Developer Guide

Quick Start

# Clone and setup
git clone https://github.com/UNFmontreal/skullduggery.git
cd skullduggery
python -m venv venv
source venv/bin/activate
pip install -e ".[test,datalad]"

Project Structure

skullduggery/
├── src/skullduggery/
│   ├── run.py              # CLI entry point
│   ├── workflow.py         # Main defacing pipeline
│   ├── align.py            # ANTs registration
│   ├── mask.py             # Mask generation
│   ├── bids.py             # BIDS utilities
│   ├── template.py         # Template handling
│   ├── report.py           # Report generation
│   └── utils.py            # Helpers
├── tests/                  # Unit tests
├── docs/                   # Documentation
└── pyproject.toml          # Project config

Development Tasks

Tests

pytest tests/                           # All tests
pytest tests/test_bids.py -v            # Single file
pytest tests/ --cov=skullduggery        # With coverage

Code Quality

black src/skullduggery tests            # Format
flake8 src/skullduggery tests           # Lint
pre-commit install                      # Auto-checks

Documentation

cd docs
make html                               # Build docs

Docstring Format

Use Google-style docstrings:

def process_image(path: str, template: str) -> bool:
    """Brief one-liner description.

    More detailed explanation if needed.

    Args:
        path: Input file path.
        template: Template name.

    Returns:
        True if successful.

    Raises:
        ValueError: If inputs are invalid.
    """

Adding Features

Create feature branch from main
Write tests first
Implement feature
Run: pytest tests/ && flake8 src/
Update docs if needed
Submit PR

Dependencies

Core: templateflow, pybids, nibabel, antspyx, nitransforms, nireports, coloredlogs

Optional: datalad (DataLad support)

Dev: specified in pyproject.toml

Debugging

DEBUG=1 skullduggery /path/to/dataset --debug debug

Or add breakpoint in code:

import pdb; pdb.set_trace()

Common Issues

Issue	Solution
`ImportError: datalad`	`pip install skullduggery[datalad]`
ANTs registration fails	`pip install antspyx`
Tests fail	`pip install -e ".[test]" && pytest tests/`

Contributing

Keep commits atomic and meaningful
Follow PEP 8
Include tests for new code
Update docstrings
Ensure all tests pass (pytest tests/)

Questions? Open an issue on GitHub