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Restructure the repo so the existing bash MD-prep workflows become resilient, dynamic Python workflows organized in layers. At the base, reusable GROMACS primitives (grompp+mdrun, solvate, energy, WAT-topology management) wrap single operations with structured errors and reproducibility metadata; on top, composable typed step functions and hardened pipelines build on those primitives, including the adaptive pressure-driven resolvation loop. This layering decouples what a step does from how it is invoked, so the same core supports multiple front ends: a Typer CLI (subcommand per step + run-pipeline), an SDK public API (run_standard_md), and eventual Prefect orchestration without rewrites. Per-system behavior is driven by a Pydantic config (YAML/TOML + flag overrides) with per-invocation GROMACS run profiles, replacing hard-coded, typo-prone shell scripts. Adopt taylor as the canonical variant and add gmx-free contract/CLI tests wired into CI.
The per-step dotted entry points are replaced by a single md-workflows Typer app, so this is a breaking interface change rather than the patch version inherited from main. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Refactor bash MD scripts into typed Python core + Typer CLI
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Refactor bash MD scripts into typed Python core + Typer CLI