diff --git a/.bumpversion.cfg b/.bumpversion.cfg new file mode 100644 index 0000000..36d51c9 --- /dev/null +++ b/.bumpversion.cfg @@ -0,0 +1,35 @@ +[bumpversion] +commit = True +tag = False +current_version = 0.1.0 + +[bumpversion:file:pyproject.toml] +search = version = "{current_version}" +replace = version = "{new_version}" + +[bumpversion:file:src/flintpy/__init__.py] +search = __version__ = "{current_version}" +replace = __version__ = "{new_version}" + +[bumpversion:file(title):CHANGELOG.md] +search = {#}{#} [Unreleased] +replace = {#}{#} [Unreleased] + + {#}{#} [{new_version}] - {now:%Y-%m-%d} + +[bumpversion:file(links):CHANGELOG.md] +search = [Unreleased]: https://github.com/rserial/flintpy/compare/v{current_version}...HEAD +replace = [Unreleased]: https://github.com/rserial/flintpy/compare/v{new_version}...HEAD + [{new_version}]: https://github.com/rserial/flintpy/compare/v{current_version}...v{new_version} + +[bumpversion:file(version):CITATION.cff] +search = version: {current_version} +replace = version: {new_version} + +[bumpversion:file(tag):CITATION.cff] +search = https://github.com/rserial/flintpy/releases/tag/v{current_version} +replace = https://github.com/rserial/flintpy/releases/tag/v{new_version} + +[bumpversion:file(description):CITATION.cff] +search = description: The Software Heritage link for version {current_version}. +replace = description: The Software Heritage link for version {new_version}. diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS new file mode 100644 index 0000000..a7eb7bf --- /dev/null +++ b/.github/CODEOWNERS @@ -0,0 +1,10 @@ +# This is a comment. +# Each line is a file pattern followed by one or more owners. + +# More details are here: https://help.github.com/articles/about-codeowners/ + +# These owners will be the default owners for everything in +# the repo. Unless a later match takes precedence, +# @rserial will be requested for review when someone opens +# a pull request. +* @rserial diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md new file mode 100644 index 0000000..7cd5ec2 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -0,0 +1,25 @@ +--- +name: 🐛 Bug report +about: Create a report to help us improve +labels: bug +assignees: '' + +--- + +## Expected Behavior + + +## Actual Behavior + + +## Steps to Reproduce the Problem + + 1. + 1. + 1. + +## Specifications + + - Version: + - Platform: + - Subsystem: diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml new file mode 100644 index 0000000..8005e32 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/config.yml @@ -0,0 +1,2 @@ +blank_issues_enabled: false +contact_links: [] diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md new file mode 100644 index 0000000..248cac5 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feature_request.md @@ -0,0 +1,19 @@ +--- +name: 🚀 Feature request +about: Suggest an idea for this project +labels: enhancement +assignees: '' + +--- + +**Is your feature request related to a problem? Please describe.** +A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] + +**Describe the solution you'd like** +A clear and concise description of what you want to happen. + +**Describe alternatives you've considered** +A clear and concise description of any alternative solutions or features you've considered. + +**Additional context** +Add any other context or screenshots about the feature request here. diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md new file mode 100644 index 0000000..4030f6f --- /dev/null +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -0,0 +1,7 @@ +Fixes # + +## Proposed Changes + + - + - + - diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 0000000..801cc12 --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,14 @@ +version: 2 +updates: + - package-ecosystem: github-actions + directory: "/" + schedule: + interval: daily + - package-ecosystem: pip + directory: "/docs" + schedule: + interval: daily + - package-ecosystem: pip + directory: "/" + schedule: + interval: daily diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml new file mode 100644 index 0000000..27fc369 --- /dev/null +++ b/.github/workflows/codeql-analysis.yml @@ -0,0 +1,41 @@ +name: "CodeQL" + +on: + push: + branches: + pull_request: + branches: + schedule: + - cron: '0 6 * * 1' + +jobs: + analyze: + name: Analyze + runs-on: ubuntu-latest + permissions: + actions: read + contents: read + security-events: write + + strategy: + fail-fast: false + matrix: + language: [ 'python' ] + + steps: + - name: Checkout repository + uses: actions/checkout@v4.1.1 + + # Initializes the CodeQL tools for scanning. + - name: Initialize CodeQL + uses: github/codeql-action/init@v3 + with: + languages: ${{ matrix.language }} + + # Autobuild attempts to build any compiled languages (C/C++, C#, or Java). + # If this step fails, then you should remove it and run the build manually (see below) + - name: Autobuild + uses: github/codeql-action/autobuild@v3 + + - name: Perform CodeQL Analysis + uses: github/codeql-action/analyze@v3 diff --git a/.github/workflows/pre-commit-autoupdate.yml