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Contributing to BioContext

We love your input! We want to make contributing to BioContext as easy and transparent as possible, whether it's:

  • Reporting a bug
  • Discussing the current state of the code
  • Submitting a fix
  • Proposing new features
  • Becoming a maintainer

Development Process

We use GitHub to host code, to track issues and feature requests, as well as accept pull requests.

  1. Fork the repo and create your branch from main.
  2. If you've added code that should be tested, add tests.
  3. If you've changed APIs, update the documentation.
  4. Ensure the test suite passes.
  5. Make sure your code lints.
  6. Issue that pull request!

Any contributions you make will be under the MIT Software License

In short, when you submit code changes, your submissions are understood to be under the same MIT License that covers the project. Feel free to contact the maintainers if that's a concern.

Report bugs using GitHub's issue tracker

We use GitHub issues to track public bugs. Report a bug by opening a new issue; it's that easy!

Write bug reports with detail, background, and sample code

Great Bug Reports tend to have:

  • A quick summary and/or background
  • Steps to reproduce
    • Be specific!
    • Give sample code if you can.
  • What you expected would happen
  • What actually happens
  • Notes (possibly including why you think this might be happening, or stuff you tried that didn't work)

Development Setup

  1. Clone the repository with submodules:
git clone --recursive https://github.com/BioContext/BioContext-main.git
cd BioContext-main
  1. Set up development environment:
./setup.sh
  1. Run tests:
# Run tests for all submodules
for module in modules/*; do
    if [ -d "$module" ]; then
        (cd "$module" && python -m pytest)
    fi
done

Pull Request Process

  1. Update the README.md with details of changes to the interface, if applicable.
  2. Update the version numbers in any examples files and the README.md to the new version that this Pull Request would represent.
  3. The PR will be merged once you have the sign-off of at least one other developer.

Coding Style

  • Use Black for Python code formatting
  • Follow PEP 8 style guidelines
  • Write docstrings for all public functions
  • Comment your code where necessary

License

By contributing, you agree that your contributions will be licensed under its MIT License.