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Contributing to GenAIRR

GenAIRR welcomes contributions from everyone — bug reports, documentation improvements, new features, and code patches. No contribution is too small.

Large changes should be discussed first via GitHub Issues.

Development Setup

git clone https://github.com/MuteJester/GenAIRR.git
cd GenAIRR
python -m venv .venv && source .venv/bin/activate
pip install maturin pytest pandas
maturin develop --release -m engine_rs/Cargo.toml   # builds the Rust kernel
pip install -e .                                    # editable Python install
pytest tests/ -x -q                                 # run the test suite

Or, if you prefer the Makefile:

make build       # rebuilds Rust + reinstalls Python
make test        # pytest
make test-rust   # cargo test

Requirements: Python 3.9+ and a stable Rust toolchain (rustup install stable). No C compiler or CMake needed — the simulation kernel is pure Rust.

Project Structure

.
├── engine_rs/                 # Rust simulation kernel (cargo workspace)
│   ├── Cargo.toml
│   └── src/
│       ├── ir.rs              # Persistent IR
│       ├── pass.rs            # Pass trait + runtime
│       ├── passes/            # Concrete passes (recombination, mutation, corruption)
│       ├── contract/          # Contract trait + filter/verify implementations
│       ├── dist.rs            # Distribution trait + concrete distributions
│       └── python/            # PyO3 wrappers exposed as `genairr_engine`
└── src/GenAIRR/
    ├── experiment.py          # Experiment DSL (public entry point)
    ├── dataconfig/            # DataConfig + species metadata
    ├── data/                  # 106+ built-in DataConfig pickles
    └── utilities/             # Helpers, IMGT regions

Running Tests

pytest tests/ -x -q                  # Python tests (DSL + integration)
cd engine_rs && cargo test           # Rust tests (unit + integration)

Release Process

GenAIRR ships two PyPI packages:

  • genairr_engine — Rust kernel built per OS/arch via maturin (abi3-py39, so one wheel per platform covers Python 3.9+).
  • GenAIRR — pure Python (single universal wheel + sdist).

GitHub Actions handles CI and publishing:

  1. Tests run on every push/PR (Linux, macOS, Windows × Python 3.10–3.12) plus a separate cargo test job.
  2. Wheels are built when a tag is pushed: maturin builds engine wheels for Linux x86_64+aarch64, macOS x86_64+arm64, Windows x64; setuptools builds a universal Python wheel.
  3. Publishing to PyPI happens automatically on GitHub Release or version tag.

Creating a Release

  1. Update the version in setup.py and engine_rs/Cargo.toml (keep them in sync).
  2. Update CHANGELOG.md.
  3. Commit, tag, and push: 
    git tag v1.0.0
git push origin v1.0.0
  4. Create a GitHub Release from the tag.

Prerequisites

  • PYPI_API_TOKEN secret must be configured in GitHub repository settings.