b/.github/workflows/pre-commit-autoupdate.yml new file mode 100644 index 0000000..c02bdf9 --- /dev/null +++ b/.github/workflows/pre-commit-autoupdate.yml @@ -0,0 +1,43 @@ +name: "Pre-commit autoupdate" + +on: + schedule: + - cron: '0 6 * * 1' + workflow_dispatch: + +jobs: + autoupdate: + name: autoupdate + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4.1.1 + + - name: Set up Python 3.9 + uses: actions/setup-python@v5.0.0 + with: + python-version: 3.9 + + - name: Install system deps + shell: bash + run: | + pip install poetry + poetry config virtualenvs.in-project true + poetry install --no-root --only dev --only linters --sync + + - name: Run autoupdate + run: poetry run pre-commit autoupdate + + - name: Run pre-commit + run: poetry run pre-commit run --all-files + + - uses: peter-evans/create-pull-request@v6.0.0 + with: + token: ${{ secrets.GITHUB_TOKEN }} + branch: chore-update-pre-commit-hooks + title: Update pre-commit hooks + commit-message: "Update pre-commit hooks" + body: | + # Update pre-commit hooks + + - Update pre-commit hooks to the latest version. + delete-branch: true diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml new file mode 100644 index 0000000..9714f63 --- /dev/null +++ b/.github/workflows/release.yml @@ -0,0 +1,72 @@ +name: release + +on: + push: + tags: + - 'v*' + +jobs: + release: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4.1.1 + + - name: Set up Python 3.9 + uses: actions/setup-python@v5.0.0 + with: + python-version: 3.9 + + - name: Install system deps + shell: bash + run: | + pip install poetry + poetry config virtualenvs.in-project true + + - name: Build package + run: | + poetry build --ansi + + - name: Publish package on PyPI + uses: pypa/gh-action-pypi-publish@v1.8.11 + with: + user: __token__ + password: ${{ secrets.PYPI_TOKEN }} + + - name: Publish package on TestPyPI + uses: pypa/gh-action-pypi-publish@v1.8.11 + with: + user: __token__ + password: ${{ secrets.TEST_PYPI_TOKEN }} + repository_url: https://test.pypi.org/legacy/ + + github_release: + needs: release + name: Create Github Release + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4.1.1 + + - name: Get version from tag + id: tag_name + shell: bash + run: | + echo ::set-output name=current_version::${GITHUB_REF#refs/tags/v} + + - name: Get Changelog Entry + id: changelog_reader + uses: mindsers/changelog-reader-action@v2.2.2 + with: + version: ${{ steps.tag_name.outputs.current_version }} + path: ./CHANGELOG.md + + - name: Create Release + id: create_release + uses: actions/create-release@v1.1.4 + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + with: + tag_name: ${{ github.ref }} + release_name: Release ${{ github.ref }} + body: ${{ steps.changelog_reader.outputs.changes }} + draft: false + prerelease: false diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml new file mode 100644 index 0000000..741ac8f --- /dev/null +++ b/.github/workflows/tests.yml @@ -0,0 +1,108 @@ +name: tests + +on: + push: + branches: + pull_request: + branches: + +jobs: + linting: + name: Linting + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4.1.1 + + - name: Set up Python 3.9 + uses: actions/setup-python@v5.0.0 + with: + python-version: 3.9 + + - name: Install system deps + shell: bash + run: | + pip install poetry + poetry config virtualenvs.in-project true + poetry install --no-root --only dev --only linters --sync + + - name: Linting + shell: bash + run: poetry run pre-commit run --all-files + + tests: + needs: linting + name: ${{ matrix.os }} / ${{ matrix.python-version }} + runs-on: ${{ matrix.os }}-latest + strategy: + matrix: + os: [Ubuntu, MacOS, Windows] + python-version: ['3.9', '3.10', '3.11', '3.12'] + fail-fast: true + steps: + - uses: actions/checkout@v4.1.1 + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v5.0.0 + with: + python-version: ${{ matrix.python-version }} + + - name: Install system deps + shell: bash + run: | + pip install nox-poetry + pip install poetry + poetry config virtualenvs.in-project true + + - name: Run mypy with nox + shell: bash + run: nox --force-color -s mypy-${{ matrix.python-version }} + + - name: Run tests with nox + shell: bash + run: nox --force-color -s tests-${{ matrix.python-version }} + + - name: Run securtity check + if: matrix.python-version == '3.12' && matrix.os == 'Ubuntu' + shell: bash + run: nox --force-color -s security + + - name: Upload coverage data + uses: actions/upload-artifact@v4 + with: + name: ${{ matrix.os }}-${{ matrix.python-version }}.coverage-data + path: ".coverage.