Contributing

Contributing#

Thank you for your interest in contributing to GATAC!

Development setup#

git clone https://github.com/Soldatov-Lab/gatac.git
cd GATAC

# Install in editable mode with all dev extras
uv sync --extra cuda12

Running tests#

Tests are located in tests/ (unit tests) and in the reproducibility/ submodule (tracked at reproducibility/) for integration/benchmark tests.

After cloning, initialise the submodule once:

git submodule update --init --recursive

# Unit tests
uv run pytest tests/

# Reproducibility benchmarks (requires GPU + data)
cd reproducibility
pixi run pytest test/

After any change to a preprocessing or analysis function, run the related reproducibility test:

cd reproducibility
pixi run pytest test/tile_matrix.py
pixi run pytest test/spectral_embedding.py

Code style#

  • Formatter: ruff format

  • Linter: ruff check

  • Type hints: encouraged for all public functions

  • Docstrings: NumPy style

uv run ruff format gatac/
uv run ruff check gatac/

Submitting changes#

  1. Fork the repository and create a feature branch.

  2. Make your changes with appropriate tests.

  3. Ensure all existing tests pass.

  4. Open a pull request with a clear description of the changes.

Reporting issues#

Please open a GitHub issue with:

  • A minimal reproducible example

  • GATAC version (gatac --version)

  • GPU model and CUDA version

  • Error traceback

Documentation#

The docs live in docs/. To build locally:

uv sync --extra docs
cd docs
make html
# Open _build/html/index.html

Analysis notebooks live in the separate gatac-notebooks repository — see Tutorials for details.