Use cached namespaces during validation #531
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stephprince
commented
Oct 24, 2024
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@rly you mentioned you had a related test file, can you let me know if this solves the issue or share the file? |
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@rly this should be ready for you to test with your example file and review |
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## dev #531 +/- ##
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+ Coverage 82.77% 86.72% +3.94%
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Files 47 47
Lines 1504 1507 +3
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+ Hits 1245 1307 +62
+ Misses 259 200 -59
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rly
approved these changes
Nov 20, 2024
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Motivation
Fix #528.
Recent Zarr-related updates switched the inspector from using
pynwb.validate(paths=paths)topynwb.validate(io=io), resulting in the inspector not using cached namespaces during validation. We will temporarily revert this change, since pynwb validation of Zarr NWB files is not yet fully supported anyway due to pending issues that need to be addressed in hdmf/pynwb.Since this is more of a bug on the pynwb side that using the
ioargument ignores theuse_cached_namespaces=Truesetting in the validator (and will be updated in the next major pynwb release), I'm not sure if there are really any specific tests to add here.While addressing this issue, I added a couple of other small updates to the Zarr support here:
inspect_allthat detected whether the path provided was a directory of NWB files or an NWB file.test_inspect_all_paralleltests had been indented and were not running