[ENH] Dynamically pull BIDS schema for auto entities and extractions.

.github/workflows/tests.yml

@@ -31,4 +31,4 @@ jobs:
         run: uv sync --group test
 
       - name: Run tests
-        run: uv run pytest
+        run: uv run pytest

dcm2bids/acquisition.py

@@ -161,8 +161,7 @@ def setExtraDstFile(self, new_entities):
         """
         Return:
             The destination filename formatted following
-            the v1.9.0 BIDS entity key table
-            https://bids-specification.readthedocs.io/en/v1.9.0/99-appendices/04-entity-table.html
+            the BIDS entity key order according to the schema
         """
 
         if self.custom_entities.strip() == "":
@@ -258,7 +257,6 @@ def setDstFile(self):
                     to:     {new_name}""")
                 self.dstFile = new_name
 
-
     def dstSidecarData(self, idList):
         """
         """

dcm2bids/cli/dcm2bids.py

@@ -15,6 +15,7 @@
 from dcm2bids.dcm2bids_gen import Dcm2BidsGen
 from dcm2bids.utils.utils import DEFAULT
 from dcm2bids.utils.tools import dcm2niix_version, check_latest
+from dcm2bids.utils.schema import load_schema
 from dcm2bids.participant import Participant
 from dcm2bids.utils.logger import setup_logging
 from dcm2bids.version import __version__
@@ -61,7 +62,7 @@ def _build_arg_parser():
     g = p.add_mutually_exclusive_group()
     g.add_argument("--auto_extract_entities",
                    action='store_true',
-                   help="If set, it will automatically try to extract entity"
+                   help="If set, it will automatically try to extract entity "
                    "information [task, dir, echo] based on the suffix and datatype."
                    " Default is [%(default)s]")
 
@@ -73,6 +74,18 @@ def _build_arg_parser():
                         "Cannot be used with --auto_extract_entities. "
                         " Default is [%(default)s]")
 
+    p.add_argument("-b", "--bids_version",
+                   default=None,
+                   help=(
+            "Set the BIDS specification version to follow (e.g. 'v1.11.1', 'stable', 'latest' or 'default')."
+            "\nThis controls which BIDS schema and rules dcm2bids uses for automatic entity extraction and ordering."
+            "\nIf not provided, dcm2bids uses the 'default' BIDS spec for reproducible, offline-friendly behavior."
+            "\nFor long-running or shared pipelines, consider pinning a specific tag (e.g. 'v1.11.1')."
+            "\nWhen internet is available, it will check once whether the remote 'stable' is newer and, if so, \n"
+            "suggest updating to that specific version tag."
+            ),
+        )
+
     p.add_argument("--bids_validate",
                    action='store_true',
                    help="If set, once your conversion is done it "
@@ -98,15 +111,20 @@ def _build_arg_parser():
                    required=False,
                    default=DEFAULT.cli_log_level,
                    choices=["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"],
-                   help="Set logging level to the console." 
+                   help="Set logging level to the console."
                         " The default level is [%(default)s]"
                 )
 
     p.add_argument("-v", "--version",
                    action="version",
-                   version=f"dcm2bids version:\t{__version__}\n"
-                   f"Based on BIDS version:\t{DEFAULT.bids_version}",
-                   help="Report dcm2bids version and the BIDS version.")
+                   # This uses version.__BIDSversion__, which reflects the bundled schema version.
+                   version=(
+                        f"dcm2bids version:\t{__version__}\n"
+                        f"default BIDS version:\t{DEFAULT.bids_version} "
+                        "unless overridden by --bids_version."
+                    ),
+                   help="Report dcm2bids version and the default BIDS specification version it follows by default."
+                   )
 
     return p
 
@@ -129,13 +147,23 @@ def main():
     logger.info("Running the following command: " + " ".join(sys.argv))
     logger.info("OS version: %s", platform.platform())
     logger.info("Python version: %s", sys.version.replace("\n", ""))
-    logger.info(f"dcm2bids version: { __version__}")
+    logger.info(f"dcm2bids version: {__version__}")
     logger.info(f"dcm2niix version: {dcm2niix_version()}")
     logger.info("Checking for software update")
 
