Ran formatter and minor code cleanup (#737)

* Refactor diff markdown title

* code clean-up

* formatted

* reverted relationships to mappings

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

src/oaklib/utilities/writers/change_handler.py

@@ -1,7 +1,7 @@
 """Change Handler Class."""
 
 from dataclasses import dataclass
-from typing import Dict
+from typing import Dict, List
 
 from kgcl_schema.datamodel.kgcl import Change
 
@@ -12,30 +12,22 @@ def __init__(self, oi, file):
         self.file = file
         self.oi = oi
 
-    def write_markdown_collapsible(self, title, content_lines):
-        # Start with the details tag for a collapsible section
+    def write_markdown_collapsible(self, title: str, content_lines: List[str]) -> None:
         self.file.write(f"<details>\n<summary>{title}</summary>\n\n")
-
-        # Write the content lines within the collapsible section
-        content = "\n".join(content_lines)
-        self.file.write(content + "\n\n")
-
-        # Close the details tag
+        self.file.write("\n".join(content_lines) + "\n\n")
         self.file.write("</details>\n\n")
 
-    def write_markdown_table(self, title, header, rows):
-        # Create the table header and separator lines
-        markdown_rows = [
-            header,
-            "|".join(["----"] * len(header.split("|")[1:-1])) + "|",
-        ]
-
-        # Add the table rows
-        markdown_rows.extend(rows)
-
-        # Write the table as a collapsible section
+    def write_markdown_table(self, title: str, header: str, rows: List[str]) -> None:
+        separator = "|".join(["----"] * len(header.split("|")[1:-1])) + "|"
+        markdown_rows = [header, separator] + rows
         self.write_markdown_collapsible(title, markdown_rows)
 
+    def handle_generic_change(
+        self, value: List[object], title: str, header: str, row_format: str
+    ) -> None:
+        rows = [row_format.format(change=change) for change in value]
+        self.write_markdown_table(f"{title}: {len(rows)}", header, rows)
+
     def handle_new_synonym(self, value):
         # Create rows for the table
         rows = [

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

@@ -41,7 +41,7 @@ deps =
     ruff
 skip_install = true
 commands =
-    black src/ tests/
+    black src/ tests/ --exclude src\/oaklib\/datamodels\/.*\.py
     ruff --fix src/ tests/
 description = Run linters.