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Contributing to Polysome

Thank you for your interest in contributing to Polysome! This document provides guidelines for contributing to the project.

How to Contribute

Reporting Bugs

If you find a bug, please create an issue on GitHub with:

  • A clear, descriptive title
  • Steps to reproduce the issue
  • Expected behavior
  • Actual behavior
  • Your environment (OS, Python version, package version)
  • Any relevant logs or error messages

Suggesting Features

Feature suggestions are welcome! Please create an issue with:

  • A clear description of the feature
  • Use cases and motivation
  • Possible implementation approach (optional)

Submitting Pull Requests

  1. Fork the repository and create a new branch from main

    git checkout -b feature/your-feature-name

  2. Make your changes following these guidelines:

    • Follow the existing code style
    • Add tests for new functionality
    • Update documentation as needed
    • Keep commits focused and atomic

  3. Test your changes locally:

    # Run tests
pytest

# Check code formatting
black --check src/

# Type checking (if applicable)
mypy src/

  4. Commit your changes with clear, descriptive commit messages:

    git commit -m "Add feature: brief description"

  5. Push to your fork and create a pull request:

    git push origin feature/your-feature-name

  6. Describe your changes in the pull request:

    • What problem does it solve?
    • How does it work?
    • Any breaking changes?
    • Related issues (if any)

Development Setup

Installation for Development

# Clone the repository
git clone https://github.com/computationalpathologygroup/Polysome.git
cd Polysome

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

Running Tests

# Run all tests
pytest

# Run with coverage
pytest --cov=polysome

# Run specific test file
pytest tests/test_specific.py

Code Style

  • Follow PEP 8 guidelines
  • Use type hints where appropriate
  • Write docstrings for public functions and classes
  • Keep functions focused and modular

Questions?

If you have questions about contributing, feel free to:

  • Open a discussion on GitHub
  • Reach out to the maintainers

Thank you for contributing to Polysome!