Merge pull request #861 from danielballan/zarr-cleanup

Zarr cleanup

CHANGELOG.md

@@ -5,6 +5,13 @@ Write the date in place of the "Unreleased" in the case a new version is release
 
 ## Unreleased
 
+### Changed
+
+- Refactor and standardize Adapter API: implement from_uris and from_catalog
+  classmethods for instantiation from files and registered Tiled nodes, respectively.
+- Refactor CSVAdapter to allow pd.read_csv kwargs
+- Removed `tiled.adapters.zarr.read_zarr` utility function.
+
 ### Added
 
 - Added `.get` methods on TableAdapter and ParquetDatasetAdapter
@@ -18,6 +25,7 @@ Write the date in place of the "Unreleased" in the case a new version is release
   mode in the `AboutAuthenticationProvider` schema to be `internal`|`external`.
 - Improved type hinting and efficiency of caching singleton values
 
+
 ## v0.1.0-b16 (2024-01-23)
 
 ### Maintenance
@@ -39,9 +47,6 @@ Write the date in place of the "Unreleased" in the case a new version is release
   `public_keys`, which can be fetched at initialization (server startup) time.
   See examples `example_configs/orcid_auth.yml`,
   `example_configs/google_auth.yml`, and `example_configs/simple_oidc`.
-- Refactor and standardize Adapter API: implement from_uris and from_catalog
-  classmethods for instantiation from files and registered Tiled nodes, respectively.
-- Refactor CSVAdapter to allow pd.read_csv kwargs
 
 ### Maintenance
 

tiled/adapters/zarr.py

@@ -23,24 +23,6 @@
 INLINED_DEPTH = int(os.getenv("TILED_HDF5_INLINED_CONTENTS_MAX_DEPTH", "7"))
 
 
-def read_zarr(
-    data_uri: str,
-    structure: Optional[ArrayStructure] = None,
-    **kwargs: Any,
-) -> Union["ZarrGroupAdapter", ArrayAdapter]:
-    filepath = path_from_uri(data_uri)
-    zarr_obj = zarr.open(filepath)  # Group or Array
-    adapter: Union[ZarrGroupAdapter, ArrayAdapter]
-    if isinstance(zarr_obj, zarr.hierarchy.Group):
-        adapter = ZarrGroupAdapter(zarr_obj, **kwargs)
-    else:
-        if structure is None:
-            adapter = ZarrArrayAdapter.from_array(zarr_obj, **kwargs)
-        else:
-            adapter = ZarrArrayAdapter(zarr_obj, structure=structure, **kwargs)
-    return adapter
-
-
 class ZarrArrayAdapter(ArrayAdapter):
     """ """
 
@@ -381,7 +363,7 @@ def from_catalog(
         zarr_obj = zarr.open(
             path_from_uri(data_source.assets[0].data_uri)
         )  # Group or Array
-        if isinstance(zarr_obj, zarr.hierarchy.Group):
+        if node.structure_family == StructureFamily.container:
             return ZarrGroupAdapter(
                 zarr_obj,
                 structure=data_source.structure,