Merge branch 'main' into dependabot/pip/numpy-lte-2.1.3

Author: tsalo

.circleci/config.yml

@@ -1,6 +1,6 @@
 version: 2.1
 orbs:
-  codecov: codecov/codecov@1.0.5
+  codecov: codecov/codecov@3.2.4
 
 jobs:
   run_pytests:
@@ -31,10 +31,8 @@ jobs:
             source activate cubids
             conda install -c conda-forge -y datalad
 
-            # Add nodejs and the validator
-            conda install nodejs
-            npm install -g yarn && \
-            npm install -g [email protected]
+            # Add deno to run the schema validator
+            conda install deno
 
             # Install CuBIDS
             pip install -e .[tests]
@@ -64,7 +62,8 @@ jobs:
 
             # We need curl for the codecov upload
             apt-get update
-            apt-get install -yqq curl
+            apt-get install -y -qq curl
+            apt-get install -y gnupg
 
             cd /home/circleci/src/coverage/
             echo "Merge coverage files"

cubids/cli.py

@@ -43,7 +43,7 @@ def _parse_validate():
         type=PathExists,
         action="store",
         help=(
-            "the root of a BIDS dataset. It should contain "
+            "The root of a BIDS dataset. It should contain "
             "sub-X directories and dataset_description.json"
         ),
     )
@@ -107,6 +107,41 @@ def _enter_validate(argv=None):
     workflows.validate(**args)
 
 
+def _parse_bids_version():
+    parser = argparse.ArgumentParser(
+        description="cubids bids-version: Get BIDS Validator and Schema version",
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+    )
+    PathExists = partial(_path_exists, parser=parser)
+
+    parser.add_argument(
+        "bids_dir",
+        type=PathExists,
+        action="store",
+        help=(
+            "The root of a BIDS dataset. It should contain "
+            "sub-X directories and dataset_description.json"
+        ),
+    )
+    parser.add_argument(
+        "--write",
+        action="store_true",
+        default=False,
+        help=(
+            "Save the validator and schema version to 'dataset_description.json' "
+            "when using `cubids bids-version /bids/path --write`. "
+            "By default, `cubids bids-version /bids/path` prints to the terminal."
+        ),
+    )
+    return parser
+
+
+def _enter_bids_version(argv=None):
+    options = _parse_bids_version().parse_args(argv)
+    args = vars(options).copy()
+    workflows.bids_version(**args)
+
+
 def _parse_bids_sidecar_merge():
     parser = argparse.ArgumentParser(
         description=("bids-sidecar-merge: merge critical keys from one sidecar to another"),
@@ -153,7 +188,7 @@ def _parse_group():
         type=PathExists,
         action="store",
         help=(
-            "the root of a BIDS dataset. It should contain "
+            "The root of a BIDS dataset. It should contain "
             "sub-X directories and dataset_description.json"
         ),
     )
@@ -220,7 +255,7 @@ def _parse_apply():
         type=PathExists,
         action="store",
         help=(
-            "the root of a BIDS dataset. It should contain "
+            "The root of a BIDS dataset. It should contain "
             "sub-X directories and dataset_description.json"
         ),
     )
@@ -316,7 +351,7 @@ def _parse_datalad_save():
         type=PathExists,
         action="store",
         help=(
-            "the root of a BIDS dataset. It should contain "
+            "The root of a BIDS dataset. It should contain "
             "sub-X directories and dataset_description.json"
         ),
     )
@@ -358,7 +393,7 @@ def _parse_undo():
         type=PathExists,
         action="store",
         help=(
-            "the root of a BIDS dataset. It should contain "
+            "The root of a BIDS dataset. It should contain "
             "sub-X directories and dataset_description.json"
         ),
     )
@@ -582,7 +617,7 @@ def _parse_remove_metadata_fields():
         type=PathExists,
         action="store",
         help=(
-            "the root of a BIDS dataset. It should contain "
+            "The root of a BIDS dataset. It should contain "
             "sub-X directories and dataset_description.json"
         ),
     )
@@ -628,7 +663,7 @@ def _parse_print_metadata_fields():
         type=PathExists,
         action="store",
         help=(
-            "the root of a BIDS dataset. It should contain "
+            "The root of a BIDS dataset. It should contain "
             "sub-X directories and dataset_description.json"
         ),
     )
@@ -655,6 +690,7 @@ def _enter_print_metadata_fields(argv=None):
 
 COMMANDS = [
     ("validate", _parse_validate, workflows.validate),
+    ("bids-version", _parse_bids_version, workflows.bids_version),
     ("sidecar-merge", _parse_bids_sidecar_merge, workflows.bids_sidecar_merge),
     ("group", _parse_group, workflows.group),
     ("apply", _parse_apply, workflows.apply),

cubids/cubids.py

@@ -1336,9 +1336,20 @@ def get_all_metadata_fields(self):
         found_fields = set()
         for json_file in Path(self.path).rglob("*.json"):
             if ".git" not in str(json_file):
-                with open(json_file, "r") as jsonr:
-                    metadata = json.load(jsonr)
-                found_fields.update(metadata.keys())
+                # add this in case `print-metadata-fields` is run before validate
+                try:
+                    with open(json_file, "r", encoding="utf-8") as jsonr:
+                        content = jsonr.read().strip()
+                        if not content:
+                            print(f"Empty file: {json_file}")
+                            continue
+                        metadata = json.loads(content)
+                    found_fields.update(metadata.keys())
+                except json.JSONDecodeError as e:
+                    warnings.warn(f"Error decoding JSON in {json_file}: {e}")
+                except Exception as e:
+                    warnings.warn(f"Unexpected error with file {json_file}: {e}")
+
         return sorted(found_fields)
 
     def remove_metadata_fields(self, fields_to_remove):

cubids/tests/test_bond.py

@@ -9,6 +9,7 @@
 import numpy as np
 import pandas as pd
 import pytest
+from packaging.version import Version
 
 from cubids.cubids import CuBIDS
 from cubids.metadata_merge import merge_json_into_json, merge_without_overwrite
@@ -22,7 +23,15 @@
     file_hash,
     get_data,
 )
-from cubids.validator import build_validator_call, parse_validator_output, run_validator
+from cubids.validator import (
+    build_validator_call,
+    parse_validator_output,
+    run_validator,
+    get_bids_validator_version,
+    extract_summary_info,
+    update_dataset_description,
+    bids_validator_version,
+)
 
 COMPLETE_KEY_GROUPS = [
     "acquisition-HASC55AP_datatype-dwi_suffix-dwi",
@@ -1028,6 +1037,39 @@ def test_validator(tmp_path):
     assert isinstance(parsed, pd.DataFrame)
 
 
+def test_bids_version(tmp_path):
+    """Test workflows.bids_version."""
+    data_root = get_data(tmp_path)
+    bids_dir = Path(data_root) / "complete"
+
+    # Ensure the test directory exists
+    assert bids_dir.exists()
+
+    # test the validator in valid dataset
+    call = build_validator_call(bids_dir)
+    ret = run_validator(call)
+
+    assert ret.returncode == 0
+
+    decoded = ret.stdout.decode("UTF-8")
+
+    # Get the BIDS validator version
+    validator_version = Version(get_bids_validator_version()["ValidatorVersion"])
+    # Extract schemaVersion
+    schema_version = Version(extract_summary_info(decoded)["SchemaVersion"])
+
+    # Set baseline versions to compare against
+    min_validator_version = Version("2.0.0")
+    min_schema_version = Version("0.11.3")
+
+    assert (
+        validator_version >= min_validator_version
+    ), f"Validator version {validator_version} is less than minimum {min_validator_version}"
+    assert (
+        schema_version >= min_schema_version
+    ), f"Schema version {schema_version} is less than minimum {min_schema_version}"
+
+
 def test_docker():
     """Verify that docker is installed and the user has permission to run docker images.
 

cubids/tests/test_cli.py

@@ -14,9 +14,10 @@
 """
 
 import argparse
+
 import pytest
 
-from cubids.cli import _path_exists, _is_file, _get_parser, _main
+from cubids.cli import _get_parser, _is_file, _main, _path_exists
 
 
 def _test_path_exists():