*" + retention-days: 2 + + coverage: + needs: tests + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4.1.1 + + - name: Set up Python 3.9 + uses: actions/setup-python@v5.0.0 + with: + python-version: 3.9 + + - name: Install system deps + shell: bash + run: | + pip install nox-poetry + pip install poetry + poetry config virtualenvs.in-project true + + - name: Download coverage data + uses: actions/download-artifact@v4 + with: + pattern: "*.coverage-data" + merge-multiple: true + + - name: Create coverage report + shell: bash + run: | + nox --force-color --session=coverage -- --fmt xml + + - name: Upload coverage report + uses: codecov/codecov-action@v3.1.4 + with: + token: ${{ secrets.CODECOV_TOKEN }} diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..b8eb5b1 --- /dev/null +++ b/.gitignore @@ -0,0 +1,135 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +pip-wheel-metadata/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +.python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# pytype +.pytype/ + +# Pyre type checker +.pyre/ + +# Code editors +.vscode diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..da07c6d --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,42 @@ +--- +default_install_hook_types: + - pre-commit + - post-checkout + - post-merge +repos: + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.5.0 + hooks: + - id: check-toml + - id: check-json + - id: check-yaml + - id: debug-statements + - id: check-merge-conflict + - id: pretty-format-json + args: [--autofix, '--no-sort-keys'] + exclude: .ipynb + - id: end-of-file-fixer + - id: trailing-whitespace + exclude: .bumpversion.cfg + - repo: https://github.com/timothycrosley/isort + rev: 5.13.2 + hooks: + - id: isort + - repo: https://github.com/psf/black + rev: 24.2.0 + hooks: + - id: black + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.2.1 + hooks: + - id: ruff + args: [ --fix ] + - repo: https://github.com/citation-file-format/cffconvert + rev: 5295f87c0e261da61a7b919fc754e3a77edd98a7 + hooks: + - id: validate-cff + - repo: https://github.com/python-poetry/poetry + rev: 1.7.1 + hooks: + - id: poetry-check + - id: poetry-install diff --git a/.readthedocs.yml b/.readthedocs.yml new file mode 100644 index 0000000..ab4d0dd --- /dev/null +++ b/.readthedocs.yml @@ -0,0 +1,17 @@ +version: 2 + +build: + os: ubuntu-22.04 + tools: + python: "3.9" + +formats: all + +sphinx: + configuration: docs/conf.py + +python: + install: + - requirements: docs/requirements.txt + - method: pip + path: . diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 0000000..01633eb --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,15 @@ +# Changelog +All notable changes to this project will be documented in this file. + +The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), +and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). + + +## [Unreleased] + +## [0.1.0] - 2024-07-06 +### Added +- First release on PyPI. + +[Unreleased]: https://github.com/rserial/flintpy/compare/v0.1.0...HEAD +[0.1.0]: https://github.com/rserial/flintpy/compare/releases/tag/v0.1.0 diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..101fa8e --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,24 @@ +# This CITATION.cff file was generated with cffinit. +# Visit https://bit.ly/cffinit to generate yours today! + +cff-version: 1.2.0 +title: Flintpy +message: >- + If you use this software, please cite it using the + metadata from this file. +type: software +authors: + - given-names: Raquel + family-names: Serial + alias: fedejaure +identifiers: + - type: url + value: >- + https://github.com/rserial/flintpy/releases/tag/v0.1.0 + description: The Software Heritage link for version 0.1.0. +repository-code: 'https://github.com/rserial/flintpy' +abstract: Cookiecutter template for a modern Python package. +keywords: + - flintpy +license: MIT +version: 0.1.0 diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 0000000..a02f5ac --- /dev/null +++ b/CODE_OF_CONDUCT.md @@ -0,0 +1,133 @@ + +# Contributor Covenant Code of Conduct + +## Our Pledge + +We as members, contributors, and leaders pledge to make participation in our +community a harassment-free experience for everyone, regardless of age, body +size, visible or invisible disability, ethnicity, sex characteristics, gender +identity and expression, level of experience, education, socio-economic status, +nationality, personal appearance, race, caste, color, religion, or sexual +identity and orientation. + +We pledge to act and interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community. + +## Our Standards + +Examples of behavior that contributes to a positive environment for our +community include: + +* Demonstrating empathy and kindness toward other people +* Being respectful of differing opinions, viewpoints, and experiences +* Giving and gracefully accepting constructive feedback +* Accepting responsibility and apologizing to those affected by our mistakes, + and learning from the experience +* Focusing on what is best not just for us as individuals, but for the overall + community + +Examples of unacceptable behavior include: + +* The use of sexualized language or imagery, and sexual attention or advances of + any kind +* Trolling, insulting or derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or email address, + without their explicit permission +* Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Enforcement Responsibilities + +Community leaders are responsible for clarifying and enforcing our standards of +acceptable behavior and will take appropriate and fair corrective action in +response to any behavior that they deem inappropriate, threatening, offensive, +or harmful. + +Community leaders have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are +not aligned to this Code of Conduct, and will communicate reasons for moderation +decisions when appropriate. + +## Scope + +This Code of Conduct applies within all community spaces, and also applies when +an individual is officially representing the community in public spaces. +Examples of representing our community include using an official email address, +posting via an official social media account, or acting as an appointed +representative at an online or offline event. