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Contributing to BackBonus

First off, thank you for considering contributing to BackBonus!

Code of Conduct

This project and everyone participating in it is governed by our Code of Conduct. By participating, you are expected to uphold this code.

How Can I Contribute?

Reporting Bugs

Before creating bug reports, please check existing issues as you might find out that you don't need to create one. When you are creating a bug report, please include as many details as possible:

  • Use a clear and descriptive title
  • Describe the exact steps which reproduce the problem
  • Provide specific examples to demonstrate the steps
  • Describe the behavior you observed after following the steps
  • Explain which behavior you expected to see instead and why
  • Include mol2 files if possible (sanitized if necessary)

Suggesting Enhancements

Enhancement suggestions are tracked as GitHub issues. When creating an enhancement suggestion, please include:

  • Use a clear and descriptive title
  • Provide a step-by-step description of the suggested enhancement
  • Provide specific examples to demonstrate the steps
  • Describe the current behavior and explain which behavior you expected to see instead
  • Explain why this enhancement would be useful

Pull Requests

  1. Fork the repo and create your branch from main
  2. If you've added code that should be tested, add tests
  3. If you've changed APIs, update the documentation
  4. Ensure the test suite passes
  5. Make sure your code follows the style guidelines
  6. Issue that pull request!

Development Setup

  1. Fork and clone the repository:

    git clone https://github.com/yourusername/backbonus.git
cd backbonus

  2. Create a virtual environment:

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

  3. Install in development mode:

    pip install -e ".[dev]"
pre-commit install

  4. Create a branch:

    git checkout -b feature/your-feature-name

Style Guidelines

Python Style

  • We use Black for code formatting
  • We use isort for import sorting
  • We use flake8 for linting
  • We use mypy for type checking

Run all checks with:

black backbonus tests
isort backbonus tests
flake8 backbonus tests
mypy backbonus

Git Commit Messages

  • Use the present tense ("Add feature" not "Added feature")
  • Use the imperative mood ("Move cursor to..." not "Moves cursor to...")
  • Limit the first line to 72 characters or less
  • Reference issues and pull requests liberally after the first line

Documentation

  • Use Google style docstrings
  • Include type hints for all function parameters
  • Update the README.md if you change functionality

Testing

# Run all tests
pytest

# Run with coverage
pytest --cov=backbonus

# Run specific test file
pytest tests/test_correspondence.py -v

Release Process

  1. Update version in backbonus/__init__.py
  2. Update CHANGELOG.md
  3. Create a tagged release on GitHub
  4. Package will be automatically published to PyPI

Thank you for contributing!