Clean

Author: cthoyt

src/pyobo/ner/normalizer.py

@@ -16,6 +16,7 @@
 ]
 
 
+# docstr-coverage:excused `overload`
 @overload
 def ground(
     prefix: str | Iterable[str],
@@ -26,6 +27,7 @@ def ground(
 ) -> Reference: ...
 
 
+# docstr-coverage:excused `overload`
 @overload
 def ground(
     prefix: str | Iterable[str],

src/pyobo/sources/nlm/utils.py

@@ -1,8 +1,8 @@
 """Utilities for NLM."""
 
 from collections.abc import Iterable
-from xml.etree import ElementTree
 
+from lxml.etree import Element, ElementTree
 from tqdm import tqdm
 
 from pyobo import Reference, Term, TypeDef, default_reference, ensure_path
@@ -72,9 +72,7 @@ def get_journals(
             yield term
 
 
-def _process_journal(
-    element: ElementTree.Element[str], journal_id_to_publisher_key: dict[str, Term]
-) -> Term | None:
+def _process_journal(element: Element, journal_id_to_publisher_key: dict[str, Term]) -> Term | None:
     # TODO enrich with context from https://ftp.ncbi.nlm.nih.gov/pubmed/J_Entrez.txt and https://ftp.ncbi.nlm.nih.gov/pubmed/J_Medline.txt
 
     nlm_id = element.findtext("NlmUniqueID")

src/pyobo/struct/struct.py

@@ -393,9 +393,11 @@ def set_species(self, identifier: str, name: str | None = None) -> Self:
             v.from_species, Reference(prefix=NCBITAXON_PREFIX, identifier=identifier, name=name)
         )
 
+    # docstr-coverage:excused `overload`
     @overload
     def get_species(self, prefix: str = ..., *, strict: Literal[True] = ...) -> Reference: ...
 
+    # docstr-coverage:excused `overload`
     @overload
     def get_species(
         self, prefix: str = ..., *, strict: Literal[False] = ...

src/pyobo/struct/struct_utils.py

@@ -600,11 +600,13 @@ def get_relationships(self, typedef: ReferenceHint) -> list[Reference]:
         """Get relationships from the given type."""
         return self.relationships.get(_ensure_ref(typedef), [])
 
+    # docstr-coverage:excused `overload`
     @overload
     def get_relationship(
         self, typedef: ReferenceHint, *, strict: Literal[False] = ...
     ) -> Reference | None: ...
 
+    # docstr-coverage:excused `overload`
     @overload
     def get_relationship(
         self, typedef: ReferenceHint, *, strict: Literal[True] = ...