Contributing

Contributing#

We welcome contributions to grassp! 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/grassp.git
cd grassp

  3. Create a development environment:

This installs the package with the -e option and development and documentation dependencies as well as pre-commit hooks.

make setup-develop

Testing#

  1. Tests can be added to grassp/tests

  2. Run the tests:

    pytest grassp/tests

Code Style#

Documentation#

  • Update docstrings for any changed functions.

  • Update tutorials if adding new features.

  • Build docs locally to check formatting:

    cd docs
# Optional (if running into errors): make clean
make html

Adding New public functions#

When adding support for new functionality:

  1. Add the code for the function in the most appropriate submodule

    1. preprocessing is for data filtering, enrichment, qc

    2. tools is for dimensionality reduction, classification, differential testing

    3. plotting is for visualization

    4. io is for reading from diffferent sources and writing outputs

  2. Make sure you follow the recommended code style and describe the function and parameters accurately with a docstring

  3. Expose the function as public by importing it in the __init__.py file of the submodule

  4. Add the function to the documentation by adding it to the api documentation.

  5. Build the documentation to check proper formatting.

  6. Add tests and run them

  7. Create a PR against main

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