Repository Layout

The repository is centered on a single Cargo package, alchemrs.

That package contains:

• the alchemrs library crate
• the alchemrs command-line binary

alchemrs library layout

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

• data: domain types and scientific data-model structures
• error: shared crate-level error handling
• parse: engine-specific parsers; today this means AMBER parsing
• prep: time-series preparation such as duplicate cleanup, sorting, equilibration detection, and decorrelation
• estimators: TI, BAR, MBAR, EXP, and DEXP implementations
• analysis: overlap diagnostics built on top of MBAR log weights

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

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 binary depends on the library through the same package source tree.