pre-commit test4

sopa/cli/patchify.py

@@ -37,6 +37,7 @@ def image(
 
     _save_cache(sdata_path, SopaFiles.PATCHES_FILE_IMAGE, str(len(patches)))
 
+
 @app_patchify.command()
 def baysor(
     sdata_path: str = typer.Argument(help=SDATA_HELPER),
@@ -82,7 +83,7 @@ def baysor(
         config=config,
         cell_key=cell_key,
         unassigned_value=unassigned_value,
-        use_prior = use_prior,
+        use_prior=use_prior,
     )
 
 
@@ -130,6 +131,7 @@ def comseg(
         unassigned_value=unassigned_value,
         use_prior=True,
     )
+
 @app_patchify.command()
 def transcript_segmentation(
     sdata_path: str = typer.Argument(help=SDATA_HELPER),
@@ -217,6 +219,7 @@ def transcript_segmentation(
     )
     _save_cache(sdata_path, filename, "\n".join(map(str, valid_indices)))
 
+
 def _save_cache(sdata_path: str, filename: str, content: str):
     from pathlib import Path
 

sopa/cli/segmentation.py

@@ -197,12 +197,12 @@ def comseg(
 ):
     """Perform ComSeg segmentation. This can be done on all patches directly, or on one individual patch."""
     import json
+
     from sopa._constants import SopaFiles, SopaKeys
     from sopa.segmentation.methods import comseg_patch
 
     from .utils import _default_boundary_dir
 
-
     config_name = SopaFiles.JSON_CONFIG_FILE
 
     if patch_dir is None: