[yarikoptic]

Motivation

check_subject_sex (CRITICAL in the dandi config) requires Subject.sex to be XX (hermaphrodite) or XO (male) when the species is C. elegans. The CElegansSubject type of ndx-subjects instead fixes sex to "O", and records XX/XO in a separate c_elegans_sex field (for example DANDI:001075). Every such file therefore fails check_subject_sex, and so fails dandi validate/dandi upload, even though the sex is recorded.

Discussed with @CodyCBakerPhD in

• Map C. elegans sex XX/XO to hermaphrodite/male dandi/dandi-cli#1976

That PR makes dandi-cli read c_elegans_sex for the asset metadata.

Changes

• check_subject_sex passes when c_elegans_sex is XX or XO and sex is "O" or unset.
• The C. elegans message now names the c_elegans_sex alternative.
• The "Subject Sex" best practice mentions the ndx-subjects case.
• Tests use a Subject subclass with a c_elegans_sex attribute, standing in for CElegansSubject, so the tests do not depend on ndx-subjects. They cover both codes with sex "O" or unset, and an invalid c_elegans_sex.

Testing

• tests/unit_tests: 345 passed, 7 skipped. pre-commit passes.

• I wrote two NWB files with ndx-subjects 0.2.0, then ran inspect_nwbfile(..., config=load_config("dandi")) without ndx-subjects installed, so the extension came from the namespace cached in the file:

  file	before	after
  sex="O", c_elegans_sex="XO"	check_subject_sex fails	passes
  sex unset, c_elegans_sex="XX"	n/a (not run)	passes

A changelog entry (changelog_entries/<PR>.fix.md) will be added once the PR number is known.

🤖 Generated with Claude Code

https://claude.ai/code/session_01NdN9xPzPo1AzsnEMuU8UQs

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 89.21%. Comparing base (fe72b42) to head (65ff014).

Additional details and impacted files

@@            Coverage Diff             @@
##              dev     #774      +/-   ##
==========================================
+ Coverage   86.30%   89.21%   +2.90%     
==========================================
  Files          48       48              
  Lines        2001     2003       +2     
==========================================
+ Hits         1727     1787      +60     
+ Misses        274      216      -58     

Files with missing lines	Coverage Δ
src/nwbinspector/checks/_nwbfile_metadata.py	96.63% <100.00%> (+0.03%)	⬆️

... and 4 files with indirect coverage changes

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.