Fix 22 audit findings across calculation, UI, and packaging - #120

Merged

jonathanschultzNU merged 30 commits into

mainfrom

claude/gpt-astra-audit-fixes-iqa1om

Sep 8, 2026

Commits on Sep 7, 2026

fix(freq): correct entropy units so Gibbs free energy is not corrupted (AUDIT F01)

NCCU-Schultz-Lab
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83589e6
fix(raman): apply the missing a0^3->Angstrom^3 polarizability conversion (AUDIT F02)

NCCU-Schultz-Lab
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0400aac
fix(dft): resolve wB97X-D to its true functional, not bare wb97x+D3 (AUDIT F03)

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9f7a257
fix(dft): surface D3-dispersion status instead of silently degrading (AUDIT F04)

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4436cf1
fix(freq): serialize ECPs into parallel IR/Raman displacement workers (AUDIT F05)

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93a56b1
fix(export): embed the resolved ECP mapping in exported scripts (AUDIT F06)

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2e83f7e
fix(cc): stop reporting unconverged CCSD/CCSD(T) as a converged result (AUDIT F07)

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1bf70ba
fix(tddft): stop reporting unconverged TD roots as a successful calculation (AUDIT F08)

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2b472c5
fix(optimizer): reject gradients from an unconverged SCF (AUDIT F09)

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3ce4554
fix(pes): make checkpoint identity and point reuse coordinate-aware (AUDIT F10)

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2b6cb01
fix(solvent): stop silently ignoring PCM for unsupported calc types (AUDIT F11)

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6cc9594
fix(slurm): stop discarding computed properties/provenance at ingest (AUDIT F12)

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48d48cb
fix(export): generate real MP2/CCSD/CCSD(T) scripts instead of a DFT branch (AUDIT F13)

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499ee2e
fix(cube): correct charge/spin inference for ROHF and ECP systems (AUDIT F14)

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d1013c0
fix(freq): stop reporting a failed Hessian as a converged result (AUDIT F15)

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d9da698
fix(app): wire the interactive Frequency run into its own checkpoint (AUDIT F16)

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38d40f2
fix(nmr): persist and surface fallback-reference metadata on local save (AUDIT F17)

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4c8527a
fix(freq): persist and restore frequency thermochemistry (AUDIT F18)

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c19ca38
fix(freq): parallel IR/Raman workers now honor density fitting and SCF rescue (AUDIT F19)

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c8dfe16
fix(packaging): ship quantui.engines in the built wheel (AUDIT F20)

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5154b0f
fix(slurm): quote generated command/directive paths for spaces (AUDIT F21)

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a437fd0
fix(tests): stop optimizer tests skipping on an obsolete dependency check (AUDIT F22)

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bc9010d
docs(labels): clarify TDHF/RPA, alpha-channel, and HF-reference scope (audit additional concerns)

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eaa4804
fix(export): exported NPZ carries cube-helper fields; cube provenance is immutable (audit additional concerns)

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26e62c4
fix(workers): size parallel IR/Raman pools from the SLURM/cgroup allocation (audit additional concerns)

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8440e55
fix(plots): spectral x-range covers every real mode; document height-normalized broadening (audit additional concerns)

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86f6337
chore(tests): drop unused variable flagged by ruff in test_raman_calc.py

NCCU-Schultz-Lab
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adbbd41

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Fix 22 audit findings across calculation, UI, and packaging - #120

Fix 22 audit findings across calculation, UI, and packaging#120
jonathanschultzNU merged 30 commits into
mainfrom
claude/gpt-astra-audit-fixes-iqa1om

Commits on Sep 7, 2026

fix(freq): correct entropy units so Gibbs free energy is not corrupted (AUDIT F01)

fix(raman): apply the missing a0^3->Angstrom^3 polarizability conversion (AUDIT F02)

fix(dft): resolve wB97X-D to its true functional, not bare wb97x+D3 (AUDIT F03)

fix(dft): surface D3-dispersion status instead of silently degrading (AUDIT F04)

fix(freq): serialize ECPs into parallel IR/Raman displacement workers (AUDIT F05)

fix(export): embed the resolved ECP mapping in exported scripts (AUDIT F06)

fix(cc): stop reporting unconverged CCSD/CCSD(T) as a converged result (AUDIT F07)

fix(tddft): stop reporting unconverged TD roots as a successful calculation (AUDIT F08)

fix(optimizer): reject gradients from an unconverged SCF (AUDIT F09)

fix(pes): make checkpoint identity and point reuse coordinate-aware (AUDIT F10)

fix(solvent): stop silently ignoring PCM for unsupported calc types (AUDIT F11)

fix(slurm): stop discarding computed properties/provenance at ingest (AUDIT F12)

fix(export): generate real MP2/CCSD/CCSD(T) scripts instead of a DFT branch (AUDIT F13)

fix(cube): correct charge/spin inference for ROHF and ECP systems (AUDIT F14)

fix(freq): stop reporting a failed Hessian as a converged result (AUDIT F15)

fix(app): wire the interactive Frequency run into its own checkpoint (AUDIT F16)

fix(nmr): persist and surface fallback-reference metadata on local save (AUDIT F17)

fix(freq): persist and restore frequency thermochemistry (AUDIT F18)

fix(freq): parallel IR/Raman workers now honor density fitting and SCF rescue (AUDIT F19)

fix(packaging): ship quantui.engines in the built wheel (AUDIT F20)

fix(slurm): quote generated command/directive paths for spaces (AUDIT F21)

fix(tests): stop optimizer tests skipping on an obsolete dependency check (AUDIT F22)

docs(labels): clarify TDHF/RPA, alpha-channel, and HF-reference scope (audit additional concerns)

fix(export): exported NPZ carries cube-helper fields; cube provenance is immutable (audit additional concerns)

fix(workers): size parallel IR/Raman pools from the SLURM/cgroup allocation (audit additional concerns)

fix(plots): spectral x-range covers every real mode; document height-normalized broadening (audit additional concerns)

chore(tests): drop unused variable flagged by ruff in test_raman_calc.py

Commits on Sep 8, 2026

fix(ci): restore Windows PySCF-free script generation and pes_scan test gating; satisfy mypy in ir_plot.py

fix(ci): actually satisfy mypy~=1.10.0 (pinned) on ir_plot.py

fix(tests): guard the ECP-embedding assertion test with a PySCF skip