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[Bug] spatialdata==0.3.0 pins zarr<3 which is incompatible with latest numcodecs (0.16.0) #3917

@ryan-williams

Description

@ryan-williams

Describe the bug
Per zarr-developers/zarr-python#2963.

This resulted in import zarr raising ImportError in unrelated GHA on #3916:

  File "/home/runner/work/TileDB-SOMA/TileDB-SOMA/venv-soma/lib/python3.11/site-packages/zarr/convenience.py", line 8, in <module>
    from zarr._storage.store import data_root, meta_root, assert_zarr_v3_api_available
  File "/home/runner/work/TileDB-SOMA/TileDB-SOMA/venv-soma/lib/python3.11/site-packages/zarr/_storage/store.py", line 10, in <module>
    from zarr.meta import Metadata2, Metadata3
  File "/home/runner/work/TileDB-SOMA/TileDB-SOMA/venv-soma/lib/python3.11/site-packages/zarr/meta.py", line 10, in <module>
    from zarr.util import json_dumps, json_loads
  File "/home/runner/work/TileDB-SOMA/TileDB-SOMA/venv-soma/lib/python3.11/site-packages/zarr/util.py", line 34, in <module>
    from numcodecs.blosc import cbuffer_sizes, cbuffer_metainfo
ImportError: cannot import name 'cbuffer_sizes' from 'numcodecs.blosc' (/home/runner/work/TileDB-SOMA/TileDB-SOMA/venv-soma/lib/python3.11/site-packages/numcodecs/blosc.cpython-311-x86_64-linux-gnu.so)
Error: Process completed with exit code 1.

To Reproduce
See GHA example.

Versions (please complete the following information):

  • TileDB-SOMA version: main
  • Language and language version: Python 3.11 (but probably all versions)
  • OS: macOS, Ubuntu

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