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Add streaming example for NWB files from DANDI using Zarr #2037

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Motivation

Cline-assisted

This PR adds documentation for streaming Zarr files from DANDI (Fix #1930). DANDI provides access to large neuroscience datasets, and many of these are stored in Zarr format. Adding a dedicated section to the Zarr I/O tutorial will help users understand how to efficiently stream and process these large datasets without loading them entirely into memory.

The changes add a new section to the existing Zarr I/O tutorial that demonstrates:

  • Connecting to DANDI and accessing datasets
  • Setting up S3 access for cloud storage
  • Efficiently streaming and processing data in chunks
  • Proper resource cleanup

How to test the behavior?

  1. Install required packages:
pip install pynwb hdmf-zarr dandi s3fs
  1. Run the updated Zarr I/O tutorial:
cd docs/gallery/advanced_io
python plot_zarr_io.py
  1. Verify that the new DANDI streaming section executes successfully and demonstrates efficient data access patterns.

Changes Made

  1. Added new section "Streaming from DANDI" to docs/gallery/advanced_io/plot_zarr_io.py
  2. Updated CHANGELOG.md with new documentation addition

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 ruff check . && codespell 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 [Documentation]: How to stream Zarr files from DANDI #1930" notation?

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codecov bot commented Feb 11, 2025

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 91.73%. Comparing base (bc12931) to head (1328668).

Additional details and impacted files
@@           Coverage Diff           @@
##              dev    #2037   +/-   ##
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  Coverage   91.73%   91.73%           
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  Files          27       27           
  Lines        2722     2722           
  Branches      710      710           
=======================================
  Hits         2497     2497           
  Misses        149      149           
  Partials       76       76           
Flag Coverage Δ
integration 72.96% <ø> (ø)
unit 82.29% <ø> (ø)

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[Documentation]: How to stream Zarr files from DANDI
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