Change os.rename to shutil.move (#951)

angelolab · Mar 21, 2023 · e06838f · e06838f
1 parent ad4e42f
commit e06838f
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/src/ark/phenotyping/pixel_meta_clustering.py b/src/ark/phenotyping/pixel_meta_clustering.py
@@ -2,7 +2,7 @@
 import os
 import random
 from functools import partial
-from shutil import rmtree
+from shutil import rmtree, move
 
 import feather
 import numpy as np
@@ -185,7 +185,7 @@ def pixel_consensus_cluster(fovs, channels, base_dir, max_k=20, cap=3,
 
     # remove the data directory and rename the temp directory to the data directory
     rmtree(pixel_data_path)
-    os.rename(pixel_data_path + '_temp', pixel_data_path)
+    move(pixel_data_path + '_temp', pixel_data_path)
 
     return pixel_cc
 
@@ -435,7 +435,7 @@ def apply_pixel_meta_cluster_remapping(fovs, channels, base_dir,
 
     # remove the data directory and rename the temp directory to the data directory
     rmtree(pixel_data_path)
-    os.rename(pixel_data_path + '_temp', pixel_data_path)
+    move(pixel_data_path + '_temp', pixel_data_path)
 
 
 def generate_remap_avg_files(fovs, channels, base_dir, pixel_data_dir, pixel_remapped_name,

diff --git a/src/ark/phenotyping/pixel_som_clustering.py b/src/ark/phenotyping/pixel_som_clustering.py
@@ -1,7 +1,7 @@
 import multiprocessing
 import os
 from functools import partial
-from shutil import rmtree
+from shutil import rmtree, move
 
 import feather
 from pyarrow.lib import ArrowInvalid
@@ -269,7 +269,7 @@ def cluster_pixels(fovs, channels, base_dir, pixel_pysom, data_dir='pixel_mat_da
 
     # remove the data directory and rename the temp directory to the data directory
     rmtree(data_path)
-    os.rename(data_path + '_temp', data_path)
+    move(data_path + '_temp', data_path)
 
 
 def generate_som_avg_files(fovs, channels, base_dir, pixel_pysom, data_dir='pixel_data_dir',