} + +div.highlight .-Color[class*=-C195] { + color: #D7FFFF +} + +div.highlight .-Color[class*=-BGC195] { + background-color: #D7FFFF +} + +div.highlight .-Color[class*=-C196] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC196] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C197] { + color: #FF005F +} + +div.highlight .-Color[class*=-BGC197] { + background-color: #FF005F +} + +div.highlight .-Color[class*=-C198] { + color: #FF0087 +} + +div.highlight .-Color[class*=-BGC198] { + background-color: #FF0087 +} + +div.highlight .-Color[class*=-C199] { + color: #FF00AF +} + +div.highlight .-Color[class*=-BGC199] { + background-color: #FF00AF +} + +div.highlight .-Color[class*=-C200] { + color: #FF00D7 +} + +div.highlight .-Color[class*=-BGC200] { + background-color: #FF00D7 +} + +div.highlight .-Color[class*=-C201] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC201] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C202] { + color: #FF5F00 +} + +div.highlight .-Color[class*=-BGC202] { + background-color: #FF5F00 +} + +div.highlight .-Color[class*=-C203] { + color: #FF5F5F +} + +div.highlight .-Color[class*=-BGC203] { + background-color: #FF5F5F +} + +div.highlight .-Color[class*=-C204] { + color: #FF5F87 +} + +div.highlight .-Color[class*=-BGC204] { + background-color: #FF5F87 +} + +div.highlight .-Color[class*=-C205] { + color: #FF5FAF +} + +div.highlight .-Color[class*=-BGC205] { + background-color: #FF5FAF +} + +div.highlight .-Color[class*=-C206] { + color: #FF5FD7 +} + +div.highlight .-Color[class*=-BGC206] { + background-color: #FF5FD7 +} + +div.highlight .-Color[class*=-C207] { + color: #FF5FFF +} + +div.highlight .-Color[class*=-BGC207] { + background-color: #FF5FFF +} + +div.highlight .-Color[class*=-C208] { + color: #FF8700 +} + +div.highlight .-Color[class*=-BGC208] { + background-color: #FF8700 +} + +div.highlight .-Color[class*=-C209] { + color: #FF875F +} + +div.highlight .-Color[class*=-BGC209] { + background-color: #FF875F +} + +div.highlight .-Color[class*=-C210] { + color: #FF8787 +} + +div.highlight .-Color[class*=-BGC210] { + background-color: #FF8787 +} + +div.highlight .-Color[class*=-C211] { + color: #FF87AF +} + +div.highlight .-Color[class*=-BGC211] { + background-color: #FF87AF +} + +div.highlight .-Color[class*=-C212] { + color: #FF87D7 +} + +div.highlight .-Color[class*=-BGC212] { + background-color: #FF87D7 +} + +div.highlight .-Color[class*=-C213] { + color: #FF87FF +} + +div.highlight .-Color[class*=-BGC213] { + background-color: #FF87FF +} + +div.highlight .-Color[class*=-C214] { + color: #FFAF00 +} + +div.highlight .-Color[class*=-BGC214] { + background-color: #FFAF00 +} + +div.highlight .-Color[class*=-C215] { + color: #FFAF5F +} + +div.highlight .-Color[class*=-BGC215] { + background-color: #FFAF5F +} + +div.highlight .-Color[class*=-C216] { + color: #FFAF87 +} + +div.highlight .-Color[class*=-BGC216] { + background-color: #FFAF87 +} + +div.highlight .-Color[class*=-C217] { + color: #FFAFAF +} + +div.highlight .-Color[class*=-BGC217] { + background-color: #FFAFAF +} + +div.highlight .-Color[class*=-C218] { + color: #FFAFD7 +} + +div.highlight .-Color[class*=-BGC218] { + background-color: #FFAFD7 +} + +div.highlight .-Color[class*=-C219] { + color: #FFAFFF +} + +div.highlight .-Color[class*=-BGC219] { + background-color: #FFAFFF +} + +div.highlight .-Color[class*=-C220] { + color: #FFD700 +} + +div.highlight .-Color[class*=-BGC220] { + background-color: #FFD700 +} + +div.highlight .-Color[class*=-C221] { + color: #FFD75F +} + +div.highlight .-Color[class*=-BGC221] { + background-color: #FFD75F +} + +div.highlight .-Color[class*=-C222] { + color: #FFD787 +} + +div.highlight .-Color[class*=-BGC222] { + background-color: #FFD787 +} + +div.highlight .-Color[class*=-C223] { + color: #FFD7AF +} + +div.highlight .-Color[class*=-BGC223] { + background-color: #FFD7AF +} + +div.highlight .-Color[class*=-C224] { + color: #FFD7D7 +} + +div.highlight .-Color[class*=-BGC224] { + background-color: #FFD7D7 +} + +div.highlight .-Color[class*=-C225] { + color: #FFD7FF +} + +div.highlight .-Color[class*=-BGC225] { + background-color: #FFD7FF +} + +div.highlight .-Color[class*=-C226] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC226] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C227] { + color: #FFFF5F +} + +div.highlight .-Color[class*=-BGC227] { + background-color: #FFFF5F +} + +div.highlight .-Color[class*=-C228] { + color: #FFFF87 +} + +div.highlight .-Color[class*=-BGC228] { + background-color: #FFFF87 +} + +div.highlight .-Color[class*=-C229] { + color: #FFFFAF +} + +div.highlight .-Color[class*=-BGC229] { + background-color: #FFFFAF +} + +div.highlight .-Color[class*=-C230] { + color: #FFFFD7 +} + +div.highlight .-Color[class*=-BGC230] { + background-color: #FFFFD7 +} + +div.highlight .-Color[class*=-C231] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC231] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C232] { + color: #080808 +} + +div.highlight .-Color[class*=-BGC232] { + background-color: #080808 +} + +div.highlight .-Color[class*=-C233] { + color: #121212 +} + +div.highlight .-Color[class*=-BGC233] { + background-color: #121212 +} + +div.highlight .-Color[class*=-C234] { + color: #1C1C1C +} + +div.highlight .-Color[class*=-BGC234] { + background-color: #1C1C1C +} + +div.highlight .-Color[class*=-C235] { + color: #262626 +} + +div.highlight .-Color[class*=-BGC235] { + background-color: #262626 +} + +div.highlight .-Color[class*=-C236] { + color: #303030 +} + +div.highlight .-Color[class*=-BGC236] { + background-color: #303030 +} + +div.highlight .-Color[class*=-C237] { + color: #3A3A3A +} + +div.highlight .-Color[class*=-BGC237] { + background-color: #3A3A3A +} + +div.highlight .-Color[class*=-C238] { + color: #444444 +} + +div.highlight .-Color[class*=-BGC238] { + background-color: #444444 +} + +div.highlight .-Color[class*=-C239] { + color: #4E4E4E +} + +div.highlight .-Color[class*=-BGC239] { + background-color: #4E4E4E +} + +div.highlight .-Color[class*=-C240] { + color: #585858 +} + +div.highlight .-Color[class*=-BGC240] { + background-color: #585858 +} + +div.highlight .-Color[class*=-C241] { + color: #626262 +} + +div.highlight .-Color[class*=-BGC241] { + background-color: #626262 +} + +div.highlight .-Color[class*=-C242] { + color: #6C6C6C +} + +div.highlight .-Color[class*=-BGC242] { + background-color: #6C6C6C +} + +div.highlight .-Color[class*=-C243] { + color: #767676 +} + +div.highlight .-Color[class*=-BGC243] { + background-color: #767676 +} + +div.highlight .-Color[class*=-C244] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC244] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C245] { + color: #8A8A8A +} + +div.highlight .-Color[class*=-BGC245] { + background-color: #8A8A8A +} + +div.highlight .-Color[class*=-C246] { + color: #949494 +} + +div.highlight .-Color[class*=-BGC246] { + background-color: #949494 +} + +div.highlight .-Color[class*=-C247] { + color: #9E9E9E +} + +div.highlight .-Color[class*=-BGC247] { + background-color: #9E9E9E +} + +div.highlight .-Color[class*=-C248] { + color: #A8A8A8 +} + +div.highlight .-Color[class*=-BGC248] { + background-color: #A8A8A8 +} + +div.highlight .-Color[class*=-C249] { + color: #B2B2B2 +} + +div.highlight .-Color[class*=-BGC249] { + background-color: #B2B2B2 +} + +div.highlight .-Color[class*=-C250] { + color: #BCBCBC +} + +div.highlight .-Color[class*=-BGC250] { + background-color: #BCBCBC +} + +div.highlight .-Color[class*=-C251] { + color: #C6C6C6 +} + +div.highlight .-Color[class*=-BGC251] { + background-color: #C6C6C6 +} + +div.highlight .-Color[class*=-C252] { + color: #D0D0D0 +} + +div.highlight .-Color[class*=-BGC252] { + background-color: #D0D0D0 +} + +div.highlight .-Color[class*=-C253] { + color: #DADADA +} + +div.highlight .-Color[class*=-BGC253] { + background-color: #DADADA +} + +div.highlight .-Color[class*=-C254] { + color: #E4E4E4 +} + +div.highlight .-Color[class*=-BGC254] { + background-color: #E4E4E4 +} + +div.highlight .-Color[class*=-C255] { + color: #EEEEEE +} + +div.highlight .-Color[class*=-BGC255] { + background-color: #EEEEEE +} diff --git a/branch/main/_static/plus.png b/branch/main/_static/plus.png new file mode 100644 index 0000000..7107cec Binary files /dev/null and b/branch/main/_static/plus.png differ diff --git a/branch/main/_static/pygments.css b/branch/main/_static/pygments.css new file mode 100644 index 0000000..84ab303 --- /dev/null +++ b/branch/main/_static/pygments.css @@ -0,0 +1,75 @@ +pre { line-height: 125%; } +td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +.highlight .hll { background-color: #ffffcc } 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#19177C } /* Literal.String.Symbol */ +.highlight .bp { color: #008000 } /* Name.Builtin.Pseudo */ +.highlight .fm { color: #0000FF } /* Name.Function.Magic */ +.highlight .vc { color: #19177C } /* Name.Variable.Class */ +.highlight .vg { color: #19177C } /* Name.Variable.Global */ +.highlight .vi { color: #19177C } /* Name.Variable.Instance */ +.highlight .vm { color: #19177C } /* Name.Variable.Magic */ +.highlight .il { color: #666666 } /* Literal.Number.Integer.Long */ \ No newline at end of file diff --git a/branch/main/_static/searchtools.js b/branch/main/_static/searchtools.js new file mode 100644 index 0000000..b08d58c --- /dev/null +++ b/branch/main/_static/searchtools.js @@ -0,0 +1,620 @@ +/* + * searchtools.js + * ~~~~~~~~~~~~~~~~ + * + * Sphinx JavaScript utilities for the full-text search. + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ +"use strict"; + +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms, anchor) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + "Search finished, found ${resultCount} page(s) matching the search query." + ).replace('${resultCount}', resultCount); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString, anchor) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + for (const removalQuery of [".headerlink", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent) return docContent.textContent; + + console.warn( + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + _parseQuery: (query) => { + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename]. + const normalResults = []; + const nonMainIndexResults = []; + + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase().trim(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + const score = Math.round(Scorer.title * queryLower.length / title.length); + const boost = titles[file] === title ? 1 : 0; // add a boost for document titles + normalResults.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score + boost, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } + } + } + } + + // lookup as object + objectTerms.forEach((term) => + normalResults.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/branch/main/_static/sphinx_highlight.js b/branch/main/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/branch/main/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/branch/main/_static/sphinx_lesson.css b/branch/main/_static/sphinx_lesson.css new file mode 100644 index 0000000..14b20c6 --- /dev/null +++ b/branch/main/_static/sphinx_lesson.css @@ -0,0 +1,51 @@ +/* sphinx_lesson.css */ + +body.wy-body-for-nav img.with-border { + border: 2px solid; +} + +.rst-content .admonition-no-content { + padding-bottom: 0px; +} + +.rst-content .demo > .admonition-title::before { + content: "\01F440"; /* Eyes */ } +.rst-content .type-along > .admonition-title::before { + content: "\02328\0FE0F"; /* Keyboard */ } +.rst-content .exercise > .admonition-title::before { + content: "\0270D\0FE0F"; /* Hand */ } +.rst-content .solution > .admonition-title::before { + content: "\02714\0FE0E"; /* Check mark */ } +.rst-content .homework > .admonition-title::before { + content: "\01F4DD"; /* Memo */ } +.rst-content .discussion > .admonition-title::before { + content: "\01F4AC"; /* Speech balloon */ } +.rst-content .questions > .admonition-title::before { + content: "\02753\0FE0E"; /* Question mark */ } +.rst-content .prerequisites > .admonition-title::before { + content: "\02699"; /* Gear */ } +.rst-content .seealso > .admonition-title::before { + content: "\027A1\0FE0E"; /* Question mark */ } + + +/* instructor-note */ +.rst-content .instructor-note { + background: #e7e7e7; +} +.rst-content .instructor-note > .admonition-title { + background: #6a6a6a; +} +.rst-content .instructor-note > .admonition-title::before { + content: ""; +} + + +/* sphinx_toggle_button, make the font white */ +.rst-content .toggle.admonition button.toggle-button { + color: white; +} + +/* sphinx-togglebutton, remove underflow when toggled to hidden mode */ +.rst-content .admonition.toggle-hidden { + padding-bottom: 0px; +} diff --git a/branch/main/_static/sphinx_rtd_theme_ext_color_contrast.css b/branch/main/_static/sphinx_rtd_theme_ext_color_contrast.css new file mode 100644 index 0000000..e68feb8 --- /dev/null +++ b/branch/main/_static/sphinx_rtd_theme_ext_color_contrast.css @@ -0,0 +1,47 @@ +/* The following are for web accessibility of sphinx_rtd_theme: they + * solve some of the most frequent contrast issues. Remove when this + * solved: + * https://github.com/readthedocs/sphinx_rtd_theme/issues/971 + */ +/* background: #fcfcfc, note boxes #E7F2FA */ +a { color: #2573A7; } /* original #2980B9, #1F5C84; */ +body { color: #242424; } /* original #404040, #383838 */ +.wy-side-nav-search>a, .wy-side-nav-search .wy-dropdown>a { + color: #ffffff; +} /* original #fcfcfc */ +footer { color: #737373; } /* original gray=#808080*/ +footer span.commit code, footer span.commit .rst-content tt, .rst-content footer span.commit tt { + color: #737373; +} /* original gray=#808080*/ +.rst-content tt.literal, .rst-content tt.literal, .rst-content code.literal { + color: #AB2314; +} +/* Sidebar background */ +.wy-side-nav-search { background-color: #277CB4;} + +/* Same, but for pygments */ +.highlight .ch { color: #3E7A89; } /* #! line */ +.highlight .c1 { color: #3E7A89; } /* also comments */ +.highlight .nv { color: #AD3ECC; } /* variable */ +.highlight .gp { color: #B45608; } /* prompt character, $*/ +.highlight .si { color: #3975B1; } /* ${} variable text */ +.highlight .nc { color: #0C78A7; } + +/* Sphinx admonitions */ +/* warning */ +.wy-alert.wy-alert-warning .wy-alert-title, .rst-content .wy-alert-warning.note .wy-alert-title, .rst-content .attention .wy-alert-title, .rst-content .caution .wy-alert-title, .rst-content .wy-alert-warning.danger .wy-alert-title, .rst-content .wy-alert-warning.error .wy-alert-title, .rst-content .wy-alert-warning.hint .wy-alert-title, .rst-content .wy-alert-warning.important .wy-alert-title, .rst-content .wy-alert-warning.tip .wy-alert-title, .rst-content .warning .wy-alert-title, .rst-content .wy-alert-warning.seealso .wy-alert-title, .rst-content .admonition-todo .wy-alert-title, .rst-content .wy-alert-warning.admonition .wy-alert-title, .wy-alert.wy-alert-warning .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-warning .admonition-title, .rst-content .wy-alert-warning.note .admonition-title, .rst-content .attention .admonition-title, .rst-content .caution .admonition-title, .rst-content .wy-alert-warning.danger .admonition-title, .rst-content .wy-alert-warning.error .admonition-title, .rst-content .wy-alert-warning.hint .admonition-title, .rst-content .wy-alert-warning.important .admonition-title, .rst-content .wy-alert-warning.tip .admonition-title, .rst-content .warning .admonition-title, .rst-content .wy-alert-warning.seealso .admonition-title, .rst-content .admonition-todo .admonition-title, .rst-content .wy-alert-warning.admonition .admonition-title { + background: #B15E16; } +/* important */ +.wy-alert.wy-alert-success .wy-alert-title, .rst-content .wy-alert-success.note .wy-alert-title, .rst-content .wy-alert-success.attention .wy-alert-title, .rst-content .wy-alert-success.caution .wy-alert-title, .rst-content .wy-alert-success.danger .wy-alert-title, .rst-content .wy-alert-success.error .wy-alert-title, .rst-content .hint .wy-alert-title, .rst-content .important .wy-alert-title, .rst-content .tip .wy-alert-title, .rst-content .wy-alert-success.warning .wy-alert-title, .rst-content .wy-alert-success.seealso .wy-alert-title, .rst-content .wy-alert-success.admonition-todo .wy-alert-title, .rst-content .wy-alert-success.admonition .wy-alert-title, .wy-alert.wy-alert-success .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-success .admonition-title, .rst-content .wy-alert-success.note .admonition-title, .rst-content .wy-alert-success.attention .admonition-title, .rst-content .wy-alert-success.caution .admonition-title, .rst-content .wy-alert-success.danger .admonition-title, .rst-content .wy-alert-success.error .admonition-title, .rst-content .hint .admonition-title, .rst-content .important .admonition-title, .rst-content .tip .admonition-title, .rst-content .wy-alert-success.warning .admonition-title, .rst-content .wy-alert-success.seealso .admonition-title, .rst-content .wy-alert-success.admonition-todo .admonition-title, .rst-content .wy-alert-success.admonition .admonition-title { + background: #12826C; } +/* seealso, note, etc */ +.wy-alert.wy-alert-info .wy-alert-title, .rst-content .note .wy-alert-title, .rst-content .wy-alert-info.attention .wy-alert-title, .rst-content .wy-alert-info.caution .wy-alert-title, .rst-content .wy-alert-info.danger .wy-alert-title, .rst-content .wy-alert-info.error .wy-alert-title, .rst-content .wy-alert-info.hint .wy-alert-title, .rst-content .wy-alert-info.important .wy-alert-title, .rst-content .wy-alert-info.tip .wy-alert-title, .rst-content .wy-alert-info.warning .wy-alert-title, .rst-content .seealso .wy-alert-title, .rst-content .wy-alert-info.admonition-todo .wy-alert-title, .rst-content .wy-alert-info.admonition .wy-alert-title, .wy-alert.wy-alert-info .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-info .admonition-title, .rst-content .note .admonition-title, .rst-content .wy-alert-info.attention .admonition-title, .rst-content .wy-alert-info.caution .admonition-title, .rst-content .wy-alert-info.danger .admonition-title, .rst-content .wy-alert-info.error .admonition-title, .rst-content .wy-alert-info.hint .admonition-title, .rst-content .wy-alert-info.important .admonition-title, .rst-content .wy-alert-info.tip .admonition-title, .rst-content .wy-alert-info.warning .admonition-title, .rst-content .seealso .admonition-title, .rst-content .wy-alert-info.admonition-todo .admonition-title, .rst-content .wy-alert-info.admonition .admonition-title { + background: #277CB4; } +/* error, danger */ +.rst-content .danger .admonition-title, .rst-content .danger .wy-alert-title, .rst-content .error .admonition-title, .rst-content .error .wy-alert-title, .rst-content .wy-alert-danger.admonition-todo .admonition-title, .rst-content .wy-alert-danger.admonition-todo .wy-alert-title, .rst-content .wy-alert-danger.admonition .admonition-title, .rst-content .wy-alert-danger.admonition .wy-alert-title, .rst-content .wy-alert-danger.attention .admonition-title, .rst-content .wy-alert-danger.attention .wy-alert-title, .rst-content .wy-alert-danger.caution .admonition-title, .rst-content .wy-alert-danger.caution .wy-alert-title, .rst-content .wy-alert-danger.hint .admonition-title, .rst-content .wy-alert-danger.hint .wy-alert-title, .rst-content .wy-alert-danger.important .admonition-title, .rst-content .wy-alert-danger.important .wy-alert-title, .rst-content .wy-alert-danger.note .admonition-title, .rst-content .wy-alert-danger.note .wy-alert-title, .rst-content .wy-alert-danger.seealso .admonition-title, .rst-content .wy-alert-danger.seealso .wy-alert-title, .rst-content .wy-alert-danger.tip .admonition-title, .rst-content .wy-alert-danger.tip .wy-alert-title, .rst-content .wy-alert-danger.warning .admonition-title, .rst-content .wy-alert-danger.warning .wy-alert-title, .rst-content .wy-alert.wy-alert-danger .admonition-title, .wy-alert.wy-alert-danger .rst-content .admonition-title, .wy-alert.wy-alert-danger .wy-alert-title { + background: #e31704; +} + +/* Generic admonition titles */ +.wy-alert-title, .rst-content .admonition-title { + background: #277CB4; } diff --git a/branch/main/_static/style.css b/branch/main/_static/style.css new file mode 100644 index 0000000..59e60ee --- /dev/null +++ b/branch/main/_static/style.css @@ -0,0 +1,6 @@ +.rst-content .objectives { + background: #fee0d2; +} +.rst-content .objectives > .admonition-title { + background: #fc9272; +} diff --git a/branch/main/_static/tabs.css b/branch/main/_static/tabs.css new file mode 100644 index 0000000..957ba60 --- /dev/null +++ b/branch/main/_static/tabs.css @@ -0,0 +1,89 @@ +.sphinx-tabs { + margin-bottom: 1rem; +} + +[role="tablist"] { + border-bottom: 1px solid #a0b3bf; +} + +.sphinx-tabs-tab { + position: relative; + font-family: Lato,'Helvetica Neue',Arial,Helvetica,sans-serif; + color: #1D5C87; + line-height: 24px; + margin: 0; + font-size: 16px; + font-weight: 400; + background-color: rgba(255, 255, 255, 0); + border-radius: 5px 5px 0 0; + border: 0; + padding: 1rem 1.5rem; + margin-bottom: 0; +} + +.sphinx-tabs-tab[aria-selected="true"] { + font-weight: 700; + border: 1px solid #a0b3bf; + border-bottom: 1px solid white; + margin: -1px; + background-color: white; +} + +.sphinx-tabs-tab:focus { + z-index: 1; + outline-offset: 1px; +} + +.sphinx-tabs-panel { + position: relative; + padding: 1rem; + border: 1px solid #a0b3bf; + margin: 0px -1px -1px -1px; + border-radius: 0 0 5px 5px; + border-top: 0; + background: white; +} + +.sphinx-tabs-panel.code-tab { + padding: 0.4rem; +} + +.sphinx-tab img { + margin-bottom: 24 px; +} + +/* Dark theme preference styling */ + +@media (prefers-color-scheme: dark) { + body[data-theme="auto"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); + } + + body[data-theme="auto"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); + } + + body[data-theme="auto"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 1px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); + } +} + +/* Explicit dark theme styling */ + +body[data-theme="dark"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); +} + +body[data-theme="dark"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); +} + +body[data-theme="dark"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 2px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); +} diff --git a/branch/main/_static/tabs.js b/branch/main/_static/tabs.js new file mode 100644 index 0000000..48dc303 --- /dev/null +++ b/branch/main/_static/tabs.js @@ -0,0 +1,145 @@ +try { + var session = window.sessionStorage || {}; +} catch (e) { + var session = {}; +} + +window.addEventListener("DOMContentLoaded", () => { + const allTabs = document.querySelectorAll('.sphinx-tabs-tab'); + const tabLists = document.querySelectorAll('[role="tablist"]'); + + allTabs.forEach(tab => { + tab.addEventListener("click", changeTabs); + }); + + tabLists.forEach(tabList => { + tabList.addEventListener("keydown", keyTabs); + }); + + // Restore group tab selection from session + const lastSelected = session.getItem('sphinx-tabs-last-selected'); + if (lastSelected != null) selectNamedTabs(lastSelected); +}); + +/** + * Key focus left and right between sibling elements using arrows + * @param {Node} e the element in focus when key was pressed + */ +function keyTabs(e) { + const tab = e.target; + let nextTab = null; + if (e.keyCode === 39 || e.keyCode === 37) { + tab.setAttribute("tabindex", -1); + // Move right + if (e.keyCode === 39) { + nextTab = tab.nextElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.firstElementChild; + } + // Move left + } else if (e.keyCode === 37) { + nextTab = tab.previousElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.lastElementChild; + } + } + } + + if (nextTab !== null) { + nextTab.setAttribute("tabindex", 0); + nextTab.focus(); + } +} + +/** + * Select or deselect clicked tab. If a group tab + * is selected, also select tab in other tabLists. + * @param {Node} e the element that was clicked + */ +function changeTabs(e) { + // Use this instead of the element that was clicked, in case it's a child + const notSelected = this.getAttribute("aria-selected") === "false"; + const positionBefore = this.parentNode.getBoundingClientRect().top; + const notClosable = !this.parentNode.classList.contains("closeable"); + + deselectTabList(this); + + if (notSelected || notClosable) { + selectTab(this); + const name = this.getAttribute("name"); + selectNamedTabs(name, this.id); + + if (this.classList.contains("group-tab")) { + // Persist during session + session.setItem('sphinx-tabs-last-selected', name); + } + } + + const positionAfter = this.parentNode.getBoundingClientRect().top; + const positionDelta = positionAfter - positionBefore; + // Scroll to offset content resizing + window.scrollTo(0, window.scrollY + positionDelta); +} + +/** + * Select tab and show associated panel. + * @param {Node} tab tab to select + */ +function selectTab(tab) { + tab.setAttribute("aria-selected", true); + + // Show the associated panel + document + .getElementById(tab.getAttribute("aria-controls")) + .removeAttribute("hidden"); +} + +/** + * Hide the panels associated with all tabs within the + * tablist containing this tab. + * @param {Node} tab a tab within the tablist to deselect + */ +function deselectTabList(tab) { + const parent = tab.parentNode; + const grandparent = parent.parentNode; + + Array.from(parent.children) + .forEach(t => t.setAttribute("aria-selected", false)); + + Array.from(grandparent.children) + .slice(1) // Skip tablist + .forEach(panel => panel.setAttribute("hidden", true)); +} + +/** + * Select grouped tabs with the same name, but no the tab + * with the given id. + * @param {Node} name name of grouped tab to be selected + * @param {Node} clickedId id of clicked tab + */ +function selectNamedTabs(name, clickedId=null) { + const groupedTabs = document.querySelectorAll(`.sphinx-tabs-tab[name="${name}"]`); + const tabLists = Array.from(groupedTabs).map(tab => tab.parentNode); + + tabLists + .forEach(tabList => { + // Don't want to change the tabList containing the clicked tab + const clickedTab = tabList.querySelector(`[id="${clickedId}"]`); + if (clickedTab === null ) { + // Select first tab with matching name + const tab = tabList.querySelector(`.sphinx-tabs-tab[name="${name}"]`); + deselectTabList(tab); + selectTab(tab); + } + }) +} + +if (typeof exports === 'undefined') { + exports = {}; +} + +exports.keyTabs = keyTabs; +exports.changeTabs = changeTabs; +exports.selectTab = selectTab; +exports.deselectTabList = deselectTabList; +exports.selectNamedTabs = selectNamedTabs; diff --git a/branch/main/_static/term_role_formatting.css b/branch/main/_static/term_role_formatting.css new file mode 100644 index 0000000..0b66095 --- /dev/null +++ b/branch/main/_static/term_role_formatting.css @@ -0,0 +1,4 @@ +/* Make terms bold */ +a.reference span.std-term { + font-weight: bold; +} diff --git a/branch/main/_static/togglebutton.css b/branch/main/_static/togglebutton.css new file mode 100644 index 0000000..54a6787 --- /dev/null +++ b/branch/main/_static/togglebutton.css @@ -0,0 +1,160 @@ +/** + * Admonition-based toggles + */ + +/* Visibility of the target */ +.admonition.toggle .admonition-title ~ * { + transition: opacity .3s, height .3s; +} + +/* Toggle buttons inside admonitions so we see the title */ +.admonition.toggle { + position: relative; +} + +/* Titles should cut off earlier to avoid overlapping w/ button */ +.admonition.toggle .admonition-title { + padding-right: 25%; + cursor: pointer; +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:hover { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 1%); +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:active { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 3%); +} + +/* Remove extra whitespace below the admonition title when hidden */ +.admonition.toggle-hidden { + padding-bottom: 0; +} + +.admonition.toggle-hidden .admonition-title { + margin-bottom: 0; +} + +/* hides all the content of a page until de-toggled */ +.admonition.toggle-hidden .admonition-title ~ * { + height: 0; + margin: 0; + opacity: 0; + visibility: hidden; +} + +/* General button style and position*/ +button.toggle-button { + /** + * Background and shape. By default there's no background + * but users can style as they wish + */ + background: none; + border: none; + outline: none; + + /* Positioning just inside the admonition title */ + position: absolute; + right: 0.5em; + padding: 0px; + border: none; + outline: none; +} + +/* Display the toggle hint on wide screens */ +@media (min-width: 768px) { + button.toggle-button.toggle-button-hidden:before { + content: attr(data-toggle-hint); /* This will be filled in by JS */ + font-size: .8em; + align-self: center; + } +} + +/* Icon behavior */ +.tb-icon { + transition: transform .2s ease-out; + height: 1.5em; + width: 1.5em; + stroke: currentColor; /* So that we inherit the color of other text */ +} + +/* The icon should point right when closed, down when open. */ +/* Open */ +.admonition.toggle button .tb-icon { + transform: rotate(90deg); +} + +/* Closed */ +.admonition.toggle button.toggle-button-hidden .tb-icon { + transform: rotate(0deg); +} + +/* With details toggles, we don't rotate the icon so it points right */ +details.toggle-details .tb-icon { + height: 1.4em; + width: 1.4em; + margin-top: 0.1em; /* To center the button vertically */ +} + + +/** + * Details-based toggles. + * In this case, we wrap elements with `.toggle` in a details block. + */ + +/* Details blocks */ +details.toggle-details { + margin: 1em 0; +} + + +details.toggle-details summary { + display: flex; + align-items: center; + cursor: pointer; + list-style: none; + border-radius: .2em; + border-left: 3px solid #1976d2; + background-color: rgb(204 204 204 / 10%); + padding: 0.2em 0.7em 0.3em 0.5em; /* Less padding on left because the SVG has left margin */ + font-size: 0.9em; +} + +details.toggle-details summary:hover { + background-color: rgb(204 204 204 / 20%); +} + +details.toggle-details summary:active { + background: rgb(204 204 204 / 28%); +} + +.toggle-details__summary-text { + margin-left: 0.2em; +} + +details.toggle-details[open] summary { + margin-bottom: .5em; +} + +details.toggle-details[open] summary .tb-icon { + transform: rotate(90deg); +} + +details.toggle-details[open] summary ~ * { + animation: toggle-fade-in .3s ease-out; +} + +@keyframes toggle-fade-in { + from {opacity: 0%;} + to {opacity: 100%;} +} + +/* Print rules - we hide all toggle button elements at print */ +@media print { + /* Always hide the summary so the button doesn't show up */ + details.toggle-details summary { + display: none; + } +} \ No newline at end of file diff --git a/branch/main/_static/togglebutton.js b/branch/main/_static/togglebutton.js new file mode 100644 index 0000000..215a7ee --- /dev/null +++ b/branch/main/_static/togglebutton.js @@ -0,0 +1,187 @@ +/** + * Add Toggle Buttons to elements + */ + +let toggleChevron = ` + + + +`; + +var initToggleItems = () => { + var itemsToToggle = document.querySelectorAll(togglebuttonSelector); + console.log(`[togglebutton]: Adding toggle buttons to ${itemsToToggle.length} items`) + // Add the button to each admonition and hook up a callback to toggle visibility + itemsToToggle.forEach((item, index) => { + if (item.classList.contains("admonition")) { + // If it's an admonition block, then we'll add a button inside + // Generate unique IDs for this item + var toggleID = `toggle-${index}`; + var buttonID = `button-${toggleID}`; + + item.setAttribute('id', toggleID); + if (!item.classList.contains("toggle")){ + item.classList.add("toggle"); + } + // This is the button that will be added to each item to trigger the toggle + var collapseButton = ` + `; + + title = item.querySelector(".admonition-title") + title.insertAdjacentHTML("beforeend", collapseButton); + thisButton = document.getElementById(buttonID); + + // Add click handlers for the button + admonition title (if admonition) + admonitionTitle = document.querySelector(`#${toggleID} > .admonition-title`) + if (admonitionTitle) { + // If an admonition, then make the whole title block clickable + admonitionTitle.addEventListener('click', toggleClickHandler); + admonitionTitle.dataset.target = toggleID + admonitionTitle.dataset.button = buttonID + } else { + // If not an admonition then we'll listen for the button click + thisButton.addEventListener('click', toggleClickHandler); + } + + // Now hide the item for this toggle button unless explicitly noted to show + if (!item.classList.contains("toggle-shown")) { + toggleHidden(thisButton); + } + } else { + // If not an admonition, wrap the block in a
block + // Define the structure of the details block and insert it as a sibling + var detailsBlock = ` +
+ + ${toggleChevron} + ${toggleHintShow} + +
`; + item.insertAdjacentHTML("beforebegin", detailsBlock); + + // Now move the toggle-able content inside of the details block + details = item.previousElementSibling + details.appendChild(item) + item.classList.add("toggle-details__container") + + // Set up a click trigger to change the text as needed + details.addEventListener('click', (click) => { + let parent = click.target.parentElement; + if (parent.tagName.toLowerCase() == "details") { + summary = parent.querySelector("summary"); + details = parent; + } else { + summary = parent; + details = parent.parentElement; + } + // Update the inner text for the proper hint + if (details.open) { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintShow; + } else { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintHide; + } + + }); + + // If we have a toggle-shown class, open details block should be open + if (item.classList.contains("toggle-shown")) { + details.click(); + } + } + }) +}; + +// This should simply add / remove the collapsed class and change the button text +var toggleHidden = (button) => { + target = button.dataset['target'] + var itemToToggle = document.getElementById(target); + if (itemToToggle.classList.contains("toggle-hidden")) { + itemToToggle.classList.remove("toggle-hidden"); + button.classList.remove("toggle-button-hidden"); + } else { + itemToToggle.classList.add("toggle-hidden"); + button.classList.add("toggle-button-hidden"); + } +} + +var toggleClickHandler = (click) => { + // Be cause the admonition title is clickable and extends to the whole admonition + // We only look for a click event on this title to trigger the toggle. + + if (click.target.classList.contains("admonition-title")) { + button = click.target.querySelector(".toggle-button"); + } else if (click.target.classList.contains("tb-icon")) { + // We've clicked the icon and need to search up one parent for the button + button = click.target.parentElement; + } else if (click.target.tagName == "polyline") { + // We've clicked the SVG elements inside the button, need to up 2 layers + button = click.target.parentElement.parentElement; + } else if (click.target.classList.contains("toggle-button")) { + // We've clicked the button itself and so don't need to do anything + button = click.target; + } else { + console.log(`[togglebutton]: Couldn't find button for ${click.target}`) + } + target = document.getElementById(button.dataset['button']); + toggleHidden(target); +} + +// If we want to blanket-add toggle classes to certain cells +var addToggleToSelector = () => { + const selector = ""; + if (selector.length > 0) { + document.querySelectorAll(selector).forEach((item) => { + item.classList.add("toggle"); + }) + } +} + +// Helper function to run when the DOM is finished +const sphinxToggleRunWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} +sphinxToggleRunWhenDOMLoaded(addToggleToSelector) +sphinxToggleRunWhenDOMLoaded(initToggleItems) + +/** Toggle details blocks to be open when printing */ +if (toggleOpenOnPrint == "true") { + window.addEventListener("beforeprint", () => { + // Open the details + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.dataset["togglestatus"] = el.open; + el.open = true; + }); + + // Open the admonitions + document.querySelectorAll(".admonition.toggle.toggle-hidden").forEach((el) => { + console.log(el); + el.querySelector("button.toggle-button").click(); + el.dataset["toggle_after_print"] = "true"; + }); + }); + window.addEventListener("afterprint", () => { + // Re-close the details that were closed + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.open = el.dataset["togglestatus"] == "true"; + delete el.dataset["togglestatus"]; + }); + + // Re-close the admonition toggle buttons + document.querySelectorAll(".admonition.toggle").forEach((el) => { + if (el.dataset["toggle_after_print"] == "true") { + el.querySelector("button.toggle-button").click(); + delete el.dataset["toggle_after_print"]; + } + }); + }); +} diff --git a/branch/main/collaboration/code-review/index.html b/branch/main/collaboration/code-review/index.html new file mode 100644 index 0000000..2db66b2 --- /dev/null +++ b/branch/main/collaboration/code-review/index.html @@ -0,0 +1,289 @@ + + + + + + + Practicing code review — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Practicing code review

+

In this episode we will practice the code review process. We will learn how to +ask for changes in a pull request, how to suggest a change in a pull request, +and how to modify a pull request.

+

This will enable research groups to work more collaboratively and to not only +improve the code quality but also to learn from each other.

+
+

Exercise

+
+

Exercise preparation

+

We can continue in the same exercise repository which we have used in the +previous episode.

+
+
+

Exercise: Practicing code review (25 min)

+

Technical requirements:

+ +

What is familiar from previous lessons:

+
    +

  • Creating a branch.

    • +

  • Committing a change on the new branch.

    • +

  • Opening and merging pull requests.

    • +
+

What will be new in this exercise:

+
    +

  • As a reviewer, we will learn how to ask for changes in a pull request.

    • +

  • As a reviewer, we will learn how to suggest a change in a pull request.

    • +

  • As a submitter, we will learn how to modify a pull request without closing +the incomplete one and opening a new one.

    • +
+

Exercise tasks:

+
    +

  1. Create a new branch and one or few commits: in these improve something but also +deliberately introduce a typo and also a larger mistake which we will want to fix during the code review.

    2. +

  2. Open a pull request towards the main branch.

    3. +

  3. As a reviewer to somebody else’s pull request, ask for an improvement and +also directly suggest a change for the small typo. (Hint: +suggestions are possible through the GitHub web interface, view of +a pull request, “Files changed” view, after selecting some lines. +Look for the “±” button.)

    4. +

  4. As the submitter, learn how to accept the suggested change. (Hint: +GitHub web interface, “Files Changed” view.)

    5. +

  5. As the submitter, improve the pull request without having to close and open +a new one: by adding a new commit to the same branch. (Hint: push +to the branch again.)

    6. +

  6. Once the changes are addressed, merge the pull request.

    7. +
+
+
+
+

Help and discussion

+

From here on out, we don’t give detailed steps to the solution. You +need to combine what you know, and the extra info below, in order to +solve the above.

+
+

How to ask for changes in a pull request

+

Technically, there are at least two common ways to ask for changes in a pull +request.

+

Either in the comment field of the pull request:

+
+Screenshot of a pull request comment field +
+

Or by using the “Review changes”:

+
+Screenshot of a pull request navigating to the "Review changes" tab +
+

And always please be kind and constructive in your comments. Remember that the +goal is not gate-keeping but collaborative learning.

+
+
+

How to suggest a change in a pull request as a reviewer

+

If you see a very small problem that is easy to fix, you can suggest a change +as a reviewer.

+

Instead of asking the submitter to tiny problem, you can suggest a change by +clicking on the plus sign next to the line number in the “Files changed” tab:

+
+Screenshot of leaving a comment to a line in a pull request +
+

Here you can comment on specific lines or even line ranges.

+

But now the interesting part is to click on the “Add a suggestion” symbol (the +one that looks like plus and minus). Now you can fix the tiny problem (in this +case a typo) and then click on the “Add single comment” button:

+
+Sequence of clicks to add a suggestion to a line in a pull request +
+

The result is this and the submitter can accept the change with a single click:

+
+Screenshot of a pull request with a suggested change +
+

After accepting with “Commit suggestion”, the improvement gets added to the +pull request.

+
+
+

How to modify a pull request to address the review comments

+

If the reviewer asks for changes, it is not necessary to close the pull request +and later open a new one. It can even be counter-productive to do so: This can +fragment the discussion and the history of the pull request and can make it +harder to understand the context of the changes.

+

A much better mechanism to recognize that pull requests are not implemented +from a specific commit to a specific branch, but always from a branch to a +branch.

+

This means that you can make amendments to the pull request by adding new +commits to the same source branch. This way the pull request will be updated +automatically and the reviewer can see the new changes and comment on them.

+

The fact that pull requests are from branch to branch also strongly suggests +that it is a good practice to create a new branch for each pull request. +Otherwise you could accidentally modify an open pull request by adding new +commits to the source branch.

+
+
+
+

Summary

+
    +

  • Our process isn’t just about code now. It’s about discussion and +working together to make the whole process better.

    • +

  • GitHub discussions and reviewing are quite powerful and can make +small changes easy.

    • +
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/collaboration/concepts/index.html b/branch/main/collaboration/concepts/index.html new file mode 100644 index 0000000..f4c073d --- /dev/null +++ b/branch/main/collaboration/concepts/index.html @@ -0,0 +1,234 @@ + + + + + + + Concepts around collaboration — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Concepts around collaboration

+
+

Objectives

+
    +

  • Be able to decide whether to divide work at the branch level or at the repository level.

    • +
+
+
+

Commits, branches, repositories, forks, clones

+
    +

  • repository: The project, contains all data and history (commits, branches, tags).

    • +

  • commit: Snapshot of the project, gets a unique identifier (e.g. c7f0e8bfc718be04525847fc7ac237f470add76e).

    • +

  • branch: Independent development line. The main development line is often called main.

    • +

  • tag: A pointer to one commit, to be able to refer to it later. Like a commemorative plaque +that you attach to a particular commit (e.g. phd-printed or paper-submitted).

    • +

  • cloning: Copying the whole repository to your laptop - the first time. It is not necessary to download each file one by one.

    • +

  • forking: Taking a copy of a repository (which is typically not yours) - your +copy (fork) stays on GitHub/GitLab and you can make changes to your copy.

    • +
+
+
+

Cloning a repository

+

In order to make a complete copy a whole repository, the git clone command +can be used. When cloning, all the files, of all or selected branches, of a +repository are copied in one operation. Cloning of a repository is of relevance +in a few different situations:

+
    +

  • Working on your own, cloning is the operation that you can use to create +multiple instances of a repository on, for instance, a personal computer, a +server, and a supercomputer.

    • +

  • The parent repository could be a repository that you or your colleague own. A +common use case for cloning is when working together within a smaller team +where everyone has read and write access to the same git repository.

    • +

  • Alternatively, cloning can be made from a public repository of a code that +you would like to use. Perhaps you have no intention to work on the code, but +would like to stay in tune with the latest developments, also in-between +releases of new versions of the code.

    • +
+
+Forking and cloning +
+

Forking and cloning

+
+
+
+
+

Forking a repository

+

When a fork is made on GitHub/GitLab a complete copy, of all or selected +branches, of the repository is made. The copy will reside under a different +account on GitHub/GitLab. Forking of a repository is of high relevance when +working with a git repository to which you do not have write access.

+
    +

  • In the fork repository commits can be made to the base branch (main or +master), and to other branches.

    • +

  • The commits that are made within the branches of the fork repository can be +contributed back to the parent repository by means of pull or merge requests.

    • +
+
+
+

Synchronizing changes between repositories

+
    +

  • We need a mechanism to communicate changes between the repositories.

    • +

  • We will pull or fetch updates from remote repositories (we will soon discuss the difference between pull and fetch).

    • +

  • We will push updates to remote repositories.

    • +

  • We will learn how to suggest changes within repositories on GitHub and across repositories (pull request).

    • +

  • Repositories that are forked or cloned do not automatically synchronize themselves: +We will learn how to update forks (by pulling from the “central” repository).

    • +

  • A main difference between cloning a repository and forking a repository is that the former is a general operation for generating copies of a repository to different computers, whereas forking is a particular operation implemented on GitHub/GitLab.

    • +
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/collaboration/demo-discussion/index.html b/branch/main/collaboration/demo-discussion/index.html new file mode 100644 index 0000000..405df1b --- /dev/null +++ b/branch/main/collaboration/demo-discussion/index.html @@ -0,0 +1,160 @@ + + + + + + + Conclict resolution, rebasing, and organizational strategies — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Conclict resolution, rebasing, and organizational strategies

+

(40 min demo and discussion)

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/collaboration/forking-workflow/index.html b/branch/main/collaboration/forking-workflow/index.html new file mode 100644 index 0000000..ed602bb --- /dev/null +++ b/branch/main/collaboration/forking-workflow/index.html @@ -0,0 +1,376 @@ + + + + + + + How to contribute changes to repositories that belong to others — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

How to contribute changes to repositories that belong to others

+

In this episode we prepare you to suggest and contribute changes to +repositories that belong to others. These might be open source projects that +you use in your work.

+

We will see how Git and services like GitHub or GitLab can be used to suggest +modification without having to ask for write access to the repository and +accept modifications without having to grant write access to others.

+
+

Exercise

+
+

Exercise preparation

+
    +

  • The exercise repository is now different: +https://github.com/workshop-material/recipe-book-forking-exercise (note the -forking-exercise).

    • +

  • First fork the exercise repository to your GitHub account.

    • +

  • Then clone your fork to your computer (if you wish to work locally).

    • +

  • Double-check that you have forked the correct repository.

    • +
+
+
+

Exercise: Collaborating within the same repository (25 min)

+

Technical requirements:

+ +

What is familiar from previous lessons:

+
    +

  • Forking a repository.

    • +

  • Creating a branch.

    • +

  • Committing a change on the new branch.

    • +

  • Opening and merging pull requests.

    • +
+

What will be new in this exercise:

+
    +

  • Opening a pull request towards the upstream repository.

    • +

  • Pull requests can be coupled with automated testing.

    • +

  • Learning that your fork can get out of date.

    • +

  • After the pull requests are merged, updating your fork with the changes.

    • +

  • Learn how to approach other people’s repositories with ideas, changes, and requests.

    • +
+

Exercise tasks:

+
    +

  1. Open an issue in the upstream exercise repository where you describe the +change you want to make. Take note of the issue number.

    2. +

  2. Create a new branch in your fork of the repository.

    3. +

  3. Make a change to the recipe book on the new branch and in the commit cross-reference the issue you opened. +See the walk-through below for how to do this.

    4. +

  4. Open a pull request towards the upstream repository.

    5. +

  5. The instructor will review and merge the pull requests. +During the review, pay attention to the automated test step (here for +demonstration purposes, we test whether the recipe contains an ingredients +and an instructions sections).

    6. +

  6. After few pull requests are merged, update your fork with the changes.

    7. +

  7. Check that in your fork you can see changes from other people’s pull requests.

    8. +
+
+
+
+

Help and discussion

+
+

Help! I don’t have permissions to push my local changes

+

Maybe you see an error like this one:

+
Please make sure you have the correct access rights
+and the repository exists.
+
+
+

Or like this one:

+
failed to push some refs to workshop-material/recipe-book-forking-exercise.git
+
+
+

In this case you probably try to push the changes not to your fork but to the original repository +and in this exercise you do not have write access to the original repository.

+

The simpler solution is to clone again but this time your fork.

+ +
+
+

Opening a pull request towards the upstream repository

+

We have learned in the previous episode that pull requests are always from +branch to branch. But the branch can be in a different repository.

+

When you open a pull request in a fork, by default GitHub will suggest to +direct it towards the default branch of the upstream repository.

+

This can be changed and it should always be verified, but in this case this is +exactly what we want to do, from fork towards upstream:

+
+Screenshot of a pull request from fork towards upstream +
+
+
+

Pull requests can be coupled with automated testing

+

We added an automated test here just for fun and so that you see that this is +possible to do.

+

In this exercise, the test is silly. It will check whether the recipe contains +both an ingredients and an instructions section.

+

In this example the test failed:

+
+Screenshot of a failed test in a pull request +
+

Click on the “Details” link to see the details of the failed test:

+
+Screenshot of details why the test failed +
+

How can this be useful?

+
    +

  • The project can define what kind of tests are expected to pass before a pull +request can be merged.

    • +

  • The reviewer can see the results of the tests, without having to run them +locally.

    • +
+

How does it work?

+
    +

  • We added a GitHub Actions workflow +to automatically run on each push or pull request towards the main branch.

    • +
+

What tests or steps can you image for your project to run automatically with +each pull request?

+
+
+

How to update your fork with changes from upstream

+

This used to be difficult but now it is two mouse clicks.

+

Navigate to your fork and notice how GitHub tells you that your fork is behind. +In my case, it is 9 commits behind upstream. To fix this, click on “Sync fork” +and then “Update branch”:

+
+Screenshot on GitHub fork page showing that the fork is behind +
+

After the update my “branch is up to date” with the upstream repository:

+
+Screenshot on GitHub after fork has been updated +
+
+
+

How to approach other people’s repositories with ideas, changes, and requests

+

Contributing very minor changes

+
    +

  • Clone or fork+clone repository

    • +

  • Create a branch

    • +

  • Commit and push change

    • +

  • Open a pull request or merge request

    • +
+

If you observe an issue and have an idea how to fix it

+
    +

  • Open an issue in the repository you wish to contribute to

    • +

  • Describe the problem

    • +

  • If you have a suggestion on how to fix it, describe your suggestion

    • +

  • Possibly discuss and get feedback

    • +

  • If you are working on the fix, indicate it in the issue so that others know that somebody is working on it and who is working on it

    • +

  • Submit your fix as pull request or merge request which references/closes the issue

    • +
+
+

Motivation

+
    +

  • Inform others about an observed problem

    • +

  • Make it clear whether this issue is up for grabs or already being worked on

    • +
+
+

If you have an idea for a new feature

+
    +

  • Open an issue in the repository you wish to contribute to

    • +

  • In the issue, write a short proposal for your suggested change or new feature

    • +

  • Motivate why and how you wish to do this

    • +

  • Also indicate where you are unsure and where you would like feedback

    • +

  • Discuss and get feedback before you code

    • +

  • Once you start coding, indicate that you are working on it

    • +

  • Once you are done, submit your new feature as pull request or merge request which references/closes the issue/proposal

    • +
+
+

Motivation

+
    +

  • Get agreement and feedback before writing 5000 lines of code which might be rejected

    • +

  • If we later wonder why something was done, we have the issue/proposal as +reference and can read up on the reasoning behind a code change

    • +
+
+
+
+
+

Summary

+
    +

  • This forking workflow lets you propose changes to repositories for +which you have no write access.

    • +

  • This is the way that much modern open-source software works.

    • +

  • You can now contribute to any project you can view.

    • +
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/collaboration/index.html b/branch/main/collaboration/index.html new file mode 100644 index 0000000..975bbbe --- /dev/null +++ b/branch/main/collaboration/index.html @@ -0,0 +1,167 @@ + + + + + + + Collaborative version control and code review — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+ +
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/collaboration/same-repository/index.html b/branch/main/collaboration/same-repository/index.html new file mode 100644 index 0000000..e901473 --- /dev/null +++ b/branch/main/collaboration/same-repository/index.html @@ -0,0 +1,423 @@ + + + + + + + Collaborating within the same repository — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Collaborating within the same repository

+

In this episode, we will learn how to collaborate within the same repository. +We will learn how to cross-reference issues and pull requests, how to review +pull requests, and how to use draft pull requests.

+

This exercise will form a good basis for collaboration that is suitable for +most research groups.

+
+

Note

+

When you read or hear pull request, please think of a change proposal.

+
+
+

Exercise

+

In this exercise, we will contribute to a repository via a pull request. +This means that you propose some change, and then it is accepted (or not).

+
+

Exercise preparation

+
    +

  • First we need to get access to the exercise repository to which we will +contribute.

    +
      +

    • Instructor collects GitHub usernames from learners and adds them as collaborators to the exercise repository +(Settings -> Collaborators and teams -> Manage access -> Add people).

      • +
    +
    • +

  • Don’t forget to accept the invitation

    +
      +

    • Check https://github.com/settings/organizations/

      • +

    • Alternatively check the inbox for the email account you registered with +GitHub. GitHub emails you an invitation link, but if you don’t receive it +you can go to your GitHub notifications in the top right corner. The +maintainer can also “copy invite link” and share it within the group.

      • +
    +
    • +

  • Watching and unwatching repositories

    +
      +

    • Now that you are a collaborator, you get notified about new issues and pull +requests via email.

      • +

    • If you do not wish this, you can “unwatch” a repository (top of +the project page).

      • +

    • However, we recommend watching repositories you are interested +in. You can learn things from experts just by watching the +activity that come through a popular project.

      • +
    +
    +Unwatching a repository +
    +

    Unwatch a repository by clicking “Unwatch” in the repository view, +then “Participating and @mentions” - this way, you will get +notifications about your own interactions.

    +
    +
    +
    • +
+
+
+

Exercise: Collaborating within the same repository (25 min)

+

Technical requirements (from installation instructions):

+ +

What is familiar from the previous workshop day (not repeated here):

+
    +

  • Cloning a repository.

    • +

  • Creating a branch.

    • +

  • Committing a change on the new branch.

    • +

  • Submit a pull request towards the main branch.

    • +
+

What will be new in this exercise:

+
    +

  • If you create the changes locally, you will need to push them to the remote repository.

    • +

  • Learning what a protected branch is and how to modify a protected branch: using a pull request.

    • +

  • Cross-referencing issues and pull requests.

    • +

  • Practice to review a pull request.

    • +

  • Learn about the value of draft pull requests.

    • +
+

Exercise tasks:

+
    +

  1. Start in the exercise +repository and open an +issue where you describe the change you want to make. Note down the issue +number since you will need it later.

    2. +

  2. Create a new branch.

    3. +

  3. Make a change to the recipe book on the new branch and in the commit +cross-reference the issue you opened (see the walk-through below +for how to do that).

    4. +

  4. Push your new branch (with the new commit) to the repository you +are working on.

    5. +

  5. Open a pull request towards the main branch.

    6. +

  6. Review somebody else’s pull request and give constructive feedback. Merge their pull request.

    7. +

  7. Try to create a new branch with some half-finished work and open a draft +pull request. Verify that the draft pull request cannot be merged since it +is not meant to be merged yet.

    8. +
+
+
+
+

Solution and hints

+
+

(1) Opening an issue

+

This is done through the GitHub web interface. For example, you could +give the name of the recipe you want to add (so that others don’t add +the same one). It is the “Issues” tab.

+
+
+

(2) Create a new branch.

+

If on GitHub, you can make the branch in the web interface.

+
+
+

(3) Make a change adding the recipe

+

Add a new file with the recipe in it. Commit the file. In the commit +message, include the note about the issue number, saying that this +will close that issue.

+
+

Cross-referencing issues and pull requests

+

Each issue and each pull request gets a number and you can cross-reference them.

+

When you open an issue, note down the issue number (in this case it is #2):

+
+Each issue gets a number +
+

You can reference this issue number in a commit message or in a pull request, like in this +commit message:

+
this is the new recipe; fixes #2
+
+
+

If you forget to do that in your commit message, you can also reference the issue +in the pull request description. And instead of fixes you can also use closes or resolves +or fix or close or resolve (case insensitive).

+

Here are all the keywords that GitHub recognizes: +https://help.github.com/en/articles/closing-issues-using-keywords

+

Then observe what happens in the issue once your commit gets merged: it will +automatically close the issue and create a link between the issue and the +commit. This is very useful for tracking what changes were made in response to +which issue and to know from when until when precisely the issue was open.

+
+
+
+

(4) Push to GitHub as a new branch

+

Push the branch to the repository. You should end up with a branch +visible in the GitHub web view.

+

This is only necessary if you created the changes locally. If you created the +changes directly on GitHub, you can skip this step.

+
+

In VS Code, you can “publish the branch” to the remote repository by clicking +the cloud icon in the bottom left corner of the window:

+
+Publishing a branch in VS Code +
+
+
+
+

(5) Open a pull request towards the main branch

+

This is done through the GitHub web interface.

+
+
+

(6) Reviewing pull requests

+

You review through the GitHub web interface.

+

Checklist for reviewing a pull request:

+
    +

  • Be kind, on the other side is a human who has put effort into this.

    • +

  • Be constructive: if you see a problem, suggest a solution.

    • +

  • Towards which branch is this directed?

    • +

  • Is the title descriptive?

    • +

  • Is the description informative?

    • +

  • Scroll down to see commits.

    • +

  • Scroll down to see the changes.

    • +

  • If you get incredibly many changes, also consider the license or copyright +and ask where all that code is coming from.

    • +

  • Again, be kind and constructive.

    • +

  • Later we will learn how to suggest changes directly in the pull request.

    • +
+

If someone is new, it’s often nice to say something encouraging in the +comments before merging (even if it’s just “thanks”). If all is good +and there’s not much else to say, you could merge directly.

+
+
+

(7) Draft pull requests

+

Try to create a draft pull request:

+
+Creating a draft pull request +
+

Verify that the draft pull request cannot be merged until it is marked as ready +for review:

+
+Draft pull request cannot be merged +
+

Draft pull requests can be useful for:

+
    +

  • Feedback: You can open a pull request early to get feedback on your work without +signaling that it is ready to merge.

    • +

  • Information: They can help communicating to others that a change is coming up and in +progress.

    • +
+
+
+

What is a protected branch? And how to modify it?

+

A protected branch on GitHub or GitLab is a branch that cannot (accidentally) +deleted or force-pushed to. It is also possible to require that a branch cannot +be directly pushed to or modified, but that changes must be submitted via a +pull request.

+

To protect a branch in your own repository, go to “Settings” -> “Branches”.

+
+
+

Summary

+
    +

  • We used all the same pieces that we’ve learned previously.

    • +

  • But we successfully contributed to a collaborative project!

    • +

  • The pull request allowed us to contribute without changing directly: +this is very good when it’s not mainly our project.

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/credit/index.html b/branch/main/credit/index.html new file mode 100644 index 0000000..e4d14e5 --- /dev/null +++ b/branch/main/credit/index.html @@ -0,0 +1,158 @@ + + + + + + + Credit — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Credit

+

The following material (all CC-BY) was reused to create this workshop material:

+ +

(I will also summarize what changes have been made to the original material)

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/documentation/index.html b/branch/main/documentation/index.html new file mode 100644 index 0000000..74b8b75 --- /dev/null +++ b/branch/main/documentation/index.html @@ -0,0 +1,540 @@ + + + + + + + Code documentation — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Code documentation

+
+

Objectives

+
    +

  • Discuss what makes good documentation.

    • +

  • Improve the README of your project or our example project.

    • +

  • Explore Sphinx which is a popular tool to build documentation websites.

    • +

  • Learn how to leverage GitHub Actions and GitHub Pages to build and deploy documentation.

    • +
+
+
+

Instructor note

+
    +

  • (30 min) Discussion

    • +

  • (30 min) Exercise: Set up a Sphinx documentation and add API documentation

    • +

  • (15 min) Demo: Building documentation with GitHub Actions

    • +
+
+
+

Why? 💗✉️ to your future self

+
    +

  • You will probably use your code in the future and may forget details.

    • +

  • You may want others to use your code or contribute +(almost impossible without documentation).

    • +
+
+
+

In-code documentation

+

Not very useful (more commentary than comment):

+
# now we check if temperature is below -50
+if temperature < -50:
+    print("ERROR: temperature is too low")
+
+
+

More useful (explaining why):

+
# we regard temperatures below -50 degrees as measurement errors
+if temperature < -50:
+    print("ERROR: temperature is too low")
+
+
+

Keeping zombie code “just in case” (rather use version control):

+
# do not run this code!
+# if temperature > 0:
+#     print("It is warm")
+
+
+

Emulating version control:

+
# John Doe: threshold changed from 0 to 15 on August 5, 2013
+if temperature > 15:
+    print("It is warm")
+
+
+
+
+

Many languages allow “docstrings”

+

Example (Python):

+
def kelvin_to_celsius(temp_k: float) -> float:
+    """
+    Converts temperature in Kelvin to Celsius.
+
+    Parameters
+    ----------
+    temp_k : float
+        temperature in Kelvin
+
+    Returns
+    -------
+    temp_c : float
+        temperature in Celsius
+    """
+    assert temp_k >= 0.0, "ERROR: negative T_K"
+
+    temp_c = temp_k - 273.15
+
+    return temp_c
+
+
+
+

Keypoints

+
    +

  • Documentation which is only in the source code is not enough.

    • +

  • Often a README is enough.

    • +

  • Documentation needs to be kept +in the same Git repository as the code since we want it to evolve with +the code.

    • +
+
+
+
+

Often a README is enough - checklist

+
    +

  • Purpose

    • +

  • Requirements

    • +

  • Installation instructions

    • +

  • Copy-paste-able example to get started

    • +

  • Tutorials covering key functionality

    • +

  • Reference documentation (e.g. API) covering all functionality

    • +

  • Authors and recommended citation

    • +

  • License

    • +

  • Contribution guide

    • +
+

See also the +JOSS review checklist.

+
+
+

What if you need more than a README?

+ +
+
+

Diátaxis

+

Diátaxis is a systematic approach to technical documentation authoring.

+ +
+
+

Exercise: Set up a Sphinx documentation

+
+

Preparation

+

In this episode we will use the following 5 packages which we installed +previously as part of the Conda environment or Virtual environment:

+
myst-parser
+sphinx
+sphinx-rtd-theme
+sphinx-autoapi
+sphinx-autobuild
+
+
+

Which repository to use? You have 3 options:

+
    +

  • Clone your fork of the planets example repository.

    • +

  • If you don’t have that, you can clone the original repository itself: +https://github.com/workshop-material/planets

    • +

  • You can try this with your own project and the project does not have to +be a Python project.

    • +
+
+

There are at least two ways to get started with Sphinx:

+
    +

  1. Use sphinx-quickstart to create a new Sphinx project.

    2. +

  2. This is what we will do: Create three files (doc/conf.py, doc/index.md, and doc/about.md) +as starting point and improve from there.

    3. +
+
+

Exercise: Set up a Sphinx documentation

+
    +

  1. Create the following three files in your project:

    +
    planets/
+├── doc/
+│   ├── conf.py
+│   ├── index.md
+│   └── about.md
+└── ...
+
    +
    +

    This is conf.py:

    +
    project = "planets"
+copyright = "2024, Authors"
+author = "Authors"
+release = "0.1"
+
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+extensions = [
+    "myst_parser",  # in order to use markdown
+]
+
+myst_enable_extensions = [
+    "colon_fence",  # ::: can be used instead of ``` for better rendering
+]
+
+html_theme = "sphinx_rtd_theme"
+
    +
    +

    This is index.md (feel free to adjust):

    +
    # Our code documentation
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor
+incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis
+nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.
+Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu
+fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in
+culpa qui officia deserunt mollit anim id est laborum.
+
+:::{toctree}
+:maxdepth: 2
+:caption: Some caption
+
+about.md
+:::
+
    +
    +

    This is about.md (feel free to adjust):

    +
    # About this code
+
+Work in progress ...
+
    +
    +
    2. +

  2. Run sphinx-build to build the HTML documentation:

    +
    $ sphinx-build doc _build
+
+... lots of output ...
+The HTML pages are in _build.
+
    +
    +
    3. +

  3. Try to open _build/index.html in your browser.

    4. +

  4. Experiment with adding more content, images, equations, code blocks, …

    + +
    5. +
+
+

There is a lot more you can do:

+
    +

  • This is useful if you want to check the integrity of all internal and external links:

    +
    $ sphinx-build doc -W -b linkcheck _build
+
    +
    +
    • +

  • sphinx-autobuild +provides a local web server that will automatically refresh your view +every time you save a file - which makes writing and testing much easier.

    • +
+
+
+

Demo: Building documentation with GitHub Actions

+

First we need to extend the environment.yml file to include the necessary packages:

+
name: planets
+channels:
+  - conda-forge
+dependencies:
+  - python=3.12
+  - numpy
+  - click
+  - matplotlib
+  - myst-parser
+  - sphinx
+  - sphinx-rtd-theme
+  - sphinx-autoapi
+
+
+

Then we add a GitHub Actions workflow .github/workflow/sphinx.yml to build the documentation:

+
name: Build documentation
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+permissions:
+  contents: write
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+
+    - uses: mamba-org/setup-micromamba@v1
+      with:
+        micromamba-version: '1.5.8-0' # any version from https://github.com/mamba-org/micromamba-releases
+        environment-file: environment.yml
+        init-shell: bash
+        cache-environment: true
+        post-cleanup: 'all'
+        generate-run-shell: false
+
+    - name: Sphinx build
+      run: |
+        sphinx-build doc _build
+      shell: bash -el {0}
+
+    - name: Deploy to GitHub Pages
+      uses: peaceiris/actions-gh-pages@v4
+      if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+      with:
+        publish_branch: gh-pages
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: _build/
+        force_orphan: true
+
+
+

Now:

+
    +

  • Add these two changes to the GitHub repository.

    • +

  • Go to “Settings” -> “Pages” -> “Branch” -> gh-pages -> “Save”.

    • +

  • Look at “Actions” tab and observe the workflow running and hopefully +deploying the website.

    • +

  • Finally visit the generated site. You find it by clicking the About wheel +icon on top right of your repository. There, select “Use your GitHub Pages +website”.

    • +

  • This is how we build almost all of our lesson websites (including this one).

    • +

  • Another popular place to deploy Sphinx documentation is ReadTheDocs.

    • +
+
+
+

Optional: How to auto-generate API documentation in Python

+

Add three tiny modifications (highlighted) to doc/conf.py to auto-generate API documentation +(this requires the sphinx-autoapi package):

+
project = "planets"
+copyright = "2024, Authors"
+author = "Authors"
+release = "0.1"
+
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+extensions = [
+    "myst_parser",  # in order to use markdown
+    "autoapi.extension",  # in order to use markdown
+]
+
+# search this directory for Python files
+autoapi_dirs = [".."]
+
+# ignore this file when generating API documentation
+autoapi_ignore = ["*/conf.py"]
+
+myst_enable_extensions = [
+    "colon_fence",  # ::: can be used instead of ``` for better rendering
+]
+
+html_theme = "sphinx_rtd_theme"
+
+
+

Then rebuild the documentation (or push the changes and let GitHub rebuild it) +and you should see a new section “API Reference”.

+
+
+

Confused about reStructuredText vs. Markdown vs. MyST?

+
    +

  • At the beginning there was reStructuredText and Sphinx was built for reStructuredText.

    • +

  • Independently, Markdown was invented and evolved into a couple of flavors.

    • +

  • Markdown became more and more popular but was limited compared to reStructuredText.

    • +

  • Later, MyST +was invented to be able to write +something that looks like Markdown but in addition can do everything that +reStructuredText can do with extra directives.

    • +
+
+
+

Where to read more

+ +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/example/index.html b/branch/main/example/index.html new file mode 100644 index 0000000..c0c506a --- /dev/null +++ b/branch/main/example/index.html @@ -0,0 +1,237 @@ + + + + + + + Example project: Simulating the motion of planets — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Example project: Simulating the motion of planets
    • +
  • + Edit on GitHub +
    • +
+
+
+
+
+ +
+

Example project: Simulating the motion of planets

+

The example code that we will study +is a hopefully simple N-body simulation written in Python. It is not important +or expected that we understand the code in any detail.

+

The big picture is that the code simulates the motion of a number of +planets:

+
    +

  • We can choose the number of planets.

    • +

  • Each planet starts with a random position, velocity, and mass.

    • +

  • At each time step, the code calculates the gravitational force between each +pair of planets.

    • +

  • The forces accelerate each planet, the acceleration modifies the velocity, +the velocity modifies the position of each planet.

    • +

  • We can choose the number of time steps.

    • +

  • The units were chosen to make numbers easy to read.

    • +
+
+

Example run

+
+

Instructor note

+

The instructor demonstrates running the code on their computer.

+
+

The code is written to accept command-line arguments to specify the number +of planets and the number of time steps.

+

We first generate starting data:

+
$ python generate-data.py --num-planets 10 --output-file initial.csv
+
+
+

The generated file (initial.csv) could look like this:

+
px,py,pz,vx,vy,vz,mass
+-46.88,-42.51,88.33,-0.86,-0.18,0.55,6.70
+-5.29,17.09,-96.13,0.66,0.45,-0.17,3.51
+83.53,-92.83,-68.77,-0.26,-0.48,0.24,6.84
+-36.31,25.48,64.16,0.85,0.75,-0.56,1.53
+-68.38,-17.21,-97.07,0.60,0.26,0.69,6.63
+-48.37,-48.74,3.92,-0.92,-0.33,-0.93,8.60
+40.53,-75.50,44.18,-0.62,-0.31,-0.53,8.04
+-27.21,10.78,-78.82,-0.09,-0.55,-0.03,5.35
+88.42,-74.95,-45.85,0.81,0.68,0.56,5.36
+39.09,53.12,-59.54,-0.54,0.56,0.07,8.98
+
+
+

Then we can simulate their motion (in this case for 20 steps):

+
$ python simulate.py --num-steps 20 \
+                     --input-file initial.csv \
+                     --output-file final.csv
+
+
+

The --output-file (final.csv) is again a CSV file (comma-separated values) +and contains the final positions of all planets.

+

It is possible to run on multiple cores and to animate the result. +Here is an example with 100 planets:

+
$ python generate-data.py --num-planets 100 --output-file initial.csv
+
+$ python simulate.py --num-steps 50 \
+                     --input-file initial.csv \
+                     --output-file final.csv \
+                     --trajectories-file trajectories.npz \
+                     --num-cores 8
+
+$ python animate.py --initial-file initial.csv \
+                    --trajectories-file trajectories.npz \
+                    --output-file animation.mp4
+
+
+
+

Learning goals

+
    +

  • What are the most important steps to make this code reusable by others +and our future selves?

    • +

  • Be able to apply these techniques to your own code/script.

    • +
+
+
+

We will not focus on …

+
    +

  • … how the code works internally in detail.

    • +

  • … whether this is the most efficient algorithm.

    • +

  • … whether the code is numerically stable.

    • +

  • … how to code scales with the number of cores.

    • +

  • … whether it is portable to other operating systems (we will discuss this later).

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/genindex/index.html b/branch/main/genindex/index.html new file mode 100644 index 0000000..99f0d30 --- /dev/null +++ b/branch/main/genindex/index.html @@ -0,0 +1,149 @@ + + + + + + Index — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ + +

Index

+ +
+ +
+ + +
+
+
+ +
+ +
+

© Copyright CodeRefinery team (CC-BY license).

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/index.html b/branch/main/index.html new file mode 100644 index 0000000..a97289d --- /dev/null +++ b/branch/main/index.html @@ -0,0 +1,290 @@ + + + + + + + Reproducible research software development using Python — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Reproducible research software development using Python
    • +
  • + Edit on GitHub +
    • +
+
+
+
+
+ +
+

Reproducible research software development using Python

+
+

Big-picture goal

+

This is a hands-on course on research software engineering. In this +workshop we assume that most workshop participants use Python in their work or +a leading a group which uses Python. Therefore, some of the examples will use +Python as the example language.

+

We will work with an example project and go through all the steps of a typical +software project. Once we have seen the building blocks, we will try to apply +them to own projects. Workshop participants will receive and also learn to give +constructive code feedback.

+
+
+

Prerequisites

+
+

Preparation

+
    +

  1. Get a GitHub account following these instructions.

    2. +

  2. You will need a text editor. If you don’t have a favorite one, we recommend +VS Code.

    3. +

  3. If you prefer to work in the terminal and not in VS Code, set up these two (skip this if you use VS Code):

    + +
    4. +

  4. One of these two software environments (if you are not sure which one to +choose or have no preference, choose Conda):

    + +
    5. +

  5. Optional and only on Linux: Apptainer following +these instructions.

    6. +
+
+
+
+

Schedule

+
+

Day 1

+ +
+
+

Day 2

+ +
+
+

Day 3

+ +
+
+

If we have time left

+ +
+
+
+
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/installation/conda/index.html b/branch/main/installation/conda/index.html new file mode 100644 index 0000000..70fe17a --- /dev/null +++ b/branch/main/installation/conda/index.html @@ -0,0 +1,252 @@ + + + + + + + Conda environment — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Conda environment

+

A Conda environment is an isolated software environment that is used to manage dependencies for a project +and you decide where it is located.

+

You will need a environment.yml file that documents the dependencies:

+
name: coderefinery
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - python >= 3.10
+  - black
+  - click
+  - flit
+  - ipywidgets
+  - isort
+  - jupyterlab
+  - jupyterlab_code_formatter
+  - jupyterlab-git
+  - matplotlib
+  - myst-parser
+  - nbdime
+  - numpy
+  - pandas
+  - pytest
+  - pytest-cov
+  - scalene
+  - seaborn
+  - snakemake-minimal
+  - sphinx
+  - sphinx-autoapi
+  - sphinx-autobuild
+  - sphinx_rtd_theme >= 2.0
+  - vulture
+  - scikit-image
+
+
+
+

Before you create a virtual environment

+
    +

  1. Create a new directory for this course.

    2. +

  2. In this directory, create an environment.yml file and copy-paste the dependencies above into it.

    3. +
+
+
+

Choose the tool to manage the environment

+

If you are already using one of these tools, please continue using the tool that you like and know. +If you are new to this, we recommend using Miniconda or Miniforge.

+
    +

  • Anaconda

    +
      +

    • Advantages: easy to install, easy to use, good for beginners

      • +

    • Disadvantages: large download, installs more than we will need, license restrictions

      • +
    +
    • +

  • Miniconda

    +
      +

    • Advantages: small size, installs only what you need

      • +

    • Disadvantages: no graphical interface, license restrictions

      • +
    +
    • +

  • Miniforge

    +
      +

    • Advantages: small size, no license restrictions

      • +

    • Disadvantages: no graphical interface

      • +
    +
    • +

  • Micromamba

    +
      +

    • Advantages: fast, small size

      • +

    • Disadvantages: no graphical interface

      • +
    +
    • +

  • Pixi

    +
      +

    • Advantages: fast and new

      • +

    • Disadvantages: new and less tested and not documented here

      • +
    +
    • +
+
+
+

Creating the virtual environment

+
    +

  1. Open your terminal shell (e.g. Bash or Zsh).

    2. +

  2. Activate conda using conda activate or source ~/miniconda3/bin/activate.

    3. +

  3. Run the following command:

    +
    $ conda env create --file environment.yml
+
    +
    +
    4. +

  4. Make sure that you see “coderefinery” in the output when you ask for a list of all available environments:

    +
    $ conda env list
+
    +
    +
    5. +
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/installation/virtual-environment/index.html b/branch/main/installation/virtual-environment/index.html new file mode 100644 index 0000000..72439ff --- /dev/null +++ b/branch/main/installation/virtual-environment/index.html @@ -0,0 +1,217 @@ + + + + + + + Virtual environment — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Virtual environment

+

A virtual environment is an isolated software environment that is used to manage dependencies for a project +and you decide where it is located.

+

You will need a requirements.txt file that documents the dependencies:

+
black
+click
+flit
+ipywidgets
+isort
+jupyterlab
+jupyterlab-code-formatter
+jupyterlab-git
+matplotlib
+myst-parser
+nbdime
+numpy
+pandas
+pytest
+pytest-cov
+scalene
+seaborn
+sphinx
+sphinx-autoapi
+sphinx-autobuild
+sphinx_rtd_theme >= 2.0
+vulture
+scikit-image
+
+
+
+

Before you create a virtual environment

+
    +

  1. Create a new directory for this course.

    2. +

  2. In this directory, create a requirements.txt file and copy-paste the dependencies above into it.

    3. +
+
+
+

Creating the virtual environment

+

Now create a virtual environment in this directory either using pip and +venv +(more traditional and safer) or using uv (more modern but also less tested):

+
+

Create a new virtual environment and activate it:

+
$ python3 -m venv coderefinery-environment
+$ source coderefinery-environment/bin/activate
+
+
+

Install the dependencies into the environment:

+
$ python3 -m pip install -r requirements.txt
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/lesson.pdf b/branch/main/lesson.pdf new file mode 100644 index 0000000..d032217 Binary files /dev/null and b/branch/main/lesson.pdf differ diff --git a/branch/main/objects.inv b/branch/main/objects.inv new file mode 100644 index 0000000..31aff9c Binary files /dev/null and b/branch/main/objects.inv differ diff --git a/branch/main/profiling/index.html b/branch/main/profiling/index.html new file mode 100644 index 0000000..ea98d96 --- /dev/null +++ b/branch/main/profiling/index.html @@ -0,0 +1,164 @@ + + + + + + + Profiling memory and CPU usage — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Profiling memory and CPU usage

+

Profilers:

+
    +

  • cProfile or profile

    • +

  • line_profiler

    • +

  • viztracer

    • +

  • scalene

    • +

  • Intel VTune

    • +

  • PyInstrument

    • +

  • py-spy

    • +

  • Pyflame

    • +

  • timeit

    • +
+

(here I will add some examples that we can profile together)

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/publishing/index.html b/branch/main/publishing/index.html new file mode 100644 index 0000000..24ea5b1 --- /dev/null +++ b/branch/main/publishing/index.html @@ -0,0 +1,161 @@ + + + + + + + How to release and publish your code — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

How to release and publish your code

+

Part 1:

+
    +

  • 30 min: Overview over software licenses and code publishing

    • +

  • 15 min: We add a license, CFF file, and publish to Zenodo (sandbox)

    • +
+

Part 2:

+
    +

  • 30 min: Creating a Python package with the help of flit

    • +

  • 15 min: Deploy the package to test-PyPI using GitHub Actions

    • +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/refactoring-concepts/index.html b/branch/main/refactoring-concepts/index.html new file mode 100644 index 0000000..ca7705e --- /dev/null +++ b/branch/main/refactoring-concepts/index.html @@ -0,0 +1,157 @@ + + + + + + + Concepts in refactoring and modular code design — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Concepts in refactoring and modular code design
    • +
  • + Edit on GitHub +
    • +
+
+
+
+
+ +
+

Concepts in refactoring and modular code design

+

Topics:

+
    +

  • Pure functions

    • +

  • Design patterns: functional design vs. object-oriented design

    • +

  • How to design your code before writing it: document-driven development

    • +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/refactoring-demo/index.html b/branch/main/refactoring-demo/index.html new file mode 100644 index 0000000..235a7cd --- /dev/null +++ b/branch/main/refactoring-demo/index.html @@ -0,0 +1,349 @@ + + + + + + + Demo: From a script towards a workflow — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Demo: From a script towards a workflow

+

In this episode we will explore code quality and good practices in Python using +a hands-on approach. We will together build up a small project and improve it +step by step.

+

We will start from a relatively simple image processing script which can read a +telescope image of stars and our goal is to count the number of stars in +the image. Later we will want to be able to process many such images.

+

The (fictional) telescope images look like the one below here (in this +repository we can find more):

+
+Generated image representing a telescope image of stars +
+

Generated image representing a telescope image of stars.

+
+
+
+

Rough plan for this demo

+
    +

  • (15 min) Discuss how we would solve the problem, run example code, and make it work (as part of a Jupyter notebook)?

    • +

  • (15 min) Refactor the positioning code into a function and a module

    • +

  • (15 min) Now we wish to process many images - discuss how we would approach this

    • +

  • (15 min) Introduce CLI and discuss the benefits

    • +

  • (30 min) From a script to a workflow (using Snakemake)

    • +
+
+ +
+

Plan

+

Topics we wish to show and discuss:

+
    +

  • Naming (and other) conventions, project organization, modularity

    • +

  • The value of pure functions and immutability

    • +

  • Refactoring (explained through examples)

    • +

  • Auto-formatting and linting with tools like black, vulture, ruff

    • +

  • Moving a project under Git

    • +

  • How to document dependencies

    • +

  • Structuring larger software projects in a modular way

    • +

  • Command-line interfaces

    • +

  • Workflows with Snakemake

    • +
+

We will work together on the code on the big screen, and participants will be +encouraged to give suggestions and ask questions. We will end up with a Git +repository which will be shared with workshop participants.

+
+
+

Possible solutions

+ + +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/reusable/index.html b/branch/main/reusable/index.html new file mode 100644 index 0000000..b17c103 --- /dev/null +++ b/branch/main/reusable/index.html @@ -0,0 +1,163 @@ + + + + + + + How to make the project more reusable — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

How to make the project more reusable

+

Part 1:

+
    +

  • 15 min: Motivation

    • +

  • 15 min: Best practices for managing dependencies in Python

    • +

  • 20 min: Exercise

    • +
+

Part 2:

+
    +

  • 10 min: Introduction to containers

    • +

  • 20 min: Demonstration

    • +

  • 10 min: Discussion

    • +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/search/index.html b/branch/main/search/index.html new file mode 100644 index 0000000..655dc57 --- /dev/null +++ b/branch/main/search/index.html @@ -0,0 +1,163 @@ + + + + + + Search — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Search
    • +
  • +
    • +
+
+
+
+
+ + + + +
+ +
+ +
+
+
+ +
+ +
+

© Copyright CodeRefinery team (CC-BY license).

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + + + + + + \ No newline at end of file diff --git a/branch/main/searchindex.js b/branch/main/searchindex.js new file mode 100644 index 0000000..abec3f0 --- /dev/null +++ b/branch/main/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({"alltitles": {"(1) Basic browsing": [[20, "basic-browsing"]], "(1) Create a new branch and a new commit": [[19, "create-a-new-branch-and-a-new-commit"]], "(1) Opening an issue": [[5, "opening-an-issue"]], "(2) Compare commit history with network graph": [[20, "compare-commit-history-with-network-graph"]], "(2) Create a new branch.": [[5, "create-a-new-branch"]], "(2) Modify the file again with a new commit": [[19, "modify-the-file-again-with-a-new-commit"]], "(3) How can you browse the history of a single file?": [[20, "how-can-you-browse-the-history-of-a-single-file"]], "(3) Make a change adding the recipe": [[5, "make-a-change-adding-the-recipe"]], "(3) Switch to the main branch and create a commit there": [[19, "switch-to-the-main-branch-and-create-a-commit-there"]], "(4) Browse the commits you just made": [[19, "browse-the-commits-you-just-made"]], "(4) Push to GitHub as a new branch": [[5, "push-to-github-as-a-new-branch"]], "(4) Which files include the word \u201cposition\u201d?": [[20, "which-files-include-the-word-position"]], "(5) Compare the branches": [[19, "compare-the-branches"]], "(5) Open a pull request towards the main branch": [[5, "open-a-pull-request-towards-the-main-branch"]], "(5) Who modified each line last and when?": [[20, "who-modified-each-line-last-and-when"]], "(6) Can you use this code yourself? 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diff --git a/branch/main/singlehtml/_static/_sphinx_javascript_frameworks_compat.js b/branch/main/singlehtml/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 0000000..8141580 --- /dev/null +++ b/branch/main/singlehtml/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. Multiple values per key are supported, + * it will always return arrays of strings for the value parts. + */ +jQuery.getQueryParameters = function(s) { + if (typeof s === 'undefined') + s = document.location.search; + var parts = s.substr(s.indexOf('?') + 1).split('&'); + var result = {}; + for (var i = 0; i < parts.length; i++) { + var tmp = parts[i].split('=', 2); + var key = jQuery.urldecode(tmp[0]); + var value = jQuery.urldecode(tmp[1]); + if (key in result) + result[key].push(value); + else + result[key] = [value]; + } + return result; +}; + +/** + * highlight a given string on a jquery object by wrapping it in + * span elements with the given class name. + */ +jQuery.fn.highlightText = function(text, className) { + function highlight(node, addItems) { + if (node.nodeType === 3) { + var val = node.nodeValue; + var pos = val.toLowerCase().indexOf(text); + if (pos >= 0 && + !jQuery(node.parentNode).hasClass(className) && + !jQuery(node.parentNode).hasClass("nohighlight")) { + var span; + var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.className = className; + } + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + node.parentNode.insertBefore(span, node.parentNode.insertBefore( + document.createTextNode(val.substr(pos + text.length)), + node.nextSibling)); + node.nodeValue = val.substr(0, pos); + if (isInSVG) { + var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); + var bbox = node.parentElement.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute('class', className); + addItems.push({ + "parent": node.parentNode, + "target": rect}); + } + } + } + else if (!jQuery(node).is("button, select, textarea")) { + jQuery.each(node.childNodes, function() { + highlight(this, addItems); + }); + } + } + var addItems = []; + var result = this.each(function() { + highlight(this, addItems); + }); + for (var i = 0; i < addItems.length; ++i) { + jQuery(addItems[i].parent).before(addItems[i].target); + } + return result; +}; + +/* + * backward compatibility for jQuery.browser + * This will be supported until firefox bug is fixed. + */ +if (!jQuery.browser) { + jQuery.uaMatch = function(ua) { + ua = ua.toLowerCase(); + + var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || + /(webkit)[ \/]([\w.]+)/.exec(ua) || + /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || + /(msie) ([\w.]+)/.exec(ua) || + ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || + []; + + return { + browser: match[ 1 ] || "", + version: match[ 2 ] || "0" + }; + }; + jQuery.browser = {}; + jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; +} diff --git a/branch/main/singlehtml/_static/basic.css b/branch/main/singlehtml/_static/basic.css new file mode 100644 index 0000000..f316efc --- /dev/null +++ b/branch/main/singlehtml/_static/basic.css @@ -0,0 +1,925 @@ +/* + * basic.css + * ~~~~~~~~~ + * + * Sphinx stylesheet -- basic theme. + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; +} + +div.section::after { + display: block; + content: ''; + clear: left; +} + +/* -- relbar ---------------------------------------------------------------- */ + +div.related { + width: 100%; + font-size: 90%; +} + +div.related h3 { + display: none; +} + +div.related ul { + margin: 0; + padding: 0 0 0 10px; + list-style: none; +} + +div.related li { + display: inline; +} + +div.related li.right { + float: right; + margin-right: 5px; +} + +/* -- sidebar --------------------------------------------------------------- */ + +div.sphinxsidebarwrapper { + padding: 10px 5px 0 10px; +} + +div.sphinxsidebar { + float: left; + width: 230px; + margin-left: -100%; + font-size: 90%; + word-wrap: break-word; + overflow-wrap : break-word; +} + +div.sphinxsidebar ul { + list-style: none; +} + +div.sphinxsidebar ul ul, +div.sphinxsidebar ul.want-points { + margin-left: 20px; + list-style: square; +} + +div.sphinxsidebar ul ul { + margin-top: 0; + margin-bottom: 0; +} + +div.sphinxsidebar form { + margin-top: 10px; +} + +div.sphinxsidebar input { + border: 1px solid #98dbcc; + font-family: sans-serif; + font-size: 1em; +} + +div.sphinxsidebar #searchbox form.search { + overflow: hidden; +} + +div.sphinxsidebar #searchbox input[type="text"] { + float: left; + width: 80%; + padding: 0.25em; + box-sizing: border-box; +} + +div.sphinxsidebar #searchbox input[type="submit"] { + float: left; + width: 20%; + border-left: none; + padding: 0.25em; + box-sizing: border-box; +} + + +img { + border: 0; + max-width: 100%; +} + +/* -- search page ----------------------------------------------------------- */ + +ul.search { + margin: 10px 0 0 20px; + padding: 0; +} + +ul.search li { + padding: 5px 0 5px 20px; + background-image: url(file.png); + background-repeat: no-repeat; + background-position: 0 7px; +} + +ul.search li a { + font-weight: bold; +} + +ul.search li p.context { + color: #888; + margin: 2px 0 0 30px; + text-align: left; +} + +ul.keywordmatches li.goodmatch a { + font-weight: bold; +} + +/* -- index page ------------------------------------------------------------ */ + +table.contentstable { + width: 90%; + margin-left: auto; + margin-right: auto; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable ul { + margin-top: 0; + margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: 360px; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, figure.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, figure.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, figure.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-default, figure.align-default, .figure.align-default { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-default { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar, +aside.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px; + background-color: #ffe; + width: 40%; + float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; +} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} + +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +.translated { + background-color: rgba(207, 255, 207, 0.2) +} + +.untranslated { + background-color: rgba(255, 207, 207, 0.2) +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + +td.linenos pre { + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; +} + +table.highlighttable td { + margin: 0; + padding: 0; +} + +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; +} + +div.code-block-caption code { + background-color: transparent; +} + +table.highlighttable td.linenos, +span.linenos, +div.highlight span.gp { /* gp: Generic.Prompt */ + user-select: none; + -webkit-user-select: text; /* Safari fallback only */ + -webkit-user-select: none; /* Chrome/Safari */ + -moz-user-select: none; /* Firefox */ + -ms-user-select: none; /* IE10+ */ +} + +div.code-block-caption span.caption-number { + padding: 0.1em 0.3em; + font-style: italic; +} + +div.code-block-caption span.caption-text { +} + +div.literal-block-wrapper { + margin: 1em 0; +} + +code.xref, a code { + background-color: transparent; + font-weight: bold; +} + +h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { + background-color: transparent; +} + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family: sans-serif; +} + +div.viewcode-block:target { + margin: -1px -10px; + padding: 0 10px; +} + +/* -- math display ---------------------------------------------------------- */ + +img.math { + vertical-align: middle; +} + +div.body div.math p { + text-align: center; +} + +span.eqno { + float: right; +} + +span.eqno a.headerlink { + position: absolute; + z-index: 1; +} + +div.math:hover a.headerlink { + visibility: visible; +} + +/* -- printout stylesheet --------------------------------------------------- */ + +@media print { + div.document, + div.documentwrapper, + div.bodywrapper { + margin: 0 !important; + width: 100%; + } + + div.sphinxsidebar, + div.related, + div.footer, + #top-link { + display: none; + } +} \ No newline at end of file diff --git a/branch/main/singlehtml/_static/check-solid.svg b/branch/main/singlehtml/_static/check-solid.svg new file mode 100644 index 0000000..92fad4b --- /dev/null +++ b/branch/main/singlehtml/_static/check-solid.svg @@ -0,0 +1,4 @@ + + + + diff --git a/branch/main/singlehtml/_static/clipboard.min.js b/branch/main/singlehtml/_static/clipboard.min.js new file mode 100644 index 0000000..54b3c46 --- /dev/null +++ b/branch/main/singlehtml/_static/clipboard.min.js @@ -0,0 +1,7 @@ +/*! + * clipboard.js v2.0.8 + * https://clipboardjs.com/ + * + * Licensed MIT © Zeno Rocha + */ +!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return o}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),c=n.n(e);function a(t){try{return document.execCommand(t)}catch(t){return}}var f=function(t){t=c()(t);return a("cut"),t};var l=function(t){var e,n,o,r=1 + + + + diff --git a/branch/main/singlehtml/_static/copybutton.css b/branch/main/singlehtml/_static/copybutton.css new file mode 100644 index 0000000..40eafe5 --- /dev/null +++ b/branch/main/singlehtml/_static/copybutton.css @@ -0,0 +1,93 @@ +/* Copy buttons */ +button.copybtn { + position: absolute; + display: flex; + top: .3em; + right: .3em; + width: 1.7em; + height: 1.7em; + opacity: 0; + transition: opacity 0.3s, border .3s, background-color .3s; + user-select: none; + padding: 0; + border: none; + outline: none; + border-radius: 0.4em; + /* The colors that GitHub uses */ + border: #1b1f2426 1px solid; + background-color: #f6f8fa; + color: #57606a; +} + +button.copybtn.success { + border-color: #22863a; + color: #22863a; +} + +button.copybtn svg { + stroke: currentColor; + width: 1.5em; + height: 1.5em; + padding: 0.1em; +} + +div.highlight { + position: relative; +} + +.highlight:hover button.copybtn { + opacity: 1; +} + +.highlight button.copybtn:hover { + background-color: rgb(235, 235, 235); +} + +.highlight button.copybtn:active { + background-color: rgb(187, 187, 187); +} + +/** + * A minimal CSS-only tooltip copied from: + * https://codepen.io/mildrenben/pen/rVBrpK + * + * To use, write HTML like the following: + * + *

