API coherence: WorkflowResult return type, public-surface hygiene, config de-dup - #106
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main() now returns a WorkflowResult -- a str subclass whose value is the output SDF path (a drop-in for the path string it returned before: isinstance(str), Path(), open(), ==, hashing, pickling all behave identically) that also exposes n_molecules / n_conformers, computed lazily from the output and cached. The CLI run command reads those counts off the result instead of re-opening the SDF, and cli.results.count_from_output now delegates to the single-source core Auto3D.results.count_output. Backwards-compatible.
- Promote get_stable_tautomers/select_tautomers into the public API (Auto3D.__all__) and add a self-describing generate_conformers alias for main(); refactor the lazy __getattr__ into a single name->(module,attr) table. - Add module-level __all__ to SPE.py, ASE/geometry.py, ASE/thermo.py, and tautomer.py to pin each module's exported surface. - Replace hardcoded opt_tol/opt_steps/batchsize_atoms literals in opt_geometry/calc_thermo with the DEFAULT_* constants (same values; the thermo-specific 2e-4 tolerance becomes DEFAULT_THERMO_CONVERGENCE_THRESHOLD), and add a test asserting CLIConfig covers every public Auto3DOptions field so the config layers cannot silently drift.
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Jul 11, 2026
API coherence: WorkflowResult return type, public-surface hygiene, config de-dup
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The deferred API-coherence work from the CLI review. Two independent reviews (architecture + correctness) verified the change set is backwards-compatible and ship-able; the one actionable finding (defensive count read in
run.py) was applied.main()returns aWorkflowResultA
strsubclass whose value is the output SDF path — a verified drop-in for the previous return (isinstance(str),Path(),open(),==, hashing, pickling,json.dumpsall behave identically) — that also exposesn_molecules/n_conformers, computed lazily and cached. The CLI reads these off the result instead of re-opening the SDF;count_from_outputnow delegates to a single-source corecount_output.Public-surface hygiene
get_stable_tautomers/select_tautomerspromoted intoAuto3D.__all__; added a self-describinggenerate_conformersalias formain()(mainstays exported); lazy__getattr__refactored into onename -> (module, attr)table.__all__added toSPE.py,ASE/geometry.py,ASE/thermo.py,tautomer.py.Config coherence
opt_tol/opt_steps/batchsize_atomsliterals inopt_geometry/calc_thermowith theDEFAULT_*constants (same values; thermo's 2e-4 becomesDEFAULT_THERMO_CONVERGENCE_THRESHOLD).CLIConfigcovers every publicAuto3DOptionsfield, so the config layers can't silently drift.All values preserved (no behavior change). Fast gate: 671 passed (+8 new tests); ruff clean on
src/. CHANGELOG updated.Still deferred (CLI/feature, not API coherence): registry-aware
models(models test <engine>), wiringprogress.py's live display into the run loop.