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

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

Author: pre-commit-ci[bot]

.isort.cfg

@@ -1,2 +1,2 @@
 [settings]
-known_third_party = dask,numpy,ome_zarr,omero,omero_zarr,setuptools,skimage,zarr
+known_third_party = dask,numpy,ome_zarr,omero,omero_sys_ParametersI,omero_zarr,setuptools,skimage,zarr

src/omero_zarr/cli.py

@@ -29,6 +29,7 @@
 from zarr.hierarchy import open_group
 from zarr.storage import FSStore
 
+from .extinfo import get_images, set_external_info
 from .masks import (
     MASK_DTYPE_SIZE,
     MaskSaver,
@@ -41,10 +42,6 @@
     image_to_zarr,
     plate_to_zarr,
 )
-from .extinfo import (
-    get_images,
-    set_external_info,
-)
 
 HELP = """Export data in zarr format.
 
@@ -114,6 +111,7 @@
 
 EXTINFO_HELP = """Set the external info path for an ome.zarr image."""
 
+
 def gateway_required(func: Callable) -> Callable:
     """
     Decorator which initializes a client (self.client),
@@ -290,9 +288,9 @@ def _configure(self, parser: Parser) -> None:
         )
 
         exinfo = parser.add(sub, self.extinfo, EXTINFO_HELP)
-        exinfo.add_argument("object",
-            type=ProxyStringType(),
-            help="Object in Class:ID format")
+        exinfo.add_argument(
+            "object", type=ProxyStringType(), help="Object in Class:ID format"
+        )
 
         for subcommand in (polygons, masks, export):
             subcommand.add_argument(
@@ -352,10 +350,13 @@ def extinfo(self, args: argparse.Namespace) -> None:
             try:
                 img = set_external_info(self.gateway, img, well, idx)
                 img = self.gateway.getUpdateService().saveAndReturnObject(img)
-                self.ctx.out(f"Set path to '{img.details.externalInfo.lsid._val}' for image {img.id._val}")
+                self.ctx.out(
+                    f"Set path to '{img.details.externalInfo.lsid._val}' for image {img.id._val}"
+                )
             except Exception as e:
-                self.ctx.err(f"Failed to set external info for image {img.id._val}: {e}")
-
+                self.ctx.err(
+                    f"Failed to set external info for image {img.id._val}: {e}"
+                )
 
     def _lookup(
         self, gateway: BlitzGateway, otype: str, oid: int

src/omero_zarr/extinfo.py

@@ -1,15 +1,9 @@
-from omero.gateway import BlitzGateway
-from omero.gateway import BlitzObjectWrapper
-from omero.model import ExternalInfoI, ImageI
-from omero.rtypes import rstring, rlong
-from omero_sys_ParametersI import ParametersI
-from omero.model import Image
-from omero.model import Plate
-from omero.model import Screen
-from omero.model import Dataset
-from omero.model import Project
 import re
 
+from omero.gateway import BlitzGateway, BlitzObjectWrapper
+from omero.model import Dataset, ExternalInfoI, Image, ImageI, Plate, Project, Screen
+from omero.rtypes import rlong, rstring
+from omero_sys_ParametersI import ParametersI
 
 # Regex to match well positions (eg. A1)
 WELL_POS_RE = re.compile(r"(?P<row>\D+)(?P<col>\d+)")
@@ -65,7 +59,9 @@ def _lookup(conn: BlitzGateway, type: str, oid: int) -> BlitzObjectWrapper:
     return obj
 
 
-def get_images(conn: BlitzGateway, object) -> tuple[BlitzObjectWrapper, str | None, int | None]:
+def get_images(
+    conn: BlitzGateway, object
+) -> tuple[BlitzObjectWrapper, str | None, int | None]:
     """
     Generator that yields images from any OMERO container object.
 
@@ -117,30 +113,30 @@ def get_images(conn: BlitzGateway, object) -> tuple[BlitzObjectWrapper, str | No
 def set_external_info(conn: BlitzGateway, img: ImageI, well: str, idx: int) -> ImageI:
     """
     Set external info for an image to enable omero zarr pixel buffer handling.
-    
+
     This function configures an image for use with the omero-zarr-pixel-buffer by:
     1. Retrieving the original file path
     2. Converting it to point to the 5d multiscale image directory
     3. Setting up the external info with the path and metadata
-    
+
     For plate-based images (with wells), the path structure follows:
     /<base_path>/<row>/<column>/<field index>
-    
+
     For regular images:
     /<base_path>/0
-    
+
     Args:
         conn (BlitzGateway): Active OMERO gateway connection
         img (ImageI): OMERO image object to modify
         well (str): Well position (e.g., 'A1', 'B2') for plate-based images, or None
         idx (int): Well sample / field index for plate-based images, or None
-        
+
     Returns:
         ImageI: Modified image object with updated external info
-        
+
     Raises:
         ValueError: If the image path is not an OME-Zarr format or if well position is invalid
-        
+
     Note:
         The external info is configured with entity type 'com.glencoesoftware.ngff:multiscales'
         and entity ID 3, which are required by the omero-zarr-pixel-buffer.