Contributing¶

Before you start¶

Open an issue first — use the templates:

Setup¶

git clone https://github.com/BasselShaheen06/MLenz.git
cd MLenz
python -m venv venv
venv\Scripts\activate
pip install -r requirements.txt
pip install -r requirements-dev.txt

Hard boundary — never cross this¶

core/ modules must never import PyQt5, pyqtgraph, or matplotlib. They take a path or numpy array, return a VolumeData or numpy array. No side effects.

Adding a new file format¶

Add a loader function to core/loader.py and add the extension to guess_loader(). SimpleITK supports most formats (.mhd, .nrrd, .mha, .vtk) without extra code — just let it fall through to the SimpleITK fallback.

Code standards¶

Type hints on all public functions
Google-style docstrings
ruff check . must pass before committing
Run pytest — all tests must pass

Commit messages¶

feat: add pixel value readout on hover
fix: annotation stroke duplicated on fast mouse-move
docs: update Window/Level explanation in science.md
refactor: extract cine logic to CineController
test: add loader roundtrip test for NIfTI

Pull request checklist¶

[ ] ruff check . passes
[ ] pytest passes
[ ] core/ has no UI imports
[ ] Docs updated if behaviour changed
[ ] changelog.md updated