Sync docs, guides, and example configs with current code - #104
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Audited the active docs (docs/source, top-level, example notebooks) against the current source and fixed the divergences: Docs (docs/source): - usage/quickstart: output SDF property names corrected (E_rel/E_relative -> E_rel(kcal/mol); E_tot also exposed as E_tot(Hartree)). - usage: replace the non-existent `--job-name` CLI flag example with a config-file one. - cli: `auto3d validate` description trimmed to what it actually checks (format + RDKit parse), dropping the unimplemented element/engine check. - migration: `use_ensemble` / AUTO3D_USE_ENSEMBLE described as deprecated no-op (they warn) rather than "removed". - howto/quickstart: replace the unverifiable `conda install -c conda-forge auto3d` with the documented `conda env create -f installation.yml`. - howto/troubleshooting: error strings match the real messages (GPU index validation; "Only k OR window needs to be specified"). - howto/drug_discovery: clarify tauto_k/tauto_window are get_stable_tautomers() arguments (not Auto3DOptions fields) and document the _Name grouping key. Top-level: - SECURITY.md supported-versions table updated to 3.5.x. - CHANGELOG.md: add an [Unreleased] section for the recent fixes. Example notebooks: - thermodynamic_calculation: fix the removed `get_mol_idx_t=` kwarg -> `mol_info_func=`, refresh 298 -> 298.15 K prose, clear stale help() output. - tautomer_with_userNNP: was non-runnable (empty model cells, bogus optimizing_engine="userNNP"); populate the userNNP wrapper, save it, and pass the saved model path. Code (to make the shipped example config valid via the documented CLI): - cli/config_schema: expose `batchsize_atoms` and `allow_tf32` in CLIConfig and forward them to Auto3DOptions; parameters.yaml previously failed to load via `auto3d run -c` (extra=forbid) and used an invalid `window: False`.
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Jul 11, 2026
Sync docs, guides, and example configs with current code
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Audited the active documentation (the
docs/sourceSphinx site, top-level docs, andexample/notebooks) against the current source after the recent bug-hunt merges, and fixed every divergence found by a four-agent parallel review. Leftdocs/legacy-v2/(frozen v2 snapshot) and auto-generated API stubs untouched.Docs (
docs/source)E_rel/E_relative→E_rel(kcal/mol);E_totalso shown asE_tot(Hartree)).--job-nameCLI flag example (it's a config-file field).auto3d validatedescription trimmed to what it actually does.use_ensemble/AUTO3D_USE_ENSEMBLEdocumented as deprecated no-ops (they warn), not "removed".conda install -c conda-forge auto3dwithconda env create -f installation.yml.tauto_k/tauto_windowareget_stable_tautomers()arguments.Top-level
SECURITY.mdsupported-versions table → 3.5.x.CHANGELOG.mdgains an[Unreleased]section for the recent fixes.Example notebooks
thermodynamic_calculation: fixed the removedget_mol_idx_t=kwarg →mol_info_func=, refreshed 298 → 298.15 K prose, cleared stalehelp()output.tautomer_with_userNNP: was non-runnable (empty model cells, bogusoptimizing_engine="userNNP") — populated the userNNP wrapper and pass the saved model path.Small code change (to make the shipped example valid)
cli/config_schema: exposebatchsize_atomsandallow_tf32inCLIConfigand forward toAuto3DOptions. The shippedparameters.yamlpreviously failed to load via the documentedauto3d run -cpath (extra=forbid) and used an invalidwindow: False; both fixed, with tests.Fast gate: 649 passed (+2 new CLIConfig tests). All edited .rst parse cleanly.