format with black

Author: bendhouseart

petdeface/petdeface.py

@@ -1271,7 +1271,6 @@ def main():  # noqa: max-complexity: 12
         print("=" * 60)
 
         try:
-
             # Determine the defaced directory based on placement
             if args.placement == "adjacent":
                 defaced_dir = args.bids_dir.parent / f"{args.bids_dir.name}_defaced"
@@ -1291,9 +1290,7 @@ def main():  # noqa: max-complexity: 12
                 faced_dir=str(args.bids_dir),
                 defaced_dir=str(defaced_dir),
                 subject=(
-                    " ".join(args.participant_label)
-                    if args.participant_label
-                    else None
+                    " ".join(args.participant_label) if args.participant_label else None
                 ),
                 open_browser=args.open_browser,
             )
@@ -1305,9 +1302,7 @@ def main():  # noqa: max-complexity: 12
 
         except Exception as e:
             print(f"\nError generating QA reports: {e}")
-            print(
-                "QA report generation failed, but defacing completed successfully."
-            )
+            print("QA report generation failed, but defacing completed successfully.")
 
 
 if __name__ == "__main__":

petdeface/qa.py

@@ -22,9 +22,6 @@
 from pathlib import Path
 
 
-
-
-
 def preprocess_single_subject(s, output_dir):
     """Preprocess a single subject's images (for parallel processing)."""
     temp_dir = os.path.join(output_dir, "temp_3d_images")

tests/test_dir_layouts.py

@@ -129,7 +129,7 @@ def test_participant_exclusion():
     """Test that participant exclusion works correctly by excluding sub-02"""
     with tempfile.TemporaryDirectory() as temp_dir:
         test_dir = Path(temp_dir)
-        
+
         # Create the test directory and copy our data
         shutil.copytree(data_dir, test_dir / "participant_exclusion")
 
@@ -145,37 +145,45 @@ def test_participant_exclusion():
 
         # Check the final defaced dataset directory
         final_defaced_dir = test_dir / "participant_exclusion_defaced"
-        
+
         # Count files in the final defaced dataset
         all_files = list(final_defaced_dir.rglob("*"))
         all_files = [f for f in all_files if f.is_file()]  # Only files, not directories
-        
+
         # Count files by subject
         sub01_files = [f for f in all_files if "sub-01" in str(f)]
         sub02_files = [f for f in all_files if "sub-02" in str(f)]
-        
+
         print(f"Total files in defaced dataset: {len(all_files)}")
         print(f"sub-01 files: {len(sub01_files)}")
         print(f"sub-02 files: {len(sub02_files)}")
-        
+
         # Verify that sub-02 does NOT appear anywhere in the final defaced dataset
-        assert len(sub02_files) == 0, f"sub-02 should be completely excluded from final defaced dataset, but found {len(sub02_files)} files: {[str(f) for f in sub02_files]}"
-        
+        assert (
+            len(sub02_files) == 0
+        ), f"sub-02 should be completely excluded from final defaced dataset, but found {len(sub02_files)} files: {[str(f) for f in sub02_files]}"
+
         # Verify that sub-01 exists and was processed
         assert len(sub01_files) > 0, "sub-01 should exist in final defaced dataset"
-        assert (final_defaced_dir / "sub-01").exists(), "sub-01 directory should exist in final defaced dataset"
-        
+        assert (
+            final_defaced_dir / "sub-01"
+        ).exists(), "sub-01 directory should exist in final defaced dataset"
+
         # Verify processing artifacts exist for sub-01 in derivatives
         derivatives_dir = final_defaced_dir / "derivatives" / "petdeface"
         if derivatives_dir.exists():
             sub01_defacemasks = list(derivatives_dir.glob("**/sub-01*defacemask*"))
             sub01_lta_files = list(derivatives_dir.glob("**/sub-01*.lta"))
-            
+
             print(f"sub-01 defacemasks found: {len(sub01_defacemasks)}")
             print(f"sub-01 lta files found: {len(sub01_lta_files)}")
-            
-            assert len(sub01_defacemasks) > 0, "sub-01 should have been processed and have defacemasks"
-            assert len(sub01_lta_files) > 0, "sub-01 should have been processed and have lta registration files"
+
+            assert (
+                len(sub01_defacemasks) > 0
+            ), "sub-01 should have been processed and have defacemasks"
+            assert (
+                len(sub01_lta_files) > 0
+            ), "sub-01 should have been processed and have lta registration files"
 
 
 def test_no_anat():