Contributing

We welcome contributions to sr2silo! Whether you're fixing bugs, adding features, improving documentation, or reporting issues, your help is appreciated.

Ways to Contribute

• Report bugs: Open an issue describing the problem and how to reproduce it
• Suggest features: Open an issue to discuss new functionality
• Submit pull requests: Fix bugs or implement new features
• Improve documentation: Help make the docs clearer and more complete

Development Setup

We use Poetry for dependency management and packaging. The project provides multiple environment configurations in the environments/ directory.

Environment Options

Core Environment (basic usage):

make setup

Development Environment (recommended for contributors):

make setup-dev

Workflow Environment (for Snakemake workflows):

make setup-workflow

All Environments:

make setup-all

After Setup

conda activate sr2silo-dev
poetry install --with dev
poetry run pre-commit install

Running Tests

make test
# or directly:
pytest

Getting Started

1. Fork the repository
2. Clone your fork:

   git clone https://github.com/YOUR_USERNAME/sr2silo.git
   cd sr2silo
   

3. Set up the development environment (see above)
4. Create a feature branch following our branching strategy
5. Make your changes and run tests
6. Submit a pull request to the dev branch

Code Guidelines

• Follow existing code style and patterns
• Add tests for new functionality
• Update documentation as needed
• Keep commits focused and write descriptive commit messages

Questions?

Open an issue on GitHub if you have questions about contributing.