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Contributing to BOND

Thank you for your interest in contributing to BOND! This document provides guidelines and instructions for contributing.

Code of Conduct

  • Be respectful and inclusive
  • Welcome newcomers and help them learn
  • Focus on constructive feedback
  • Respect different viewpoints and experiences

How to Contribute

Reporting Bugs

  1. Check if the bug has already been reported in Issues
  2. If not, create a new issue with:
    • Clear title and description
    • Steps to reproduce
    • Expected vs actual behavior
    • Environment details (OS, Python version, etc.)
    • Relevant error messages or logs

Suggesting Features

  1. Check if the feature has already been suggested
  2. Open an issue with:
    • Clear description of the feature
    • Use case and motivation
    • Potential implementation approach (if you have ideas)

Pull Requests

  1. Fork the repository and create a feature branch:

    git checkout -b feature/your-feature-name

  2. Make your changes:

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

  3. Run tests and linting:

    make test
make lint

  4. Commit your changes:

    git commit -m "Add: descriptive commit message"

    Follow conventional commit format when possible:

    • Add: for new features
    • Fix: for bug fixes
    • Update: for improvements
    • Docs: for documentation
    • Refactor: for code refactoring

  5. Push and create a PR:

    git push origin feature/your-feature-name

    Then create a pull request on GitHub with:

    • Clear description of changes
    • Reference to related issues
    • Screenshots/examples if applicable

Development Setup

  1. Clone and setup:

    git clone https://github.com/pankajrajdeo/BOND.git
cd BOND
python3.11 -m venv bond_venv
source bond_venv/bin/activate
pip install -e ".[dev]"

  2. Install pre-commit hooks (optional):

    pip install pre-commit
pre-commit install

Code Style

  • Follow PEP 8 style guide
  • Use type hints where possible
  • Keep functions focused and small
  • Add docstrings for public functions/classes
  • Maximum line length: 100 characters (flexible for readability)

Testing

  • Write tests for new functionality
  • Aim for high test coverage
  • Run tests before submitting PR: 
    pytest

Documentation

  • Update README.md for user-facing changes
  • Add docstrings to new functions/classes
  • Update API documentation if endpoints change
  • Keep examples in code current

Project Structure

BOND/
├── bond/              # Main package
│   ├── pipeline.py   # Core BondMatcher class
│   ├── retrieval/    # Retrieval modules
│   ├── server.py     # FastAPI service
│   └── ...
├── scripts/          # Utility scripts
├── benchmark-metrics/ # Benchmark evaluation results and scripts
├── assets/           # Data files (gitignored)

Areas for Contribution

  • Performance improvements: Optimization of retrieval or fusion
  • New ontology support: Adding support for additional ontologies
  • Better error handling: More informative error messages
  • Documentation: Improving guides and examples
  • Benchmarking: Evaluation on new datasets

Questions?

Feel free to open an issue with the question label or reach out to the maintainers.

Thank you for contributing to BOND! 🎉