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Contributing

Contributions to AToM-OpenMM are welcome. Useful contributions include bug reports, fixes, new examples, clearer documentation, tests, and workflow improvements for ABFE and RBFE calculations.

Before You Start

  • Check the issue tracker for related reports or ongoing work.
  • Open an issue for larger changes so the approach can be discussed before implementation.
  • Keep changes focused and describe the scientific or workflow motivation clearly.

Development Setup

Use an isolated conda or mamba environment with the runtime dependencies described in Installation, then install the repository from source:

git clone https://github.com/Gallicchio-Lab/AToM-OpenMM.git
cd AToM-OpenMM
pip install .

For changes to package code, run the relevant tests or a small representative example before opening a pull request:

pytest

Some tests and examples may require OpenMM-compatible hardware and the full runtime environment.

Pull Requests

  • Create a feature branch from the current upstream branch.
  • Include a concise summary of the change and any tests or examples you ran.
  • Avoid mixing unrelated refactors with behavior changes.
  • Update examples or user-facing documentation when behavior, inputs, or outputs change.

Research Software Note

AToM-OpenMM is research software under active development. Please include enough detail in issues and pull requests for maintainers to reproduce and review the scientific workflow affected by the change.