Contribute

Guidelines for contributing to SpinalfMRIprep development.

Getting Started

Development Setup

# Clone the repository
git clone https://github.com/SpinalfMRIprep/SpinalfMRIprep.git
cd SpinalfMRIprep

# Install in development mode
pip install poetry
poetry install

# Install pre-commit hooks
poetry run pre-commit install

Run Tests

# Run all tests
poetry run pytest

# Run specific test file
poetry run pytest tests/test_S1_input_verify.py

# Run with coverage
poetry run pytest --cov=spinalfmriprep

Development Workflow

Branch Naming

Commit Messages

Follow Conventional Commits:

feat: add slice-timing correction to S4
fix: handle missing JSON sidecar gracefully
docs: expand S1 method specification
test: add integration test for multi-session

Pull Request Process

1. Create a feature branch from main
2. Make your changes with tests
3. Run poetry run pytest to ensure tests pass
4. Run poetry run pre-commit run --all-files
5. Open a PR with clear description
6. Address review feedback
7. Squash and merge when approved

Code Style

Python

• Follow PEP 8
• Use type hints
• Docstrings in Google style
• Maximum line length: 100 characters

Pre-commit Hooks

The repository uses pre-commit for automated checks:

• ruff - Linting and formatting
• mypy - Type checking
• pytest - Test execution

Adding a New Step

To add a new processing step (e.g., S12):

1. Create the module: src/spinalfmriprep/S12_new_step.py

2. Implement required functions:

   def run_S12_new_step(...) -> StepResult:
       """Run the step."""
       ...
   
   def check_S12_new_step(...) -> StepResult:
       """Validate step outputs."""
       ...
   

3. Add CLI integration: Update src/spinalfmriprep/cli.py

4. Add tests: Create tests/test_S12_new_step.py

5. Add documentation: Create docs/methods/S12_new_step.md

6. Update navigation: Add to mkdocs.yml

Reporting Issues

Bug Reports

Please include:

• SpinalfMRIprep version (poetry run spinalfmriprep --version)
• Operating system
• Container runtime and version
• Minimal reproducible example
• Full error traceback

Feature Requests

Open a GitHub issue with:

• Use case description
• Proposed solution
• Alternatives considered

Contact

• GitHub Issues: SpinalfMRIprep/SpinalfMRIprep
• Discussions: Use GitHub Discussions for questions

Thank you for contributing to SpinalfMRIprep!