Short

+ */ + .o-tooltip--left { + position: relative; + } + + .o-tooltip--left:after { + opacity: 0; + visibility: hidden; + position: absolute; + content: attr(data-tooltip); + padding: .2em; + font-size: .8em; + left: -.2em; + background: grey; + color: white; + white-space: nowrap; + z-index: 2; + border-radius: 2px; + transform: translateX(-102%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); +} + +.o-tooltip--left:hover:after { + display: block; + opacity: 1; + visibility: visible; + transform: translateX(-100%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); + transition-delay: .5s; +} + +/* By default the copy button shouldn't show up when printing a page */ +@media print { + button.copybtn { + display: none; + } +} diff --git a/branch/main/singlehtml/_static/copybutton.js b/branch/main/singlehtml/_static/copybutton.js new file mode 100644 index 0000000..f3ecd03 --- /dev/null +++ b/branch/main/singlehtml/_static/copybutton.js @@ -0,0 +1,241 @@ +// Localization support +const messages = { + 'en': { + 'copy': 'Copy', + 'copy_to_clipboard': 'Copy to clipboard', + 'copy_success': 'Copied!', + 'copy_failure': 'Failed to copy', + }, + 'es' : { + 'copy': 'Copiar', + 'copy_to_clipboard': 'Copiar al portapapeles', + 'copy_success': '¡Copiado!', + 'copy_failure': 'Error al copiar', + }, + 'de' : { + 'copy': 'Kopieren', + 'copy_to_clipboard': 'In die Zwischenablage kopieren', + 'copy_success': 'Kopiert!', + 'copy_failure': 'Fehler beim Kopieren', + }, + 'fr' : { + 'copy': 'Copier', + 'copy_to_clipboard': 'Copié dans le presse-papier', + 'copy_success': 'Copié !', + 'copy_failure': 'Échec de la copie', + }, + 'ru': { + 'copy': 'Скопировать', + 'copy_to_clipboard': 'Скопировать в буфер', + 'copy_success': 'Скопировано!', + 'copy_failure': 'Не удалось скопировать', + }, + 'zh-CN': { + 'copy': '复制', + 'copy_to_clipboard': '复制到剪贴板', + 'copy_success': '复制成功!', + 'copy_failure': '复制失败', + }, + 'it' : { + 'copy': 'Copiare', + 'copy_to_clipboard': 'Copiato negli appunti', + 'copy_success': 'Copiato!', + 'copy_failure': 'Errore durante la copia', + } +} + +let locale = 'en' +if( document.documentElement.lang !== undefined + && messages[document.documentElement.lang] !== undefined ) { + locale = document.documentElement.lang +} + +let doc_url_root = DOCUMENTATION_OPTIONS.URL_ROOT; +if (doc_url_root == '#') { + doc_url_root = ''; +} + +/** + * SVG files for our copy buttons + */ +let iconCheck = ` + ${messages[locale]['copy_success']} + + +` + +// If the user specified their own SVG use that, otherwise use the default +let iconCopy = ``; +if (!iconCopy) { + iconCopy = ` + ${messages[locale]['copy_to_clipboard']} + + + +` +} + +/** + * Set up copy/paste for code blocks + */ + +const runWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} + +const codeCellId = index => `codecell${index}` + +// Clears selected text since ClipboardJS will select the text when copying +const clearSelection = () => { + if (window.getSelection) { + window.getSelection().removeAllRanges() + } else if (document.selection) { + document.selection.empty() + } +} + +// Changes tooltip text for two seconds, then changes it back +const temporarilyChangeTooltip = (el, oldText, newText) => { + el.setAttribute('data-tooltip', newText) + el.classList.add('success') + setTimeout(() => el.setAttribute('data-tooltip', oldText), 2000) + setTimeout(() => el.classList.remove('success'), 2000) +} + +// Changes the copy button icon for two seconds, then changes it back +const temporarilyChangeIcon = (el) => { + el.innerHTML = iconCheck; + setTimeout(() => {el.innerHTML = iconCopy}, 2000) +} + +const addCopyButtonToCodeCells = () => { + // If ClipboardJS hasn't loaded, wait a bit and try again. This + // happens because we load ClipboardJS asynchronously. + if (window.ClipboardJS === undefined) { + setTimeout(addCopyButtonToCodeCells, 250) + return + } + + // Add copybuttons to all of our code cells + const COPYBUTTON_SELECTOR = 'div.highlight pre'; + const codeCells = document.querySelectorAll(COPYBUTTON_SELECTOR) + codeCells.forEach((codeCell, index) => { + const id = codeCellId(index) + codeCell.setAttribute('id', id) + + const clipboardButton = id => + `` + codeCell.insertAdjacentHTML('afterend', clipboardButton(id)) + }) + +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} + + +var copyTargetText = (trigger) => { + var target = document.querySelector(trigger.attributes['data-clipboard-target'].value); + + // get filtered text + let exclude = '.linenos, .gp'; + + let text = filterText(target, exclude); + return formatCopyText(text, '', false, true, true, true, '', '') +} + + // Initialize with a callback so we can modify the text before copy + const clipboard = new ClipboardJS('.copybtn', {text: copyTargetText}) + + // Update UI with error/success messages + clipboard.on('success', event => { + clearSelection() + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_success']) + temporarilyChangeIcon(event.trigger) + }) + + clipboard.on('error', event => { + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_failure']) + }) +} + +runWhenDOMLoaded(addCopyButtonToCodeCells) \ No newline at end of file diff --git a/branch/main/singlehtml/_static/copybutton_funcs.js b/branch/main/singlehtml/_static/copybutton_funcs.js new file mode 100644 index 0000000..dbe1aaa --- /dev/null +++ b/branch/main/singlehtml/_static/copybutton_funcs.js @@ -0,0 +1,73 @@ +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +export function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +export function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} diff --git a/branch/main/singlehtml/_static/css/badge_only.css b/branch/main/singlehtml/_static/css/badge_only.css new file mode 100644 index 0000000..c718cee --- /dev/null +++ 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+ return this; // for chaining... + } +})(jQuery); + +// NO good way to do this!. Copy a hack from here +// https://stackoverflow.com/questions/901115/how-can-i-get-query-string-values-in-javascript +// https://stackoverflow.com/a/2880929 +var urlParams; +(window.onpopstate = function () { + var match, + pl = /\+/g, // Regex for replacing addition symbol with a space + search = /([^&=]+)=?([^&]*)/g, + decode = function (s) { return decodeURIComponent(s.replace(pl, " ")); }, + query = window.location.search.substring(1); + urlParams = {}; + while (match = search.exec(query)) + urlParams[decode(match[1])] = decode(match[2]); +})(); + +// Select heading levels +var maxHeading = urlParams['h'] +if (maxHeading === undefined) maxHeading = 2 +var headingLevels = []; +for (h=2 ; h (sections.length-1) ) { + // if we would scroll past bottom, or above top, do nothing + return; + } + + console.log('xxxxxx'); + var targetSection = sections[targetPos]; + console.log(targetSection, typeof(targetSection)); + + // Return targetSection top and height + var secProperties = section_top_and_height(targetSection); + var top = secProperties['top']; + var height = secProperties['height'] + var win_height = window.innerHeight; + //console.info(top, height, win_height) + + var scroll_to = 0; + if (height >= win_height || height == 0) { + scroll_to = top; + } else { + scroll_to = top - (win_height-height)/3.; + } + //console.info(top, height, win_height, scroll_to) + + $('html, body').animate({ + scrollTop: scroll_to //+ 'px' + }, 'fast'); + +} + + +function minipres() { + /* Enable the minipres mode: + - call the hide() function + - set up the scrolling listener + */ + document.addEventListener('keydown', function (event) { + switch(event.which) { + case 37: // left + switch_slide(-1); + event.preventDefault(); + return false; + break; + //case 38: // up + case 39: // right + switch_slide(+1); + event.preventDefault(); + return false; + break; + //case 40: // down + default: + return; // exit this handler for other keys + } + }, true) + + hide() + + // Increase space between sections + //$("div .section").css('margin-bottom', '50%'); 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+} + +/* Math align to the left */ +.cell_output .MathJax_Display { + text-align: left !important; +} + +/* Pandas tables. Pulled from the Jupyter / nbsphinx CSS */ +div.cell_output table { + border: none; + border-collapse: collapse; + border-spacing: 0; + color: black; + font-size: 1em; + table-layout: fixed; +} + +div.cell_output thead { + border-bottom: 1px solid black; + vertical-align: bottom; +} + +div.cell_output tr, +div.cell_output th, +div.cell_output td { + text-align: right; + vertical-align: middle; + padding: 0.5em 0.5em; + line-height: normal; + white-space: normal; + max-width: none; + border: none; +} + +div.cell_output th { + font-weight: bold; +} + +div.cell_output tbody tr:nth-child(odd) { + background: #f5f5f5; +} + +div.cell_output tbody tr:hover { + background: rgba(66, 165, 245, 0.2); +} + +/** source code line numbers **/ +span.linenos { + opacity: 0.5; +} + +/* Inline text from `paste` operation */ + +span.pasted-text { + font-weight: bold; +} + +span.pasted-inline img { + max-height: 2em; +} + +tbody span.pasted-inline img { + max-height: none; +} + +/* Font colors for 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background-color: #E75C58 +} + +div.highlight .-Color[class*=-BGGreen] { + background-color: #00A250 +} + +div.highlight .-Color[class*=-BGYellow] { + background-color: #DDB62B +} + +div.highlight .-Color[class*=-BGBlue] { + background-color: #208FFB +} + +div.highlight .-Color[class*=-BGMagenta] { + background-color: #D160C4 +} + +div.highlight .-Color[class*=-BGCyan] { + background-color: #60C6C8 +} + +div.highlight .-Color[class*=-BGWhite] { + background-color: #C5C1B4 +} + +/* Font colors for 8-bit ANSI */ + +div.highlight .-Color[class*=-C0] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC0] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C1] { + color: #800000 +} + +div.highlight .-Color[class*=-BGC1] { + background-color: #800000 +} + +div.highlight .-Color[class*=-C2] { + color: #008000 +} + +div.highlight .-Color[class*=-BGC2] { + background-color: #008000 +} + +div.highlight .-Color[class*=-C3] { + color: #808000 +} + +div.highlight .-Color[class*=-BGC3] { + background-color: #808000 +} + +div.highlight .-Color[class*=-C4] { + color: #000080 +} + +div.highlight .-Color[class*=-BGC4] { + background-color: #000080 +} + +div.highlight .-Color[class*=-C5] { + color: #800080 +} + +div.highlight .-Color[class*=-BGC5] { + background-color: #800080 +} + +div.highlight .-Color[class*=-C6] { + color: #008080 +} + +div.highlight .-Color[class*=-BGC6] { + background-color: #008080 +} + +div.highlight .-Color[class*=-C7] { + color: #C0C0C0 +} + +div.highlight .-Color[class*=-BGC7] { + background-color: #C0C0C0 +} + +div.highlight .-Color[class*=-C8] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC8] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C9] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC9] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C10] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC10] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C11] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC11] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C12] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC12] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C13] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC13] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C14] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC14] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C15] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC15] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C16] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC16] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C17] { + color: #00005F +} + +div.highlight .-Color[class*=-BGC17] { + background-color: #00005F +} + +div.highlight .-Color[class*=-C18] { + color: #000087 +} + +div.highlight .-Color[class*=-BGC18] { + background-color: #000087 +} + +div.highlight .-Color[class*=-C19] { + color: #0000AF +} + +div.highlight .-Color[class*=-BGC19] { + background-color: #0000AF +} + +div.highlight .-Color[class*=-C20] { + color: #0000D7 +} + +div.highlight .-Color[class*=-BGC20] { + background-color: #0000D7 +} + +div.highlight .-Color[class*=-C21] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC21] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C22] { + color: #005F00 +} + +div.highlight .-Color[class*=-BGC22] { + background-color: #005F00 +} + +div.highlight .-Color[class*=-C23] { + color: #005F5F +} + +div.highlight .-Color[class*=-BGC23] { + background-color: #005F5F +} + +div.highlight .-Color[class*=-C24] { + color: #005F87 +} + +div.highlight .-Color[class*=-BGC24] { + background-color: #005F87 +} + +div.highlight .-Color[class*=-C25] { + color: #005FAF +} + +div.highlight .-Color[class*=-BGC25] { + background-color: #005FAF +} + +div.highlight .-Color[class*=-C26] { + color: #005FD7 +} + +div.highlight .-Color[class*=-BGC26] { + background-color: #005FD7 +} + +div.highlight .-Color[class*=-C27] { + color: #005FFF +} + +div.highlight .-Color[class*=-BGC27] { + background-color: #005FFF +} + +div.highlight .-Color[class*=-C28] { + color: #008700 +} + +div.highlight .-Color[class*=-BGC28] { + background-color: #008700 +} + +div.highlight .-Color[class*=-C29] { + color: #00875F +} + +div.highlight .-Color[class*=-BGC29] { + background-color: #00875F +} + +div.highlight .-Color[class*=-C30] { + color: #008787 +} + +div.highlight .-Color[class*=-BGC30] { + background-color: #008787 +} + +div.highlight .-Color[class*=-C31] { + color: #0087AF +} + +div.highlight .-Color[class*=-BGC31] { + background-color: #0087AF +} + +div.highlight .-Color[class*=-C32] { + color: #0087D7 +} + +div.highlight .-Color[class*=-BGC32] { + background-color: #0087D7 +} + +div.highlight .-Color[class*=-C33] { + color: #0087FF +} + +div.highlight .-Color[class*=-BGC33] { + background-color: #0087FF +} + +div.highlight .-Color[class*=-C34] { + color: #00AF00 +} + +div.highlight .-Color[class*=-BGC34] { + background-color: #00AF00 +} + +div.highlight .-Color[class*=-C35] { + color: #00AF5F +} + +div.highlight .-Color[class*=-BGC35] { + background-color: #00AF5F +} + +div.highlight .-Color[class*=-C36] { + color: #00AF87 +} + +div.highlight .-Color[class*=-BGC36] { + background-color: #00AF87 +} + +div.highlight .-Color[class*=-C37] { + color: #00AFAF +} + +div.highlight .-Color[class*=-BGC37] { + background-color: #00AFAF +} + +div.highlight .-Color[class*=-C38] { + color: #00AFD7 +} + +div.highlight .-Color[class*=-BGC38] { + background-color: #00AFD7 +} + +div.highlight .-Color[class*=-C39] { + color: #00AFFF +} + +div.highlight .-Color[class*=-BGC39] { + background-color: #00AFFF +} + +div.highlight .-Color[class*=-C40] { + color: #00D700 +} + +div.highlight .-Color[class*=-BGC40] { + background-color: #00D700 +} + +div.highlight .-Color[class*=-C41] { + color: #00D75F +} + +div.highlight .-Color[class*=-BGC41] { + background-color: #00D75F +} + +div.highlight .-Color[class*=-C42] { + color: #00D787 +} + +div.highlight .-Color[class*=-BGC42] { + background-color: #00D787 +} + +div.highlight .-Color[class*=-C43] { + color: #00D7AF +} + +div.highlight .-Color[class*=-BGC43] { + background-color: #00D7AF +} + +div.highlight .-Color[class*=-C44] { + color: #00D7D7 +} + +div.highlight .-Color[class*=-BGC44] { + background-color: #00D7D7 +} + +div.highlight .-Color[class*=-C45] { + color: #00D7FF +} + +div.highlight .-Color[class*=-BGC45] { + background-color: #00D7FF +} + +div.highlight .-Color[class*=-C46] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC46] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C47] { + color: #00FF5F +} + +div.highlight .-Color[class*=-BGC47] { + background-color: #00FF5F +} + +div.highlight .-Color[class*=-C48] { + color: #00FF87 +} + +div.highlight .-Color[class*=-BGC48] { + background-color: #00FF87 +} + +div.highlight .-Color[class*=-C49] { + color: #00FFAF +} + +div.highlight .-Color[class*=-BGC49] { + background-color: #00FFAF +} + +div.highlight .-Color[class*=-C50] { + color: #00FFD7 +} + +div.highlight .-Color[class*=-BGC50] { + background-color: #00FFD7 +} + +div.highlight .-Color[class*=-C51] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC51] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C52] { + color: #5F0000 +} + +div.highlight .-Color[class*=-BGC52] { + background-color: #5F0000 +} + +div.highlight .-Color[class*=-C53] { + color: #5F005F +} + +div.highlight .-Color[class*=-BGC53] { + background-color: #5F005F +} + +div.highlight .-Color[class*=-C54] { + color: #5F0087 +} + +div.highlight .-Color[class*=-BGC54] { + background-color: #5F0087 +} + +div.highlight .-Color[class*=-C55] { + color: #5F00AF +} + +div.highlight .-Color[class*=-BGC55] { + background-color: #5F00AF +} + +div.highlight .-Color[class*=-C56] { + color: #5F00D7 +} + +div.highlight .-Color[class*=-BGC56] { + background-color: #5F00D7 +} + +div.highlight .-Color[class*=-C57] { + color: #5F00FF +} + +div.highlight .-Color[class*=-BGC57] { + background-color: #5F00FF +} + +div.highlight .-Color[class*=-C58] { + color: #5F5F00 +} + +div.highlight .-Color[class*=-BGC58] { + background-color: #5F5F00 +} + +div.highlight .-Color[class*=-C59] { + color: #5F5F5F +} + +div.highlight .-Color[class*=-BGC59] { + background-color: #5F5F5F +} + +div.highlight .-Color[class*=-C60] { + color: #5F5F87 +} + +div.highlight .-Color[class*=-BGC60] { + background-color: #5F5F87 +} + +div.highlight .-Color[class*=-C61] { + color: #5F5FAF +} + +div.highlight .-Color[class*=-BGC61] { + background-color: #5F5FAF +} + +div.highlight .-Color[class*=-C62] { + color: #5F5FD7 +} + +div.highlight .-Color[class*=-BGC62] { + background-color: #5F5FD7 +} + +div.highlight .-Color[class*=-C63] { + color: #5F5FFF +} + +div.highlight .-Color[class*=-BGC63] { + background-color: #5F5FFF +} + +div.highlight .-Color[class*=-C64] { + color: #5F8700 +} + +div.highlight .-Color[class*=-BGC64] { + background-color: #5F8700 +} + +div.highlight .-Color[class*=-C65] { + color: #5F875F +} + +div.highlight .-Color[class*=-BGC65] { + background-color: #5F875F +} + +div.highlight .-Color[class*=-C66] { + color: #5F8787 +} + +div.highlight .-Color[class*=-BGC66] { + background-color: #5F8787 +} + +div.highlight .-Color[class*=-C67] { + color: #5F87AF +} + +div.highlight .-Color[class*=-BGC67] { + background-color: #5F87AF +} + +div.highlight .-Color[class*=-C68] { + color: #5F87D7 +} + +div.highlight .-Color[class*=-BGC68] { + background-color: #5F87D7 +} + +div.highlight .-Color[class*=-C69] { + color: #5F87FF +} + +div.highlight .-Color[class*=-BGC69] { + background-color: #5F87FF +} + +div.highlight .-Color[class*=-C70] { + color: #5FAF00 +} + +div.highlight .-Color[class*=-BGC70] { + background-color: #5FAF00 +} + +div.highlight .-Color[class*=-C71] { + color: #5FAF5F +} + +div.highlight .-Color[class*=-BGC71] { + background-color: #5FAF5F +} + +div.highlight .-Color[class*=-C72] { + color: #5FAF87 +} + +div.highlight .-Color[class*=-BGC72] { + background-color: #5FAF87 +} + +div.highlight .-Color[class*=-C73] { + color: #5FAFAF +} + +div.highlight .-Color[class*=-BGC73] { + background-color: #5FAFAF +} + +div.highlight .-Color[class*=-C74] { + color: #5FAFD7 +} + +div.highlight .-Color[class*=-BGC74] { + background-color: #5FAFD7 +} + +div.highlight .-Color[class*=-C75] { + color: #5FAFFF +} + +div.highlight .-Color[class*=-BGC75] { + background-color: #5FAFFF +} + +div.highlight .-Color[class*=-C76] { + color: #5FD700 +} + +div.highlight .-Color[class*=-BGC76] { + background-color: #5FD700 +} + +div.highlight .-Color[class*=-C77] { + color: #5FD75F +} + +div.highlight .-Color[class*=-BGC77] { + background-color: #5FD75F +} + +div.highlight .-Color[class*=-C78] { + color: #5FD787 +} + +div.highlight .-Color[class*=-BGC78] { + background-color: #5FD787 +} + +div.highlight .-Color[class*=-C79] { + color: #5FD7AF +} + +div.highlight .-Color[class*=-BGC79] { + background-color: #5FD7AF +} + +div.highlight .-Color[class*=-C80] { + color: #5FD7D7 +} + +div.highlight .-Color[class*=-BGC80] { + background-color: #5FD7D7 +} + +div.highlight .-Color[class*=-C81] { + color: #5FD7FF +} + +div.highlight .-Color[class*=-BGC81] { + background-color: #5FD7FF +} + +div.highlight .-Color[class*=-C82] { + color: #5FFF00 +} + +div.highlight .-Color[class*=-BGC82] { + background-color: #5FFF00 +} + +div.highlight .-Color[class*=-C83] { + color: #5FFF5F +} + +div.highlight .-Color[class*=-BGC83] { + background-color: #5FFF5F +} + +div.highlight .-Color[class*=-C84] { + color: #5FFF87 +} + +div.highlight .-Color[class*=-BGC84] { + background-color: #5FFF87 +} + +div.highlight .-Color[class*=-C85] { + color: #5FFFAF +} + +div.highlight .-Color[class*=-BGC85] { + background-color: #5FFFAF +} + +div.highlight .-Color[class*=-C86] { + color: #5FFFD7 +} + +div.highlight .-Color[class*=-BGC86] { + background-color: #5FFFD7 +} + +div.highlight .-Color[class*=-C87] { + color: #5FFFFF +} + +div.highlight .-Color[class*=-BGC87] { + background-color: #5FFFFF +} + +div.highlight .-Color[class*=-C88] { + color: #870000 +} + +div.highlight .-Color[class*=-BGC88] { + background-color: #870000 +} + +div.highlight .-Color[class*=-C89] { + color: #87005F +} + +div.highlight .-Color[class*=-BGC89] { + background-color: #87005F +} + +div.highlight .-Color[class*=-C90] { + color: #870087 +} + +div.highlight .-Color[class*=-BGC90] { + background-color: #870087 +} + +div.highlight .-Color[class*=-C91] { + color: #8700AF +} + +div.highlight .-Color[class*=-BGC91] { + background-color: #8700AF +} + +div.highlight .-Color[class*=-C92] { + color: #8700D7 +} + +div.highlight .-Color[class*=-BGC92] { + background-color: #8700D7 +} + +div.highlight .-Color[class*=-C93] { + color: #8700FF +} + +div.highlight .-Color[class*=-BGC93] { + background-color: #8700FF +} + +div.highlight .-Color[class*=-C94] { + color: #875F00 +} + +div.highlight .-Color[class*=-BGC94] { + background-color: #875F00 +} + +div.highlight .-Color[class*=-C95] { + color: #875F5F +} + +div.highlight .-Color[class*=-BGC95] { + background-color: #875F5F +} + +div.highlight .-Color[class*=-C96] { + color: #875F87 +} + +div.highlight .-Color[class*=-BGC96] { + background-color: #875F87 +} + +div.highlight .-Color[class*=-C97] { + color: #875FAF +} + +div.highlight .-Color[class*=-BGC97] { + background-color: #875FAF +} + +div.highlight .-Color[class*=-C98] { + color: #875FD7 +} + +div.highlight .-Color[class*=-BGC98] { + background-color: #875FD7 +} + +div.highlight .-Color[class*=-C99] { + color: #875FFF +} + +div.highlight .-Color[class*=-BGC99] { + background-color: #875FFF +} + +div.highlight .-Color[class*=-C100] { + color: #878700 +} + +div.highlight .-Color[class*=-BGC100] { + background-color: #878700 +} + +div.highlight .-Color[class*=-C101] { + color: #87875F +} + +div.highlight .-Color[class*=-BGC101] { + background-color: #87875F +} + +div.highlight .-Color[class*=-C102] { + color: #878787 +} + +div.highlight .-Color[class*=-BGC102] { + background-color: #878787 +} + +div.highlight .-Color[class*=-C103] { + color: #8787AF +} + +div.highlight .-Color[class*=-BGC103] { + background-color: #8787AF +} + +div.highlight .-Color[class*=-C104] { + color: #8787D7 +} + +div.highlight .-Color[class*=-BGC104] { + background-color: #8787D7 +} + +div.highlight .-Color[class*=-C105] { + color: #8787FF +} + +div.highlight .-Color[class*=-BGC105] { + background-color: #8787FF +} + +div.highlight .-Color[class*=-C106] { + color: #87AF00 +} + +div.highlight .-Color[class*=-BGC106] { + background-color: #87AF00 +} + +div.highlight .-Color[class*=-C107] { + color: #87AF5F +} + +div.highlight .-Color[class*=-BGC107] { + background-color: #87AF5F +} + +div.highlight .-Color[class*=-C108] { + color: #87AF87 +} + +div.highlight .-Color[class*=-BGC108] { + background-color: #87AF87 +} + +div.highlight .-Color[class*=-C109] { + color: #87AFAF +} + +div.highlight .-Color[class*=-BGC109] { + background-color: #87AFAF +} + +div.highlight .-Color[class*=-C110] { + color: #87AFD7 +} + +div.highlight .-Color[class*=-BGC110] { + background-color: #87AFD7 +} + +div.highlight .-Color[class*=-C111] { + color: #87AFFF +} + +div.highlight .-Color[class*=-BGC111] { + background-color: #87AFFF +} + +div.highlight .-Color[class*=-C112] { + color: #87D700 +} + +div.highlight .-Color[class*=-BGC112] { + background-color: #87D700 +} + +div.highlight .-Color[class*=-C113] { + color: #87D75F +} + +div.highlight .-Color[class*=-BGC113] { + background-color: #87D75F +} + +div.highlight .-Color[class*=-C114] { + color: #87D787 +} + +div.highlight .-Color[class*=-BGC114] { + background-color: #87D787 +} + +div.highlight .-Color[class*=-C115] { + color: #87D7AF +} + +div.highlight .-Color[class*=-BGC115] { + background-color: #87D7AF +} + +div.highlight .-Color[class*=-C116] { + color: #87D7D7 +} + +div.highlight .-Color[class*=-BGC116] { + background-color: #87D7D7 +} + +div.highlight .-Color[class*=-C117] { + color: #87D7FF +} + +div.highlight .-Color[class*=-BGC117] { + background-color: #87D7FF +} + +div.highlight .-Color[class*=-C118] { + color: #87FF00 +} + +div.highlight .-Color[class*=-BGC118] { + background-color: #87FF00 +} + +div.highlight .-Color[class*=-C119] { + color: #87FF5F +} + +div.highlight .-Color[class*=-BGC119] { + background-color: #87FF5F +} + +div.highlight .-Color[class*=-C120] { + color: #87FF87 +} + +div.highlight .-Color[class*=-BGC120] { + background-color: #87FF87 +} + +div.highlight .-Color[class*=-C121] { + color: #87FFAF +} + +div.highlight .-Color[class*=-BGC121] { + background-color: #87FFAF +} + +div.highlight .-Color[class*=-C122] { + color: #87FFD7 +} + +div.highlight .-Color[class*=-BGC122] { + background-color: #87FFD7 +} + +div.highlight .-Color[class*=-C123] { + color: #87FFFF +} + +div.highlight .-Color[class*=-BGC123] { + background-color: #87FFFF +} + +div.highlight .-Color[class*=-C124] { + color: #AF0000 +} + +div.highlight .-Color[class*=-BGC124] { + background-color: #AF0000 +} + +div.highlight .-Color[class*=-C125] { + color: #AF005F +} + +div.highlight .-Color[class*=-BGC125] { + background-color: #AF005F +} + +div.highlight .-Color[class*=-C126] { + color: #AF0087 +} + +div.highlight .-Color[class*=-BGC126] { + background-color: #AF0087 +} + +div.highlight .-Color[class*=-C127] { + color: #AF00AF +} + +div.highlight .-Color[class*=-BGC127] { + background-color: #AF00AF +} + +div.highlight .-Color[class*=-C128] { + color: #AF00D7 +} + +div.highlight .-Color[class*=-BGC128] { + background-color: #AF00D7 +} + +div.highlight .-Color[class*=-C129] { + color: #AF00FF +} + +div.highlight .-Color[class*=-BGC129] { + background-color: #AF00FF +} + +div.highlight .-Color[class*=-C130] { + color: #AF5F00 +} + +div.highlight .-Color[class*=-BGC130] { + background-color: #AF5F00 +} + +div.highlight .-Color[class*=-C131] { + color: #AF5F5F +} + +div.highlight .-Color[class*=-BGC131] { + background-color: #AF5F5F +} + +div.highlight .-Color[class*=-C132] { + color: #AF5F87 +} + +div.highlight .-Color[class*=-BGC132] { + background-color: #AF5F87 +} + +div.highlight .-Color[class*=-C133] { + color: #AF5FAF +} + +div.highlight .-Color[class*=-BGC133] { + background-color: #AF5FAF +} + +div.highlight .-Color[class*=-C134] { + color: #AF5FD7 +} + +div.highlight .-Color[class*=-BGC134] { + background-color: #AF5FD7 +} + +div.highlight .-Color[class*=-C135] { + color: #AF5FFF +} + +div.highlight .-Color[class*=-BGC135] { + background-color: #AF5FFF +} + +div.highlight .-Color[class*=-C136] { + color: #AF8700 +} + +div.highlight .-Color[class*=-BGC136] { + background-color: #AF8700 +} + +div.highlight .-Color[class*=-C137] { + color: #AF875F +} + +div.highlight .-Color[class*=-BGC137] { + background-color: #AF875F +} + +div.highlight .-Color[class*=-C138] { + color: #AF8787 +} + +div.highlight .-Color[class*=-BGC138] { + background-color: #AF8787 +} + +div.highlight .-Color[class*=-C139] { + color: #AF87AF +} + +div.highlight .-Color[class*=-BGC139] { + background-color: #AF87AF +} + +div.highlight .-Color[class*=-C140] { + color: #AF87D7 +} + +div.highlight .-Color[class*=-BGC140] { + background-color: #AF87D7 +} + +div.highlight .-Color[class*=-C141] { + color: #AF87FF +} + +div.highlight .-Color[class*=-BGC141] { + background-color: #AF87FF +} + +div.highlight .-Color[class*=-C142] { + color: #AFAF00 +} + +div.highlight .-Color[class*=-BGC142] { + background-color: #AFAF00 +} + +div.highlight .-Color[class*=-C143] { + color: #AFAF5F +} + +div.highlight .-Color[class*=-BGC143] { + background-color: #AFAF5F +} + +div.highlight .-Color[class*=-C144] { + color: #AFAF87 +} + +div.highlight .-Color[class*=-BGC144] { + background-color: #AFAF87 +} + +div.highlight .-Color[class*=-C145] { + color: #AFAFAF +} + +div.highlight .-Color[class*=-BGC145] { + background-color: #AFAFAF +} + +div.highlight .-Color[class*=-C146] { + color: #AFAFD7 +} + +div.highlight .-Color[class*=-BGC146] { + background-color: #AFAFD7 +} + +div.highlight .-Color[class*=-C147] { + color: #AFAFFF +} + +div.highlight .-Color[class*=-BGC147] { + background-color: #AFAFFF +} + +div.highlight .-Color[class*=-C148] { + color: #AFD700 +} + +div.highlight .-Color[class*=-BGC148] { + background-color: #AFD700 +} + +div.highlight .-Color[class*=-C149] { + color: #AFD75F +} + +div.highlight .-Color[class*=-BGC149] { + background-color: #AFD75F +} + +div.highlight .-Color[class*=-C150] { + color: #AFD787 +} + +div.highlight .-Color[class*=-BGC150] { + background-color: #AFD787 +} + +div.highlight .-Color[class*=-C151] { + color: #AFD7AF +} + +div.highlight .-Color[class*=-BGC151] { + background-color: #AFD7AF +} + +div.highlight .-Color[class*=-C152] { + color: #AFD7D7 +} + +div.highlight .-Color[class*=-BGC152] { + background-color: #AFD7D7 +} + +div.highlight .-Color[class*=-C153] { + color: #AFD7FF +} + +div.highlight .-Color[class*=-BGC153] { + background-color: #AFD7FF +} + +div.highlight .-Color[class*=-C154] { + color: #AFFF00 +} + +div.highlight .-Color[class*=-BGC154] { + background-color: #AFFF00 +} + +div.highlight .-Color[class*=-C155] { + color: #AFFF5F +} + +div.highlight .-Color[class*=-BGC155] { + background-color: #AFFF5F +} + +div.highlight .-Color[class*=-C156] { + color: #AFFF87 +} + +div.highlight .-Color[class*=-BGC156] { + background-color: #AFFF87 +} + +div.highlight .-Color[class*=-C157] { + color: #AFFFAF +} + +div.highlight .-Color[class*=-BGC157] { + background-color: #AFFFAF +} + +div.highlight .-Color[class*=-C158] { + color: #AFFFD7 +} + +div.highlight .-Color[class*=-BGC158] { + background-color: #AFFFD7 +} + +div.highlight .-Color[class*=-C159] { + color: #AFFFFF +} + +div.highlight .-Color[class*=-BGC159] { + background-color: #AFFFFF +} + +div.highlight .-Color[class*=-C160] { + color: #D70000 +} + +div.highlight .-Color[class*=-BGC160] { + background-color: #D70000 +} + +div.highlight .-Color[class*=-C161] { + color: #D7005F +} + +div.highlight .-Color[class*=-BGC161] { + background-color: #D7005F +} + +div.highlight .-Color[class*=-C162] { + color: #D70087 +} + +div.highlight .-Color[class*=-BGC162] { + background-color: #D70087 +} + +div.highlight .-Color[class*=-C163] { + color: #D700AF +} + +div.highlight .-Color[class*=-BGC163] { + background-color: #D700AF +} + +div.highlight .-Color[class*=-C164] { + color: #D700D7 +} + +div.highlight .-Color[class*=-BGC164] { + background-color: #D700D7 +} + +div.highlight .-Color[class*=-C165] { + color: #D700FF +} + +div.highlight .-Color[class*=-BGC165] { + background-color: #D700FF +} + +div.highlight .-Color[class*=-C166] { + color: #D75F00 +} + +div.highlight .-Color[class*=-BGC166] { + background-color: #D75F00 +} + +div.highlight .-Color[class*=-C167] { + color: #D75F5F +} + +div.highlight .-Color[class*=-BGC167] { + background-color: #D75F5F +} + +div.highlight .-Color[class*=-C168] { + color: #D75F87 +} + +div.highlight .-Color[class*=-BGC168] { + background-color: #D75F87 +} + +div.highlight .-Color[class*=-C169] { + color: #D75FAF +} + +div.highlight .-Color[class*=-BGC169] { + background-color: #D75FAF +} + +div.highlight .-Color[class*=-C170] { + color: #D75FD7 +} + +div.highlight .-Color[class*=-BGC170] { + background-color: #D75FD7 +} + +div.highlight .-Color[class*=-C171] { + color: #D75FFF +} + +div.highlight .-Color[class*=-BGC171] { + background-color: #D75FFF +} + +div.highlight .-Color[class*=-C172] { + color: #D78700 +} + +div.highlight .-Color[class*=-BGC172] { + background-color: #D78700 +} + +div.highlight .-Color[class*=-C173] { + color: #D7875F +} + +div.highlight .-Color[class*=-BGC173] { + background-color: #D7875F +} + +div.highlight .-Color[class*=-C174] { + color: #D78787 +} + +div.highlight .-Color[class*=-BGC174] { + background-color: #D78787 +} + +div.highlight .-Color[class*=-C175] { + color: #D787AF +} + +div.highlight .-Color[class*=-BGC175] { + background-color: #D787AF +} + +div.highlight .-Color[class*=-C176] { + color: #D787D7 +} + +div.highlight .-Color[class*=-BGC176] { + background-color: #D787D7 +} + +div.highlight .-Color[class*=-C177] { + color: #D787FF +} + +div.highlight .-Color[class*=-BGC177] { + background-color: #D787FF +} + +div.highlight .-Color[class*=-C178] { + color: #D7AF00 +} + +div.highlight .-Color[class*=-BGC178] { + background-color: #D7AF00 +} + +div.highlight .-Color[class*=-C179] { + color: #D7AF5F +} + +div.highlight .-Color[class*=-BGC179] { + background-color: #D7AF5F +} + +div.highlight .-Color[class*=-C180] { + color: #D7AF87 +} + +div.highlight .-Color[class*=-BGC180] { + background-color: #D7AF87 +} + +div.highlight .-Color[class*=-C181] { + color: #D7AFAF +} + +div.highlight .-Color[class*=-BGC181] { + background-color: #D7AFAF +} + +div.highlight .-Color[class*=-C182] { + color: #D7AFD7 +} + +div.highlight .-Color[class*=-BGC182] { + background-color: #D7AFD7 +} + +div.highlight .-Color[class*=-C183] { + color: #D7AFFF +} + +div.highlight .-Color[class*=-BGC183] { + background-color: #D7AFFF +} + +div.highlight .-Color[class*=-C184] { + color: #D7D700 +} + +div.highlight .-Color[class*=-BGC184] { + background-color: #D7D700 +} + +div.highlight .-Color[class*=-C185] { + color: #D7D75F +} + +div.highlight .-Color[class*=-BGC185] { + background-color: #D7D75F +} + +div.highlight .-Color[class*=-C186] { + color: #D7D787 +} + +div.highlight .-Color[class*=-BGC186] { + background-color: #D7D787 +} + +div.highlight .-Color[class*=-C187] { + color: #D7D7AF +} + +div.highlight .-Color[class*=-BGC187] { + background-color: #D7D7AF +} + +div.highlight .-Color[class*=-C188] { + color: #D7D7D7 +} + +div.highlight .-Color[class*=-BGC188] { + background-color: #D7D7D7 +} + +div.highlight .-Color[class*=-C189] { + color: #D7D7FF +} + +div.highlight .-Color[class*=-BGC189] { + background-color: #D7D7FF +} + +div.highlight .-Color[class*=-C190] { + color: #D7FF00 +} + +div.highlight .-Color[class*=-BGC190] { + background-color: #D7FF00 +} + +div.highlight .-Color[class*=-C191] { + color: #D7FF5F +} + +div.highlight .-Color[class*=-BGC191] { + background-color: #D7FF5F +} + +div.highlight .-Color[class*=-C192] { + color: #D7FF87 +} + +div.highlight .-Color[class*=-BGC192] { + background-color: #D7FF87 +} + +div.highlight .-Color[class*=-C193] { + color: #D7FFAF +} + +div.highlight .-Color[class*=-BGC193] { + background-color: #D7FFAF +} + +div.highlight .-Color[class*=-C194] { + color: #D7FFD7 +} + +div.highlight .-Color[class*=-BGC194] { + background-color: #D7FFD7 +} + +div.highlight .-Color[class*=-C195] { + color: #D7FFFF +} + +div.highlight .-Color[class*=-BGC195] { + background-color: #D7FFFF +} + +div.highlight .-Color[class*=-C196] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC196] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C197] { + color: #FF005F +} + +div.highlight .-Color[class*=-BGC197] { + background-color: #FF005F +} + +div.highlight .-Color[class*=-C198] { + color: #FF0087 +} + +div.highlight .-Color[class*=-BGC198] { + background-color: #FF0087 +} + +div.highlight .-Color[class*=-C199] { + color: #FF00AF +} + +div.highlight .-Color[class*=-BGC199] { + background-color: #FF00AF +} + +div.highlight .-Color[class*=-C200] { + color: #FF00D7 +} + +div.highlight .-Color[class*=-BGC200] { + background-color: #FF00D7 +} + +div.highlight .-Color[class*=-C201] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC201] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C202] { + color: #FF5F00 +} + +div.highlight .-Color[class*=-BGC202] { + background-color: #FF5F00 +} + +div.highlight .-Color[class*=-C203] { + color: #FF5F5F +} + +div.highlight .-Color[class*=-BGC203] { + background-color: #FF5F5F +} + +div.highlight .-Color[class*=-C204] { + color: #FF5F87 +} + +div.highlight .-Color[class*=-BGC204] { + background-color: #FF5F87 +} + +div.highlight .-Color[class*=-C205] { + color: #FF5FAF +} + +div.highlight .-Color[class*=-BGC205] { + background-color: #FF5FAF +} + +div.highlight .-Color[class*=-C206] { + color: #FF5FD7 +} + +div.highlight .-Color[class*=-BGC206] { + background-color: #FF5FD7 +} + +div.highlight .-Color[class*=-C207] { + color: #FF5FFF +} + +div.highlight .-Color[class*=-BGC207] { + background-color: #FF5FFF +} + +div.highlight .-Color[class*=-C208] { + color: #FF8700 +} + +div.highlight .-Color[class*=-BGC208] { + background-color: #FF8700 +} + +div.highlight .-Color[class*=-C209] { + color: #FF875F +} + +div.highlight .-Color[class*=-BGC209] { + background-color: #FF875F +} + +div.highlight .-Color[class*=-C210] { + color: #FF8787 +} + +div.highlight .-Color[class*=-BGC210] { + background-color: #FF8787 +} + +div.highlight .-Color[class*=-C211] { + color: #FF87AF +} + +div.highlight .-Color[class*=-BGC211] { + background-color: #FF87AF +} + +div.highlight .-Color[class*=-C212] { + color: #FF87D7 +} + +div.highlight .-Color[class*=-BGC212] { + background-color: #FF87D7 +} + +div.highlight .-Color[class*=-C213] { + color: #FF87FF +} + +div.highlight .-Color[class*=-BGC213] { + background-color: #FF87FF +} + +div.highlight .-Color[class*=-C214] { + color: #FFAF00 +} + +div.highlight .-Color[class*=-BGC214] { + background-color: #FFAF00 +} + +div.highlight .-Color[class*=-C215] { + color: #FFAF5F +} + +div.highlight .-Color[class*=-BGC215] { + background-color: #FFAF5F +} + +div.highlight .-Color[class*=-C216] { + color: #FFAF87 +} + +div.highlight .-Color[class*=-BGC216] { + background-color: #FFAF87 +} + +div.highlight .-Color[class*=-C217] { + color: #FFAFAF +} + +div.highlight .-Color[class*=-BGC217] { + background-color: #FFAFAF +} + +div.highlight .-Color[class*=-C218] { + color: #FFAFD7 +} + +div.highlight .-Color[class*=-BGC218] { + background-color: #FFAFD7 +} + +div.highlight .-Color[class*=-C219] { + color: #FFAFFF +} + +div.highlight .-Color[class*=-BGC219] { + background-color: #FFAFFF +} + +div.highlight .-Color[class*=-C220] { + color: #FFD700 +} + +div.highlight .-Color[class*=-BGC220] { + background-color: #FFD700 +} + +div.highlight .-Color[class*=-C221] { + color: #FFD75F +} + +div.highlight .-Color[class*=-BGC221] { + background-color: #FFD75F +} + +div.highlight .-Color[class*=-C222] { + color: #FFD787 +} + +div.highlight .-Color[class*=-BGC222] { + background-color: #FFD787 +} + +div.highlight .-Color[class*=-C223] { + color: #FFD7AF +} + +div.highlight .-Color[class*=-BGC223] { + background-color: #FFD7AF +} + +div.highlight .-Color[class*=-C224] { + color: #FFD7D7 +} + +div.highlight .-Color[class*=-BGC224] { + background-color: #FFD7D7 +} + +div.highlight .-Color[class*=-C225] { + color: #FFD7FF +} + +div.highlight .-Color[class*=-BGC225] { + background-color: #FFD7FF +} + +div.highlight .-Color[class*=-C226] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC226] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C227] { + color: #FFFF5F +} + +div.highlight .-Color[class*=-BGC227] { + background-color: #FFFF5F +} + +div.highlight .-Color[class*=-C228] { + color: #FFFF87 +} + +div.highlight .-Color[class*=-BGC228] { + background-color: #FFFF87 +} + +div.highlight .-Color[class*=-C229] { + color: #FFFFAF +} + +div.highlight .-Color[class*=-BGC229] { + background-color: #FFFFAF +} + +div.highlight .-Color[class*=-C230] { + color: #FFFFD7 +} + +div.highlight .-Color[class*=-BGC230] { + background-color: #FFFFD7 +} + +div.highlight .-Color[class*=-C231] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC231] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C232] { + color: #080808 +} + +div.highlight .-Color[class*=-BGC232] { + background-color: #080808 +} + +div.highlight .-Color[class*=-C233] { + color: #121212 +} + +div.highlight .-Color[class*=-BGC233] { + background-color: #121212 +} + +div.highlight .-Color[class*=-C234] { + color: #1C1C1C +} + +div.highlight .-Color[class*=-BGC234] { + background-color: #1C1C1C +} + +div.highlight .-Color[class*=-C235] { + color: #262626 +} + +div.highlight .-Color[class*=-BGC235] { + background-color: #262626 +} + +div.highlight .-Color[class*=-C236] { + color: #303030 +} + +div.highlight .-Color[class*=-BGC236] { + background-color: #303030 +} + +div.highlight .-Color[class*=-C237] { + color: #3A3A3A +} + +div.highlight .-Color[class*=-BGC237] { + background-color: #3A3A3A +} + +div.highlight .-Color[class*=-C238] { + color: #444444 +} + +div.highlight .-Color[class*=-BGC238] { + background-color: #444444 +} + +div.highlight .-Color[class*=-C239] { + color: #4E4E4E +} + +div.highlight .-Color[class*=-BGC239] { + background-color: #4E4E4E +} + +div.highlight .-Color[class*=-C240] { + color: #585858 +} + +div.highlight .-Color[class*=-BGC240] { + background-color: #585858 +} + +div.highlight .-Color[class*=-C241] { + color: #626262 +} + +div.highlight .-Color[class*=-BGC241] { + background-color: #626262 +} + +div.highlight .-Color[class*=-C242] { + color: #6C6C6C +} + +div.highlight .-Color[class*=-BGC242] { + background-color: #6C6C6C +} + +div.highlight .-Color[class*=-C243] { + color: #767676 +} + +div.highlight .-Color[class*=-BGC243] { + background-color: #767676 +} + +div.highlight .-Color[class*=-C244] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC244] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C245] { + color: #8A8A8A +} + +div.highlight .-Color[class*=-BGC245] { + background-color: #8A8A8A +} + +div.highlight .-Color[class*=-C246] { + color: #949494 +} + +div.highlight .-Color[class*=-BGC246] { + background-color: #949494 +} + +div.highlight .-Color[class*=-C247] { + color: #9E9E9E +} + +div.highlight .-Color[class*=-BGC247] { + background-color: #9E9E9E +} + +div.highlight .-Color[class*=-C248] { + color: #A8A8A8 +} + +div.highlight .-Color[class*=-BGC248] { + background-color: #A8A8A8 +} + +div.highlight .-Color[class*=-C249] { + color: #B2B2B2 +} + +div.highlight .-Color[class*=-BGC249] { + background-color: #B2B2B2 +} + +div.highlight .-Color[class*=-C250] { + color: #BCBCBC +} + +div.highlight .-Color[class*=-BGC250] { + background-color: #BCBCBC +} + +div.highlight .-Color[class*=-C251] { + color: #C6C6C6 +} + +div.highlight .-Color[class*=-BGC251] { + background-color: #C6C6C6 +} + +div.highlight .-Color[class*=-C252] { + color: #D0D0D0 +} + +div.highlight .-Color[class*=-BGC252] { + background-color: #D0D0D0 +} + +div.highlight .-Color[class*=-C253] { + color: #DADADA +} + +div.highlight .-Color[class*=-BGC253] { + background-color: #DADADA +} + +div.highlight .-Color[class*=-C254] { + color: #E4E4E4 +} + +div.highlight .-Color[class*=-BGC254] { + background-color: #E4E4E4 +} + +div.highlight .-Color[class*=-C255] { + color: #EEEEEE +} + +div.highlight .-Color[class*=-BGC255] { + background-color: #EEEEEE +} diff --git a/branch/main/singlehtml/_static/plus.png b/branch/main/singlehtml/_static/plus.png new file mode 100644 index 0000000..7107cec Binary files /dev/null and b/branch/main/singlehtml/_static/plus.png differ diff --git a/branch/main/singlehtml/_static/pygments.css b/branch/main/singlehtml/_static/pygments.css new file mode 100644 index 0000000..84ab303 --- /dev/null +++ b/branch/main/singlehtml/_static/pygments.css @@ -0,0 +1,75 @@ +pre { line-height: 125%; } +td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +.highlight .hll { background-color: #ffffcc } +.highlight { background: #f8f8f8; } +.highlight .c { color: #3D7B7B; font-style: italic } /* Comment */ +.highlight .err { border: 1px solid #FF0000 } /* Error */ +.highlight .k { color: #008000; font-weight: bold } /* Keyword */ +.highlight .o { color: #666666 } /* Operator */ +.highlight .ch { color: #3D7B7B; font-style: italic } /* Comment.Hashbang */ +.highlight .cm { color: #3D7B7B; font-style: italic } /* Comment.Multiline */ +.highlight .cp { color: #9C6500 } /* Comment.Preproc */ +.highlight .cpf { color: #3D7B7B; font-style: italic } /* Comment.PreprocFile */ +.highlight .c1 { color: #3D7B7B; font-style: italic } /* Comment.Single */ +.highlight .cs { color: #3D7B7B; font-style: italic } /* Comment.Special */ +.highlight .gd { color: #A00000 } /* Generic.Deleted */ +.highlight .ge { font-style: italic } /* Generic.Emph */ +.highlight .ges { font-weight: bold; font-style: italic } /* Generic.EmphStrong */ 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+.highlight .s1 { color: #BA2121 } /* Literal.String.Single */ +.highlight .ss { color: #19177C } /* Literal.String.Symbol */ +.highlight .bp { color: #008000 } /* Name.Builtin.Pseudo */ +.highlight .fm { color: #0000FF } /* Name.Function.Magic */ +.highlight .vc { color: #19177C } /* Name.Variable.Class */ +.highlight .vg { color: #19177C } /* Name.Variable.Global */ +.highlight .vi { color: #19177C } /* Name.Variable.Instance */ +.highlight .vm { color: #19177C } /* Name.Variable.Magic */ +.highlight .il { color: #666666 } /* Literal.Number.Integer.Long */ \ No newline at end of file diff --git a/branch/main/singlehtml/_static/searchtools.js b/branch/main/singlehtml/_static/searchtools.js new file mode 100644 index 0000000..b08d58c --- /dev/null +++ b/branch/main/singlehtml/_static/searchtools.js @@ -0,0 +1,620 @@ +/* + * searchtools.js + * ~~~~~~~~~~~~~~~~ + * + * Sphinx JavaScript utilities for the full-text search. + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ +"use strict"; + +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms, anchor) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + "Search finished, found ${resultCount} page(s) matching the search query." + ).replace('${resultCount}', resultCount); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString, anchor) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + for (const removalQuery of [".headerlink", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent) return docContent.textContent; + + console.warn( + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + _parseQuery: (query) => { + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename]. + const normalResults = []; + const nonMainIndexResults = []; + + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase().trim(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + const score = Math.round(Scorer.title * queryLower.length / title.length); + const boost = titles[file] === title ? 1 : 0; // add a boost for document titles + normalResults.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score + boost, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } + } + } + } + + // lookup as object + objectTerms.forEach((term) => + normalResults.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/branch/main/singlehtml/_static/sphinx_highlight.js b/branch/main/singlehtml/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/branch/main/singlehtml/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/branch/main/singlehtml/_static/sphinx_lesson.css b/branch/main/singlehtml/_static/sphinx_lesson.css new file mode 100644 index 0000000..14b20c6 --- /dev/null +++ b/branch/main/singlehtml/_static/sphinx_lesson.css @@ -0,0 +1,51 @@ +/* sphinx_lesson.css */ + +body.wy-body-for-nav img.with-border { + border: 2px solid; +} + +.rst-content .admonition-no-content { + padding-bottom: 0px; +} + +.rst-content .demo > .admonition-title::before { + content: "\01F440"; /* Eyes */ } +.rst-content .type-along > .admonition-title::before { + content: "\02328\0FE0F"; /* Keyboard */ } +.rst-content .exercise > .admonition-title::before { + content: "\0270D\0FE0F"; /* Hand */ } +.rst-content .solution > .admonition-title::before { + content: "\02714\0FE0E"; /* Check mark */ } +.rst-content .homework > .admonition-title::before { + content: "\01F4DD"; /* Memo */ } +.rst-content .discussion > .admonition-title::before { + content: "\01F4AC"; /* Speech balloon */ } +.rst-content .questions > .admonition-title::before { + content: "\02753\0FE0E"; /* Question mark */ } +.rst-content .prerequisites > .admonition-title::before { + content: "\02699"; /* Gear */ } +.rst-content .seealso > .admonition-title::before { + content: "\027A1\0FE0E"; /* Question mark */ } + + +/* instructor-note */ +.rst-content .instructor-note { + background: #e7e7e7; +} +.rst-content .instructor-note > .admonition-title { + background: #6a6a6a; +} +.rst-content .instructor-note > .admonition-title::before { + content: ""; +} + + +/* sphinx_toggle_button, make the font white */ +.rst-content .toggle.admonition button.toggle-button { + color: white; +} + +/* sphinx-togglebutton, remove underflow when toggled to hidden mode */ +.rst-content .admonition.toggle-hidden { + padding-bottom: 0px; +} diff --git a/branch/main/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css b/branch/main/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css new file mode 100644 index 0000000..e68feb8 --- /dev/null +++ b/branch/main/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css @@ -0,0 +1,47 @@ +/* The following are for web accessibility of sphinx_rtd_theme: they + * solve some of the most frequent contrast issues. Remove when this + * solved: + * https://github.com/readthedocs/sphinx_rtd_theme/issues/971 + */ +/* background: #fcfcfc, note boxes #E7F2FA */ +a { color: #2573A7; } /* original #2980B9, #1F5C84; */ +body { color: #242424; } /* original #404040, #383838 */ +.wy-side-nav-search>a, .wy-side-nav-search .wy-dropdown>a { + color: #ffffff; +} /* original #fcfcfc */ +footer { color: #737373; } /* original gray=#808080*/ +footer span.commit code, footer span.commit .rst-content tt, .rst-content footer span.commit tt { + color: #737373; +} /* original gray=#808080*/ +.rst-content tt.literal, .rst-content tt.literal, .rst-content code.literal { + color: #AB2314; +} +/* Sidebar background */ +.wy-side-nav-search { background-color: #277CB4;} + +/* Same, but for pygments */ +.highlight .ch { color: #3E7A89; } /* #! line */ +.highlight .c1 { color: #3E7A89; } /* also comments */ +.highlight .nv { color: #AD3ECC; } /* variable */ +.highlight .gp { color: #B45608; } /* prompt character, $*/ +.highlight .si { color: #3975B1; } /* ${} variable text */ +.highlight .nc { color: #0C78A7; } + +/* Sphinx admonitions */ +/* warning */ +.wy-alert.wy-alert-warning .wy-alert-title, .rst-content .wy-alert-warning.note .wy-alert-title, .rst-content .attention .wy-alert-title, .rst-content .caution .wy-alert-title, .rst-content .wy-alert-warning.danger .wy-alert-title, .rst-content .wy-alert-warning.error .wy-alert-title, .rst-content .wy-alert-warning.hint .wy-alert-title, .rst-content .wy-alert-warning.important .wy-alert-title, .rst-content .wy-alert-warning.tip .wy-alert-title, .rst-content .warning .wy-alert-title, .rst-content .wy-alert-warning.seealso .wy-alert-title, .rst-content .admonition-todo .wy-alert-title, .rst-content .wy-alert-warning.admonition .wy-alert-title, .wy-alert.wy-alert-warning .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-warning .admonition-title, .rst-content .wy-alert-warning.note .admonition-title, .rst-content .attention .admonition-title, .rst-content .caution .admonition-title, .rst-content .wy-alert-warning.danger .admonition-title, .rst-content .wy-alert-warning.error .admonition-title, .rst-content .wy-alert-warning.hint .admonition-title, .rst-content .wy-alert-warning.important .admonition-title, .rst-content .wy-alert-warning.tip .admonition-title, .rst-content .warning .admonition-title, .rst-content .wy-alert-warning.seealso .admonition-title, .rst-content .admonition-todo .admonition-title, .rst-content .wy-alert-warning.admonition .admonition-title { + background: #B15E16; } +/* important */ +.wy-alert.wy-alert-success .wy-alert-title, .rst-content .wy-alert-success.note .wy-alert-title, .rst-content .wy-alert-success.attention .wy-alert-title, .rst-content .wy-alert-success.caution .wy-alert-title, .rst-content .wy-alert-success.danger .wy-alert-title, .rst-content .wy-alert-success.error .wy-alert-title, .rst-content .hint .wy-alert-title, .rst-content .important .wy-alert-title, .rst-content .tip .wy-alert-title, .rst-content .wy-alert-success.warning .wy-alert-title, .rst-content .wy-alert-success.seealso .wy-alert-title, .rst-content .wy-alert-success.admonition-todo .wy-alert-title, .rst-content .wy-alert-success.admonition .wy-alert-title, .wy-alert.wy-alert-success .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-success .admonition-title, .rst-content .wy-alert-success.note .admonition-title, .rst-content .wy-alert-success.attention .admonition-title, .rst-content .wy-alert-success.caution .admonition-title, .rst-content .wy-alert-success.danger .admonition-title, .rst-content .wy-alert-success.error .admonition-title, .rst-content .hint .admonition-title, .rst-content .important .admonition-title, .rst-content .tip .admonition-title, .rst-content .wy-alert-success.warning .admonition-title, .rst-content .wy-alert-success.seealso .admonition-title, .rst-content .wy-alert-success.admonition-todo .admonition-title, .rst-content .wy-alert-success.admonition .admonition-title { + background: #12826C; } +/* seealso, note, etc */ +.wy-alert.wy-alert-info .wy-alert-title, .rst-content .note .wy-alert-title, .rst-content .wy-alert-info.attention .wy-alert-title, .rst-content .wy-alert-info.caution .wy-alert-title, .rst-content .wy-alert-info.danger .wy-alert-title, .rst-content .wy-alert-info.error .wy-alert-title, .rst-content .wy-alert-info.hint .wy-alert-title, .rst-content .wy-alert-info.important .wy-alert-title, .rst-content .wy-alert-info.tip .wy-alert-title, .rst-content .wy-alert-info.warning .wy-alert-title, .rst-content .seealso .wy-alert-title, .rst-content .wy-alert-info.admonition-todo .wy-alert-title, .rst-content .wy-alert-info.admonition .wy-alert-title, .wy-alert.wy-alert-info .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-info .admonition-title, .rst-content .note .admonition-title, .rst-content .wy-alert-info.attention .admonition-title, .rst-content .wy-alert-info.caution .admonition-title, .rst-content .wy-alert-info.danger .admonition-title, .rst-content .wy-alert-info.error .admonition-title, .rst-content .wy-alert-info.hint .admonition-title, .rst-content .wy-alert-info.important .admonition-title, .rst-content .wy-alert-info.tip .admonition-title, .rst-content .wy-alert-info.warning .admonition-title, .rst-content .seealso .admonition-title, .rst-content .wy-alert-info.admonition-todo .admonition-title, .rst-content .wy-alert-info.admonition .admonition-title { + background: #277CB4; } +/* error, danger */ +.rst-content .danger .admonition-title, .rst-content .danger .wy-alert-title, .rst-content .error .admonition-title, .rst-content .error .wy-alert-title, .rst-content .wy-alert-danger.admonition-todo .admonition-title, .rst-content .wy-alert-danger.admonition-todo .wy-alert-title, .rst-content .wy-alert-danger.admonition .admonition-title, .rst-content .wy-alert-danger.admonition .wy-alert-title, .rst-content .wy-alert-danger.attention .admonition-title, .rst-content .wy-alert-danger.attention .wy-alert-title, .rst-content .wy-alert-danger.caution .admonition-title, .rst-content .wy-alert-danger.caution .wy-alert-title, .rst-content .wy-alert-danger.hint .admonition-title, .rst-content .wy-alert-danger.hint .wy-alert-title, .rst-content .wy-alert-danger.important .admonition-title, .rst-content .wy-alert-danger.important .wy-alert-title, .rst-content .wy-alert-danger.note .admonition-title, .rst-content .wy-alert-danger.note .wy-alert-title, .rst-content .wy-alert-danger.seealso .admonition-title, .rst-content .wy-alert-danger.seealso .wy-alert-title, .rst-content .wy-alert-danger.tip .admonition-title, .rst-content .wy-alert-danger.tip .wy-alert-title, .rst-content .wy-alert-danger.warning .admonition-title, .rst-content .wy-alert-danger.warning .wy-alert-title, .rst-content .wy-alert.wy-alert-danger .admonition-title, .wy-alert.wy-alert-danger .rst-content .admonition-title, .wy-alert.wy-alert-danger .wy-alert-title { + background: #e31704; +} + +/* Generic admonition titles */ +.wy-alert-title, .rst-content .admonition-title { + background: #277CB4; } diff --git a/branch/main/singlehtml/_static/style.css b/branch/main/singlehtml/_static/style.css new file mode 100644 index 0000000..59e60ee --- /dev/null +++ b/branch/main/singlehtml/_static/style.css @@ -0,0 +1,6 @@ +.rst-content .objectives { + background: #fee0d2; +} +.rst-content .objectives > .admonition-title { + background: #fc9272; +} diff --git a/branch/main/singlehtml/_static/tabs.css b/branch/main/singlehtml/_static/tabs.css new file mode 100644 index 0000000..957ba60 --- /dev/null +++ b/branch/main/singlehtml/_static/tabs.css @@ -0,0 +1,89 @@ +.sphinx-tabs { + margin-bottom: 1rem; +} + +[role="tablist"] { + border-bottom: 1px solid #a0b3bf; +} + +.sphinx-tabs-tab { + position: relative; + font-family: Lato,'Helvetica Neue',Arial,Helvetica,sans-serif; + color: #1D5C87; + line-height: 24px; + margin: 0; + font-size: 16px; + font-weight: 400; + background-color: rgba(255, 255, 255, 0); + border-radius: 5px 5px 0 0; + border: 0; + padding: 1rem 1.5rem; + margin-bottom: 0; +} + +.sphinx-tabs-tab[aria-selected="true"] { + font-weight: 700; + border: 1px solid #a0b3bf; + border-bottom: 1px solid white; + margin: -1px; + background-color: white; +} + +.sphinx-tabs-tab:focus { + z-index: 1; + outline-offset: 1px; +} + +.sphinx-tabs-panel { + position: relative; + padding: 1rem; + border: 1px solid #a0b3bf; + margin: 0px -1px -1px -1px; + border-radius: 0 0 5px 5px; + border-top: 0; + background: white; +} + +.sphinx-tabs-panel.code-tab { + padding: 0.4rem; +} + +.sphinx-tab img { + margin-bottom: 24 px; +} + +/* Dark theme preference styling */ + +@media (prefers-color-scheme: dark) { + body[data-theme="auto"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); + } + + body[data-theme="auto"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); + } + + body[data-theme="auto"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 1px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); + } +} + +/* Explicit dark theme styling */ + +body[data-theme="dark"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); +} + +body[data-theme="dark"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); +} + +body[data-theme="dark"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 2px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); +} diff --git a/branch/main/singlehtml/_static/tabs.js b/branch/main/singlehtml/_static/tabs.js new file mode 100644 index 0000000..48dc303 --- /dev/null +++ b/branch/main/singlehtml/_static/tabs.js @@ -0,0 +1,145 @@ +try { + var session = window.sessionStorage || {}; +} catch (e) { + var session = {}; +} + +window.addEventListener("DOMContentLoaded", () => { + const allTabs = document.querySelectorAll('.sphinx-tabs-tab'); + const tabLists = document.querySelectorAll('[role="tablist"]'); + + allTabs.forEach(tab => { + tab.addEventListener("click", changeTabs); + }); + + tabLists.forEach(tabList => { + tabList.addEventListener("keydown", keyTabs); + }); + + // Restore group tab selection from session + const lastSelected = session.getItem('sphinx-tabs-last-selected'); + if (lastSelected != null) selectNamedTabs(lastSelected); +}); + +/** + * Key focus left and right between sibling elements using arrows + * @param {Node} e the element in focus when key was pressed + */ +function keyTabs(e) { + const tab = e.target; + let nextTab = null; + if (e.keyCode === 39 || e.keyCode === 37) { + tab.setAttribute("tabindex", -1); + // Move right + if (e.keyCode === 39) { + nextTab = tab.nextElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.firstElementChild; + } + // Move left + } else if (e.keyCode === 37) { + nextTab = tab.previousElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.lastElementChild; + } + } + } + + if (nextTab !== null) { + nextTab.setAttribute("tabindex", 0); + nextTab.focus(); + } +} + +/** + * Select or deselect clicked tab. If a group tab + * is selected, also select tab in other tabLists. + * @param {Node} e the element that was clicked + */ +function changeTabs(e) { + // Use this instead of the element that was clicked, in case it's a child + const notSelected = this.getAttribute("aria-selected") === "false"; + const positionBefore = this.parentNode.getBoundingClientRect().top; + const notClosable = !this.parentNode.classList.contains("closeable"); + + deselectTabList(this); + + if (notSelected || notClosable) { + selectTab(this); + const name = this.getAttribute("name"); + selectNamedTabs(name, this.id); + + if (this.classList.contains("group-tab")) { + // Persist during session + session.setItem('sphinx-tabs-last-selected', name); + } + } + + const positionAfter = this.parentNode.getBoundingClientRect().top; + const positionDelta = positionAfter - positionBefore; + // Scroll to offset content resizing + window.scrollTo(0, window.scrollY + positionDelta); +} + +/** + * Select tab and show associated panel. + * @param {Node} tab tab to select + */ +function selectTab(tab) { + tab.setAttribute("aria-selected", true); + + // Show the associated panel + document + .getElementById(tab.getAttribute("aria-controls")) + .removeAttribute("hidden"); +} + +/** + * Hide the panels associated with all tabs within the + * tablist containing this tab. + * @param {Node} tab a tab within the tablist to deselect + */ +function deselectTabList(tab) { + const parent = tab.parentNode; + const grandparent = parent.parentNode; + + Array.from(parent.children) + .forEach(t => t.setAttribute("aria-selected", false)); + + Array.from(grandparent.children) + .slice(1) // Skip tablist + .forEach(panel => panel.setAttribute("hidden", true)); +} + +/** + * Select grouped tabs with the same name, but no the tab + * with the given id. + * @param {Node} name name of grouped tab to be selected + * @param {Node} clickedId id of clicked tab + */ +function selectNamedTabs(name, clickedId=null) { + const groupedTabs = document.querySelectorAll(`.sphinx-tabs-tab[name="${name}"]`); + const tabLists = Array.from(groupedTabs).map(tab => tab.parentNode); + + tabLists + .forEach(tabList => { + // Don't want to change the tabList containing the clicked tab + const clickedTab = tabList.querySelector(`[id="${clickedId}"]`); + if (clickedTab === null ) { + // Select first tab with matching name + const tab = tabList.querySelector(`.sphinx-tabs-tab[name="${name}"]`); + deselectTabList(tab); + selectTab(tab); + } + }) +} + +if (typeof exports === 'undefined') { + exports = {}; +} + +exports.keyTabs = keyTabs; +exports.changeTabs = changeTabs; +exports.selectTab = selectTab; +exports.deselectTabList = deselectTabList; +exports.selectNamedTabs = selectNamedTabs; diff --git a/branch/main/singlehtml/_static/term_role_formatting.css b/branch/main/singlehtml/_static/term_role_formatting.css new file mode 100644 index 0000000..0b66095 --- /dev/null +++ b/branch/main/singlehtml/_static/term_role_formatting.css @@ -0,0 +1,4 @@ +/* Make terms bold */ +a.reference span.std-term { + font-weight: bold; +} diff --git a/branch/main/singlehtml/_static/togglebutton.css b/branch/main/singlehtml/_static/togglebutton.css new file mode 100644 index 0000000..54a6787 --- /dev/null +++ b/branch/main/singlehtml/_static/togglebutton.css @@ -0,0 +1,160 @@ +/** + * Admonition-based toggles + */ + +/* Visibility of the target */ +.admonition.toggle .admonition-title ~ * { + transition: opacity .3s, height .3s; +} + +/* Toggle buttons inside admonitions so we see the title */ +.admonition.toggle { + position: relative; +} + +/* Titles should cut off earlier to avoid overlapping w/ button */ +.admonition.toggle .admonition-title { + padding-right: 25%; + cursor: pointer; +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:hover { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 1%); +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:active { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 3%); +} + +/* Remove extra whitespace below the admonition title when hidden */ +.admonition.toggle-hidden { + padding-bottom: 0; +} + +.admonition.toggle-hidden .admonition-title { + margin-bottom: 0; +} + +/* hides all the content of a page until de-toggled */ +.admonition.toggle-hidden .admonition-title ~ * { + height: 0; + margin: 0; + opacity: 0; + visibility: hidden; +} + +/* General button style and position*/ +button.toggle-button { + /** + * Background and shape. By default there's no background + * but users can style as they wish + */ + background: none; + border: none; + outline: none; + + /* Positioning just inside the admonition title */ + position: absolute; + right: 0.5em; + padding: 0px; + border: none; + outline: none; +} + +/* Display the toggle hint on wide screens */ +@media (min-width: 768px) { + button.toggle-button.toggle-button-hidden:before { + content: attr(data-toggle-hint); /* This will be filled in by JS */ + font-size: .8em; + align-self: center; + } +} + +/* Icon behavior */ +.tb-icon { + transition: transform .2s ease-out; + height: 1.5em; + width: 1.5em; + stroke: currentColor; /* So that we inherit the color of other text */ +} + +/* The icon should point right when closed, down when open. */ +/* Open */ +.admonition.toggle button .tb-icon { + transform: rotate(90deg); +} + +/* Closed */ +.admonition.toggle button.toggle-button-hidden .tb-icon { + transform: rotate(0deg); +} + +/* With details toggles, we don't rotate the icon so it points right */ +details.toggle-details .tb-icon { + height: 1.4em; + width: 1.4em; + margin-top: 0.1em; /* To center the button vertically */ +} + + +/** + * Details-based toggles. + * In this case, we wrap elements with `.toggle` in a details block. + */ + +/* Details blocks */ +details.toggle-details { + margin: 1em 0; +} + + +details.toggle-details summary { + display: flex; + align-items: center; + cursor: pointer; + list-style: none; + border-radius: .2em; + border-left: 3px solid #1976d2; + background-color: rgb(204 204 204 / 10%); + padding: 0.2em 0.7em 0.3em 0.5em; /* Less padding on left because the SVG has left margin */ + font-size: 0.9em; +} + +details.toggle-details summary:hover { + background-color: rgb(204 204 204 / 20%); +} + +details.toggle-details summary:active { + background: rgb(204 204 204 / 28%); +} + +.toggle-details__summary-text { + margin-left: 0.2em; +} + +details.toggle-details[open] summary { + margin-bottom: .5em; +} + +details.toggle-details[open] summary .tb-icon { + transform: rotate(90deg); +} + +details.toggle-details[open] summary ~ * { + animation: toggle-fade-in .3s ease-out; +} + +@keyframes toggle-fade-in { + from {opacity: 0%;} + to {opacity: 100%;} +} + +/* Print rules - we hide all toggle button elements at print */ +@media print { + /* Always hide the summary so the button doesn't show up */ + details.toggle-details summary { + display: none; + } +} \ No newline at end of file diff --git a/branch/main/singlehtml/_static/togglebutton.js b/branch/main/singlehtml/_static/togglebutton.js new file mode 100644 index 0000000..215a7ee --- /dev/null +++ b/branch/main/singlehtml/_static/togglebutton.js @@ -0,0 +1,187 @@ +/** + * Add Toggle Buttons to elements + */ + +let toggleChevron = ` + + + +`; + +var initToggleItems = () => { + var itemsToToggle = document.querySelectorAll(togglebuttonSelector); + console.log(`[togglebutton]: Adding toggle buttons to ${itemsToToggle.length} items`) + // Add the button to each admonition and hook up a callback to toggle visibility + itemsToToggle.forEach((item, index) => { + if (item.classList.contains("admonition")) { + // If it's an admonition block, then we'll add a button inside + // Generate unique IDs for this item + var toggleID = `toggle-${index}`; + var buttonID = `button-${toggleID}`; + + item.setAttribute('id', toggleID); + if (!item.classList.contains("toggle")){ + item.classList.add("toggle"); + } + // This is the button that will be added to each item to trigger the toggle + var collapseButton = ` + `; + + title = item.querySelector(".admonition-title") + title.insertAdjacentHTML("beforeend", collapseButton); + thisButton = document.getElementById(buttonID); + + // Add click handlers for the button + admonition title (if admonition) + admonitionTitle = document.querySelector(`#${toggleID} > .admonition-title`) + if (admonitionTitle) { + // If an admonition, then make the whole title block clickable + admonitionTitle.addEventListener('click', toggleClickHandler); + admonitionTitle.dataset.target = toggleID + admonitionTitle.dataset.button = buttonID + } else { + // If not an admonition then we'll listen for the button click + thisButton.addEventListener('click', toggleClickHandler); + } + + // Now hide the item for this toggle button unless explicitly noted to show + if (!item.classList.contains("toggle-shown")) { + toggleHidden(thisButton); + } + } else { + // If not an admonition, wrap the block in a
block + // Define the structure of the details block and insert it as a sibling + var detailsBlock = ` +
+ + ${toggleChevron} + ${toggleHintShow} + +
`; + item.insertAdjacentHTML("beforebegin", detailsBlock); + + // Now move the toggle-able content inside of the details block + details = item.previousElementSibling + details.appendChild(item) + item.classList.add("toggle-details__container") + + // Set up a click trigger to change the text as needed + details.addEventListener('click', (click) => { + let parent = click.target.parentElement; + if (parent.tagName.toLowerCase() == "details") { + summary = parent.querySelector("summary"); + details = parent; + } else { + summary = parent; + details = parent.parentElement; + } + // Update the inner text for the proper hint + if (details.open) { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintShow; + } else { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintHide; + } + + }); + + // If we have a toggle-shown class, open details block should be open + if (item.classList.contains("toggle-shown")) { + details.click(); + } + } + }) +}; + +// This should simply add / remove the collapsed class and change the button text +var toggleHidden = (button) => { + target = button.dataset['target'] + var itemToToggle = document.getElementById(target); + if (itemToToggle.classList.contains("toggle-hidden")) { + itemToToggle.classList.remove("toggle-hidden"); + button.classList.remove("toggle-button-hidden"); + } else { + itemToToggle.classList.add("toggle-hidden"); + button.classList.add("toggle-button-hidden"); + } +} + +var toggleClickHandler = (click) => { + // Be cause the admonition title is clickable and extends to the whole admonition + // We only look for a click event on this title to trigger the toggle. + + if (click.target.classList.contains("admonition-title")) { + button = click.target.querySelector(".toggle-button"); + } else if (click.target.classList.contains("tb-icon")) { + // We've clicked the icon and need to search up one parent for the button + button = click.target.parentElement; + } else if (click.target.tagName == "polyline") { + // We've clicked the SVG elements inside the button, need to up 2 layers + button = click.target.parentElement.parentElement; + } else if (click.target.classList.contains("toggle-button")) { + // We've clicked the button itself and so don't need to do anything + button = click.target; + } else { + console.log(`[togglebutton]: Couldn't find button for ${click.target}`) + } + target = document.getElementById(button.dataset['button']); + toggleHidden(target); +} + +// If we want to blanket-add toggle classes to certain cells +var addToggleToSelector = () => { + const selector = ""; + if (selector.length > 0) { + document.querySelectorAll(selector).forEach((item) => { + item.classList.add("toggle"); + }) + } +} + +// Helper function to run when the DOM is finished +const sphinxToggleRunWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} +sphinxToggleRunWhenDOMLoaded(addToggleToSelector) +sphinxToggleRunWhenDOMLoaded(initToggleItems) + +/** Toggle details blocks to be open when printing */ +if (toggleOpenOnPrint == "true") { + window.addEventListener("beforeprint", () => { + // Open the details + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.dataset["togglestatus"] = el.open; + el.open = true; + }); + + // Open the admonitions + document.querySelectorAll(".admonition.toggle.toggle-hidden").forEach((el) => { + console.log(el); + el.querySelector("button.toggle-button").click(); + el.dataset["toggle_after_print"] = "true"; + }); + }); + window.addEventListener("afterprint", () => { + // Re-close the details that were closed + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.open = el.dataset["togglestatus"] == "true"; + delete el.dataset["togglestatus"]; + }); + + // Re-close the admonition toggle buttons + document.querySelectorAll(".admonition.toggle").forEach((el) => { + if (el.dataset["toggle_after_print"] == "true") { + el.querySelector("button.toggle-button").click(); + delete el.dataset["toggle_after_print"]; + } + }); + }); +} diff --git a/branch/main/singlehtml/index.html b/branch/main/singlehtml/index.html new file mode 100644 index 0000000..8dac0a1 --- /dev/null +++ b/branch/main/singlehtml/index.html @@ -0,0 +1,3103 @@ + + + + + + + Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Reproducible research software development using Python documentation
    • +
  • + Edit on GitHub +
    • +
+
+
+
+
+ +
+

Reproducible research software development using Python

+
+

Big-picture goal

+

This is a hands-on course on research software engineering. In this +workshop we assume that most workshop participants use Python in their work or +a leading a group which uses Python. Therefore, some of the examples will use +Python as the example language.

+

We will work with an example project and go through all the steps of a typical +software project. Once we have seen the building blocks, we will try to apply +them to own projects. Workshop participants will receive and also learn to give +constructive code feedback.

+
+
+

Prerequisites

+
+

Preparation

+
    +

  1. Get a GitHub account following these instructions.

    2. +

  2. You will need a text editor. If you don’t have a favorite one, we recommend +VS Code.

    3. +

  3. If you prefer to work in the terminal and not in VS Code, set up these two (skip this if you use VS Code):

    + +
    4. +

  4. One of these two software environments (if you are not sure which one to +choose or have no preference, choose Conda):

    + +
    5. +

  5. Optional and only on Linux: Apptainer following +these instructions.

    6. +
+
+
+
+

Schedule

+
+

Day 1

+ +
+
+

Day 2

+ +
+
+

Day 3

+ +
+
+

If we have time left

+ +
+
+

Conda environment

+

A Conda environment is an isolated software environment that is used to manage dependencies for a project +and you decide where it is located.

+

You will need a environment.yml file that documents the dependencies:

+
name: coderefinery
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - python >= 3.10
+  - black
+  - click
+  - flit
+  - ipywidgets
+  - isort
+  - jupyterlab
+  - jupyterlab_code_formatter
+  - jupyterlab-git
+  - matplotlib
+  - myst-parser
+  - nbdime
+  - numpy
+  - pandas
+  - pytest
+  - pytest-cov
+  - scalene
+  - seaborn
+  - snakemake-minimal
+  - sphinx
+  - sphinx-autoapi
+  - sphinx-autobuild
+  - sphinx_rtd_theme >= 2.0
+  - vulture
+  - scikit-image
+
+
+
+
Before you create a virtual environment
+
    +

  1. Create a new directory for this course.

    2. +

  2. In this directory, create an environment.yml file and copy-paste the dependencies above into it.

    3. +
+
+
+
Choose the tool to manage the environment
+

If you are already using one of these tools, please continue using the tool that you like and know. +If you are new to this, we recommend using Miniconda or Miniforge.

+
    +

  • Anaconda

    +
      +

    • Advantages: easy to install, easy to use, good for beginners

      • +

    • Disadvantages: large download, installs more than we will need, license restrictions

      • +
    +
    • +

  • Miniconda

    +
      +

    • Advantages: small size, installs only what you need

      • +

    • Disadvantages: no graphical interface, license restrictions

      • +
    +
    • +

  • Miniforge

    +
      +

    • Advantages: small size, no license restrictions

      • +

    • Disadvantages: no graphical interface

      • +
    +
    • +

  • Micromamba

    +
      +

    • Advantages: fast, small size

      • +

    • Disadvantages: no graphical interface

      • +
    +
    • +

  • Pixi

    +
      +

    • Advantages: fast and new

      • +

    • Disadvantages: new and less tested and not documented here

      • +
    +
    • +
+
+
+
Creating the virtual environment
+
    +

  1. Open your terminal shell (e.g. Bash or Zsh).

    2. +

  2. Activate conda using conda activate or source ~/miniconda3/bin/activate.

    3. +

  3. Run the following command:

    +
    $ conda env create --file environment.yml
+
    +
    +
    4. +

  4. Make sure that you see “coderefinery” in the output when you ask for a list of all available environments:

    +
    $ conda env list
+
    +
    +
    5. +
+
+
+
+

Virtual environment

+

A virtual environment is an isolated software environment that is used to manage dependencies for a project +and you decide where it is located.

+

You will need a requirements.txt file that documents the dependencies:

+
black
+click
+flit
+ipywidgets
+isort
+jupyterlab
+jupyterlab-code-formatter
+jupyterlab-git
+matplotlib
+myst-parser
+nbdime
+numpy
+pandas
+pytest
+pytest-cov
+scalene
+seaborn
+sphinx
+sphinx-autoapi
+sphinx-autobuild
+sphinx_rtd_theme >= 2.0
+vulture
+scikit-image
+
+
+
+
Before you create a virtual environment
+
    +

  1. Create a new directory for this course.

    2. +

  2. In this directory, create a requirements.txt file and copy-paste the dependencies above into it.

    3. +
+
+
+
Creating the virtual environment
+

Now create a virtual environment in this directory either using pip and +venv +(more traditional and safer) or using uv (more modern but also less tested):

+
+

Create a new virtual environment and activate it:

+
$ python3 -m venv coderefinery-environment
+$ source coderefinery-environment/bin/activate
+
+
+

Install the dependencies into the environment:

+
$ python3 -m pip install -r requirements.txt
+
+
+
+
+
+
+
+
+

Example project: Simulating the motion of planets

+

The example code that we will study +is a hopefully simple N-body simulation written in Python. It is not important +or expected that we understand the code in any detail.

+

The big picture is that the code simulates the motion of a number of +planets:

+
    +

  • We can choose the number of planets.

    • +

  • Each planet starts with a random position, velocity, and mass.

    • +

  • At each time step, the code calculates the gravitational force between each +pair of planets.

    • +

  • The forces accelerate each planet, the acceleration modifies the velocity, +the velocity modifies the position of each planet.

    • +

  • We can choose the number of time steps.

    • +

  • The units were chosen to make numbers easy to read.

    • +
+
+
Example run
+
+

Instructor note

+

The instructor demonstrates running the code on their computer.

+
+

The code is written to accept command-line arguments to specify the number +of planets and the number of time steps.

+

We first generate starting data:

+
$ python generate-data.py --num-planets 10 --output-file initial.csv
+
+
+

The generated file (initial.csv) could look like this:

+
px,py,pz,vx,vy,vz,mass
+-46.88,-42.51,88.33,-0.86,-0.18,0.55,6.70
+-5.29,17.09,-96.13,0.66,0.45,-0.17,3.51
+83.53,-92.83,-68.77,-0.26,-0.48,0.24,6.84
+-36.31,25.48,64.16,0.85,0.75,-0.56,1.53
+-68.38,-17.21,-97.07,0.60,0.26,0.69,6.63
+-48.37,-48.74,3.92,-0.92,-0.33,-0.93,8.60
+40.53,-75.50,44.18,-0.62,-0.31,-0.53,8.04
+-27.21,10.78,-78.82,-0.09,-0.55,-0.03,5.35
+88.42,-74.95,-45.85,0.81,0.68,0.56,5.36
+39.09,53.12,-59.54,-0.54,0.56,0.07,8.98
+
+
+

Then we can simulate their motion (in this case for 20 steps):

+
$ python simulate.py --num-steps 20 \
+                     --input-file initial.csv \
+                     --output-file final.csv
+
+
+

The --output-file (final.csv) is again a CSV file (comma-separated values) +and contains the final positions of all planets.

+

It is possible to run on multiple cores and to animate the result. +Here is an example with 100 planets:

+
$ python generate-data.py --num-planets 100 --output-file initial.csv
+
+$ python simulate.py --num-steps 50 \
+                     --input-file initial.csv \
+                     --output-file final.csv \
+                     --trajectories-file trajectories.npz \
+                     --num-cores 8
+
+$ python animate.py --initial-file initial.csv \
+                    --trajectories-file trajectories.npz \
+                    --output-file animation.mp4
+
+
+
+

Learning goals

+
    +

  • What are the most important steps to make this code reusable by others +and our future selves?

    • +

  • Be able to apply these techniques to your own code/script.

    • +
+
+
+

We will not focus on …

+
    +

  • … how the code works internally in detail.

    • +

  • … whether this is the most efficient algorithm.

    • +

  • … whether the code is numerically stable.

    • +

  • … how to code scales with the number of cores.

    • +

  • … whether it is portable to other operating systems (we will discuss this later).

    • +
+
+
+
+
+

Introduction to version control with Git and GitHub

+
+
+
Motivation
+
+

Objectives

+
    +

  • Browse commits and branches of a Git repository.

    • +

  • Remember that commits are like snapshots of the repository at a certain +point in time.

    • +

  • Know the difference between Git (something that tracks changes) and +GitHub/GitLab (a platform to host Git repositories).

    • +
+
+
+
Why do we need to keep track of versions?
+

Version control is an answer to the following questions (do you recognize some +of them?):

+
    +

  • “It broke … hopefully I have a working version somewhere?”

    • +

  • “Can you please send me the latest version?”

    • +

  • “Where is the latest version?”

    • +

  • “Which version are you using?”

    • +

  • “Which version have the authors used in the paper I am trying to reproduce?”

    • +

  • “Found a bug! Since when was it there?”

    • +

  • “I am sure it used to work. When did it change?”

    • +

  • “My laptop is gone. Is my thesis now gone?”

    • +
+
+
+
Demonstration
+
    +

  • Example repository: https://github.com/workshop-material/planets

    • +

  • Commits are like snapshots and if we break something we can go back to a +previous snapshot.

    • +

  • Commits carry metadata about changes: author, date, commit message, and +a checksum.

    • +

  • Branches are like parallel universes where you can experiment with +changes without affecting the default branch: +https://github.com/workshop-material/planets/network +(“Insights” -> “Network”)

    • +

  • With version control we can annotate code +(example).

    • +

  • Collaboration: We can fork (make a copy on GitHub), clone (make a copy +to our computer), review, compare, share, and discuss.

    • +

  • Code review: Others can suggest changes using pull requests or merge +requests. These can be reviewed and discussed before they are merged. +Conceptually, they are similar to “suggesting changes” in Google Docs.

    • +
+
+
+
Features: roll-back, branching, merging, collaboration
+
    +

  • Roll-back: you can always go back to a previous version and compare

    • +

  • Branching and merging:

    +
      +

    • Work on different ideas at the same time

      • +

    • Different people can work on the same code/project without interfering

      • +

    • You can experiment with an idea and discard it if it turns out to be a bad idea

      • +
    +
    • +
+
+Branching explained with a gopher +
+

Image created using https://gopherize.me/ +(inspiration).

+
+
+ +
+
+
Talking about code
+

Which of these two is more practical?

+
    +

  1. “Clone the code, go to the file ‘simulate.py’, and search for ‘force_between_planets’. +Oh! But make sure you use the version from September 2024.”

    2. +

  2. Or I can send you a permalink: https://github.com/workshop-material/planets/blob/1343ac0/simulate.py#L31C5-L39

    3. +
+
+
+
What we typically like to snapshot
+
    +

  • Software (this is how it started but Git/GitHub can track a lot more)

    • +

  • Scripts

    • +

  • Documents (plain text files much better suitable than Word documents)

    • +

  • Manuscripts (Git is great for collaborating/sharing LaTeX or Quarto manuscripts)

    • +

  • Configuration files

    • +

  • Website sources

    • +

  • Data

    • +
+
+

Discussion

+

In this example somebody tried to keep track of versions without a version +control system tool like Git. Discuss the following directory listing. What +possible problems do you anticipate with this kind of “version control”:

+
myproject-2019.zip
+myproject-2020-february.zip
+myproject-2021-august.zip
+myproject-2023-09-19-working.zip
+myproject-2023-09-21.zip
+myproject-2023-09-21-test.zip
+myproject-2023-09-21-myversion.zip
+myproject-2023-09-21-newfeature.zip
+...
+(100 more files like these)
+
+
+ +
+
+
+
+
Forking, cloning, and browsing
+

In this episode, we will look at an existing repository to understand how +all the pieces work together. Along the way, we will make a copy (by +forking and/or cloning) of the repository for us, which will be used +for our own changes.

+
+

Objectives

+
    +

  • See a real Git repository and understand what is inside of it.

    • +

  • Understand how version control allows advanced inspection of a +repository.

    • +

  • See how Git allows multiple people to work on the same project at the same time.

    • +

  • See the big picture instead of remembering a bunch of commands.

    • +
+
+
+
GitHub, VS Code, or command line
+

We offer three different paths for this exercise:

+
    +

  • GitHub (this is the one we will demonstrate)

    • +

  • VS Code (if you prefer to follow along using an editor)

    • +

  • Command line (for people comfortable with the command line)

    • +
+
+
+
Creating a copy of the repository by “forking” or “cloning”
+

A repository is a collection of files in one directory tracked by Git. A +GitHub repository is GitHub’s copy, which adds things like access control, +issue tracking, and discussions. Each GitHub repository is owned by a user or +organization, who controls access.

+

First, we need to make our own copy of the exercise repository. This will +become important later, when we make our own changes.

+
+Illustration of forking a repository on GitHub +
+

Illustration of forking a repository on GitHub.

+
+
+
+Illustration of cloning a repository to your computer +
+

Illustration of cloning a repository to your computer.

+
+
+
+Illustration of cloning a forked repository to your computer +
+

It is also possible to do this: to clone a forked repository to your computer.

+
+
+

At all times you should be aware of if you are looking at your repository +or the upstream repository (original repository):

+
    +

  • Your repository: https://github.com/USER/planets

    • +

  • Upstream repository: https://github.com/workshop-material/planets

    • +
+
+

How to create a fork

+
    +

  1. Go to the repository view on GitHub: https://github.com/workshop-material/planets

    2. +

  2. First, on GitHub, click the button that says “Fork”. It is towards +the top-right of the screen.

    3. +

  3. You should shortly be redirected to your copy of the repository +USER/planets.

    4. +
+
+
+

Instructor note

+

Before starting the exercise session show +how to fork the repository to own account +(above).

+
+
+
+
Exercise: Copy and browse an existing project
+

Work on this by yourself or in pairs.

+
+

Exercise preparation

+
+

In this case you will work on a fork.

+

You only need to open your own view, as described above. The browser +URL should look like https://github.com/USER/planets, where +USER is your GitHub username.

+
+
+
+

Exercise: Browsing an existing project (20 min)

+

Browse the example project and +explore commits and branches, either on a fork or on a clone. Take notes and +prepare questions. The hints are for the GitHub path in the browser.

+
    +

  1. Browse the commit history: Are commit messages understandable? +(Hint: “Commit history”, the timeline symbol, above the file list)

    2. +

  2. Compare the commit history with the network graph (“Insights” -> “Network”). Can you find the branches?

    3. +

  3. Try to find the history of commits for a single file, e.g. simulate.py. +(Hint: “History” button in the file view)

    4. +

  4. Which files include the word “position”? +(Hint: the GitHub search on top of the repository view)

    5. +

  5. In the simulate.py file, find out who modified each line last and when +(click on file, then click “Blame” button). Find out who modified the gravitational constant +last and in which commit. +(Hint: “Blame” view in the file view)

    6. +

  6. Can you use this code yourself? Are you allowed to share +modifications? +(Hint: look for a license file)

    7. +
+
+

The solution below goes over most of the answers, and you are +encouraged to use it when the hints aren’t enough - this is by +design.

+
+
+
Solution and walk-through
+
+
(1) Basic browsing
+

The most basic thing to look at is the history of commits.

+
    +

  • This is visible from a button in the repository view. We see every +change, when, and who has committed.

    • +

  • Every change has a unique identifier, such as 244c993. This can +be used to identify both this change, and the whole project’s +version as of that change.

    • +

  • Clicking on a change in the view shows more.

    • +
+
+

Click on the timeline symbol in the repository view:

+
+Screenshot on GitHub of where to find the commit history +
+
+
+
+
(2) Compare commit history with network graph
+

The commit history we saw above looks linear: one commit after +another. But if we look at the network view, we see some branches and +merges. We’ll see how to do these later. This is another one of the +basic Git views.

+
+

In a new browser tab, open the “Insights” tab, and click on “Network”. +You can hover over the commit dots to see the person who committed and +how they correspond with the commits in the other view:

+
+Screenshot on GitHub of the network graph +
+
+
+
+
(3) How can you browse the history of a single file?
+

We see the history for the whole repository, but we can also see it +for a single file.

+
+

Navigate to the file view: Main page → simulate.py. +Click the “History” button near the top right.

+
+
+
+
(4) Which files include the word “position”?
+

Version control makes it very easy to find all occurrences of a single +word. This is useful for things like finding where functions or +variables are defined or used.

+
+

We go to the main file view. We click the Search magnifying +class at the very top, type “position”, and click enter. We see every +instance, including the context.

+
+

Searching in a forked repository will not work instantaneously!

+

It usually takes a few minutes before one can search for keywords in a forked repository +since it first needs to build the search index the very first time we search. +Start it, continue with other steps, then come back to this.

+
+
+
+
+
(5) Who modified each line last and when?
+

This is called the “annotate” or “blame” view. The name “blame” +is very unfortunate, but it is the standard term for historical reasons +for this functionality and it is not meant to blame anyone.

+
+

From a file view, change preview to “Blame” towards the top-left. +To get the actual commit, click on the commit message.

+
+
+
+
(6) Can you use this code yourself? Are you allowed to share modifications?
+
    +

  • Look at the file LICENSE.

    • +

  • On GitHub, click on the file to see a nice summary of what we can do with this:

    +
    +Screenshot on GitHub summarizing license terms +
    +
    • +
+
+
+
Summary
+
    +

  • Git allowed us to understand this simple project much better than we +could, if it was just a few files on our own computer.

    • +

  • It was easy to share the project with the course.

    • +

  • By forking the repository, we created our own copy. This is +important for the following, where we will make changes to +our copy.

    • +
+
+
+
+
+
Creating branches and commits
+

The first and most basic task to do in Git is record changes using +commits. In this part, we will record changes in two +ways: on a new branch (which supports multiple lines of work at once), and directly +on the “main” branch (which happens to be the default branch here).

+
+

Objectives

+
    +

  • Record new changes to our own copy of the project.

    • +

  • Understand adding changes in two separate branches.

    • +

  • See how to compare different versions.

    • +
+
+
+
Background
+
    +

  • In the previous episode we have browsed an existing repository and saw commits +and branches.

    • +

  • Each commit is a snapshot of the entire project at a certain +point in time and has a unique identifier (hash) .

    • +

  • A branch is a line of development, and the main branch or master branch +are often the default branch in Git.

    • +

  • A branch in Git is like a sticky note that is attached to a commit. When we add +new commits to a branch, the sticky note moves to the new commit.

    • +

  • Tags are a way to mark a specific commit as important, for example a release +version. They are also like a sticky note, but they don’t move when new +commits are added.

    • +
+
+Branching explained with a gopher +
+

What if two people, at the same time, make two different changes? Git +can merge them together easily. Image created using https://gopherize.me/ +(inspiration).

+
+
+
+
+
Exercise: Creating branches and commits
+
+Illustration of what we want to achieve in this exercise +
+

Illustration of what we want to achieve in this exercise.

+
+
+
+

Exercise: Practice creating commits and branches (20 min)

+
    +

  1. First create a new branch and then either add a new file or modify an +existing file and commit the change. Make sure that you now work on your +copy of the example repository. In your commit you can share a Git or +programming trick you like.

    2. +

  2. In a new commit, modify the file again.

    3. +

  3. Switch to the main branch and create a commit there.

    4. +

  4. Browse the network and locate the commits that you just created (“Insights” -> “Network”).

    5. +

  5. Compare the branch that you created with the main branch. Can you find an easy way to see the differences?

    6. +

  6. Can you find a way to compare versions between two arbitrary commits in the repository?

    7. +

  7. Try to rename the branch that you created and then browse the network again.

    8. +

  8. Try to create a tag for one of the commits that you created (on GitHub, +create a “release”).

    9. +
+
+

The solution below goes over most of the answers, and you are +encouraged to use it when the hints aren’t enough - this is by +design.

+
+
+
Solution and walk-through
+
+
(1) Create a new branch and a new commit
+
+
    +

  1. Where it says “main” at the top left, click, enter a new branch +name new-tutorial, click on the offer to create the new branch +(“Create branch new-tutorial from main”).

    2. +

  2. Make sure you are still on the new-tutorial branch (it should say +it at the top), and click “Add file” → “Create new file” from the +upper right.

    3. +

  3. Enter a filename where it says “Name your file…”.

    4. +

  4. Share some Git or programming trick you like.

    5. +

  5. Click “Commit changes”

    6. +

  6. Enter a commit message. Then click “Commit +changes”.

    7. +
+

You should appear back at the file browser view, and see your +modification there.

+
+
+
+
(2) Modify the file again with a new commit
+
+

This is similar to before, but we click on the existing file to +modify.

+
    +

  1. Click on the file you added or modified previously.

    2. +

  2. Click the edit button, the pencil icon at top-right.

    3. +

  3. Follow the “Commit changes” instructions as in the previous step.

    4. +
+
+
+
+
(3) Switch to the main branch and create a commit there
+
+
    +

  1. Go back to the main repository page (your user’s page).

    2. +

  2. In the branch switch view (top left above the file view), switch to +main.

    3. +

  3. Modify another file that already exists, following the pattern +from above.

    4. +
+
+
+
+
(4) Browse the commits you just made
+

Let’s look at what we did. Now, the main and new-tutorial branches +have diverged: both have some modifications. Try to find the commits +you created.

+
+

Insights tab → Network view (just like we have done before).

+
+
+
+
(5) Compare the branches
+

Comparing changes is an important thing we need to do. When using the +GitHub view only, this may not be so common, but we’ll show it so that +it makes sense later on.

+
+

A nice way to compare branches is to add /compare to the URL of the repository, +for example (replace USER): +https://github.com/USER/planets/compare

+
+
+
+
(6) Compare two arbitrary commits
+

This is similar to above, but not only between branches.

+
+

Following the /compare-trick above, one can compare commits on GitHub by +adjusting the following URL: +https://github.com/USER/planets/compare/VERSION1..VERSION2

+

Replace USER with your username and VERSION1 and VERSION2 with a commit hash or branch name. +Please try it out.

+
+
+
+
(7) Renaming a branch
+
+

Branch button → View all branches → three dots at right side → Rename branch.

+
+
+
+
(8) Creating a tag
+

Tags are a way to mark a specific commit as important, for example a release +version. They are also like a sticky note, but they don’t move when new +commits are added.

+
+

On the right side, below “Releases”, click on “Create a new release”.

+

What GitHub calls releases are actually tags in Git with additional metadata. +For the purpose of this exercise we can use them interchangeably.

+
+
+
+
+
Summary
+

In this part, we saw how we can make changes to our files. With branches, we +can track several lines of work at once, and can compare their differences.

+
    +

  • You could commit directly to main if there is only one single line +of work and it’s only you.

    • +

  • You could commit to branches if there are multiple lines of work at +once, and you don’t want them to interfere with each other.

    • +

  • Tags are useful to mark a specific commit as important, for example a +release version.

    • +

  • In Git, commits form a so-called “graph”. Branches are tags in Git function +like sticky notes that stick to specific commits. What this means for us is +that it does not cost any significant disk space to create new branches.

    • +

  • Not all files should be added to Git. For example, temporary files or +files with sensitive information or files which are generated as part of +the build process should not be added to Git. For this we use +.gitignore (more about this later: Practical advice: How much Git is necessary?).

    • +

  • Unsure on which branch you are or what state the repository is in? +On the command line, use git status frequently to get a quick overview.

    • +
+
+
+
+
Practical advice: How much Git is necessary?
+
+
Writing useful commit messages
+

Useful commit messages summarize the change and provide context.

+

If you need a commit message that is longer than one line, +then the convention is: one line summarizing the commit, then one empty line, +then paragraph(s) with more details in free form, if necessary.

+

Good example:

+
increase alpha to 2.0 for faster convergence
+
+the motivation for this change is
+to enable ...
+...
+(more context)
+...
+this is based on a discussion in #123
+
+
+
    +

  • Why something was changed is more important than what has changed.

    • +

  • Cross-reference to issues and discussions if possible/relevant.

    • +

  • Bad commit messages: “fix”, “oops”, “save work”

    • +

  • Bad examples: http://whatthecommit.com

    • +

  • Write commit messages that will be understood +15 years from now by someone else than you. Or by your future you.

    • +

  • Many projects start out as projects “just for me” and end up to be successful projects +that are developed by 50 people over decades.

    • +

  • Commits with multiple authors are possible.

    • +
+

Good references:

+ +
+

Note

+

A great way to learn how to write commit messages and to get inspired by their +style choices: browse repositories of codes that you use/like:

+

Some examples (but there are so many good examples):

+ +

When designing commit message styles consider also these:

+
    +

  • How will you easily generate a changelog or release notes?

    • +

  • During code review, you can help each other improving commit messages.

    • +
+
+

But remember: it is better to make any commit, than no commit. Especially in small projects. +Let not the perfect be the enemy of the good enough.

+
+
+
What level of branching complexity is necessary for each project?
+

Simple personal projects:

+
    +

  • Typically start with just the main branch.

    • +

  • Use branches for unfinished/untested ideas.

    • +

  • Use branches when you are not sure about a change.

    • +

  • Use tags to mark important milestones.

    • +

  • If you are unsure what to do with unfinished and not working code, commit it +to a branch.

    • +
+

Projects with few persons: you accept things breaking sometimes

+
    +

  • It might be reasonable to commit to the main branch and feature branches.

    • +
+

Projects with few persons: changes are reviewed by others

+
    +

  • You create new feature branches for changes.

    • +

  • Changes are reviewed before they are merged to the main branch.

    • +

  • Consider to write-protect the main branch so that it can only be changed +with pull requests or merge requests.

    • +
+
+
+
How large should a commit be?
+
    +

  • Better too small than too large (easier to combine than to split).

    • +

  • Often I make a commit at the end of the day (this is a unit I would not like to lose).

    • +

  • Smaller sized commits may be easier to review for others than huge commits.

    • +

  • Imperfect commits are better than no commits.

    • +

  • A commit should not contain unrelated changes to simplify review and possible +repair/adjustments/undo later (but again: imperfect commits are better than no commits).

    • +
+
+
+
Working on the command line? Use “git status” all the time
+

The git status command is one of the most useful commands in Git +to inform about which branch we are on, what we are about to commit, +which files might not be tracked, etc.

+
+
+
How about staging and committing?
+
    +

  • Commit early and often: rather create too many commits than too few. +You can always combine commits later.

    • +

  • Once you commit, it is very, very hard to really lose your code.

    • +

  • Always fully commit (or stash) before you do dangerous things, so that you know you are safe. +Otherwise it can be hard to recover.

    • +

  • Later you can start using the staging area (where you first stage and then commit in a second step).

    • +

  • Later start using git add -p and/or git commit -p.

    • +
+
+
+
What to avoid
+
    +

  • Committing generated files/directories (example: __pycache__, *.pyc) -> +use .gitignore +files +(collection of .gitignore templates).

    • +

  • Committing huge files -> use code review to detect this.

    • +

  • Committing unrelated changes together.

    • +

  • Postponing commits because the changes are “unfinished”/”ugly” -> better ugly +commits than no commits.

    • +

  • When working with branches:

    +
      +

    • Not updating your branch before starting new work.

      • +

    • Too ambitious branch which risks to never get completed.

      • +

    • Over-engineering the branch layout and safeguards in small projects.

      • +

    • Working on unrelated things on the same branch.

      • +
    +
    • +
+
+
+
+
Optional: How to turn your project to a Git repo and share it
+
+

Objectives

+
    +

  • Turn our own coding project (small or large, finished or unfinished) into a +Git repository.

    • +

  • Be able to share a repository on the web to have a backup or so that others +can reuse and collaborate or even just find it.

    • +
+
+
+
Exercise
+
+Illustration of how we turn a project into a Git repository and share it +
+

From a bunch of files to a local repository which we then share on GitHub.

+
+
+
+

Exercise: Turn your project to a Git repo and share it (20 min)

+
    +

  1. Create a new directory called myproject with one or few files in it. +This represents our own project. It is not yet a Git repository. You can try +that with your own project or use a simple placeholder example.

    2. +

  2. Turn this new directory into a Git repository.

    3. +

  3. Share this repository on GitHub (or GitLab, since it really works the same).

    4. +
+

We offer three different paths of how to do this exercise.

+
    +

  • Via GitHub web interface: easy and can be a good starting point if you are completely +new to Git.

    • +

  • VS Code is quite easy, since VS Code can offer to create the +GitHub repositories for you.

    • +

  • Command line: you need to create the +repository on GitHub and link it yourself.

    • +
+
+

Create an repository on GitHub

+

First log into GitHub, then follow the screenshots and descriptions below.

+
+Screenshot on GitHub before a new repository form is opened +
+

Click on the “plus” symbol on top right, then on “New repository”.

+
+
+

Then:

+
+Screenshot on GitHub just before a new repository is created +
+

Choose a repository name, add a short description, and in this case make sure to check “Add a +README file”. Finally “Create repository”.

+
+
+

Upload your files

+

Now that the repository is created, you can upload your files:

+
+Screenshot on GitHub just before uploading files +
+

Click on the “+” symbol and then on “Upload files”.

+
+
+
+
+
+
+
Is putting software on GitHub/GitLab/… publishing?
+

It is a good first step but to make your code truly findable and +accessible, consider making your code citable and persistent: Get a +persistent identifier (PID) such as DOI in addition to sharing the code +publicly, by using services like Zenodo or similar +services.

+
+
+
+
+
+

Code documentation

+
+

Objectives

+
    +

  • Discuss what makes good documentation.

    • +

  • Improve the README of your project or our example project.

    • +

  • Explore Sphinx which is a popular tool to build documentation websites.

    • +

  • Learn how to leverage GitHub Actions and GitHub Pages to build and deploy documentation.

    • +
+
+
+

Instructor note

+
    +

  • (30 min) Discussion

    • +

  • (30 min) Exercise: Set up a Sphinx documentation and add API documentation

    • +

  • (15 min) Demo: Building documentation with GitHub Actions

    • +
+
+
+
Why? 💗✉️ to your future self
+
    +

  • You will probably use your code in the future and may forget details.

    • +

  • You may want others to use your code or contribute +(almost impossible without documentation).

    • +
+
+
+
In-code documentation
+

Not very useful (more commentary than comment):

+
# now we check if temperature is below -50
+if temperature < -50:
+    print("ERROR: temperature is too low")
+
+
+

More useful (explaining why):

+
# we regard temperatures below -50 degrees as measurement errors
+if temperature < -50:
+    print("ERROR: temperature is too low")
+
+
+

Keeping zombie code “just in case” (rather use version control):

+
# do not run this code!
+# if temperature > 0:
+#     print("It is warm")
+
+
+

Emulating version control:

+
# John Doe: threshold changed from 0 to 15 on August 5, 2013
+if temperature > 15:
+    print("It is warm")
+
+
+
+
+
Many languages allow “docstrings”
+

Example (Python):

+
def kelvin_to_celsius(temp_k: float) -> float:
+    """
+    Converts temperature in Kelvin to Celsius.
+
+    Parameters
+    ----------
+    temp_k : float
+        temperature in Kelvin
+
+    Returns
+    -------
+    temp_c : float
+        temperature in Celsius
+    """
+    assert temp_k >= 0.0, "ERROR: negative T_K"
+
+    temp_c = temp_k - 273.15
+
+    return temp_c
+
+
+
+

Keypoints

+
    +

  • Documentation which is only in the source code is not enough.

    • +

  • Often a README is enough.

    • +

  • Documentation needs to be kept +in the same Git repository as the code since we want it to evolve with +the code.

    • +
+
+
+
+
Often a README is enough - checklist
+
    +

  • Purpose

    • +

  • Requirements

    • +

  • Installation instructions

    • +

  • Copy-paste-able example to get started

    • +

  • Tutorials covering key functionality

    • +

  • Reference documentation (e.g. API) covering all functionality

    • +

  • Authors and recommended citation

    • +

  • License

    • +

  • Contribution guide

    • +
+

See also the +JOSS review checklist.

+
+
+
What if you need more than a README?
+ +
+
+
Diátaxis
+

Diátaxis is a systematic approach to technical documentation authoring.

+ +
+
+
Exercise: Set up a Sphinx documentation
+
+

Preparation

+

In this episode we will use the following 5 packages which we installed +previously as part of the Conda environment or Virtual environment:

+
myst-parser
+sphinx
+sphinx-rtd-theme
+sphinx-autoapi
+sphinx-autobuild
+
+
+

Which repository to use? You have 3 options:

+
    +

  • Clone your fork of the planets example repository.

    • +

  • If you don’t have that, you can clone the original repository itself: +https://github.com/workshop-material/planets

    • +

  • You can try this with your own project and the project does not have to +be a Python project.

    • +
+
+

There are at least two ways to get started with Sphinx:

+
    +

  1. Use sphinx-quickstart to create a new Sphinx project.

    2. +

  2. This is what we will do: Create three files (doc/conf.py, doc/index.md, and doc/about.md) +as starting point and improve from there.

    3. +
+
+

Exercise: Set up a Sphinx documentation

+
    +

  1. Create the following three files in your project:

    +
    planets/
+├── doc/
+│   ├── conf.py
+│   ├── index.md
+│   └── about.md
+└── ...
+
    +
    +

    This is conf.py:

    +
    project = "planets"
+copyright = "2024, Authors"
+author = "Authors"
+release = "0.1"
+
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+extensions = [
+    "myst_parser",  # in order to use markdown
+]
+
+myst_enable_extensions = [
+    "colon_fence",  # ::: can be used instead of ``` for better rendering
+]
+
+html_theme = "sphinx_rtd_theme"
+
    +
    +

    This is index.md (feel free to adjust):

    +
    # Our code documentation
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor
+incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis
+nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.
+Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu
+fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in
+culpa qui officia deserunt mollit anim id est laborum.
+
+:::{toctree}
+:maxdepth: 2
+:caption: Some caption
+
+about.md
+:::
+
    +
    +

    This is about.md (feel free to adjust):

    +
    # About this code
+
+Work in progress ...
+
    +
    +
    2. +

  2. Run sphinx-build to build the HTML documentation:

    +
    $ sphinx-build doc _build
+
+... lots of output ...
+The HTML pages are in _build.
+
    +
    +
    3. +

  3. Try to open _build/index.html in your browser.

    4. +

  4. Experiment with adding more content, images, equations, code blocks, …

    + +
    5. +
+
+

There is a lot more you can do:

+
    +

  • This is useful if you want to check the integrity of all internal and external links:

    +
    $ sphinx-build doc -W -b linkcheck _build
+
    +
    +
    • +

  • sphinx-autobuild +provides a local web server that will automatically refresh your view +every time you save a file - which makes writing and testing much easier.

    • +
+
+
+
Demo: Building documentation with GitHub Actions
+

First we need to extend the environment.yml file to include the necessary packages:

+
name: planets
+channels:
+  - conda-forge
+dependencies:
+  - python=3.12
+  - numpy
+  - click
+  - matplotlib
+  - myst-parser
+  - sphinx
+  - sphinx-rtd-theme
+  - sphinx-autoapi
+
+
+

Then we add a GitHub Actions workflow .github/workflow/sphinx.yml to build the documentation:

+
name: Build documentation
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+permissions:
+  contents: write
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+
+    - uses: mamba-org/setup-micromamba@v1
+      with:
+        micromamba-version: '1.5.8-0' # any version from https://github.com/mamba-org/micromamba-releases
+        environment-file: environment.yml
+        init-shell: bash
+        cache-environment: true
+        post-cleanup: 'all'
+        generate-run-shell: false
+
+    - name: Sphinx build
+      run: |
+        sphinx-build doc _build
+      shell: bash -el {0}
+
+    - name: Deploy to GitHub Pages
+      uses: peaceiris/actions-gh-pages@v4
+      if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+      with:
+        publish_branch: gh-pages
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: _build/
+        force_orphan: true
+
+
+

Now:

+
    +

  • Add these two changes to the GitHub repository.

    • +

  • Go to “Settings” -> “Pages” -> “Branch” -> gh-pages -> “Save”.

    • +

  • Look at “Actions” tab and observe the workflow running and hopefully +deploying the website.

    • +

  • Finally visit the generated site. You find it by clicking the About wheel +icon on top right of your repository. There, select “Use your GitHub Pages +website”.

    • +

  • This is how we build almost all of our lesson websites (including this one).

    • +

  • Another popular place to deploy Sphinx documentation is ReadTheDocs.

    • +
+
+
+
Optional: How to auto-generate API documentation in Python
+

Add three tiny modifications (highlighted) to doc/conf.py to auto-generate API documentation +(this requires the sphinx-autoapi package):

+
project = "planets"
+copyright = "2024, Authors"
+author = "Authors"
+release = "0.1"
+
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+extensions = [
+    "myst_parser",  # in order to use markdown
+    "autoapi.extension",  # in order to use markdown
+]
+
+# search this directory for Python files
+autoapi_dirs = [".."]
+
+# ignore this file when generating API documentation
+autoapi_ignore = ["*/conf.py"]
+
+myst_enable_extensions = [
+    "colon_fence",  # ::: can be used instead of ``` for better rendering
+]
+
+html_theme = "sphinx_rtd_theme"
+
+
+

Then rebuild the documentation (or push the changes and let GitHub rebuild it) +and you should see a new section “API Reference”.

+
+
+
Confused about reStructuredText vs. Markdown vs. MyST?
+
    +

  • At the beginning there was reStructuredText and Sphinx was built for reStructuredText.

    • +

  • Independently, Markdown was invented and evolved into a couple of flavors.

    • +

  • Markdown became more and more popular but was limited compared to reStructuredText.

    • +

  • Later, MyST +was invented to be able to write +something that looks like Markdown but in addition can do everything that +reStructuredText can do with extra directives.

    • +
+
+
+
Where to read more
+ +
+
+
+

Collaborative version control and code review

+
+
+
Concepts around collaboration
+
+

Objectives

+
    +

  • Be able to decide whether to divide work at the branch level or at the repository level.

    • +
+
+
+
Commits, branches, repositories, forks, clones
+
    +

  • repository: The project, contains all data and history (commits, branches, tags).

    • +

  • commit: Snapshot of the project, gets a unique identifier (e.g. c7f0e8bfc718be04525847fc7ac237f470add76e).

    • +

  • branch: Independent development line. The main development line is often called main.

    • +

  • tag: A pointer to one commit, to be able to refer to it later. Like a commemorative plaque +that you attach to a particular commit (e.g. phd-printed or paper-submitted).

    • +

  • cloning: Copying the whole repository to your laptop - the first time. It is not necessary to download each file one by one.

    • +

  • forking: Taking a copy of a repository (which is typically not yours) - your +copy (fork) stays on GitHub/GitLab and you can make changes to your copy.

    • +
+
+
+
Cloning a repository
+

In order to make a complete copy a whole repository, the git clone command +can be used. When cloning, all the files, of all or selected branches, of a +repository are copied in one operation. Cloning of a repository is of relevance +in a few different situations:

+
    +

  • Working on your own, cloning is the operation that you can use to create +multiple instances of a repository on, for instance, a personal computer, a +server, and a supercomputer.

    • +

  • The parent repository could be a repository that you or your colleague own. A +common use case for cloning is when working together within a smaller team +where everyone has read and write access to the same git repository.

    • +

  • Alternatively, cloning can be made from a public repository of a code that +you would like to use. Perhaps you have no intention to work on the code, but +would like to stay in tune with the latest developments, also in-between +releases of new versions of the code.

    • +
+
+Forking and cloning +
+

Forking and cloning

+
+
+
+
+
Forking a repository
+

When a fork is made on GitHub/GitLab a complete copy, of all or selected +branches, of the repository is made. The copy will reside under a different +account on GitHub/GitLab. Forking of a repository is of high relevance when +working with a git repository to which you do not have write access.

+
    +

  • In the fork repository commits can be made to the base branch (main or +master), and to other branches.

    • +

  • The commits that are made within the branches of the fork repository can be +contributed back to the parent repository by means of pull or merge requests.

    • +
+
+
+
Synchronizing changes between repositories
+
    +

  • We need a mechanism to communicate changes between the repositories.

    • +

  • We will pull or fetch updates from remote repositories (we will soon discuss the difference between pull and fetch).

    • +

  • We will push updates to remote repositories.

    • +

  • We will learn how to suggest changes within repositories on GitHub and across repositories (pull request).

    • +

  • Repositories that are forked or cloned do not automatically synchronize themselves: +We will learn how to update forks (by pulling from the “central” repository).

    • +

  • A main difference between cloning a repository and forking a repository is that the former is a general operation for generating copies of a repository to different computers, whereas forking is a particular operation implemented on GitHub/GitLab.

    • +
+
+
+
+
Collaborating within the same repository
+

In this episode, we will learn how to collaborate within the same repository. +We will learn how to cross-reference issues and pull requests, how to review +pull requests, and how to use draft pull requests.

+

This exercise will form a good basis for collaboration that is suitable for +most research groups.

+
+

Note

+

When you read or hear pull request, please think of a change proposal.

+
+
+
Exercise
+

In this exercise, we will contribute to a repository via a pull request. +This means that you propose some change, and then it is accepted (or not).

+
+

Exercise preparation

+
    +

  • First we need to get access to the exercise repository to which we will +contribute.

    +
      +

    • Instructor collects GitHub usernames from learners and adds them as collaborators to the exercise repository +(Settings -> Collaborators and teams -> Manage access -> Add people).

      • +
    +
    • +

  • Don’t forget to accept the invitation

    +
      +

    • Check https://github.com/settings/organizations/

      • +

    • Alternatively check the inbox for the email account you registered with +GitHub. GitHub emails you an invitation link, but if you don’t receive it +you can go to your GitHub notifications in the top right corner. The +maintainer can also “copy invite link” and share it within the group.

      • +
    +
    • +

  • Watching and unwatching repositories

    +
      +

    • Now that you are a collaborator, you get notified about new issues and pull +requests via email.

      • +

    • If you do not wish this, you can “unwatch” a repository (top of +the project page).

      • +

    • However, we recommend watching repositories you are interested +in. You can learn things from experts just by watching the +activity that come through a popular project.

      • +
    +
    +Unwatching a repository +
    +

    Unwatch a repository by clicking “Unwatch” in the repository view, +then “Participating and @mentions” - this way, you will get +notifications about your own interactions.

    +
    +
    +
    • +
+
+
+

Exercise: Collaborating within the same repository (25 min)

+

Technical requirements (from installation instructions):

+ +

What is familiar from the previous workshop day (not repeated here):

+
    +

  • Cloning a repository.

    • +

  • Creating a branch.

    • +

  • Committing a change on the new branch.

    • +

  • Submit a pull request towards the main branch.

    • +
+

What will be new in this exercise:

+
    +

  • If you create the changes locally, you will need to push them to the remote repository.

    • +

  • Learning what a protected branch is and how to modify a protected branch: using a pull request.

    • +

  • Cross-referencing issues and pull requests.

    • +

  • Practice to review a pull request.

    • +

  • Learn about the value of draft pull requests.

    • +
+

Exercise tasks:

+
    +

  1. Start in the exercise +repository and open an +issue where you describe the change you want to make. Note down the issue +number since you will need it later.

    2. +

  2. Create a new branch.

    3. +

  3. Make a change to the recipe book on the new branch and in the commit +cross-reference the issue you opened (see the walk-through below +for how to do that).

    4. +

  4. Push your new branch (with the new commit) to the repository you +are working on.

    5. +

  5. Open a pull request towards the main branch.

    6. +

  6. Review somebody else’s pull request and give constructive feedback. Merge their pull request.

    7. +

  7. Try to create a new branch with some half-finished work and open a draft +pull request. Verify that the draft pull request cannot be merged since it +is not meant to be merged yet.

    8. +
+
+
+
+
Solution and hints
+
+
(1) Opening an issue
+

This is done through the GitHub web interface. For example, you could +give the name of the recipe you want to add (so that others don’t add +the same one). It is the “Issues” tab.

+
+
+
(2) Create a new branch.
+

If on GitHub, you can make the branch in the web interface.

+
+
+
(3) Make a change adding the recipe
+

Add a new file with the recipe in it. Commit the file. In the commit +message, include the note about the issue number, saying that this +will close that issue.

+
+
Cross-referencing issues and pull requests
+

Each issue and each pull request gets a number and you can cross-reference them.

+

When you open an issue, note down the issue number (in this case it is #2):

+
+Each issue gets a number +
+

You can reference this issue number in a commit message or in a pull request, like in this +commit message:

+
this is the new recipe; fixes #2
+
+
+

If you forget to do that in your commit message, you can also reference the issue +in the pull request description. And instead of fixes you can also use closes or resolves +or fix or close or resolve (case insensitive).

+

Here are all the keywords that GitHub recognizes: +https://help.github.com/en/articles/closing-issues-using-keywords

+

Then observe what happens in the issue once your commit gets merged: it will +automatically close the issue and create a link between the issue and the +commit. This is very useful for tracking what changes were made in response to +which issue and to know from when until when precisely the issue was open.

+
+
+
+
(4) Push to GitHub as a new branch
+

Push the branch to the repository. You should end up with a branch +visible in the GitHub web view.

+

This is only necessary if you created the changes locally. If you created the +changes directly on GitHub, you can skip this step.

+
+

In VS Code, you can “publish the branch” to the remote repository by clicking +the cloud icon in the bottom left corner of the window:

+
+Publishing a branch in VS Code +
+
+
+
+
(5) Open a pull request towards the main branch
+

This is done through the GitHub web interface.

+
+
+
(6) Reviewing pull requests
+

You review through the GitHub web interface.

+

Checklist for reviewing a pull request:

+
    +

  • Be kind, on the other side is a human who has put effort into this.

    • +

  • Be constructive: if you see a problem, suggest a solution.

    • +

  • Towards which branch is this directed?

    • +

  • Is the title descriptive?

    • +

  • Is the description informative?

    • +

  • Scroll down to see commits.

    • +

  • Scroll down to see the changes.

    • +

  • If you get incredibly many changes, also consider the license or copyright +and ask where all that code is coming from.

    • +

  • Again, be kind and constructive.

    • +

  • Later we will learn how to suggest changes directly in the pull request.

    • +
+

If someone is new, it’s often nice to say something encouraging in the +comments before merging (even if it’s just “thanks”). If all is good +and there’s not much else to say, you could merge directly.

+
+
+
(7) Draft pull requests
+

Try to create a draft pull request:

+
+Creating a draft pull request +
+

Verify that the draft pull request cannot be merged until it is marked as ready +for review:

+
+Draft pull request cannot be merged +
+

Draft pull requests can be useful for:

+
    +

  • Feedback: You can open a pull request early to get feedback on your work without +signaling that it is ready to merge.

    • +

  • Information: They can help communicating to others that a change is coming up and in +progress.

    • +
+
+
+
What is a protected branch? And how to modify it?
+

A protected branch on GitHub or GitLab is a branch that cannot (accidentally) +deleted or force-pushed to. It is also possible to require that a branch cannot +be directly pushed to or modified, but that changes must be submitted via a +pull request.

+

To protect a branch in your own repository, go to “Settings” -> “Branches”.

+
+
+
Summary
+
    +

  • We used all the same pieces that we’ve learned previously.

    • +

  • But we successfully contributed to a collaborative project!

    • +

  • The pull request allowed us to contribute without changing directly: +this is very good when it’s not mainly our project.

    • +
+
+
+
+
+
Practicing code review
+

In this episode we will practice the code review process. We will learn how to +ask for changes in a pull request, how to suggest a change in a pull request, +and how to modify a pull request.

+

This will enable research groups to work more collaboratively and to not only +improve the code quality but also to learn from each other.

+
+
Exercise
+
+

Exercise preparation

+

We can continue in the same exercise repository which we have used in the +previous episode.

+
+
+

Exercise: Practicing code review (25 min)

+

Technical requirements:

+ +

What is familiar from previous lessons:

+
    +

  • Creating a branch.

    • +

  • Committing a change on the new branch.

    • +

  • Opening and merging pull requests.

    • +
+

What will be new in this exercise:

+
    +

  • As a reviewer, we will learn how to ask for changes in a pull request.

    • +

  • As a reviewer, we will learn how to suggest a change in a pull request.

    • +

  • As a submitter, we will learn how to modify a pull request without closing +the incomplete one and opening a new one.

    • +
+

Exercise tasks:

+
    +

  1. Create a new branch and one or few commits: in these improve something but also +deliberately introduce a typo and also a larger mistake which we will want to fix during the code review.

    2. +

  2. Open a pull request towards the main branch.

    3. +

  3. As a reviewer to somebody else’s pull request, ask for an improvement and +also directly suggest a change for the small typo. (Hint: +suggestions are possible through the GitHub web interface, view of +a pull request, “Files changed” view, after selecting some lines. +Look for the “±” button.)

    4. +

  4. As the submitter, learn how to accept the suggested change. (Hint: +GitHub web interface, “Files Changed” view.)

    5. +

  5. As the submitter, improve the pull request without having to close and open +a new one: by adding a new commit to the same branch. (Hint: push +to the branch again.)

    6. +

  6. Once the changes are addressed, merge the pull request.

    7. +
+
+
+
+
Help and discussion
+

From here on out, we don’t give detailed steps to the solution. You +need to combine what you know, and the extra info below, in order to +solve the above.

+
+
How to ask for changes in a pull request
+

Technically, there are at least two common ways to ask for changes in a pull +request.

+

Either in the comment field of the pull request:

+
+Screenshot of a pull request comment field +
+

Or by using the “Review changes”:

+
+Screenshot of a pull request navigating to the "Review changes" tab +
+

And always please be kind and constructive in your comments. Remember that the +goal is not gate-keeping but collaborative learning.

+
+
+
How to suggest a change in a pull request as a reviewer
+

If you see a very small problem that is easy to fix, you can suggest a change +as a reviewer.

+

Instead of asking the submitter to tiny problem, you can suggest a change by +clicking on the plus sign next to the line number in the “Files changed” tab:

+
+Screenshot of leaving a comment to a line in a pull request +
+

Here you can comment on specific lines or even line ranges.

+

But now the interesting part is to click on the “Add a suggestion” symbol (the +one that looks like plus and minus). Now you can fix the tiny problem (in this +case a typo) and then click on the “Add single comment” button:

+
+Sequence of clicks to add a suggestion to a line in a pull request +
+

The result is this and the submitter can accept the change with a single click:

+
+Screenshot of a pull request with a suggested change +
+

After accepting with “Commit suggestion”, the improvement gets added to the +pull request.

+
+
+
How to modify a pull request to address the review comments
+

If the reviewer asks for changes, it is not necessary to close the pull request +and later open a new one. It can even be counter-productive to do so: This can +fragment the discussion and the history of the pull request and can make it +harder to understand the context of the changes.

+

A much better mechanism to recognize that pull requests are not implemented +from a specific commit to a specific branch, but always from a branch to a +branch.

+

This means that you can make amendments to the pull request by adding new +commits to the same source branch. This way the pull request will be updated +automatically and the reviewer can see the new changes and comment on them.

+

The fact that pull requests are from branch to branch also strongly suggests +that it is a good practice to create a new branch for each pull request. +Otherwise you could accidentally modify an open pull request by adding new +commits to the source branch.

+
+
+
+
Summary
+
    +

  • Our process isn’t just about code now. It’s about discussion and +working together to make the whole process better.

    • +

  • GitHub discussions and reviewing are quite powerful and can make +small changes easy.

    • +
+
+
+
+
How to contribute changes to repositories that belong to others
+

In this episode we prepare you to suggest and contribute changes to +repositories that belong to others. These might be open source projects that +you use in your work.

+

We will see how Git and services like GitHub or GitLab can be used to suggest +modification without having to ask for write access to the repository and +accept modifications without having to grant write access to others.

+
+
Exercise
+
+

Exercise preparation

+
    +

  • The exercise repository is now different: +https://github.com/workshop-material/recipe-book-forking-exercise (note the -forking-exercise).

    • +

  • First fork the exercise repository to your GitHub account.

    • +

  • Then clone your fork to your computer (if you wish to work locally).

    • +

  • Double-check that you have forked the correct repository.

    • +
+
+
+

Exercise: Collaborating within the same repository (25 min)

+

Technical requirements:

+ +

What is familiar from previous lessons:

+
    +

  • Forking a repository.

    • +

  • Creating a branch.

    • +

  • Committing a change on the new branch.

    • +

  • Opening and merging pull requests.

    • +
+

What will be new in this exercise:

+
    +

  • Opening a pull request towards the upstream repository.

    • +

  • Pull requests can be coupled with automated testing.

    • +

  • Learning that your fork can get out of date.

    • +

  • After the pull requests are merged, updating your fork with the changes.

    • +

  • Learn how to approach other people’s repositories with ideas, changes, and requests.

    • +
+

Exercise tasks:

+
    +

  1. Open an issue in the upstream exercise repository where you describe the +change you want to make. Take note of the issue number.

    2. +

  2. Create a new branch in your fork of the repository.

    3. +

  3. Make a change to the recipe book on the new branch and in the commit cross-reference the issue you opened. +See the walk-through below for how to do this.

    4. +

  4. Open a pull request towards the upstream repository.

    5. +

  5. The instructor will review and merge the pull requests. +During the review, pay attention to the automated test step (here for +demonstration purposes, we test whether the recipe contains an ingredients +and an instructions sections).

    6. +

  6. After few pull requests are merged, update your fork with the changes.

    7. +

  7. Check that in your fork you can see changes from other people’s pull requests.

    8. +
+
+
+
+
Help and discussion
+
+
Help! I don’t have permissions to push my local changes
+

Maybe you see an error like this one:

+
Please make sure you have the correct access rights
+and the repository exists.
+
+
+

Or like this one:

+
failed to push some refs to workshop-material/recipe-book-forking-exercise.git
+
+
+

In this case you probably try to push the changes not to your fork but to the original repository +and in this exercise you do not have write access to the original repository.

+

The simpler solution is to clone again but this time your fork.

+ +
+
+
Opening a pull request towards the upstream repository
+

We have learned in the previous episode that pull requests are always from +branch to branch. But the branch can be in a different repository.

+

When you open a pull request in a fork, by default GitHub will suggest to +direct it towards the default branch of the upstream repository.

+

This can be changed and it should always be verified, but in this case this is +exactly what we want to do, from fork towards upstream:

+
+Screenshot of a pull request from fork towards upstream +
+
+
+
Pull requests can be coupled with automated testing
+

We added an automated test here just for fun and so that you see that this is +possible to do.

+

In this exercise, the test is silly. It will check whether the recipe contains +both an ingredients and an instructions section.

+

In this example the test failed:

+
+Screenshot of a failed test in a pull request +
+

Click on the “Details” link to see the details of the failed test:

+
+Screenshot of details why the test failed +
+

How can this be useful?

+
    +

  • The project can define what kind of tests are expected to pass before a pull +request can be merged.

    • +

  • The reviewer can see the results of the tests, without having to run them +locally.

    • +
+

How does it work?

+
    +

  • We added a GitHub Actions workflow +to automatically run on each push or pull request towards the main branch.

    • +
+

What tests or steps can you image for your project to run automatically with +each pull request?

+
+
+
How to update your fork with changes from upstream
+

This used to be difficult but now it is two mouse clicks.

+

Navigate to your fork and notice how GitHub tells you that your fork is behind. +In my case, it is 9 commits behind upstream. To fix this, click on “Sync fork” +and then “Update branch”:

+
+Screenshot on GitHub fork page showing that the fork is behind +
+

After the update my “branch is up to date” with the upstream repository:

+
+Screenshot on GitHub after fork has been updated +
+
+
+
How to approach other people’s repositories with ideas, changes, and requests
+

Contributing very minor changes

+
    +

  • Clone or fork+clone repository

    • +

  • Create a branch

    • +

  • Commit and push change

    • +

  • Open a pull request or merge request

    • +
+

If you observe an issue and have an idea how to fix it

+
    +

  • Open an issue in the repository you wish to contribute to

    • +

  • Describe the problem

    • +

  • If you have a suggestion on how to fix it, describe your suggestion

    • +

  • Possibly discuss and get feedback

    • +

  • If you are working on the fix, indicate it in the issue so that others know that somebody is working on it and who is working on it

    • +

  • Submit your fix as pull request or merge request which references/closes the issue

    • +
+
+

Motivation

+
    +

  • Inform others about an observed problem

    • +

  • Make it clear whether this issue is up for grabs or already being worked on

    • +
+
+

If you have an idea for a new feature

+
    +

  • Open an issue in the repository you wish to contribute to

    • +

  • In the issue, write a short proposal for your suggested change or new feature

    • +

  • Motivate why and how you wish to do this

    • +

  • Also indicate where you are unsure and where you would like feedback

    • +

  • Discuss and get feedback before you code

    • +

  • Once you start coding, indicate that you are working on it

    • +

  • Once you are done, submit your new feature as pull request or merge request which references/closes the issue/proposal

    • +
+
+

Motivation

+
    +

  • Get agreement and feedback before writing 5000 lines of code which might be rejected

    • +

  • If we later wonder why something was done, we have the issue/proposal as +reference and can read up on the reasoning behind a code change

    • +
+
+
+
+
+
Summary
+
    +

  • This forking workflow lets you propose changes to repositories for +which you have no write access.

    • +

  • This is the way that much modern open-source software works.

    • +

  • You can now contribute to any project you can view.

    • +
+
+
+
+
Conclict resolution, rebasing, and organizational strategies
+

(40 min demo and discussion)

+
+
+
+
+

Automated testing

+
+

Objectives

+
    +

  • Know where to start in your own project.

    • +

  • Have an example for how to make the testing part of code review.

    • +
+
+
+

Instructor note

+
    +

  • (15 min) Motivation

    • +

  • (15 min) End-to-end tests

    • +

  • (15 min) Pytest

    • +

  • (15 min) Adding the unit test to GitHub Actions

    • +

  • (10 min) What else is possible

    • +

  • (20 min) Exercise

    • +
+
+
+
Motivation
+

Testing is a way to check that the code does what it is expected to.

+
    +

  • Less scary to change code: tests will tell you whether something broke.

    • +

  • Easier for new people to join.

    • +

  • Easier for somebody to revive an old code.

    • +

  • End-to-end test: run the whole code and compare result to a reference.

    • +

  • Unit tests: test one unit (function or module). Can guide towards better +structured code: complicated code is more difficult to test.

    • +
+
+
+
How testing is often taught
+
def add(a, b):
+    return a + b
+
+
+def test_add():
+    assert add(1, 2) == 3
+
+
+

How this feels:

+
+Instruction on how to draw an owl +
+

[Citation needed]

+
+
+

Instead, we will look at and discuss a real example where we test components +from our example project.

+
+
+
Where to start
+

Short answer: Start with an end-to-end test.

+ +
+
+
End-to-end tests
+ +
+

Discussion

+

Is the end-to-end test +perfect? No. But it’s a good starting point. Discuss its limitations.

+
+
+
+
Pytest
+

First we need to add a test function, for instance +for this function:

+
def force_between_planets(position1, mass1, position2, mass2):
+    G = 1.0  # gravitational constant
+
+    r = position2 - position1
+    distance = (r[0] ** 2 + r[1] ** 2 + r[2] ** 2) ** 0.5
+    force_magnitude = G * mass1 * mass2 / distance**2
+    force = (r / distance) * force_magnitude
+
+    return force
+
+
+def test_force_between_planets():
+    position1 = np.array([0.0, 0.0, 0.0])
+    mass1 = 1.0
+    position2 = np.array([1.0, 0.0, 0.0])
+    mass2 = 2.0
+
+    force = force_between_planets(position1, mass1, position2, mass2)
+
+    assert np.allclose(force, [2.0, 0.0, 0.0])
+
+
+

Let us run the test with:

+
$ pytest simulate.py
+
+
+

Explanation: pytest will look for functions starting with test_ in files +and directories given as arguments. It will run them and report the results.

+

Now let us try this:

+
    +

  • Commit the test.

    • +

  • Break the function on purpose and run the test.

    • +

  • Does the test fail as expected?

    • +
+
+
+
Adding the unit test to GitHub Actions
+

Our next goal is that we want GitHub to run the unit test +automatically on every change.

+

First we need to extend our +environment.yml:

+
name: planets
+channels:
+  - conda-forge
+dependencies:
+  - python=3.12
+  - numpy
+  - click
+  - matplotlib
+  - pytest
+
+
+

We also need to extend .github/workflows/test.yml (highlighted line):

+
name: Test
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+
+    - uses: mamba-org/setup-micromamba@v1
+      with:
+        micromamba-version: '1.5.8-0' # any version from https://github.com/mamba-org/micromamba-releases
+        environment-file: environment.yml
+        init-shell: bash
+        cache-environment: true
+        post-cleanup: 'all'
+        generate-run-shell: false
+
+    - name: Run tests
+      run: |
+        ./test.sh
+        pytest simulate.py
+      shell: bash -el {0}
+
+
+

If we have time, we can try to create a pull request which would break the +code and see how the test fails.

+
+
+
What else is possible
+
    +

  • The testing above used example-based testing.

    • +

  • Test coverage: how much of the code is traversed by tests?

    + +
    • +

  • Property-based testing: generates arbitrary data matching your specification and checks that your guarantee still holds in that case.

    + +
    • +

  • Snapshot-based testing: makes it easier to generate snapshots for regression tests.

    + +
    • +

  • Mutation testing: tests pass -> change a line of code (make a mutant) -> test again and check whether all mutants get “killed”.

    + +
    • +
+
+
+
Exercises
+

Experiment with the example project and what we learned above or try it on your +own project:

+
    +

  • Add a unit test.

    • +

  • Try to run it locally.

    • +

  • Check whether it fails when you break the corresponding function.

    • +

  • Try to run it on GitHub Actions.

    • +

  • Create a pull request which would break the code and see whether the automatic test would catch it.

    • +

  • Try to design an end-to-end test for your project.

    • +
+
+
+
+

How to make the project more reusable

+

Part 1:

+
    +

  • 15 min: Motivation

    • +

  • 15 min: Best practices for managing dependencies in Python

    • +

  • 20 min: Exercise

    • +
+

Part 2:

+
    +

  • 10 min: Introduction to containers

    • +

  • 20 min: Demonstration

    • +

  • 10 min: Discussion

    • +
+
+
+

Demo: From a script towards a workflow

+

In this episode we will explore code quality and good practices in Python using +a hands-on approach. We will together build up a small project and improve it +step by step.

+

We will start from a relatively simple image processing script which can read a +telescope image of stars and our goal is to count the number of stars in +the image. Later we will want to be able to process many such images.

+

The (fictional) telescope images look like the one below here (in this +repository we can find more):

+
+Generated image representing a telescope image of stars +
+

Generated image representing a telescope image of stars.

+
+
+
+

Rough plan for this demo

+
    +

  • (15 min) Discuss how we would solve the problem, run example code, and make it work (as part of a Jupyter notebook)?

    • +

  • (15 min) Refactor the positioning code into a function and a module

    • +

  • (15 min) Now we wish to process many images - discuss how we would approach this

    • +

  • (15 min) Introduce CLI and discuss the benefits

    • +

  • (30 min) From a script to a workflow (using Snakemake)

    • +
+
+ +
+
Plan
+

Topics we wish to show and discuss:

+
    +

  • Naming (and other) conventions, project organization, modularity

    • +

  • The value of pure functions and immutability

    • +

  • Refactoring (explained through examples)

    • +

  • Auto-formatting and linting with tools like black, vulture, ruff

    • +

  • Moving a project under Git

    • +

  • How to document dependencies

    • +

  • Structuring larger software projects in a modular way

    • +

  • Command-line interfaces

    • +

  • Workflows with Snakemake

    • +
+

We will work together on the code on the big screen, and participants will be +encouraged to give suggestions and ask questions. We will end up with a Git +repository which will be shared with workshop participants.

+
+
+
Possible solutions
+ + +
+
+
+

Concepts in refactoring and modular code design

+

Topics:

+
    +

  • Pure functions

    • +

  • Design patterns: functional design vs. object-oriented design

    • +

  • How to design your code before writing it: document-driven development

    • +
+
+
+

How to release and publish your code

+

Part 1:

+
    +

  • 30 min: Overview over software licenses and code publishing

    • +

  • 15 min: We add a license, CFF file, and publish to Zenodo (sandbox)

    • +
+

Part 2:

+
    +

  • 30 min: Creating a Python package with the help of flit

    • +

  • 15 min: Deploy the package to test-PyPI using GitHub Actions

    • +
+
+
+

Profiling memory and CPU usage

+

Profilers:

+
    +

  • cProfile or profile

    • +

  • line_profiler

    • +

  • viztracer

    • +

  • scalene

    • +

  • Intel VTune

    • +

  • PyInstrument

    • +

  • py-spy

    • +

  • Pyflame

    • +

  • timeit

    • +
+

(here I will add some examples that we can profile together)

+
+
+
+
+

Credit

+

The following material (all CC-BY) was reused to create this workshop material:

+ +

(I will also summarize what changes have been made to the original material)

+
+
+
+
+
+ + +
+
+
+ +
+ +
+

© Copyright CodeRefinery team (CC-BY license).

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/singlehtml/objects.inv b/branch/main/singlehtml/objects.inv new file mode 100644 index 0000000..636e87a Binary files /dev/null and b/branch/main/singlehtml/objects.inv differ diff --git a/branch/main/testing/index.html b/branch/main/testing/index.html new file mode 100644 index 0000000..1ec8c5e --- /dev/null +++ b/branch/main/testing/index.html @@ -0,0 +1,379 @@ + + + + + + + Automated testing — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Automated testing

+
+

Objectives

+
    +

  • Know where to start in your own project.

    • +

  • Have an example for how to make the testing part of code review.

    • +
+
+
+

Instructor note

+
    +

  • (15 min) Motivation

    • +

  • (15 min) End-to-end tests

    • +

  • (15 min) Pytest

    • +

  • (15 min) Adding the unit test to GitHub Actions

    • +

  • (10 min) What else is possible

    • +

  • (20 min) Exercise

    • +
+
+
+

Motivation

+

Testing is a way to check that the code does what it is expected to.

+
    +

  • Less scary to change code: tests will tell you whether something broke.

    • +

  • Easier for new people to join.

    • +

  • Easier for somebody to revive an old code.

    • +

  • End-to-end test: run the whole code and compare result to a reference.

    • +

  • Unit tests: test one unit (function or module). Can guide towards better +structured code: complicated code is more difficult to test.

    • +
+
+
+

How testing is often taught

+
def add(a, b):
+    return a + b
+
+
+def test_add():
+    assert add(1, 2) == 3
+
+
+

How this feels:

+
+Instruction on how to draw an owl +
+

[Citation needed]

+
+
+

Instead, we will look at and discuss a real example where we test components +from our example project.

+
+
+

Where to start

+

Short answer: Start with an end-to-end test.

+ +
+
+

End-to-end tests

+ +
+

Discussion

+

Is the end-to-end test +perfect? No. But it’s a good starting point. Discuss its limitations.

+
+
+
+

Pytest

+

First we need to add a test function, for instance +for this function:

+
def force_between_planets(position1, mass1, position2, mass2):
+    G = 1.0  # gravitational constant
+
+    r = position2 - position1
+    distance = (r[0] ** 2 + r[1] ** 2 + r[2] ** 2) ** 0.5
+    force_magnitude = G * mass1 * mass2 / distance**2
+    force = (r / distance) * force_magnitude
+
+    return force
+
+
+def test_force_between_planets():
+    position1 = np.array([0.0, 0.0, 0.0])
+    mass1 = 1.0
+    position2 = np.array([1.0, 0.0, 0.0])
+    mass2 = 2.0
+
+    force = force_between_planets(position1, mass1, position2, mass2)
+
+    assert np.allclose(force, [2.0, 0.0, 0.0])
+
+
+

Let us run the test with:

+
$ pytest simulate.py
+
+
+

Explanation: pytest will look for functions starting with test_ in files +and directories given as arguments. It will run them and report the results.

+

Now let us try this:

+
    +

  • Commit the test.

    • +

  • Break the function on purpose and run the test.

    • +

  • Does the test fail as expected?

    • +
+
+
+

Adding the unit test to GitHub Actions

+

Our next goal is that we want GitHub to run the unit test +automatically on every change.

+

First we need to extend our +environment.yml:

+
name: planets
+channels:
+  - conda-forge
+dependencies:
+  - python=3.12
+  - numpy
+  - click
+  - matplotlib
+  - pytest
+
+
+

We also need to extend .github/workflows/test.yml (highlighted line):

+
name: Test
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+
+    - uses: mamba-org/setup-micromamba@v1
+      with:
+        micromamba-version: '1.5.8-0' # any version from https://github.com/mamba-org/micromamba-releases
+        environment-file: environment.yml
+        init-shell: bash
+        cache-environment: true
+        post-cleanup: 'all'
+        generate-run-shell: false
+
+    - name: Run tests
+      run: |
+        ./test.sh
+        pytest simulate.py
+      shell: bash -el {0}
+
+
+

If we have time, we can try to create a pull request which would break the +code and see how the test fails.

+
+
+

What else is possible

+
    +

  • The testing above used example-based testing.

    • +

  • Test coverage: how much of the code is traversed by tests?

    + +
    • +

  • Property-based testing: generates arbitrary data matching your specification and checks that your guarantee still holds in that case.

    + +
    • +

  • Snapshot-based testing: makes it easier to generate snapshots for regression tests.

    + +
    • +

  • Mutation testing: tests pass -> change a line of code (make a mutant) -> test again and check whether all mutants get “killed”.

    + +
    • +
+
+
+

Exercises

+

Experiment with the example project and what we learned above or try it on your +own project:

+
    +

  • Add a unit test.

    • +

  • Try to run it locally.

    • +

  • Check whether it fails when you break the corresponding function.

    • +

  • Try to run it on GitHub Actions.

    • +

  • Create a pull request which would break the code and see whether the automatic test would catch it.

    • +

  • Try to design an end-to-end test for your project.

    • +
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/version-control/branching-and-committing/index.html b/branch/main/version-control/branching-and-committing/index.html new file mode 100644 index 0000000..2827392 --- /dev/null +++ b/branch/main/version-control/branching-and-committing/index.html @@ -0,0 +1,432 @@ + + + + + + + Creating branches and commits — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Creating branches and commits

+

The first and most basic task to do in Git is record changes using +commits. In this part, we will record changes in two +ways: on a new branch (which supports multiple lines of work at once), and directly +on the “main” branch (which happens to be the default branch here).

+
+

Objectives

+
    +

  • Record new changes to our own copy of the project.

    • +

  • Understand adding changes in two separate branches.

    • +

  • See how to compare different versions.

    • +
+
+
+

Background

+
    +

  • In the previous episode we have browsed an existing repository and saw commits +and branches.

    • +

  • Each commit is a snapshot of the entire project at a certain +point in time and has a unique identifier (hash) .

    • +

  • A branch is a line of development, and the main branch or master branch +are often the default branch in Git.

    • +

  • A branch in Git is like a sticky note that is attached to a commit. When we add +new commits to a branch, the sticky note moves to the new commit.

    • +

  • Tags are a way to mark a specific commit as important, for example a release +version. They are also like a sticky note, but they don’t move when new +commits are added.

    • +
+
+Branching explained with a gopher +
+

What if two people, at the same time, make two different changes? Git +can merge them together easily. Image created using https://gopherize.me/ +(inspiration).

+
+
+
+
+

Exercise: Creating branches and commits

+
+Illustration of what we want to achieve in this exercise +
+

Illustration of what we want to achieve in this exercise.

+
+
+
+

Exercise: Practice creating commits and branches (20 min)

+
    +

  1. First create a new branch and then either add a new file or modify an +existing file and commit the change. Make sure that you now work on your +copy of the example repository. In your commit you can share a Git or +programming trick you like.

    2. +

  2. In a new commit, modify the file again.

    3. +

  3. Switch to the main branch and create a commit there.

    4. +

  4. Browse the network and locate the commits that you just created (“Insights” -> “Network”).

    5. +

  5. Compare the branch that you created with the main branch. Can you find an easy way to see the differences?

    6. +

  6. Can you find a way to compare versions between two arbitrary commits in the repository?

    7. +

  7. Try to rename the branch that you created and then browse the network again.

    8. +

  8. Try to create a tag for one of the commits that you created (on GitHub, +create a “release”).

    9. +
+
+

The solution below goes over most of the answers, and you are +encouraged to use it when the hints aren’t enough - this is by +design.

+
+
+

Solution and walk-through

+
+

(1) Create a new branch and a new commit

+
+
    +

  1. Where it says “main” at the top left, click, enter a new branch +name new-tutorial, click on the offer to create the new branch +(“Create branch new-tutorial from main”).

    2. +

  2. Make sure you are still on the new-tutorial branch (it should say +it at the top), and click “Add file” → “Create new file” from the +upper right.

    3. +

  3. Enter a filename where it says “Name your file…”.

    4. +

  4. Share some Git or programming trick you like.

    5. +

  5. Click “Commit changes”

    6. +

  6. Enter a commit message. Then click “Commit +changes”.

    7. +
+

You should appear back at the file browser view, and see your +modification there.

+
+
+
+

(2) Modify the file again with a new commit

+
+

This is similar to before, but we click on the existing file to +modify.

+
    +

  1. Click on the file you added or modified previously.

    2. +

  2. Click the edit button, the pencil icon at top-right.

    3. +

  3. Follow the “Commit changes” instructions as in the previous step.

    4. +
+
+
+
+

(3) Switch to the main branch and create a commit there

+
+
    +

  1. Go back to the main repository page (your user’s page).

    2. +

  2. In the branch switch view (top left above the file view), switch to +main.

    3. +

  3. Modify another file that already exists, following the pattern +from above.

    4. +
+
+
+
+

(4) Browse the commits you just made

+

Let’s look at what we did. Now, the main and new-tutorial branches +have diverged: both have some modifications. Try to find the commits +you created.

+
+

Insights tab → Network view (just like we have done before).

+
+
+
+

(5) Compare the branches

+

Comparing changes is an important thing we need to do. When using the +GitHub view only, this may not be so common, but we’ll show it so that +it makes sense later on.

+
+

A nice way to compare branches is to add /compare to the URL of the repository, +for example (replace USER): +https://github.com/USER/planets/compare

+
+
+
+

(6) Compare two arbitrary commits

+

This is similar to above, but not only between branches.

+
+

Following the /compare-trick above, one can compare commits on GitHub by +adjusting the following URL: +https://github.com/USER/planets/compare/VERSION1..VERSION2

+

Replace USER with your username and VERSION1 and VERSION2 with a commit hash or branch name. +Please try it out.

+
+
+
+

(7) Renaming a branch

+
+

Branch button → View all branches → three dots at right side → Rename branch.

+
+
+
+

(8) Creating a tag

+

Tags are a way to mark a specific commit as important, for example a release +version. They are also like a sticky note, but they don’t move when new +commits are added.

+
+

On the right side, below “Releases”, click on “Create a new release”.

+

What GitHub calls releases are actually tags in Git with additional metadata. +For the purpose of this exercise we can use them interchangeably.

+
+
+
+
+

Summary

+

In this part, we saw how we can make changes to our files. With branches, we +can track several lines of work at once, and can compare their differences.

+
    +

  • You could commit directly to main if there is only one single line +of work and it’s only you.

    • +

  • You could commit to branches if there are multiple lines of work at +once, and you don’t want them to interfere with each other.

    • +

  • Tags are useful to mark a specific commit as important, for example a +release version.

    • +

  • In Git, commits form a so-called “graph”. Branches are tags in Git function +like sticky notes that stick to specific commits. What this means for us is +that it does not cost any significant disk space to create new branches.

    • +

  • Not all files should be added to Git. For example, temporary files or +files with sensitive information or files which are generated as part of +the build process should not be added to Git. For this we use +.gitignore (more about this later: Practical advice: How much Git is necessary?).

    • +

  • Unsure on which branch you are or what state the repository is in? +On the command line, use git status frequently to get a quick overview.

    • +
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/version-control/browsing/index.html b/branch/main/version-control/browsing/index.html new file mode 100644 index 0000000..b36d1e3 --- /dev/null +++ b/branch/main/version-control/browsing/index.html @@ -0,0 +1,456 @@ + + + + + + + Forking, cloning, and browsing — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Forking, cloning, and browsing

+

In this episode, we will look at an existing repository to understand how +all the pieces work together. Along the way, we will make a copy (by +forking and/or cloning) of the repository for us, which will be used +for our own changes.

