Set Up a Contributor Environment

Use this page when you want to modify PolyzyMD, run tests, build the docs, or work on new analysis plugins.

What This Environment Is For

The contributor setup gives you:

  • an editable PolyzyMD install through pixi.toml

  • the test and docs toolchain

  • the same dependency story used by the project itself

1. Clone the Repository

git clone https://github.com/joelaforet/polyzymd.git
cd polyzymd

2. Install the Build Environment

pixi install -e build

PolyzyMD is installed in editable mode by default, so source changes are picked up immediately. If you want an interactive shell inside the environment, run pixi shell -e build.

3. Run the Core Contributor Checks

pixi run -e build pytest tests/ -x -q --tb=short --ignore=tests/utils/test_packmol.py
pixi run -e build ruff check src/
pixi run -e build black --check src/
pixi run -e build make -C docs clean html

4. Optional Tooling Notes

OpenEye Toolkit

If you have an OpenEye license and want the commercial charging backend:

pixi run -e build python -m pip install openeye-toolkits

If you prefer an interactive shell, enter it first with pixi shell -e build and then run python -m pip install openeye-toolkits inside that shell. Avoid installing OpenEye into a system Python that PolyzyMD will not use.

CUDA Environments for Cluster Work

If you are debugging or developing on GPU clusters, install the CUDA-specific pixi environment that matches the target cluster driver version:

pixi install -e cuda-12-6
pixi shell -e cuda-12-6

5. Keep Your Environment Updated

git pull
pixi install -e build