Add age.reference support - #250
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Port the age.reference support from the 2022 WIP PR #250 onto the current restructured codebase and complete its open TODOs (best-practice docs + tests). Adds check_subject_age_reference, which flags Subject.age__reference values outside {"birth", "gestational"}. PyNWB now enforces this constraint at construction time, so the check is defensive against files written by other tools (e.g. MatNWB) and read back. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Port the age.reference support from the 2022 WIP PR #250 onto the current restructured codebase and complete its open TODOs (best-practice docs + tests). Adds check_subject_age_reference, which flags Subject.age__reference values outside {"birth", "gestational"}. PyNWB now enforces this constraint at construction time, so the check is defensive against files written by other tools (e.g. MatNWB) and read back. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## dev #250 +/- ##
==========================================
+ Coverage 79.44% 82.93% +3.49%
==========================================
Files 48 48
Lines 1897 1910 +13
==========================================
+ Hits 1507 1584 +77
+ Misses 390 326 -64
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Adds
check_subject_age_reference, which validates thatSubject.age__reference, when present, is one of the supported values ("birth"or"gestational").This revives and completes the original 2022 WIP (rebased onto the current restructured
dev), finishing both open TODOs:docs/best_practices/nwbfile_metadata.rst, under Subject Age)tests/unit_tests/test_nwbfile_metadata.py, 5 cases)Note on scope
The original dependency (pynwb PR #1540) merged long ago, and current PyNWB now enforces
age__reference ∈ {birth, gestational}at construction time (raisesValueError), defaulting to"birth". The check therefore serves a defensive role: catching invalid references in files written by other tools (e.g. MatNWB) and read back. Tests simulate that case by overriding the field after construction.Not added to the DANDI critical config, since the value is schema-enforced and defaulted.
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