Set Up a Contributor Environment

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

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 and Activate the Build Environment

pixi install -e build
pixi shell -e build

PolyzyMD is installed in editable mode by default, so source changes are picked up immediately.

3. Run the Core Contributor Checks

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

4. Optional Tooling Notes

OpenEye Toolkit

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

pixi shell -e build
pip install openeye-toolkits

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