Merge branch 'main' into dependabot/pip/pybids-lte-0.17.2

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:
@@ -9,7 +9,7 @@ jobs:
         type: string
         default: "3.8"
     machine:
-      image: ubuntu-2004:202201-02
+      image: ubuntu-2404:2024.08.1
     working_directory: /home/circleci/src/CuBIDS
     steps:
       - checkout:
@@ -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 bids-validator
+            # 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"
@@ -83,7 +82,7 @@ jobs:
 
   deploy_pypi:
     machine:
-      image: ubuntu-2004:202201-02
+      image: ubuntu-2404:2024.08.1
     working_directory: /home/circleci/src/CuBIDS
     steps:
       - checkout:

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"
         ),
     )
@@ -230,7 +265,7 @@ def _parse_apply():
         action="store",
         help=(
             "path to the _summary.tsv that has been edited "
-            "in the MergeInto and RenameKeyGroup columns. If the "
+            "in the MergeInto and RenameEntitySet columns. If the "
             " summary table is located in the code/CuBIDS "
             "directory, then users can just pass the summary tsv "
             "filename instead of the full path to the tsv"
@@ -242,7 +277,7 @@ def _parse_apply():
         action="store",
         help=(
             "path to the _files.tsv that has been edited "
-            "in the MergeInto and RenameKeyGroup columns. If the "
+            "in the MergeInto and RenameEntitySet columns. If the "
             "files table is located in the code/CuBIDS "
             "directory, then users can just pass the files tsv "
             "filename instead of the full path to the tsv"
@@ -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/constants.py

@@ -1,9 +1,9 @@
 """Constants for CuBIDS."""
 
 # Names of identifier variables.
-# Used to place KeyGroup and ParamGroup at the beginning of a dataframe,
+# Used to place EntitySet and ParamGroup at the beginning of a dataframe,
 # but both are hardcoded in the relevant function.
-ID_VARS = set(["KeyGroup", "ParamGroup", "FilePath"])
+ID_VARS = set(["EntitySet", "ParamGroup", "FilePath"])
 # Entities that should not be used to group parameter sets
 NON_KEY_ENTITIES = set(["subject", "session", "extension"])
 # Multi-dimensional keys SliceTiming  XXX: what is this line about?