Contributing

Welcome to cellarr-se. Contributions of all kinds are appreciated — bug reports, documentation improvements, and code changes.

All contributors are expected to be open, considerate, reasonable, and respectful. When in doubt, the Python Software Foundation’s Code of Conduct is a good reference.

Issue Reports

If you encounter a bug or have a feature request, please open an issue on the issue tracker. Include:

  • Your operating system and Python version

  • Steps to reproduce the problem

  • A minimal example that demonstrates the issue

Documentation Improvements

Documentation lives in the docs/ folder alongside the source code. To build it locally:

tox -e docs
python3 -m http.server --directory docs/_build/html

Then open http://localhost:8000 in your browser.

Code Contributions

Set up a development environment

git clone https://github.com/CellArr/cellarr-se.git
cd cellarr-se
pip install -e ".[testing]"

Or with micromamba/conda:

micromamba create -n cellarr-se -c conda-forge python=3.11 pip -y
micromamba run -n cellarr-se pip install -e ".[testing]"

Workflow

  1. Open an issue to discuss non-trivial changes before starting work.

  2. Create a branch:

    git checkout -b my-feature

  3. Make your changes. Add unit tests for new behaviour.

  4. Run the test suite:

    pytest tests/
# or via tox
tox

  5. Run the linter:

    ruff check src/ tests/
ruff format --check src/ tests/

  6. Commit and push, then open a pull request against main.

Releases (maintainers)

  1. Ensure all tests pass on main.

  2. Tag the commit: git tag v0.1.0 && git push origin v0.1.0

  3. The CI pipeline will build the wheel and publish to PyPI automatically on tag push. Requires TWINE_USERNAME and TWINE_PASSWORD set as CI/CD variables (TWINE_USERNAME=__token__, TWINE_PASSWORD=<your-pypi-token>).

Note

This project was scaffolded with PyScaffold and BiocSetup.