Update

Author: cthoyt

src/pyobo/struct/jskos_utils.py

@@ -3,21 +3,22 @@
 from pathlib import Path
 
 import curies
-
-from .struct import Obo, build_ontology
 import jskos
 from jskos import ProcessedConcept, ProcessedKOS
 
+from .struct import Obo, build_ontology
+
 __all__ = [
-    "read_jskos",
     "from_pkos",
+    "read_jskos",
 ]
 
 
 def read_jskos(path: str | Path, *, prefix: str, converter: curies.Converter | None = None) -> Obo:
     """Read JSKOS into an ontology."""
     if converter is None:
         from ..identifier_utils import get_converter
+
         converter = get_converter()
     kos = jskos.read(path)
     pkos = jskos.process(kos, converter)

src/pyobo/utils/misc.py

@@ -5,12 +5,13 @@
 import logging
 from collections.abc import Callable, Iterable
 from datetime import datetime
-from typing import TYPE_CHECKING, TypeAlias
+from typing import TypeAlias
 
 import bioversions.utils
-from pyobo.constants import ONTOLOGY_GETTERS, OntologyFormat
 from bioregistry.schema.struct import AnnotatedURL
 
+from ..constants import ONTOLOGY_GETTERS, OntologyFormat
+
 __all__ = [
     "VERSION_GETTERS",
     "cleanup_version",
@@ -49,8 +50,8 @@
     "https://w3id.org/lehrplan/ontology/",  # like in https://w3id.org/lehrplan/ontology/1.0.0-4
     "http://www.ebi.ac.uk/swo/version/",  # http://www.ebi.ac.uk/swo/version/6.0
     "https://w3id.org/emi/version/",
-    "https://nfdi4culture.de/ontology/", # https://nfdi4culture.de/ontology/3.0.0
-    "http://purls.helmholtz-metadaten.de/mwo/mwo.owl/", # http://purls.helmholtz-metadaten.de/mwo/mwo.owl/3.0.0
+    "https://nfdi4culture.de/ontology/",  # https://nfdi4culture.de/ontology/3.0.0
+    "http://purls.helmholtz-metadaten.de/mwo/mwo.owl/",  # http://purls.helmholtz-metadaten.de/mwo/mwo.owl/3.0.0
 ]
 VERSION_PREFIX_SPLITS = [
     "http://www.ebi.ac.uk/efo/releases/v",
@@ -59,7 +60,7 @@
     "http://ontology.neuinfo.org/NIF/ttl/nif/version/",
     "http://nmrml.org/cv/v",  # as in http://nmrml.org/cv/v1.1.0/nmrCV
     "http://enanomapper.github.io/ontologies/releases/",  # as in http://enanomapper.github.io/ontologies/releases/10.0/enanomapper
-    "https://w3id.org/sulo/sulo-", # as in https://w3id.org/sulo/sulo-0.2.4.ttl
+    "https://w3id.org/sulo/sulo-",  # as in https://w3id.org/sulo/sulo-0.2.4.ttl
 ]
 BAD = {
     "http://purl.obolibrary.org/obo",

tests/test_struct/test_jskos/test_jskos.py

@@ -1,10 +1,11 @@
 """Test JSKOS."""
 
 import unittest
-from pyobo.struct.jskos_utils import read_jskos
 
 import curies
 
+from pyobo.struct.jskos_utils import read_jskos
+
 URL = "https://skohub.io/KDSF-FFK/kdsf-ffk/heads/main/w3id.org/kdsf-ffk/index.json"
 
 
@@ -13,9 +14,11 @@ class TestJSKOS(unittest.TestCase):
 
     def test_jskos(self) -> None:
         """Test JSKOS."""
-        converter = curies.Converter.from_prefix_map({
-            "ksdf.fkk": "https://w3id.org/kdsf-ffk/",
-        })
+        converter = curies.Converter.from_prefix_map(
+            {
+                "ksdf.fkk": "https://w3id.org/kdsf-ffk/",
+            }
+        )
         ontology = read_jskos(prefix="ksdf.fkk", path=URL, converter=converter)
         names = ontology.get_id_name_mapping()
         self.assertIn("ArbeitUndWirtschaft", names)