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[ENH] Add Study and NipoppyDataAPI classes #816

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[ENH] Add Study and NipoppyDataAPI classes #816

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@michellewang michellewang commented Nov 6, 2025 •
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Changes proposed in this pull request:

  • Extract Study class from BaseDatasetWorkflow in preparation for eventual deeper refactor
    • Contains layout, manifest, config, curation_status_table and processing_status_table
    • Does not have dicom_dir_map for now, I'm not sure how to handle this since the map is not necessarily a file on disk
  • Create NipoppyDataAPI class for getting tabular data from disk
    • Currently only supports tabular derivatives (output/IDP) data, but will add demographics data soon (need to discuss a bit more/check with Neurobagel team)

Checklist (for reviewers)

This section is for the PR reviewer

  • PR has an interpretable title with a prefix (e.g. [BUG], [DOC], [ENH], [MAINT])
    Refer to NumPy Development Guide for a full list
  • PR links to GitHub issue with mention Closes #XXXX
  • Tests pass
  • Checks pass

For new features:

  • Tests have been added

For bug fixes:

  • There is at least one test that would fail under the original bug conditions

📚 Documentation preview 📚: https://nipoppy--816.org.readthedocs.build/en/816/

@github-actions github-actions bot added the T.1 - Enhancement New feature or request label Nov 6, 2025
@nipoppy-bot nipoppy-bot bot added this to Software Nov 6, 2025
@nipoppy-bot nipoppy-bot bot moved this to Pending review in Software Nov 6, 2025
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codecov bot commented Nov 6, 2025 •
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Codecov Report

❌ Patch coverage is 99.24242% with 1 line in your changes missing coverage. Please review.

Files with missing lines Patch % Lines
nipoppy/data_api.py 97.05% 1 Missing ⚠️
Files with missing lines Coverage Δ
nipoppy/study.py 100.00% <100.00%> (ø)
nipoppy/workflows/base.py 98.83% <100.00%> (-0.14%) ⬇️
nipoppy/workflows/bids_conversion.py 100.00% <100.00%> (ø)
nipoppy/workflows/dataset_init.py 98.96% <100.00%> (ø)
nipoppy/workflows/dataset_status.py 100.00% <100.00%> (ø)
nipoppy/workflows/dicom_reorg.py 100.00% <ø> (ø)
nipoppy/workflows/extractor.py 100.00% <100.00%> (ø)
nipoppy/workflows/pipeline.py 99.74% <100.00%> (ø)
nipoppy/workflows/pipeline_store/install.py 100.00% <100.00%> (ø)
nipoppy/workflows/pipeline_store/list.py 100.00% <ø> (ø)
... and 5 more

... and 1 file with indirect coverage changes

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mathdugre
mathdugre requested changes Nov 11, 2025
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@github-project-automation github-project-automation bot moved this from Pending review to Reviewed in Software Nov 11, 2025
@nipoppy-bot nipoppy-bot bot moved this from Reviewed to Pending review in Software Nov 12, 2025
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@mathdugre mathdugre Awaiting requested review from mathdugre

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[ENH] Create NipoppyStudy class for representing a Nipoppy dataset

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@michellewang @mathdugre