+
+

Objectives

+
    +

  • See a real Git repository and understand what is inside of it.

    • +

  • Understand how version control allows advanced inspection of a +repository.

    • +

  • See how Git allows multiple people to work on the same project at the same time.

    • +

  • See the big picture instead of remembering a bunch of commands.

    • +
+
+
+

GitHub, VS Code, or command line

+

We offer three different paths for this exercise:

+
    +

  • GitHub (this is the one we will demonstrate)

    • +

  • VS Code (if you prefer to follow along using an editor)

    • +

  • Command line (for people comfortable with the command line)

    • +
+
+
+

Creating a copy of the repository by “forking” or “cloning”

+

A repository is a collection of files in one directory tracked by Git. A +GitHub repository is GitHub’s copy, which adds things like access control, +issue tracking, and discussions. Each GitHub repository is owned by a user or +organization, who controls access.

+

First, we need to make our own copy of the exercise repository. This will +become important later, when we make our own changes.

+
+Illustration of forking a repository on GitHub +
+

Illustration of forking a repository on GitHub.

+
+
+
+Illustration of cloning a repository to your computer +
+

Illustration of cloning a repository to your computer.

+
+
+
+Illustration of cloning a forked repository to your computer +
+

It is also possible to do this: to clone a forked repository to your computer.

+
+
+

At all times you should be aware of if you are looking at your repository +or the upstream repository (original repository):

+
    +

  • Your repository: https://github.com/USER/planets

    • +

  • Upstream repository: https://github.com/workshop-material/planets

    • +
+
+

How to create a fork

+
    +

  1. Go to the repository view on GitHub: https://github.com/workshop-material/planets

    2. +

  2. First, on GitHub, click the button that says “Fork”. It is towards +the top-right of the screen.

    3. +

  3. You should shortly be redirected to your copy of the repository +USER/planets.

    4. +
+
+
+

Instructor note

+

Before starting the exercise session show +how to fork the repository to own account +(above).

+
+
+
+

Exercise: Copy and browse an existing project

+

Work on this by yourself or in pairs.

+
+

Exercise preparation

+
+

In this case you will work on a fork.

+

You only need to open your own view, as described above. The browser +URL should look like https://github.com/USER/planets, where +USER is your GitHub username.

+
+
+
+

Exercise: Browsing an existing project (20 min)

+

Browse the example project and +explore commits and branches, either on a fork or on a clone. Take notes and +prepare questions. The hints are for the GitHub path in the browser.

+
    +

  1. Browse the commit history: Are commit messages understandable? +(Hint: “Commit history”, the timeline symbol, above the file list)

    2. +

  2. Compare the commit history with the network graph (“Insights” -> “Network”). Can you find the branches?

    3. +

  3. Try to find the history of commits for a single file, e.g. simulate.py. +(Hint: “History” button in the file view)

    4. +

  4. Which files include the word “position”? +(Hint: the GitHub search on top of the repository view)

    5. +

  5. In the simulate.py file, find out who modified each line last and when +(click on file, then click “Blame” button). Find out who modified the gravitational constant +last and in which commit. +(Hint: “Blame” view in the file view)

    6. +

  6. Can you use this code yourself? Are you allowed to share +modifications? +(Hint: look for a license file)

    7. +
+
+

The solution below goes over most of the answers, and you are +encouraged to use it when the hints aren’t enough - this is by +design.

+
+
+

Solution and walk-through

+
+

(1) Basic browsing

+

The most basic thing to look at is the history of commits.

+
    +

  • This is visible from a button in the repository view. We see every +change, when, and who has committed.

    • +

  • Every change has a unique identifier, such as 244c993. This can +be used to identify both this change, and the whole project’s +version as of that change.

    • +

  • Clicking on a change in the view shows more.

    • +
+
+

Click on the timeline symbol in the repository view:

+
+Screenshot on GitHub of where to find the commit history +
+
+
+
+

(2) Compare commit history with network graph

+

The commit history we saw above looks linear: one commit after +another. But if we look at the network view, we see some branches and +merges. We’ll see how to do these later. This is another one of the +basic Git views.

+
+

In a new browser tab, open the “Insights” tab, and click on “Network”. +You can hover over the commit dots to see the person who committed and +how they correspond with the commits in the other view:

+
+Screenshot on GitHub of the network graph +
+
+
+
+

(3) How can you browse the history of a single file?

+

We see the history for the whole repository, but we can also see it +for a single file.

+
+

Navigate to the file view: Main page → simulate.py. +Click the “History” button near the top right.

+
+
+
+

(4) Which files include the word “position”?

+

Version control makes it very easy to find all occurrences of a single +word. This is useful for things like finding where functions or +variables are defined or used.

+
+

We go to the main file view. We click the Search magnifying +class at the very top, type “position”, and click enter. We see every +instance, including the context.

+
+

Searching in a forked repository will not work instantaneously!

+

It usually takes a few minutes before one can search for keywords in a forked repository +since it first needs to build the search index the very first time we search. +Start it, continue with other steps, then come back to this.

+
+
+
+
+

(5) Who modified each line last and when?

+

This is called the “annotate” or “blame” view. The name “blame” +is very unfortunate, but it is the standard term for historical reasons +for this functionality and it is not meant to blame anyone.

+
+

From a file view, change preview to “Blame” towards the top-left. +To get the actual commit, click on the commit message.

+
+
+
+

(6) Can you use this code yourself? Are you allowed to share modifications?

+
    +

  • Look at the file LICENSE.

    • +

  • On GitHub, click on the file to see a nice summary of what we can do with this:

    +
    +Screenshot on GitHub summarizing license terms +
    +
    • +
+
+
+

Summary

+
    +

  • Git allowed us to understand this simple project much better than we +could, if it was just a few files on our own computer.

    • +

  • It was easy to share the project with the course.

    • +

  • By forking the repository, we created our own copy. This is +important for the following, where we will make changes to +our copy.

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/version-control/index.html b/branch/main/version-control/index.html new file mode 100644 index 0000000..f5e96bc --- /dev/null +++ b/branch/main/version-control/index.html @@ -0,0 +1,167 @@ + + + + + + + Introduction to version control with Git and GitHub — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Introduction to version control with Git and GitHub
    • +
  • + Edit on GitHub +
    • +
+
+
+
+ +
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/version-control/motivation/index.html b/branch/main/version-control/motivation/index.html new file mode 100644 index 0000000..454a972 --- /dev/null +++ b/branch/main/version-control/motivation/index.html @@ -0,0 +1,283 @@ + + + + + + + Motivation — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+ +
+
+ +
+

Motivation

+
+

Objectives

+
    +

  • Browse commits and branches of a Git repository.

    • +

  • Remember that commits are like snapshots of the repository at a certain +point in time.

    • +

  • Know the difference between Git (something that tracks changes) and +GitHub/GitLab (a platform to host Git repositories).

    • +
+
+
+

Why do we need to keep track of versions?

+

Version control is an answer to the following questions (do you recognize some +of them?):

+
    +

  • “It broke … hopefully I have a working version somewhere?”

    • +

  • “Can you please send me the latest version?”

    • +

  • “Where is the latest version?”

    • +

  • “Which version are you using?”

    • +

  • “Which version have the authors used in the paper I am trying to reproduce?”

    • +

  • “Found a bug! Since when was it there?”

    • +

  • “I am sure it used to work. When did it change?”

    • +

  • “My laptop is gone. Is my thesis now gone?”

    • +
+
+
+

Demonstration

+
    +

  • Example repository: https://github.com/workshop-material/planets

    • +

  • Commits are like snapshots and if we break something we can go back to a +previous snapshot.

    • +

  • Commits carry metadata about changes: author, date, commit message, and +a checksum.

    • +

  • Branches are like parallel universes where you can experiment with +changes without affecting the default branch: +https://github.com/workshop-material/planets/network +(“Insights” -> “Network”)

    • +

  • With version control we can annotate code +(example).

    • +

  • Collaboration: We can fork (make a copy on GitHub), clone (make a copy +to our computer), review, compare, share, and discuss.

    • +

  • Code review: Others can suggest changes using pull requests or merge +requests. These can be reviewed and discussed before they are merged. +Conceptually, they are similar to “suggesting changes” in Google Docs.

    • +
+
+
+

Features: roll-back, branching, merging, collaboration

+
    +

  • Roll-back: you can always go back to a previous version and compare

    • +

  • Branching and merging:

    +
      +

    • Work on different ideas at the same time

      • +

    • Different people can work on the same code/project without interfering

      • +

    • You can experiment with an idea and discard it if it turns out to be a bad idea

      • +
    +
    • +
+
+Branching explained with a gopher +
+

Image created using https://gopherize.me/ +(inspiration).

+
+
+ +
+
+

Talking about code

+

Which of these two is more practical?

+
    +

  1. “Clone the code, go to the file ‘simulate.py’, and search for ‘force_between_planets’. +Oh! But make sure you use the version from September 2024.”

    2. +

  2. Or I can send you a permalink: https://github.com/workshop-material/planets/blob/1343ac0/simulate.py#L31C5-L39

    3. +
+
+
+

What we typically like to snapshot

+
    +

  • Software (this is how it started but Git/GitHub can track a lot more)

    • +

  • Scripts

    • +

  • Documents (plain text files much better suitable than Word documents)

    • +

  • Manuscripts (Git is great for collaborating/sharing LaTeX or Quarto manuscripts)

    • +

  • Configuration files

    • +

  • Website sources

    • +

  • Data

    • +
+
+

Discussion

+

In this example somebody tried to keep track of versions without a version +control system tool like Git. Discuss the following directory listing. What +possible problems do you anticipate with this kind of “version control”:

+
myproject-2019.zip
+myproject-2020-february.zip
+myproject-2021-august.zip
+myproject-2023-09-19-working.zip
+myproject-2023-09-21.zip
+myproject-2023-09-21-test.zip
+myproject-2023-09-21-myversion.zip
+myproject-2023-09-21-newfeature.zip
+...
+(100 more files like these)
+
+
+ +
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/version-control/practical-advice/index.html b/branch/main/version-control/practical-advice/index.html new file mode 100644 index 0000000..bcc49ec --- /dev/null +++ b/branch/main/version-control/practical-advice/index.html @@ -0,0 +1,300 @@ + + + + + + + Practical advice: How much Git is necessary? — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Practical advice: How much Git is necessary?

+
+

Writing useful commit messages

+

Useful commit messages summarize the change and provide context.

+

If you need a commit message that is longer than one line, +then the convention is: one line summarizing the commit, then one empty line, +then paragraph(s) with more details in free form, if necessary.

+

Good example:

+
increase alpha to 2.0 for faster convergence
+
+the motivation for this change is
+to enable ...
+...
+(more context)
+...
+this is based on a discussion in #123
+
+
+
    +

  • Why something was changed is more important than what has changed.

    • +

  • Cross-reference to issues and discussions if possible/relevant.

    • +

  • Bad commit messages: “fix”, “oops”, “save work”

    • +

  • Bad examples: http://whatthecommit.com

    • +

  • Write commit messages that will be understood +15 years from now by someone else than you. Or by your future you.

    • +

  • Many projects start out as projects “just for me” and end up to be successful projects +that are developed by 50 people over decades.

    • +

  • Commits with multiple authors are possible.

    • +
+

Good references:

+ +
+

Note

+

A great way to learn how to write commit messages and to get inspired by their +style choices: browse repositories of codes that you use/like:

+

Some examples (but there are so many good examples):

+ +

When designing commit message styles consider also these:

+
    +

  • How will you easily generate a changelog or release notes?

    • +

  • During code review, you can help each other improving commit messages.

    • +
+
+

But remember: it is better to make any commit, than no commit. Especially in small projects. +Let not the perfect be the enemy of the good enough.

+
+
+

What level of branching complexity is necessary for each project?

+

Simple personal projects:

+
    +

  • Typically start with just the main branch.

    • +

  • Use branches for unfinished/untested ideas.

    • +

  • Use branches when you are not sure about a change.

    • +

  • Use tags to mark important milestones.

    • +

  • If you are unsure what to do with unfinished and not working code, commit it +to a branch.

    • +
+

Projects with few persons: you accept things breaking sometimes

+
    +

  • It might be reasonable to commit to the main branch and feature branches.

    • +
+

Projects with few persons: changes are reviewed by others

+
    +

  • You create new feature branches for changes.

    • +

  • Changes are reviewed before they are merged to the main branch.

    • +

  • Consider to write-protect the main branch so that it can only be changed +with pull requests or merge requests.

    • +
+
+
+

How large should a commit be?

+
    +

  • Better too small than too large (easier to combine than to split).

    • +

  • Often I make a commit at the end of the day (this is a unit I would not like to lose).

    • +

  • Smaller sized commits may be easier to review for others than huge commits.

    • +

  • Imperfect commits are better than no commits.

    • +

  • A commit should not contain unrelated changes to simplify review and possible +repair/adjustments/undo later (but again: imperfect commits are better than no commits).

    • +
+
+
+

Working on the command line? Use “git status” all the time

+

The git status command is one of the most useful commands in Git +to inform about which branch we are on, what we are about to commit, +which files might not be tracked, etc.

+
+
+

How about staging and committing?

+
    +

  • Commit early and often: rather create too many commits than too few. +You can always combine commits later.

    • +

  • Once you commit, it is very, very hard to really lose your code.

    • +

  • Always fully commit (or stash) before you do dangerous things, so that you know you are safe. +Otherwise it can be hard to recover.

    • +

  • Later you can start using the staging area (where you first stage and then commit in a second step).

    • +

  • Later start using git add -p and/or git commit -p.

    • +
+
+
+

What to avoid

+
    +

  • Committing generated files/directories (example: __pycache__, *.pyc) -> +use .gitignore +files +(collection of .gitignore templates).

    • +

  • Committing huge files -> use code review to detect this.

    • +

  • Committing unrelated changes together.

    • +

  • Postponing commits because the changes are “unfinished”/”ugly” -> better ugly +commits than no commits.

    • +

  • When working with branches:

    +
      +

    • Not updating your branch before starting new work.

      • +

    • Too ambitious branch which risks to never get completed.

      • +

    • Over-engineering the branch layout and safeguards in small projects.

      • +

    • Working on unrelated things on the same branch.

      • +
    +
    • +
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/version-control/sharing/index.html b/branch/main/version-control/sharing/index.html new file mode 100644 index 0000000..7621f54 --- /dev/null +++ b/branch/main/version-control/sharing/index.html @@ -0,0 +1,405 @@ + + + + + + + Optional: How to turn your project to a Git repo and share it — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Optional: How to turn your project to a Git repo and share it

+
+

Objectives

+
    +

  • Turn our own coding project (small or large, finished or unfinished) into a +Git repository.

    • +

  • Be able to share a repository on the web to have a backup or so that others +can reuse and collaborate or even just find it.

    • +
+
+
+

Exercise

+
+Illustration of how we turn a project into a Git repository and share it +
+

From a bunch of files to a local repository which we then share on GitHub.

+
+
+
+

Exercise: Turn your project to a Git repo and share it (20 min)

+
    +

  1. Create a new directory called myproject with one or few files in it. +This represents our own project. It is not yet a Git repository. You can try +that with your own project or use a simple placeholder example.

    2. +

  2. Turn this new directory into a Git repository.

    3. +

  3. Share this repository on GitHub (or GitLab, since it really works the same).

    4. +
+

We offer three different paths of how to do this exercise.

+
    +

  • Via GitHub web interface: easy and can be a good starting point if you are completely +new to Git.

    • +

  • VS Code is quite easy, since VS Code can offer to create the +GitHub repositories for you.

    • +

  • Command line: you need to create the +repository on GitHub and link it yourself.

    • +
+
+

Create an repository on GitHub

+

First log into GitHub, then follow the screenshots and descriptions below.

+
+Screenshot on GitHub before a new repository form is opened +
+

Click on the “plus” symbol on top right, then on “New repository”.

+
+
+

Then:

+
+Screenshot on GitHub just before a new repository is created +
+

Choose a repository name, add a short description, and in this case make sure to check “Add a +README file”. Finally “Create repository”.

+
+
+

Upload your files

+

Now that the repository is created, you can upload your files:

+
+Screenshot on GitHub just before uploading files +
+

Click on the “+” symbol and then on “Upload files”.

+
+
+
+
+
+
+

Is putting software on GitHub/GitLab/… publishing?

+

It is a good first step but to make your code truly findable and +accessible, consider making your code citable and persistent: Get a +persistent identifier (PID) such as DOI in addition to sharing the code +publicly, by using services like Zenodo or similar +services.

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/collaboration/code-review/index.html b/collaboration/code-review/index.html new file mode 100644 index 0000000..2db66b2 --- /dev/null +++ b/collaboration/code-review/index.html @@ -0,0 +1,289 @@ + + + + + + + Practicing code review — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Practicing code review

+

In this episode we will practice the code review process. We will learn how to +ask for changes in a pull request, how to suggest a change in a pull request, +and how to modify a pull request.

+

This will enable research groups to work more collaboratively and to not only +improve the code quality but also to learn from each other.

+
+

Exercise

+
+

Exercise preparation

+

We can continue in the same exercise repository which we have used in the +previous episode.

+
+
+

Exercise: Practicing code review (25 min)

+

Technical requirements:

+ +

What is familiar from previous lessons:

+
    +

  • Creating a branch.

    • +

  • Committing a change on the new branch.

    • +

  • Opening and merging pull requests.

    • +
+

What will be new in this exercise:

+
    +

  • As a reviewer, we will learn how to ask for changes in a pull request.

    • +

  • As a reviewer, we will learn how to suggest a change in a pull request.

    • +

  • As a submitter, we will learn how to modify a pull request without closing +the incomplete one and opening a new one.

    • +
+

Exercise tasks:

+
    +

  1. Create a new branch and one or few commits: in these improve something but also +deliberately introduce a typo and also a larger mistake which we will want to fix during the code review.

    2. +

  2. Open a pull request towards the main branch.

    3. +

  3. As a reviewer to somebody else’s pull request, ask for an improvement and +also directly suggest a change for the small typo. (Hint: +suggestions are possible through the GitHub web interface, view of +a pull request, “Files changed” view, after selecting some lines. +Look for the “±” button.)

    4. +

  4. As the submitter, learn how to accept the suggested change. (Hint: +GitHub web interface, “Files Changed” view.)

    5. +

  5. As the submitter, improve the pull request without having to close and open +a new one: by adding a new commit to the same branch. (Hint: push +to the branch again.)

    6. +

  6. Once the changes are addressed, merge the pull request.

    7. +
+
+
+
+

Help and discussion

+

From here on out, we don’t give detailed steps to the solution. You +need to combine what you know, and the extra info below, in order to +solve the above.

+
+

How to ask for changes in a pull request

+

Technically, there are at least two common ways to ask for changes in a pull +request.

+

Either in the comment field of the pull request:

+
+Screenshot of a pull request comment field +
+

Or by using the “Review changes”:

+
+Screenshot of a pull request navigating to the "Review changes" tab +
+

And always please be kind and constructive in your comments. Remember that the +goal is not gate-keeping but collaborative learning.

+
+
+

How to suggest a change in a pull request as a reviewer

+

If you see a very small problem that is easy to fix, you can suggest a change +as a reviewer.

+

Instead of asking the submitter to tiny problem, you can suggest a change by +clicking on the plus sign next to the line number in the “Files changed” tab:

+
+Screenshot of leaving a comment to a line in a pull request +
+

Here you can comment on specific lines or even line ranges.

+

But now the interesting part is to click on the “Add a suggestion” symbol (the +one that looks like plus and minus). Now you can fix the tiny problem (in this +case a typo) and then click on the “Add single comment” button:

+
+Sequence of clicks to add a suggestion to a line in a pull request +
+

The result is this and the submitter can accept the change with a single click:

+
+Screenshot of a pull request with a suggested change +
+

After accepting with “Commit suggestion”, the improvement gets added to the +pull request.

+
+
+

How to modify a pull request to address the review comments

+

If the reviewer asks for changes, it is not necessary to close the pull request +and later open a new one. It can even be counter-productive to do so: This can +fragment the discussion and the history of the pull request and can make it +harder to understand the context of the changes.

+

A much better mechanism to recognize that pull requests are not implemented +from a specific commit to a specific branch, but always from a branch to a +branch.

+

This means that you can make amendments to the pull request by adding new +commits to the same source branch. This way the pull request will be updated +automatically and the reviewer can see the new changes and comment on them.

+

The fact that pull requests are from branch to branch also strongly suggests +that it is a good practice to create a new branch for each pull request. +Otherwise you could accidentally modify an open pull request by adding new +commits to the source branch.

+
+
+
+

Summary

+
    +

  • Our process isn’t just about code now. It’s about discussion and +working together to make the whole process better.

    • +

  • GitHub discussions and reviewing are quite powerful and can make +small changes easy.

    • +
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/collaboration/concepts/index.html b/collaboration/concepts/index.html new file mode 100644 index 0000000..f4c073d --- /dev/null +++ b/collaboration/concepts/index.html @@ -0,0 +1,234 @@ + + + + + + + Concepts around collaboration — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Concepts around collaboration

+
+

Objectives

+
    +

  • Be able to decide whether to divide work at the branch level or at the repository level.

    • +
+
+
+

Commits, branches, repositories, forks, clones

+
    +

  • repository: The project, contains all data and history (commits, branches, tags).

    • +

  • commit: Snapshot of the project, gets a unique identifier (e.g. c7f0e8bfc718be04525847fc7ac237f470add76e).

    • +

  • branch: Independent development line. The main development line is often called main.

    • +

  • tag: A pointer to one commit, to be able to refer to it later. Like a commemorative plaque +that you attach to a particular commit (e.g. phd-printed or paper-submitted).

    • +

  • cloning: Copying the whole repository to your laptop - the first time. It is not necessary to download each file one by one.

    • +

  • forking: Taking a copy of a repository (which is typically not yours) - your +copy (fork) stays on GitHub/GitLab and you can make changes to your copy.

    • +
+
+
+

Cloning a repository

+

In order to make a complete copy a whole repository, the git clone command +can be used. When cloning, all the files, of all or selected branches, of a +repository are copied in one operation. Cloning of a repository is of relevance +in a few different situations:

+
    +

  • Working on your own, cloning is the operation that you can use to create +multiple instances of a repository on, for instance, a personal computer, a +server, and a supercomputer.

    • +

  • The parent repository could be a repository that you or your colleague own. A +common use case for cloning is when working together within a smaller team +where everyone has read and write access to the same git repository.

    • +

  • Alternatively, cloning can be made from a public repository of a code that +you would like to use. Perhaps you have no intention to work on the code, but +would like to stay in tune with the latest developments, also in-between +releases of new versions of the code.

    • +
+
+Forking and cloning +
+

Forking and cloning

+
+
+
+
+

Forking a repository

+

When a fork is made on GitHub/GitLab a complete copy, of all or selected +branches, of the repository is made. The copy will reside under a different +account on GitHub/GitLab. Forking of a repository is of high relevance when +working with a git repository to which you do not have write access.

+
    +

  • In the fork repository commits can be made to the base branch (main or +master), and to other branches.

    • +

  • The commits that are made within the branches of the fork repository can be +contributed back to the parent repository by means of pull or merge requests.

    • +
+
+
+

Synchronizing changes between repositories

+
    +

  • We need a mechanism to communicate changes between the repositories.

    • +

  • We will pull or fetch updates from remote repositories (we will soon discuss the difference between pull and fetch).

    • +

  • We will push updates to remote repositories.

    • +

  • We will learn how to suggest changes within repositories on GitHub and across repositories (pull request).

    • +

  • Repositories that are forked or cloned do not automatically synchronize themselves: +We will learn how to update forks (by pulling from the “central” repository).

    • +

  • A main difference between cloning a repository and forking a repository is that the former is a general operation for generating copies of a repository to different computers, whereas forking is a particular operation implemented on GitHub/GitLab.

    • +
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/collaboration/demo-discussion/index.html b/collaboration/demo-discussion/index.html new file mode 100644 index 0000000..405df1b --- /dev/null +++ b/collaboration/demo-discussion/index.html @@ -0,0 +1,160 @@ + + + + + + + Conclict resolution, rebasing, and organizational strategies — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Conclict resolution, rebasing, and organizational strategies

+

(40 min demo and discussion)

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/collaboration/forking-workflow/index.html b/collaboration/forking-workflow/index.html new file mode 100644 index 0000000..ed602bb --- /dev/null +++ b/collaboration/forking-workflow/index.html @@ -0,0 +1,376 @@ + + + + + + + How to contribute changes to repositories that belong to others — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

How to contribute changes to repositories that belong to others

+

In this episode we prepare you to suggest and contribute changes to +repositories that belong to others. These might be open source projects that +you use in your work.

+

We will see how Git and services like GitHub or GitLab can be used to suggest +modification without having to ask for write access to the repository and +accept modifications without having to grant write access to others.

+
+

Exercise

+
+

Exercise preparation

+
    +

  • The exercise repository is now different: +https://github.com/workshop-material/recipe-book-forking-exercise (note the -forking-exercise).

    • +

  • First fork the exercise repository to your GitHub account.

    • +

  • Then clone your fork to your computer (if you wish to work locally).

    • +

  • Double-check that you have forked the correct repository.

    • +
+
+
+

Exercise: Collaborating within the same repository (25 min)

+

Technical requirements:

+ +

What is familiar from previous lessons:

+
    +

  • Forking a repository.

    • +

  • Creating a branch.

    • +

  • Committing a change on the new branch.

    • +

  • Opening and merging pull requests.

    • +
+

What will be new in this exercise:

+
    +

  • Opening a pull request towards the upstream repository.

    • +

  • Pull requests can be coupled with automated testing.

    • +

  • Learning that your fork can get out of date.

    • +

  • After the pull requests are merged, updating your fork with the changes.

    • +

  • Learn how to approach other people’s repositories with ideas, changes, and requests.

    • +
+

Exercise tasks:

+
    +

  1. Open an issue in the upstream exercise repository where you describe the +change you want to make. Take note of the issue number.

    2. +

  2. Create a new branch in your fork of the repository.

    3. +

  3. Make a change to the recipe book on the new branch and in the commit cross-reference the issue you opened. +See the walk-through below for how to do this.

    4. +

  4. Open a pull request towards the upstream repository.

    5. +

  5. The instructor will review and merge the pull requests. +During the review, pay attention to the automated test step (here for +demonstration purposes, we test whether the recipe contains an ingredients +and an instructions sections).

    6. +

  6. After few pull requests are merged, update your fork with the changes.

    7. +

  7. Check that in your fork you can see changes from other people’s pull requests.

    8. +
+
+
+
+

Help and discussion

+
+

Help! I don’t have permissions to push my local changes

+

Maybe you see an error like this one:

+
Please make sure you have the correct access rights
+and the repository exists.
+
+
+

Or like this one:

+
failed to push some refs to workshop-material/recipe-book-forking-exercise.git
+
+
+

In this case you probably try to push the changes not to your fork but to the original repository +and in this exercise you do not have write access to the original repository.

+

The simpler solution is to clone again but this time your fork.

+ +
+
+

Opening a pull request towards the upstream repository

+

We have learned in the previous episode that pull requests are always from +branch to branch. But the branch can be in a different repository.

+

When you open a pull request in a fork, by default GitHub will suggest to +direct it towards the default branch of the upstream repository.

+

This can be changed and it should always be verified, but in this case this is +exactly what we want to do, from fork towards upstream:

+
+Screenshot of a pull request from fork towards upstream +
+
+
+

Pull requests can be coupled with automated testing

+

We added an automated test here just for fun and so that you see that this is +possible to do.

+

In this exercise, the test is silly. It will check whether the recipe contains +both an ingredients and an instructions section.

+

In this example the test failed:

+
+Screenshot of a failed test in a pull request +
+

Click on the “Details” link to see the details of the failed test:

+
+Screenshot of details why the test failed +
+

How can this be useful?

+
    +

  • The project can define what kind of tests are expected to pass before a pull +request can be merged.

    • +

  • The reviewer can see the results of the tests, without having to run them +locally.

    • +
+

How does it work?

+
    +

  • We added a GitHub Actions workflow +to automatically run on each push or pull request towards the main branch.

    • +
+

What tests or steps can you image for your project to run automatically with +each pull request?

+
+
+

How to update your fork with changes from upstream

+

This used to be difficult but now it is two mouse clicks.

+

Navigate to your fork and notice how GitHub tells you that your fork is behind. +In my case, it is 9 commits behind upstream. To fix this, click on “Sync fork” +and then “Update branch”:

+
+Screenshot on GitHub fork page showing that the fork is behind +
+

After the update my “branch is up to date” with the upstream repository:

+
+Screenshot on GitHub after fork has been updated +
+
+
+

How to approach other people’s repositories with ideas, changes, and requests

+

Contributing very minor changes

+
    +

  • Clone or fork+clone repository

    • +

  • Create a branch

    • +

  • Commit and push change

    • +

  • Open a pull request or merge request

    • +
+

If you observe an issue and have an idea how to fix it

+
    +

  • Open an issue in the repository you wish to contribute to

    • +

  • Describe the problem

    • +

  • If you have a suggestion on how to fix it, describe your suggestion

    • +

  • Possibly discuss and get feedback

    • +

  • If you are working on the fix, indicate it in the issue so that others know that somebody is working on it and who is working on it

    • +

  • Submit your fix as pull request or merge request which references/closes the issue

    • +
+
+

Motivation

+
    +

  • Inform others about an observed problem

    • +

  • Make it clear whether this issue is up for grabs or already being worked on

    • +
+
+

If you have an idea for a new feature

+
    +

  • Open an issue in the repository you wish to contribute to

    • +

  • In the issue, write a short proposal for your suggested change or new feature

    • +

  • Motivate why and how you wish to do this

    • +

  • Also indicate where you are unsure and where you would like feedback

    • +

  • Discuss and get feedback before you code

    • +

  • Once you start coding, indicate that you are working on it

    • +

  • Once you are done, submit your new feature as pull request or merge request which references/closes the issue/proposal

    • +
+
+

Motivation

+
    +

  • Get agreement and feedback before writing 5000 lines of code which might be rejected

    • +

  • If we later wonder why something was done, we have the issue/proposal as +reference and can read up on the reasoning behind a code change

    • +
+
+
+
+
+

Summary

+
    +

  • This forking workflow lets you propose changes to repositories for +which you have no write access.

    • +

  • This is the way that much modern open-source software works.

    • +

  • You can now contribute to any project you can view.

    • +
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/collaboration/index.html b/collaboration/index.html new file mode 100644 index 0000000..975bbbe --- /dev/null +++ b/collaboration/index.html @@ -0,0 +1,167 @@ + + + + + + + Collaborative version control and code review — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+ +
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/collaboration/same-repository/index.html b/collaboration/same-repository/index.html new file mode 100644 index 0000000..e901473 --- /dev/null +++ b/collaboration/same-repository/index.html @@ -0,0 +1,423 @@ + + + + + + + Collaborating within the same repository — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Collaborating within the same repository

+

In this episode, we will learn how to collaborate within the same repository. +We will learn how to cross-reference issues and pull requests, how to review +pull requests, and how to use draft pull requests.

+

This exercise will form a good basis for collaboration that is suitable for +most research groups.

+
+

Note

+

When you read or hear pull request, please think of a change proposal.

+
+
+

Exercise

+

In this exercise, we will contribute to a repository via a pull request. +This means that you propose some change, and then it is accepted (or not).

+
+

Exercise preparation

+
    +

  • First we need to get access to the exercise repository to which we will +contribute.

    +
      +

    • Instructor collects GitHub usernames from learners and adds them as collaborators to the exercise repository +(Settings -> Collaborators and teams -> Manage access -> Add people).

      • +
    +
    • +

  • Don’t forget to accept the invitation

    +
      +

    • Check https://github.com/settings/organizations/

      • +

    • Alternatively check the inbox for the email account you registered with +GitHub. GitHub emails you an invitation link, but if you don’t receive it +you can go to your GitHub notifications in the top right corner. The +maintainer can also “copy invite link” and share it within the group.

      • +
    +
    • +

  • Watching and unwatching repositories

    +
      +

    • Now that you are a collaborator, you get notified about new issues and pull +requests via email.

      • +

    • If you do not wish this, you can “unwatch” a repository (top of +the project page).

      • +

    • However, we recommend watching repositories you are interested +in. You can learn things from experts just by watching the +activity that come through a popular project.

      • +
    +
    +Unwatching a repository +
    +

    Unwatch a repository by clicking “Unwatch” in the repository view, +then “Participating and @mentions” - this way, you will get +notifications about your own interactions.

    +
    +
    +
    • +
+
+
+

Exercise: Collaborating within the same repository (25 min)

+

Technical requirements (from installation instructions):

+ +

What is familiar from the previous workshop day (not repeated here):

+
    +

  • Cloning a repository.

    • +

  • Creating a branch.

    • +

  • Committing a change on the new branch.

    • +

  • Submit a pull request towards the main branch.

    • +
+

What will be new in this exercise:

+
    +

  • If you create the changes locally, you will need to push them to the remote repository.

    • +

  • Learning what a protected branch is and how to modify a protected branch: using a pull request.

    • +

  • Cross-referencing issues and pull requests.

    • +

  • Practice to review a pull request.

    • +

  • Learn about the value of draft pull requests.

    • +
+

Exercise tasks:

+
    +

  1. Start in the exercise +repository and open an +issue where you describe the change you want to make. Note down the issue +number since you will need it later.

    2. +

  2. Create a new branch.

    3. +

  3. Make a change to the recipe book on the new branch and in the commit +cross-reference the issue you opened (see the walk-through below +for how to do that).

    4. +

  4. Push your new branch (with the new commit) to the repository you +are working on.

    5. +

  5. Open a pull request towards the main branch.

    6. +

  6. Review somebody else’s pull request and give constructive feedback. Merge their pull request.

    7. +

  7. Try to create a new branch with some half-finished work and open a draft +pull request. Verify that the draft pull request cannot be merged since it +is not meant to be merged yet.

    8. +
+
+
+
+

Solution and hints

+
+

(1) Opening an issue

+

This is done through the GitHub web interface. For example, you could +give the name of the recipe you want to add (so that others don’t add +the same one). It is the “Issues” tab.

+
+
+

(2) Create a new branch.

+

If on GitHub, you can make the branch in the web interface.

+
+
+

(3) Make a change adding the recipe

+

Add a new file with the recipe in it. Commit the file. In the commit +message, include the note about the issue number, saying that this +will close that issue.

+
+

Cross-referencing issues and pull requests

+

Each issue and each pull request gets a number and you can cross-reference them.

+

When you open an issue, note down the issue number (in this case it is #2):

+
+Each issue gets a number +
+

You can reference this issue number in a commit message or in a pull request, like in this +commit message:

+
this is the new recipe; fixes #2
+
+
+

If you forget to do that in your commit message, you can also reference the issue +in the pull request description. And instead of fixes you can also use closes or resolves +or fix or close or resolve (case insensitive).

+

Here are all the keywords that GitHub recognizes: +https://help.github.com/en/articles/closing-issues-using-keywords

+

Then observe what happens in the issue once your commit gets merged: it will +automatically close the issue and create a link between the issue and the +commit. This is very useful for tracking what changes were made in response to +which issue and to know from when until when precisely the issue was open.

+
+
+
+

(4) Push to GitHub as a new branch

+

Push the branch to the repository. You should end up with a branch +visible in the GitHub web view.

+

This is only necessary if you created the changes locally. If you created the +changes directly on GitHub, you can skip this step.

+
+

In VS Code, you can “publish the branch” to the remote repository by clicking +the cloud icon in the bottom left corner of the window:

+
+Publishing a branch in VS Code +
+
+
+
+

(5) Open a pull request towards the main branch

+

This is done through the GitHub web interface.

+
+
+

(6) Reviewing pull requests

+

You review through the GitHub web interface.

+

Checklist for reviewing a pull request:

+
    +

  • Be kind, on the other side is a human who has put effort into this.

    • +

  • Be constructive: if you see a problem, suggest a solution.

    • +

  • Towards which branch is this directed?

    • +

  • Is the title descriptive?

    • +

  • Is the description informative?

    • +

  • Scroll down to see commits.

    • +

  • Scroll down to see the changes.

    • +

  • If you get incredibly many changes, also consider the license or copyright +and ask where all that code is coming from.

    • +

  • Again, be kind and constructive.

    • +

  • Later we will learn how to suggest changes directly in the pull request.

    • +
+

If someone is new, it’s often nice to say something encouraging in the +comments before merging (even if it’s just “thanks”). If all is good +and there’s not much else to say, you could merge directly.

+
+
+

(7) Draft pull requests

+

Try to create a draft pull request:

+
+Creating a draft pull request +
+

Verify that the draft pull request cannot be merged until it is marked as ready +for review:

+
+Draft pull request cannot be merged +
+

Draft pull requests can be useful for:

+
    +

  • Feedback: You can open a pull request early to get feedback on your work without +signaling that it is ready to merge.

    • +

  • Information: They can help communicating to others that a change is coming up and in +progress.

    • +
+
+
+

What is a protected branch? And how to modify it?

+

A protected branch on GitHub or GitLab is a branch that cannot (accidentally) +deleted or force-pushed to. It is also possible to require that a branch cannot +be directly pushed to or modified, but that changes must be submitted via a +pull request.

+

To protect a branch in your own repository, go to “Settings” -> “Branches”.

+
+
+

Summary

+
    +

  • We used all the same pieces that we’ve learned previously.

    • +

  • But we successfully contributed to a collaborative project!

    • +

  • The pull request allowed us to contribute without changing directly: +this is very good when it’s not mainly our project.

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/credit/index.html b/credit/index.html new file mode 100644 index 0000000..e4d14e5 --- /dev/null +++ b/credit/index.html @@ -0,0 +1,158 @@ + + + + + + + Credit — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Credit

+

The following material (all CC-BY) was reused to create this workshop material:

+ +

(I will also summarize what changes have been made to the original material)

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/documentation/index.html b/documentation/index.html new file mode 100644 index 0000000..74b8b75 --- /dev/null +++ b/documentation/index.html @@ -0,0 +1,540 @@ + + + + + + + Code documentation — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Code documentation

+
+

Objectives

+
    +

  • Discuss what makes good documentation.

    • +

  • Improve the README of your project or our example project.

    • +

  • Explore Sphinx which is a popular tool to build documentation websites.

    • +

  • Learn how to leverage GitHub Actions and GitHub Pages to build and deploy documentation.

    • +
+
+
+

Instructor note

+
    +

  • (30 min) Discussion

    • +

  • (30 min) Exercise: Set up a Sphinx documentation and add API documentation

    • +

  • (15 min) Demo: Building documentation with GitHub Actions

    • +
+
+
+

Why? 💗✉️ to your future self

+
    +

  • You will probably use your code in the future and may forget details.

    • +

  • You may want others to use your code or contribute +(almost impossible without documentation).

    • +
+
+
+

In-code documentation

+

Not very useful (more commentary than comment):

+
# now we check if temperature is below -50
+if temperature < -50:
+    print("ERROR: temperature is too low")
+
+
+

More useful (explaining why):

+
# we regard temperatures below -50 degrees as measurement errors
+if temperature < -50:
+    print("ERROR: temperature is too low")
+
+
+

Keeping zombie code “just in case” (rather use version control):

+
# do not run this code!
+# if temperature > 0:
+#     print("It is warm")
+
+
+

Emulating version control:

+
# John Doe: threshold changed from 0 to 15 on August 5, 2013
+if temperature > 15:
+    print("It is warm")
+
+
+
+
+

Many languages allow “docstrings”

+

Example (Python):

+
def kelvin_to_celsius(temp_k: float) -> float:
+    """
+    Converts temperature in Kelvin to Celsius.
+
+    Parameters
+    ----------
+    temp_k : float
+        temperature in Kelvin
+
+    Returns
+    -------
+    temp_c : float
+        temperature in Celsius
+    """
+    assert temp_k >= 0.0, "ERROR: negative T_K"
+
+    temp_c = temp_k - 273.15
+
+    return temp_c
+
+
+
+

Keypoints

+
    +

  • Documentation which is only in the source code is not enough.

    • +

  • Often a README is enough.

    • +

  • Documentation needs to be kept +in the same Git repository as the code since we want it to evolve with +the code.

    • +
+
+
+
+

Often a README is enough - checklist

+
    +

  • Purpose

    • +

  • Requirements

    • +

  • Installation instructions

    • +

  • Copy-paste-able example to get started

    • +

  • Tutorials covering key functionality

    • +

  • Reference documentation (e.g. API) covering all functionality

    • +

  • Authors and recommended citation

    • +

  • License

    • +

  • Contribution guide

    • +
+

See also the +JOSS review checklist.

+
+
+

What if you need more than a README?

+ +
+
+

Diátaxis

+

Diátaxis is a systematic approach to technical documentation authoring.

+ +
+
+

Exercise: Set up a Sphinx documentation

+
+

Preparation

+

In this episode we will use the following 5 packages which we installed +previously as part of the Conda environment or Virtual environment:

+
myst-parser
+sphinx
+sphinx-rtd-theme
+sphinx-autoapi
+sphinx-autobuild
+
+
+

Which repository to use? You have 3 options:

+
    +

  • Clone your fork of the planets example repository.

    • +

  • If you don’t have that, you can clone the original repository itself: +https://github.com/workshop-material/planets

    • +

  • You can try this with your own project and the project does not have to +be a Python project.

    • +
+
+

There are at least two ways to get started with Sphinx:

+
    +

  1. Use sphinx-quickstart to create a new Sphinx project.

    2. +

  2. This is what we will do: Create three files (doc/conf.py, doc/index.md, and doc/about.md) +as starting point and improve from there.

    3. +
+
+

Exercise: Set up a Sphinx documentation

+
    +

  1. Create the following three files in your project:

    +
    planets/
+├── doc/
+│   ├── conf.py
+│   ├── index.md
+│   └── about.md
+└── ...
+
    +
    +

    This is conf.py:

    +
    project = "planets"
+copyright = "2024, Authors"
+author = "Authors"
+release = "0.1"
+
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+extensions = [
+    "myst_parser",  # in order to use markdown
+]
+
+myst_enable_extensions = [
+    "colon_fence",  # ::: can be used instead of ``` for better rendering
+]
+
+html_theme = "sphinx_rtd_theme"
+
    +
    +

    This is index.md (feel free to adjust):

    +
    # Our code documentation
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor
+incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis
+nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.
+Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu
+fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in
+culpa qui officia deserunt mollit anim id est laborum.
+
+:::{toctree}
+:maxdepth: 2
+:caption: Some caption
+
+about.md
+:::
+
    +
    +

    This is about.md (feel free to adjust):

    +
    # About this code
+
+Work in progress ...
+
    +
    +
    2. +

  2. Run sphinx-build to build the HTML documentation:

    +
    $ sphinx-build doc _build
+
+... lots of output ...
+The HTML pages are in _build.
+
    +
    +
    3. +

  3. Try to open _build/index.html in your browser.

    4. +

  4. Experiment with adding more content, images, equations, code blocks, …

    + +
    5. +
+
+

There is a lot more you can do:

+
    +

  • This is useful if you want to check the integrity of all internal and external links:

    +
    $ sphinx-build doc -W -b linkcheck _build
+
    +
    +
    • +

  • sphinx-autobuild +provides a local web server that will automatically refresh your view +every time you save a file - which makes writing and testing much easier.

    • +
+
+
+

Demo: Building documentation with GitHub Actions

+

First we need to extend the environment.yml file to include the necessary packages:

+
name: planets
+channels:
+  - conda-forge
+dependencies:
+  - python=3.12
+  - numpy
+  - click
+  - matplotlib
+  - myst-parser
+  - sphinx
+  - sphinx-rtd-theme
+  - sphinx-autoapi
+
+
+

Then we add a GitHub Actions workflow .github/workflow/sphinx.yml to build the documentation:

+
name: Build documentation
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+permissions:
+  contents: write
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+
+    - uses: mamba-org/setup-micromamba@v1
+      with:
+        micromamba-version: '1.5.8-0' # any version from https://github.com/mamba-org/micromamba-releases
+        environment-file: environment.yml
+        init-shell: bash
+        cache-environment: true
+        post-cleanup: 'all'
+        generate-run-shell: false
+
+    - name: Sphinx build
+      run: |
+        sphinx-build doc _build
+      shell: bash -el {0}
+
+    - name: Deploy to GitHub Pages
+      uses: peaceiris/actions-gh-pages@v4
+      if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+      with:
+        publish_branch: gh-pages
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: _build/
+        force_orphan: true
+
+
+

Now:

+
    +

  • Add these two changes to the GitHub repository.

    • +

  • Go to “Settings” -> “Pages” -> “Branch” -> gh-pages -> “Save”.

    • +

  • Look at “Actions” tab and observe the workflow running and hopefully +deploying the website.

    • +

  • Finally visit the generated site. You find it by clicking the About wheel +icon on top right of your repository. There, select “Use your GitHub Pages +website”.

    • +

  • This is how we build almost all of our lesson websites (including this one).

    • +

  • Another popular place to deploy Sphinx documentation is ReadTheDocs.

    • +
+
+
+

Optional: How to auto-generate API documentation in Python

+

Add three tiny modifications (highlighted) to doc/conf.py to auto-generate API documentation +(this requires the sphinx-autoapi package):

+
project = "planets"
+copyright = "2024, Authors"
+author = "Authors"
+release = "0.1"
+
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+extensions = [
+    "myst_parser",  # in order to use markdown
+    "autoapi.extension",  # in order to use markdown
+]
+
+# search this directory for Python files
+autoapi_dirs = [".."]
+
+# ignore this file when generating API documentation
+autoapi_ignore = ["*/conf.py"]
+
+myst_enable_extensions = [
+    "colon_fence",  # ::: can be used instead of ``` for better rendering
+]
+
+html_theme = "sphinx_rtd_theme"
+
+
+

Then rebuild the documentation (or push the changes and let GitHub rebuild it) +and you should see a new section “API Reference”.

+
+
+

Confused about reStructuredText vs. Markdown vs. MyST?

+
    +

  • At the beginning there was reStructuredText and Sphinx was built for reStructuredText.

    • +

  • Independently, Markdown was invented and evolved into a couple of flavors.

    • +

  • Markdown became more and more popular but was limited compared to reStructuredText.

    • +

  • Later, MyST +was invented to be able to write +something that looks like Markdown but in addition can do everything that +reStructuredText can do with extra directives.

    • +
+
+
+

Where to read more

+ +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/example/index.html b/example/index.html new file mode 100644 index 0000000..c0c506a --- /dev/null +++ b/example/index.html @@ -0,0 +1,237 @@ + + + + + + + Example project: Simulating the motion of planets — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Example project: Simulating the motion of planets
    • +
  • + Edit on GitHub +
    • +
+
+
+
+
+ +
+

Example project: Simulating the motion of planets

+

The example code that we will study +is a hopefully simple N-body simulation written in Python. It is not important +or expected that we understand the code in any detail.

+

The big picture is that the code simulates the motion of a number of +planets:

+
    +

  • We can choose the number of planets.

    • +

  • Each planet starts with a random position, velocity, and mass.

    • +

  • At each time step, the code calculates the gravitational force between each +pair of planets.

    • +

  • The forces accelerate each planet, the acceleration modifies the velocity, +the velocity modifies the position of each planet.

    • +

  • We can choose the number of time steps.

    • +

  • The units were chosen to make numbers easy to read.

    • +
+
+

Example run

+
+

Instructor note

+

The instructor demonstrates running the code on their computer.

+
+

The code is written to accept command-line arguments to specify the number +of planets and the number of time steps.

+

We first generate starting data:

+
$ python generate-data.py --num-planets 10 --output-file initial.csv
+
+
+

The generated file (initial.csv) could look like this:

+
px,py,pz,vx,vy,vz,mass
+-46.88,-42.51,88.33,-0.86,-0.18,0.55,6.70
+-5.29,17.09,-96.13,0.66,0.45,-0.17,3.51
+83.53,-92.83,-68.77,-0.26,-0.48,0.24,6.84
+-36.31,25.48,64.16,0.85,0.75,-0.56,1.53
+-68.38,-17.21,-97.07,0.60,0.26,0.69,6.63
+-48.37,-48.74,3.92,-0.92,-0.33,-0.93,8.60
+40.53,-75.50,44.18,-0.62,-0.31,-0.53,8.04
+-27.21,10.78,-78.82,-0.09,-0.55,-0.03,5.35
+88.42,-74.95,-45.85,0.81,0.68,0.56,5.36
+39.09,53.12,-59.54,-0.54,0.56,0.07,8.98
+
+
+

Then we can simulate their motion (in this case for 20 steps):

+
$ python simulate.py --num-steps 20 \
+                     --input-file initial.csv \
+                     --output-file final.csv
+
+
+

The --output-file (final.csv) is again a CSV file (comma-separated values) +and contains the final positions of all planets.

+

It is possible to run on multiple cores and to animate the result. +Here is an example with 100 planets:

+
$ python generate-data.py --num-planets 100 --output-file initial.csv
+
+$ python simulate.py --num-steps 50 \
+                     --input-file initial.csv \
+                     --output-file final.csv \
+                     --trajectories-file trajectories.npz \
+                     --num-cores 8
+
+$ python animate.py --initial-file initial.csv \
+                    --trajectories-file trajectories.npz \
+                    --output-file animation.mp4
+
+
+
+

Learning goals

+
    +

  • What are the most important steps to make this code reusable by others +and our future selves?

    • +

  • Be able to apply these techniques to your own code/script.

    • +
+
+
+

We will not focus on …

+
    +

  • … how the code works internally in detail.

    • +

  • … whether this is the most efficient algorithm.

    • +

  • … whether the code is numerically stable.

    • +

  • … how to code scales with the number of cores.

    • +

  • … whether it is portable to other operating systems (we will discuss this later).

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/genindex/index.html b/genindex/index.html new file mode 100644 index 0000000..99f0d30 --- /dev/null +++ b/genindex/index.html @@ -0,0 +1,149 @@ + + + + + + Index — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ + +

Index

+ +
+ +
+ + +
+
+
+ +
+ +
+

© Copyright CodeRefinery team (CC-BY license).

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/index.html b/index.html new file mode 100644 index 0000000..a97289d --- /dev/null +++ b/index.html @@ -0,0 +1,290 @@ + + + + + + + Reproducible research software development using Python — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Reproducible research software development using Python
    • +
  • + Edit on GitHub +
    • +
+
+
+
+
+ +
+

Reproducible research software development using Python

+
+

Big-picture goal

+

This is a hands-on course on research software engineering. In this +workshop we assume that most workshop participants use Python in their work or +a leading a group which uses Python. Therefore, some of the examples will use +Python as the example language.

+

We will work with an example project and go through all the steps of a typical +software project. Once we have seen the building blocks, we will try to apply +them to own projects. Workshop participants will receive and also learn to give +constructive code feedback.

+
+
+

Prerequisites

+
+

Preparation

+
    +

  1. Get a GitHub account following these instructions.

    2. +

  2. You will need a text editor. If you don’t have a favorite one, we recommend +VS Code.

    3. +

  3. If you prefer to work in the terminal and not in VS Code, set up these two (skip this if you use VS Code):

    + +
    4. +

  4. One of these two software environments (if you are not sure which one to +choose or have no preference, choose Conda):

    + +
    5. +

  5. Optional and only on Linux: Apptainer following +these instructions.

    6. +
+
+
+
+

Schedule

+
+

Day 1

+ +
+
+

Day 2

+ +
+
+

Day 3

+ +
+
+

If we have time left

+ +
+
+
+
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/installation/conda/index.html b/installation/conda/index.html new file mode 100644 index 0000000..70fe17a --- /dev/null +++ b/installation/conda/index.html @@ -0,0 +1,252 @@ + + + + + + + Conda environment — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Conda environment

+

A Conda environment is an isolated software environment that is used to manage dependencies for a project +and you decide where it is located.

+

You will need a environment.yml file that documents the dependencies:

+
name: coderefinery
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - python >= 3.10
+  - black
+  - click
+  - flit
+  - ipywidgets
+  - isort
+  - jupyterlab
+  - jupyterlab_code_formatter
+  - jupyterlab-git
+  - matplotlib
+  - myst-parser
+  - nbdime
+  - numpy
+  - pandas
+  - pytest
+  - pytest-cov
+  - scalene
+  - seaborn
+  - snakemake-minimal
+  - sphinx
+  - sphinx-autoapi
+  - sphinx-autobuild
+  - sphinx_rtd_theme >= 2.0
+  - vulture
+  - scikit-image
+
+
+
+

Before you create a virtual environment

+
    +

  1. Create a new directory for this course.

    2. +

  2. In this directory, create an environment.yml file and copy-paste the dependencies above into it.

    3. +
+
+
+

Choose the tool to manage the environment

+

If you are already using one of these tools, please continue using the tool that you like and know. +If you are new to this, we recommend using Miniconda or Miniforge.

+
    +

  • Anaconda

    +
      +

    • Advantages: easy to install, easy to use, good for beginners

      • +

    • Disadvantages: large download, installs more than we will need, license restrictions

      • +
    +
    • +

  • Miniconda

    +
      +

    • Advantages: small size, installs only what you need

      • +

    • Disadvantages: no graphical interface, license restrictions

      • +
    +
    • +

  • Miniforge

    +
      +

    • Advantages: small size, no license restrictions

      • +

    • Disadvantages: no graphical interface

      • +
    +
    • +

  • Micromamba

    +
      +

    • Advantages: fast, small size

      • +

    • Disadvantages: no graphical interface

      • +
    +
    • +

  • Pixi

    +
      +

    • Advantages: fast and new

      • +

    • Disadvantages: new and less tested and not documented here

      • +
    +
    • +
+
+
+

Creating the virtual environment

+
    +

  1. Open your terminal shell (e.g. Bash or Zsh).

    2. +

  2. Activate conda using conda activate or source ~/miniconda3/bin/activate.

    3. +

  3. Run the following command:

    +
    $ conda env create --file environment.yml
+
    +
    +
    4. +

  4. Make sure that you see “coderefinery” in the output when you ask for a list of all available environments:

    +
    $ conda env list
+
    +
    +
    5. +
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/installation/virtual-environment/index.html b/installation/virtual-environment/index.html new file mode 100644 index 0000000..72439ff --- /dev/null +++ b/installation/virtual-environment/index.html @@ -0,0 +1,217 @@ + + + + + + + Virtual environment — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Virtual environment

+

A virtual environment is an isolated software environment that is used to manage dependencies for a project +and you decide where it is located.

+

You will need a requirements.txt file that documents the dependencies:

+
black
+click
+flit
+ipywidgets
+isort
+jupyterlab
+jupyterlab-code-formatter
+jupyterlab-git
+matplotlib
+myst-parser
+nbdime
+numpy
+pandas
+pytest
+pytest-cov
+scalene
+seaborn
+sphinx
+sphinx-autoapi
+sphinx-autobuild
+sphinx_rtd_theme >= 2.0
+vulture
+scikit-image
+
+
+
+

Before you create a virtual environment

+
    +

  1. Create a new directory for this course.

    2. +

  2. In this directory, create a requirements.txt file and copy-paste the dependencies above into it.

    3. +
+
+
+

Creating the virtual environment

+

Now create a virtual environment in this directory either using pip and +venv +(more traditional and safer) or using uv (more modern but also less tested):

+
+

Create a new virtual environment and activate it:

+
$ python3 -m venv coderefinery-environment
+$ source coderefinery-environment/bin/activate
+
+
+

Install the dependencies into the environment:

+
$ python3 -m pip install -r requirements.txt
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/lesson.pdf b/lesson.pdf new file mode 100644 index 0000000..d032217 Binary files /dev/null and b/lesson.pdf differ diff --git a/objects.inv b/objects.inv new file mode 100644 index 0000000..31aff9c Binary files /dev/null and b/objects.inv differ diff --git a/profiling/index.html b/profiling/index.html new file mode 100644 index 0000000..ea98d96 --- /dev/null +++ b/profiling/index.html @@ -0,0 +1,164 @@ + + + + + + + Profiling memory and CPU usage — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Profiling memory and CPU usage

+

Profilers:

+
    +

  • cProfile or profile

    • +

  • line_profiler

    • +

  • viztracer

    • +

  • scalene

    • +

  • Intel VTune

    • +

  • PyInstrument

    • +

  • py-spy

    • +

  • Pyflame

    • +

  • timeit

    • +
+

(here I will add some examples that we can profile together)

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/publishing/index.html b/publishing/index.html new file mode 100644 index 0000000..24ea5b1 --- /dev/null +++ b/publishing/index.html @@ -0,0 +1,161 @@ + + + + + + + How to release and publish your code — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

How to release and publish your code

+

Part 1:

+
    +

  • 30 min: Overview over software licenses and code publishing

    • +

  • 15 min: We add a license, CFF file, and publish to Zenodo (sandbox)

    • +
+

Part 2:

+
    +

  • 30 min: Creating a Python package with the help of flit

    • +

  • 15 min: Deploy the package to test-PyPI using GitHub Actions

    • +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/refactoring-concepts/index.html b/refactoring-concepts/index.html new file mode 100644 index 0000000..ca7705e --- /dev/null +++ b/refactoring-concepts/index.html @@ -0,0 +1,157 @@ + + + + + + + Concepts in refactoring and modular code design — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
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  • Concepts in refactoring and modular code design
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Concepts in refactoring and modular code design

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Topics:

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  • Pure functions

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  • Design patterns: functional design vs. object-oriented design

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  • How to design your code before writing it: document-driven development

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Demo: From a script towards a workflow

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In this episode we will explore code quality and good practices in Python using +a hands-on approach. We will together build up a small project and improve it +step by step.

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We will start from a relatively simple image processing script which can read a +telescope image of stars and our goal is to count the number of stars in +the image. Later we will want to be able to process many such images.

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The (fictional) telescope images look like the one below here (in this +repository we can find more):

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+Generated image representing a telescope image of stars +
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Generated image representing a telescope image of stars.

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Rough plan for this demo

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  • (15 min) Discuss how we would solve the problem, run example code, and make it work (as part of a Jupyter notebook)?

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  • (15 min) Refactor the positioning code into a function and a module

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  • (15 min) Now we wish to process many images - discuss how we would approach this

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  • (15 min) Introduce CLI and discuss the benefits

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  • (30 min) From a script to a workflow (using Snakemake)

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Plan

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Topics we wish to show and discuss:

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  • Naming (and other) conventions, project organization, modularity

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  • The value of pure functions and immutability

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  • Refactoring (explained through examples)

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  • Auto-formatting and linting with tools like black, vulture, ruff

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  • Moving a project under Git

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  • How to document dependencies

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  • Structuring larger software projects in a modular way

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  • Command-line interfaces

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  • Workflows with Snakemake

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We will work together on the code on the big screen, and participants will be +encouraged to give suggestions and ask questions. We will end up with a Git +repository which will be shared with workshop participants.

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Possible solutions

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+ + + + \ No newline at end of file diff --git a/reusable/index.html b/reusable/index.html new file mode 100644 index 0000000..b17c103 --- /dev/null +++ b/reusable/index.html @@ -0,0 +1,163 @@ + + + + + + + How to make the project more reusable — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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How to make the project more reusable

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Part 1:

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  • 15 min: Motivation

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  • 15 min: Best practices for managing dependencies in Python

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  • 20 min: Exercise

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Part 2:

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  • 10 min: Introduction to containers

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  • 20 min: Demonstration

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  • 10 min: Discussion

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+ + + + \ No newline at end of file diff --git a/search/index.html b/search/index.html new file mode 100644 index 0000000..655dc57 --- /dev/null +++ b/search/index.html @@ -0,0 +1,163 @@ + + + + + + Search — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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© Copyright CodeRefinery team (CC-BY license).

