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Contributing to Machine Boss

Building and testing

C++

brew install gsl boost htslib pkg-config   # macOS
make
npm install
make test

Requires clang++ or g++ with C++11 support. Tests use t/testexpect.py and require Node.js.

Python

cd python
pip install -e '.[jax]'
pip install pytest
pytest machineboss/

Requires Python 3.10+. The [jax] extra is needed for JAX-based tests.

Pull request workflow

Fork the repository
Create a feature branch from master
Make your changes
Run both C++ and Python tests
Open a pull request against master

Code style

C++: C++11, consistent with existing src/ conventions
Python: Python 3.10+, tested with pytest
Keep commits focused and well-described

Reporting bugs

Open an issue at https://github.com/evoldoers/machineboss/issues with:

Steps to reproduce
Expected vs actual behavior
Environment details (OS, compiler, Python version)