update test_bond

Author: tien-tong

cubids/cli.py

@@ -1012,7 +1012,7 @@ def _parse_print_metadata_fields():
 COMMANDS = [
     ("validate", _parse_validate, workflows.validate),
     ("bids-version", _parse_bids_version, workflows.bids_version),
-    ("sidecar-merge", _parse_bids_sidecar_merge, workflows.bids_sidecar_merge),
+    ("bids-sidecar-merge", _parse_bids_sidecar_merge, workflows.bids_sidecar_merge),
     ("group", _parse_group, workflows.group),
     ("apply", _parse_apply, workflows.apply),
     ("purge", _parse_purge, workflows.purge),

cubids/cubids.py

@@ -490,7 +490,7 @@ def apply_tsv_changes(self, summary_tsv, files_tsv, new_prefix, raise_on_error=T
             for dest_nii in dest_files.FilePath:
                 dest_json = utils.img_to_new_ext(self.path + dest_nii, ".json")
                 if Path(dest_json).exists() and Path(source_json).exists():
-                    merge_commands.append(f"bids-sidecar-merge {source_json} {dest_json}")
+                    merge_commands.append(f"cubids bids-sidecar-merge {source_json} {dest_json}")
 
         # Get the delete commands
         to_remove = []

cubids/tests/test_bond.py

@@ -107,7 +107,7 @@ def test_ok_json_merge_cli(tmp_path):
 
     assert os.path.isfile(source_json)
     assert os.path.isfile(dest_json)
-    merge_proc = subprocess.run(["bids-sidecar-merge", str(source_json), str(dest_json)])
+    merge_proc = subprocess.run(["cubids", "bids-sidecar-merge", str(source_json), str(dest_json)])
     assert merge_proc.returncode == 0
     assert not _get_json_string(dest_json) == orig_dest_json_content
 
@@ -331,7 +331,9 @@ def test_bad_json_merge_cli(tmp_path):
         / "sub-01_ses-phdiff_acq-HASC55AP_dwi.json"
     )
 
-    merge_proc = subprocess.run(["bids-sidecar-merge", str(invalid_source_json), str(dest_json)])
+    merge_proc = subprocess.run(
+        ["cubids", "bids-sidecar-merge", str(invalid_source_json), str(dest_json)]
+    )
     assert merge_proc.returncode > 0
     assert _get_json_string(dest_json) == orig_dest_json_content