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+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
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+ + + + + + + + + \ No newline at end of file diff --git a/searchindex.js b/searchindex.js new file mode 100644 index 0000000..abec3f0 --- /dev/null +++ b/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({"alltitles": {"(1) Basic browsing": [[20, "basic-browsing"]], "(1) Create a new branch and a new commit": [[19, "create-a-new-branch-and-a-new-commit"]], "(1) Opening an issue": [[5, "opening-an-issue"]], "(2) Compare commit history with network graph": [[20, "compare-commit-history-with-network-graph"]], "(2) Create a new branch.": [[5, "create-a-new-branch"]], "(2) Modify the file again with a new commit": [[19, "modify-the-file-again-with-a-new-commit"]], "(3) How can you browse the history of a single file?": [[20, "how-can-you-browse-the-history-of-a-single-file"]], "(3) Make a change adding the recipe": [[5, "make-a-change-adding-the-recipe"]], "(3) Switch to the main branch and create a commit there": [[19, "switch-to-the-main-branch-and-create-a-commit-there"]], "(4) Browse the commits you just made": [[19, "browse-the-commits-you-just-made"]], "(4) Push to GitHub as a new branch": [[5, "push-to-github-as-a-new-branch"]], "(4) Which files include the word \u201cposition\u201d?": [[20, "which-files-include-the-word-position"]], "(5) Compare the branches": [[19, "compare-the-branches"]], "(5) Open a pull request towards the main branch": [[5, "open-a-pull-request-towards-the-main-branch"]], "(5) Who modified each line last and when?": [[20, "who-modified-each-line-last-and-when"]], "(6) Can you use this code yourself? Are you allowed to share modifications?": [[20, "can-you-use-this-code-yourself-are-you-allowed-to-share-modifications"]], "(6) Compare two arbitrary commits": [[19, "compare-two-arbitrary-commits"]], "(6) Reviewing pull requests": [[5, "reviewing-pull-requests"]], "(7) Draft pull requests": [[5, "draft-pull-requests"]], "(7) Renaming a branch": [[19, "renaming-a-branch"]], "(8) Creating a tag": [[19, "creating-a-tag"]], "Adding the unit test to GitHub Actions": [[17, "adding-the-unit-test-to-github-actions"]], "Automated testing": [[17, null]], "Background": [[19, "background"]], "Before you create a virtual environment": [[10, "before-you-create-a-virtual-environment"], [11, "before-you-create-a-virtual-environment"]], "Big-picture goal": [[9, "big-picture-goal"]], "Choose the tool to manage the environment": [[10, "choose-the-tool-to-manage-the-environment"]], "Cloning a repository": [[2, "cloning-a-repository"]], "Code documentation": [[7, null]], "Collaborating within the same repository": [[5, null]], "Collaborative version control and code review": [[0, null]], "Commits, branches, repositories, forks, clones": [[2, "commits-branches-repositories-forks-clones"]], "Concepts around collaboration": [[2, null]], "Concepts in refactoring and modular code design": [[14, null]], "Conclict resolution, rebasing, and organizational strategies": [[3, null]], "Conda environment": [[10, null]], "Confused about reStructuredText vs. Markdown vs. MyST?": [[7, "confused-about-restructuredtext-vs-markdown-vs-myst"]], "Creating a copy of the repository by \u201cforking\u201d or \u201ccloning\u201d": [[20, "creating-a-copy-of-the-repository-by-forking-or-cloning"]], "Creating branches and commits": [[19, null]], "Creating the virtual environment": [[10, "creating-the-virtual-environment"], [11, "creating-the-virtual-environment"]], "Credit": [[6, null]], "Cross-referencing issues and pull requests": [[5, "cross-referencing-issues-and-pull-requests"]], "Day 1": [[9, "day-1"]], "Day 2": [[9, "day-2"]], "Day 3": [[9, "day-3"]], "Demo: Building documentation with GitHub Actions": [[7, "demo-building-documentation-with-github-actions"]], "Demo: From a script towards a workflow": [[15, null]], "Demonstration": [[21, "demonstration"]], "Discussion": [[17, "discussion-0"], [21, "discussion-0"]], "Di\u00e1taxis": [[7, "diataxis"]], "End-to-end tests": [[17, "end-to-end-tests"]], "Example project: Simulating the motion of planets": [[8, null]], "Example run": [[8, "example-run"]], "Exercise": [[1, "exercise"], [4, "exercise"], [5, "exercise"], [23, "exercise"]], "Exercise preparation": [[1, "prerequisites-0"], [4, "prerequisites-0"], [5, "prerequisites-0"], [20, "prerequisites-0"]], "Exercise: Browsing an existing project (20 min)": [[20, "exercise-0"]], "Exercise: Collaborating within the same repository (25 min)": [[4, "exercise-0"], [5, "exercise-0"]], "Exercise: Copy and browse an existing project": [[20, "exercise-copy-and-browse-an-existing-project"]], "Exercise: Creating branches and commits": [[19, "exercise-creating-branches-and-commits"]], "Exercise: Practice creating commits and branches (20 min)": [[19, "exercise-0"]], "Exercise: Practicing code review (25 min)": [[1, "exercise-0"]], "Exercise: Set up a Sphinx documentation": [[7, "exercise-set-up-a-sphinx-documentation"], [7, "exercise-0"]], "Exercise: Turn your project to a Git repo and share it (20 min)": [[23, "exercise-0"]], "Exercises": [[17, "exercises"]], "Features: roll-back, branching, merging, collaboration": [[21, "features-roll-back-branching-merging-collaboration"]], "Forking a repository": [[2, "forking-a-repository"]], "Forking, cloning, and browsing": [[20, null]], "GitHub, VS Code, or command line": [[20, "github-vs-code-or-command-line"]], "Help and discussion": [[1, "help-and-discussion"], [4, "help-and-discussion"]], "Help! I don\u2019t have permissions to push my local changes": [[4, "help-i-don-t-have-permissions-to-push-my-local-changes"]], "How about staging and committing?": [[22, "how-about-staging-and-committing"]], "How large should a commit be?": [[22, "how-large-should-a-commit-be"]], "How testing is often taught": [[17, "how-testing-is-often-taught"]], "How to approach other people\u2019s repositories with ideas, changes, and requests": [[4, "how-to-approach-other-peoples-repositories-with-ideas-changes-and-requests"]], "How to ask for changes in a pull request": [[1, "how-to-ask-for-changes-in-a-pull-request"]], "How to contribute changes to repositories that belong to others": [[4, null]], "How to create a fork": [[20, null]], "How to make the project more reusable": [[16, null]], "How to modify a pull request to address the review comments": [[1, "how-to-modify-a-pull-request-to-address-the-review-comments"]], "How to release and publish your code": [[13, null]], "How to suggest a change in a pull request as a reviewer": [[1, "how-to-suggest-a-change-in-a-pull-request-as-a-reviewer"]], "How to update your fork with changes from upstream": [[4, "how-to-update-your-fork-with-changes-from-upstream"]], "If we have time left": [[9, "if-we-have-time-left"]], "In-code documentation": [[7, "in-code-documentation"]], "Instructor note": [[7, "instructor-note-0"], [8, "instructor-note-0"], [17, "instructor-note-0"], [20, "instructor-note-0"]], "Introduction to version control with Git and GitHub": [[18, null]], "Is putting software on GitHub/GitLab/\u2026 publishing?": [[23, "is-putting-software-on-github-gitlab-publishing"]], "Keypoints": [[7, "keypoints-0"]], "Learning goals": [[8, null]], "Longer answer": [[17, "solution-0"]], "Many languages allow \u201cdocstrings\u201d": [[7, "many-languages-allow-docstrings"]], "Motivation": [[4, null], [4, null], [17, "motivation"], [21, null]], "Objectives": [[2, "objectives-0"], [7, "objectives-0"], [17, "objectives-0"], [19, "objectives-0"], [20, "objectives-0"], [21, "objectives-0"], [23, "objectives-0"]], "Often a README is enough - checklist": [[7, "often-a-readme-is-enough-checklist"]], "Opening a pull request towards the upstream repository": [[4, "opening-a-pull-request-towards-the-upstream-repository"]], "Optional: How to auto-generate API documentation in Python": [[7, "optional-how-to-auto-generate-api-documentation-in-python"]], "Optional: How to turn your project to a Git repo and share it": [[23, null]], "Plan": [[15, "plan"]], "Possible solutions": [[15, "possible-solutions"]], "Practical advice: How much Git is necessary?": [[22, null]], "Practicing code review": [[1, null]], "Preparation": [[7, "prerequisites-0"], [9, "prerequisites-0"]], "Prerequisites": [[9, "prerequisites"]], "Profiling memory and CPU usage": [[12, null]], "Pull requests can be coupled with automated testing": [[4, "pull-requests-can-be-coupled-with-automated-testing"]], "Pytest": [[17, "pytest"]], "Recovery": [[4, "solution-0"]], "Reproducible research software development using Python": [[9, null]], "Rough plan for this demo": [[15, null]], "Schedule": [[9, "schedule"]], "Script after some work, with command-line interface (spoiler alert)": [[15, "solution-1"]], "Searching in a forked repository will not work instantaneously!": [[20, null]], "Snakemake rules which define a workflow (spoiler alert)": [[15, "solution-2"]], "Solution": [[21, "solution-0"]], "Solution and hints": [[5, "solution-and-hints"]], "Solution and walk-through": [[19, "solution-and-walk-through"], [20, "solution-and-walk-through"]], "Starting point (spoiler alert)": [[15, "solution-0"]], "Summary": [[1, "summary"], [4, "summary"], [5, "summary"], [19, "summary"], [20, "summary"]], "Synchronizing changes between repositories": [[2, "synchronizing-changes-between-repositories"]], "Talking about code": [[21, "talking-about-code"]], "Virtual environment": [[11, null]], "We will not focus on \u2026": [[8, null]], "What else is possible": [[17, "what-else-is-possible"]], "What if you need more than a README?": [[7, "what-if-you-need-more-than-a-readme"]], "What is a protected branch? 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Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. Multiple values per key are supported, + * it will always return arrays of strings for the value parts. + */ +jQuery.getQueryParameters = function(s) { + if (typeof s === 'undefined') + s = document.location.search; + var parts = s.substr(s.indexOf('?') + 1).split('&'); + var result = {}; + for (var i = 0; i < parts.length; i++) { + var tmp = parts[i].split('=', 2); + var key = jQuery.urldecode(tmp[0]); + var value = jQuery.urldecode(tmp[1]); + if (key in result) + result[key].push(value); + else + result[key] = [value]; + } + return result; +}; + +/** + * highlight a given string on a jquery object by wrapping it in + * span elements with the given class name. + */ +jQuery.fn.highlightText = function(text, className) { + function highlight(node, addItems) { + if (node.nodeType === 3) { + var val = node.nodeValue; + var pos = val.toLowerCase().indexOf(text); + if (pos >= 0 && + !jQuery(node.parentNode).hasClass(className) && + !jQuery(node.parentNode).hasClass("nohighlight")) { + var span; + var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.className = className; + } + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + node.parentNode.insertBefore(span, node.parentNode.insertBefore( + document.createTextNode(val.substr(pos + text.length)), + node.nextSibling)); + node.nodeValue = val.substr(0, pos); + if (isInSVG) { + var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); + var bbox = node.parentElement.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute('class', className); + addItems.push({ + "parent": node.parentNode, + "target": rect}); + } + } + } + else if (!jQuery(node).is("button, select, textarea")) { + jQuery.each(node.childNodes, function() { + highlight(this, addItems); + }); + } + } + var addItems = []; + var result = this.each(function() { + highlight(this, addItems); + }); + for (var i = 0; i < addItems.length; ++i) { + jQuery(addItems[i].parent).before(addItems[i].target); + } + return result; +}; + +/* + * backward compatibility for jQuery.browser + * This will be supported until firefox bug is fixed. + */ +if (!jQuery.browser) { + jQuery.uaMatch = function(ua) { + ua = ua.toLowerCase(); + + var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || + /(webkit)[ \/]([\w.]+)/.exec(ua) || + /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || + /(msie) ([\w.]+)/.exec(ua) || + ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || + []; + + return { + browser: match[ 1 ] || "", + version: match[ 2 ] || "0" + }; + }; + jQuery.browser = {}; + jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; +} diff --git a/singlehtml/_static/basic.css b/singlehtml/_static/basic.css new file mode 100644 index 0000000..f316efc --- /dev/null +++ b/singlehtml/_static/basic.css @@ -0,0 +1,925 @@ +/* + * basic.css + * ~~~~~~~~~ + * + * Sphinx stylesheet -- basic theme. + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; +} + +div.section::after { + display: block; + content: ''; + clear: left; +} + +/* -- relbar ---------------------------------------------------------------- */ + +div.related { + width: 100%; + font-size: 90%; +} + +div.related h3 { + display: none; +} + +div.related ul { + margin: 0; + padding: 0 0 0 10px; + list-style: none; +} + +div.related li { + display: inline; +} + +div.related li.right { + float: right; + margin-right: 5px; +} + +/* -- sidebar --------------------------------------------------------------- */ + +div.sphinxsidebarwrapper { + padding: 10px 5px 0 10px; +} + +div.sphinxsidebar { + float: left; + width: 230px; + margin-left: -100%; + font-size: 90%; + word-wrap: break-word; + overflow-wrap : break-word; +} + +div.sphinxsidebar ul { + list-style: none; +} + +div.sphinxsidebar ul ul, +div.sphinxsidebar ul.want-points { + margin-left: 20px; + list-style: square; +} + +div.sphinxsidebar ul ul { + margin-top: 0; + margin-bottom: 0; +} + +div.sphinxsidebar form { + margin-top: 10px; +} + +div.sphinxsidebar input { + border: 1px solid #98dbcc; + font-family: sans-serif; + font-size: 1em; +} + +div.sphinxsidebar #searchbox form.search { + overflow: hidden; +} + +div.sphinxsidebar #searchbox input[type="text"] { + float: left; + width: 80%; + padding: 0.25em; + box-sizing: border-box; +} + +div.sphinxsidebar #searchbox input[type="submit"] { + float: left; + width: 20%; + border-left: none; + padding: 0.25em; + box-sizing: border-box; +} + + +img { + border: 0; + max-width: 100%; +} + +/* -- search page ----------------------------------------------------------- */ + +ul.search { + margin: 10px 0 0 20px; + padding: 0; +} + +ul.search li { + padding: 5px 0 5px 20px; + background-image: url(file.png); + background-repeat: no-repeat; + background-position: 0 7px; +} + +ul.search li a { + font-weight: bold; +} + +ul.search li p.context { + color: #888; + margin: 2px 0 0 30px; + text-align: left; +} + +ul.keywordmatches li.goodmatch a { + font-weight: bold; +} + +/* -- index page ------------------------------------------------------------ */ + +table.contentstable { + width: 90%; + margin-left: auto; + margin-right: auto; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable ul { + margin-top: 0; + margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: 360px; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, figure.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, figure.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, figure.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-default, figure.align-default, .figure.align-default { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-default { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar, +aside.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px; + background-color: #ffe; + width: 40%; + float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; +} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} + +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +.translated { + background-color: rgba(207, 255, 207, 0.2) +} + +.untranslated { + background-color: rgba(255, 207, 207, 0.2) +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + +td.linenos pre { + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; +} + +table.highlighttable td { + margin: 0; + padding: 0; +} + +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; +} + +div.code-block-caption code { + background-color: transparent; +} + +table.highlighttable td.linenos, +span.linenos, +div.highlight span.gp { /* gp: Generic.Prompt */ + user-select: none; + -webkit-user-select: text; /* Safari fallback only */ + -webkit-user-select: none; /* Chrome/Safari */ + -moz-user-select: none; /* Firefox */ + -ms-user-select: none; /* IE10+ */ +} + +div.code-block-caption span.caption-number { + padding: 0.1em 0.3em; + font-style: italic; +} + +div.code-block-caption span.caption-text { +} + +div.literal-block-wrapper { + margin: 1em 0; +} + +code.xref, a code { + background-color: transparent; + font-weight: bold; +} + +h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { + background-color: transparent; +} + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family: sans-serif; +} + +div.viewcode-block:target { + margin: -1px -10px; + padding: 0 10px; +} + +/* -- math display ---------------------------------------------------------- */ + +img.math { + vertical-align: middle; +} + +div.body div.math p { + text-align: center; +} + +span.eqno { + float: right; +} + +span.eqno a.headerlink { + position: absolute; + z-index: 1; +} + +div.math:hover a.headerlink { + visibility: visible; +} + +/* -- printout stylesheet --------------------------------------------------- */ + +@media print { + div.document, + div.documentwrapper, + div.bodywrapper { + margin: 0 !important; + width: 100%; + } + + div.sphinxsidebar, + div.related, + div.footer, + #top-link { + display: none; + } +} \ No newline at end of file diff --git a/singlehtml/_static/check-solid.svg b/singlehtml/_static/check-solid.svg new file mode 100644 index 0000000..92fad4b --- /dev/null +++ b/singlehtml/_static/check-solid.svg @@ -0,0 +1,4 @@ + + + + diff --git a/singlehtml/_static/clipboard.min.js b/singlehtml/_static/clipboard.min.js new file mode 100644 index 0000000..54b3c46 --- /dev/null +++ b/singlehtml/_static/clipboard.min.js @@ -0,0 +1,7 @@ +/*! + * clipboard.js v2.0.8 + * https://clipboardjs.com/ + * + * Licensed MIT © Zeno Rocha + */ +!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return o}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),c=n.n(e);function a(t){try{return document.execCommand(t)}catch(t){return}}var f=function(t){t=c()(t);return a("cut"),t};var l=function(t){var e,n,o,r=1 + + + + diff --git a/singlehtml/_static/copybutton.css b/singlehtml/_static/copybutton.css new file mode 100644 index 0000000..40eafe5 --- /dev/null +++ b/singlehtml/_static/copybutton.css @@ -0,0 +1,93 @@ +/* Copy buttons */ +button.copybtn { + position: absolute; + display: flex; + top: .3em; + right: .3em; + width: 1.7em; + height: 1.7em; + opacity: 0; + transition: opacity 0.3s, border .3s, background-color .3s; + user-select: none; + padding: 0; + border: none; + outline: none; + border-radius: 0.4em; + /* The colors that GitHub uses */ + border: #1b1f2426 1px solid; + background-color: #f6f8fa; + color: #57606a; +} + +button.copybtn.success { + border-color: #22863a; + color: #22863a; +} + +button.copybtn svg { + stroke: currentColor; + width: 1.5em; + height: 1.5em; + padding: 0.1em; +} + +div.highlight { + position: relative; +} + +.highlight:hover button.copybtn { + opacity: 1; +} + +.highlight button.copybtn:hover { + background-color: rgb(235, 235, 235); +} + +.highlight button.copybtn:active { + background-color: rgb(187, 187, 187); +} + +/** + * A minimal CSS-only tooltip copied from: + * https://codepen.io/mildrenben/pen/rVBrpK + * + * To use, write HTML like the following: + * + *

Short

+ */ + .o-tooltip--left { + position: relative; + } + + .o-tooltip--left:after { + opacity: 0; + visibility: hidden; + position: absolute; + content: attr(data-tooltip); + padding: .2em; + font-size: .8em; + left: -.2em; + background: grey; + color: white; + white-space: nowrap; + z-index: 2; + border-radius: 2px; + transform: translateX(-102%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); +} + +.o-tooltip--left:hover:after { + display: block; + opacity: 1; + visibility: visible; + transform: translateX(-100%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); + transition-delay: .5s; +} + +/* By default the copy button shouldn't show up when printing a page */ +@media print { + button.copybtn { + display: none; + } +} diff --git a/singlehtml/_static/copybutton.js b/singlehtml/_static/copybutton.js new file mode 100644 index 0000000..f3ecd03 --- /dev/null +++ b/singlehtml/_static/copybutton.js @@ -0,0 +1,241 @@ +// Localization support +const messages = { + 'en': { + 'copy': 'Copy', + 'copy_to_clipboard': 'Copy to clipboard', + 'copy_success': 'Copied!', + 'copy_failure': 'Failed to copy', + }, + 'es' : { + 'copy': 'Copiar', + 'copy_to_clipboard': 'Copiar al portapapeles', + 'copy_success': '¡Copiado!', + 'copy_failure': 'Error al copiar', + }, + 'de' : { + 'copy': 'Kopieren', + 'copy_to_clipboard': 'In die Zwischenablage kopieren', + 'copy_success': 'Kopiert!', + 'copy_failure': 'Fehler beim Kopieren', + }, + 'fr' : { + 'copy': 'Copier', + 'copy_to_clipboard': 'Copié dans le presse-papier', + 'copy_success': 'Copié !', + 'copy_failure': 'Échec de la copie', + }, + 'ru': { + 'copy': 'Скопировать', + 'copy_to_clipboard': 'Скопировать в буфер', + 'copy_success': 'Скопировано!', + 'copy_failure': 'Не удалось скопировать', + }, + 'zh-CN': { + 'copy': '复制', + 'copy_to_clipboard': '复制到剪贴板', + 'copy_success': '复制成功!', + 'copy_failure': '复制失败', + }, + 'it' : { + 'copy': 'Copiare', + 'copy_to_clipboard': 'Copiato negli appunti', + 'copy_success': 'Copiato!', + 'copy_failure': 'Errore durante la copia', + } +} + +let locale = 'en' +if( document.documentElement.lang !== undefined + && messages[document.documentElement.lang] !== undefined ) { + locale = document.documentElement.lang +} + +let doc_url_root = DOCUMENTATION_OPTIONS.URL_ROOT; +if (doc_url_root == '#') { + doc_url_root = ''; +} + +/** + * SVG files for our copy buttons + */ +let iconCheck = ` + ${messages[locale]['copy_success']} + + +` + +// If the user specified their own SVG use that, otherwise use the default +let iconCopy = ``; +if (!iconCopy) { + iconCopy = ` + ${messages[locale]['copy_to_clipboard']} + + + +` +} + +/** + * Set up copy/paste for code blocks + */ + +const runWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} + +const codeCellId = index => `codecell${index}` + +// Clears selected text since ClipboardJS will select the text when copying +const clearSelection = () => { + if (window.getSelection) { + window.getSelection().removeAllRanges() + } else if (document.selection) { + document.selection.empty() + } +} + +// Changes tooltip text for two seconds, then changes it back +const temporarilyChangeTooltip = (el, oldText, newText) => { + el.setAttribute('data-tooltip', newText) + el.classList.add('success') + setTimeout(() => el.setAttribute('data-tooltip', oldText), 2000) + setTimeout(() => el.classList.remove('success'), 2000) +} + +// Changes the copy button icon for two seconds, then changes it back +const temporarilyChangeIcon = (el) => { + el.innerHTML = iconCheck; + setTimeout(() => {el.innerHTML = iconCopy}, 2000) +} + +const addCopyButtonToCodeCells = () => { + // If ClipboardJS hasn't loaded, wait a bit and try again. This + // happens because we load ClipboardJS asynchronously. + if (window.ClipboardJS === undefined) { + setTimeout(addCopyButtonToCodeCells, 250) + return + } + + // Add copybuttons to all of our code cells + const COPYBUTTON_SELECTOR = 'div.highlight pre'; + const codeCells = document.querySelectorAll(COPYBUTTON_SELECTOR) + codeCells.forEach((codeCell, index) => { + const id = codeCellId(index) + codeCell.setAttribute('id', id) + + const clipboardButton = id => + `` + codeCell.insertAdjacentHTML('afterend', clipboardButton(id)) + }) + +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} + + +var copyTargetText = (trigger) => { + var target = document.querySelector(trigger.attributes['data-clipboard-target'].value); + + // get filtered text + let exclude = '.linenos, .gp'; + + let text = filterText(target, exclude); + return formatCopyText(text, '', false, true, true, true, '', '') +} + + // Initialize with a callback so we can modify the text before copy + const clipboard = new ClipboardJS('.copybtn', {text: copyTargetText}) + + // Update UI with error/success messages + clipboard.on('success', event => { + clearSelection() + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_success']) + temporarilyChangeIcon(event.trigger) + }) + + clipboard.on('error', event => { + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_failure']) + }) +} + +runWhenDOMLoaded(addCopyButtonToCodeCells) \ No newline at end of file diff --git a/singlehtml/_static/copybutton_funcs.js b/singlehtml/_static/copybutton_funcs.js new file mode 100644 index 0000000..dbe1aaa --- /dev/null +++ b/singlehtml/_static/copybutton_funcs.js @@ -0,0 +1,73 @@ +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +export function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +export function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} diff --git a/singlehtml/_static/css/badge_only.css b/singlehtml/_static/css/badge_only.css new file mode 100644 index 0000000..c718cee --- /dev/null +++ b/singlehtml/_static/css/badge_only.css @@ -0,0 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+ return this; // for chaining... + } +})(jQuery); + +// NO good way to do this!. Copy a hack from here +// https://stackoverflow.com/questions/901115/how-can-i-get-query-string-values-in-javascript +// https://stackoverflow.com/a/2880929 +var urlParams; +(window.onpopstate = function () { + var match, + pl = /\+/g, // Regex for replacing addition symbol with a space + search = /([^&=]+)=?([^&]*)/g, + decode = function (s) { return decodeURIComponent(s.replace(pl, " ")); }, + query = window.location.search.substring(1); + urlParams = {}; + while (match = search.exec(query)) + urlParams[decode(match[1])] = decode(match[2]); +})(); + +// Select heading levels +var maxHeading = urlParams['h'] +if (maxHeading === undefined) maxHeading = 2 +var headingLevels = []; +for (h=2 ; h (sections.length-1) ) { + // if we would scroll past bottom, or above top, do nothing + return; + } + + console.log('xxxxxx'); + var targetSection = sections[targetPos]; + console.log(targetSection, typeof(targetSection)); + + // Return targetSection top and height + var secProperties = section_top_and_height(targetSection); 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+} + +/* Pandas tables. Pulled from the Jupyter / nbsphinx CSS */ +div.cell_output table { + border: none; + border-collapse: collapse; + border-spacing: 0; + color: black; + font-size: 1em; + table-layout: fixed; +} + +div.cell_output thead { + border-bottom: 1px solid black; + vertical-align: bottom; +} + +div.cell_output tr, +div.cell_output th, +div.cell_output td { + text-align: right; + vertical-align: middle; + padding: 0.5em 0.5em; + line-height: normal; + white-space: normal; + max-width: none; + border: none; +} + +div.cell_output th { + font-weight: bold; +} + +div.cell_output tbody tr:nth-child(odd) { + background: #f5f5f5; +} + +div.cell_output tbody tr:hover { + background: rgba(66, 165, 245, 0.2); +} + +/** source code line numbers **/ +span.linenos { + opacity: 0.5; +} + +/* Inline text from `paste` operation */ + +span.pasted-text { + font-weight: bold; +} + +span.pasted-inline img { + max-height: 2em; +} + +tbody span.pasted-inline img { + max-height: none; +} + +/* Font colors for 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background-color: #E75C58 +} + +div.highlight .-Color[class*=-BGGreen] { + background-color: #00A250 +} + +div.highlight .-Color[class*=-BGYellow] { + background-color: #DDB62B +} + +div.highlight .-Color[class*=-BGBlue] { + background-color: #208FFB +} + +div.highlight .-Color[class*=-BGMagenta] { + background-color: #D160C4 +} + +div.highlight .-Color[class*=-BGCyan] { + background-color: #60C6C8 +} + +div.highlight .-Color[class*=-BGWhite] { + background-color: #C5C1B4 +} + +/* Font colors for 8-bit ANSI */ + +div.highlight .-Color[class*=-C0] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC0] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C1] { + color: #800000 +} + +div.highlight .-Color[class*=-BGC1] { + background-color: #800000 +} + +div.highlight .-Color[class*=-C2] { + color: #008000 +} + +div.highlight .-Color[class*=-BGC2] { + background-color: #008000 +} + +div.highlight .-Color[class*=-C3] { + color: #808000 +} + +div.highlight .-Color[class*=-BGC3] { + background-color: #808000 +} + +div.highlight .-Color[class*=-C4] { + color: #000080 +} + +div.highlight .-Color[class*=-BGC4] { + background-color: #000080 +} + +div.highlight .-Color[class*=-C5] { + color: #800080 +} + +div.highlight .-Color[class*=-BGC5] { + background-color: #800080 +} + +div.highlight .-Color[class*=-C6] { + color: #008080 +} + +div.highlight .-Color[class*=-BGC6] { + background-color: #008080 +} + +div.highlight .-Color[class*=-C7] { + color: #C0C0C0 +} + +div.highlight .-Color[class*=-BGC7] { + background-color: #C0C0C0 +} + +div.highlight .-Color[class*=-C8] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC8] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C9] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC9] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C10] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC10] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C11] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC11] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C12] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC12] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C13] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC13] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C14] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC14] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C15] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC15] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C16] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC16] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C17] { + color: #00005F +} + +div.highlight .-Color[class*=-BGC17] { + background-color: #00005F +} + +div.highlight .-Color[class*=-C18] { + color: #000087 +} + +div.highlight .-Color[class*=-BGC18] { + background-color: #000087 +} + +div.highlight .-Color[class*=-C19] { + color: #0000AF +} + +div.highlight .-Color[class*=-BGC19] { + background-color: #0000AF +} + +div.highlight .-Color[class*=-C20] { + color: #0000D7 +} + +div.highlight .-Color[class*=-BGC20] { + background-color: #0000D7 +} + +div.highlight .-Color[class*=-C21] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC21] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C22] { + color: #005F00 +} + +div.highlight .-Color[class*=-BGC22] { + background-color: #005F00 +} + +div.highlight .-Color[class*=-C23] { + color: #005F5F +} + +div.highlight .-Color[class*=-BGC23] { + background-color: #005F5F +} + +div.highlight .-Color[class*=-C24] { + color: #005F87 +} + +div.highlight .-Color[class*=-BGC24] { + background-color: #005F87 +} + +div.highlight .-Color[class*=-C25] { + color: #005FAF +} + +div.highlight .-Color[class*=-BGC25] { + background-color: #005FAF +} + +div.highlight .-Color[class*=-C26] { + color: #005FD7 +} + +div.highlight .-Color[class*=-BGC26] { + background-color: #005FD7 +} + +div.highlight .-Color[class*=-C27] { + color: #005FFF +} + +div.highlight .-Color[class*=-BGC27] { + background-color: #005FFF +} + +div.highlight .-Color[class*=-C28] { + color: #008700 +} + +div.highlight .-Color[class*=-BGC28] { + background-color: #008700 +} + +div.highlight .-Color[class*=-C29] { + color: #00875F +} + +div.highlight .-Color[class*=-BGC29] { + background-color: #00875F +} + +div.highlight .-Color[class*=-C30] { + color: #008787 +} + +div.highlight .-Color[class*=-BGC30] { + background-color: #008787 +} + +div.highlight .-Color[class*=-C31] { + color: #0087AF +} + +div.highlight .-Color[class*=-BGC31] { + background-color: #0087AF +} + +div.highlight .-Color[class*=-C32] { + color: #0087D7 +} + +div.highlight .-Color[class*=-BGC32] { + background-color: #0087D7 +} + +div.highlight .-Color[class*=-C33] { + color: #0087FF +} + +div.highlight .-Color[class*=-BGC33] { + background-color: #0087FF +} + +div.highlight .-Color[class*=-C34] { + color: #00AF00 +} + +div.highlight .-Color[class*=-BGC34] { + background-color: #00AF00 +} + +div.highlight .-Color[class*=-C35] { + color: #00AF5F +} + +div.highlight .-Color[class*=-BGC35] { + background-color: #00AF5F +} + +div.highlight .-Color[class*=-C36] { + color: #00AF87 +} + +div.highlight .-Color[class*=-BGC36] { + background-color: #00AF87 +} + +div.highlight .-Color[class*=-C37] { + color: #00AFAF +} + +div.highlight .-Color[class*=-BGC37] { + background-color: #00AFAF +} + +div.highlight .-Color[class*=-C38] { + color: #00AFD7 +} + +div.highlight .-Color[class*=-BGC38] { + background-color: #00AFD7 +} + +div.highlight .-Color[class*=-C39] { + color: #00AFFF +} + +div.highlight .-Color[class*=-BGC39] { + background-color: #00AFFF +} + +div.highlight .-Color[class*=-C40] { + color: #00D700 +} + +div.highlight .-Color[class*=-BGC40] { + background-color: #00D700 +} + +div.highlight .-Color[class*=-C41] { + color: #00D75F +} + +div.highlight .-Color[class*=-BGC41] { + background-color: #00D75F +} + +div.highlight .-Color[class*=-C42] { + color: #00D787 +} + +div.highlight .-Color[class*=-BGC42] { + background-color: #00D787 +} + +div.highlight .-Color[class*=-C43] { + color: #00D7AF +} + +div.highlight .-Color[class*=-BGC43] { + background-color: #00D7AF +} + +div.highlight .-Color[class*=-C44] { + color: #00D7D7 +} + +div.highlight .-Color[class*=-BGC44] { + background-color: #00D7D7 +} + +div.highlight .-Color[class*=-C45] { + color: #00D7FF +} + +div.highlight .-Color[class*=-BGC45] { + background-color: #00D7FF +} + +div.highlight .-Color[class*=-C46] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC46] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C47] { + color: #00FF5F +} + +div.highlight .-Color[class*=-BGC47] { + background-color: #00FF5F +} + +div.highlight .-Color[class*=-C48] { + color: #00FF87 +} + +div.highlight .-Color[class*=-BGC48] { + background-color: #00FF87 +} + +div.highlight .-Color[class*=-C49] { + color: #00FFAF +} + +div.highlight .-Color[class*=-BGC49] { + background-color: #00FFAF +} + +div.highlight .-Color[class*=-C50] { + color: #00FFD7 +} + +div.highlight .-Color[class*=-BGC50] { + background-color: #00FFD7 +} + +div.highlight .-Color[class*=-C51] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC51] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C52] { + color: #5F0000 +} + +div.highlight .-Color[class*=-BGC52] { + background-color: #5F0000 +} + +div.highlight .-Color[class*=-C53] { + color: #5F005F +} + +div.highlight .-Color[class*=-BGC53] { + background-color: #5F005F +} + +div.highlight .-Color[class*=-C54] { + color: #5F0087 +} + +div.highlight .-Color[class*=-BGC54] { + background-color: #5F0087 +} + +div.highlight .-Color[class*=-C55] { + color: #5F00AF +} + +div.highlight .-Color[class*=-BGC55] { + background-color: #5F00AF +} + +div.highlight .-Color[class*=-C56] { + color: #5F00D7 +} + +div.highlight .-Color[class*=-BGC56] { + background-color: #5F00D7 +} + +div.highlight .-Color[class*=-C57] { + color: #5F00FF +} + +div.highlight .-Color[class*=-BGC57] { + background-color: #5F00FF +} + +div.highlight .-Color[class*=-C58] { + color: #5F5F00 +} + +div.highlight .-Color[class*=-BGC58] { + background-color: #5F5F00 +} + +div.highlight .-Color[class*=-C59] { + color: #5F5F5F +} + +div.highlight .-Color[class*=-BGC59] { + background-color: #5F5F5F +} + +div.highlight .-Color[class*=-C60] { + color: #5F5F87 +} + +div.highlight .-Color[class*=-BGC60] { + background-color: #5F5F87 +} + +div.highlight .-Color[class*=-C61] { + color: #5F5FAF +} + +div.highlight .-Color[class*=-BGC61] { + background-color: #5F5FAF +} + +div.highlight .-Color[class*=-C62] { + color: #5F5FD7 +} + +div.highlight .-Color[class*=-BGC62] { + background-color: #5F5FD7 +} + +div.highlight .-Color[class*=-C63] { + color: #5F5FFF +} + +div.highlight .-Color[class*=-BGC63] { + background-color: #5F5FFF +} + +div.highlight .-Color[class*=-C64] { + color: #5F8700 +} + +div.highlight .-Color[class*=-BGC64] { + background-color: #5F8700 +} + +div.highlight .-Color[class*=-C65] { + color: #5F875F +} + +div.highlight .-Color[class*=-BGC65] { + background-color: #5F875F +} + +div.highlight .-Color[class*=-C66] { + color: #5F8787 +} + +div.highlight .-Color[class*=-BGC66] { + background-color: #5F8787 +} + +div.highlight .-Color[class*=-C67] { + color: #5F87AF +} + +div.highlight .-Color[class*=-BGC67] { + background-color: #5F87AF +} + +div.highlight .-Color[class*=-C68] { + color: #5F87D7 +} + +div.highlight .-Color[class*=-BGC68] { + background-color: #5F87D7 +} + +div.highlight .-Color[class*=-C69] { + color: #5F87FF +} + +div.highlight .-Color[class*=-BGC69] { + background-color: #5F87FF +} + +div.highlight .-Color[class*=-C70] { + color: #5FAF00 +} + +div.highlight .-Color[class*=-BGC70] { + background-color: #5FAF00 +} + +div.highlight .-Color[class*=-C71] { + color: #5FAF5F +} + +div.highlight .-Color[class*=-BGC71] { + background-color: #5FAF5F +} + +div.highlight .-Color[class*=-C72] { + color: #5FAF87 +} + +div.highlight .-Color[class*=-BGC72] { + background-color: #5FAF87 +} + +div.highlight .-Color[class*=-C73] { + color: #5FAFAF +} + +div.highlight .-Color[class*=-BGC73] { + background-color: #5FAFAF +} + +div.highlight .-Color[class*=-C74] { + color: #5FAFD7 +} + +div.highlight .-Color[class*=-BGC74] { + background-color: #5FAFD7 +} + +div.highlight .-Color[class*=-C75] { + color: #5FAFFF +} + +div.highlight .-Color[class*=-BGC75] { + background-color: #5FAFFF +} + +div.highlight .-Color[class*=-C76] { + color: #5FD700 +} + +div.highlight .-Color[class*=-BGC76] { + background-color: #5FD700 +} + +div.highlight .-Color[class*=-C77] { + color: #5FD75F +} + +div.highlight .-Color[class*=-BGC77] { + background-color: #5FD75F +} + +div.highlight .-Color[class*=-C78] { + color: #5FD787 +} + +div.highlight .-Color[class*=-BGC78] { + background-color: #5FD787 +} + +div.highlight .-Color[class*=-C79] { + color: #5FD7AF +} + +div.highlight .-Color[class*=-BGC79] { + background-color: #5FD7AF +} + +div.highlight .-Color[class*=-C80] { + color: #5FD7D7 +} + +div.highlight .-Color[class*=-BGC80] { + background-color: #5FD7D7 +} + +div.highlight .-Color[class*=-C81] { + color: #5FD7FF +} + +div.highlight .-Color[class*=-BGC81] { + background-color: #5FD7FF +} + +div.highlight .-Color[class*=-C82] { + color: #5FFF00 +} + +div.highlight .-Color[class*=-BGC82] { + background-color: #5FFF00 +} + +div.highlight .-Color[class*=-C83] { + color: #5FFF5F +} + +div.highlight .-Color[class*=-BGC83] { + background-color: #5FFF5F +} + +div.highlight .-Color[class*=-C84] { + color: #5FFF87 +} + +div.highlight .-Color[class*=-BGC84] { + background-color: #5FFF87 +} + +div.highlight .-Color[class*=-C85] { + color: #5FFFAF +} + +div.highlight .-Color[class*=-BGC85] { + background-color: #5FFFAF +} + +div.highlight .-Color[class*=-C86] { + color: #5FFFD7 +} + +div.highlight .-Color[class*=-BGC86] { + background-color: #5FFFD7 +} + +div.highlight .-Color[class*=-C87] { + color: #5FFFFF +} + +div.highlight .-Color[class*=-BGC87] { + background-color: #5FFFFF +} + +div.highlight .-Color[class*=-C88] { + color: #870000 +} + +div.highlight .-Color[class*=-BGC88] { + background-color: #870000 +} + +div.highlight .-Color[class*=-C89] { + color: #87005F +} + +div.highlight .-Color[class*=-BGC89] { + background-color: #87005F +} + +div.highlight .-Color[class*=-C90] { + color: #870087 +} + +div.highlight .-Color[class*=-BGC90] { + background-color: #870087 +} + +div.highlight .-Color[class*=-C91] { + color: #8700AF +} + +div.highlight .-Color[class*=-BGC91] { + background-color: #8700AF +} + +div.highlight .-Color[class*=-C92] { + color: #8700D7 +} + +div.highlight .-Color[class*=-BGC92] { + background-color: #8700D7 +} + +div.highlight .-Color[class*=-C93] { + color: #8700FF +} + +div.highlight .-Color[class*=-BGC93] { + background-color: #8700FF +} + +div.highlight .-Color[class*=-C94] { + color: #875F00 +} + +div.highlight .-Color[class*=-BGC94] { + background-color: #875F00 +} + +div.highlight .-Color[class*=-C95] { + color: #875F5F +} + +div.highlight .-Color[class*=-BGC95] { + background-color: #875F5F +} + +div.highlight .-Color[class*=-C96] { + color: #875F87 +} + +div.highlight .-Color[class*=-BGC96] { + background-color: #875F87 +} + +div.highlight .-Color[class*=-C97] { + color: #875FAF +} + +div.highlight .-Color[class*=-BGC97] { + background-color: #875FAF +} + +div.highlight .-Color[class*=-C98] { + color: #875FD7 +} + +div.highlight .-Color[class*=-BGC98] { + background-color: #875FD7 +} + +div.highlight .-Color[class*=-C99] { + color: #875FFF +} + +div.highlight .-Color[class*=-BGC99] { + background-color: #875FFF +} + +div.highlight .-Color[class*=-C100] { + color: #878700 +} + +div.highlight .-Color[class*=-BGC100] { + background-color: #878700 +} + +div.highlight .-Color[class*=-C101] { + color: #87875F +} + +div.highlight .-Color[class*=-BGC101] { + background-color: #87875F +} + +div.highlight .-Color[class*=-C102] { + color: #878787 +} + +div.highlight .-Color[class*=-BGC102] { + background-color: #878787 +} + +div.highlight .-Color[class*=-C103] { + color: #8787AF +} + +div.highlight .-Color[class*=-BGC103] { + background-color: #8787AF +} + +div.highlight .-Color[class*=-C104] { + color: #8787D7 +} + +div.highlight .-Color[class*=-BGC104] { + background-color: #8787D7 +} + +div.highlight .-Color[class*=-C105] { + color: #8787FF +} + +div.highlight .-Color[class*=-BGC105] { + background-color: #8787FF +} + +div.highlight .-Color[class*=-C106] { + color: #87AF00 +} + +div.highlight .-Color[class*=-BGC106] { + background-color: #87AF00 +} + +div.highlight .-Color[class*=-C107] { + color: #87AF5F +} + +div.highlight .-Color[class*=-BGC107] { + background-color: #87AF5F +} + +div.highlight .-Color[class*=-C108] { + color: #87AF87 +} + +div.highlight .-Color[class*=-BGC108] { + background-color: #87AF87 +} + +div.highlight .-Color[class*=-C109] { + color: #87AFAF +} + +div.highlight .-Color[class*=-BGC109] { + background-color: #87AFAF +} + +div.highlight .-Color[class*=-C110] { + color: #87AFD7 +} + +div.highlight .-Color[class*=-BGC110] { + background-color: #87AFD7 +} + +div.highlight .-Color[class*=-C111] { + color: #87AFFF +} + +div.highlight .-Color[class*=-BGC111] { + background-color: #87AFFF +} + +div.highlight .-Color[class*=-C112] { + color: #87D700 +} + +div.highlight .-Color[class*=-BGC112] { + background-color: #87D700 +} + +div.highlight .-Color[class*=-C113] { + color: #87D75F +} + +div.highlight .-Color[class*=-BGC113] { + background-color: #87D75F +} + +div.highlight .-Color[class*=-C114] { + color: #87D787 +} + +div.highlight .-Color[class*=-BGC114] { + background-color: #87D787 +} + +div.highlight .-Color[class*=-C115] { + color: #87D7AF +} + +div.highlight .-Color[class*=-BGC115] { + background-color: #87D7AF +} + +div.highlight .-Color[class*=-C116] { + color: #87D7D7 +} + +div.highlight .-Color[class*=-BGC116] { + background-color: #87D7D7 +} + +div.highlight .-Color[class*=-C117] { + color: #87D7FF +} + +div.highlight .-Color[class*=-BGC117] { + background-color: #87D7FF +} + +div.highlight .-Color[class*=-C118] { + color: #87FF00 +} + +div.highlight .-Color[class*=-BGC118] { + background-color: #87FF00 +} + +div.highlight .-Color[class*=-C119] { + color: #87FF5F +} + +div.highlight .-Color[class*=-BGC119] { + background-color: #87FF5F +} + +div.highlight .-Color[class*=-C120] { + color: #87FF87 +} + +div.highlight .-Color[class*=-BGC120] { + background-color: #87FF87 +} + +div.highlight .-Color[class*=-C121] { + color: #87FFAF +} + +div.highlight .-Color[class*=-BGC121] { + background-color: #87FFAF +} + +div.highlight .-Color[class*=-C122] { + color: #87FFD7 +} + +div.highlight .-Color[class*=-BGC122] { + background-color: #87FFD7 +} + +div.highlight .-Color[class*=-C123] { + color: #87FFFF +} + +div.highlight .-Color[class*=-BGC123] { + background-color: #87FFFF +} + +div.highlight .-Color[class*=-C124] { + color: #AF0000 +} + +div.highlight .-Color[class*=-BGC124] { + background-color: #AF0000 +} + +div.highlight .-Color[class*=-C125] { + color: #AF005F +} + +div.highlight .-Color[class*=-BGC125] { + background-color: #AF005F +} + +div.highlight .-Color[class*=-C126] { + color: #AF0087 +} + +div.highlight .-Color[class*=-BGC126] { + background-color: #AF0087 +} + +div.highlight .-Color[class*=-C127] { + color: #AF00AF +} + +div.highlight .-Color[class*=-BGC127] { + background-color: #AF00AF +} + +div.highlight .-Color[class*=-C128] { + color: #AF00D7 +} + +div.highlight .-Color[class*=-BGC128] { + background-color: #AF00D7 +} + +div.highlight .-Color[class*=-C129] { + color: #AF00FF +} + +div.highlight .-Color[class*=-BGC129] { + background-color: #AF00FF +} + +div.highlight .-Color[class*=-C130] { + color: #AF5F00 +} + +div.highlight .-Color[class*=-BGC130] { + background-color: #AF5F00 +} + +div.highlight .-Color[class*=-C131] { + color: #AF5F5F +} + +div.highlight .-Color[class*=-BGC131] { + background-color: #AF5F5F +} + +div.highlight .-Color[class*=-C132] { + color: #AF5F87 +} + +div.highlight .-Color[class*=-BGC132] { + background-color: #AF5F87 +} + +div.highlight .-Color[class*=-C133] { + color: #AF5FAF +} + +div.highlight .-Color[class*=-BGC133] { + background-color: #AF5FAF +} + +div.highlight .-Color[class*=-C134] { + color: #AF5FD7 +} + +div.highlight .-Color[class*=-BGC134] { + background-color: #AF5FD7 +} + +div.highlight .-Color[class*=-C135] { + color: #AF5FFF +} + +div.highlight .-Color[class*=-BGC135] { + background-color: #AF5FFF +} + +div.highlight .-Color[class*=-C136] { + color: #AF8700 +} + +div.highlight .-Color[class*=-BGC136] { + background-color: #AF8700 +} + +div.highlight .-Color[class*=-C137] { + color: #AF875F +} + +div.highlight .-Color[class*=-BGC137] { + background-color: #AF875F +} + +div.highlight .-Color[class*=-C138] { + color: #AF8787 +} + +div.highlight .-Color[class*=-BGC138] { + background-color: #AF8787 +} + +div.highlight .-Color[class*=-C139] { + color: #AF87AF +} + +div.highlight .-Color[class*=-BGC139] { + background-color: #AF87AF +} + +div.highlight .-Color[class*=-C140] { + color: #AF87D7 +} + +div.highlight .-Color[class*=-BGC140] { + background-color: #AF87D7 +} + +div.highlight .-Color[class*=-C141] { + color: #AF87FF +} + +div.highlight .-Color[class*=-BGC141] { + background-color: #AF87FF +} + +div.highlight .-Color[class*=-C142] { + color: #AFAF00 +} + +div.highlight .-Color[class*=-BGC142] { + background-color: #AFAF00 +} + +div.highlight .-Color[class*=-C143] { + color: #AFAF5F +} + +div.highlight .-Color[class*=-BGC143] { + background-color: #AFAF5F +} + +div.highlight .-Color[class*=-C144] { + color: #AFAF87 +} + +div.highlight .-Color[class*=-BGC144] { + background-color: #AFAF87 +} + +div.highlight .-Color[class*=-C145] { + color: #AFAFAF +} + +div.highlight .-Color[class*=-BGC145] { + background-color: #AFAFAF +} + +div.highlight .-Color[class*=-C146] { + color: #AFAFD7 +} + +div.highlight .-Color[class*=-BGC146] { + background-color: #AFAFD7 +} + +div.highlight .-Color[class*=-C147] { + color: #AFAFFF +} + +div.highlight .-Color[class*=-BGC147] { + background-color: #AFAFFF +} + +div.highlight .-Color[class*=-C148] { + color: #AFD700 +} + +div.highlight .-Color[class*=-BGC148] { + background-color: #AFD700 +} + +div.highlight .-Color[class*=-C149] { + color: #AFD75F +} + +div.highlight .-Color[class*=-BGC149] { + background-color: #AFD75F +} + +div.highlight .-Color[class*=-C150] { + color: #AFD787 +} + +div.highlight .-Color[class*=-BGC150] { + background-color: #AFD787 +} + +div.highlight .-Color[class*=-C151] { + color: #AFD7AF +} + +div.highlight .-Color[class*=-BGC151] { + background-color: #AFD7AF +} + +div.highlight .-Color[class*=-C152] { + color: #AFD7D7 +} + +div.highlight .-Color[class*=-BGC152] { + background-color: #AFD7D7 +} + +div.highlight .-Color[class*=-C153] { + color: #AFD7FF +} + +div.highlight .-Color[class*=-BGC153] { + background-color: #AFD7FF +} + +div.highlight .-Color[class*=-C154] { + color: #AFFF00 +} + +div.highlight .-Color[class*=-BGC154] { + background-color: #AFFF00 +} + +div.highlight .-Color[class*=-C155] { + color: #AFFF5F +} + +div.highlight .-Color[class*=-BGC155] { + background-color: #AFFF5F +} + +div.highlight .-Color[class*=-C156] { + color: #AFFF87 +} + +div.highlight .-Color[class*=-BGC156] { + background-color: #AFFF87 +} + +div.highlight .-Color[class*=-C157] { + color: #AFFFAF +} + +div.highlight .-Color[class*=-BGC157] { + background-color: #AFFFAF +} + +div.highlight .-Color[class*=-C158] { + color: #AFFFD7 +} + +div.highlight .-Color[class*=-BGC158] { + background-color: #AFFFD7 +} + +div.highlight .-Color[class*=-C159] { + color: #AFFFFF +} + +div.highlight .-Color[class*=-BGC159] { + background-color: #AFFFFF +} + +div.highlight .-Color[class*=-C160] { + color: #D70000 +} + +div.highlight .-Color[class*=-BGC160] { + background-color: #D70000 +} + +div.highlight .-Color[class*=-C161] { + color: #D7005F +} + +div.highlight .-Color[class*=-BGC161] { + background-color: #D7005F +} + +div.highlight .-Color[class*=-C162] { + color: #D70087 +} + +div.highlight .-Color[class*=-BGC162] { + background-color: #D70087 +} + +div.highlight .-Color[class*=-C163] { + color: #D700AF +} + +div.highlight .-Color[class*=-BGC163] { + background-color: #D700AF +} + +div.highlight .-Color[class*=-C164] { + color: #D700D7 +} + +div.highlight .-Color[class*=-BGC164] { + background-color: #D700D7 +} + +div.highlight .-Color[class*=-C165] { + color: #D700FF +} + +div.highlight .-Color[class*=-BGC165] { + background-color: #D700FF +} + +div.highlight .-Color[class*=-C166] { + color: #D75F00 +} + +div.highlight .-Color[class*=-BGC166] { + background-color: #D75F00 +} + +div.highlight .-Color[class*=-C167] { + color: #D75F5F +} + +div.highlight .-Color[class*=-BGC167] { + background-color: #D75F5F +} + +div.highlight .-Color[class*=-C168] { + color: #D75F87 +} + +div.highlight .-Color[class*=-BGC168] { + background-color: #D75F87 +} + +div.highlight .-Color[class*=-C169] { + color: #D75FAF +} + +div.highlight .-Color[class*=-BGC169] { + background-color: #D75FAF +} + +div.highlight .-Color[class*=-C170] { + color: #D75FD7 +} + +div.highlight .-Color[class*=-BGC170] { + background-color: #D75FD7 +} + +div.highlight .-Color[class*=-C171] { + color: #D75FFF +} + +div.highlight .-Color[class*=-BGC171] { + background-color: #D75FFF +} + +div.highlight .-Color[class*=-C172] { + color: #D78700 +} + +div.highlight .-Color[class*=-BGC172] { + background-color: #D78700 +} + +div.highlight .-Color[class*=-C173] { + color: #D7875F +} + +div.highlight .-Color[class*=-BGC173] { + background-color: #D7875F +} + +div.highlight .-Color[class*=-C174] { + color: #D78787 +} + +div.highlight .-Color[class*=-BGC174] { + background-color: #D78787 +} + +div.highlight .-Color[class*=-C175] { + color: #D787AF +} + +div.highlight .-Color[class*=-BGC175] { + background-color: #D787AF +} + +div.highlight .-Color[class*=-C176] { + color: #D787D7 +} + +div.highlight .-Color[class*=-BGC176] { + background-color: #D787D7 +} + +div.highlight .-Color[class*=-C177] { + color: #D787FF +} + +div.highlight .-Color[class*=-BGC177] { + background-color: #D787FF +} + +div.highlight .-Color[class*=-C178] { + color: #D7AF00 +} + +div.highlight .-Color[class*=-BGC178] { + background-color: #D7AF00 +} + +div.highlight .-Color[class*=-C179] { + color: #D7AF5F +} + +div.highlight .-Color[class*=-BGC179] { + background-color: #D7AF5F +} + +div.highlight .-Color[class*=-C180] { + color: #D7AF87 +} + +div.highlight .-Color[class*=-BGC180] { + background-color: #D7AF87 +} + +div.highlight .-Color[class*=-C181] { + color: #D7AFAF +} + +div.highlight .-Color[class*=-BGC181] { + background-color: #D7AFAF +} + +div.highlight .-Color[class*=-C182] { + color: #D7AFD7 +} + +div.highlight .-Color[class*=-BGC182] { + background-color: #D7AFD7 +} + +div.highlight .-Color[class*=-C183] { + color: #D7AFFF +} + +div.highlight .-Color[class*=-BGC183] { + background-color: #D7AFFF +} + +div.highlight .-Color[class*=-C184] { + color: #D7D700 +} + +div.highlight .-Color[class*=-BGC184] { + background-color: #D7D700 +} + +div.highlight .-Color[class*=-C185] { + color: #D7D75F +} + +div.highlight .-Color[class*=-BGC185] { + background-color: #D7D75F +} + +div.highlight .-Color[class*=-C186] { + color: #D7D787 +} + +div.highlight .-Color[class*=-BGC186] { + background-color: #D7D787 +} + +div.highlight .-Color[class*=-C187] { + color: #D7D7AF +} + +div.highlight .-Color[class*=-BGC187] { + background-color: #D7D7AF +} + +div.highlight .-Color[class*=-C188] { + color: #D7D7D7 +} + +div.highlight .-Color[class*=-BGC188] { + background-color: #D7D7D7 +} + +div.highlight .-Color[class*=-C189] { + color: #D7D7FF +} + +div.highlight .-Color[class*=-BGC189] { + background-color: #D7D7FF +} + +div.highlight .-Color[class*=-C190] { + color: #D7FF00 +} + +div.highlight .-Color[class*=-BGC190] { + background-color: #D7FF00 +} + +div.highlight .-Color[class*=-C191] { + color: #D7FF5F +} + +div.highlight .-Color[class*=-BGC191] { + background-color: #D7FF5F +} + +div.highlight .-Color[class*=-C192] { + color: #D7FF87 +} + +div.highlight .-Color[class*=-BGC192] { + background-color: #D7FF87 +} + +div.highlight .-Color[class*=-C193] { + color: #D7FFAF +} + +div.highlight .-Color[class*=-BGC193] { + background-color: #D7FFAF +} + +div.highlight .-Color[class*=-C194] { + color: #D7FFD7 +} + +div.highlight .-Color[class*=-BGC194] { + background-color: #D7FFD7 +} + +div.highlight .-Color[class*=-C195] { + color: #D7FFFF +} + +div.highlight .-Color[class*=-BGC195] { + background-color: #D7FFFF +} + +div.highlight .-Color[class*=-C196] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC196] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C197] { + color: #FF005F +} + +div.highlight .-Color[class*=-BGC197] { + background-color: #FF005F +} + +div.highlight .-Color[class*=-C198] { + color: #FF0087 +} + +div.highlight .-Color[class*=-BGC198] { + background-color: #FF0087 +} + +div.highlight .-Color[class*=-C199] { + color: #FF00AF +} + +div.highlight .-Color[class*=-BGC199] { + background-color: #FF00AF +} + +div.highlight .-Color[class*=-C200] { + color: #FF00D7 +} + +div.highlight .-Color[class*=-BGC200] { + background-color: #FF00D7 +} + +div.highlight .-Color[class*=-C201] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC201] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C202] { + color: #FF5F00 +} + +div.highlight .-Color[class*=-BGC202] { + background-color: #FF5F00 +} + +div.highlight .-Color[class*=-C203] { + color: #FF5F5F +} + +div.highlight .-Color[class*=-BGC203] { + background-color: #FF5F5F +} + +div.highlight .-Color[class*=-C204] { + color: #FF5F87 +} + +div.highlight .-Color[class*=-BGC204] { + background-color: #FF5F87 +} + +div.highlight .-Color[class*=-C205] { + color: #FF5FAF +} + +div.highlight .-Color[class*=-BGC205] { + background-color: #FF5FAF +} + +div.highlight .-Color[class*=-C206] { + color: #FF5FD7 +} + +div.highlight .-Color[class*=-BGC206] { + background-color: #FF5FD7 +} + +div.highlight .-Color[class*=-C207] { + color: #FF5FFF +} + +div.highlight .-Color[class*=-BGC207] { + background-color: #FF5FFF +} + +div.highlight .-Color[class*=-C208] { + color: #FF8700 +} + +div.highlight .-Color[class*=-BGC208] { + background-color: #FF8700 +} + +div.highlight .-Color[class*=-C209] { + color: #FF875F +} + +div.highlight .-Color[class*=-BGC209] { + background-color: #FF875F +} + +div.highlight .-Color[class*=-C210] { + color: #FF8787 +} + +div.highlight .-Color[class*=-BGC210] { + background-color: #FF8787 +} + +div.highlight .-Color[class*=-C211] { + color: #FF87AF +} + +div.highlight .-Color[class*=-BGC211] { + background-color: #FF87AF +} + +div.highlight .-Color[class*=-C212] { + color: #FF87D7 +} + +div.highlight .-Color[class*=-BGC212] { + background-color: #FF87D7 +} + +div.highlight .-Color[class*=-C213] { + color: #FF87FF +} + +div.highlight .-Color[class*=-BGC213] { + background-color: #FF87FF +} + +div.highlight .-Color[class*=-C214] { + color: #FFAF00 +} + +div.highlight .-Color[class*=-BGC214] { + background-color: #FFAF00 +} + +div.highlight .-Color[class*=-C215] { + color: #FFAF5F +} + +div.highlight .-Color[class*=-BGC215] { + background-color: #FFAF5F +} + +div.highlight .-Color[class*=-C216] { + color: #FFAF87 +} + +div.highlight .-Color[class*=-BGC216] { + background-color: #FFAF87 +} + +div.highlight .-Color[class*=-C217] { + color: #FFAFAF +} + +div.highlight .-Color[class*=-BGC217] { + background-color: #FFAFAF +} + +div.highlight .-Color[class*=-C218] { + color: #FFAFD7 +} + +div.highlight .-Color[class*=-BGC218] { + background-color: #FFAFD7 +} + +div.highlight .-Color[class*=-C219] { + color: #FFAFFF +} + +div.highlight .-Color[class*=-BGC219] { + background-color: #FFAFFF +} + +div.highlight .-Color[class*=-C220] { + color: #FFD700 +} + +div.highlight .-Color[class*=-BGC220] { + background-color: #FFD700 +} + +div.highlight .-Color[class*=-C221] { + color: #FFD75F +} + +div.highlight .-Color[class*=-BGC221] { + background-color: #FFD75F +} + +div.highlight .-Color[class*=-C222] { + color: #FFD787 +} + +div.highlight .-Color[class*=-BGC222] { + background-color: #FFD787 +} + +div.highlight .-Color[class*=-C223] { + color: #FFD7AF +} + +div.highlight .-Color[class*=-BGC223] { + background-color: #FFD7AF +} + +div.highlight .-Color[class*=-C224] { + color: #FFD7D7 +} + +div.highlight .-Color[class*=-BGC224] { + background-color: #FFD7D7 +} + +div.highlight .-Color[class*=-C225] { + color: #FFD7FF +} + +div.highlight .-Color[class*=-BGC225] { + background-color: #FFD7FF +} + +div.highlight .-Color[class*=-C226] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC226] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C227] { + color: #FFFF5F +} + +div.highlight .-Color[class*=-BGC227] { + background-color: #FFFF5F +} + +div.highlight .-Color[class*=-C228] { + color: #FFFF87 +} + +div.highlight .-Color[class*=-BGC228] { + background-color: #FFFF87 +} + +div.highlight .-Color[class*=-C229] { + color: #FFFFAF +} + +div.highlight .-Color[class*=-BGC229] { + background-color: #FFFFAF +} + +div.highlight .-Color[class*=-C230] { + color: #FFFFD7 +} + +div.highlight .-Color[class*=-BGC230] { + background-color: #FFFFD7 +} + +div.highlight .-Color[class*=-C231] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC231] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C232] { + color: #080808 +} + +div.highlight .-Color[class*=-BGC232] { + background-color: #080808 +} + +div.highlight .-Color[class*=-C233] { + color: #121212 +} + +div.highlight .-Color[class*=-BGC233] { + background-color: #121212 +} + +div.highlight .-Color[class*=-C234] { + color: #1C1C1C +} + +div.highlight .-Color[class*=-BGC234] { + background-color: #1C1C1C +} + +div.highlight .-Color[class*=-C235] { + color: #262626 +} + +div.highlight .-Color[class*=-BGC235] { + background-color: #262626 +} + +div.highlight .-Color[class*=-C236] { + color: #303030 +} + +div.highlight .-Color[class*=-BGC236] { + background-color: #303030 +} + +div.highlight .-Color[class*=-C237] { + color: #3A3A3A +} + +div.highlight .-Color[class*=-BGC237] { + background-color: #3A3A3A +} + +div.highlight .-Color[class*=-C238] { + color: #444444 +} + +div.highlight .-Color[class*=-BGC238] { + background-color: #444444 +} + +div.highlight .-Color[class*=-C239] { + color: #4E4E4E +} + +div.highlight .-Color[class*=-BGC239] { + background-color: #4E4E4E +} + +div.highlight .-Color[class*=-C240] { + color: #585858 +} + +div.highlight .-Color[class*=-BGC240] { + background-color: #585858 +} + +div.highlight .-Color[class*=-C241] { + color: #626262 +} + +div.highlight .-Color[class*=-BGC241] { + background-color: #626262 +} + +div.highlight .-Color[class*=-C242] { + color: #6C6C6C +} + +div.highlight .-Color[class*=-BGC242] { + background-color: #6C6C6C +} + +div.highlight .-Color[class*=-C243] { + color: #767676 +} + +div.highlight .-Color[class*=-BGC243] { + background-color: #767676 +} + +div.highlight .-Color[class*=-C244] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC244] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C245] { + color: #8A8A8A +} + +div.highlight .-Color[class*=-BGC245] { + background-color: #8A8A8A +} + +div.highlight .-Color[class*=-C246] { + color: #949494 +} + +div.highlight .-Color[class*=-BGC246] { + background-color: #949494 +} + +div.highlight .-Color[class*=-C247] { + color: #9E9E9E +} + +div.highlight .-Color[class*=-BGC247] { + background-color: #9E9E9E +} + +div.highlight .-Color[class*=-C248] { + color: #A8A8A8 +} + +div.highlight .-Color[class*=-BGC248] { + background-color: #A8A8A8 +} + +div.highlight .-Color[class*=-C249] { + color: #B2B2B2 +} + +div.highlight .-Color[class*=-BGC249] { + background-color: #B2B2B2 +} + +div.highlight .-Color[class*=-C250] { + color: #BCBCBC +} + +div.highlight .-Color[class*=-BGC250] { + background-color: #BCBCBC +} + +div.highlight .-Color[class*=-C251] { + color: #C6C6C6 +} + +div.highlight .-Color[class*=-BGC251] { + background-color: #C6C6C6 +} + +div.highlight .-Color[class*=-C252] { + color: #D0D0D0 +} + +div.highlight .-Color[class*=-BGC252] { + background-color: #D0D0D0 +} + +div.highlight .-Color[class*=-C253] { + color: #DADADA +} + +div.highlight .-Color[class*=-BGC253] { + background-color: #DADADA +} + +div.highlight .-Color[class*=-C254] { + color: #E4E4E4 +} + +div.highlight .-Color[class*=-BGC254] { + background-color: #E4E4E4 +} + +div.highlight .-Color[class*=-C255] { + color: #EEEEEE +} + +div.highlight .-Color[class*=-BGC255] { + background-color: #EEEEEE +} diff --git a/singlehtml/_static/plus.png b/singlehtml/_static/plus.png new file mode 100644 index 0000000..7107cec Binary files /dev/null and b/singlehtml/_static/plus.png differ diff --git a/singlehtml/_static/pygments.css b/singlehtml/_static/pygments.css new file mode 100644 index 0000000..84ab303 --- /dev/null +++ b/singlehtml/_static/pygments.css @@ -0,0 +1,75 @@ +pre { line-height: 125%; } +td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } +td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } +.highlight .hll { background-color: #ffffcc } 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#19177C } /* Literal.String.Symbol */ +.highlight .bp { color: #008000 } /* Name.Builtin.Pseudo */ +.highlight .fm { color: #0000FF } /* Name.Function.Magic */ +.highlight .vc { color: #19177C } /* Name.Variable.Class */ +.highlight .vg { color: #19177C } /* Name.Variable.Global */ +.highlight .vi { color: #19177C } /* Name.Variable.Instance */ +.highlight .vm { color: #19177C } /* Name.Variable.Magic */ +.highlight .il { color: #666666 } /* Literal.Number.Integer.Long */ \ No newline at end of file diff --git a/singlehtml/_static/searchtools.js b/singlehtml/_static/searchtools.js new file mode 100644 index 0000000..b08d58c --- /dev/null +++ b/singlehtml/_static/searchtools.js @@ -0,0 +1,620 @@ +/* + * searchtools.js + * ~~~~~~~~~~~~~~~~ + * + * Sphinx JavaScript utilities for the full-text search. + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ +"use strict"; + +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms, anchor) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + "Search finished, found ${resultCount} page(s) matching the search query." + ).replace('${resultCount}', resultCount); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString, anchor) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + for (const removalQuery of [".headerlink", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent) return docContent.textContent; + + console.warn( + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + _parseQuery: (query) => { + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename]. + const normalResults = []; + const nonMainIndexResults = []; + + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase().trim(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + const score = Math.round(Scorer.title * queryLower.length / title.length); + const boost = titles[file] === title ? 1 : 0; // add a boost for document titles + normalResults.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score + boost, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } + } + } + } + + // lookup as object + objectTerms.forEach((term) => + normalResults.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/singlehtml/_static/sphinx_highlight.js b/singlehtml/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/singlehtml/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/singlehtml/_static/sphinx_lesson.css b/singlehtml/_static/sphinx_lesson.css new file mode 100644 index 0000000..14b20c6 --- /dev/null +++ b/singlehtml/_static/sphinx_lesson.css @@ -0,0 +1,51 @@ +/* sphinx_lesson.css */ + +body.wy-body-for-nav img.with-border { + border: 2px solid; +} + +.rst-content .admonition-no-content { + padding-bottom: 0px; +} + +.rst-content .demo > .admonition-title::before { + content: "\01F440"; /* Eyes */ } +.rst-content .type-along > .admonition-title::before { + content: "\02328\0FE0F"; /* Keyboard */ } +.rst-content .exercise > .admonition-title::before { + content: "\0270D\0FE0F"; /* Hand */ } +.rst-content .solution > .admonition-title::before { + content: "\02714\0FE0E"; /* Check mark */ } +.rst-content .homework > .admonition-title::before { + content: "\01F4DD"; /* Memo */ } +.rst-content .discussion > .admonition-title::before { + content: "\01F4AC"; /* Speech balloon */ } +.rst-content .questions > .admonition-title::before { + content: "\02753\0FE0E"; /* Question mark */ } +.rst-content .prerequisites > .admonition-title::before { + content: "\02699"; /* Gear */ } +.rst-content .seealso > .admonition-title::before { + content: "\027A1\0FE0E"; /* Question mark */ } + + +/* instructor-note */ +.rst-content .instructor-note { + background: #e7e7e7; +} +.rst-content .instructor-note > .admonition-title { + background: #6a6a6a; +} +.rst-content .instructor-note > .admonition-title::before { + content: ""; +} + + +/* sphinx_toggle_button, make the font white */ +.rst-content .toggle.admonition button.toggle-button { + color: white; +} + +/* sphinx-togglebutton, remove underflow when toggled to hidden mode */ +.rst-content .admonition.toggle-hidden { + padding-bottom: 0px; +} diff --git a/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css b/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css new file mode 100644 index 0000000..e68feb8 --- /dev/null +++ b/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css @@ -0,0 +1,47 @@ +/* The following are for web accessibility of sphinx_rtd_theme: they + * solve some of the most frequent contrast issues. Remove when this + * solved: + * https://github.com/readthedocs/sphinx_rtd_theme/issues/971 + */ +/* background: #fcfcfc, note boxes #E7F2FA */ +a { color: #2573A7; } /* original #2980B9, #1F5C84; */ +body { color: #242424; } /* original #404040, #383838 */ +.wy-side-nav-search>a, .wy-side-nav-search .wy-dropdown>a { + color: #ffffff; +} /* original #fcfcfc */ +footer { color: #737373; } /* original gray=#808080*/ +footer span.commit code, footer span.commit .rst-content tt, .rst-content footer span.commit tt { + color: #737373; +} /* original gray=#808080*/ +.rst-content tt.literal, .rst-content tt.literal, .rst-content code.literal { + color: #AB2314; +} +/* Sidebar background */ +.wy-side-nav-search { background-color: #277CB4;} + +/* Same, but for pygments */ +.highlight .ch { color: #3E7A89; } /* #! line */ +.highlight .c1 { color: #3E7A89; } /* also comments */ +.highlight .nv { color: #AD3ECC; } /* variable */ +.highlight .gp { color: #B45608; } /* prompt character, $*/ +.highlight .si { color: #3975B1; } /* ${} variable text */ +.highlight .nc { color: #0C78A7; } + +/* Sphinx admonitions */ +/* warning */ +.wy-alert.wy-alert-warning .wy-alert-title, .rst-content .wy-alert-warning.note .wy-alert-title, .rst-content .attention .wy-alert-title, .rst-content .caution .wy-alert-title, .rst-content .wy-alert-warning.danger .wy-alert-title, .rst-content .wy-alert-warning.error .wy-alert-title, .rst-content .wy-alert-warning.hint .wy-alert-title, .rst-content .wy-alert-warning.important .wy-alert-title, .rst-content .wy-alert-warning.tip .wy-alert-title, .rst-content .warning .wy-alert-title, .rst-content .wy-alert-warning.seealso .wy-alert-title, .rst-content .admonition-todo .wy-alert-title, .rst-content .wy-alert-warning.admonition .wy-alert-title, .wy-alert.wy-alert-warning .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-warning .admonition-title, .rst-content .wy-alert-warning.note .admonition-title, .rst-content .attention .admonition-title, .rst-content .caution .admonition-title, .rst-content .wy-alert-warning.danger .admonition-title, .rst-content .wy-alert-warning.error .admonition-title, .rst-content .wy-alert-warning.hint .admonition-title, .rst-content .wy-alert-warning.important .admonition-title, .rst-content .wy-alert-warning.tip .admonition-title, .rst-content .warning .admonition-title, .rst-content .wy-alert-warning.seealso .admonition-title, .rst-content .admonition-todo .admonition-title, .rst-content .wy-alert-warning.admonition .admonition-title { + background: #B15E16; } +/* important */ +.wy-alert.wy-alert-success .wy-alert-title, .rst-content .wy-alert-success.note .wy-alert-title, .rst-content .wy-alert-success.attention .wy-alert-title, .rst-content .wy-alert-success.caution .wy-alert-title, .rst-content .wy-alert-success.danger .wy-alert-title, .rst-content .wy-alert-success.error .wy-alert-title, .rst-content .hint .wy-alert-title, .rst-content .important .wy-alert-title, .rst-content .tip .wy-alert-title, .rst-content .wy-alert-success.warning .wy-alert-title, .rst-content .wy-alert-success.seealso .wy-alert-title, .rst-content .wy-alert-success.admonition-todo .wy-alert-title, .rst-content .wy-alert-success.admonition .wy-alert-title, .wy-alert.wy-alert-success .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-success .admonition-title, .rst-content .wy-alert-success.note .admonition-title, .rst-content .wy-alert-success.attention .admonition-title, .rst-content .wy-alert-success.caution .admonition-title, .rst-content .wy-alert-success.danger .admonition-title, .rst-content .wy-alert-success.error .admonition-title, .rst-content .hint .admonition-title, .rst-content .important .admonition-title, .rst-content .tip .admonition-title, .rst-content .wy-alert-success.warning .admonition-title, .rst-content .wy-alert-success.seealso .admonition-title, .rst-content .wy-alert-success.admonition-todo .admonition-title, .rst-content .wy-alert-success.admonition .admonition-title { + background: #12826C; } +/* seealso, note, etc */ +.wy-alert.wy-alert-info .wy-alert-title, .rst-content .note .wy-alert-title, .rst-content .wy-alert-info.attention .wy-alert-title, .rst-content .wy-alert-info.caution .wy-alert-title, .rst-content .wy-alert-info.danger .wy-alert-title, .rst-content .wy-alert-info.error .wy-alert-title, .rst-content .wy-alert-info.hint .wy-alert-title, .rst-content .wy-alert-info.important .wy-alert-title, .rst-content .wy-alert-info.tip .wy-alert-title, .rst-content .wy-alert-info.warning .wy-alert-title, .rst-content .seealso .wy-alert-title, .rst-content .wy-alert-info.admonition-todo .wy-alert-title, .rst-content .wy-alert-info.admonition .wy-alert-title, .wy-alert.wy-alert-info .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-info .admonition-title, .rst-content .note .admonition-title, .rst-content .wy-alert-info.attention .admonition-title, .rst-content .wy-alert-info.caution .admonition-title, .rst-content .wy-alert-info.danger .admonition-title, .rst-content .wy-alert-info.error .admonition-title, .rst-content .wy-alert-info.hint .admonition-title, .rst-content .wy-alert-info.important .admonition-title, .rst-content .wy-alert-info.tip .admonition-title, .rst-content .wy-alert-info.warning .admonition-title, .rst-content .seealso .admonition-title, .rst-content .wy-alert-info.admonition-todo .admonition-title, .rst-content .wy-alert-info.admonition .admonition-title { + background: #277CB4; } +/* error, danger */ +.rst-content .danger .admonition-title, .rst-content .danger .wy-alert-title, .rst-content .error .admonition-title, .rst-content .error .wy-alert-title, .rst-content .wy-alert-danger.admonition-todo .admonition-title, .rst-content .wy-alert-danger.admonition-todo .wy-alert-title, .rst-content .wy-alert-danger.admonition .admonition-title, .rst-content .wy-alert-danger.admonition .wy-alert-title, .rst-content .wy-alert-danger.attention .admonition-title, .rst-content .wy-alert-danger.attention .wy-alert-title, .rst-content .wy-alert-danger.caution .admonition-title, .rst-content .wy-alert-danger.caution .wy-alert-title, .rst-content .wy-alert-danger.hint .admonition-title, .rst-content .wy-alert-danger.hint .wy-alert-title, .rst-content .wy-alert-danger.important .admonition-title, .rst-content .wy-alert-danger.important .wy-alert-title, .rst-content .wy-alert-danger.note .admonition-title, .rst-content .wy-alert-danger.note .wy-alert-title, .rst-content .wy-alert-danger.seealso .admonition-title, .rst-content .wy-alert-danger.seealso .wy-alert-title, .rst-content .wy-alert-danger.tip .admonition-title, .rst-content .wy-alert-danger.tip .wy-alert-title, .rst-content .wy-alert-danger.warning .admonition-title, .rst-content .wy-alert-danger.warning .wy-alert-title, .rst-content .wy-alert.wy-alert-danger .admonition-title, .wy-alert.wy-alert-danger .rst-content .admonition-title, .wy-alert.wy-alert-danger .wy-alert-title { + background: #e31704; +} + +/* Generic admonition titles */ +.wy-alert-title, .rst-content .admonition-title { + background: #277CB4; } diff --git a/singlehtml/_static/style.css b/singlehtml/_static/style.css new file mode 100644 index 0000000..59e60ee --- /dev/null +++ b/singlehtml/_static/style.css @@ -0,0 +1,6 @@ +.rst-content .objectives { + background: #fee0d2; +} +.rst-content .objectives > .admonition-title { + background: #fc9272; +} diff --git a/singlehtml/_static/tabs.css b/singlehtml/_static/tabs.css new file mode 100644 index 0000000..957ba60 --- /dev/null +++ b/singlehtml/_static/tabs.css @@ -0,0 +1,89 @@ +.sphinx-tabs { + margin-bottom: 1rem; +} + +[role="tablist"] { + border-bottom: 1px solid #a0b3bf; +} + +.sphinx-tabs-tab { + position: relative; + font-family: Lato,'Helvetica Neue',Arial,Helvetica,sans-serif; + color: #1D5C87; + line-height: 24px; + margin: 0; + font-size: 16px; + font-weight: 400; + background-color: rgba(255, 255, 255, 0); + border-radius: 5px 5px 0 0; + border: 0; + padding: 1rem 1.5rem; + margin-bottom: 0; +} + +.sphinx-tabs-tab[aria-selected="true"] { + font-weight: 700; + border: 1px solid #a0b3bf; + border-bottom: 1px solid white; + margin: -1px; + background-color: white; +} + +.sphinx-tabs-tab:focus { + z-index: 1; + outline-offset: 1px; +} + +.sphinx-tabs-panel { + position: relative; + padding: 1rem; + border: 1px solid #a0b3bf; + margin: 0px -1px -1px -1px; + border-radius: 0 0 5px 5px; + border-top: 0; + background: white; +} + +.sphinx-tabs-panel.code-tab { + padding: 0.4rem; +} + +.sphinx-tab img { + margin-bottom: 24 px; +} + +/* Dark theme preference styling */ + +@media (prefers-color-scheme: dark) { + body[data-theme="auto"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); + } + + body[data-theme="auto"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); + } + + body[data-theme="auto"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 1px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); + } +} + +/* Explicit dark theme styling */ + +body[data-theme="dark"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); +} + +body[data-theme="dark"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); +} + +body[data-theme="dark"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 2px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); +} diff --git a/singlehtml/_static/tabs.js b/singlehtml/_static/tabs.js new file mode 100644 index 0000000..48dc303 --- /dev/null +++ b/singlehtml/_static/tabs.js @@ -0,0 +1,145 @@ +try { + var session = window.sessionStorage || {}; +} catch (e) { + var session = {}; +} + +window.addEventListener("DOMContentLoaded", () => { + const allTabs = document.querySelectorAll('.sphinx-tabs-tab'); + const tabLists = document.querySelectorAll('[role="tablist"]'); + + allTabs.forEach(tab => { + tab.addEventListener("click", changeTabs); + }); + + tabLists.forEach(tabList => { + tabList.addEventListener("keydown", keyTabs); + }); + + // Restore group tab selection from session + const lastSelected = session.getItem('sphinx-tabs-last-selected'); + if (lastSelected != null) selectNamedTabs(lastSelected); +}); + +/** + * Key focus left and right between sibling elements using arrows + * @param {Node} e the element in focus when key was pressed + */ +function keyTabs(e) { + const tab = e.target; + let nextTab = null; + if (e.keyCode === 39 || e.keyCode === 37) { + tab.setAttribute("tabindex", -1); + // Move right + if (e.keyCode === 39) { + nextTab = tab.nextElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.firstElementChild; + } + // Move left + } else if (e.keyCode === 37) { + nextTab = tab.previousElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.lastElementChild; + } + } + } + + if (nextTab !== null) { + nextTab.setAttribute("tabindex", 0); + nextTab.focus(); + } +} + +/** + * Select or deselect clicked tab. If a group tab + * is selected, also select tab in other tabLists. + * @param {Node} e the element that was clicked + */ +function changeTabs(e) { + // Use this instead of the element that was clicked, in case it's a child + const notSelected = this.getAttribute("aria-selected") === "false"; + const positionBefore = this.parentNode.getBoundingClientRect().top; + const notClosable = !this.parentNode.classList.contains("closeable"); + + deselectTabList(this); + + if (notSelected || notClosable) { + selectTab(this); + const name = this.getAttribute("name"); + selectNamedTabs(name, this.id); + + if (this.classList.contains("group-tab")) { + // Persist during session + session.setItem('sphinx-tabs-last-selected', name); + } + } + + const positionAfter = this.parentNode.getBoundingClientRect().top; + const positionDelta = positionAfter - positionBefore; + // Scroll to offset content resizing + window.scrollTo(0, window.scrollY + positionDelta); +} + +/** + * Select tab and show associated panel. + * @param {Node} tab tab to select + */ +function selectTab(tab) { + tab.setAttribute("aria-selected", true); + + // Show the associated panel + document + .getElementById(tab.getAttribute("aria-controls")) + .removeAttribute("hidden"); +} + +/** + * Hide the panels associated with all tabs within the + * tablist containing this tab. + * @param {Node} tab a tab within the tablist to deselect + */ +function deselectTabList(tab) { + const parent = tab.parentNode; + const grandparent = parent.parentNode; + + Array.from(parent.children) + .forEach(t => t.setAttribute("aria-selected", false)); + + Array.from(grandparent.children) + .slice(1) // Skip tablist + .forEach(panel => panel.setAttribute("hidden", true)); +} + +/** + * Select grouped tabs with the same name, but no the tab + * with the given id. + * @param {Node} name name of grouped tab to be selected + * @param {Node} clickedId id of clicked tab + */ +function selectNamedTabs(name, clickedId=null) { + const groupedTabs = document.querySelectorAll(`.sphinx-tabs-tab[name="${name}"]`); + const tabLists = Array.from(groupedTabs).map(tab => tab.parentNode); + + tabLists + .forEach(tabList => { + // Don't want to change the tabList containing the clicked tab + const clickedTab = tabList.querySelector(`[id="${clickedId}"]`); + if (clickedTab === null ) { + // Select first tab with matching name + const tab = tabList.querySelector(`.sphinx-tabs-tab[name="${name}"]`); + deselectTabList(tab); + selectTab(tab); + } + }) +} + +if (typeof exports === 'undefined') { + exports = {}; +} + +exports.keyTabs = keyTabs; +exports.changeTabs = changeTabs; +exports.selectTab = selectTab; +exports.deselectTabList = deselectTabList; +exports.selectNamedTabs = selectNamedTabs; diff --git a/singlehtml/_static/term_role_formatting.css b/singlehtml/_static/term_role_formatting.css new file mode 100644 index 0000000..0b66095 --- /dev/null +++ b/singlehtml/_static/term_role_formatting.css @@ -0,0 +1,4 @@ +/* Make terms bold */ +a.reference span.std-term { + font-weight: bold; +} diff --git a/singlehtml/_static/togglebutton.css b/singlehtml/_static/togglebutton.css new file mode 100644 index 0000000..54a6787 --- /dev/null +++ b/singlehtml/_static/togglebutton.css @@ -0,0 +1,160 @@ +/** + * Admonition-based toggles + */ + +/* Visibility of the target */ +.admonition.toggle .admonition-title ~ * { + transition: opacity .3s, height .3s; +} + +/* Toggle buttons inside admonitions so we see the title */ +.admonition.toggle { + position: relative; +} + +/* Titles should cut off earlier to avoid overlapping w/ button */ +.admonition.toggle .admonition-title { + padding-right: 25%; + cursor: pointer; +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:hover { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 1%); +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:active { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 3%); +} + +/* Remove extra whitespace below the admonition title when hidden */ +.admonition.toggle-hidden { + padding-bottom: 0; +} + +.admonition.toggle-hidden .admonition-title { + margin-bottom: 0; +} + +/* hides all the content of a page until de-toggled */ +.admonition.toggle-hidden .admonition-title ~ * { + height: 0; + margin: 0; + opacity: 0; + visibility: hidden; +} + +/* General button style and position*/ +button.toggle-button { + /** + * Background and shape. By default there's no background + * but users can style as they wish + */ + background: none; + border: none; + outline: none; + + /* Positioning just inside the admonition title */ + position: absolute; + right: 0.5em; + padding: 0px; + border: none; + outline: none; +} + +/* Display the toggle hint on wide screens */ +@media (min-width: 768px) { + button.toggle-button.toggle-button-hidden:before { + content: attr(data-toggle-hint); /* This will be filled in by JS */ + font-size: .8em; + align-self: center; + } +} + +/* Icon behavior */ +.tb-icon { + transition: transform .2s ease-out; + height: 1.5em; + width: 1.5em; + stroke: currentColor; /* So that we inherit the color of other text */ +} + +/* The icon should point right when closed, down when open. */ +/* Open */ +.admonition.toggle button .tb-icon { + transform: rotate(90deg); +} + +/* Closed */ +.admonition.toggle button.toggle-button-hidden .tb-icon { + transform: rotate(0deg); +} + +/* With details toggles, we don't rotate the icon so it points right */ +details.toggle-details .tb-icon { + height: 1.4em; + width: 1.4em; + margin-top: 0.1em; /* To center the button vertically */ +} + + +/** + * Details-based toggles. + * In this case, we wrap elements with `.toggle` in a details block. + */ + +/* Details blocks */ +details.toggle-details { + margin: 1em 0; +} + + +details.toggle-details summary { + display: flex; + align-items: center; + cursor: pointer; + list-style: none; + border-radius: .2em; + border-left: 3px solid #1976d2; + background-color: rgb(204 204 204 / 10%); + padding: 0.2em 0.7em 0.3em 0.5em; /* Less padding on left because the SVG has left margin */ + font-size: 0.9em; +} + +details.toggle-details summary:hover { + background-color: rgb(204 204 204 / 20%); +} + +details.toggle-details summary:active { + background: rgb(204 204 204 / 28%); +} + +.toggle-details__summary-text { + margin-left: 0.2em; +} + +details.toggle-details[open] summary { + margin-bottom: .5em; +} + +details.toggle-details[open] summary .tb-icon { + transform: rotate(90deg); +} + +details.toggle-details[open] summary ~ * { + animation: toggle-fade-in .3s ease-out; +} + +@keyframes toggle-fade-in { + from {opacity: 0%;} + to {opacity: 100%;} +} + +/* Print rules - we hide all toggle button elements at print */ +@media print { + /* Always hide the summary so the button doesn't show up */ + details.toggle-details summary { + display: none; + } +} \ No newline at end of file diff --git a/singlehtml/_static/togglebutton.js b/singlehtml/_static/togglebutton.js new file mode 100644 index 0000000..215a7ee --- /dev/null +++ b/singlehtml/_static/togglebutton.js @@ -0,0 +1,187 @@ +/** + * Add Toggle Buttons to elements + */ + +let toggleChevron = ` + + + +`; + +var initToggleItems = () => { + var itemsToToggle = document.querySelectorAll(togglebuttonSelector); + console.log(`[togglebutton]: Adding toggle buttons to ${itemsToToggle.length} items`) + // Add the button to each admonition and hook up a callback to toggle visibility + itemsToToggle.forEach((item, index) => { + if (item.classList.contains("admonition")) { + // If it's an admonition block, then we'll add a button inside + // Generate unique IDs for this item + var toggleID = `toggle-${index}`; + var buttonID = `button-${toggleID}`; + + item.setAttribute('id', toggleID); + if (!item.classList.contains("toggle")){ + item.classList.add("toggle"); + } + // This is the button that will be added to each item to trigger the toggle + var collapseButton = ` + `; + + title = item.querySelector(".admonition-title") + title.insertAdjacentHTML("beforeend", collapseButton); + thisButton = document.getElementById(buttonID); + + // Add click handlers for the button + admonition title (if admonition) + admonitionTitle = document.querySelector(`#${toggleID} > .admonition-title`) + if (admonitionTitle) { + // If an admonition, then make the whole title block clickable + admonitionTitle.addEventListener('click', toggleClickHandler); + admonitionTitle.dataset.target = toggleID + admonitionTitle.dataset.button = buttonID + } else { + // If not an admonition then we'll listen for the button click + thisButton.addEventListener('click', toggleClickHandler); + } + + // Now hide the item for this toggle button unless explicitly noted to show + if (!item.classList.contains("toggle-shown")) { + toggleHidden(thisButton); + } + } else { + // If not an admonition, wrap the block in a
block + // Define the structure of the details block and insert it as a sibling + var detailsBlock = ` +
+ + ${toggleChevron} + ${toggleHintShow} + +
`; + item.insertAdjacentHTML("beforebegin", detailsBlock); + + // Now move the toggle-able content inside of the details block + details = item.previousElementSibling + details.appendChild(item) + item.classList.add("toggle-details__container") + + // Set up a click trigger to change the text as needed + details.addEventListener('click', (click) => { + let parent = click.target.parentElement; + if (parent.tagName.toLowerCase() == "details") { + summary = parent.querySelector("summary"); + details = parent; + } else { + summary = parent; + details = parent.parentElement; + } + // Update the inner text for the proper hint + if (details.open) { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintShow; + } else { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintHide; + } + + }); + + // If we have a toggle-shown class, open details block should be open + if (item.classList.contains("toggle-shown")) { + details.click(); + } + } + }) +}; + +// This should simply add / remove the collapsed class and change the button text +var toggleHidden = (button) => { + target = button.dataset['target'] + var itemToToggle = document.getElementById(target); + if (itemToToggle.classList.contains("toggle-hidden")) { + itemToToggle.classList.remove("toggle-hidden"); + button.classList.remove("toggle-button-hidden"); + } else { + itemToToggle.classList.add("toggle-hidden"); + button.classList.add("toggle-button-hidden"); + } +} + +var toggleClickHandler = (click) => { + // Be cause the admonition title is clickable and extends to the whole admonition + // We only look for a click event on this title to trigger the toggle. + + if (click.target.classList.contains("admonition-title")) { + button = click.target.querySelector(".toggle-button"); + } else if (click.target.classList.contains("tb-icon")) { + // We've clicked the icon and need to search up one parent for the button + button = click.target.parentElement; + } else if (click.target.tagName == "polyline") { + // We've clicked the SVG elements inside the button, need to up 2 layers + button = click.target.parentElement.parentElement; + } else if (click.target.classList.contains("toggle-button")) { + // We've clicked the button itself and so don't need to do anything + button = click.target; + } else { + console.log(`[togglebutton]: Couldn't find button for ${click.target}`) + } + target = document.getElementById(button.dataset['button']); + toggleHidden(target); +} + +// If we want to blanket-add toggle classes to certain cells +var addToggleToSelector = () => { + const selector = ""; + if (selector.length > 0) { + document.querySelectorAll(selector).forEach((item) => { + item.classList.add("toggle"); + }) + } +} + +// Helper function to run when the DOM is finished +const sphinxToggleRunWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} +sphinxToggleRunWhenDOMLoaded(addToggleToSelector) +sphinxToggleRunWhenDOMLoaded(initToggleItems) + +/** Toggle details blocks to be open when printing */ +if (toggleOpenOnPrint == "true") { + window.addEventListener("beforeprint", () => { + // Open the details + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.dataset["togglestatus"] = el.open; + el.open = true; + }); + + // Open the admonitions + document.querySelectorAll(".admonition.toggle.toggle-hidden").forEach((el) => { + console.log(el); + el.querySelector("button.toggle-button").click(); + el.dataset["toggle_after_print"] = "true"; + }); + }); + window.addEventListener("afterprint", () => { + // Re-close the details that were closed + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.open = el.dataset["togglestatus"] == "true"; + delete el.dataset["togglestatus"]; + }); + + // Re-close the admonition toggle buttons + document.querySelectorAll(".admonition.toggle").forEach((el) => { + if (el.dataset["toggle_after_print"] == "true") { + el.querySelector("button.toggle-button").click(); + delete el.dataset["toggle_after_print"]; + } + }); + }); +} diff --git a/singlehtml/index.html b/singlehtml/index.html new file mode 100644 index 0000000..8dac0a1 --- /dev/null +++ b/singlehtml/index.html @@ -0,0 +1,3103 @@ + + + + + + + Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Reproducible research software development using Python documentation
    • +
  • + Edit on GitHub +
    • +
+
+
+
+
+ +
+

