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Fix export cache spec and fix read cached spec #232

Merged
merged 2 commits into from
Nov 10, 2024
Merged

Fix export cache spec and fix read cached spec #232

merged 2 commits into from
Nov 10, 2024

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rly
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@rly rly commented Nov 10, 2024

Motivation

Fix #145. Cached extensions that are not one of {core, hdmf-common, hdmf-experimental} were not being exported into the Zarr store. In addition, cached extensions were not being read correctly because the name of the ZarrSpecReader source was being set to "./namespace" rather than something unique to the spec. The specs were also not being cached. This PR makes the code for ZarrSpecReader more aligned with H5SpecReader.

How to test the behavior?

Run example code in #145 but you need to use this branch in HDMF to read the file hdmf-dev/hdmf#1205

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 ruff 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-commenter commented Nov 10, 2024

Codecov Report

Attention: Patch coverage is 83.33333% with 2 lines in your changes missing coverage. Please review.

Project coverage is 85.58%. Comparing base (049402f) to head (bbc4ecd).

Files with missing lines Patch % Lines
src/hdmf_zarr/backend.py 66.66% 0 Missing and 1 partial ⚠️
src/hdmf_zarr/utils.py 88.88% 0 Missing and 1 partial ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##              dev     #232      +/-   ##
==========================================
- Coverage   85.67%   85.58%   -0.10%     
==========================================
  Files           5        5              
  Lines        1208     1214       +6     
  Branches      301      304       +3     
==========================================
+ Hits         1035     1039       +4     
  Misses        113      113              
- Partials       60       62       +2     

☔ View full report in Codecov by Sentry.
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@rly rly requested review from mavaylon1 and oruebel November 10, 2024 02:12
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@oruebel oruebel left a comment

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Looks good to me

@rly rly merged commit bdf8950 into dev Nov 10, 2024
23 checks passed
@rly rly deleted the cache_spec branch November 10, 2024 20:05
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Successfully merging this pull request may close these issues.

[Bug]: Extension namespaces not exported from HDF5 NWB
3 participants