Contributing
============

We welcome contributions to LymphoSeq!

Getting Started
---------------

1. Fork the repository on GitHub
2. Clone your fork locally
3. Create a new branch for your changes
4. Make your changes
5. Run the tests
6. Submit a pull request

Development Setup
-----------------

.. code-block:: bash

   git clone https://github.com/yourusername/lymphoseq.git
   cd lymphoseq
   pip install -e ".[dev]"

Running Tests
-------------

.. code-block:: bash

   pytest

Code Style
----------

We use:

- Black for code formatting
- isort for import sorting
- Ruff for linting
- mypy for type checking

Run all checks with:

.. code-block:: bash

   black lymphoseq tests
   isort lymphoseq tests
   ruff check lymphoseq tests
   mypy lymphoseq

Pull Request Guidelines
-----------------------

- Include tests for new features
- Update documentation as needed
- Follow existing code style
- Write clear commit messages