Fix?

cubids/tests/test_cli.py

@@ -151,11 +151,17 @@ def test_validate_command(tmp_path):
     bids_dir.mkdir()
     (bids_dir / "dataset_description.json").touch()
 
+    # Create output prefix
+    output_prefix = tmp_path / "validation_output"
+
     # Test validation
     with pytest.raises(SystemExit) as excinfo:
-        _main(["validate", str(bids_dir)])
+        _main(["validate", str(bids_dir), str(output_prefix)])
     assert excinfo.value.code == 0
 
+    # Check that output files were created
+    assert (output_prefix.parent / f"{output_prefix.name}_validation.txt").exists()
+
 
 def test_validate_command_invalid_dir(tmp_path):
     """Test the validate command with an invalid directory."""

cubids/workflows.py

@@ -86,7 +86,7 @@ def validate(
         parsed = parse_validator_output(ret.stdout.decode("UTF-8"))
         if parsed.shape[1] < 1:
             logger.info("No issues/warnings parsed, your dataset is BIDS valid.")
-            sys.exit(0)
+            return
         else:
             logger.info("BIDS issues/warnings found in the dataset")
 
@@ -110,7 +110,7 @@ def validate(
                     json.dump(val_dict, outfile, indent=4)
 
                 logger.info("Writing issues out to %s", val_tsv)
-                sys.exit(0)
+                return
             else:
                 # user may be in python session, return dataframe
                 return parsed