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Contributing

Thanks for your interest in mdfs!

Setup

make venv          # creates .venv (Python 3.12) and installs everything
.venv/bin/python -c "import jax; print(jax.devices())"   # check GPU

Development workflow

  1. Branch off main.
  2. Write tests first (the suite mirrors src/mdfs/; physics changes must keep tests/test_params_vs_openmm.py green).
  3. Implement, keeping energy functions pure and units in the OpenMM convention (nm / ps / amu / kJ/mol / e -- see src/mdfs/constants.py).
  4. Run the local gate before committing: 
    make format lint mypy bandit test
    Slow / end-to-end tests: make slow-test.
  5. Use conventional-commit messages (feat:, fix:, refactor:, test:, docs:, chore:). Never bypass hooks with --no-verify.
  6. Open a PR once CI is green.

Conventions

See CLAUDE.md for the full list (absolute imports, pathlib, logging over print, Google docstrings, type hints, immutable aggregates, parameters sourced from OpenMM's resolved System).