Contributing

Contributing#

We welcome contributions to protdata! This guide will help you get started with contributing to the project.

Getting Started#

  1. Fork the repository on GitHub

  2. Clone your fork locally:

git clone https://github.com/yourusername/protdata.git
cd protdata

  1. Create a development environment:

pip install -e ".[dev,docs]"

Development Workflow#

  1. Make your changes

  2. Run the tests:

pytest tests/

Code Style#

  • Follow PEP 8 style guidelines

  • Use type hints where appropriate

  • Add docstrings to all public functions

  • Use numpy-style docstrings

Documentation#

  • Update docstrings for any changed functions

  • Update tutorials if adding new features

  • Build docs locally to check formatting:

cd docs
make html

Adding New Loaders#

When adding support for a new proteomics tool:

  1. Create a new loader function in protdata/io/

  2. Follow the existing pattern: - Return an AnnData object - Use consistent variable naming (X, obs, var, uns, layers) - Add proper error handling - Include comprehensive docstrings

  3. Add the loader to protdata/io/__init__.py

  4. Write comprehensive tests

  5. Add tutorial documentation

  6. Update the API reference

Contact#

Code of Conduct#

This project follows the standard open-source code of conduct. Be respectful and inclusive in all interactions.

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