Contributing

We welcome contributions to PhenoQC! This document provides guidelines for contributing to the project.

Setting Up Development Environment

1. Fork the repository on GitHub

2. Clone your fork locally:

   git clone https://github.com/YOUR_USERNAME/PhenoQC.git
   cd PhenoQC
   

3. Create a virtual environment and install dependencies:

   python -m venv venv
   source venv/bin/activate  # On Windows: venv\Scripts\activate
   pip install -e ".[dev]"
   

4. Install pre-commit hooks:

   pre-commit install
   

Making Changes

1. Create a new branch for your changes:

   git checkout -b feature-name
   

2. Make your changes

3. Add tests for any new functionality

4. Run the test suite:

   pytest
   

5. Format your code:

   black .
   

6. Commit your changes:

   git add .
   git commit -m "Description of changes"
   

7. Push to your fork:

   git push origin feature-name
   

8. Submit a Pull Request

Pull Request Guidelines

1. Include tests for any new functionality

2. Update documentation as needed

3. Follow the existing code style

4. Include a clear description of the changes

5. Link any related issues

Code Style

We use Black for code formatting and follow PEP 8 guidelines.

Running Tests

Run the full test suite:

pytest

Run with coverage:

pytest --cov=src tests/

Building Documentation

Build the documentation locally:

cd docs
make html

The built documentation will be in docs/build/html.