Reproducible research software development using Python

+
+

Big-picture goal

+

This is a hands-on course on research software engineering. In this +workshop we assume that most workshop participants use Python in their work or +a leading a group which uses Python. Therefore, some of the examples will use +Python as the example language.

+

We will work with an example project and go through all the steps of a typical +software project. Once we have seen the building blocks, we will try to apply +them to own projects. Workshop participants will receive and also learn to give +constructive code feedback.

+
+
+

Prerequisites

+
+

Preparation

+
    +

  1. Get a GitHub account following these instructions.

    2. +

  2. You will need a text editor. If you don’t have a favorite one, we recommend +VS Code.

    3. +

  3. If you prefer to work in the terminal and not in VS Code, set up these two (skip this if you use VS Code):

    + +
    4. +

  4. One of these two software environments (if you are not sure which one to +choose or have no preference, choose Conda):

    + +
    5. +

  5. Optional and only on Linux: Apptainer following +these instructions.

    6. +
+
+
+
+

Schedule

+
+

Day 1

+ +
+
+

Day 2

+ +
+
+

Day 3

+ +
+
+

If we have time left

+ +
+
+

Conda environment

+

A Conda environment is an isolated software environment that is used to manage dependencies for a project +and you decide where it is located.

+

You will need a environment.yml file that documents the dependencies:

+
name: coderefinery
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - python >= 3.10
+  - black
+  - click
+  - flit
+  - ipywidgets
+  - isort
+  - jupyterlab
+  - jupyterlab_code_formatter
+  - jupyterlab-git
+  - matplotlib
+  - myst-parser
+  - nbdime
+  - numpy
+  - pandas
+  - pytest
+  - pytest-cov
+  - scalene
+  - seaborn
+  - snakemake-minimal
+  - sphinx
+  - sphinx-autoapi
+  - sphinx-autobuild
+  - sphinx_rtd_theme >= 2.0
+  - vulture
+  - scikit-image
+
+
+
+
Before you create a virtual environment
+
    +

  1. Create a new directory for this course.

    2. +

  2. In this directory, create an environment.yml file and copy-paste the dependencies above into it.

    3. +
+
+
+
Choose the tool to manage the environment
+

If you are already using one of these tools, please continue using the tool that you like and know. +If you are new to this, we recommend using Miniconda or Miniforge.

+
    +

  • Anaconda

    +
      +

    • Advantages: easy to install, easy to use, good for beginners

      • +

    • Disadvantages: large download, installs more than we will need, license restrictions

      • +
    +
    • +

  • Miniconda

    +
      +

    • Advantages: small size, installs only what you need

      • +

    • Disadvantages: no graphical interface, license restrictions

      • +
    +
    • +

  • Miniforge

    +
      +

    • Advantages: small size, no license restrictions

      • +

    • Disadvantages: no graphical interface

      • +
    +
    • +

  • Micromamba

    +
      +

    • Advantages: fast, small size

      • +

    • Disadvantages: no graphical interface

      • +
    +
    • +

  • Pixi

    +
      +

    • Advantages: fast and new

      • +

    • Disadvantages: new and less tested and not documented here

      • +
    +
    • +
+
+
+
Creating the virtual environment
+
    +

  1. Open your terminal shell (e.g. Bash or Zsh).

    2. +

  2. Activate conda using conda activate or source ~/miniconda3/bin/activate.

    3. +

  3. Run the following command:

    +
    $ conda env create --file environment.yml
+
    +
    +
    4. +

  4. Make sure that you see “coderefinery” in the output when you ask for a list of all available environments:

    +
    $ conda env list
+
    +
    +
    5. +
+
+
+
+

Virtual environment

+

A virtual environment is an isolated software environment that is used to manage dependencies for a project +and you decide where it is located.

+

You will need a requirements.txt file that documents the dependencies:

+
black
+click
+flit
+ipywidgets
+isort
+jupyterlab
+jupyterlab-code-formatter
+jupyterlab-git
+matplotlib
+myst-parser
+nbdime
+numpy
+pandas
+pytest
+pytest-cov
+scalene
+seaborn
+sphinx
+sphinx-autoapi
+sphinx-autobuild
+sphinx_rtd_theme >= 2.0
+vulture
+scikit-image
+
+
+
+
Before you create a virtual environment
+
    +

  1. Create a new directory for this course.

    2. +

  2. In this directory, create a requirements.txt file and copy-paste the dependencies above into it.

    3. +
+
+
+
Creating the virtual environment
+

Now create a virtual environment in this directory either using pip and +venv +(more traditional and safer) or using uv (more modern but also less tested):

+
+

Create a new virtual environment and activate it:

+
$ python3 -m venv coderefinery-environment
+$ source coderefinery-environment/bin/activate
+
+
+

Install the dependencies into the environment:

+
$ python3 -m pip install -r requirements.txt
+
+
+
+
+
+
+
+
+

Example project: Simulating the motion of planets

+

The example code that we will study +is a hopefully simple N-body simulation written in Python. It is not important +or expected that we understand the code in any detail.

+

The big picture is that the code simulates the motion of a number of +planets:

+
    +

  • We can choose the number of planets.

    • +

  • Each planet starts with a random position, velocity, and mass.

    • +

  • At each time step, the code calculates the gravitational force between each +pair of planets.

    • +

  • The forces accelerate each planet, the acceleration modifies the velocity, +the velocity modifies the position of each planet.

    • +

  • We can choose the number of time steps.

    • +

  • The units were chosen to make numbers easy to read.

    • +
+
+
Example run
+
+

Instructor note

+

The instructor demonstrates running the code on their computer.

+
+

The code is written to accept command-line arguments to specify the number +of planets and the number of time steps.

+

We first generate starting data:

+
$ python generate-data.py --num-planets 10 --output-file initial.csv
+
+
+

The generated file (initial.csv) could look like this:

+
px,py,pz,vx,vy,vz,mass
+-46.88,-42.51,88.33,-0.86,-0.18,0.55,6.70
+-5.29,17.09,-96.13,0.66,0.45,-0.17,3.51
+83.53,-92.83,-68.77,-0.26,-0.48,0.24,6.84
+-36.31,25.48,64.16,0.85,0.75,-0.56,1.53
+-68.38,-17.21,-97.07,0.60,0.26,0.69,6.63
+-48.37,-48.74,3.92,-0.92,-0.33,-0.93,8.60
+40.53,-75.50,44.18,-0.62,-0.31,-0.53,8.04
+-27.21,10.78,-78.82,-0.09,-0.55,-0.03,5.35
+88.42,-74.95,-45.85,0.81,0.68,0.56,5.36
+39.09,53.12,-59.54,-0.54,0.56,0.07,8.98
+
+
+

Then we can simulate their motion (in this case for 20 steps):

+
$ python simulate.py --num-steps 20 \
+                     --input-file initial.csv \
+                     --output-file final.csv
+
+
+

The --output-file (final.csv) is again a CSV file (comma-separated values) +and contains the final positions of all planets.

+

It is possible to run on multiple cores and to animate the result. +Here is an example with 100 planets:

+
$ python generate-data.py --num-planets 100 --output-file initial.csv
+
+$ python simulate.py --num-steps 50 \
+                     --input-file initial.csv \
+                     --output-file final.csv \
+                     --trajectories-file trajectories.npz \
+                     --num-cores 8
+
+$ python animate.py --initial-file initial.csv \
+                    --trajectories-file trajectories.npz \
+                    --output-file animation.mp4
+
+
+
+

Learning goals

+
    +

  • What are the most important steps to make this code reusable by others +and our future selves?

    • +

  • Be able to apply these techniques to your own code/script.

    • +
+
+
+

We will not focus on …

+
    +

  • … how the code works internally in detail.

    • +

  • … whether this is the most efficient algorithm.

    • +

  • … whether the code is numerically stable.

    • +

  • … how to code scales with the number of cores.

    • +

  • … whether it is portable to other operating systems (we will discuss this later).

    • +
+
+
+
+
+

Introduction to version control with Git and GitHub

+
+
+
Motivation
+
+

Objectives

+
    +

  • Browse commits and branches of a Git repository.

    • +

  • Remember that commits are like snapshots of the repository at a certain +point in time.

    • +

  • Know the difference between Git (something that tracks changes) and +GitHub/GitLab (a platform to host Git repositories).

    • +
+
+
+
Why do we need to keep track of versions?
+

Version control is an answer to the following questions (do you recognize some +of them?):

+
    +

  • “It broke … hopefully I have a working version somewhere?”

    • +

  • “Can you please send me the latest version?”

    • +

  • “Where is the latest version?”

    • +

  • “Which version are you using?”

    • +

  • “Which version have the authors used in the paper I am trying to reproduce?”

    • +

  • “Found a bug! Since when was it there?”

    • +

  • “I am sure it used to work. When did it change?”

    • +

  • “My laptop is gone. Is my thesis now gone?”

    • +
+
+
+
Demonstration
+
    +

  • Example repository: https://github.com/workshop-material/planets

    • +

  • Commits are like snapshots and if we break something we can go back to a +previous snapshot.

    • +

  • Commits carry metadata about changes: author, date, commit message, and +a checksum.

    • +

  • Branches are like parallel universes where you can experiment with +changes without affecting the default branch: +https://github.com/workshop-material/planets/network +(“Insights” -> “Network”)

    • +

  • With version control we can annotate code +(example).

    • +

  • Collaboration: We can fork (make a copy on GitHub), clone (make a copy +to our computer), review, compare, share, and discuss.

    • +

  • Code review: Others can suggest changes using pull requests or merge +requests. These can be reviewed and discussed before they are merged. +Conceptually, they are similar to “suggesting changes” in Google Docs.

    • +
+
+
+
Features: roll-back, branching, merging, collaboration
+
    +

  • Roll-back: you can always go back to a previous version and compare

    • +

  • Branching and merging:

    +
      +

    • Work on different ideas at the same time

      • +

    • Different people can work on the same code/project without interfering

      • +

    • You can experiment with an idea and discard it if it turns out to be a bad idea

      • +
    +
    • +
+
+Branching explained with a gopher +
+

Image created using https://gopherize.me/ +(inspiration).

+
+
+ +
+
+
Talking about code
+

Which of these two is more practical?

+
    +

  1. “Clone the code, go to the file ‘simulate.py’, and search for ‘force_between_planets’. +Oh! But make sure you use the version from September 2024.”

    2. +

  2. Or I can send you a permalink: https://github.com/workshop-material/planets/blob/1343ac0/simulate.py#L31C5-L39

    3. +
+
+
+
What we typically like to snapshot
+
    +

  • Software (this is how it started but Git/GitHub can track a lot more)

    • +

  • Scripts

    • +

  • Documents (plain text files much better suitable than Word documents)

    • +

  • Manuscripts (Git is great for collaborating/sharing LaTeX or Quarto manuscripts)

    • +

  • Configuration files

    • +

  • Website sources

    • +

  • Data

    • +
+
+

Discussion

+

In this example somebody tried to keep track of versions without a version +control system tool like Git. Discuss the following directory listing. What +possible problems do you anticipate with this kind of “version control”:

+
myproject-2019.zip
+myproject-2020-february.zip
+myproject-2021-august.zip
+myproject-2023-09-19-working.zip
+myproject-2023-09-21.zip
+myproject-2023-09-21-test.zip
+myproject-2023-09-21-myversion.zip
+myproject-2023-09-21-newfeature.zip
+...
+(100 more files like these)
+
+
+ +
+
+
+
+
Forking, cloning, and browsing
+

In this episode, we will look at an existing repository to understand how +all the pieces work together. Along the way, we will make a copy (by +forking and/or cloning) of the repository for us, which will be used +for our own changes.

+
+

Objectives

+
    +

  • See a real Git repository and understand what is inside of it.

    • +

  • Understand how version control allows advanced inspection of a +repository.

    • +

  • See how Git allows multiple people to work on the same project at the same time.

    • +

  • See the big picture instead of remembering a bunch of commands.

    • +
+
+
+
GitHub, VS Code, or command line
+

We offer three different paths for this exercise:

+
    +

  • GitHub (this is the one we will demonstrate)

    • +

  • VS Code (if you prefer to follow along using an editor)

    • +

  • Command line (for people comfortable with the command line)

    • +
+
+
+
Creating a copy of the repository by “forking” or “cloning”
+

A repository is a collection of files in one directory tracked by Git. A +GitHub repository is GitHub’s copy, which adds things like access control, +issue tracking, and discussions. Each GitHub repository is owned by a user or +organization, who controls access.

+

First, we need to make our own copy of the exercise repository. This will +become important later, when we make our own changes.

+
+Illustration of forking a repository on GitHub +
+

Illustration of forking a repository on GitHub.

+
+
+
+Illustration of cloning a repository to your computer +
+

Illustration of cloning a repository to your computer.

+
+
+
+Illustration of cloning a forked repository to your computer +
+

It is also possible to do this: to clone a forked repository to your computer.

+
+
+

At all times you should be aware of if you are looking at your repository +or the upstream repository (original repository):

+
    +

  • Your repository: https://github.com/USER/planets

    • +

  • Upstream repository: https://github.com/workshop-material/planets

    • +
+
+

How to create a fork

+
    +

  1. Go to the repository view on GitHub: https://github.com/workshop-material/planets

    2. +

  2. First, on GitHub, click the button that says “Fork”. It is towards +the top-right of the screen.

    3. +

  3. You should shortly be redirected to your copy of the repository +USER/planets.

    4. +
+
+
+

Instructor note

+

Before starting the exercise session show +how to fork the repository to own account +(above).

+
+
+
+
Exercise: Copy and browse an existing project
+

Work on this by yourself or in pairs.

+
+

Exercise preparation

+
+

In this case you will work on a fork.

+

You only need to open your own view, as described above. The browser +URL should look like https://github.com/USER/planets, where +USER is your GitHub username.

+
+
+
+

Exercise: Browsing an existing project (20 min)

+

Browse the example project and +explore commits and branches, either on a fork or on a clone. Take notes and +prepare questions. The hints are for the GitHub path in the browser.

+
    +

  1. Browse the commit history: Are commit messages understandable? +(Hint: “Commit history”, the timeline symbol, above the file list)

    2. +

  2. Compare the commit history with the network graph (“Insights” -> “Network”). Can you find the branches?

    3. +

  3. Try to find the history of commits for a single file, e.g. simulate.py. +(Hint: “History” button in the file view)

    4. +

  4. Which files include the word “position”? +(Hint: the GitHub search on top of the repository view)

    5. +

  5. In the simulate.py file, find out who modified each line last and when +(click on file, then click “Blame” button). Find out who modified the gravitational constant +last and in which commit. +(Hint: “Blame” view in the file view)

    6. +

  6. Can you use this code yourself? Are you allowed to share +modifications? +(Hint: look for a license file)

    7. +
+
+

The solution below goes over most of the answers, and you are +encouraged to use it when the hints aren’t enough - this is by +design.

+
+
+
Solution and walk-through
+
+
(1) Basic browsing
+

The most basic thing to look at is the history of commits.

+
    +

  • This is visible from a button in the repository view. We see every +change, when, and who has committed.

    • +

  • Every change has a unique identifier, such as 244c993. This can +be used to identify both this change, and the whole project’s +version as of that change.

    • +

  • Clicking on a change in the view shows more.

    • +
+
+

Click on the timeline symbol in the repository view:

+
+Screenshot on GitHub of where to find the commit history +
+
+
+
+
(2) Compare commit history with network graph
+

The commit history we saw above looks linear: one commit after +another. But if we look at the network view, we see some branches and +merges. We’ll see how to do these later. This is another one of the +basic Git views.

+
+

In a new browser tab, open the “Insights” tab, and click on “Network”. +You can hover over the commit dots to see the person who committed and +how they correspond with the commits in the other view:

+
+Screenshot on GitHub of the network graph +
+
+
+
+
(3) How can you browse the history of a single file?
+

We see the history for the whole repository, but we can also see it +for a single file.

+
+

Navigate to the file view: Main page → simulate.py. +Click the “History” button near the top right.

+
+
+
+
(4) Which files include the word “position”?
+

Version control makes it very easy to find all occurrences of a single +word. This is useful for things like finding where functions or +variables are defined or used.

+
+

We go to the main file view. We click the Search magnifying +class at the very top, type “position”, and click enter. We see every +instance, including the context.

+
+

Searching in a forked repository will not work instantaneously!

+

It usually takes a few minutes before one can search for keywords in a forked repository +since it first needs to build the search index the very first time we search. +Start it, continue with other steps, then come back to this.

+
+
+
+
+
(5) Who modified each line last and when?
+

This is called the “annotate” or “blame” view. The name “blame” +is very unfortunate, but it is the standard term for historical reasons +for this functionality and it is not meant to blame anyone.

+
+

From a file view, change preview to “Blame” towards the top-left. +To get the actual commit, click on the commit message.

+
+
+
+
(6) Can you use this code yourself? Are you allowed to share modifications?
+
    +

  • Look at the file LICENSE.

    • +

  • On GitHub, click on the file to see a nice summary of what we can do with this:

    +
    +Screenshot on GitHub summarizing license terms +
    +
    • +
+
+
+
Summary
+
    +

  • Git allowed us to understand this simple project much better than we +could, if it was just a few files on our own computer.

    • +

  • It was easy to share the project with the course.

    • +

  • By forking the repository, we created our own copy. This is +important for the following, where we will make changes to +our copy.

    • +
+
+
+
+
+
Creating branches and commits
+

The first and most basic task to do in Git is record changes using +commits. In this part, we will record changes in two +ways: on a new branch (which supports multiple lines of work at once), and directly +on the “main” branch (which happens to be the default branch here).

+
+

Objectives

+
    +

  • Record new changes to our own copy of the project.

    • +

  • Understand adding changes in two separate branches.

    • +

  • See how to compare different versions.

    • +
+
+
+
Background
+
    +

  • In the previous episode we have browsed an existing repository and saw commits +and branches.

    • +

  • Each commit is a snapshot of the entire project at a certain +point in time and has a unique identifier (hash) .

    • +

  • A branch is a line of development, and the main branch or master branch +are often the default branch in Git.

    • +

  • A branch in Git is like a sticky note that is attached to a commit. When we add +new commits to a branch, the sticky note moves to the new commit.

    • +

  • Tags are a way to mark a specific commit as important, for example a release +version. They are also like a sticky note, but they don’t move when new +commits are added.

    • +
+
+Branching explained with a gopher +
+

What if two people, at the same time, make two different changes? Git +can merge them together easily. Image created using https://gopherize.me/ +(inspiration).

+
+
+
+
+
Exercise: Creating branches and commits
+
+Illustration of what we want to achieve in this exercise +
+

Illustration of what we want to achieve in this exercise.

+
+
+
+

Exercise: Practice creating commits and branches (20 min)

+
    +

  1. First create a new branch and then either add a new file or modify an +existing file and commit the change. Make sure that you now work on your +copy of the example repository. In your commit you can share a Git or +programming trick you like.

    2. +

  2. In a new commit, modify the file again.

    3. +

  3. Switch to the main branch and create a commit there.

    4. +

  4. Browse the network and locate the commits that you just created (“Insights” -> “Network”).

    5. +

  5. Compare the branch that you created with the main branch. Can you find an easy way to see the differences?

    6. +

  6. Can you find a way to compare versions between two arbitrary commits in the repository?

    7. +

  7. Try to rename the branch that you created and then browse the network again.

    8. +

  8. Try to create a tag for one of the commits that you created (on GitHub, +create a “release”).

    9. +
+
+

The solution below goes over most of the answers, and you are +encouraged to use it when the hints aren’t enough - this is by +design.

+
+
+
Solution and walk-through
+
+
(1) Create a new branch and a new commit
+
+
    +

  1. Where it says “main” at the top left, click, enter a new branch +name new-tutorial, click on the offer to create the new branch +(“Create branch new-tutorial from main”).

    2. +

  2. Make sure you are still on the new-tutorial branch (it should say +it at the top), and click “Add file” → “Create new file” from the +upper right.

    3. +

  3. Enter a filename where it says “Name your file…”.

    4. +

  4. Share some Git or programming trick you like.

    5. +

  5. Click “Commit changes”

    6. +

  6. Enter a commit message. Then click “Commit +changes”.

    7. +
+

You should appear back at the file browser view, and see your +modification there.

+
+
+
+
(2) Modify the file again with a new commit
+
+

This is similar to before, but we click on the existing file to +modify.

+
    +

  1. Click on the file you added or modified previously.

    2. +

  2. Click the edit button, the pencil icon at top-right.

    3. +

  3. Follow the “Commit changes” instructions as in the previous step.

    4. +
+
+
+
+
(3) Switch to the main branch and create a commit there
+
+
    +

  1. Go back to the main repository page (your user’s page).

    2. +

  2. In the branch switch view (top left above the file view), switch to +main.

    3. +

  3. Modify another file that already exists, following the pattern +from above.

    4. +
+
+
+
+
(4) Browse the commits you just made
+

Let’s look at what we did. Now, the main and new-tutorial branches +have diverged: both have some modifications. Try to find the commits +you created.

+
+

Insights tab → Network view (just like we have done before).

+
+
+
+
(5) Compare the branches
+

Comparing changes is an important thing we need to do. When using the +GitHub view only, this may not be so common, but we’ll show it so that +it makes sense later on.

+
+

A nice way to compare branches is to add /compare to the URL of the repository, +for example (replace USER): +https://github.com/USER/planets/compare

+
+
+
+
(6) Compare two arbitrary commits
+

This is similar to above, but not only between branches.

+
+

Following the /compare-trick above, one can compare commits on GitHub by +adjusting the following URL: +https://github.com/USER/planets/compare/VERSION1..VERSION2

+

Replace USER with your username and VERSION1 and VERSION2 with a commit hash or branch name. +Please try it out.

+
+
+
+
(7) Renaming a branch
+
+

Branch button → View all branches → three dots at right side → Rename branch.

+
+
+
+
(8) Creating a tag
+

Tags are a way to mark a specific commit as important, for example a release +version. They are also like a sticky note, but they don’t move when new +commits are added.

+
+

On the right side, below “Releases”, click on “Create a new release”.

+

What GitHub calls releases are actually tags in Git with additional metadata. +For the purpose of this exercise we can use them interchangeably.

+
+
+
+
+
Summary
+

In this part, we saw how we can make changes to our files. With branches, we +can track several lines of work at once, and can compare their differences.

+
    +

  • You could commit directly to main if there is only one single line +of work and it’s only you.

    • +

  • You could commit to branches if there are multiple lines of work at +once, and you don’t want them to interfere with each other.

    • +

  • Tags are useful to mark a specific commit as important, for example a +release version.

    • +

  • In Git, commits form a so-called “graph”. Branches are tags in Git function +like sticky notes that stick to specific commits. What this means for us is +that it does not cost any significant disk space to create new branches.

    • +

  • Not all files should be added to Git. For example, temporary files or +files with sensitive information or files which are generated as part of +the build process should not be added to Git. For this we use +.gitignore (more about this later: Practical advice: How much Git is necessary?).

    • +

  • Unsure on which branch you are or what state the repository is in? +On the command line, use git status frequently to get a quick overview.

    • +
+
+
+
+
Practical advice: How much Git is necessary?
+
+
Writing useful commit messages
+

Useful commit messages summarize the change and provide context.

+

If you need a commit message that is longer than one line, +then the convention is: one line summarizing the commit, then one empty line, +then paragraph(s) with more details in free form, if necessary.

+

Good example:

+
increase alpha to 2.0 for faster convergence
+
+the motivation for this change is
+to enable ...
+...
+(more context)
+...
+this is based on a discussion in #123
+
+
+
    +

  • Why something was changed is more important than what has changed.

    • +

  • Cross-reference to issues and discussions if possible/relevant.

    • +

  • Bad commit messages: “fix”, “oops”, “save work”

    • +

  • Bad examples: http://whatthecommit.com

    • +

  • Write commit messages that will be understood +15 years from now by someone else than you. Or by your future you.

    • +

  • Many projects start out as projects “just for me” and end up to be successful projects +that are developed by 50 people over decades.

    • +

  • Commits with multiple authors are possible.

    • +
+

Good references:

+ +
+

Note

+

A great way to learn how to write commit messages and to get inspired by their +style choices: browse repositories of codes that you use/like:

+

Some examples (but there are so many good examples):

+ +

When designing commit message styles consider also these:

+
    +

  • How will you easily generate a changelog or release notes?

    • +

  • During code review, you can help each other improving commit messages.

    • +
+
+

But remember: it is better to make any commit, than no commit. Especially in small projects. +Let not the perfect be the enemy of the good enough.

+
+
+
What level of branching complexity is necessary for each project?
+

Simple personal projects:

+
    +

  • Typically start with just the main branch.

    • +

  • Use branches for unfinished/untested ideas.

    • +

  • Use branches when you are not sure about a change.

    • +

  • Use tags to mark important milestones.

    • +

  • If you are unsure what to do with unfinished and not working code, commit it +to a branch.

    • +
+

Projects with few persons: you accept things breaking sometimes

+
    +

  • It might be reasonable to commit to the main branch and feature branches.

    • +
+

Projects with few persons: changes are reviewed by others

+
    +

  • You create new feature branches for changes.

    • +

  • Changes are reviewed before they are merged to the main branch.

    • +

  • Consider to write-protect the main branch so that it can only be changed +with pull requests or merge requests.

    • +
+
+
+
How large should a commit be?
+
    +

  • Better too small than too large (easier to combine than to split).

    • +

  • Often I make a commit at the end of the day (this is a unit I would not like to lose).

    • +

  • Smaller sized commits may be easier to review for others than huge commits.

    • +

  • Imperfect commits are better than no commits.

    • +

  • A commit should not contain unrelated changes to simplify review and possible +repair/adjustments/undo later (but again: imperfect commits are better than no commits).

    • +
+
+
+
Working on the command line? Use “git status” all the time
+

The git status command is one of the most useful commands in Git +to inform about which branch we are on, what we are about to commit, +which files might not be tracked, etc.

+
+
+
How about staging and committing?
+
    +

  • Commit early and often: rather create too many commits than too few. +You can always combine commits later.

    • +

  • Once you commit, it is very, very hard to really lose your code.

    • +

  • Always fully commit (or stash) before you do dangerous things, so that you know you are safe. +Otherwise it can be hard to recover.

    • +

  • Later you can start using the staging area (where you first stage and then commit in a second step).

    • +

  • Later start using git add -p and/or git commit -p.

    • +
+
+
+
What to avoid
+
    +

  • Committing generated files/directories (example: __pycache__, *.pyc) -> +use .gitignore +files +(collection of .gitignore templates).

    • +

  • Committing huge files -> use code review to detect this.

    • +

  • Committing unrelated changes together.

    • +

  • Postponing commits because the changes are “unfinished”/”ugly” -> better ugly +commits than no commits.

    • +

  • When working with branches:

    +
      +

    • Not updating your branch before starting new work.

      • +

    • Too ambitious branch which risks to never get completed.

      • +

    • Over-engineering the branch layout and safeguards in small projects.

      • +

    • Working on unrelated things on the same branch.

      • +
    +
    • +
+
+
+
+
Optional: How to turn your project to a Git repo and share it
+
+

Objectives

+
    +

  • Turn our own coding project (small or large, finished or unfinished) into a +Git repository.

    • +

  • Be able to share a repository on the web to have a backup or so that others +can reuse and collaborate or even just find it.

    • +
+
+
+
Exercise
+
+Illustration of how we turn a project into a Git repository and share it +
+

From a bunch of files to a local repository which we then share on GitHub.

+
+
+
+

Exercise: Turn your project to a Git repo and share it (20 min)

+
    +

  1. Create a new directory called myproject with one or few files in it. +This represents our own project. It is not yet a Git repository. You can try +that with your own project or use a simple placeholder example.

    2. +

  2. Turn this new directory into a Git repository.

    3. +

  3. Share this repository on GitHub (or GitLab, since it really works the same).

    4. +
+

We offer three different paths of how to do this exercise.

+
    +

  • Via GitHub web interface: easy and can be a good starting point if you are completely +new to Git.

    • +

  • VS Code is quite easy, since VS Code can offer to create the +GitHub repositories for you.

    • +

  • Command line: you need to create the +repository on GitHub and link it yourself.

    • +
+
+

Create an repository on GitHub

+

First log into GitHub, then follow the screenshots and descriptions below.

+
+Screenshot on GitHub before a new repository form is opened +
+

Click on the “plus” symbol on top right, then on “New repository”.

+
+
+

Then:

+
+Screenshot on GitHub just before a new repository is created +
+

Choose a repository name, add a short description, and in this case make sure to check “Add a +README file”. Finally “Create repository”.

+
+
+

Upload your files

+

Now that the repository is created, you can upload your files:

+
+Screenshot on GitHub just before uploading files +
+

Click on the “+” symbol and then on “Upload files”.

+
+
+
+
+
+
+
Is putting software on GitHub/GitLab/… publishing?
+

It is a good first step but to make your code truly findable and +accessible, consider making your code citable and persistent: Get a +persistent identifier (PID) such as DOI in addition to sharing the code +publicly, by using services like Zenodo or similar +services.

+
+
+
+
+
+

Code documentation

+
+

Objectives

+
    +

  • Discuss what makes good documentation.

    • +

  • Improve the README of your project or our example project.

    • +

  • Explore Sphinx which is a popular tool to build documentation websites.

    • +

  • Learn how to leverage GitHub Actions and GitHub Pages to build and deploy documentation.

    • +
+
+
+

Instructor note

+
    +

  • (30 min) Discussion

    • +

  • (30 min) Exercise: Set up a Sphinx documentation and add API documentation

    • +

  • (15 min) Demo: Building documentation with GitHub Actions

    • +
+
+
+
Why? 💗✉️ to your future self
+
    +

  • You will probably use your code in the future and may forget details.

    • +

  • You may want others to use your code or contribute +(almost impossible without documentation).

    • +
+
+
+
In-code documentation
+

Not very useful (more commentary than comment):

+
# now we check if temperature is below -50
+if temperature < -50:
+    print("ERROR: temperature is too low")
+
+
+

More useful (explaining why):

+
# we regard temperatures below -50 degrees as measurement errors
+if temperature < -50:
+    print("ERROR: temperature is too low")
+
+
+

Keeping zombie code “just in case” (rather use version control):

+
# do not run this code!
+# if temperature > 0:
+#     print("It is warm")
+
+
+

Emulating version control:

+
# John Doe: threshold changed from 0 to 15 on August 5, 2013
+if temperature > 15:
+    print("It is warm")
+
+
+
+
+
Many languages allow “docstrings”
+

Example (Python):

+
def kelvin_to_celsius(temp_k: float) -> float:
+    """
+    Converts temperature in Kelvin to Celsius.
+
+    Parameters
+    ----------
+    temp_k : float
+        temperature in Kelvin
+
+    Returns
+    -------
+    temp_c : float
+        temperature in Celsius
+    """
+    assert temp_k >= 0.0, "ERROR: negative T_K"
+
+    temp_c = temp_k - 273.15
+
+    return temp_c
+
+
+
+

Keypoints

+
    +

  • Documentation which is only in the source code is not enough.

