[ericchansen]

Summary

Simplify the core provenance, canonicalization, settings, preparation, and application modules (177 insertions, 346 deletions, -169 net lines) while preserving all public, architectural, and lazy-import contracts.

Changes

• Replace the dual _CREDENTIAL_KEY regex + startswith/endswith check in q2mm/_provenance.py with a normalized alphanumeric substring check against _CREDENTIAL_KEY_TERMS, and export thaw_json_value for reuse in q2mm/settings.py (including BackendSettings.factory_options()).
• Factor the recursive normalization closure in q2mm/_canonical.py (json_value) to eliminate repeated keyword-argument forwarding and _screen_key boilerplate.
• Reuse ActiveParameterSpace.pack/expand/with_baseline, QFuerzaSettings.model_dump(), and PreparationProvenance.__post_init__ freezing in q2mm/preparation.py.
• Share _validate_execution_controls and _validate_result_vectors across q2mm/application/models.py and q2mm/application/optimization.py, collapse _result_gradient_mode and _settings_gradient_mode into one function, replace manual dataclass-to-dict reconstructions in OptimizationRun.from_result and _manifest_payload with vars(...), and inline _install_staged in q2mm/application/persistence.py.

Testing

• python -m pytest test/ -x -q -m "not (openmm or tinker or jax or jax_md or psi4)" (7582 passed, 185 skipped)
• python -m ruff check q2mm/ test/ scripts/ (All checks passed!)
• python -m ruff format --check q2mm test scripts examples (288 files already formatted)
• python -m mypy q2mm/ (Success: no issues found in 109 source files)

[Copilot]

🟡 Changes recommended

Credential screening now accepts previously blocked auth keys, allowing opaque credentials into saved manifests.

1 open issue

• Restore boundary-aware auth key rejection · New

What changed in this PR

Simplifies shared provenance, preparation, and application code by reusing normalization, validation, and serialization helpers.

Changes:

• Consolidates JSON handling and credential screening.
• Reuses parameter-space operations and settings serialization.
• Shares execution validation and simplifies persistence staging.

File	Description
q2mm/​settings.py	Reuses JSON thawing for options and serialization.
q2mm/​preparation.py	Reuses parameter-space helpers and settings exports.
q2mm/​application/​persistence.py	Simplifies manifest construction and staged writes.
q2mm/​application/​optimization.py	Consolidates gradient resolution and validation.
q2mm/​application/​models.py	Shares validators and simplifies provenance capture.
q2mm/​application/​configuration.py	Passes configured finite-difference step directly.
q2mm/​_provenance.py	Adds shared thawing and changes credential-key screening.
q2mm/​_canonical.py	Consolidates recursive JSON normalization.

_{Review effort: Balanced}

[Copilot]

🟢 Approval recommended

The refactors have no identified blocking issues, and regression coverage addresses the previously reported credential-screening gap.

No open issues 🎉

1 resolved since last review

• Restore boundary-aware auth key rejection

_{Review effort: Balanced}