Fix typing

Author: cthoyt

scripts/educational_resources.py

@@ -1,21 +1,11 @@
 # /// script
 # requires-python = ">=3.14"
 # dependencies = [
-#     "biomappings",
-#     "bioregistry",
-#     "curies-processing",
-#     "pyobo[gilda-slim]",
-#     "sssom-curator",
-#     "sssom-pydantic",
+#     "biomappings[predict-lexical]",
 # ]
 #
 # [tool.uv.sources]
 # biomappings = { path = "../", editable = true }
-# sssom-curator = { path = "../../sssom-curator", editable = true }
-# sssom-pydantic = { path = "../../sssom-pydantic", editable = true }
-# pyobo = { path = "../../pyobo", editable = true }
-# bioregistry = { path = "../../bioregistry", editable = true }
-# curies-processing = { path = "../../curies-processing" }
 # ///
 
 """Generate mappings between educational resources."""

scripts/generate_cl_mesh_mappings.py

@@ -36,15 +36,15 @@
     matches = gilda.ground(data["name"])
     if not matches:
         if data["name"].endswith(" cells"):
-            matches = gilda.ground(data["name"].replace(" cells", ""))
+            matches = gilda.ground(data["name"].replace(" cells", ""))  # type:ignore[no-untyped-call]
         elif data["name"].endswith(" cell"):
-            matches = gilda.ground(data["name"].replace(" cell", ""))
+            matches = gilda.ground(data["name"].replace(" cell", ""))  # type:ignore[no-untyped-call]
     if not matches:
         continue
 
     mesh_ids = set()
     for match in matches:
-        groundings = match.get_groundings()
+        groundings = match.get_groundings()  # type:ignore[no-untyped-call]
         mesh_ids |= {id for ns, id in groundings if ns == "MESH"}
     if len(mesh_ids) > 1:
         print(f"Multiple MESH IDs for {node}")

scripts/generate_vaccine_mappings.py

@@ -23,7 +23,7 @@ def main() -> None:
     for term in iter_terms():
         texts = [term.name, *(s.name for s in term.synonyms)]
         for text in texts:
-            for scored_match in grounder.get_matches(text + " vaccine"):
+            for scored_match in grounder.get_matches(text + " vaccine"):  # type:ignore[no-untyped-call]
                 pred = SemanticMapping(
                     subject=term.reference,
                     predicate=exact_match,

scripts/generate_wikipathways_orthologs.py

@@ -16,7 +16,7 @@
 
 
 def _lexical_exact_match(name1: str, name2: str) -> bool:
-    return cast(str, normalize(name1)) == cast(str, normalize(name2))
+    return cast(str, normalize(name1)) == cast(str, normalize(name2))  # type:ignore[no-untyped-call]
 
 
 def iterate_orthologous_lexical_matches(prefix: str = "wikipathways") -> Iterable[SemanticMapping]: