BioPython MCP Server

# Contributing to BioPython MCP Thank you for your interest in contributing to BioPython MCP! This document provides guidelines and instructions for contributing. ## Code of Conduct By participating in this project, you agree to abide by our code of conduct: - Be respectful and inclusive - Welcome newcomers and help them get started - Focus on what is best for the community - Show empathy towards other community members ## Getting Started ### Development Setup 1. **Fork the repository** ```bash git clone https://github.com/yourusername/biopython-mcp.git cd biopython-mcp ``` 2. **Create a virtual environment** ```bash python -m venv venv source venv/bin/activate # On Windows: venv\Scripts\activate ``` 3. **Install development dependencies** ```bash pip install -e ".[dev]" ``` 4. **Install pre-commit hooks** ```bash pre-commit install ``` ### Development Workflow 1. **Create a feature branch** ```bash git checkout -b feature/your-feature-name ``` 2. **Make your changes** - Write code following our style guidelines - Add tests for new functionality - Update documentation as needed 3. **Run tests and checks** ```bash # Run tests pytest # Run type checking mypy biopython_mcp/ # Run linting black src/ tests/ ruff check src/ tests/ # Run all pre-commit hooks pre-commit run --all-files ``` 4. **Commit your changes** ```bash git add . git commit -m "feat: add new feature" ``` 5. **Push and create a pull request** ```bash git push origin feature/your-feature-name ``` ## Contribution Guidelines ### Code Style We follow these style guidelines: - **Black** for code formatting (line length: 100) - **Ruff** for linting - **PEP 8** for general Python style - **Type hints** required for all functions - **Docstrings** required for all public functions and classes ### Type Hints All functions must include type hints: ```python def calculate_gc_content(sequence: str) -> dict[str, Any]: """ Calculate GC content of a sequence. Args: sequence: DNA or RNA sequence Returns: Dictionary containing GC content and statistics """ pass ``` ### Docstrings Use Google-style docstrings: ```python def example_function(param1: str, param2: int) -> bool: """ Brief description of function. Longer description if needed. Args: param1: Description of param1 param2: Description of param2 Returns: Description of return value Raises: ValueError: When input is invalid """ pass ``` ### Testing - Write tests for all new features - Maintain or improve code coverage - Use pytest fixtures for common test data - Mock external API calls Example test: ```python def test_translate_sequence() -> None: """Test DNA translation.""" result = translate_sequence("ATGGCC") assert result["success"] is True assert result["protein_sequence"] == "MA" ``` ### Commit Messages Follow [Conventional Commits](https://www.conventionalcommits.org/): - `feat:` New feature - `fix:` Bug fix - `docs:` Documentation changes - `test:` Test updates - `refactor:` Code refactoring - `style:` Code style changes - `chore:` Maintenance tasks Examples: ``` feat: add support for protein structure prediction fix: correct GC content calculation for RNA docs: update installation instructions test: add tests for alignment functions ``` ### Pull Request Process 1. **Update documentation** for any new features 2. **Add tests** that cover your changes 3. **Ensure all tests pass** and pre-commit hooks succeed 4. **Update CHANGELOG** if applicable 5. **Reference related issues** in the PR description 6. **Request review** from maintainers ### PR Description Template ```markdown ## Description Brief description of changes ## Type of Change - [ ] Bug fix - [ ] New feature - [ ] Breaking change - [ ] Documentation update ## Testing Describe testing performed ## Checklist - [ ] Tests added/updated - [ ] Documentation updated - [ ] Type hints added - [ ] Pre-commit hooks pass - [ ] All tests pass ``` ## Areas for Contribution ### High Priority - Additional BioPython tool integrations - Performance optimizations - Documentation improvements - Test coverage improvements - Bug fixes ### New Features - BLAST search integration - Protein structure prediction - Sequence feature annotation - Custom HMM profile support - Batch processing capabilities ### Documentation - Usage examples - Tutorial notebooks - API documentation - Video tutorials - Blog posts ### Testing - Unit tests - Integration tests - Performance benchmarks - Edge case coverage ## Reporting Bugs ### Before Submitting 1. Check existing issues 2. Test with the latest version 3. Collect relevant information ### Bug Report Template ```markdown **Describe the bug** Clear description of the bug **To Reproduce** Steps to reproduce: 1. Call function X with parameter Y 2. See error **Expected behavior** What should happen **Actual behavior** What actually happens **Environment** - OS: [e.g., macOS 13.0] - Python version: [e.g., 3.11] - BioPython MCP version: [e.g., 0.1.0] **Additional context** Any other relevant information ``` ## Requesting Features ### Feature Request Template ```markdown **Feature Description** Clear description of the feature **Use Case** Why is this feature needed? **Proposed Solution** How should this work? **Alternatives Considered** Other approaches you've considered **Additional Context** Any other relevant information ``` ## Code Review Process ### For Contributors - Respond to review comments promptly - Make requested changes in new commits - Update the PR description if scope changes - Be open to feedback and suggestions ### For Reviewers - Be constructive and respectful - Explain the reasoning behind suggestions - Approve when changes meet standards - Help contributors improve their code ## Development Tips ### Running Specific Tests ```bash # Run specific test file pytest tests/test_sequence.py # Run specific test pytest tests/test_sequence.py::test_translate_sequence # Run with verbose output pytest -v # Run with coverage pytest --cov=biopython_mcp --cov-report=html ``` ### Debugging ```bash # Run with debugging pytest --pdb # Run with print statements visible pytest -s ``` ### Type Checking ```bash # Check specific file mypy biopython_mcp/sequence.py # Check all source mypy biopython_mcp/ # Generate coverage report mypy --html-report mypy-report src/ ``` ## Release Process Maintainers handle releases following this process: 1. Update version in `pyproject.toml` 2. Update `CHANGELOG.md` 3. Create release tag 4. GitHub Actions publishes to PyPI 5. Announce release ## Questions? - Open a [Discussion](https://github.com/kmaneesh/biopython-mcp/discussions) - Ask in [Issues](https://github.com/kmaneesh/biopython-mcp/issues) - Email maintainers ## Recognition Contributors are recognized in: - README acknowledgments - CHANGELOG entries - GitHub contributors page - Release notes Thank you for contributing to BioPython MCP!