Use zarr.hierarchy.Group for type hints (ref #587)

fractal_tasks_core/lib_ngff.py

@@ -6,7 +6,7 @@
 from typing import Optional
 from typing import Union
 
-import zarr
+import zarr.hierarchy
 from pydantic import BaseModel
 from pydantic import Field
 from pydantic import validator
@@ -422,7 +422,7 @@ def load_NgffWellMeta(zarr_path: str) -> NgffWellMeta:
         raise e
 
 
-def detect_ome_ngff_type(group: zarr.Group) -> str:
+def detect_ome_ngff_type(group: zarr.hierarchy.Group) -> str:
     """
     Given a Zarr group, find whether it is an OME-NGFF plate, well or image.
 

fractal_tasks_core/lib_write.py

@@ -18,7 +18,7 @@
 from typing import Union
 
 import anndata as ad
-import zarr
+import zarr.hierarchy
 from anndata.experimental import write_elem
 from zarr.errors import ContainsGroupError
 from zarr.errors import GroupNotFoundError
@@ -36,7 +36,7 @@ def open_zarr_group_with_overwrite(
     overwrite: bool,
     logger: Optional[logging.Logger] = None,
     **open_group_kwargs: Any,
-) -> zarr.Group:
+) -> zarr.hierarchy.Group:
     """
     Wrap `zarr.open_group` and add `overwrite` argument.
 
@@ -124,7 +124,7 @@ def open_zarr_group_with_overwrite(
 
 
 def _write_elem_with_overwrite(
-    group: zarr.Group,
+    group: zarr.hierarchy.Group,
     key: str,
     elem: Any,
     *,
@@ -186,7 +186,7 @@ def _write_elem_with_overwrite(
 
 
 def write_table(
-    image_group: zarr.Group,
+    image_group: zarr.hierarchy.Group,
     table_name: str,
     table: ad.AnnData,
     overwrite: bool = False,
@@ -300,7 +300,7 @@ def write_table(
 
 
 def prepare_label_group(
-    image_group: zarr.Group,
+    image_group: zarr.hierarchy.Group,
     label_name: str,
     overwrite: bool = False,
     label_attrs: Optional[dict[str, Any]] = None,