[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_rois,omero_zarr,pytest,setuptools,skimage,zarr
+known_third_party = dask,numpy,ome_zarr,omero,omero_rois,omero_sys_ParametersI,omero_zarr,pytest,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.
 
@@ -205,8 +200,7 @@ def _configure(self, parser: Parser) -> None:
         polygons.add_argument(
             "--label-name",
             help=(
-                "Name of the array that will be stored. Ignored for "
-                "--style=split"
+                "Name of the array that will be stored. Ignored for " "--style=split"
             ),
             default="0",
         )
@@ -236,8 +230,7 @@ def _configure(self, parser: Parser) -> None:
         masks.add_argument(
             "--label-name",
             help=(
-                "Name of the array that will be stored. Ignored for "
-                "--style=split"
+                "Name of the array that will be stored. Ignored for " "--style=split"
             ),
             default="0",
         )
@@ -302,10 +295,7 @@ def _configure(self, parser: Parser) -> None:
         export.add_argument(
             "--max_workers",
             default=None,
-            help=(
-                "Maximum number of workers (only for "
-                "use with bioformats2raw)"
-            ),
+            help=("Maximum number of workers (only for " "use with bioformats2raw)"),
         )
         export.add_argument(
             "object",
@@ -428,8 +418,7 @@ def extinfo(self, args: argparse.Namespace) -> None:
                         args.entityType,
                         int(args.entityId),
                     )
-                    img = self.gateway.getUpdateService()\
-                        .saveAndReturnObject(img)
+                    img = self.gateway.getUpdateService().saveAndReturnObject(img)
                     self.ctx.out(
                         f"Set ExternalInfo for image ({img.id._val}) "
                         f"{img.name._val}:\n"
@@ -443,16 +432,14 @@ def extinfo(self, args: argparse.Namespace) -> None:
             elif args.reset:
                 if extinfo:
                     img.details.externalInfo = None
-                    img = self.gateway.getUpdateService()\
-                        .saveAndReturnObject(img)
+                    img = self.gateway.getUpdateService().saveAndReturnObject(img)
                     self.ctx.out(
                         f"Removed ExternalInfo from image "
                         f"({img.id._val}) {img.name._val}"
                     )
                 else:
                     self.ctx.out(
-                        f"Image ({img.id._val}) {img.name._val} "
-                        "has no ExternalInfo"
+                        f"Image ({img.id._val}) {img.name._val} " "has no ExternalInfo"
                     )
             else:
                 if extinfo:
@@ -463,8 +450,7 @@ def extinfo(self, args: argparse.Namespace) -> None:
                     )
                 else:
                     self.ctx.out(
-                        f"Image ({img.id._val}) {img.name._val} has no "
-                        "ExternalInfo"
+                        f"Image ({img.id._val}) {img.name._val} has no " "ExternalInfo"
                     )
 
     def _lookup(
@@ -477,9 +463,7 @@ def _lookup(
             self.ctx.die(110, f"No such {otype}: {oid}")
         return obj
 
-    def _bf_export(
-        self, image: BlitzObjectWrapper, args: argparse.Namespace
-    ) -> None:
+    def _bf_export(self, image: BlitzObjectWrapper, args: argparse.Namespace) -> None:
         if args.bfpath:
             abs_path = Path(args.bfpath)
         elif image.getInplaceImport():

src/omero_zarr/extinfo.py

@@ -1,25 +1,17 @@
 import re
 
 from omero.gateway import BlitzGateway, BlitzObjectWrapper, ImageWrapper
-from omero.model import (
-    Dataset,
-    ExternalInfoI,
-    Image,
-    ImageI,
-    Plate,
-    Project,
-    Screen,
-)
+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+)")
 # Regex to match the metadata.xml (could be any xml under xyz.zarr/ directory,
 # not only xyz.zarr/OME/METADATA.ome.xml)
 METADATA_XML_RE = re.compile(r".+\.zarr\/(.+\.xml)")
 
+
 def get_extinfo(conn: BlitzGateway, image: ImageWrapper) -> ExternalInfoI:
     """
     Get the external info for an OMERO image.
@@ -157,7 +149,7 @@ def set_external_info(
     idx: int,
     overwrite_path: str,
     entityType: str,
-    entityId: int
+    entityId: int,
 ) -> ImageI:
     """
     Set the external info for an OMERO image.
@@ -194,12 +186,10 @@ def set_external_info(
     else:
         if METADATA_XML_RE.match(img_path):
             metadata_xml = METADATA_XML_RE.match(img_path).group(1)
-            path = img_path.replace(metadata_xml,"")
+            path = img_path.replace(metadata_xml, "")
             path = f"/{path}"
         else:
-            raise ValueError(
-                f"Doesn't seem to be an ome.zarr: {img_path}"
-            )
+            raise ValueError(f"Doesn't seem to be an ome.zarr: {img_path}")
 
     if well:
         match = WELL_POS_RE.match(well)
@@ -213,7 +203,6 @@ def set_external_info(
         series = img.getSeries()._val
         path = f"{path}{series}"
 
-
     info = ExternalInfoI()
     info.entityType = rstring(entityType)
     info.entityId = rlong(entityId)