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Add Support for Zarr-backed DelayedArray reading - #507

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Artur-man:delayed_zarr
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Add Support for Zarr-backed DelayedArray reading#507
Artur-man wants to merge 7 commits into
scverse:develfrom
Artur-man:delayed_zarr

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@Artur-man

@Artur-man Artur-man commented Aug 21, 2026

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Description

This is a draft PR that adds new support for reading dense and sparse matrices as Zarr-backed DelayedArray objects.

  • Use the {ZarrArray} package for lazily reading dense and sparse arrays from Zarr stores
  • Add a backed argument to ZarrAnnData, read_zarr etc.
  • Conversion of Zarr-backed AnnData objects to SingleCellExperiment/Seurat while keeping dense and sparse matrices as {ZarrArray} objects.

Checklist

Before review

  • Update and regenerate man pages (needed?)
  • Add/update tests
  • Add/update examples in vignettes (needed?)
  • Pass CI checks

Before merge

  • Update NEWS
  • Bump devel version

@Artur-man
Artur-man marked this pull request as draft August 21, 2026 15:30
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github-actions Bot commented Aug 21, 2026

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🐰 Bencher Report

ProjectanndataR
Branchdelayed_zarr
Testbedubuntu-latest

⚠️ WARNING: Truncated view!

The full continuous benchmarking report exceeds the maximum length allowed on this platform.

🚨 1 Alert

🐰 View full continuous benchmarking report in Bencher

@Artur-man

Artur-man commented Aug 23, 2026

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These errors are caused by a novel warning thrown by rhdf5, caused by warnings for writing numeric vectors with NAs which is now deprecated, otherwise works as intended.

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