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Integrate TypeConfig #1829

Merged
merged 51 commits into from
May 22, 2024
Merged

Integrate TypeConfig #1829

merged 51 commits into from
May 22, 2024

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mavaylon1
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@mavaylon1 mavaylon1 commented Jan 18, 2024 •
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Motivation

Integrate TypeConfigurator from HDMF to pynwb. Also provide documentation.

  • load and unload should use the load and unload from hdmf
  • [x ] tutorial
  • restructure the default configs to match the new structure set in hdmf
  • [x ] tests

What was the reasoning behind this change? Please explain the changes briefly.

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.

oruebel
oruebel reviewed Jan 19, 2024
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src/pynwb/__init__.py Outdated Show resolved Hide resolved
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codecov bot commented Mar 3, 2024 •
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 92.09%. Comparing base (014b143) to head (4fe39f0).
Report is 18 commits behind head on dev.

Additional details and impacted files 
@@            Coverage Diff             @@
##              dev    #1829      +/-   ##
==========================================
+ Coverage   92.02%   92.09%   +0.06%     
==========================================
  Files          27       27              
  Lines        2620     2643      +23     
  Branches      685      689       +4     
==========================================
+ Hits         2411     2434      +23     
  Misses        139      139              
  Partials       70       70
Flag Coverage Δ
integration 73.13% <60.86%> (-0.11%) ⬇️
unit 84.07% <100.00%> (+0.13%) ⬆️

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@mavaylon1 mavaylon1 changed the title Integrate TermSetConfigurator Integrate TypeConfig May 20, 2024
rly
rly reviewed May 21, 2024
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rly
rly reviewed May 21, 2024
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rly commented May 21, 2024

I think we need to figure out the workflow for a user who has installed pynwb via pip. Otherwise this all looks good.

@mavaylon1 mavaylon1 requested a review from rly May 22, 2024 17:16
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@rly issue ticket has been made, link has been added with what would be the link after merge.

@mavaylon1 mavaylon1 requested a review from rly May 22, 2024 20:55
@rly rly mentioned this pull request May 22, 2024
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rly
rly previously approved these changes May 22, 2024
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@mavaylon1 mavaylon1 enabled auto-merge (squash) May 22, 2024 22:30
rly
rly previously approved these changes May 22, 2024
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rly commented May 22, 2024 •
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In a separate PR, I updated the dev branch to use HDMF 3.14.0 throughout, so the ros3 test should pass now.

@mavaylon1 mavaylon1 merged commit 2f851df into dev May 22, 2024
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@mavaylon1 mavaylon1 deleted the tmc branch May 22, 2024 23:36
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@rly rly rly approved these changes

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@mavaylon1 @rly @oruebel