[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

ome_zarr/format.py

@@ -4,11 +4,9 @@
 from abc import ABC, abstractmethod
 from typing import Any, Dict, Iterator, List, Optional
 
-from zarr.v2.storage import FSStore
-
-from zarr.store import LocalStore, RemoteStore
-from zarr.store import StoreLike, StorePath
 from zarr.abc.store import Store
+from zarr.store import LocalStore, RemoteStore, StoreLike, StorePath
+from zarr.v2.storage import FSStore
 
 LOGGER = logging.getLogger("ome_zarr.format")
 
@@ -200,7 +198,6 @@ def version(self) -> str:
 
     #     mkdir = True
 
-
     #     if "r" in mode or path.startswith(("http", "s3")):
     #         # Could be simplified on the fsspec side
     #         mkdir = False
@@ -214,7 +211,7 @@ def version(self) -> str:
     #     )  # TODO: open issue for using Path
     #     LOGGER.debug("Created nested FSStore(%s, %s, %s)", path, mode, kwargs)
     #     return store
-    
+
     def init_store(self, path: str, mode: str = "r") -> Store:
         """
         Returns a Zarr v3 PathStore
@@ -231,7 +228,9 @@ def init_store(self, path: str, mode: str = "r") -> Store:
             mode=mode,
             **kwargs,
         )  # TODO: open issue for using Path
-        print("Created %s store %s(%s, %s, %s)" % (self.version, cls, path, mode, kwargs))
+        print(
+            "Created {} store {}({}, {}, {})".format(self.version, cls, path, mode, kwargs)
+        )
         return store
 
 
@@ -389,7 +388,7 @@ def matches(self, metadata: dict) -> bool:
         version = self._get_metadata_version(metadata)
         LOGGER.debug("%s matches %s?", self.version, version)
         return version == self.version_key
-    
+
     def _get_metadata_version(self, metadata: dict) -> Optional[str]:
         """
         For version 0.5+ we use the NGFF_URL_0_5 key

ome_zarr/io.py

@@ -10,7 +10,7 @@
 from urllib.parse import urljoin
 
 import dask.array as da
-from zarr import Group, Array, open
+from zarr import Array, Group, open
 
 # from zarr.v2.storage import FSStore
 from zarr.abc.store import Store
@@ -75,9 +75,7 @@ def __init__(
         detected = detect_format(self.__metadata, loader)
         print("ZarrLocation.__init__ %s detected: %s", self.__path, detected)
         if detected != self.__fmt:
-            print(
-                "version mismatch: detected: %s, requested: %s", detected, self.__fmt
-            )
+            print("version mismatch: detected: %s, requested: %s", detected, self.__fmt)
             self.__fmt = detected
             self.__store = detected.init_store(self.__path, self.__mode)
             self.__init_metadata()
@@ -112,7 +110,7 @@ def __init_metadata(self) -> None:
             print("ZarrLocation __init_metadata: TRY to open group...")
             # zarr_group = Group.open(self.__store)  #, zarr_format=None)
 
-            # NB: If the store is writable, open() will fail IF location doesn't exist because 
+            # NB: If the store is writable, open() will fail IF location doesn't exist because
             # zarr v3 will try to create an Array (instead of looking instead for a Group)
             # and fails because 'shape' is not provided - see TypeError below.
             # NB: we need zarr_format here to open V2 groups
@@ -134,7 +132,7 @@ def __init_metadata(self) -> None:
         except TypeError:
             # open() tried to open_array() but we didn't supply 'shape' argument
             self.__exists = False
-                
+
         # self.zarray: JSONDict = await self.get_json(".zarray")
         # self.zgroup: JSONDict = await self.get_json(".zgroup")
         # v3_json = await self.get_json("zarr.json")
@@ -189,6 +187,7 @@ def load(self, subpath: str = "") -> da.core.Array:
         """Use dask.array.from_zarr to load the subpath."""
         # return da.from_zarr(self.__store, subpath)
         from zarr import load
+
         # returns zarr Array (no chunks) instead of Dask
         return load(store=self.__store, path=subpath)
 
@@ -229,9 +228,9 @@ async def get_json(self, subpath: str) -> JSONDict:
         All other exceptions log at the ERROR level.
         """
         try:
-            print('get_json', subpath)
+            print("get_json", subpath)
             data = await self.__store.get(subpath)
-            print('data', data)
+            print("data", data)
 
             if not data:
                 return {}

ome_zarr/reader.py

@@ -9,7 +9,7 @@
 import numpy as np
 
 from .axes import Axes
-from .format import format_from_version, NGFF_URL_0_5
+from .format import NGFF_URL_0_5, format_from_version
 from .io import ZarrLocation
 from .types import JSONDict
 
@@ -179,7 +179,11 @@ def lookup(self, key: str, default: Any) -> Any:
 
         # Handle zarr V3 where everything is under "attributes"
         if NGFF_URL_0_5 in self.zarr.root_attrs.get("attributes", {}):
-            return self.zarr.root_attrs.get("attributes", {}).get(NGFF_URL_0_5, {}).get(key, default)
+            return (
+                self.zarr.root_attrs.get("attributes", {})
+                .get(NGFF_URL_0_5, {})
+                .get(key, default)
+            )
 
         return self.zarr.root_attrs.get(key, default)
 
@@ -281,7 +285,9 @@ def matches(zarr: ZarrLocation) -> bool:
         if zarr.zgroup:
             if "multiscales" in zarr.root_attrs:
                 return True
-            if "multiscales" in (zarr.root_attrs.get("attributes", {}).get(NGFF_URL_0_5, {})):
+            if "multiscales" in (
+                zarr.root_attrs.get("attributes", {}).get(NGFF_URL_0_5, {})
+            ):
                 return True
         return False
 
@@ -331,7 +337,9 @@ def __init__(self, node: Node) -> None:
         # e.g. 6001240.zarr/labels/0/labels doesn't exist
         # BUT calling this with zarr v3 fails since
         child_zarr = self.zarr.create("labels")
-        print("Multiscales child_zarr 'labels' exists??", child_zarr, child_zarr.exists())
+        print(
+            "Multiscales child_zarr 'labels' exists??", child_zarr, child_zarr.exists()
+        )
         if child_zarr.exists():
             node.add(child_zarr, visibility=False)
         print("Multiscales __init__ END")

ome_zarr/writer.py

@@ -265,7 +265,13 @@ def write_multiscale(
 
         else:
             # We create the array and write data to it immediately...
-            a = group.create_array(str(path), chunks=chunks_opt, shape=data.shape, dtype=data.dtype, **options)
+            a = group.create_array(
+                str(path),
+                chunks=chunks_opt,
+                shape=data.shape,
+                dtype=data.dtype,
+                **options,
+            )
             # These 2 lines are equivalent to e.g. a[:,:] = data (for any number of dimensions)
             s = [np.s_[:]] * len(data.shape)
             a[tuple(s)] = data