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CONTRIBUTING.md

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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
git clone git@github.com:jfnavarro/st_pipeline.git
  1. Ensure poetry is installed.
  2. Ensure STAR and samtools are installed.
  3. Install dependencies and start your virtualenv:
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:

poetry config virtualenvs.create false
  1. Create a branch for local development:
git checkout -b name-of-your-bugfix-or-feature

Now you can make your changes locally.

  1. When you're done making changes, check that your changes pass the tests, including testing other Python versions, with pytest:
poetry run pytest
  1. Commit your changes and push your branch to GitHub:
git add .
git commit -m "Your detailed description of your changes."
git push origin name-of-your-bugfix-or-feature
  1. 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:

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

make format

To run linting tools

make lint

To run the tests

make unittet

To run the tests with coverage

make coverage

To clean the temporary files and cache

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). Make sure you have updated the version in pyproject.toml and stpipeline/version.py. Then run:

git tag <version> -m "message"
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:

poetry run mkdocs build

Publish package

Ensure that you have configured your PyPi tokens.

poetry config repositories.testpypi https://test.pypi.org/legacy/
poetry config repositories.pypi https://upload.pypi.org/legacy/

and

poetry config pypi-token.pypi YOUR_PYPI_API_TOKEN
poetry config pypi-token.testpypi YOUR_TEST_PYPI_API_TOKEN

Then run:

poetry build
poetry publish -r test-pypi # optional
poetry publish