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Prepare ophys metadata for dict-based format#1680

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h-mayorquin merged 13 commits intomainfrom
prepare_ophys_metadata
Mar 3, 2026
Merged

Prepare ophys metadata for dict-based format#1680
h-mayorquin merged 13 commits intomainfrom
prepare_ophys_metadata

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Preparation for the ophys metadata restructuring described in PR #1653.

Removes deprecated wrapper functions from roiextractors_pending_deprecation.py (March 2026 deadline). Adds keyword-only parameter enforcement to add_imaging_to_nwbfile via *args with FutureWarning. Renames internal functions with _old_list_format / _old_metadata_list suffixes to make it explicit that they operate on the current list-based metadata format.

@h-mayorquin h-mayorquin marked this pull request as ready for review March 3, 2026 04:08
@h-mayorquin h-mayorquin requested a review from pauladkisson March 3, 2026 04:08
@h-mayorquin h-mayorquin self-assigned this Mar 3, 2026
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Looks good to me!

@h-mayorquin h-mayorquin enabled auto-merge (squash) March 3, 2026 20:43
@h-mayorquin h-mayorquin merged commit dac02a7 into main Mar 3, 2026
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@h-mayorquin h-mayorquin deleted the prepare_ophys_metadata branch March 3, 2026 22:01
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codecov bot commented Mar 3, 2026

Codecov Report

❌ Patch coverage is 63.88889% with 13 lines in your changes missing coverage. Please review.
✅ Project coverage is 81.01%. Comparing base (c7f0869) to head (3b5d576).
⚠️ Report is 4 commits behind head on main.

Files with missing lines Patch % Lines
src/neuroconv/tools/roiextractors/roiextractors.py 55.17% 13 Missing ⚠️
Additional details and impacted files

Impacted file tree graph

@@            Coverage Diff             @@
##             main    #1680      +/-   ##
==========================================
+ Coverage   80.23%   81.01%   +0.78%     
==========================================
  Files         160      160              
  Lines       12663    12471     -192     
==========================================
- Hits        10160    10104      -56     
+ Misses       2503     2367     -136     
Flag Coverage Δ
unittests 81.01% <63.88%> (+0.78%) ⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines Coverage Δ
...rfaces/ophys/basesegmentationextractorinterface.py 79.31% <100.00%> (ø)
...tainterfaces/ophys/miniscope/miniscopeconverter.py 95.23% <100.00%> (ø)
...s/ophys/miniscope/miniscopeimagingdatainterface.py 78.04% <100.00%> (ø)
src/neuroconv/tools/roiextractors/__init__.py 100.00% <ø> (ø)
...roiextractors/roiextractors_pending_deprecation.py 87.50% <100.00%> (+51.37%) ⬆️
src/neuroconv/tools/roiextractors/roiextractors.py 75.18% <55.17%> (-1.78%) ⬇️
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