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Require zarr 3.1.2 or newer #1257

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5f9a120
Require zarr 3.1.2 or newer
Darlokt Sep 21, 2026
00dfd27
Add issue number to changelog
Darlokt Sep 22, 2026
f266d36
Merge branch 'main' into fix-zarr-lower-bound
Darlokt Sep 27, 2026
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1 change: 1 addition & 0 deletions docs/changelog.md
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Expand Up @@ -13,4 +13,5 @@ For developers, please consult the [contributing guide](https://github.com/scver

### Fixed

- Require Zarr 3.1.2 or newer, which provides the `ArrayNotFoundError` used by SpatialData's persistence layer. (#1256)
- Querying a `SpatialData` object with multiple (batched) bounding boxes now raises an explicit `NotImplementedError` instead of failing with an opaque `AssertionError`. Batched queries are supported when querying a `SpatialElement` directly, but not when querying a `SpatialData` object, since that would require returning one `SpatialData` object per bounding box.
5 changes: 3 additions & 2 deletions pyproject.toml
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Expand Up @@ -53,7 +53,7 @@ dependencies = [
"universal-pathlib>=0.2.6",
"xarray>=2024.10",
"xarray-spatial>=0.3.5",
"zarr>=3",
"zarr>=3.1.2",
]
optional-dependencies.extra = [
"napari-spatialdata[all]",
Expand Down Expand Up @@ -140,6 +140,7 @@ envs.hatch-test.overrides.matrix.deps.env-vars = [
envs.hatch-test.overrides.matrix.deps.extra-dependencies = [
{ value = "dask==2026.3.0", if = [ "min" ] },
{ value = "distributed==2026.3.0", if = [ "min" ] },
{ value = "zarr==3.1.2", if = [ "min" ] },
]
envs.hatch-test.dependency-groups = [ "dev", "test" ]
envs.hatch-check-fmt.dependencies = [ "prek" ]
Expand All @@ -151,7 +152,7 @@ envs.hatch-check-code.scripts.lint-fix = "prek run -a --no-group=format --no-gro
envs.hatch-check-types.scripts.check = [ "mypy" ]
envs.hatch-check-types.dependency-groups = [ "typecheck", "test" ]
# Not part of the CI matrix; run locally with `hatch run test-anndata-pandas:test`.
envs.test-anndata-pandas.extra-dependencies = [ "zarr>=3" ]
envs.test-anndata-pandas.extra-dependencies = [ "zarr>=3.1.2" ]
envs.test-anndata-pandas.scripts.test = [ "pip list|grep anndata && pip list|grep pandas && pytest {args}" ]
envs.test-anndata-pandas.scripts.test-all = [ "pip list|grep anndata && pip list|grep pandas && pytest ." ]
envs.test-anndata-pandas.scripts.test-readwrite = [
Expand Down
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