Update api.py

Author: cthoyt

src/pyobo/struct/functional/obo_to_functional.py

@@ -78,7 +78,8 @@ def get_ontology_axioms(obo_ontology: Obo) -> Iterable[f.Box]:
         used_has_scope = False
         for synonym_typedef in obo_ontology.synonym_typedefs:
             yield f.Declaration(synonym_typedef, type="AnnotationProperty")
-            yield m.LabelMacro(synonym_typedef, synonym_typedef.name)
+            if synonym_typedef.name is not None:
+                yield m.LabelMacro(synonym_typedef, synonym_typedef.name)
             yield f.SubAnnotationPropertyOf(synonym_typedef, "oboInOwl:SynonymTypeProperty")
             if synonym_typedef.specificity:
                 used_has_scope = True

src/pyobo/struct/reference.py

@@ -86,18 +86,20 @@ def __eq__(self, other: Any) -> bool:
             return self.prefix == other.prefix and self.identifier == other.identifier
         raise TypeError
 
-    def __lt__(self, other: Referenced) -> bool:
-        if not isinstance(other, curies.Reference | Referenced):
-            raise TypeError
-        return self.reference < other.reference
+    def __lt__(self, other: curies.Reference | Referenced) -> bool:
+        if isinstance(other, curies.Reference):
+            return self.reference < other
+        if isinstance(other, Referenced):
+            return self.reference < other.reference
+        raise TypeError
 
     @property
-    def prefix(self):
+    def prefix(self) -> str:
         """The prefix of the typedef."""
         return self.reference.prefix
 
     @property
-    def name(self):
+    def name(self) -> str | None:
         """The name of the typedef."""
         return self.reference.name
 

src/pyobo/struct/struct.py

@@ -1568,14 +1568,14 @@ def get_typedef_df(self, use_tqdm: bool = False) -> pd.DataFrame:
         ]
         return pd.DataFrame(rows, columns=["prefix", "identifier", "name"])
 
-    def iter_typedef_id_name(self) -> Iterable[tuple[str, str]]:
+    def iter_typedef_id_name(self) -> Iterable[tuple[str, str | None]]:
         """Iterate over typedefs' identifiers and their respective names."""
         for typedef in self.typedefs or []:
             yield typedef.identifier, typedef.name
 
     def get_typedef_id_name_mapping(self) -> Mapping[str, str]:
         """Get a mapping from typedefs' identifiers to names."""
-        return dict(self.iter_typedef_id_name())
+        return {identifier: name for identifier, name in self.iter_typedef_id_name() if name}
 
     #########
     # PROPS #
@@ -2031,7 +2031,7 @@ def get_literal_mappings_df(self) -> pd.DataFrame:
 
     def iterate_mapping_rows(
         self, *, use_tqdm: bool = False
-    ) -> Iterable[tuple[str, str, str, str, str, float | None, str | None]]:
+    ) -> Iterable[tuple[str, str | None, str, str, str, float | None, str | None]]:
         """Iterate over SSSOM rows for mappings."""
         for stanza in self._iter_stanzas(use_tqdm=use_tqdm):
             for predicate, obj_ref, context in stanza.get_mappings(