format

src/oaklib/implementations/amigo/amigo_implementation.py

@@ -172,6 +172,7 @@ def __post_init__(self):
     def go_adapter(self) -> OboGraphInterface:
         if not self._go_adapter:
             from oaklib import get_adapter
+
             self._go_adapter = get_adapter("sqlite:obo:go")
         return self._go_adapter
 

src/oaklib/implementations/sparql/abstract_sparql_implementation.py

@@ -522,11 +522,13 @@ def relationships(
                     _sparql_values("s", s_uris),
                     _sparql_values("p", [self.curie_to_sparql(IS_A)]),
                     _sparql_values("o", o_uris),
-                ]
+                ],
             )
             bindings = self._sparql_query(q)
             for row in bindings:
-                yield self.uri_to_curie(row["s"]["value"]), IS_A, self.uri_to_curie(row["o"]["value"])
+                yield self.uri_to_curie(row["s"]["value"]), IS_A, self.uri_to_curie(
+                    row["o"]["value"]
+                )
         if predicates != [IS_A]:
             # existentials
             q = SparqlQuery(
@@ -538,7 +540,7 @@ def relationships(
                     _sparql_values("s", s_uris),
                     _sparql_values("p", p_uris),
                     _sparql_values("o", o_uris),
-                ]
+                ],
             )
             bindings = self._sparql_query(q)
             for row in bindings:
@@ -548,8 +550,6 @@ def relationships(
                     self.uri_to_curie(row["o"]["value"]),
                 )
 
-
-
     def outgoing_relationship_map(self, *args, **kwargs) -> RELATIONSHIP_MAP:
         return pairs_as_dict(self.outgoing_relationships(*args, **kwargs))
 

src/oaklib/implementations/sqldb/sql_implementation.py

@@ -365,10 +365,10 @@ def __post_init__(self):
             logging.info(f"Locator, post-processed: {locator}")
             self.engine = create_engine(locator)
 
-            if(logging.root.level <= logging.DEBUG):
-                #If oaklib is running at DEBUG level logging; record all queries from sqlachemy on execution.
-                #This line is equivalent to create_engine(locator,echo=True)
-                logging.getLogger('sqlalchemy.engine.Engine').setLevel(logging.INFO)
+            if logging.root.level <= logging.DEBUG:
+                # If oaklib is running at DEBUG level logging; record all queries from sqlachemy on execution.
+                # This line is equivalent to create_engine(locator,echo=True)
+                logging.getLogger("sqlalchemy.engine.Engine").setLevel(logging.INFO)
 
     @property
     def session(self):

src/oaklib/interfaces/association_provider_interface.py

@@ -367,7 +367,8 @@ def association_pairwise_coassociations(
         symmetric = curies1 == curies2
         logging.info(f"Finding co-associations between {curies1} and {curies2}")
         assocmap = {
-            c: list(self.associations(objects=[c], limit=-1, **kwargs)) for c in curies1.union(curies2)
+            c: list(self.associations(objects=[c], limit=-1, **kwargs))
+            for c in curies1.union(curies2)
         }
         assocmap1 = {c: assocmap[c] for c in curies1}
         assocmap2 = {c: assocmap[c] for c in curies2}
@@ -382,7 +383,9 @@ def association_pairwise_coassociations(
                 elements1 = {a.subject for a in assocs1}
                 elements2 = {a.subject for a in assocs2}
                 if not elements1 or not elements2:
-                    logging.debug(f"No associations for {c1} or {c2}, so a coassociation is not meaningful")
+                    logging.debug(
+                        f"No associations for {c1} or {c2}, so a coassociation is not meaningful"
+                    )
                     continue
                 common = elements1.intersection(elements2)
                 assocs_to_common = [a for a in assocs1 + assocs2 if a.subject in common]

src/oaklib/interfaces/usages_interface.py

@@ -193,5 +193,9 @@ def _source_id():
         if include_unused:
             for c in curies:
                 if c not in used_curies:
-                    yield Usage(used_id=c, used_by_id="None", source=_source_id(), context=UsageContext.MULTIPLE)
-
+                    yield Usage(
+                        used_id=c,
+                        used_by_id="None",
+                        source=_source_id(),
+                        context=UsageContext.MULTIPLE,
+                    )

src/oaklib/io/heatmap_writer.py

@@ -63,13 +63,13 @@ def finish(self):
         # ax = sns.heatmap(df, annot=mask, fmt=".2f", mask=~mask)  # Annotates only non-zero cells
         ax = sns.heatmap(df, annot=True, fmt=".2f")
         # Rotate x and y labels if necessary
-        plt.xticks(rotation=45, ha='right')  # Rotate term2 labels for better fit
+        plt.xticks(rotation=45, ha="right")  # Rotate term2 labels for better fit
         plt.yticks(rotation=0)  # Keep term1 labels horizontal
         # Adjust font size of the labels
-        ax.tick_params(axis='both', which='major', labelsize=24)
+        ax.tick_params(axis="both", which="major", labelsize=24)
 
         # Manually set x-axis labels to ensure correct alignment
-        ax.set_xticklabels(ax.get_xticklabels(), rotation=45, horizontalalignment='right')
+        ax.set_xticklabels(ax.get_xticklabels(), rotation=45, horizontalalignment="right")
 
         ax.get_figure().savefig(self.output, bbox_inches="tight")
         # plt.savefig(self.output, bbox_inches="tight")

src/oaklib/utilities/lexical/lexical_indexer.py

@@ -82,7 +82,6 @@ def add_labels_from_uris(oi: BasicOntologyInterface):
             oi.set_label(curie, label)
 
 
-
 def create_lexical_index(
     oi: BasicOntologyInterface,
     pipelines: Optional[List[LexicalTransformationPipeline]] = None,