Hardcode up to date list of entities for BIDS and boost specified BIDSVersion to 1.10.1

.pre-commit-config.yaml

@@ -25,7 +25,7 @@ repos:
       - id: isort
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
+    rev: 7.1.1
     hooks:
       - id: flake8
         additional_dependencies:

heudiconv/bids.py

@@ -68,7 +68,7 @@ class BIDSError(Exception):
     pass
 
 
-BIDS_VERSION = "1.8.0"
+BIDS_VERSION = "1.10.1"
 
 # List defining allowed parameter matching for fmap assignment:
 SHIM_KEY = "ShimSetting"
@@ -1067,17 +1067,33 @@ def populate_intended_for(
 
 
 class BIDSFile:
-    """as defined in https://bids-specification.readthedocs.io/en/stable/99-appendices/04-entity-table.html
-    which might soon become machine readable
-    order matters
+    """Representation of a BIDS file with order of entities following BIDS
+
+    Full ordered list from
+    http://github.com/bids-standard/bids-specification/blob/HEAD/src/schema/rules/entities.yaml
+    while taking shortened versions from
+    https://github.com/bids-standard/bids-specification/blob/master/src/schema/objects/entities.yaml
+
+    Use
+
+         python -c 'from heudiconv.bids import BIDSFile; BIDSFile._print_entities()'
+
+    to print the current list of entities to plug in below.
     """
 
+    # For release 1.10.1
     _known_entities = [
         "sub",
         "ses",
+        "sample",
         "task",
+        "tracksys",
         "acq",
+        "nuc",
+        "voi",
         "ce",
+        "trc",
+        "stain",
         "rec",
         "dir",
         "run",
@@ -1087,9 +1103,54 @@ class BIDSFile:
         "inv",
         "mt",
         "part",
+        "proc",
+        "hemi",
+        "space",
+        "split",
         "recording",
+        "chunk",
+        "seg",
+        "res",
+        "den",
+        "label",
+        "desc",
     ]
 
+    @staticmethod
+    def _get_entities(version: str = BIDS_VERSION) -> list[str]:
+        """Load BIDS entity rules and print entity names to plug above."""
+
+        import json
+        from urllib.request import Request, urlopen
+
+        is_released = version and version[0].isdigit()
+        version_url = f"v{version}" if is_released else version
+
+        schema_url = (
+            f"https://bids-specification.readthedocs.io/en/{version_url}/schema.json"
+        )
+        headers = {
+            "User-Agent": "heudiconv/{__version__}",
+        }
+        with urlopen(Request(schema_url, headers=headers)) as response:
+            schema = json.loads(response.read().decode())
+
+        return [
+            schema["objects"]["entities"][key]["name"]
+            for key in schema["rules"]["entities"]
+        ]
+
+    @staticmethod
+    def _print_entities(version: str = BIDS_VERSION) -> None:
+        # Print the name for each entity
+        is_released = version and version[0].isdigit()
+        if is_released:
+            print(f"    # For release {version}")
+        print("    _known_entities = [")
+        for ent in BIDSFile._get_entities(version=version):
+            print(f'        "{ent}",')
+        print("    ]")
+
     def __init__(
         self, entities: dict[str, str], suffix: str, extension: Optional[str]
     ) -> None:

heudiconv/convert.py

@@ -1088,6 +1088,10 @@ def rename_files() -> None:
             # If we have failed to modify this_prefix_basename, because it didn't fall
             #   into any of the options above, just add the suffix at the end:
             if this_prefix_basename == prefix_basename:
+                # TODO: never hit by tests! So what are the suffixes for?!
+                import pdb
+
+                pdb.set_trace()
                 this_prefix_basename += suffix
 
             # Finally, form the outname by stitching the directory and outtype:

tox.ini

@@ -55,7 +55,7 @@ exclude = .*/,build/,dist/,test/data,venv/
 hang-closing = False
 unused-arguments-ignore-stub-functions = True
 select = A,B,B902,C,E,E242,F,U100,W
-ignore = A003,B005,E203,E262,E266,E501,W503
+ignore = A003,A005,B005,E203,E262,E266,E501,W503
 
 [isort]
 atomic = True