lint

src/oaklib/cli.py

@@ -1687,7 +1687,9 @@ def annotate(
         if match_column:
             writer = _get_writer(output_type, impl, StreamingCsvWriter)
             writer.output = output
-            for row in impl.annotate_tabular_file(text_file, configuration=configuration, match_column=match_column):
+            for row in impl.annotate_tabular_file(
+                text_file, configuration=configuration, match_column=match_column
+            ):
                 writer.emit(row)
         else:
             for ann in impl.annotate_file(text_file, configuration):

src/oaklib/implementations/translator/translator_implementation.py

@@ -9,15 +9,21 @@
 """
 import logging
 from dataclasses import dataclass
-from typing import Iterable, Mapping, Optional, Union, List
+from typing import Iterable, List, Mapping, Optional, Union
 
 import requests
 import sssom_schema.datamodel.sssom_schema as sssom
 
 from oaklib.datamodels.search import SearchConfiguration
-from oaklib.datamodels.vocabulary import SEMAPV, SKOS_CLOSE_MATCH, SKOS_EXACT_MATCH, RDFS_LABEL, HAS_RELATED_SYNONYM
+from oaklib.datamodels.vocabulary import (
+    HAS_RELATED_SYNONYM,
+    RDFS_LABEL,
+    SEMAPV,
+    SKOS_CLOSE_MATCH,
+    SKOS_EXACT_MATCH,
+)
 from oaklib.interfaces import SearchInterface
-from oaklib.interfaces.basic_ontology_interface import LANGUAGE_TAG, ALIAS_MAP
+from oaklib.interfaces.basic_ontology_interface import ALIAS_MAP, LANGUAGE_TAG
 from oaklib.interfaces.mapping_provider_interface import MappingProviderInterface
 from oaklib.types import CURIE
 
@@ -101,10 +107,12 @@ def inject_mapping_labels(self, mappings: Iterable[Mapping]) -> None:
         return
 
     def basic_search(
-            self, search_term: str, config: Optional[SearchConfiguration] = None
+        self, search_term: str, config: Optional[SearchConfiguration] = None
     ) -> Iterable[CURIE]:
-        r = requests.get(f"{NAME_NORMALIZER_ENDPOINT}/lookup",
-                         params={"string": search_term, "autocomplete": "true"})
+        r = requests.get(
+            f"{NAME_NORMALIZER_ENDPOINT}/lookup",
+            params={"string": search_term, "autocomplete": "true"},
+        )
         r.raise_for_status()
         results = r.json()
         for result in results:
@@ -117,17 +125,15 @@ def label(self, curie: CURIE, lang: Optional[LANGUAGE_TAG] = None) -> Optional[s
             raise NotImplementedError
         if self.property_cache.contains(curie, RDFS_LABEL):
             return self.property_cache.get(curie, RDFS_LABEL)
-        r = requests.get(f"{NAME_NORMALIZER_ENDPOINT}/reverse_lookup",
-                         params={"curies": curie})
+        r = requests.get(f"{NAME_NORMALIZER_ENDPOINT}/reverse_lookup", params={"curies": curie})
         r.raise_for_status()
         results = r.json()
         if curie not in results:
             return None
         return results[curie]["preferred_name"]
 
     def entity_aliases(self, curie: CURIE) -> List[str]:
-        r = requests.get(f"{NAME_NORMALIZER_ENDPOINT}/reverse_lookup",
-                         params={"curies": curie})
+        r = requests.get(f"{NAME_NORMALIZER_ENDPOINT}/reverse_lookup", params={"curies": curie})
         r.raise_for_status()
         results = r.json()
         if curie not in results:
@@ -136,5 +142,3 @@ def entity_aliases(self, curie: CURIE) -> List[str]:
 
     def entity_alias_map(self, curie: CURIE) -> ALIAS_MAP:
         return {HAS_RELATED_SYNONYM: self.entity_aliases(curie)}
-
-

src/oaklib/interfaces/text_annotator_interface.py

@@ -3,7 +3,7 @@
 from abc import ABC
 from io import TextIOWrapper
 from pathlib import Path
-from typing import Iterable, Iterator, Optional, Dict
+from typing import Dict, Iterable, Iterator, Optional
 
 from oaklib.datamodels.lexical_index import LexicalIndex
 from oaklib.datamodels.mapping_rules_datamodel import MappingRuleCollection