SpatialData 0.8.0 permits Zarr versions that do not provide ArrayNotFoundError

Start by checking the published dependency metadata and the persistence module used by read_zarr. Reproduce the failure with the provided isolated Python commands using Zarr 3.1.1 and 3.1.2. Done means dependency resolution no longer permits versions missing ArrayNotFoundError, and importing read_zarr succeeds in the documented environment.

Report

Hej everyone,
I found and error while working.
SpatialData 0.8.0 declares zarr>=3.0.0, but its persistence module imports ArrayNotFoundError from zarr.errors.
That exception is unavailable in Zarr 3.0.0 through 3.1.1 and was added in Zarr 3.1.2.
Consequently, dependency resolution can produce a valid environment according to the published package metadata in which importing read_zarr fails.

Minimal reproduction

In a clean environment:

$ uv run --isolated --python 3.12 \
    --with 'spatialdata==0.8.0' \
    --with 'zarr==3.1.1' \
    python -c 'from spatialdata import read_zarr'
ImportError: cannot import name 'ArrayNotFoundError' from 'zarr.errors'

The same failure occurs with Zarr 3.0.0 and 3.1.0. The import succeeds with
Zarr 3.1.2:

$ uv run --isolated --python 3.12 \
    --with 'spatialdata==0.8.0' \
    --with 'zarr==3.1.2' \
    python -c 'from spatialdata import read_zarr; print(read_zarr.__name__)'
read_zarr

Versions

| Package     | Version |
| ----------- | ------- |
| spatialdata | 0.8.0   |
| zarr        | 3.1.1   |

| Dependency               | Version                |
| ------------------------ | ---------------------- |
| google-crc32c            | 1.8.0                  |
| wrapt                     | 2.1.2                  |
| dask                      | 2026.8.0               |
| numcodecs                 | 0.16.5                 |
| typing_extensions         | 4.15.0                 |
| natsort                   | 8.4.0                  |
| scipy                     | 1.17.1                 |
| packaging                 | 26.2                   |
| six                       | 1.17.0                 |
| array-api-compat          | 1.14.0                 |
| typing-inspection         | 0.4.2                  |
| crc32c                    | 2.9.post0              |
| pandas                    | 2.3.3                  |
| charset-normalizer       | 3.4.7                  |
| transformnd              | 0.7.2                  |
| zstandard                | 0.25.0                 |
| legacy-api-wrap          | 1.5                    |
| Deprecated               | 1.3.1                  |
| pydantic                 | 2.12.5                 |
| pytz                     | 2026.2                 |
| scikit-image             | 0.26.0                 |
| shapely                  | 2.1.2                  |
| setuptools               | 82.0.1                 |
| tblib                    | 3.2.2                  |
| pydantic_core            | 2.41.5                 |
| certifi                  | 2026.4.22 (2026.04.22) |
| Jinja2                   | 3.1.6                  |
| lazy-loader              | 0.5                    |
| scverse-misc             | 0.1.6                  |
| pyarrow                  | 24.0.0                 |
| pyproj                   | 3.7.2                  |
| cloudpickle              | 3.1.2                  |
| fsspec                   | 2026.4.0               |
| numpy                    | 2.4.5                  |
| PyYAML                   | 6.0.3                  |
| xarray                   | 2026.4.0               |
| ome-zarr-models          | 1.8.1                  |
| session-info2            | 0.4.1                  |
| toolz                    | 1.1.0                  |
| spatial_image            | 1.2.3                  |
| rich                     | 15.0.0                 |
| xarray-dataclass         | 3.0.0                  |
| python-dateutil          | 2.9.0.post0            |
| MarkupSafe               | 3.0.3                  |
| annotated-types          | 0.7.0                  |
| psutil                   | 7.2.2                  |
| networkx                 | 3.6.1                  |
| h5py                     | 3.16.0                 |
| anndata                  | 0.12.14                |
| pydantic-zarr            | 0.10.0                 |
| geopandas                | 1.1.3                  |
| ome-zarr                 | 0.19.2                 |
| donfig                   | 0.8.1.post1            |
| multiscale_spatial_image | 2.0.3                  |
| msgpack                  | 1.1.2                  |

| Component | Info                                                          |
| --------- | ------------------------------------------------------------- |
| Python    | 3.12.3 (main, Aug 31 2026, 10:18:26) [GCC 13.3.0]             |
| OS        | Linux-6.18.33.2-microsoft-standard-WSL2-x86_64-with-glibc2.39 |
| Updated   | 2026-09-21 20:54                                              |