[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 external_info_str, get_extinfo, get_images, set_external_info
 from .masks import (
     MASK_DTYPE_SIZE,
     MaskSaver,
@@ -41,12 +42,6 @@
     image_to_zarr,
     plate_to_zarr,
 )
-from .extinfo import (
-    get_images,
-    set_external_info,
-    get_extinfo,
-    external_info_str
-)
 
 HELP = """Export data in zarr format.
 
@@ -120,6 +115,7 @@
 or --reset in order to remove the ExternalInfo from the image.
 """
 
+
 def gateway_required(func: Callable) -> Callable:
     """
     Decorator which initializes a client (self.client),
@@ -296,33 +292,29 @@ def _configure(self, parser: Parser) -> None:
         )
 
         extinfo = parser.add(sub, self.extinfo, EXTINFO_HELP)
-        extinfo.add_argument("object",  
-                type=ProxyStringType(),
-                help="Object in Class:ID format")
         extinfo.add_argument(
-            "--set",
-            action="store_true",
-            help="Set the ExternalInfo path"
+            "object", type=ProxyStringType(), help="Object in Class:ID format"
+        )
+        extinfo.add_argument(
+            "--set", action="store_true", help="Set the ExternalInfo path"
         )
         extinfo.add_argument(
             "--path",
             default=None,
-            help="Use a specific path (default: Determine from clientPath) (only used in combination with --set)"
+            help="Use a specific path (default: Determine from clientPath) (only used in combination with --set)",
         )
         extinfo.add_argument(
             "--entityType",
             default="com.glencoesoftware.ngff:multiscales",
-            help="Use a specific entityType (default: com.glencoesoftware.ngff:multiscales) (only used in combination with --set)"
+            help="Use a specific entityType (default: com.glencoesoftware.ngff:multiscales) (only used in combination with --set)",
         )
         extinfo.add_argument(
             "--entityId",
             default="3",
-            help="Use a specific entityId (default: 3) (only used in combination with --set)"
+            help="Use a specific entityId (default: 3) (only used in combination with --set)",
         )
         extinfo.add_argument(
-            "--reset",
-            action="store_true",
-            help="Removes the ExternalInfo"
+            "--reset", action="store_true", help="Removes the ExternalInfo"
         )
 
         for subcommand in (polygons, masks, export):
@@ -376,32 +368,50 @@ def export(self, args: argparse.Namespace) -> None:
             plate = self._lookup(self.gateway, "Plate", args.object.id)
             plate_to_zarr(plate, args)
 
-
     @gateway_required
     def extinfo(self, args: argparse.Namespace) -> None:
         for img, well, idx in get_images(self.gateway, args.object):
             img = img._obj
             extinfo = get_extinfo(self.gateway, img)
             if args.set:
                 try:
-                    img = set_external_info(self.gateway, img, well, idx, args.path, args.entityType, int(args.entityId))
+                    img = set_external_info(
+                        self.gateway,
+                        img,
+                        well,
+                        idx,
+                        args.path,
+                        args.entityType,
+                        int(args.entityId),
+                    )
                     img = self.gateway.getUpdateService().saveAndReturnObject(img)
-                    self.ctx.out(f"Set ExternalInfo for image ({img.id._val}) {img.name._val}:\n{external_info_str(img.details.externalInfo)}")
+                    self.ctx.out(
+                        f"Set ExternalInfo for image ({img.id._val}) {img.name._val}:\n{external_info_str(img.details.externalInfo)}"
+                    )
                 except Exception as e:
-                    self.ctx.err(f"Failed to set external info for image ({img.id._val}) {img.name._val}: {e}")
+                    self.ctx.err(
+                        f"Failed to set external info for image ({img.id._val}) {img.name._val}: {e}"
+                    )
             elif args.reset:
                 if extinfo:
                     img.details.externalInfo = None
                     img = self.gateway.getUpdateService().saveAndReturnObject(img)
-                    self.ctx.out(f"Removed ExternalInfo from image ({img.id._val}) {img.name._val}")
+                    self.ctx.out(
+                        f"Removed ExternalInfo from image ({img.id._val}) {img.name._val}"
+                    )
                 else:
-                    self.ctx.out(f"Image ({img.id._val}) {img.name._val} has no ExternalInfo")
+                    self.ctx.out(
+                        f"Image ({img.id._val}) {img.name._val} has no ExternalInfo"
+                    )
             else:
                 if extinfo:
-                    self.ctx.out(f"ExternalInfo for image ({img.id._val}) {img.name._val}:\n{external_info_str(extinfo)}")
+                    self.ctx.out(
+                        f"ExternalInfo for image ({img.id._val}) {img.name._val}:\n{external_info_str(extinfo)}"
+                    )
                 else:
-                    self.ctx.out(f"Image ({img.id._val}) {img.name._val} has no ExternalInfo")
-
+                    self.ctx.out(
+                        f"Image ({img.id._val}) {img.name._val} has no ExternalInfo"
+                    )
 
     def _lookup(
         self, gateway: BlitzGateway, otype: str, oid: int

src/omero_zarr/extinfo.py

@@ -1,15 +1,9 @@
-from omero.gateway import BlitzGateway, ImageWrapper
-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, ImageWrapper
+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+)")
@@ -41,7 +35,7 @@ def get_extinfo(conn: BlitzGateway, image: ImageWrapper) -> ExternalInfoI:
         extinfo = conn.getQueryService().findByQuery(query, params)
         return extinfo
     return None
-    
+
 
 def _get_path(conn: BlitzGateway, image_id: int) -> str:
     """
@@ -93,7 +87,9 @@ def _lookup(conn: BlitzGateway, type: str, oid: int) -> BlitzObjectWrapper:
     return obj
 
 
-def get_images(conn: BlitzGateway, object) -> tuple[ImageWrapper, str | None, int | None]:
+def get_images(
+    conn: BlitzGateway, object
+) -> tuple[ImageWrapper, str | None, int | None]:
     """
     Generator that yields images from any OMERO container object.
 
@@ -142,8 +138,15 @@ def get_images(conn: BlitzGateway, object) -> tuple[ImageWrapper, str | None, in
         raise ValueError(f"Unsupported type: {object.__class__.__name__}")
 
 
-def set_external_info(conn: BlitzGateway, img: ImageI, well: str, idx: int, 
-    lsid: str | None = None, entityType: str | None = None, entityId: int | None = None) -> ImageI:
+def set_external_info(
+    conn: BlitzGateway,
+    img: ImageI,
+    well: str,
+    idx: int,
+    lsid: str | None = None,
+    entityType: str | None = None,
+    entityId: int | None = None,
+) -> ImageI:
     """
     Set the external info for an OMERO image.
 
@@ -166,7 +169,7 @@ def set_external_info(conn: BlitzGateway, img: ImageI, well: str, idx: int,
     if not entityType:
         entityType = "com.glencoesoftware.ngff:multiscales"
     if not entityId:
-         entityId = 3
+        entityId = 3
     if lsid:
         path = lsid
     else: