Getting Started

Install

Using uv

git clone https://github.com/EricBoittier/mmml.git
cd mmml
uv sync

Optional extras:

uv sync --extra dev    # tests + MkDocs
uv sync --extra cli    # shell tab completion (argcomplete)
uv sync --extra gpu    # JAX CUDA 13 + CuPy (GPU nodes)

Using pip

pip install -e ".[dev]"
pip install -e ".[cli]"   # tab completion

CLI quick start

mmml -h                 # compact top-level help
mmml commands           # all subcommands by category
mmml examples           # copy-paste invocations
mmml configure          # interactive YAML / Snakemake wizard
mmml env                # checkpoints + CHARMM paths
mmml md-system --help   # flags for one command

Enable tab completion (bash/zsh):

uv sync --extra cli
eval "$(register-python-argcomplete mmml)"

See the CLI overview and tab completion pages for details.

Serve docs locally

uv sync --extra dev
make docs-serve

Then open http://127.0.0.1:8000.

Per-command reference pages are auto-generated before each make docs-build from scripts/generate_cli_docs.py.