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Add --scalar-columns parameter to NIfTI and MIF CLIs#34

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tsalo wants to merge 12 commits intomainfrom
scalar-columns
Open

Add --scalar-columns parameter to NIfTI and MIF CLIs#34
tsalo wants to merge 12 commits intomainfrom
scalar-columns

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@tsalo
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@tsalo tsalo commented Mar 26, 2026

Closes #32. Closes #33.

@tsalo tsalo added the enhancement New feature or request label Mar 26, 2026
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codecov-commenter commented Mar 26, 2026

Codecov Report

❌ Patch coverage is 47.65101% with 78 lines in your changes missing coverage. Please review.
✅ Project coverage is 58.16%. Comparing base (50e1c2e) to head (f1cdfc0).

Files with missing lines Patch % Lines
src/modelarrayio/utils/mif.py 12.90% 26 Missing and 1 partial ⚠️
src/modelarrayio/cli/mif_to_h5.py 13.79% 24 Missing and 1 partial ⚠️
src/modelarrayio/cli/nifti_to_h5.py 35.48% 17 Missing and 3 partials ⚠️
src/modelarrayio/utils/misc.py 90.47% 2 Missing and 2 partials ⚠️
src/modelarrayio/cli/cifti_to_h5.py 88.88% 1 Missing ⚠️
src/modelarrayio/storage/tiledb_storage.py 0.00% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main      #34      +/-   ##
==========================================
- Coverage   61.19%   58.16%   -3.04%     
==========================================
  Files          16       17       +1     
  Lines         951     1023      +72     
  Branches      137      161      +24     
==========================================
+ Hits          582      595      +13     
- Misses        332      386      +54     
- Partials       37       42       +5     

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@mattcieslak
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I think the way to go here is to make multiple h5 files, since using that is supported in ModelArray now. This won't make a difference for tiledb, since the scalars all go into different files in its root directory anyways. Separate h5's let users mix and match when modeling and also the reshaping from long to wide during the ModelArray runs adds up

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Leverage workers and s3-workers in all to-h5 CLIs Support --scalar-columns in nifti-to-h5 and mif-to-h5

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