Minimal reproducibility code for "Protocol reversal and the limits of waiting-time inference in stochastic pumps"

Minimal reproducibility code accompanying the manuscript “Protocol reversal and the limits of waiting-time inference in stochastic pumps”.

The package implements periodic stationary-state calculations, conditional waiting-time densities, entropy-production estimates, physically paired forward/reverse comparisons, visible-edge flux bounds, and finite-record statistical diagnostics. It provides a quick check of the representative counterexample and controls, together with an ordered workflow for regenerating the parameter scans, convergence analyses, seeded event records, seven main-text figures, and supplementary reversal schematic.

The archive contains a README, pinned dependencies, eleven Python files, and one C source file for exact continuous-time trajectory simulation. Numerical tables, deterministic kernels, and forty forward/reverse record pairs are generated by the code. Python 3.11 or newer is required; full trajectory regeneration additionally requires a C compiler. The finite-record diagnostics use known phase traffic and do not constitute a fully data-calibrated inference procedure.

This version replaces the previous bundled archive with a minimal source-only distribution and introduces a unified execution entry point. The scientific model and reported results are unchanged.