cannot import name 'ConsolidatedMetadataStore' from 'zarr.storage'

Hello,

I don't succeed to export my spatialdata with the function write into a zarr and I've been able to reproduce it with the dataset blob.

from spatialdata.datasets import blobs

test = blobs()
test.write(working_dir + 'test.zarr')

Give the following error:

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
Cell In[5], line 4
      1 from spatialdata.datasets import blobs
      3 test = blobs()
----> 4 test.write(working_dir + 'test.zarr')

File /micromamba/me/envs/sopa/lib/python3.12/site-packages/spatialdata/_utils.py:263, in _deprecation_alias.<locals>.deprecation_decorator.<locals>.wrapper(*args, **kwargs)
    261     raise ValueError("version for deprecation must be specified")
    262 rename_kwargs(f.__name__, kwargs, alias_copy, class_name, library, version)
--> 263 return f(*args, **kwargs)

File /micromamba/me/envs/sopa/lib/python3.12/site-packages/spatialdata/_core/spatialdata.py:1177, in SpatialData.write(self, file_path, overwrite, consolidate_metadata, update_sdata_path, sdata_formats)
   1174 store.close()
   1176 for element_type, element_name, element in self.gen_elements():
-> 1177     self._write_element(
   1178         element=element,
   1179         zarr_container_path=file_path,
   1180         element_type=element_type,
   1181         element_name=element_name,
   1182         overwrite=False,
   1183         parsed_formats=parsed,
   1184     )
   1186 if self.path != file_path and update_sdata_path:
   1187     self.path = file_path

File /micromamba/me/envs/sopa/lib/python3.12/site-packages/spatialdata/_core/spatialdata.py:1254, in SpatialData._write_element(self, element, zarr_container_path, element_type, element_name, overwrite, parsed_formats)
   1248     write_shapes(
   1249         shapes=element,
   1250         group=element_group,
   1251         element_format=parsed_formats["shapes"],
   1252     )
   1253 elif element_type == "tables":
-> 1254     write_table(
   1255         table=element,
   1256         group=element_type_group,
   1257         name=element_name,
   1258         element_format=parsed_formats["tables"],
   1259     )
   1260 else:
   1261     raise ValueError(f"Unknown element type: {element_type}")

File /micromamba/meenvs/sopa/lib/python3.12/site-packages/spatialdata/_io/io_table.py:63, in write_table(table, group, name, group_type, element_format)
     60 else:
     61     region, region_key, instance_key = (None, None, None)
---> 63 write_adata(group, name, table)
     64 tables_group = group[name]
     65 tables_group.attrs["spatialdata-encoding-type"] = group_type

File /micromamba/me/envs/sopa/lib/python3.12/site-packages/anndata/_io/specs/registry.py:518, in write_elem(store, k, elem, dataset_kwargs)
    494 def write_elem(
    495     store: GroupStorageType,
    496     k: str,
   (...)    499     dataset_kwargs: Mapping[str, Any] = MappingProxyType({}),
    500 ) -> None:
    501     """
    502     Write an element to a storage group using anndata encoding.
    503 
   (...)    516         E.g. for zarr this would be `chunks`, `compressor`.
    517     """
--> 518     Writer(_REGISTRY).write_elem(store, k, elem, dataset_kwargs=dataset_kwargs)

File /micromamba/me/envs/sopa/lib/python3.12/site-packages/anndata/_io/utils.py:272, in report_write_key_on_error.<locals>.func_wrapper(*args, **kwargs)
    270     raise ValueError(msg)
    271 try:
--> 272     return func(*args, **kwargs)
    273 except Exception as e:
    274     path = _get_display_path(store)

File /micromamba/me/envs/sopa/lib/python3.12/site-packages/anndata/_io/specs/registry.py:372, in Writer.write_elem(self, store, k, elem, dataset_kwargs, modifiers)
    368 if (is_zarr_group and is_zarr_v2()) or (
    369     isinstance(store, h5py.Group) and not PurePosixPath(k).is_absolute()
    370 ):
    371     k = str(PurePosixPath(store.name) / k)
--> 372 is_consolidated = is_group_consolidated(store) if is_zarr_group else False
    373 if is_consolidated:
    374     msg = "Cannot overwrite/edit a store with consolidated metadata"

File /micromamba/me/envs/sopa/lib/python3.12/site-packages/anndata/_io/zarr.py:167, in is_group_consolidated(group)
    165     raise TypeError(msg)
    166 if is_zarr_v2():
--> 167     from zarr.storage import ConsolidatedMetadataStore
    169     return isinstance(group.store, ConsolidatedMetadataStore)
    170 return group.metadata.consolidated_metadata is not None

ImportError: cannot import name 'ConsolidatedMetadataStore' from 'zarr.storage' (/micromamba/me/envs/sopa/lib/python3.12/site-packages/zarr/storage/__init__.py)
Error raised while writing key 'table' of <class 'zarr.core.group.Group'> to /tables

I work with the conda package of spatialdata version 0.6.1

Desktop (optional):

• OS: RedHat 8.7

Thanks for the package !
Lea

Start at SpatialData.write and the table-writing path shown in the traceback, then inspect anndata's zarr writer and the installed zarr version. Reproduce the failure with spatialdata.datasets.blobs() and test.write(...); done means the dataset writes to a zarr store without the ConsolidatedMetadataStore import error.