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Contributing to CRISPR-HAWK

Thank you for your interest in contributing to CRISPR-HAWK! We welcome contributions from the community to help improve the codebase, fix bugs, expand documentation, or suggest new features.

Please read the following guidelines carefully to help streamline the process.

Table of Contents

📜 Code of Conduct

By participating in this project, you agree to abide by our Code of Conduct. We are committed to fostering a welcoming, respectful, and inclusive environment for all contributors.

🚀 Getting Started

To start contributing:

  1. Fork the repository.

  2. Clone your fork:

    git clone https://github.com/<your-username>/CRISPR-HAWK.git
cd CRISPR-HAWK

  3. Create a branch for your changes:

    git checkout -b my-feature-branch

🧩 Types of Contributions

You can contribute in many ways:

  • Report/Fix bugs
  • Suggest new features
  • Suggest/Improve documentation
  • Suggest/Improve tests
  • Report reproducible issues

⚙️ Development Setup

We recommend using a virtual environment or [conda/mamba] for isolation.

  1. Create a virtual environment:

    mamba create -n crisprhawk-dev python=3.8 -y
mamba activate crisprhawk-dev

  2. Install the package in editable mode with dev dependencies:

    pip install -e .[dev]

This installs pytest, black, and any additional tools needed for testing and linting.

🧪 Testing

Before submitting your changes, please make sure all tests pass:

pytest

To run a specific test:

pytest tests/test_<module_name>.py::<test_function_name>

If your contribution includes new functionality, please add corresponding unit tests under the tests/ directory.

For quick checks, you can also run:

crisprhawk --help
crisprhawk search --help

🎨 Style Guide

  • Use PEP 8 as a general style guide.

  • Format code with black (installed via [dev] extras):

    black src/ tests/

  • Use descriptive commit messages.

  • Write docstrings for public functions and modules.

📥 Pull Requests

When your contribution is ready:

  1. Push your branch to your fork:

    git push origin my-feature-branch

  2. Open a Pull Request (PR) from your fork to the main branch of the official repo.

Checklist before submitting:

  • All tests pass (pytest)
  • Code is formatted (black)
  • Relevant unit tests added or updated
  • Documentation updated if necessary
  • PR includes a clear description of the problem and solution

We’ll review your PR and provide feedback as soon as possible. Thank you for your contribution!

🐛 Reporting Issues

Found a bug? Have a suggestion?

  1. Search the existing issues.

  2. If it's new, open a new issue and include:

    • A clear description of the issue or request
    • Steps to reproduce (if applicable)
    • System info: OS, Python version, CRISPR-HAWK version
    • Any error messages or logs (use code blocks)

📬 Contact

For any questions, collaboration proposals, or off-topic inquiries, feel free to email the authors:

Thank you for contributing to CRISPR-HAWK! 🧬🔍 Let’s build a better genome editing toolbox — together.