    • +

  • Often a README is enough.

    • +

  • Documentation needs to be kept +in the same Git repository as the code since we want it to evolve with +the code.

    • +
+
+
+
+
Often a README is enough - checklist
+
    +

  • Purpose

    • +

  • Requirements

    • +

  • Installation instructions

    • +

  • Copy-paste-able example to get started

    • +

  • Tutorials covering key functionality

    • +

  • Reference documentation (e.g. API) covering all functionality

    • +

  • Authors and recommended citation

    • +

  • License

    • +

  • Contribution guide

    • +
+

See also the +JOSS review checklist.

+
+
+
What if you need more than a README?
+ +
+
+
Diátaxis
+

Diátaxis is a systematic approach to technical documentation authoring.

+ +
+
+
Exercise: Set up a Sphinx documentation
+
+

Preparation

+

In this episode we will use the following 5 packages which we installed +previously as part of the Conda environment or Virtual environment:

+
myst-parser
+sphinx
+sphinx-rtd-theme
+sphinx-autoapi
+sphinx-autobuild
+
+
+

Which repository to use? You have 3 options:

+
    +

  • Clone your fork of the planets example repository.

    • +

  • If you don’t have that, you can clone the original repository itself: +https://github.com/workshop-material/planets

    • +

  • You can try this with your own project and the project does not have to +be a Python project.

    • +
+
+

There are at least two ways to get started with Sphinx:

+
    +

  1. Use sphinx-quickstart to create a new Sphinx project.

    2. +

  2. This is what we will do: Create three files (doc/conf.py, doc/index.md, and doc/about.md) +as starting point and improve from there.

    3. +
+
+

Exercise: Set up a Sphinx documentation

+
    +

  1. Create the following three files in your project:

    +
    planets/
+├── doc/
+│   ├── conf.py
+│   ├── index.md
+│   └── about.md
+└── ...
+
    +
    +

    This is conf.py:

    +
    project = "planets"
+copyright = "2024, Authors"
+author = "Authors"
+release = "0.1"
+
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+extensions = [
+    "myst_parser",  # in order to use markdown
+]
+
+myst_enable_extensions = [
+    "colon_fence",  # ::: can be used instead of ``` for better rendering
+]
+
+html_theme = "sphinx_rtd_theme"
+
    +
    +

    This is index.md (feel free to adjust):

    +
    # Our code documentation
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor
+incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis
+nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.
+Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu
+fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in
+culpa qui officia deserunt mollit anim id est laborum.
+
+:::{toctree}
+:maxdepth: 2
+:caption: Some caption
+
+about.md
+:::
+
    +
    +

    This is about.md (feel free to adjust):

    +
    # About this code
+
+Work in progress ...
+
    +
    +
    2. +

  2. Run sphinx-build to build the HTML documentation:

    +
    $ sphinx-build doc _build
+
+... lots of output ...
+The HTML pages are in _build.
+
    +
    +
    3. +

  3. Try to open _build/index.html in your browser.

    4. +

  4. Experiment with adding more content, images, equations, code blocks, …

    + +
    5. +
+
+

There is a lot more you can do:

+
    +

  • This is useful if you want to check the integrity of all internal and external links:

    +
    $ sphinx-build doc -W -b linkcheck _build
+
    +
    +
    • +

  • sphinx-autobuild +provides a local web server that will automatically refresh your view +every time you save a file - which makes writing and testing much easier.

    • +
+
+
+
Demo: Building documentation with GitHub Actions
+

First we need to extend the environment.yml file to include the necessary packages:

+
name: planets
+channels:
+  - conda-forge
+dependencies:
+  - python=3.12
+  - numpy
+  - click
+  - matplotlib
+  - myst-parser
+  - sphinx
+  - sphinx-rtd-theme
+  - sphinx-autoapi
+
+
+

Then we add a GitHub Actions workflow .github/workflow/sphinx.yml to build the documentation:

+
name: Build documentation
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+permissions:
+  contents: write
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+
+    - uses: mamba-org/setup-micromamba@v1
+      with:
+        micromamba-version: '1.5.8-0' # any version from https://github.com/mamba-org/micromamba-releases
+        environment-file: environment.yml
+        init-shell: bash
+        cache-environment: true
+        post-cleanup: 'all'
+        generate-run-shell: false
+
+    - name: Sphinx build
+      run: |
+        sphinx-build doc _build
+      shell: bash -el {0}
+
+    - name: Deploy to GitHub Pages
+      uses: peaceiris/actions-gh-pages@v4
+      if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+      with:
+        publish_branch: gh-pages
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: _build/
+        force_orphan: true
+
+
+

Now:

+
    +

  • Add these two changes to the GitHub repository.

    • +

  • Go to “Settings” -> “Pages” -> “Branch” -> gh-pages -> “Save”.

    • +

  • Look at “Actions” tab and observe the workflow running and hopefully +deploying the website.

    • +

  • Finally visit the generated site. You find it by clicking the About wheel +icon on top right of your repository. There, select “Use your GitHub Pages +website”.

    • +

  • This is how we build almost all of our lesson websites (including this one).

    • +

  • Another popular place to deploy Sphinx documentation is ReadTheDocs.

    • +
+
+
+
Optional: How to auto-generate API documentation in Python
+

Add three tiny modifications (highlighted) to doc/conf.py to auto-generate API documentation +(this requires the sphinx-autoapi package):

+
project = "planets"
+copyright = "2024, Authors"
+author = "Authors"
+release = "0.1"
+
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+extensions = [
+    "myst_parser",  # in order to use markdown
+    "autoapi.extension",  # in order to use markdown
+]
+
+# search this directory for Python files
+autoapi_dirs = [".."]
+
+# ignore this file when generating API documentation
+autoapi_ignore = ["*/conf.py"]
+
+myst_enable_extensions = [
+    "colon_fence",  # ::: can be used instead of ``` for better rendering
+]
+
+html_theme = "sphinx_rtd_theme"
+
+
+

Then rebuild the documentation (or push the changes and let GitHub rebuild it) +and you should see a new section “API Reference”.

+
+
+
Confused about reStructuredText vs. Markdown vs. MyST?
+
    +

  • At the beginning there was reStructuredText and Sphinx was built for reStructuredText.

    • +

  • Independently, Markdown was invented and evolved into a couple of flavors.

    • +

  • Markdown became more and more popular but was limited compared to reStructuredText.

    • +

  • Later, MyST +was invented to be able to write +something that looks like Markdown but in addition can do everything that +reStructuredText can do with extra directives.

    • +
+
+
+
Where to read more
+ +
+
+
+

Collaborative version control and code review

+
+
+
Concepts around collaboration
+
+

Objectives

+
    +

  • Be able to decide whether to divide work at the branch level or at the repository level.

    • +
+
+
+
Commits, branches, repositories, forks, clones
+
    +

  • repository: The project, contains all data and history (commits, branches, tags).

    • +

  • commit: Snapshot of the project, gets a unique identifier (e.g. c7f0e8bfc718be04525847fc7ac237f470add76e).

    • +

  • branch: Independent development line. The main development line is often called main.

    • +

  • tag: A pointer to one commit, to be able to refer to it later. Like a commemorative plaque +that you attach to a particular commit (e.g. phd-printed or paper-submitted).

    • +

  • cloning: Copying the whole repository to your laptop - the first time. It is not necessary to download each file one by one.

    • +

  • forking: Taking a copy of a repository (which is typically not yours) - your +copy (fork) stays on GitHub/GitLab and you can make changes to your copy.

    • +
+
+
+
Cloning a repository
+

In order to make a complete copy a whole repository, the git clone command +can be used. When cloning, all the files, of all or selected branches, of a +repository are copied in one operation. Cloning of a repository is of relevance +in a few different situations:

+
    +

  • Working on your own, cloning is the operation that you can use to create +multiple instances of a repository on, for instance, a personal computer, a +server, and a supercomputer.

    • +

  • The parent repository could be a repository that you or your colleague own. A +common use case for cloning is when working together within a smaller team +where everyone has read and write access to the same git repository.

    • +

  • Alternatively, cloning can be made from a public repository of a code that +you would like to use. Perhaps you have no intention to work on the code, but +would like to stay in tune with the latest developments, also in-between +releases of new versions of the code.

    • +
+
+Forking and cloning +
+

Forking and cloning

+
+
+
+
+
Forking a repository
+

When a fork is made on GitHub/GitLab a complete copy, of all or selected +branches, of the repository is made. The copy will reside under a different +account on GitHub/GitLab. Forking of a repository is of high relevance when +working with a git repository to which you do not have write access.

+
    +

  • In the fork repository commits can be made to the base branch (main or +master), and to other branches.

    • +

  • The commits that are made within the branches of the fork repository can be +contributed back to the parent repository by means of pull or merge requests.

    • +
+
+
+
Synchronizing changes between repositories
+
    +

  • We need a mechanism to communicate changes between the repositories.

    • +

  • We will pull or fetch updates from remote repositories (we will soon discuss the difference between pull and fetch).

    • +

  • We will push updates to remote repositories.

    • +

  • We will learn how to suggest changes within repositories on GitHub and across repositories (pull request).

    • +

  • Repositories that are forked or cloned do not automatically synchronize themselves: +We will learn how to update forks (by pulling from the “central” repository).

    • +

  • A main difference between cloning a repository and forking a repository is that the former is a general operation for generating copies of a repository to different computers, whereas forking is a particular operation implemented on GitHub/GitLab.

    • +
+
+
+
+
Collaborating within the same repository
+

In this episode, we will learn how to collaborate within the same repository. +We will learn how to cross-reference issues and pull requests, how to review +pull requests, and how to use draft pull requests.

+

This exercise will form a good basis for collaboration that is suitable for +most research groups.

+
+

Note

+

When you read or hear pull request, please think of a change proposal.

+
+
+
Exercise
+

In this exercise, we will contribute to a repository via a pull request. +This means that you propose some change, and then it is accepted (or not).

+
+

Exercise preparation

+
    +

  • First we need to get access to the exercise repository to which we will +contribute.

    +
      +

    • Instructor collects GitHub usernames from learners and adds them as collaborators to the exercise repository +(Settings -> Collaborators and teams -> Manage access -> Add people).

      • +
    +
    • +

  • Don’t forget to accept the invitation

    +
      +

    • Check https://github.com/settings/organizations/

      • +

    • Alternatively check the inbox for the email account you registered with +GitHub. GitHub emails you an invitation link, but if you don’t receive it +you can go to your GitHub notifications in the top right corner. The +maintainer can also “copy invite link” and share it within the group.

      • +
    +
    • +

  • Watching and unwatching repositories

    +
      +

    • Now that you are a collaborator, you get notified about new issues and pull +requests via email.

      • +

    • If you do not wish this, you can “unwatch” a repository (top of +the project page).

      • +

    • However, we recommend watching repositories you are interested +in. You can learn things from experts just by watching the +activity that come through a popular project.

      • +
    +
    +Unwatching a repository +
    +

    Unwatch a repository by clicking “Unwatch” in the repository view, +then “Participating and @mentions” - this way, you will get +notifications about your own interactions.

    +
    +
    +
    • +
+
+
+

Exercise: Collaborating within the same repository (25 min)

+

Technical requirements (from installation instructions):

+ +

What is familiar from the previous workshop day (not repeated here):

+
    +

  • Cloning a repository.

    • +

  • Creating a branch.

    • +

  • Committing a change on the new branch.

    • +

  • Submit a pull request towards the main branch.

    • +
+

What will be new in this exercise:

+
    +

  • If you create the changes locally, you will need to push them to the remote repository.

    • +

  • Learning what a protected branch is and how to modify a protected branch: using a pull request.

    • +

  • Cross-referencing issues and pull requests.

    • +

  • Practice to review a pull request.

    • +

  • Learn about the value of draft pull requests.

    • +
+

Exercise tasks:

+
    +

  1. Start in the exercise +repository and open an +issue where you describe the change you want to make. Note down the issue +number since you will need it later.

    2. +

  2. Create a new branch.

    3. +

  3. Make a change to the recipe book on the new branch and in the commit +cross-reference the issue you opened (see the walk-through below +for how to do that).

    4. +

  4. Push your new branch (with the new commit) to the repository you +are working on.

    5. +

  5. Open a pull request towards the main branch.

    6. +

  6. Review somebody else’s pull request and give constructive feedback. Merge their pull request.

    7. +

  7. Try to create a new branch with some half-finished work and open a draft +pull request. Verify that the draft pull request cannot be merged since it +is not meant to be merged yet.

    8. +
+
+
+
+
Solution and hints
+
+
(1) Opening an issue
+

This is done through the GitHub web interface. For example, you could +give the name of the recipe you want to add (so that others don’t add +the same one). It is the “Issues” tab.

+
+
+
(2) Create a new branch.
+

If on GitHub, you can make the branch in the web interface.

+
+
+
(3) Make a change adding the recipe
+

Add a new file with the recipe in it. Commit the file. In the commit +message, include the note about the issue number, saying that this +will close that issue.

+
+
Cross-referencing issues and pull requests
+

Each issue and each pull request gets a number and you can cross-reference them.

+

When you open an issue, note down the issue number (in this case it is #2):

+
+Each issue gets a number +
+

You can reference this issue number in a commit message or in a pull request, like in this +commit message:

+
this is the new recipe; fixes #2
+
+
+

If you forget to do that in your commit message, you can also reference the issue +in the pull request description. And instead of fixes you can also use closes or resolves +or fix or close or resolve (case insensitive).

+

Here are all the keywords that GitHub recognizes: +https://help.github.com/en/articles/closing-issues-using-keywords

+

Then observe what happens in the issue once your commit gets merged: it will +automatically close the issue and create a link between the issue and the +commit. This is very useful for tracking what changes were made in response to +which issue and to know from when until when precisely the issue was open.

+
+
+
+
(4) Push to GitHub as a new branch
+

Push the branch to the repository. You should end up with a branch +visible in the GitHub web view.

+

This is only necessary if you created the changes locally. If you created the +changes directly on GitHub, you can skip this step.

+
+

In VS Code, you can “publish the branch” to the remote repository by clicking +the cloud icon in the bottom left corner of the window:

+
+Publishing a branch in VS Code +
+
+
+
+
(5) Open a pull request towards the main branch
+

This is done through the GitHub web interface.

+
+
+
(6) Reviewing pull requests
+

You review through the GitHub web interface.

+

Checklist for reviewing a pull request:

+
    +

  • Be kind, on the other side is a human who has put effort into this.

    • +

  • Be constructive: if you see a problem, suggest a solution.

    • +

  • Towards which branch is this directed?

    • +

  • Is the title descriptive?

    • +

  • Is the description informative?

    • +

  • Scroll down to see commits.

    • +

  • Scroll down to see the changes.

    • +

  • If you get incredibly many changes, also consider the license or copyright +and ask where all that code is coming from.

    • +

  • Again, be kind and constructive.

    • +

  • Later we will learn how to suggest changes directly in the pull request.

    • +
+

If someone is new, it’s often nice to say something encouraging in the +comments before merging (even if it’s just “thanks”). If all is good +and there’s not much else to say, you could merge directly.

+
+
+
(7) Draft pull requests
+

Try to create a draft pull request:

+
+Creating a draft pull request +
+

Verify that the draft pull request cannot be merged until it is marked as ready +for review:

+
+Draft pull request cannot be merged +
+

Draft pull requests can be useful for:

+
    +

  • Feedback: You can open a pull request early to get feedback on your work without +signaling that it is ready to merge.

    • +

  • Information: They can help communicating to others that a change is coming up and in +progress.

    • +
+
+
+
What is a protected branch? And how to modify it?
+

A protected branch on GitHub or GitLab is a branch that cannot (accidentally) +deleted or force-pushed to. It is also possible to require that a branch cannot +be directly pushed to or modified, but that changes must be submitted via a +pull request.

+

To protect a branch in your own repository, go to “Settings” -> “Branches”.

+
+
+
Summary
+
    +

  • We used all the same pieces that we’ve learned previously.

    • +

  • But we successfully contributed to a collaborative project!

    • +

  • The pull request allowed us to contribute without changing directly: +this is very good when it’s not mainly our project.

    • +
+
+
+
+
+
Practicing code review
+

In this episode we will practice the code review process. We will learn how to +ask for changes in a pull request, how to suggest a change in a pull request, +and how to modify a pull request.

+

This will enable research groups to work more collaboratively and to not only +improve the code quality but also to learn from each other.

+
+
Exercise
+
+

Exercise preparation

+

We can continue in the same exercise repository which we have used in the +previous episode.

+
+
+

Exercise: Practicing code review (25 min)

+

Technical requirements:

+ +

What is familiar from previous lessons:

+
    +

  • Creating a branch.

    • +

  • Committing a change on the new branch.

    • +

  • Opening and merging pull requests.

    • +
+

What will be new in this exercise:

+
    +

  • As a reviewer, we will learn how to ask for changes in a pull request.

    • +

  • As a reviewer, we will learn how to suggest a change in a pull request.

    • +

  • As a submitter, we will learn how to modify a pull request without closing +the incomplete one and opening a new one.

    • +
+

Exercise tasks:

+
    +

  1. Create a new branch and one or few commits: in these improve something but also +deliberately introduce a typo and also a larger mistake which we will want to fix during the code review.

    2. +

  2. Open a pull request towards the main branch.

    3. +

  3. As a reviewer to somebody else’s pull request, ask for an improvement and +also directly suggest a change for the small typo. (Hint: +suggestions are possible through the GitHub web interface, view of +a pull request, “Files changed” view, after selecting some lines. +Look for the “±” button.)

    4. +

  4. As the submitter, learn how to accept the suggested change. (Hint: +GitHub web interface, “Files Changed” view.)

    5. +

  5. As the submitter, improve the pull request without having to close and open +a new one: by adding a new commit to the same branch. (Hint: push +to the branch again.)

    6. +

  6. Once the changes are addressed, merge the pull request.

    7. +
+
+
+
+
Help and discussion
+

From here on out, we don’t give detailed steps to the solution. You +need to combine what you know, and the extra info below, in order to +solve the above.

+
+
How to ask for changes in a pull request
+

Technically, there are at least two common ways to ask for changes in a pull +request.

+

Either in the comment field of the pull request:

+
+Screenshot of a pull request comment field +
+

Or by using the “Review changes”:

+
+Screenshot of a pull request navigating to the "Review changes" tab +
+

And always please be kind and constructive in your comments. Remember that the +goal is not gate-keeping but collaborative learning.

+
+
+
How to suggest a change in a pull request as a reviewer
+

If you see a very small problem that is easy to fix, you can suggest a change +as a reviewer.

+

Instead of asking the submitter to tiny problem, you can suggest a change by +clicking on the plus sign next to the line number in the “Files changed” tab:

+
+Screenshot of leaving a comment to a line in a pull request +
+

Here you can comment on specific lines or even line ranges.

+

But now the interesting part is to click on the “Add a suggestion” symbol (the +one that looks like plus and minus). Now you can fix the tiny problem (in this +case a typo) and then click on the “Add single comment” button:

+
+Sequence of clicks to add a suggestion to a line in a pull request +
+

The result is this and the submitter can accept the change with a single click:

+
+Screenshot of a pull request with a suggested change +
+

After accepting with “Commit suggestion”, the improvement gets added to the +pull request.

+
+
+
How to modify a pull request to address the review comments
+

If the reviewer asks for changes, it is not necessary to close the pull request +and later open a new one. It can even be counter-productive to do so: This can +fragment the discussion and the history of the pull request and can make it +harder to understand the context of the changes.

+

A much better mechanism to recognize that pull requests are not implemented +from a specific commit to a specific branch, but always from a branch to a +branch.

+

This means that you can make amendments to the pull request by adding new +commits to the same source branch. This way the pull request will be updated +automatically and the reviewer can see the new changes and comment on them.

+

The fact that pull requests are from branch to branch also strongly suggests +that it is a good practice to create a new branch for each pull request. +Otherwise you could accidentally modify an open pull request by adding new +commits to the source branch.

+
+
+
+
Summary
+
    +

  • Our process isn’t just about code now. It’s about discussion and +working together to make the whole process better.

    • +

  • GitHub discussions and reviewing are quite powerful and can make +small changes easy.

    • +
+
+
+
+
How to contribute changes to repositories that belong to others
+

In this episode we prepare you to suggest and contribute changes to +repositories that belong to others. These might be open source projects that +you use in your work.

+

We will see how Git and services like GitHub or GitLab can be used to suggest +modification without having to ask for write access to the repository and +accept modifications without having to grant write access to others.

+
+
Exercise
+
+

Exercise preparation

+
    +

  • The exercise repository is now different: +https://github.com/workshop-material/recipe-book-forking-exercise (note the -forking-exercise).

    • +

  • First fork the exercise repository to your GitHub account.

    • +

  • Then clone your fork to your computer (if you wish to work locally).

    • +

  • Double-check that you have forked the correct repository.

    • +
+
+
+

Exercise: Collaborating within the same repository (25 min)

+

Technical requirements:

+ +

What is familiar from previous lessons:

+
    +

  • Forking a repository.

    • +

  • Creating a branch.

    • +

  • Committing a change on the new branch.

    • +

  • Opening and merging pull requests.

    • +
+

What will be new in this exercise:

+
    +

  • Opening a pull request towards the upstream repository.

    • +

  • Pull requests can be coupled with automated testing.

    • +

  • Learning that your fork can get out of date.

    • +

  • After the pull requests are merged, updating your fork with the changes.

    • +

  • Learn how to approach other people’s repositories with ideas, changes, and requests.

    • +
+

Exercise tasks:

+
    +

  1. Open an issue in the upstream exercise repository where you describe the +change you want to make. Take note of the issue number.

    2. +

  2. Create a new branch in your fork of the repository.

    3. +

  3. Make a change to the recipe book on the new branch and in the commit cross-reference the issue you opened. +See the walk-through below for how to do this.

    4. +

  4. Open a pull request towards the upstream repository.

    5. +

  5. The instructor will review and merge the pull requests. +During the review, pay attention to the automated test step (here for +demonstration purposes, we test whether the recipe contains an ingredients +and an instructions sections).

    6. +

  6. After few pull requests are merged, update your fork with the changes.

    7. +

  7. Check that in your fork you can see changes from other people’s pull requests.

    8. +
+
+
+
+
Help and discussion
+
+
Help! I don’t have permissions to push my local changes
+

Maybe you see an error like this one:

+
Please make sure you have the correct access rights
+and the repository exists.
+
+
+

Or like this one:

+
failed to push some refs to workshop-material/recipe-book-forking-exercise.git
+
+
+

In this case you probably try to push the changes not to your fork but to the original repository +and in this exercise you do not have write access to the original repository.

+

The simpler solution is to clone again but this time your fork.

+ +
+
+
Opening a pull request towards the upstream repository
+

We have learned in the previous episode that pull requests are always from +branch to branch. But the branch can be in a different repository.

+

When you open a pull request in a fork, by default GitHub will suggest to +direct it towards the default branch of the upstream repository.

+

This can be changed and it should always be verified, but in this case this is +exactly what we want to do, from fork towards upstream:

+
+Screenshot of a pull request from fork towards upstream +
+
+
+
Pull requests can be coupled with automated testing
+

We added an automated test here just for fun and so that you see that this is +possible to do.

+

In this exercise, the test is silly. It will check whether the recipe contains +both an ingredients and an instructions section.

+

In this example the test failed:

+
+Screenshot of a failed test in a pull request +
+

Click on the “Details” link to see the details of the failed test:

+
+Screenshot of details why the test failed +
+

How can this be useful?

+
    +

  • The project can define what kind of tests are expected to pass before a pull +request can be merged.

    • +

  • The reviewer can see the results of the tests, without having to run them +locally.

    • +
+

How does it work?

+
    +

  • We added a GitHub Actions workflow +to automatically run on each push or pull request towards the main branch.

    • +
+

What tests or steps can you image for your project to run automatically with +each pull request?

+
+
+
How to update your fork with changes from upstream
+

This used to be difficult but now it is two mouse clicks.

+

Navigate to your fork and notice how GitHub tells you that your fork is behind. +In my case, it is 9 commits behind upstream. To fix this, click on “Sync fork” +and then “Update branch”:

+
+Screenshot on GitHub fork page showing that the fork is behind +
+

After the update my “branch is up to date” with the upstream repository:

+
+Screenshot on GitHub after fork has been updated +
+
+
+
How to approach other people’s repositories with ideas, changes, and requests
+

Contributing very minor changes

+
    +

  • Clone or fork+clone repository

    • +

  • Create a branch

    • +

  • Commit and push change

    • +

  • Open a pull request or merge request

    • +
+

If you observe an issue and have an idea how to fix it

+
    +

  • Open an issue in the repository you wish to contribute to

    • +

  • Describe the problem

    • +

  • If you have a suggestion on how to fix it, describe your suggestion

    • +

  • Possibly discuss and get feedback

    • +

  • If you are working on the fix, indicate it in the issue so that others know that somebody is working on it and who is working on it

    • +

  • Submit your fix as pull request or merge request which references/closes the issue

    • +
+
+

Motivation

+
    +

  • Inform others about an observed problem

    • +

  • Make it clear whether this issue is up for grabs or already being worked on

    • +
+
+

If you have an idea for a new feature

+
    +

  • Open an issue in the repository you wish to contribute to

    • +

  • In the issue, write a short proposal for your suggested change or new feature

    • +

  • Motivate why and how you wish to do this

    • +

  • Also indicate where you are unsure and where you would like feedback

    • +

  • Discuss and get feedback before you code

    • +

  • Once you start coding, indicate that you are working on it

    • +

  • Once you are done, submit your new feature as pull request or merge request which references/closes the issue/proposal

    • +
+
+

Motivation

+
    +

  • Get agreement and feedback before writing 5000 lines of code which might be rejected

    • +

  • If we later wonder why something was done, we have the issue/proposal as +reference and can read up on the reasoning behind a code change

    • +
+
+
+
+
+
Summary
+
    +

  • This forking workflow lets you propose changes to repositories for +which you have no write access.

    • +

  • This is the way that much modern open-source software works.

    • +

  • You can now contribute to any project you can view.

    • +
+
+
+
+
Conclict resolution, rebasing, and organizational strategies
+

(40 min demo and discussion)

+
+
+
+
+

Automated testing

+
+

Objectives

+
    +

  • Know where to start in your own project.

    • +

  • Have an example for how to make the testing part of code review.

    • +
+
+
+

Instructor note

+
    +

  • (15 min) Motivation

    • +

  • (15 min) End-to-end tests

    • +

  • (15 min) Pytest

    • +

  • (15 min) Adding the unit test to GitHub Actions

    • +

  • (10 min) What else is possible

    • +

  • (20 min) Exercise

    • +
+
+
+
Motivation
+

Testing is a way to check that the code does what it is expected to.

+
    +

  • Less scary to change code: tests will tell you whether something broke.

    • +

  • Easier for new people to join.

    • +

  • Easier for somebody to revive an old code.

    • +

  • End-to-end test: run the whole code and compare result to a reference.

    • +

  • Unit tests: test one unit (function or module). Can guide towards better +structured code: complicated code is more difficult to test.

    • +
+
+
+
How testing is often taught
+
def add(a, b):
+    return a + b
+
+
+def test_add():
+    assert add(1, 2) == 3
+
+
+

How this feels:

+
+Instruction on how to draw an owl +
+

[Citation needed]

+
+
+

Instead, we will look at and discuss a real example where we test components +from our example project.

+
+
+
Where to start
+

Short answer: Start with an end-to-end test.

+ +
+
+
End-to-end tests
+ +
+

Discussion

+

Is the end-to-end test +perfect? No. But it’s a good starting point. Discuss its limitations.

+
+
+
+
Pytest
+

First we need to add a test function, for instance +for this function:

+
def force_between_planets(position1, mass1, position2, mass2):
+    G = 1.0  # gravitational constant
+
+    r = position2 - position1
+    distance = (r[0] ** 2 + r[1] ** 2 + r[2] ** 2) ** 0.5
+    force_magnitude = G * mass1 * mass2 / distance**2
+    force = (r / distance) * force_magnitude
+
+    return force
+
+
+def test_force_between_planets():
+    position1 = np.array([0.0, 0.0, 0.0])
+    mass1 = 1.0
+    position2 = np.array([1.0, 0.0, 0.0])
+    mass2 = 2.0
+
+    force = force_between_planets(position1, mass1, position2, mass2)
+
+    assert np.allclose(force, [2.0, 0.0, 0.0])
+
+
+

Let us run the test with:

+
$ pytest simulate.py
+
+
+

Explanation: pytest will look for functions starting with test_ in files +and directories given as arguments. It will run them and report the results.

+

Now let us try this:

+
    +

  • Commit the test.

    • +

  • Break the function on purpose and run the test.

    • +

  • Does the test fail as expected?

    • +
+
+
+
Adding the unit test to GitHub Actions
+

Our next goal is that we want GitHub to run the unit test +automatically on every change.

+

First we need to extend our +environment.yml:

+
name: planets
+channels:
+  - conda-forge
+dependencies:
+  - python=3.12
+  - numpy
+  - click
+  - matplotlib
+  - pytest
+
+
+

We also need to extend .github/workflows/test.yml (highlighted line):

+
name: Test
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+
+    - uses: mamba-org/setup-micromamba@v1
+      with:
+        micromamba-version: '1.5.8-0' # any version from https://github.com/mamba-org/micromamba-releases
+        environment-file: environment.yml
+        init-shell: bash
+        cache-environment: true
+        post-cleanup: 'all'
+        generate-run-shell: false
+
+    - name: Run tests
+      run: |
+        ./test.sh
+        pytest simulate.py
+      shell: bash -el {0}
+
+
+

If we have time, we can try to create a pull request which would break the +code and see how the test fails.

+
+
+
What else is possible
+
    +

  • The testing above used example-based testing.

    • +

  • Test coverage: how much of the code is traversed by tests?

    + +
    • +

  • Property-based testing: generates arbitrary data matching your specification and checks that your guarantee still holds in that case.

    + +
    • +

  • Snapshot-based testing: makes it easier to generate snapshots for regression tests.

    + +
    • +

  • Mutation testing: tests pass -> change a line of code (make a mutant) -> test again and check whether all mutants get “killed”.

    + +
    • +
+
+
+
Exercises
+

Experiment with the example project and what we learned above or try it on your +own project:

+
    +

  • Add a unit test.

    • +

  • Try to run it locally.

    • +

  • Check whether it fails when you break the corresponding function.

    • +

  • Try to run it on GitHub Actions.

    • +

  • Create a pull request which would break the code and see whether the automatic test would catch it.

    • +

  • Try to design an end-to-end test for your project.

    • +
+
+
+
+

How to make the project more reusable

+

Part 1:

+
    +

  • 15 min: Motivation

    • +

  • 15 min: Best practices for managing dependencies in Python

    • +

  • 20 min: Exercise

    • +
+

Part 2:

+
    +

  • 10 min: Introduction to containers

    • +

  • 20 min: Demonstration

    • +

  • 10 min: Discussion

    • +
+
+
+

Demo: From a script towards a workflow

+

In this episode we will explore code quality and good practices in Python using +a hands-on approach. We will together build up a small project and improve it +step by step.

+

We will start from a relatively simple image processing script which can read a +telescope image of stars and our goal is to count the number of stars in +the image. Later we will want to be able to process many such images.

+

The (fictional) telescope images look like the one below here (in this +repository we can find more):

+
+Generated image representing a telescope image of stars +
+

Generated image representing a telescope image of stars.

+
+
+
+

Rough plan for this demo

+
    +

  • (15 min) Discuss how we would solve the problem, run example code, and make it work (as part of a Jupyter notebook)?

    • +

  • (15 min) Refactor the positioning code into a function and a module

    • +

  • (15 min) Now we wish to process many images - discuss how we would approach this

    • +

  • (15 min) Introduce CLI and discuss the benefits

    • +

  • (30 min) From a script to a workflow (using Snakemake)

    • +
+
+ +
+
Plan
+

Topics we wish to show and discuss:

+
    +

  • Naming (and other) conventions, project organization, modularity

    • +

  • The value of pure functions and immutability

    • +

  • Refactoring (explained through examples)

    • +

  • Auto-formatting and linting with tools like black, vulture, ruff

    • +

  • Moving a project under Git

    • +

  • How to document dependencies

    • +

  • Structuring larger software projects in a modular way

    • +

  • Command-line interfaces

    • +

  • Workflows with Snakemake

    • +
+

We will work together on the code on the big screen, and participants will be +encouraged to give suggestions and ask questions. We will end up with a Git +repository which will be shared with workshop participants.

+
+
+
Possible solutions
+ + +
+
+
+

Concepts in refactoring and modular code design

+

Topics:

+
    +

  • Pure functions

    • +

  • Design patterns: functional design vs. object-oriented design

    • +

  • How to design your code before writing it: document-driven development

    • +
+
+
+

How to release and publish your code

+

Part 1:

+
    +

  • 30 min: Overview over software licenses and code publishing

    • +

  • 15 min: We add a license, CFF file, and publish to Zenodo (sandbox)

    • +
+

Part 2:

+
    +

  • 30 min: Creating a Python package with the help of flit

    • +

  • 15 min: Deploy the package to test-PyPI using GitHub Actions

    • +
+
+
+

Profiling memory and CPU usage

+

Profilers:

+
    +

  • cProfile or profile

    • +

  • line_profiler

    • +

  • viztracer

    • +

  • scalene

    • +

  • Intel VTune

    • +

  • PyInstrument

    • +

  • py-spy

    • +

  • Pyflame

    • +

  • timeit

    • +
+

(here I will add some examples that we can profile together)

+
+
+
+
+

Credit

+

The following material (all CC-BY) was reused to create this workshop material:

+ +

(I will also summarize what changes have been made to the original material)

+
+
+
+
+
+ + +
+
+
+ +
+ +
+

© Copyright CodeRefinery team (CC-BY license).

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/singlehtml/objects.inv b/singlehtml/objects.inv new file mode 100644 index 0000000..636e87a Binary files /dev/null and b/singlehtml/objects.inv differ diff --git a/testing/index.html b/testing/index.html new file mode 100644 index 0000000..1ec8c5e --- /dev/null +++ b/testing/index.html @@ -0,0 +1,379 @@ + + + + + + + Automated testing — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Automated testing

+
+

Objectives

+
    +

  • Know where to start in your own project.

    • +

  • Have an example for how to make the testing part of code review.

    • +
+
+
+

Instructor note

+
    +

  • (15 min) Motivation

    • +

  • (15 min) End-to-end tests

    • +

  • (15 min) Pytest

    • +

  • (15 min) Adding the unit test to GitHub Actions

    • +

  • (10 min) What else is possible

    • +

  • (20 min) Exercise

    • +
+
+
+

Motivation

+

Testing is a way to check that the code does what it is expected to.

+
    +

  • Less scary to change code: tests will tell you whether something broke.

    • +

  • Easier for new people to join.

    • +

  • Easier for somebody to revive an old code.

    • +

  • End-to-end test: run the whole code and compare result to a reference.

    • +

  • Unit tests: test one unit (function or module). Can guide towards better +structured code: complicated code is more difficult to test.

    • +
+
+
+

How testing is often taught

+
def add(a, b):
+    return a + b
+
+
+def test_add():
+    assert add(1, 2) == 3
+
+
+

How this feels:

+
+Instruction on how to draw an owl +
+

[Citation needed]

+
+
+

Instead, we will look at and discuss a real example where we test components +from our example project.

+
+
+

Where to start

+

Short answer: Start with an end-to-end test.

+ +
+
+

End-to-end tests

+ +
+

Discussion

+

Is the end-to-end test +perfect? No. But it’s a good starting point. Discuss its limitations.

+
+
+
+

Pytest

+

First we need to add a test function, for instance +for this function:

+
def force_between_planets(position1, mass1, position2, mass2):
+    G = 1.0  # gravitational constant
+
+    r = position2 - position1
+    distance = (r[0] ** 2 + r[1] ** 2 + r[2] ** 2) ** 0.5
+    force_magnitude = G * mass1 * mass2 / distance**2
+    force = (r / distance) * force_magnitude
+
+    return force
+
+
+def test_force_between_planets():
+    position1 = np.array([0.0, 0.0, 0.0])
+    mass1 = 1.0
+    position2 = np.array([1.0, 0.0, 0.0])
+    mass2 = 2.0
+
+    force = force_between_planets(position1, mass1, position2, mass2)
+
+    assert np.allclose(force, [2.0, 0.0, 0.0])
+
+
+

Let us run the test with:

+
$ pytest simulate.py
+
+
+

Explanation: pytest will look for functions starting with test_ in files +and directories given as arguments. It will run them and report the results.

+

Now let us try this:

+
    +

  • Commit the test.

    • +

  • Break the function on purpose and run the test.

    • +

  • Does the test fail as expected?

    • +
+
+
+

Adding the unit test to GitHub Actions

+

Our next goal is that we want GitHub to run the unit test +automatically on every change.

+

First we need to extend our +environment.yml:

+
name: planets
+channels:
+  - conda-forge
+dependencies:
+  - python=3.12
+  - numpy
+  - click
+  - matplotlib
+  - pytest
+
+
+

We also need to extend .github/workflows/test.yml (highlighted line):

+
name: Test
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+
+    - uses: mamba-org/setup-micromamba@v1
+      with:
+        micromamba-version: '1.5.8-0' # any version from https://github.com/mamba-org/micromamba-releases
+        environment-file: environment.yml
+        init-shell: bash
+        cache-environment: true
+        post-cleanup: 'all'
+        generate-run-shell: false
+
+    - name: Run tests
+      run: |
+        ./test.sh
+        pytest simulate.py
+      shell: bash -el {0}
+
+
+

If we have time, we can try to create a pull request which would break the +code and see how the test fails.

+
+
+

What else is possible

+
    +

  • The testing above used example-based testing.

    • +

  • Test coverage: how much of the code is traversed by tests?

    + +
    • +

  • Property-based testing: generates arbitrary data matching your specification and checks that your guarantee still holds in that case.

    + +
    • +

  • Snapshot-based testing: makes it easier to generate snapshots for regression tests.

    + +
    • +

  • Mutation testing: tests pass -> change a line of code (make a mutant) -> test again and check whether all mutants get “killed”.

    + +
    • +
+
+
+

Exercises

+

Experiment with the example project and what we learned above or try it on your +own project:

+
    +

  • Add a unit test.

    • +

  • Try to run it locally.

    • +

  • Check whether it fails when you break the corresponding function.

    • +

  • Try to run it on GitHub Actions.

    • +

  • Create a pull request which would break the code and see whether the automatic test would catch it.

    • +

  • Try to design an end-to-end test for your project.

    • +
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/version-control/branching-and-committing/index.html b/version-control/branching-and-committing/index.html new file mode 100644 index 0000000..2827392 --- /dev/null +++ b/version-control/branching-and-committing/index.html @@ -0,0 +1,432 @@ + + + + + + + Creating branches and commits — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Creating branches and commits

+

The first and most basic task to do in Git is record changes using +commits. In this part, we will record changes in two +ways: on a new branch (which supports multiple lines of work at once), and directly +on the “main” branch (which happens to be the default branch here).

+
+

Objectives

+
    +

  • Record new changes to our own copy of the project.

    • +

  • Understand adding changes in two separate branches.

    • +

  • See how to compare different versions.

    • +
+
+
+

Background

+
    +

  • In the previous episode we have browsed an existing repository and saw commits +and branches.

    • +

  • Each commit is a snapshot of the entire project at a certain +point in time and has a unique identifier (hash) .

    • +

  • A branch is a line of development, and the main branch or master branch +are often the default branch in Git.

    • +

  • A branch in Git is like a sticky note that is attached to a commit. When we add +new commits to a branch, the sticky note moves to the new commit.

    • +

  • Tags are a way to mark a specific commit as important, for example a release +version. They are also like a sticky note, but they don’t move when new +commits are added.

    • +
+
+Branching explained with a gopher +
+

What if two people, at the same time, make two different changes? Git +can merge them together easily. Image created using https://gopherize.me/ +(inspiration).

+
+
+
+
+

Exercise: Creating branches and commits

+
+Illustration of what we want to achieve in this exercise +
+

Illustration of what we want to achieve in this exercise.

+
+
+
+

Exercise: Practice creating commits and branches (20 min)

+
    +

  1. First create a new branch and then either add a new file or modify an +existing file and commit the change. Make sure that you now work on your +copy of the example repository. In your commit you can share a Git or +programming trick you like.

    2. +

  2. In a new commit, modify the file again.

    3. +

  3. Switch to the main branch and create a commit there.

    4. +

  4. Browse the network and locate the commits that you just created (“Insights” -> “Network”).

    5. +

  5. Compare the branch that you created with the main branch. Can you find an easy way to see the differences?

    6. +

  6. Can you find a way to compare versions between two arbitrary commits in the repository?

    7. +

  7. Try to rename the branch that you created and then browse the network again.

    8. +

  8. Try to create a tag for one of the commits that you created (on GitHub, +create a “release”).

    9. +
+
+

The solution below goes over most of the answers, and you are +encouraged to use it when the hints aren’t enough - this is by +design.

+
+
+

Solution and walk-through

+
+

(1) Create a new branch and a new commit

+
+
    +

  1. Where it says “main” at the top left, click, enter a new branch +name new-tutorial, click on the offer to create the new branch +(“Create branch new-tutorial from main”).

    2. +

  2. Make sure you are still on the new-tutorial branch (it should say +it at the top), and click “Add file” → “Create new file” from the +upper right.

    3. +

  3. Enter a filename where it says “Name your file…”.

    4. +

  4. Share some Git or programming trick you like.

    5. +

  5. Click “Commit changes”

    6. +

  6. Enter a commit message. Then click “Commit +changes”.

    7. +
+

You should appear back at the file browser view, and see your +modification there.

+
+
+
+

(2) Modify the file again with a new commit

+
+

This is similar to before, but we click on the existing file to +modify.

+
    +

  1. Click on the file you added or modified previously.

    2. +

  2. Click the edit button, the pencil icon at top-right.

    3. +

  3. Follow the “Commit changes” instructions as in the previous step.

    4. +
+
+
+
+

(3) Switch to the main branch and create a commit there

+
+
    +

  1. Go back to the main repository page (your user’s page).

    2. +

  2. In the branch switch view (top left above the file view), switch to +main.

    3. +

  3. Modify another file that already exists, following the pattern +from above.

    4. +
+
+
+
+

(4) Browse the commits you just made

+

Let’s look at what we did. Now, the main and new-tutorial branches +have diverged: both have some modifications. Try to find the commits +you created.

+
+

Insights tab → Network view (just like we have done before).

+
+
+
+

(5) Compare the branches

+

Comparing changes is an important thing we need to do. When using the +GitHub view only, this may not be so common, but we’ll show it so that +it makes sense later on.

+
+

A nice way to compare branches is to add /compare to the URL of the repository, +for example (replace USER): +https://github.com/USER/planets/compare

+
+
+
+

(6) Compare two arbitrary commits

+

This is similar to above, but not only between branches.

+
+

Following the /compare-trick above, one can compare commits on GitHub by +adjusting the following URL: +https://github.com/USER/planets/compare/VERSION1..VERSION2

+

Replace USER with your username and VERSION1 and VERSION2 with a commit hash or branch name. +Please try it out.

+
+
+
+

(7) Renaming a branch

+
+

Branch button → View all branches → three dots at right side → Rename branch.

+
+
+
+

(8) Creating a tag

+

Tags are a way to mark a specific commit as important, for example a release +version. They are also like a sticky note, but they don’t move when new +commits are added.

+
+

On the right side, below “Releases”, click on “Create a new release”.

+

What GitHub calls releases are actually tags in Git with additional metadata. +For the purpose of this exercise we can use them interchangeably.

+
+
+
+
+

Summary

+

In this part, we saw how we can make changes to our files. With branches, we +can track several lines of work at once, and can compare their differences.

+
    +

  • You could commit directly to main if there is only one single line +of work and it’s only you.

    • +

  • You could commit to branches if there are multiple lines of work at +once, and you don’t want them to interfere with each other.

    • +

  • Tags are useful to mark a specific commit as important, for example a +release version.

    • +

  • In Git, commits form a so-called “graph”. Branches are tags in Git function +like sticky notes that stick to specific commits. What this means for us is +that it does not cost any significant disk space to create new branches.

    • +

  • Not all files should be added to Git. For example, temporary files or +files with sensitive information or files which are generated as part of +the build process should not be added to Git. For this we use +.gitignore (more about this later: Practical advice: How much Git is necessary?).

    • +

  • Unsure on which branch you are or what state the repository is in? +On the command line, use git status frequently to get a quick overview.

    • +
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/version-control/browsing/index.html b/version-control/browsing/index.html new file mode 100644 index 0000000..b36d1e3 --- /dev/null +++ b/version-control/browsing/index.html @@ -0,0 +1,456 @@ + + + + + + + Forking, cloning, and browsing — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Forking, cloning, and browsing

+

In this episode, we will look at an existing repository to understand how +all the pieces work together. Along the way, we will make a copy (by +forking and/or cloning) of the repository for us, which will be used +for our own changes.

+
+

Objectives

+
    +

  • See a real Git repository and understand what is inside of it.

    • +

  • Understand how version control allows advanced inspection of a +repository.

    • +

  • See how Git allows multiple people to work on the same project at the same time.

    • +

  • See the big picture instead of remembering a bunch of commands.

    • +
+
+
+

GitHub, VS Code, or command line

+

We offer three different paths for this exercise:

+
    +

  • GitHub (this is the one we will demonstrate)

    • +

  • VS Code (if you prefer to follow along using an editor)

    • +

  • Command line (for people comfortable with the command line)

    • +
+
+
+

Creating a copy of the repository by “forking” or “cloning”

+

A repository is a collection of files in one directory tracked by Git. A +GitHub repository is GitHub’s copy, which adds things like access control, +issue tracking, and discussions. Each GitHub repository is owned by a user or +organization, who controls access.

+

First, we need to make our own copy of the exercise repository. This will +become important later, when we make our own changes.

+
+Illustration of forking a repository on GitHub +
+

Illustration of forking a repository on GitHub.

+
+
+
+Illustration of cloning a repository to your computer +
+

Illustration of cloning a repository to your computer.

+
+
+
+Illustration of cloning a forked repository to your computer +
+

It is also possible to do this: to clone a forked repository to your computer.

+
+
+

At all times you should be aware of if you are looking at your repository +or the upstream repository (original repository):

+
    +

  • Your repository: https://github.com/USER/planets

    • +

  • Upstream repository: https://github.com/workshop-material/planets

    • +
+
+

How to create a fork

+
    +

  1. Go to the repository view on GitHub: https://github.com/workshop-material/planets

    2. +

  2. First, on GitHub, click the button that says “Fork”. It is towards +the top-right of the screen.

    3. +

  3. You should shortly be redirected to your copy of the repository +USER/planets.

    4. +
+
+
+

Instructor note

+

Before starting the exercise session show +how to fork the repository to own account +(above).

+
+
+
+

Exercise: Copy and browse an existing project

+

Work on this by yourself or in pairs.

+
+

Exercise preparation

+
+

In this case you will work on a fork.

+

You only need to open your own view, as described above. The browser +URL should look like https://github.com/USER/planets, where +USER is your GitHub username.

+
+
+
+

Exercise: Browsing an existing project (20 min)

+

Browse the example project and +explore commits and branches, either on a fork or on a clone. Take notes and +prepare questions. The hints are for the GitHub path in the browser.

+
    +

  1. Browse the commit history: Are commit messages understandable? +(Hint: “Commit history”, the timeline symbol, above the file list)

    2. +

  2. Compare the commit history with the network graph (“Insights” -> “Network”). Can you find the branches?

    3. +

  3. Try to find the history of commits for a single file, e.g. simulate.py. +(Hint: “History” button in the file view)

    4. +

  4. Which files include the word “position”? +(Hint: the GitHub search on top of the repository view)

    5. +

  5. In the simulate.py file, find out who modified each line last and when +(click on file, then click “Blame” button). Find out who modified the gravitational constant +last and in which commit. +(Hint: “Blame” view in the file view)

    6. +

  6. Can you use this code yourself? Are you allowed to share +modifications? +(Hint: look for a license file)

    7. +
+
+

The solution below goes over most of the answers, and you are +encouraged to use it when the hints aren’t enough - this is by +design.

+
+
+

Solution and walk-through

+
+

(1) Basic browsing

+

The most basic thing to look at is the history of commits.

+
    +

  • This is visible from a button in the repository view. We see every +change, when, and who has committed.

    • +

  • Every change has a unique identifier, such as 244c993. This can +be used to identify both this change, and the whole project’s +version as of that change.

    • +

  • Clicking on a change in the view shows more.

    • +
+
+

Click on the timeline symbol in the repository view:

+
+Screenshot on GitHub of where to find the commit history +
+
+
+
+

(2) Compare commit history with network graph

+

The commit history we saw above looks linear: one commit after +another. But if we look at the network view, we see some branches and +merges. We’ll see how to do these later. This is another one of the +basic Git views.

+
+

In a new browser tab, open the “Insights” tab, and click on “Network”. +You can hover over the commit dots to see the person who committed and +how they correspond with the commits in the other view:

+
+Screenshot on GitHub of the network graph +
+
+
+
+

(3) How can you browse the history of a single file?

+

We see the history for the whole repository, but we can also see it +for a single file.

+
+

Navigate to the file view: Main page → simulate.py. +Click the “History” button near the top right.

+
+
+
+

(4) Which files include the word “position”?

+

Version control makes it very easy to find all occurrences of a single +word. This is useful for things like finding where functions or +variables are defined or used.

+
+

We go to the main file view. We click the Search magnifying +class at the very top, type “position”, and click enter. We see every +instance, including the context.

+
+

Searching in a forked repository will not work instantaneously!

+

It usually takes a few minutes before one can search for keywords in a forked repository +since it first needs to build the search index the very first time we search. +Start it, continue with other steps, then come back to this.

+
+
+
+
+

(5) Who modified each line last and when?

+

This is called the “annotate” or “blame” view. The name “blame” +is very unfortunate, but it is the standard term for historical reasons +for this functionality and it is not meant to blame anyone.

+
+

From a file view, change preview to “Blame” towards the top-left. +To get the actual commit, click on the commit message.

+
+
+
+

(6) Can you use this code yourself? Are you allowed to share modifications?

+
    +

  • Look at the file LICENSE.

    • +

  • On GitHub, click on the file to see a nice summary of what we can do with this:

    +
    +Screenshot on GitHub summarizing license terms +
    +
    • +
+
+
+

Summary

+
    +

  • Git allowed us to understand this simple project much better than we +could, if it was just a few files on our own computer.

    • +

  • It was easy to share the project with the course.

    • +

  • By forking the repository, we created our own copy. This is +important for the following, where we will make changes to +our copy.

    • +
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/version-control/index.html b/version-control/index.html new file mode 100644 index 0000000..f5e96bc --- /dev/null +++ b/version-control/index.html @@ -0,0 +1,167 @@ + + + + + + + Introduction to version control with Git and GitHub — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Introduction to version control with Git and GitHub
    • +
  • + Edit on GitHub +
    • +
+
+
+
+ +
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/version-control/motivation/index.html b/version-control/motivation/index.html new file mode 100644 index 0000000..454a972 --- /dev/null +++ b/version-control/motivation/index.html @@ -0,0 +1,283 @@ + + + + + + + Motivation — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+ +
+
+ +
+

Motivation

+
+

Objectives

+
    +

  • Browse commits and branches of a Git repository.

    • +

  • Remember that commits are like snapshots of the repository at a certain +point in time.

    • +

  • Know the difference between Git (something that tracks changes) and +GitHub/GitLab (a platform to host Git repositories).

    • +
+
+
+

Why do we need to keep track of versions?

+

Version control is an answer to the following questions (do you recognize some +of them?):

+
    +

  • “It broke … hopefully I have a working version somewhere?”

    • +

  • “Can you please send me the latest version?”

    • +

  • “Where is the latest version?”

    • +

  • “Which version are you using?”

    • +

  • “Which version have the authors used in the paper I am trying to reproduce?”

    • +

  • “Found a bug! Since when was it there?”

    • +

  • “I am sure it used to work. When did it change?”

    • +

  • “My laptop is gone. Is my thesis now gone?”

    • +
+
+
+

Demonstration

+
    +

  • Example repository: https://github.com/workshop-material/planets

    • +

  • Commits are like snapshots and if we break something we can go back to a +previous snapshot.

    • +

  • Commits carry metadata about changes: author, date, commit message, and +a checksum.

    • +

  • Branches are like parallel universes where you can experiment with +changes without affecting the default branch: +https://github.com/workshop-material/planets/network +(“Insights” -> “Network”)

    • +

  • With version control we can annotate code +(example).

    • +

  • Collaboration: We can fork (make a copy on GitHub), clone (make a copy +to our computer), review, compare, share, and discuss.

    • +

  • Code review: Others can suggest changes using pull requests or merge +requests. These can be reviewed and discussed before they are merged. +Conceptually, they are similar to “suggesting changes” in Google Docs.

    • +
+
+
+

Features: roll-back, branching, merging, collaboration

+
    +

  • Roll-back: you can always go back to a previous version and compare

    • +

  • Branching and merging:

    +
      +

    • Work on different ideas at the same time

      • +

    • Different people can work on the same code/project without interfering

      • +

    • You can experiment with an idea and discard it if it turns out to be a bad idea

      • +
    +
    • +
+
+Branching explained with a gopher +
+

Image created using https://gopherize.me/ +(inspiration).

+
+
+ +
+
+

Talking about code

+

Which of these two is more practical?

+
    +

  1. “Clone the code, go to the file ‘simulate.py’, and search for ‘force_between_planets’. +Oh! But make sure you use the version from September 2024.”

    2. +

  2. Or I can send you a permalink: https://github.com/workshop-material/planets/blob/1343ac0/simulate.py#L31C5-L39

    3. +
+
+
+

What we typically like to snapshot

+
    +

  • Software (this is how it started but Git/GitHub can track a lot more)

    • +

  • Scripts

    • +

  • Documents (plain text files much better suitable than Word documents)

    • +

  • Manuscripts (Git is great for collaborating/sharing LaTeX or Quarto manuscripts)

    • +

  • Configuration files

    • +

  • Website sources

    • +

  • Data

    • +
+
+

Discussion

+

In this example somebody tried to keep track of versions without a version +control system tool like Git. Discuss the following directory listing. What +possible problems do you anticipate with this kind of “version control”:

+
myproject-2019.zip
+myproject-2020-february.zip
+myproject-2021-august.zip
+myproject-2023-09-19-working.zip
+myproject-2023-09-21.zip
+myproject-2023-09-21-test.zip
+myproject-2023-09-21-myversion.zip
+myproject-2023-09-21-newfeature.zip
+...
+(100 more files like these)
+
+
+ +
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/version-control/practical-advice/index.html b/version-control/practical-advice/index.html new file mode 100644 index 0000000..bcc49ec --- /dev/null +++ b/version-control/practical-advice/index.html @@ -0,0 +1,300 @@ + + + + + + + Practical advice: How much Git is necessary? — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Practical advice: How much Git is necessary?

+
+

Writing useful commit messages

+

Useful commit messages summarize the change and provide context.

+

If you need a commit message that is longer than one line, +then the convention is: one line summarizing the commit, then one empty line, +then paragraph(s) with more details in free form, if necessary.

+

Good example:

+
increase alpha to 2.0 for faster convergence
+
+the motivation for this change is
+to enable ...
+...
+(more context)
+...
+this is based on a discussion in #123
+
+
+
    +

  • Why something was changed is more important than what has changed.

    • +

  • Cross-reference to issues and discussions if possible/relevant.

    • +

  • Bad commit messages: “fix”, “oops”, “save work”

    • +

  • Bad examples: http://whatthecommit.com

    • +

  • Write commit messages that will be understood +15 years from now by someone else than you. Or by your future you.

    • +

  • Many projects start out as projects “just for me” and end up to be successful projects +that are developed by 50 people over decades.

    • +

  • Commits with multiple authors are possible.

    • +
+

Good references:

+ +
+

Note

+

A great way to learn how to write commit messages and to get inspired by their +style choices: browse repositories of codes that you use/like:

+

Some examples (but there are so many good examples):

+ +

When designing commit message styles consider also these:

+
    +

  • How will you easily generate a changelog or release notes?

    • +

  • During code review, you can help each other improving commit messages.

    • +
+
+

But remember: it is better to make any commit, than no commit. Especially in small projects. +Let not the perfect be the enemy of the good enough.

+
+
+

What level of branching complexity is necessary for each project?

+

Simple personal projects:

+
    +

  • Typically start with just the main branch.

    • +

  • Use branches for unfinished/untested ideas.

    • +

  • Use branches when you are not sure about a change.

    • +

  • Use tags to mark important milestones.

    • +

  • If you are unsure what to do with unfinished and not working code, commit it +to a branch.

    • +
+

Projects with few persons: you accept things breaking sometimes

+
    +

  • It might be reasonable to commit to the main branch and feature branches.

    • +
+

Projects with few persons: changes are reviewed by others

+
    +

  • You create new feature branches for changes.

    • +

  • Changes are reviewed before they are merged to the main branch.

    • +

  • Consider to write-protect the main branch so that it can only be changed +with pull requests or merge requests.

    • +
+
+
+

How large should a commit be?

+
    +

  • Better too small than too large (easier to combine than to split).

    • +

  • Often I make a commit at the end of the day (this is a unit I would not like to lose).

    • +

  • Smaller sized commits may be easier to review for others than huge commits.

    • +

  • Imperfect commits are better than no commits.

    • +

  • A commit should not contain unrelated changes to simplify review and possible +repair/adjustments/undo later (but again: imperfect commits are better than no commits).

    • +
+
+
+

Working on the command line? Use “git status” all the time

+

The git status command is one of the most useful commands in Git +to inform about which branch we are on, what we are about to commit, +which files might not be tracked, etc.

+
+
+

How about staging and committing?

+
    +

  • Commit early and often: rather create too many commits than too few. +You can always combine commits later.

    • +

  • Once you commit, it is very, very hard to really lose your code.

    • +

  • Always fully commit (or stash) before you do dangerous things, so that you know you are safe. +Otherwise it can be hard to recover.

    • +

  • Later you can start using the staging area (where you first stage and then commit in a second step).

    • +

  • Later start using git add -p and/or git commit -p.

    • +
+
+
+

What to avoid

+
    +

  • Committing generated files/directories (example: __pycache__, *.pyc) -> +use .gitignore +files +(collection of .gitignore templates).

    • +

  • Committing huge files -> use code review to detect this.

    • +

  • Committing unrelated changes together.

    • +

  • Postponing commits because the changes are “unfinished”/”ugly” -> better ugly +commits than no commits.

    • +

  • When working with branches:

    +
      +

    • Not updating your branch before starting new work.

      • +

    • Too ambitious branch which risks to never get completed.

      • +

    • Over-engineering the branch layout and safeguards in small projects.

      • +

    • Working on unrelated things on the same branch.

      • +
    +
    • +
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/version-control/sharing/index.html b/version-control/sharing/index.html new file mode 100644 index 0000000..7621f54 --- /dev/null +++ b/version-control/sharing/index.html @@ -0,0 +1,405 @@ + + + + + + + Optional: How to turn your project to a Git repo and share it — Reproducible research software development using Python documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Optional: How to turn your project to a Git repo and share it

+
+

Objectives

+
    +

  • Turn our own coding project (small or large, finished or unfinished) into a +Git repository.

    • +

  • Be able to share a repository on the web to have a backup or so that others +can reuse and collaborate or even just find it.

    • +
+
+
+

Exercise

+
+Illustration of how we turn a project into a Git repository and share it +
+

From a bunch of files to a local repository which we then share on GitHub.

+
+
+
+

Exercise: Turn your project to a Git repo and share it (20 min)

+
    +

  1. Create a new directory called myproject with one or few files in it. +This represents our own project. It is not yet a Git repository. You can try +that with your own project or use a simple placeholder example.

    2. +

  2. Turn this new directory into a Git repository.

    3. +

  3. Share this repository on GitHub (or GitLab, since it really works the same).

    4. +
+

We offer three different paths of how to do this exercise.

+
    +

  • Via GitHub web interface: easy and can be a good starting point if you are completely +new to Git.

    • +

  • VS Code is quite easy, since VS Code can offer to create the +GitHub repositories for you.

    • +

  • Command line: you need to create the +repository on GitHub and link it yourself.

    • +
+
+

Create an repository on GitHub

+

First log into GitHub, then follow the screenshots and descriptions below.

+
+Screenshot on GitHub before a new repository form is opened +
+

Click on the “plus” symbol on top right, then on “New repository”.

+
+
+

Then:

+
+Screenshot on GitHub just before a new repository is created +
+

Choose a repository name, add a short description, and in this case make sure to check “Add a +README file”. Finally “Create repository”.

+
+
+

Upload your files

+

Now that the repository is created, you can upload your files:

+
+Screenshot on GitHub just before uploading files +
+

Click on the “+” symbol and then on “Upload files”.

+
+
+
+
+
+
+

Is putting software on GitHub/GitLab/… publishing?

+

It is a good first step but to make your code truly findable and +accessible, consider making your code citable and persistent: Get a +persistent identifier (PID) such as DOI in addition to sharing the code +publicly, by using services like Zenodo or similar +services.

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file