Contributing

Development Setup

git clone https://github.com/LATIS-medical-Imaging/medical-image-std.git
cd medical-image-std
python -m venv .venv
source .venv/bin/activate
pip install -e ".[dev]"

Or with uv:

uv pip install -e ".[dev]"

Running Tests

pytest medical_image/tests/ -v

The test suite includes 136+ tests covering:

  • Image loading and format handling

  • Processing operations (filters, thresholds, morphology)

  • Algorithm correctness (FEBDS, K-Means, FCM, PFCM, Deep Segmentation)

  • Patch grid creation and reconstruction

  • Dataset loading and sample format

  • Annotation serialization

  • Mammography preprocessing

Code Style

The project uses Black for formatting and Ruff for linting:

black medical_image/
ruff check medical_image/

CI runs Black and pytest on Python 3.11 and 3.12.

Pull Request Workflow

  1. Fork the repository.

  2. Create a feature branch from master.

  3. Write tests for new functionality.

  4. Ensure pytest and black --check pass.

  5. Open a pull request with a clear description.

Building Documentation

pip install -e ".[docs]"
sphinx-build -b html docs docs/_build/html

Open docs/_build/html/index.html to preview.