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Contributing to ClinTAB-ML

Thanks for considering a contribution. This project follows the Code of Conduct — please read it before participating.

Dev setup

git clone https://github.com/Applied-Clinical-AI-Initiative/ClinTab-ML.git
cd ClinTab-ML
python3 -m venv .venv
source .venv/bin/activate
pip install -r requirements-dev.txt

requirements-dev.txt installs everything in requirements.txt plus pytest. See docs/install.md for more detail, including running the web app or the CLI once dependencies are installed.

Running the tests

pytest tests/ -v

The suite covers clintab/stats.py, clintab/epi.py, clintab/ml.py, and clintab/spline.py. Any change to those modules should come with a test covering the new behavior, and any bug fix should come with a test that would have caught it. clintab/plots.py, clintab/store.py, app.py, and routes.py aren't currently under test — a PR adding coverage there is welcome.

CI (.github/workflows/tests.yml) runs this same suite on every push and pull request against main, across Python 3.10 and 3.12.

Code style

There's no configured linter or formatter in this repo yet. Match the existing style in the file you're editing: minimal comments (only where the why isn't obvious from the code), no unused imports, and keep Flask/HTTP concerns in routes.py / app.py out of clintab/ — those modules are pure Python (pandas/numpy/sklearn in, plain dicts/DataFrames out) so they stay importable and testable without a running server.

Branch and PR conventions

  • One logical change per branch and per PR — don't bundle unrelated fixes together.
  • Branch off an up-to-date main: 
    git fetch origin
git checkout main
git merge origin/main
git checkout -b <short-description>
  • Open an issue describing the bug or feature before starting work on anything non-trivial, and reference it in your commits and PR (Closes #123) so it closes automatically on merge.
  • Fill in the PR template — summary, linked issue, and the tests/docs/CI checklist.
  • Keep commits scoped and messages descriptive; squash-merge is fine for keeping main's history clean.

Reporting bugs / requesting features

Use the issue templates under New Issue on GitHub — bug report or feature request, whichever fits. Include reproduction steps for bugs, and the problem you're trying to solve (not just the solution) for feature requests.