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Add NWBZarrIO.read_nwb convenience function #226

Merged
merged 11 commits into from
Nov 8, 2024
Merged

Add NWBZarrIO.read_nwb convenience function #226

merged 11 commits into from
Nov 8, 2024

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oruebel
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@oruebel oruebel commented Nov 7, 2024

Motivation

Fix #225

TODO

  • Add NWBZarrIO.read_nwb
  • Add unit test for reading from S3 via read_nwb
  • Add unit test for reading a local file via read_nwb
  • Add documentation for read_nwb to the tutorials

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 7, 2024

Codecov Report

Attention: Patch coverage is 85.71429% with 2 lines in your changes missing coverage. Please review.

Project coverage is 85.64%. Comparing base (797275a) to head (db60493).
Report is 1 commits behind head on dev.

Files with missing lines Patch % Lines
src/hdmf_zarr/nwb.py 85.71% 1 Missing and 1 partial ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##              dev     #226      +/-   ##
==========================================
+ Coverage   85.56%   85.64%   +0.07%     
==========================================
  Files           5        5              
  Lines        1185     1198      +13     
  Branches      292      297       +5     
==========================================
+ Hits         1014     1026      +12     
+ Misses        115      113       -2     
- Partials       56       59       +3     

☔ View full report in Codecov by Sentry.
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@oruebel oruebel added this to the Next Major Release: 1.0.0 milestone Nov 7, 2024
@oruebel oruebel marked this pull request as ready for review November 7, 2024 02:11
@rly
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rly commented Nov 7, 2024

When you are done with this @oruebel, can you work on #140 and also maybe copy NWB-related tutorials to PyNWB?

@oruebel
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oruebel commented Nov 7, 2024

🆗

@oruebel oruebel enabled auto-merge (squash) November 8, 2024 20:05
@oruebel oruebel merged commit eae8fb5 into dev Nov 8, 2024
22 checks passed
@oruebel oruebel deleted the add/read_nwb_func branch November 8, 2024 20:06
@@ -12,6 +12,7 @@
* Added test for opening file with consolidated metadata from DANDI. @mavaylon1 [#206](https://github.com/hdmf-dev/hdmf-zarr/pull/206)
* Add dimension labels compatible with xarray. @mavaylon1 [#207](https://github.com/hdmf-dev/hdmf-zarr/pull/207)
* Added link_data --> clear_cache relationship to support repacking zarr nwbfiles: [#215](https://github.com/hdmf-dev/hdmf-zarr/pull/215)
* Added `NWBZarrIO.read_nwb` convenience method to simplify reading an NWB file. @oruebel [#226](https://github.com/hdmf-dev/hdmf-zarr/pull/226)

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@mavaylon1, was this released already? it is on the changelog on the 0.9.0 release but the PR was merged a week ago. Is that a changelog error?

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This has not been released yet. The changelog is a mistake that we will fix. Thanks.

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[Feature]: Add NWBZarrIO.read_nwb method
5 participants