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported to the community leaders responsible for enforcement at +rserial. +All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the +reporter of any incident. + +## Enforcement Guidelines + +Community leaders will follow these Community Impact Guidelines in determining +the consequences for any action they deem in violation of this Code of Conduct: + +### 1. Correction + +**Community Impact**: Use of inappropriate language or other behavior deemed +unprofessional or unwelcome in the community. + +**Consequence**: A private, written warning from community leaders, providing +clarity around the nature of the violation and an explanation of why the +behavior was inappropriate. A public apology may be requested. + +### 2. Warning + +**Community Impact**: A violation through a single incident or series of +actions. + +**Consequence**: A warning with consequences for continued behavior. No +interaction with the people involved, including unsolicited interaction with +those enforcing the Code of Conduct, for a specified period of time. This +includes avoiding interactions in community spaces as well as external channels +like social media. Violating these terms may lead to a temporary or permanent +ban. + +### 3. Temporary Ban + +**Community Impact**: A serious violation of community standards, including +sustained inappropriate behavior. + +**Consequence**: A temporary ban from any sort of interaction or public +communication with the community for a specified period of time. No public or +private interaction with the people involved, including unsolicited interaction +with those enforcing the Code of Conduct, is allowed during this period. +Violating these terms may lead to a permanent ban. + +### 4. Permanent Ban + +**Community Impact**: Demonstrating a pattern of violation of community +standards, including sustained inappropriate behavior, harassment of an +individual, or aggression toward or disparagement of classes of individuals. + +**Consequence**: A permanent ban from any sort of public interaction within the +community. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], +version 2.1, available at +[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1]. + +Community Impact Guidelines were inspired by +[Mozilla's code of conduct enforcement ladder][Mozilla CoC]. + +For answers to common questions about this code of conduct, see the FAQ at +[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at +[https://www.contributor-covenant.org/translations][translations]. + +[homepage]: https://www.contributor-covenant.org +[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html +[Mozilla CoC]: https://github.com/mozilla/diversity +[FAQ]: https://www.contributor-covenant.org/faq +[translations]: https://www.contributor-covenant.org/translations diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000..b0d2a81 --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,75 @@ +# Contributing to Flintpy + +👏🎉 First off all, Thanks for your interest in contributing to our project! 🎉👏 + +The following is a set of guidelines for contributing to Flintpy. These are +mostly guidelines, not rules. Use your best judgment, and feel free to propose changes to this document in a pull request. + +## Code of Conduct + +We take our open source community seriously and hold ourselves and other contributors to high standards of communication. By participating and contributing to this project, you agree to uphold our [Code of Conduct](CODE_OF_CONDUCT.md). + +## Getting Started + +### Requirements + +We use `poetry` to manage and install dependencies. [Poetry](https://python-poetry.org/) provides a custom installer that will install `poetry` isolated from the rest of your system. + +``` +curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/install-poetry.py | python - +``` + +We'll also need `nox` for automated testing in multiple Python environments so [install that too](https://nox.thea.codes/en/stable/). + +To install the local development requirements inside a virtual environment run: + +``` +$ poetry install +$ poetry run inv install-hooks +``` + +> For more information about `poetry` check the [docs](https://python-poetry.org/docs/). + +We use [invoke](http://www.pyinvoke.org/) to wrap up some useful tasks like formatting, linting, testing and more. + +Execute `inv[oke] --list` to see the list of available commands. + +## Contributing + +### Issues + +We use GitHub issues to track public bugs/enhancements. Report a new one by [opening a new issue](https://github.com/rserial/flintpy/issues). + +In this repository, we provide a couple of templates for you to fill in for: + +* Bugs +* Feature Requests/Enhancements + +Please read each section in the templates and provide as much information as you can. Please do not put any sensitive information, +such as personally identifiable information, connection strings or cloud credentials. The more information you can provide, the better we can help you. + +### Pull Requests + +Please follow these steps to have your contribution considered by the maintainers: + +1. Fork the repo and create your branch locally with a succinct but descriptive name. +2. Add tests for the new changes +3. Edit documentation if you have changed something significant +4. Make sure to follow the [styleguides](#styleguides) +5. Open a PR in our repository and follow the PR template so that we can efficiently review the changes +6. After you submit your pull request, verify that all status checks are passing + +While the prerequisites above must be satisfied prior to having your pull request reviewed, the reviewer(s) may ask you to complete additional design +work, tests, or other changes before your pull request can be ultimately accepted. + +## Styleguides + +### Python Code Style + +All Python code is linted with [Ruff](https://github.com/astral-sh/ruff) and formated with +[Isort](https://github.com/PyCQA/isort) and [Black](https://github.com/psf/black). You can +execute `inv[oke] lint` and `inv[oke] format`. + +## Additional Notes + +If you have any question feel free to contact us at rserial. diff --git a/LICENSE.rst b/LICENSE.rst new file mode 100644 index 0000000..1686c93 --- /dev/null +++ b/LICENSE.rst @@ -0,0 +1,33 @@ + +GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Python implementation of FLINT algorithm for NMR relaxation data. + Copyright (C) 2024 Raquel Serial + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/README.md b/README.md new file mode 100644 index 0000000..085c82d --- /dev/null +++ b/README.md @@ -0,0 +1,42 @@ + +# Flintpy + + +
+ +[![PyPI - Version](https://img.shields.io/pypi/v/flintpy.svg)](https://pypi.python.org/pypi/flintpy) +[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/flintpy.svg)](https://pypi.python.org/pypi/flintpy) +[![Tests](https://github.com/rserial/flintpy/workflows/tests/badge.svg)](https://github.com/rserial/flintpy/actions?workflow=tests) +[![Codecov](https://codecov.io/gh/rserial/flintpy/branch/main/graph/badge.svg)](https://codecov.io/gh/rserial/flintpy) +[![Read the Docs](https://readthedocs.org/projects/flintpy/badge/)](https://flintpy.readthedocs.io/) +[![PyPI - License](https://img.shields.io/pypi/l/flintpy.svg)](https://pypi.python.org/pypi/flintpy) + +[![Black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) +[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit) +[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](https://www.contributor-covenant.org/version/2/1/code_of_conduct/) + +
+ + +Python implementation of FLINT algorithm for NMR relaxation data. + + +* GitHub repo: +* Documentation: +* Free software: GNU General Public License v3 + + +## Features + +* TODO + +## Quickstart + +TODO + +## Credits + +This package was created with [Cookiecutter][cookiecutter] and the [fedejaure/cookiecutter-modern-pypackage][cookiecutter-modern-pypackage] project template. + +[cookiecutter]: https://github.com/cookiecutter/cookiecutter +[cookiecutter-modern-pypackage]: https://github.com/fedejaure/cookiecutter-modern-pypackage diff --git a/SECURITY.md b/SECURITY.md new file mode 100644 index 0000000..1b9c953 --- /dev/null +++ b/SECURITY.md @@ -0,0 +1,29 @@ +# Security Policy + +We takes the security of our software products seriously. + +If you believe you have found a security vulnerability, please report it to us as described below. + +## Reporting Security Issues + +**Please do not report security vulnerabilities through public GitHub issues.** + +Report security vulnerabilities by emailing the lead maintainer at rserial. + +You should receive a response within 24 hours. If for some reason you do not, please follow up via email to ensure we received your original message. + +Please include the requested information listed below (as much as you can provide) to help us better understand the nature and scope of the possible issue: + + * Type of issue (e.g. buffer overflow, SQL injection, cross-site scripting, etc.) + * Full paths of source file(s) related to the manifestation of the issue + * The location of the affected source code (tag/branch/commit or direct URL) + * Any special configuration required to reproduce the issue + * Step-by-step instructions to reproduce the issue + * Proof-of-concept or exploit code (if possible) + * Impact of the issue, including how an attacker might exploit the issue + +This information will help us triage your report more quickly. + +## Preferred Languages + +We prefer all communications to be in English. diff --git a/codecov.yml b/codecov.yml new file mode 100644 index 0000000..57c07c4 --- /dev/null +++ b/codecov.yml @@ -0,0 +1,10 @@ +coverage: + status: + project: + default: + target: "100" + patch: + default: + target: "100" +comment: + require_changes: true diff --git a/docs/_static/custom.css b/docs/_static/custom.css new file mode 100644 index 0000000..0d98645 --- /dev/null +++ b/docs/_static/custom.css @@ -0,0 +1 @@ +.logo a { overflow-wrap: normal } diff --git a/docs/changelog.md b/docs/changelog.md new file mode 120000 index 0000000..04c99a5 --- /dev/null +++ b/docs/changelog.md @@ -0,0 +1 @@ +../CHANGELOG.md \ No newline at end of file diff --git a/docs/conf.py b/docs/conf.py new file mode 100644 index 0000000..f9595c7 --- /dev/null +++ b/docs/conf.py @@ -0,0 +1,73 @@ +"""Sphinx configuration.""" + +# Configuration file for the Sphinx documentation builder. +# +# This file only contains a selection of the most common options. For a full +# list see the documentation: +# https://www.sphinx-doc.org/en/master/usage/configuration.html + + +# If extensions (or modules to document with autodoc) are in another +# directory, add these directories to sys.path here. If the directory is +# relative to the documentation root, use os.path.abspath to make it +# absolute, like shown here. +import flintpy + +# -- Project information ----------------------------------------------------- + +# General information about the project. +project = "flintpy" +copyright = "2024, Raquel Serial" # noqa: A001 +author = "Raquel Serial" +# The version info for the project you're documenting, acts as replacement +# for |version| and |release|, also used in various other places throughout +# the built documents. +# +# The short X.Y version. +version = flintpy.__version__ +# The full version, including alpha/beta/rc tags. +release = flintpy.__version__ + +# -- General configuration --------------------------------------------------- + +# Add any Sphinx extension module names here, as strings. They can be +# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom +# ones. +extensions = [ + "sphinx.ext.autodoc", + "sphinx.ext.viewcode", + "sphinx.ext.napoleon", + "recommonmark", +] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ["_templates"] + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +# This pattern also affects html_static_path and html_extra_path. +exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] + + +# -- Options for HTML output ------------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +# +html_theme = "alabaster" + +# Theme options are theme-specific and customize the look and feel of a theme +# further. For a list of options available for each theme, see the +# documentation. +html_theme_options = { + "github_user": "rserial", + "github_repo": "flintpy", + "github_banner": True, + "show_related": False, + "fixed_sidebar": True, +} + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ["_static"] diff --git a/docs/index.rst b/docs/index.rst new file mode 100644 index 0000000..86fae57 --- /dev/null +++ b/docs/index.rst @@ -0,0 +1,22 @@ +Welcome to Flintpy's documentation! +=========================================================== + +.. toctree:: + :maxdepth: 2 + + readme + installation + usage + modules + changelog + +Indices and tables +================== +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` + +.. toctree:: + :hidden: + + License diff --git a/docs/installation.rst b/docs/installation.rst new file mode 100644 index 0000000..de6678a --- /dev/null +++ b/docs/installation.rst @@ -0,0 +1,23 @@ +.. highlight:: shell + +============ +Installation +============ + + +Stable release +-------------- + +To install flintpy, run this command in your terminal: + +.. code-block:: console + + $ pip install flintpy + +This is the preferred method to install flintpy, as it will always install the most recent stable release. + +If you don't have `pip`_ installed, this `Python installation guide`_ can guide +you through the process. + +.. _pip: https://pip.pypa.io +.. _Python installation guide: http://docs.python-guide.org/en/latest/starting/installation/ diff --git a/docs/license.rst b/docs/license.rst new file mode 120000 index 0000000..19cdae7 --- /dev/null +++ b/docs/license.rst @@ -0,0 +1 @@ +../LICENSE.rst \ No newline at end of file diff --git a/docs/readme.md b/docs/readme.md new file mode 120000 index 0000000..32d46ee --- /dev/null +++ b/docs/readme.md @@ -0,0 +1 @@ +../README.md \ No newline at end of file diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 0000000..165c943 --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1,2 @@ +sphinx==7.2.6 +recommonmark==0.7.1 diff --git a/docs/usage.rst b/docs/usage.rst new file mode 100644 index 0000000..720b4f2 --- /dev/null +++ b/docs/usage.rst @@ -0,0 +1,7 @@ +===== +Usage +===== + +To use flintpy in a project:: + + import flintpy diff --git a/noxfile.py b/noxfile.py new file mode 100644 index 0000000..933664c --- /dev/null +++ b/noxfile.py @@ -0,0 +1,50 @@ +"""Nox sessions.""" + +import platform + +import nox +from nox_poetry import Session, session + +nox.options.sessions = ["tests", "mypy"] +python_versions = ["3.9", "3.10", "3.11", "3.12"] + + +@session(python=python_versions) +def tests(session: Session) -> None: + """Run the test suite.""" + session.install(".") + session.install("invoke", "pytest", "xdoctest", "coverage[toml]", "pytest-cov") + try: + session.run( + "inv", + "tests", + env={ + "COVERAGE_FILE": f".coverage.