Skip to content

CONTRIBUTING.md

Latest commit

 

History

History
30 lines (21 loc) · 947 Bytes

CONTRIBUTING.md

File metadata and controls

30 lines (21 loc) · 947 Bytes

Contributing

Contributions are welcome when they improve reproducibility, biological annotation, testing, or figure quality.

Development setup

python -m venv .venv
source .venv/bin/activate
pip install -e ".[dev]"
pytest -v
python run_pipeline.py
python scripts/validate_outputs.py

Pull request checklist

  • pytest -v passes.
  • ruff check passes for changed Python files.
  • python scripts/validate_outputs.py passes after any pipeline-output change.
  • Changed figures are regenerated intentionally.
  • Annotation changes document which marker genes or scoring rules changed.

Scientific correctness

Cluster labels and trajectory claims should be evidence-backed. If you change cell-type markers, Leiden resolution selection, QC thresholds, or pseudotime rooting, include the effect on cell counts and key figures.

Licence

By contributing, you agree that your contributions are licensed under the MIT licence.