-    check_latest("dcm2bids")
+    check_latest("dcm2bids", log_dir=log_dir)
     if not args.skip_dcm2niix:
-        check_latest("dcm2niix")
+        check_latest("dcm2niix", log_dir=log_dir)
+
+    schema, derived_entities = load_schema(args.bids_version, log_dir=log_dir)
+
+    # Update the DEFAULT based on the requested version directly, otherwise uses default values
+    if args.bids_version is not None:
+        DEFAULT.bids_version = schema["bids_version"]
+        DEFAULT.entityTableKeys = derived_entities.get("entity_table_keys",
+                                              DEFAULT.entityTableKeys)
+        DEFAULT.auto_entities = derived_entities.get("auto_entities",
+                                                DEFAULT.auto_entities)                      
 
     logger.info(f"participant: {participant.name}")
     if participant.session:

dcm2bids/cli/dcm2bids_helper.py

@@ -96,12 +96,14 @@ def main():
     logger.info("Running the following command: " + " ".join(sys.argv))
     logger.info("OS version: %s", platform.platform())
     logger.info("Python version: %s", sys.version.replace("\n", ""))
-    logger.info(f"dcm2bids version: { __version__}")
+    logger.info(f"dcm2bids version: {__version__}")
     logger.info(f"dcm2niix version: {dcm2niix_version()}")
     logger.info("Checking for software update")
 
-    check_latest("dcm2bids")
-    check_latest("dcm2niix")
+    log_dir = log_file.parent
+
+    check_latest("dcm2bids", log_dir=log_dir)
+    check_latest("dcm2niix", log_dir=log_dir)
 
     app = Dcm2niixGen(dicom_dirs=args.dicom_dir, bids_dir=out_dir, helper=True)
 

dcm2bids/cli/dcm2bids_scaffold.py

@@ -64,10 +64,12 @@ def main():
     logger.info("Running the following command: " + " ".join(sys.argv))
     logger.info("OS version: %s", platform.platform())
     logger.info("Python version: %s", sys.version.replace("\n", ""))
-    logger.info(f"dcm2bids version: { __version__}")
+    logger.info(f"dcm2bids version: {__version__}")
     logger.info("Checking for software update")
 
-    check_latest("dcm2bids")
+    log_dir = log_file.parent
+    check_latest("dcm2bids", log_dir=log_dir)
+
 
     logger.info("The files used to create your BIDS directory were taken from "
                 "https://github.com/bids-standard/bids-starter-kit. \n")

dcm2bids/dcm2bids_gen.py

@@ -40,7 +40,7 @@ def __init__(
         output_dir=DEFAULT.output_dir,
         bids_validate=DEFAULT.bids_validate,
         auto_extract_entities=DEFAULT.auto_extract_entities,
-        do_not_reorder_entities = DEFAULT.do_not_reorder_entities,
+        do_not_reorder_entities=DEFAULT.do_not_reorder_entities,
         session=DEFAULT.session,
         clobber=DEFAULT.clobber,
         force_dcm2bids=DEFAULT.force_dcm2bids,
@@ -64,8 +64,8 @@ def __init__(
 
         if self.auto_extract_entities and self.do_not_reorder_entities:
             raise ValueError("Auto extract entities is set to True and "
-                              "do not reorder entities is set to True. "
-                              "Please choose only one option.")
+                             "do not reorder entities is set to True. "
+                             "Please choose only one option.")
 
     @property
     def dicom_dirs(self):

dcm2bids/participant.py

@@ -40,7 +40,7 @@ def name(self, name):
 
         if not self._name.replace('sub-', '').isalnum():
             raise NameError(f"Participant '{self._name.replace('sub-', '')}' "
-                            "should contains only alphanumeric characters.")
+                            "should contain only alphanumeric characters.")
 
     @property
     def session(self):
@@ -64,7 +64,7 @@ def session(self, session):
 
         if not self._session.replace('ses-', '').isalnum() and self._session:
             raise NameError(f"Session '{self._session.replace('ses-', '')}' "
-                            "should contains only alphanumeric characters.")
+                            "should contain only alphanumeric characters.")
 
     @property
     def directory(self):