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Contributing to OMOPHub Python SDK

First off, thank you for considering contributing to OMOPHub!

How Can I Contribute?

Reporting Bugs

Before creating bug reports, please check the existing issues to avoid duplicates.

When creating a bug report, please include:

  • Python version (python --version)
  • SDK version (pip show omophub)
  • Operating system
  • Minimal code example that reproduces the issue
  • Full error traceback
  • Expected vs actual behavior

Suggesting Features

Feature requests are welcome! Please open an issue with:

  • Clear description of the feature
  • Use case: why would this be useful?
  • Possible implementation approach (optional)

Pull Requests

  1. Fork the repository and create your branch from main
  2. Install development dependencies: 
    git clone https://github.com/YOUR_USERNAME/omophub-python.git
cd omophub-python
pip install -e ".[dev]"
  3. Make your changes with clear, descriptive commits
  4. Add tests for new functionality
  5. Run the test suite: 
    pytest
  6. Ensure code style compliance: 
    ruff check .
ruff format .
mypy src/
  7. Update documentation if needed
  8. Submit a pull request with a clear description

Development Setup

Prerequisites

  • Python 3.10+
  • pip

Installation

# Clone your fork
git clone https://github.com/YOUR_USERNAME/omophub-python.git
cd omophub-python

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

# Install in development mode
pip install -e ".[dev]"

Running Tests

# Run all tests
pytest

# Run with coverage
pytest --cov=omophub --cov-report=html

# Run specific test file
pytest tests/test_concepts.py

# Run tests matching a pattern
pytest -k "test_search"

Code Style

We use:

  • Ruff for linting and formatting
  • mypy for type checking
# Check linting
ruff check .

# Auto-format code
ruff format .

# Type checking
mypy src/

Project Structure

omophub-python/
├── src/omophub/
│   ├── __init__.py       # Public API exports
│   ├── client.py         # OMOPHub client class
│   ├── resources/        # API resource classes
│   │   ├── concepts.py
│   │   ├── search.py
│   │   ├── hierarchy.py
│   │   └── ...
│   ├── types.py          # TypedDict definitions
│   └── exceptions.py     # Custom exceptions
├── tests/
│   ├── test_concepts.py
│   ├── test_search.py
│   └── ...
├── examples/
│   └── ...
└── pyproject.toml

Commit Messages

We follow Conventional Commits:

  • feat: New feature
  • fix: Bug fix
  • docs: Documentation changes
  • test: Adding or updating tests
  • refactor: Code refactoring
  • chore: Maintenance tasks

Examples:

feat: add semantic search endpoint
fix: handle rate limit errors correctly
docs: update README with new examples
test: add tests for batch concept lookup

Questions?

License

By contributing, you agree that your contributions will be licensed under the MIT License.

Thank you for helping make OMOPHub better!