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Contributing to TBI Lesion Analysis Pipeline

Thank you for your interest in contributing to the TBI Lesion Analysis Pipeline! This document provides guidelines for contributing to the project.

Code of Conduct

This project is committed to providing a welcoming and inclusive environment for all contributors. Please be respectful and considerate in all interactions.

How to Contribute

Reporting Issues

  • Use the GitHub issue tracker to report bugs or request features
  • Include detailed information about your environment (OS, Python version, etc.)
  • Provide reproducible examples when reporting bugs
  • Include relevant error messages and stack traces

Suggesting Enhancements

  • Open an issue to discuss the proposed enhancement
  • Describe the use case and expected benefits
  • Consider backward compatibility and performance implications

Submitting Code Changes

  1. Fork the repository and create a feature branch
  2. Make your changes following the coding standards below
  3. Add tests for new functionality
  4. Update documentation as needed
  5. Submit a pull request with a clear description of changes

Development Setup

  1. Clone your fork:

    git clone https://github.com/your-username/tbi.git
cd tbi

  2. Create a virtual environment:

    python -m venv venv
source venv/bin/activate  # On Windows: venv\Scripts\activate

  3. Install dependencies:

    pip install -r requirements.txt
pip install -r requirements_training.txt

  4. Install development dependencies:

    pip install pytest pytest-cov black flake8 mypy

Coding Standards

Python Code Style

  • Follow PEP 8 style guidelines
  • Use type hints for function parameters and return values
  • Keep functions focused and under 50 lines when possible
  • Add docstrings for all public functions and classes

Code Formatting

  • Use Black for code formatting
  • Run black . before committing
  • Use 4 spaces for indentation

Code Quality

  • Run flake8 to check for style issues
  • Run mypy for type checking
  • Ensure all tests pass before submitting

Commit Messages

  • Use clear, descriptive commit messages
  • Start with a verb in present tense (e.g., "Add", "Fix", "Update")
  • Reference issue numbers when applicable

Testing

  • Write unit tests for new functionality
  • Ensure existing tests continue to pass
  • Aim for good test coverage
  • Run tests with: pytest tests/

Documentation

  • Update README.md for user-facing changes
  • Add docstrings for new functions and classes
  • Update inline comments for complex logic
  • Keep configuration examples up to date

Medical Imaging Considerations

  • Ensure proper handling of medical data privacy
  • Validate input data formats and ranges
  • Include appropriate warnings for medical use
  • Consider performance implications for large datasets

Review Process

  1. All pull requests require review
  2. Maintainers will review for:
    • Code quality and style
    • Functionality and correctness
    • Documentation completeness
    • Test coverage
  3. Address feedback and make requested changes
  4. Once approved, maintainers will merge the PR

Getting Help

  • Open an issue for questions or problems
  • Join discussions in existing issues
  • Check the documentation for common questions

Thank you for contributing to the TBI Lesion Analysis Pipeline!