Remove duplicate output of Classes added

src/oaklib/implementations/amigo/amigo_implementation.py

@@ -211,7 +211,6 @@ def subset_members(self, subset: SUBSET_CURIE, **kwargs) -> Iterable[CURIE]:
         for doc in results:
             yield doc[ANNOTATION_CLASS]
 
-
     def associations(
         self,
         subjects: Iterable[CURIE] = None,
@@ -348,7 +347,6 @@ def association_counts(
             solr, fq, facet_field=ff, rows=0, facet_limit=limit, min_facet_count=min_facet_count
         )
 
-
     # def association_pairwise_coassociations(
     #         self,
     #         curies1: Iterable[CURIE],
@@ -389,8 +387,6 @@ def association_counts(
     #         yield ff[i], ff[i + 1]
     #
 
-
-
     def association_subject_counts(
         self,
         subjects: Iterable[CURIE] = None,
@@ -446,10 +442,6 @@ def relationships(
                 self._cache_nodes(nodes, [s, p, o])
                 yield s, p, o
 
-
-
-
-
     def basic_search(
         self, search_term: str, config: Optional[SearchConfiguration] = None
     ) -> Iterable[CURIE]:

src/oaklib/interfaces/association_provider_interface.py

@@ -365,7 +365,9 @@ def association_pairwise_coassociations(
         curies1 = list(curies1)
         curies2 = list(curies2)
         logging.info(f"Finding co-associations between {curies1} and {curies2}")
-        assocmap = {c: list(self.associations(objects=[c], **kwargs)) for c in set(curies1+curies2)}
+        assocmap = {
+            c: list(self.associations(objects=[c], **kwargs)) for c in set(curies1 + curies2)
+        }
         assocmap1 = {c: assocmap[c] for c in curies1}
         assocmap2 = {c: assocmap[c] for c in curies2}
         for c1 in curies1:
@@ -389,8 +391,9 @@ def association_pairwise_coassociations(
                     number_subject_unique_to_entity2=len(elements2.difference(elements1)),
                 )
                 if coassoc.number_subjects_in_union:
-                    coassoc.proportion_subjects_in_common = (coassoc.number_subjects_in_common /
-                                                             coassoc.number_subjects_in_union)
+                    coassoc.proportion_subjects_in_common = (
+                        coassoc.number_subjects_in_common / coassoc.number_subjects_in_union
+                    )
                 if include_entities:
                     coassoc.subjects_in_common = list(common)
                     coassoc.associations_for_subjects_in_common = assocs_to_common

src/oaklib/utilities/lexical/synonymizer.py

@@ -85,7 +85,9 @@ def apply_synonymizer_to_terms(
                                     if qualifier is None or qualifier == "":
                                         if rule.in_place or scope_pred == "definition":
                                             # preserves the original synonym type
-                                            qualifier = pred_to_qual.get(scope_pred, scope_pred).lower()
+                                            qualifier = pred_to_qual.get(
+                                                scope_pred, scope_pred
+                                            ).lower()
                                         else:
                                             qualifier = "exact"
                                     n += 1

tests/test_utilities/test_synonymizer.py

@@ -81,7 +81,6 @@ def test_synonymizer(rule, input, expected):
                     "the plasma membrane and nucleus, but including other subcellular structures.' "
                     "to 'All of the contents of a cell excluding the plasma membrane and "
                     "NUCLEUS, but including other subcellular structures.'"
-
                 )
             ],
         ),
@@ -105,7 +104,7 @@ def test_synonymizer(rule, input, expected):
     ],
 )
 def test_syonymizer_on_terms(ruleset, include_all, terms, expected):
-    #adapter = get_adapter(f"simpleobo:{TEST_SIMPLE_ONT}")
+    # adapter = get_adapter(f"simpleobo:{TEST_SIMPLE_ONT}")
     adapter = get_adapter(f"{TEST_SIMPLE_ONT}")
     if isinstance(ruleset, Synonymizer):
         ruleset = RuleSet(rules=[ruleset])

tox.ini

@@ -41,8 +41,8 @@ deps =
     ruff
 skip_install = true
 commands =
-    black src/ tests/
-    ruff --fix src/ tests/
+    black src/ tests/ --exclude src/oaklib/datamodels/*
+    ruff --fix src/ tests/ --exclude src/oaklib/datamodels
 description = Run linters.
 
 # This is used for QC checks.
@@ -51,7 +51,7 @@ deps =
     ruff
 skip_install = true
 commands =
-    ruff check src/ tests/
+    ruff check src/ tests/ --exclude src/oaklib/datamodels
 description = Run linters.
 
 [testenv:codespell]