[ericchansen]

Summary

Simplifies duplicated helpers across q2mm.models and q2mm.io (-444 net lines) and resolves all remaining static type errors across every q2mm.models.* and q2mm.io.* module so all 13 grandfathered model/I/O modules can be removed from [[tool.mypy.overrides]] in pyproject.toml.

Changes

• Consolidate shared text-file path/lazy-lines/write handling (_TextFileBase) and template path resolution (_resolve_template_path) in q2mm/io/_helpers.py, removing duplicated boilerplate across GaussLog, JaguarIn, JaguarOut, MacroModel, MacroModelLog, Mol2, amber.py, mm3.py, and tinker.py.
• Deduplicate adjacency construction and delegate bond-length/bond-angle math in q2mm/models/molecule.py to q2mm.geometry (bond_length, bond_angle).
• Deduplicate 3x3 Hessian sub-block eigendecomposition projection (_project_subblock_along) in q2mm/models/seminario.py, frequency unit conversion constants and mass_weight_scale_3n usage in q2mm/models/hessian.py, enum coercion (_coerce_enum) in q2mm/models/observations.py, and token cleaning (_clean_env_tokens) in q2mm/models/identifiers.py.
• Deduplicate CMAP grid finalization in q2mm/io/cmap.py, MM3 proper/improper torsion construction in q2mm/io/mm3.py, MacroModel term staging (_MacroModelTerm) in q2mm/io/macromodel.py, and scalar observation parsing in q2mm/io/reference.py.
• Remove all 13 q2mm.models.* and q2mm.io.* entries from [[tool.mypy.overrides]] in pyproject.toml.

Testing

• python -m ruff check q2mm/ test/ scripts/ (all checks passed)
• python -m ruff format --check q2mm test scripts examples (288 files formatted)
• python -m mypy q2mm/ (0 errors across 109 source files)
• python -m pytest test/ -x -q -m "not (openmm or tinker or jax or jax_md or psi4)" (7,582 passed, 185 skipped)

[Copilot]

🟡 Changes recommended

The refactor introduces an angle-projection division failure and repeated parsing of Gaussian logs without frequency modes.

2 open issues

• No-frequency logs are reparsed on every mode cache access · New
• Float conversion causes division by zero for cancelling projections · New

What changed in this PR

Consolidates shared model and I/O helpers and extends mypy enforcement across those modules.

Changes:

• Shares text-file handling, template resolution, and repeated model calculations.
• Simplifies parser staging and strengthens type annotations.
• Removes 13 mypy exemptions and adds shared-helper tests.

File	Description
test/​test_io_helpers.py	Tests shared helpers and parser inheritance.
q2mm/​models/​seminario.py	Shares Hessian projection logic and tightens types.
q2mm/​models/​observations.py	Centralizes enum coercion.
q2mm/​models/​molecule.py	Shares adjacency and geometry calculations.
q2mm/​models/​identifiers.py	Centralizes atom-type token cleaning.
q2mm/​models/​hessian.py	Shares conversion constants and mass weighting.
q2mm/​models/​forcefield.py	Simplifies parameter construction and keys.
q2mm/​io/​tinker.py	Strengthens types and shares template resolution.
q2mm/​io/​reference.py	Consolidates scalar observation parsing.
q2mm/​io/​openmm.py	Clarifies export variable types.
q2mm/​io/​mol2.py	Adopts shared text-file handling.
q2mm/​io/​mm3.py	Unifies torsion construction and template resolution.
q2mm/​io/​macromodel.py	Unifies staging records and file handling.
q2mm/​io/​jaguar.py	Shares file handling and simplifies parsing.
q2mm/​io/​gaussian.py	Refactors parser state and file handling.
q2mm/​io/​cmap.py	Centralizes grid finalization.
q2mm/​io/​amber.py	Tightens parameter types and shares template resolution.
q2mm/​io/​_helpers.py	Adds shared file and template helpers.
pyproject.toml	Removes model and I/O mypy exemptions.

_{Review effort: Balanced}

[Copilot]

🟢 Approval recommended

No unresolved blocking issues remain, and both previously reported regressions are addressed with focused tests.

No open issues 🎉

2 resolved since last review

• Float conversion causes division by zero for cancelling projections
• No-frequency logs are reparsed on every mode cache access

_{Review effort: Balanced}