Add comprehensive CONTRIBUTING.md guide for new contributors

- Add structured contributor onboarding guide
- Document development workflow and testing
- Clarify contribution and PR process

Author: adilraza99

CONTRIBUTING.md

@@ -0,0 +1,215 @@
+# Contributing to malariagen-data-python
+
+Thanks for your interest in contributing to this project! This guide will help you get started.
+
+## About the project
+
+This package provides Python tools for accessing and analyzing genomic data from [MalariaGEN](https://www.malariagen.net/), a global research network studying the genomic epidemiology of malaria and its vectors. The package supports multiple data releases (Ag3, Af1, Amin1, Adir1, Pf7, Pf8, Pv4) and provides functionality for variant analysis, haplotype clustering, population genetics, and visualization.
+
+## Setting up your development environment
+
+### Prerequisites
+
+You'll need:
+
+- Python 3.10.x (CI-tested version)
+- [Poetry](https://python-poetry.org/) for dependency management
+- [Git](https://git-scm.com/) for version control
+
+### Initial setup
+
+1. **Fork and clone the repository**
+
+   Fork the repository on GitHub, then clone your fork:
+
+   ```bash
+   git clone git@github.com:[your-username]/malariagen-data-python.git
+   cd malariagen-data-python
+   ```
+
+2. **Add the upstream remote**
+
+   ```bash
+   git remote add upstream https://github.com/malariagen/malariagen-data-python.git
+   ```
+
+3. **Install Poetry** (if not already installed)
+
+   ```bash
+   pipx install poetry
+   ```
+
+4. **Create and activate the development environment**
+
+   ```bash
+   poetry install
+   poetry shell
+   ```
+
+5. **Install pre-commit hooks**
+
+   ```bash
+   pipx install pre-commit
+   pre-commit install
+   ```
+
+   Pre-commit hooks will automatically run `ruff` (linter and formatter) on your changes before each commit.
+
+## Development workflow
+
+### Creating a new feature or fix
+
+1. **Sync with upstream**
+
+   ```bash
+   git checkout master
+   git pull upstream master
+   ```
+
+2. **Create a feature branch**
+
+   Use a descriptive name:
+
+   ```bash
+   git checkout -b feature/your-feature-name
+   # or
+   git checkout -b fix/issue-description
+   # or
+   git checkout -b docs/update-contributing-guide
+   ```
+
+3. **Make your changes**
+
+   Write your code, add tests, update documentation as needed.
+
+4. **Run tests locally**
+
+   Fast unit tests (no external data access):
+
+   ```bash
+   poetry run pytest -v tests/anoph
+   ```
+
+   All unit tests (requires setting up credentials for legacy tests):
+
+   ```bash
+   poetry run pytest -v tests --ignore tests/integration
+   ```
+
+5. **Check code quality**
+
+   The pre-commit hooks will run automatically, but you can also run them manually:
+
+   ```bash
+   pre-commit run --all-files
+   ```
+
+### Code style
+
+We use `ruff` for both linting and formatting. The configuration is in `pyproject.toml`. Key points:
+
+- Line length: 88 characters (black default)
+- Follow PEP 8 conventions
+- Use type hints where appropriate
+- Write clear docstrings (we use numpydoc format)
+
+The pre-commit hooks will handle most formatting automatically. If you want to run ruff manually:
+
+```bash
+ruff check .
+ruff format .
+```
+
+### Testing
+
+- **Write tests for new functionality**: Add unit tests in the `tests/` directory
+- **Test coverage**: Aim to maintain or improve test coverage
+- **Fast tests**: Unit tests should use simulated data when possible (see `tests/anoph/`)
+- **Integration tests**: Tests requiring GCS data access are slower and run separately
+
+Run type checking with:
+
+```bash
+poetry run pytest -v tests --typeguard-packages=malariagen_data,malariagen_data.anoph
+```
+
+### Documentation
+
+- Update docstrings if you modify public APIs
+- Documentation is built using Sphinx with the pydata theme
+- API docs are auto-generated from docstrings
+- Follow the [numpydoc](https://numpydoc.readthedocs.io/) style guide
+
+## Submitting your contribution
+
+### Before opening a pull request
+
+- [ ] Tests pass locally
+- [ ] Pre-commit hooks pass (or run `pre-commit run --all-files`)
+- [ ] Code is well-documented
+- [ ] Commit messages are clear and descriptive
+
+### Opening a pull request
+
+1. **Push your branch**
+
+   ```bash
+   git push origin your-branch-name
+   ```
+
+2. **Create the pull request**
+   - Go to the [repository on GitHub](https://github.com/malariagen/malariagen-data-python)
+   - Click "Pull requests" → "New pull request"
+   - Select your fork and branch
+   - Write a clear title and description
+
+3. **Pull request description should include:**
+   - What problem does this solve?
+   - How does it solve it?
+   - Any relevant issue numbers (e.g., "Fixes #123")
+   - Testing done
+   - Any breaking changes or migration notes
+
+### Review process
+
+- PRs require approval from a project maintainer
+- CI tests must pass (pytest on Python 3.10 with NumPy 1.26.4)
+- Address review feedback by pushing new commits to your branch
+- Once approved, a maintainer will merge your PR
+
+## AI-assisted contributions
+
+We welcome contributions that involve AI tools (like GitHub Copilot, ChatGPT, or similar). If you use AI assistance:
+
+- Review and understand any AI-generated code before submitting
+- Ensure the code follows project conventions and passes all tests
+- You remain responsible for the quality and correctness of the contribution
+- Disclosure of AI usage is optional. Regardless of tools used, contributors remain responsible for the quality and correctness of their submissions.
+
+## Communication
+
+- **Issues**: Use [GitHub Issues](https://github.com/malariagen/malariagen-data-python/issues) for bug reports and feature requests
+- **Discussions**: For questions and general discussion, use [GitHub Discussions](https://github.com/malariagen/malariagen-data-python/discussions)
+- **Pull requests**: Use PR comments for code review discussions
+- **Email**: For data access questions, contact [support@malariagen.net](mailto:support@malariagen.net)
+
+## Finding something to work on
+
+- Look for issues labeled [`good first issue`](https://github.com/malariagen/malariagen-data-python/labels/good%20first%20issue)
+- Check for issues labeled [`help wanted`](https://github.com/malariagen/malariagen-data-python/labels/help%20wanted)
+- Improve documentation or add examples
+- Increase test coverage
+
+## Questions?
+
+If you're unsure about anything, feel free to:
+
+- Open an issue to ask
+- Start a discussion on GitHub Discussions
+- Ask in your pull request
+
+We appreciate your contributions and will do our best to help you succeed!
+
+## License
+
+By contributing to this project, you agree that your contributions will be licensed under the [MIT License](LICENSE).