Fix failing tests by adding JSON-LD flag and correcting mock patches

- Add -j flag to NIDM conversion command when output is .json-ld format
- Fix mock patching in test_wrapper.py to patch ants.image_write at the correct import location (src.antspy.wrapper.ants.image_write)
- All 13 tests now pass successfully

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

Author: yibeichan

src/run.py

@@ -225,7 +225,11 @@ def nidm_conversion(logger, derivatives_dir, nidm_dir, bids_subject, nidm_input_
             "-subjid", f"sub-{bids_subject}",
             "-o", nidm_output
         ]
-        
+
+        # Add JSON-LD flag if output format is JSON-LD
+        if nidm_output.endswith('.json-ld'):
+            cmd.append("-j")
+
         logger.info(f"Converting segmentation to NIDM for {log_prefix}")
         logger.info(f"Running command: {' '.join(cmd)}")
 

tests/test_wrapper.py

@@ -138,7 +138,7 @@ def test_organize_bids_output_single_session(self):
             'probabilityimages': [mock_prob1, mock_prob2, mock_prob3]
         }
 
-        with patch('ants.image_write') as mock_write:
+        with patch('src.antspy.wrapper.ants.image_write') as mock_write:
             # Call the method
             result = self.segmenter._organize_bids_output(segmentation_results, "01")
 
@@ -195,7 +195,7 @@ def test_organize_bids_output_with_session(self):
             'probabilityimages': []
         }
 
-        with patch('ants.image_write') as mock_write:
+        with patch('src.antspy.wrapper.ants.image_write') as mock_write:
             # Call the method with session
             result = self.segmenter._organize_bids_output(segmentation_results, "01", "01")