[ericchansen]

Summary

This PR simplifies the q2mm.backends layer by deduplicating shared validation, topology-matching, and prepared-session helpers across contracts, conformance, reference backends, and MM backends, while making all seven q2mm.backends.mm* modules mypy-clean and removing the final [[tool.mypy.overrides]] grandfather block from pyproject.toml.

Changes

• Unify capability and functional-form validation (_normalize_capabilities_and_forms), parameter-vector request validation (_ParameterVectorRequest), and MM prepared-session _ff_for, _provenance, _raw_hessian, and _mm_frequencies helpers in q2mm/backends/contracts.py.
• Deduplicate undeclared BATCHED_HESSIAN and REUSABLE_STATE verification in q2mm/backends/conformance.py, and discovery record normalization in q2mm/backends/discovery.py.
• Share reference preparation validation (_validate_reference_prepare) across q2mm/backends/reference/ase.py and q2mm/backends/reference/qcengine.py, unify ASE Atoms state validation into _unsupported_atoms_state_reason, and share frequency wavefunction evaluation in q2mm/backends/reference/psi4.py.
• Add _require_mm_force_field in q2mm/backends/mm/_term_support.py and shared match_mm_topology + _PreparedJaxBase in q2mm/backends/mm/_jax_common.py, eliminating repeated bond/angle matching passes, duplicate PreparedJax/PreparedJaxMd session hooks, and the duplicated harmonic vs. MM3 energy_fn body in q2mm/backends/mm/jax_engine.py.
• Deduplicate OpenMM vdW force and 1-4 exception construction (_build_vdw_force, _exception_14_params) in q2mm/backends/mm/openmm.py and template export checks (_uses_template_export) in q2mm/backends/mm/tinker.py.
• Fix all type annotations across q2mm.backends.mm* and remove the remaining [[tool.mypy.overrides]] grandfather block in pyproject.toml so all 109 source files are checked with zero ignore_errors overrides.

Testing

• Verified python -m ruff check q2mm/ test/ scripts/, python -m ruff format --check q2mm test scripts examples, and python -m mypy q2mm/ pass with zero errors across all 109 source files (zero ignore_errors overrides remaining in pyproject.toml).
• Verified core and backend test suites pass (7592 passed in core tests, 340 passed in JAX/contract backend tests, plus direct unit coverage for _raw_hessian/_mm_frequencies penalty mode, _exception_14_params, TinkerBackend._uses_template_export, and match_mm_topology).
• Verified all 19 CI jobs—including native openmm-cpu, tinker, jax-cpu, jax-md-cpu, parity-openmm-jax, parity-openmm-tinker, and parity-jax-jaxmd—pass on this branch.

[Copilot]

🟡 Changes recommended

Shared frequency evaluation rejects non-finite Hessians before penalty-mode recovery can run.

1 open issue

• Penalty-mode frequencies fail on non-finite native Hessians · New

What changed in this PR

Simplifies q2mm’s backend layer by sharing validation and evaluation helpers and extending enforced type checking.

Changes:

• Consolidates backend contracts, conformance checks, and reference preparation.
• Shares MM topology matching, prepared-session operations, and force construction.
• Removes seven MM modules from mypy exemptions.

File	Description
q2mm/​backends/​reference/​qcengine.py	Uses shared preparation validation.
q2mm/​backends/​reference/​psi4.py	Shares frequency wavefunction evaluation.
q2mm/​backends/​reference/​ase.py	Consolidates preparation and state validation.
q2mm/​backends/​reference/​__init__.py	Adds shared reference preparation validation.
q2mm/​backends/​mm/​tinker.py	Shares export checks and frequency conversion.
q2mm/​backends/​mm/​openmm.py	Deduplicates nonbonded force construction and session helpers.
q2mm/​backends/​mm/​jax_md_engine.py	Adopts shared topology and session helpers.
q2mm/​backends/​mm/​jax_engine.py	Consolidates topology matching and energy kernels.
q2mm/​backends/​mm/​batched.py	Tightens typing and validates session types.
q2mm/​backends/​mm/​_term_support.py	Adds shared force-field validation.
q2mm/​backends/​mm/​_jax_common.py	Adds shared topology and prepared-session implementations.
q2mm/​backends/​mm/​__init__.py	Adjusts lazy-export typing.
q2mm/​backends/​discovery.py	Consolidates discovery-record normalization.
q2mm/​backends/​contracts.py	Shares request validation and MM session utilities.
q2mm/​backends/​conformance.py	Deduplicates capability checks.
pyproject.toml	Removes seven MM mypy exemptions.

_{Review effort: Balanced}

[Copilot]

🔵 Needs a closer look

Shared numerical paths span four MM engines and need human confirmation of backend-specific regression results beyond the reported JAX/contract coverage.

No open issues 🎉

1 resolved since last review

• Penalty-mode frequencies fail on non-finite native Hessians

_{Review effort: Balanced}

[Copilot]

🟢 Approval recommended

No unresolved blocking defects remain, and the prior frequency-penalty regression is addressed with dedicated coverage.

No open issues 🎉

_{Review effort: Balanced}