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Require zarr 3.1.2 or newer - #1257

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Darlokt wants to merge 2 commits into
scverse:mainfrom
Darlokt:fix-zarr-lower-bound
Open

Darlokt wants to merge 2 commits into
scverse:mainfrom
Darlokt:fix-zarr-lower-bound

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@Darlokt

@Darlokt Darlokt commented Sep 22, 2026

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Hej,
Here is the fix.
SpatialData imports ArrayNotFoundError from zarr.errors, but that exception was only added in Zarr 3.1.2.
The existing zarr>=3 requirement therefore allowed incompatible versions to be installed, causing imports of the persistence API to fail.

Changes

  • Raise the package requirement to zarr>=3.1.2.
  • Pin Zarr to 3.1.2 in Hatch’s minimum-dependency test environment.
  • Update the local test-anndata-pandas Hatch environment to use zarr>=3.1.2.
  • Add a changelog entry.

Refrences

SpatialData imports ArrayNotFoundError, which is unavailable in Zarr 3.0.0 through 3.1.1.

Raise the dependency floor and exercise that exact version in the minimum-dependency test environment.

This fixes the invalid dependency range introduced by scverse#985.
@codecov

codecov Bot commented Sep 22, 2026

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 91.40%. Comparing base (65dc73e) to head (00dfd27).

Additional details and impacted files
@@           Coverage Diff           @@
##             main    #1257   +/-   ##
=======================================
  Coverage   91.40%   91.40%           
=======================================
  Files          53       53           
  Lines        8381     8381           
=======================================
  Hits         7661     7661           
  Misses        720      720           
🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

@Darlokt

Darlokt commented Sep 22, 2026

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The failures are unrelated, also fyi your issue templates are broke, no tags are assigned.

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SpatialData 0.8.0 permits Zarr versions that do not provide ArrayNotFoundError

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