Contributing

We welcome contributions to TwinWeaver! Please follow these steps to contribute.

Development Setup

1. Clone the repository and install dependencies:

   git clone https://github.com/MendenLab/TwinWeaver
   cd twinweaver
   pip install -e .
   pip install -r examples/requirements.txt
   pip install pre-commit pytest pytest-cov
   pip install -r docs/requirements.txt
   

2. Install pre-commit hooks:

   We use pre-commit to ensure code formatting and quality checks run before you commit.

   pre-commit install
   

Running Tests

We use pytest for testing. To run the full test suite:

pytest tests/

With coverage reporting:

pytest tests/ --cov=twinweaver --cov-report=html

Building Documentation

The documentation is built with mkdocs. To preview it locally:

mkdocs serve

Then open http://127.0.0.1:8000 in your browser.

Contribution Workflow

1. Create a New Branch: Always create a new branch for your feature or fix.

   git checkout -b feature/my-new-feature
   

2. Make Changes: Implement your feature or fix.

3. Run Tests & Linting: Ensure your code passes all tests and pre-commit hooks.

   pytest tests/
   pre-commit run --all-files
   

4. Submit a Merge Request:

   • Push your branch to the repository.
   • Open a Merge Request (Pull Request) against the main branch.
   • Describe your changes clearly in the MR description.

Code Style

• We follow PEP 8 for Python code style
• Use type hints where appropriate
• Write docstrings in NumPy format
• Add tests for new functionality

Reporting Issues

If you find a bug or have a feature request, please open an issue on GitHub.