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Fix validation in NWB testing util classes #1782

Merged
merged 5 commits into from
Feb 7, 2024
Merged

Fix validation in NWB testing util classes #1782

merged 5 commits into from
Feb 7, 2024

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rly
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@rly rly commented Oct 21, 2023

Motivation

The validate function in the pynwb.testing.testh5io classes was not validating the exported file and was using the older pynwb_validate(io=io) which validates against the core namespace instead of all leaves of the namespace hierarchy if extensions are present. The newer pynwb_validate(paths=[...]) syntax should be used instead.

Also update the write functions to cache the spec by default.

How to test the behavior?

Show how to reproduce the new behavior (can be a bug fix or a new feature)

Checklist

  • Did you update CHANGELOG.md with your changes?
  • Have you checked our Contributing document?
  • Have you ensured the PR clearly describes the problem and the solution?
  • Is your contribution compliant with our coding style? This can be checked running flake8 from the source directory.
  • Have you checked to ensure that there aren't other open Pull Requests for the same change?
  • Have you included the relevant issue number using "Fix #XXX" notation where XXX is the issue number? By including "Fix #XXX" you allow GitHub to close issue #XXX when the PR is merged.

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codecov bot commented Oct 21, 2023

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (dd6baaa) 91.99% compared to head (8bbe51a) 91.75%.

❗ Current head 8bbe51a differs from pull request most recent head 95717c6. Consider uploading reports for the commit 95717c6 to get more accurate results

Additional details and impacted files
@@            Coverage Diff             @@
##              dev    #1782      +/-   ##
==========================================
- Coverage   91.99%   91.75%   -0.25%     
==========================================
  Files          27       27              
  Lines        2623     2619       -4     
  Branches      685      684       -1     
==========================================
- Hits         2413     2403      -10     
- Misses        138      141       +3     
- Partials       72       75       +3     
Flag Coverage Δ
integration 71.09% <ø> (+0.07%) ⬆️
unit 84.38% <ø> (+0.70%) ⬆️

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@rly rly marked this pull request as ready for review October 22, 2023 18:01
@rly rly requested a review from oruebel October 22, 2023 18:02
@rly rly added this to the Next Release milestone Oct 22, 2023
@rly rly enabled auto-merge (squash) February 5, 2024 21:46
@rly rly merged commit 5d0e98d into dev Feb 7, 2024
19 of 22 checks passed
@rly rly deleted the rly-patch-1 branch February 7, 2024 00:47
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2 participants