[aaronkanzer]

Spectrum.scan_time_in_minutes() raises in three cases:

1. The cvParam has unitAccession="UO:0000010" but no unitName: Exception: Time unit 'unicorns' unknown. In the mzML 1.1 schema unitName is optional, and unitAccession is what identifies the unit.
2. The unit is millisecond. This should work, but the second branch is an if where it should be an elif, so the millisecond value falls through to the else and raises.
3. The spectrum has no scan start time: AttributeError: 'NoneType' object has no attribute 'lower'. pyteomics/tests/tiny.pwiz.1.1.mzML (written by ProteoWizard) has such a spectrum (scan=21). Scan start time is not required by the mzML mapping rules.

Fix: fall back to the UO accession (UO:0000028, UO:0000010, UO:0000031, UO:0000032) when unitName is missing, turn the if into an elif, and return None when there is no scan start time. An unknown unit still raises, as before.

Tested:

• New tests/scan_time_unit_test.py (5 tests). 3 fail on dev and all 5 pass with the fix.
• Full suite: 135 passed before, 140 passed after (same 2 plotly-only failures, 3 skipped).
• tiny.pwiz.1.1.mzML now reads to the end, with scan=21 returning None.

[sonarqubecloud]

Quality Gate passed

Issues
3 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

[MKoesters]

Thanks for the thorough write-up and tests, looks solid to me!
I'll check if there is a way around hardcoding the terms and using OboTranslator, but I think loading the uo.obo is anyway an overkill for this PR.
I might raise an issue for that though.

I'll approve and merge once I had a closer look later this week.

Best
Manuel

[aaronkanzer]

Thanks for the thorough write-up and tests, looks solid to me! I'll check if there is a way around hardcoding the terms and using OboTranslator, but I think loading the uo.obo is anyway an overkill for this PR. I might raise an issue for that though.

I'll approve and merge once I had a closer look later this week.

Best Manuel

Thanks Manuel! Agreed the OBO lookup would be a nicer long-term fix, happy to help there if useful.