{platform.system()}.{platform.python_version()}", + }, + ) + finally: + if session.interactive: + session.notify("coverage") + + +@session +def coverage(session: Session) -> None: + """Produce the coverage report.""" + args = session.posargs if session.posargs and 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["flintpy"] +classifiers=[ + "Development Status :: 2 - Pre-Alpha", + "Intended Audience :: Developers", + "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", + "Natural Language :: English", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", +] + +[tool.poetry.urls] +"Bug Tracker" = "https://github.com/rserial/flintpy/issues" + +[tool.poetry.dependencies] +python = "<3.13,>=3.9" + +[tool.poetry.group.dev.dependencies] +pre-commit = "^3.6.1" +invoke = "^2.2.0" +bump2version = "^1.0.1" +watchdog = {version = "^4.0.0", extras = ["watchmedo"]} + +[tool.poetry.group.test.dependencies] +pytest = "^8.0.1" +xdoctest = "^1.1.3" +coverage = {version = "^7.4.1", extras = ["toml"]} +pytest-cov = "^4.1.0" + +[tool.poetry.group.linters.dependencies] +isort = "^5.13.2" +black = "^24.2.0" +ruff = "^0.2.1" + +[tool.poetry.group.security.dependencies] +safety = "^3.0.1" + +[tool.poetry.group.typing.dependencies] +mypy = "^1.8.0" + +[tool.poetry.group.docs.dependencies] +sphinx = "^7.2.6" +recommonmark = "^0.7.1" + +[tool.coverage.paths] +source = ["src", "*/site-packages"] + +[tool.coverage.run] +branch = true +source = ["flintpy"] + +[tool.coverage.report] +fail_under = 100 +exclude_lines = [ + "pragma: no cover", + "def __repr__", + "if self.debug", + "if settings.DEBUG:", + "raise AssertionError", + "raise NotImplementedError", + "if 0:", + "if __name__ == __main__:" +] +show_missing = true + +[tool.coverage.html] +directory = "htmlcov" + +[tool.ruff] +target-version = "py39" +output-format = "full" +line-length = 99 +fix = true +extend-exclude = [ + "docs/*", +] + +[tool.ruff.lint] +select = [ + "E", "F", "W", # flake8 + "C", # mccabe + "I", # isort + "N", # pep8-naming + "D", # flake8-docstrings + "ANN", # flake8-annotations + "S", # flake8-bandit + "BLE", # flake8-blind-except + "B", # flake8-bugbear + "A", # flake8-builtins + "G", # flake8-logging-format + "ERA", # eradicate + "ISC", # flake8-implicit-str-concat + "RUF", # Ruff-specific rules +] +ignore = ["ANN101"] +unfixable = [ + "ERA", # Don't remove commented-out code +] + +[tool.ruff.lint.per-file-ignores] +"tests/*" = ["S101"] + +[tool.ruff.lint.mccabe] +max-complexity = 10 + +[tool.ruff.lint.isort] +known-first-party = ["flintpy"] + +[tool.ruff.lint.pydocstyle] +convention = "google" + +[tool.isort] +multi_line_output = 3 +include_trailing_comma = true +force_grid_wrap = 0 +use_parentheses = true +line_length = 99 +known_third_party = ["invoke", "nox", "nox_poetry"] + +[tool.black] +line-length = 99 +target-version = ["py39"] + +[tool.mypy] +warn_return_any = true +warn_unused_configs = true + +[[tool.mypy.overrides]] +module = ["pytest.*", "invoke.*", "nox.*", "nox_poetry.*"] +allow_redefinition = false +check_untyped_defs = true +ignore_errors = false +ignore_missing_imports = true +implicit_reexport = true +local_partial_types = true +strict_optional = true +strict_equality = true +no_implicit_optional = true +warn_unused_ignores = true +warn_unreachable = true +warn_no_return = true + +[build-system] +requires = ["poetry>=0.12"] +build-backend = "poetry.masonry.api" diff --git a/src/flintpy/__init__.py b/src/flintpy/__init__.py new file mode 100644 index 0000000..f0d6d59 --- /dev/null +++ b/src/flintpy/__init__.py @@ -0,0 +1,5 @@ +"""Top-level package for flintpy.""" + +__author__ = """Raquel Serial""" +__email__ = "raquelserial@gmail.com" +__version__ = "0.1.0" diff --git a/src/flintpy/flintpy.py b/src/flintpy/flintpy.py new file mode 100644 index 0000000..dd0b80e --- /dev/null +++ b/src/flintpy/flintpy.py @@ -0,0 +1 @@ +"""Main module.""" diff --git a/src/flintpy/py.typed b/src/flintpy/py.typed new file mode 100644 index 0000000..e69de29 diff --git a/tasks.py b/tasks.py new file mode 100644 index 0000000..cd6bc1c --- /dev/null +++ b/tasks.py @@ -0,0 +1,171 @@ +"""Tasks for maintaining the project. + +Execute 'invoke --list' for guidance on using Invoke +""" + +import platform +import webbrowser +from pathlib import Path +from typing import Optional + +from invoke import call, task +from invoke.context import Context +from invoke.runners import Result + +ROOT_DIR = Path(__file__).parent +DOCS_DIR = ROOT_DIR.joinpath("docs") +DOCS_BUILD_DIR = DOCS_DIR.joinpath("_build") +DOCS_INDEX = DOCS_BUILD_DIR.joinpath("index.html") +COVERAGE_FILE = ROOT_DIR.joinpath(".coverage") +COVERAGE_DIR = ROOT_DIR.joinpath("htmlcov") +COVERAGE_REPORT = COVERAGE_DIR.joinpath("index.html") +SOURCE_DIR = ROOT_DIR.joinpath("src/flintpy") +TEST_DIR = ROOT_DIR.joinpath("tests") +PYTHON_TARGETS = [ + SOURCE_DIR, + TEST_DIR, + ROOT_DIR.joinpath("noxfile.py"), + Path(__file__), +] +PYTHON_TARGETS_STR = " ".join([str(p) for p in PYTHON_TARGETS]) + + +def _run(c: Context, command: str) -> Optional[Result]: + return c.run(command, pty=platform.system() != "Windows") + + +@task() +def clean_build(c: Context) -> None: + """Clean up files from package building.""" + _run(c, "rm -fr build/") + _run(c, "rm -fr dist/") + _run(c, "rm -fr .eggs/") + _run(c, "find . -name '*.egg-info' -exec rm -fr {} +") + _run(c, "find . -name '*.egg' -exec rm -f {} +") + + +@task() +def clean_python(c: Context) -> None: + """Clean up python file artifacts.""" + _run(c, "find . -name '*.pyc' -exec rm -f {} +") + _run(c, "find . -name '*.pyo' -exec rm -f {} +") + _run(c, "find . -name '*~' -exec rm -f {} +") + _run(c, "find . -name '__pycache__' -exec rm -fr {} +") + + +@task() +def clean_tests(c: Context) -> None: + """Clean up files from testing.""" + _run(c, f"rm -f {COVERAGE_FILE}") + _run(c, f"rm -fr {COVERAGE_DIR}") + _run(c, "rm -fr .pytest_cache") + + +@task() +def clean_docs(c: Context) -> None: + """Clean up files from documentation builds.""" + _run(c, f"rm -fr {DOCS_BUILD_DIR}") + + +@task(pre=[clean_build, clean_python, clean_tests, clean_docs]) +def clean(c: Context) -> None: + """Run all clean sub-tasks.""" + + +@task() +def install_hooks(c: Context) -> None: + """Install pre-commit hooks.""" + _run(c, "poetry run pre-commit install") + + +@task() +def hooks(c: Context) -> None: + """Run pre-commit hooks.""" + _run(c, "poetry run pre-commit run --all-files") + + +@task(name="format", help={"check": "Checks if source is formatted without applying changes"}) +def format_(c: Context, check: bool = False) -> None: + """Format code.""" + isort_options = ["--check-only", "--diff"] if check else [] + _run(c, f"poetry run isort {' '.join(isort_options)} {PYTHON_TARGETS_STR}") + black_options = ["--diff", "--check"] if check else ["--quiet"] + _run(c, f"poetry run black {' '.join(black_options)} {PYTHON_TARGETS_STR}") + + +@task() +def ruff(c: Context) -> None: + """Run ruff.""" + _run(c, f"poetry run ruff check {PYTHON_TARGETS_STR}") + + +@task() +def security(c: Context) -> None: + """Run security related checks.""" + _run( + c, + "poetry export --with dev --format=requirements.txt --without-hashes | " + "poetry run safety check --stdin --full-report", + ) + + +@task(pre=[ruff, security, call(format_, check=True)]) +def lint(c: Context) -> None: + """Run all linting.""" + + +@task() +def mypy(c: Context) -> None: + """Run mypy.""" + _run(c, f"poetry run mypy {PYTHON_TARGETS_STR}") + + +@task() +def tests(c: Context) -> None: + """Run tests.""" + pytest_options = ["--xdoctest", "--cov", "--cov-report=", "--cov-fail-under=0"] + _run(c, f"poetry run pytest {' '.join(pytest_options)} {TEST_DIR} {SOURCE_DIR}") + + +@task( + help={ + "fmt": "Build a local report: report, html, json, annotate, html, xml.", + "open_browser": "Open the coverage report in the web browser (requires --fmt html)", + } +) +def coverage(c: Context, fmt: str = "report", open_browser: bool = False) -> None: + """Create coverage report.""" + if any(Path().glob(".coverage.*")): + _run(c, "poetry run coverage combine") + _run(c, f"poetry run coverage {fmt} -i") + if fmt == "html" and open_browser: + webbrowser.open(COVERAGE_REPORT.as_uri()) + + +@task( + help={ + "serve": "Build the docs watching for changes", + "open_browser": "Open the docs in the web browser", + } +) +def docs(c: Context, serve: bool = False, open_browser: bool = False) -> None: + """Build documentation.""" + _run(c, f"sphinx-apidoc -o {DOCS_DIR} {SOURCE_DIR}") + build_docs = f"sphinx-build -b html {DOCS_DIR} {DOCS_BUILD_DIR}" + _run(c, build_docs) + if open_browser: + webbrowser.open(DOCS_INDEX.absolute().as_uri()) + if serve: + _run(c, f"poetry run watchmedo shell-command -p '*.rst;*.md' -c '{build_docs}' -R -D .") + + +@task( + help={ + "part": "Part of the version to be bumped.", + "dry_run": "Don't write any files, just pretend. (default: False)", + } +) +def version(c: Context, part: str, dry_run: bool = False) -> None: + """Bump version.""" + bump_options = ["--dry-run"] if dry_run else [] + _run(c, f"poetry run bump2version {' '.join(bump_options)} {part}") diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..2e61d5e --- /dev/null +++ b/tests/__init__.py @@ -0,0 +1 @@ +"""Unit test package for flintpy.""" diff --git a/tests/test_flintpy.py b/tests/test_flintpy.py new file mode 100644 index 0000000..309456a --- /dev/null +++ b/tests/test_flintpy.py @@ -0,0 +1,18 @@ +"""Tests for `flintpy` module.""" + +from typing import Generator + +import pytest + +import flintpy + + +@pytest.fixture +def version() -> Generator[str, None, None]: + """Sample pytest fixture.""" + yield flintpy.__version__ + + +def test_version(version: str) -> None: + """Sample pytest test function with the pytest fixture as an argument.""" + assert version == "0.1.0"