Repository Layout

The repository is organized as a Cargo workspace with two Rust packages:

• alchemrs: the core library crate and CLI binary
• alchemrs-py: the Python binding crate built as a cdylib

The surrounding top-level directories then hold tests, examples, fixtures, documentation, the python/ package wrapper, and pyproject.toml for the repo-local Python build workflow.

alchemrs library layout

The alchemrs crate is organized into modules rather than separate library crates:

• data: domain types and scientific data-model structures, including ATM schedules and samples
• error: shared crate-level error handling
• parse: engine-specific parsers for AMBER outputs and GROMACS dhdl.xvg files
• prep: time-series preparation such as duplicate cleanup, sorting, equilibration detection, and decorrelation
• estimators: TI, BAR, MBAR, IEXP, DEXP, NES, UWHAM, and ATM implementations
• analysis: overlap diagnostics, schedule advisors, and plot-ready convergence series
• plot: optional SVG rendering helpers behind the plotting feature

The crate root also re-exports the most common types and functions directly for a flatter API.

alchemrs-py package

alchemrs-py is a separate Rust package in the same workspace. It provides the native Python extension layer and depends on the core alchemrs crate, but the dependency does not go the other way.

python/ package wrapper

The python/ directory contains:

• the importable python/alchemrs package
• OpenMM helper utilities in python/alchemrs/openmm.py
• runnable Python examples
• Python-side tests

pyproject.toml points maturin at alchemrs-py/Cargo.toml and stages the extension into that package layout.

CLI binary

The alchemrs binary wraps parsing, preprocessing, estimation, and output formatting into a command-line workflow. The scientific logic lives in the library; the CLI is a thin consumer of that API.

Layering

The intended dependency direction inside the library is:

parse -> data + error
prep -> data + error
estimators -> data + error
analysis -> data + error + estimators

The CLI depends on the core library crate, and alchemrs-py depends on the same core library crate through the workspace.