Update

.github/workflows/dev.yml

@@ -51,7 +51,7 @@ jobs:
         fetch-depth: 0 # fetch all commits/branches for mike
     - uses: actions/setup-python@v5
       with:
-        python-version: '3.12'
+        python-version: '3.10'
 
     - name: Install dependencies
       run: |

.gitignore

@@ -18,6 +18,7 @@ eggs/
 lib/
 lib64/
 parts/
+site/
 sdist/
 var/
 wheels/

AUTHORS.md

@@ -1,2 +1,3 @@
-## Author:
+# Authors
+
 - Jose Fernandez Navarro <jc.fernandez.navarro@gmail.com>

CHANGELOG.md

@@ -6,11 +6,12 @@
 * Added pre-commit hooks
 * Change the build configuration to Poetry
 * Added Docker container
-* Added tox
+* Changed tests to pytest
 * Updated versions of dependencies
 * Perform code optimizations
-* Add test for full coveragge
+* Addded tests for full coveragge
 * Bump taggd to 0.4.0
+* Changed documentation
 
 ## Version 1.8.2
 * Added annotation (htseq) feature type as parameter

CONTRIBUTING.md

@@ -0,0 +1,169 @@
+# Contributing
+
+Contributions are welcome, and they are greatly appreciated! Every little bit
+helps, and credit will always be given.
+
+You can contribute in many ways:
+
+## Types of Contributions
+
+### Report Bugs
+
+Report bugs at https://github.com/jfnavarro/st_pipeline/issues.
+
+If you are reporting a bug, please include:
+
+* Your operating system name and version.
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+### Fix Bugs
+
+Look through the GitHub issues for bugs. Anything tagged with "bug" and "help
+wanted" is open to whoever wants to implement it.
+
+### Implement Features
+
+Look through the GitHub issues for features. Anything tagged with "enhancement"
+and "help wanted" is open to whoever wants to implement it.
+
+### Write Documentation
+
+ST Pipeline could always use more documentation, whether as part of the
+official ST Pipeline docs, in docstrings, or even on the web in blog posts,
+articles, and such.
+
+### Submit Feedback
+
+The best way to send feedback is to file an issue at https://github.com/jfnavarro/st_pipeline/issues.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+
+## Get Started!
+
+Ready to contribute? Here's how to set up `ST Pipeline` for local development.
+
+1. Fork the `ST Pipeline` repo on GitHub.
+2. Clone your fork locally
+
+``` console
+git clone git@github.com:jfnavarro/st_pipeline.git
+```
+
+3. Ensure [poetry](https://python-poetry.org/docs/) is installed.
+4. Install dependencies and start your virtualenv:
+
+``` console
+poetry install -E test -E doc -E dev
+```
+
+Note that you can use your own Python environment (e.g Anaconda) by
+changing the default behaviour in poetry with this command:
+
+``` console
+poetry config virtualenvs.create false
+```
+
+5. Create a branch for local development:
+
+``` console
+git checkout -b name-of-your-bugfix-or-feature
+```
+
+Now you can make your changes locally.
+
+6. When you're done making changes, check that your changes pass the
+   tests, including testing other Python versions, with pytest:
+
+``` console
+poetry run pytest
+```
+
+7. Commit your changes and push your branch to GitHub:
+
+``` console
+git add .
+git commit -m "Your detailed description of your changes."
+git push origin name-of-your-bugfix-or-feature
+```
+
+8. Submit a pull request through the GitHub website.
+
+## Pull Request Guidelines
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include tests.
+2. If the pull request adds functionality, the docs should be updated. Put
+   your new functionality into a function with a docstring, and add the
+   feature to the list in README.md.
+3. The pull request should work for Python 3.10, 3.11 and 3.12. Check
+   https://github.com/jfnavarro/st_pipeline/actions
+   and make sure that the tests pass for all supported Python versions.
+
+## Testing
+
+You can run the tests with pytest:
+
+``` console
+poetry run pytest
+```
+
+Replace test_your_module.py with the actual name of your test file.
+
+## Makefile
+
+A `makefile`is included in the repo with the following actions:
+
+To run formatting tools
+
+```bash
+make format
+```
+
+To run linting tools
+
+```bash
+make lint
+```
+
+To run the tests
+
+```bash
+make unittet
+```
+
+To run the tests with coverage
+
+```bash
+make coverage
+```
+
+To clean the temporary files and cache
+
+```bash
+make clean
+```
+
+## Deploying
+
+A reminder for the maintainers on how to deploy.
+Make sure all your changes are committed (including an entry in CHANGELOG.md).
+Then run:
+
+``` console
+poetry run bump2version patch # possible: major / minor / patch
+git push
+git push --tags
+```
+
+GitHub Actions will then create a release and publish documentation if tests pass.
+
+You can also create the documentation manually by running:
+
+``` console
+poetry run mkdocs build
+```

Dockerfile

@@ -0,0 +1,39 @@
+FROM python:3.11-slim
+
+# Set environment variables
+ENV POETRY_VERSION=1.7.2 \
+    PYTHONUNBUFFERED=1 \
+    POETRY_NO_INTERACTION=1 \
+    PATH="/root/.local/bin:$PATH"
+
+# Install system dependencies and Poetry
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends \
+       build-essential \
+       curl \
+       libpq-dev \
+       libffi-dev \
+       libssl-dev \
+       git \
+       gcc \
+    && curl -sSL https://install.python-poetry.org | python3 - \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+# Set working directory
+WORKDIR /app
+
+# Copy project files
+COPY pyproject.toml poetry.lock README.md /app/
+
+# Install dependencies using Poetry
+RUN poetry install --no-root --only main
+
+# Copy the entire project
+COPY . /app
+
+# Ensure scripts are executable
+RUN chmod +x /app/stpipeline/scripts/*.py
+
+# Set entrypoint for the container
+ENTRYPOINT ["poetry", "run"]