fix_cli

sopa/cli/patchify.py

@@ -125,7 +125,9 @@ def comseg(
     ),
 ):
     """Prepare patches for transcript-based segmentation with ComSeg"""
+
     from sopa._constants import SopaKeys, SopaFiles
+
     from .utils import _default_boundary_dir
 
     if comseg_temp_dir is None:
@@ -190,7 +192,7 @@ def _transcript_segmentation(
 
     df_key = get_key(sdata, "points")
     patches = Patches2D(sdata, df_key, patch_width_microns, patch_overlap_microns)
-    if filename==SopaKeys.COMSEG_BOUNDARIES:
+    if filename == SopaKeys.COMSEG_BOUNDARIES:
         patches.patchify_centroids(temp_dir)
         assert (
             use_prior

sopa/cli/segmentation.py

@@ -2,7 +2,6 @@
 
 import ast
 
-
 import typer
 from tqdm import tqdm
 
@@ -195,14 +194,17 @@ def comseg(
 ):
     """Perform ComSeg segmentation. This can be done on all patches directly, or on one individual patch."""
     import json
+    import logging
 
     from sopa._constants import SopaFiles, SopaKeys
     from sopa.segmentation.methods import comseg_patch
-    import logging
-    log = logging.getLogger(__name__)
+
     from pathlib import Path
+
     from .utils import _default_boundary_dir
 
+    log = logging.getLogger(__name__)
+
     config_name = SopaFiles.JSON_CONFIG_FILE
 
     if patch_dir is None: