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Add Zarr reader for CLI and library - #164

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Dhanush010 wants to merge 11 commits into
idtlab:developfrom
Dhanush010:feat/zarr-reader
Open

Add Zarr reader for CLI and library#164
Dhanush010 wants to merge 11 commits into
idtlab:developfrom
Dhanush010:feat/zarr-reader

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@Dhanush010

@Dhanush010 Dhanush010 commented Jul 21, 2026

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Description

Add a Zarr directory store reader for CLI and library use (Globus type list included; local browser upload intentionally not enabled yet, Zarr stores are directories; zip/UI upload is deferred).

Summary

  • Add zarrReader with inventory(), read(), get_metadata(), and selected_keys for multi array stores (same selection model as HDF5)
  • Register .zarr in READER_MAP for CLI/library; expose Zarr via GLOBUS_FILE_TYPES only (not the local upload dropdown)
  • Add CLI/library/batch -selected keys / selected keys for HDF5 and Zarr path selection
  • Add optional aidrin[zarr] dependency (zarr>=3.0.8,<3.2 on Python ≥3.11)
  • Docs: CLI usage notes for Zarr and selected keys

Scope / limitations

  • Directory path Zarr only (CLI, library, Globus listed but not the focus of this PR)
  • Metrics expect tabular / compatible 1D arrays (or a single 2D array). Multi dim grids (ndim ≥ 3) are refused, no averaging/flattening inside AIDRIN, so metrics see raw values only
  • Local web upload of .zarr is out of scope

What changes are proposed in this pull request?

  • Bug fix (non-breaking change which fixes an issue)
  • New feature (non-breaking change which adds functionality)
  • Breaking change (fix or feature that would cause existing functionality not to work as expected; for instance, examples in this repository must be updated too)
  • This change requires a documentation update

Checklist:

  • My code modifies existing public API, or introduces new public API, and I updated or wrote documentation
  • I have commented my code
  • My code requires documentation updates, and I have made corresponding changes to the documentation
  • I have added tests that prove my fix is effective or that my feature works
  • New and existing unit tests pass locally with my changes

@Dhanush010 Dhanush010 changed the title Add Zarr reader for CLI, library, and Globus. Add Zarr reader for CLI and library Aug 4, 2026
@Dhanush010
Dhanush010 marked this pull request as ready for review August 4, 2026 18:29
@Dhanush010
Dhanush010 requested a review from a team as a code owner August 4, 2026 18:29
@Dhanush010
Dhanush010 requested a review from kaveenh August 4, 2026 18:29
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