Contributing

Contributions are welcome — bug reports, documentation improvements, and pull requests all help.

Getting started

Fork and clone the repository, then install in editable mode with dev dependencies:

git clone https://github.com/GalKepler/qsiparc.git
cd qsiparc
pip install -e ".[dev]"

Running the test suite

pytest
pytest --cov=qsiparc   # with coverage

All tests use synthetic 10×10×10 NIfTI volumes — no real QSIRecon data required. Tests that exercise MRtrix3 integration are automatically skipped when tck2connectome is not on $PATH.

Code style

QSIParc uses ruff for linting and formatting, and mypy for type checking.

ruff check src tests   # lint
ruff format src tests  # format
mypy src/qsiparc       # type check

These checks run in CI on every push and pull request.

Submitting a pull request

1. Create a branch from main with a descriptive name (fix/discovery-glob, feat/add-afd-scalar, etc.).
2. Make your changes, add or update tests as needed.
3. Ensure pytest, ruff check, and mypy all pass locally.
4. Open a pull request against main and describe what changed and why.

Reporting bugs

Please open an issue on GitHub with:

• QSIParc version (qsiparc --version)
• Python and MRtrix3 versions
• A minimal reproduction (command, input layout, error message / traceback)

Out-of-scope contributions

QSIParc is intentionally narrow. The following are out of scope and pull requests for them will not be merged:

• Atlas warping or registration logic
• FreeSurfer surface metric extraction (see fsatlas)
• Reimplementing tck2connectome in Python
• Support for non-QSIRecon input layouts

If you are unsure whether a contribution fits, open an issue to discuss before writing code.

License

By contributing you agree that your work will be released under the MIT License.