Add assertions for version to fix mypy linting issues

src/pyobo/cli/lookup.py

@@ -282,7 +282,7 @@ def ancestors(prefix: str, identifier: str, force: bool, version: Optional[str])
     """Look up ancestors."""
     curies = get_ancestors(prefix=prefix, identifier=identifier, force=force, version=version)
     for curie in sorted(curies or []):
-        click.echo(f"{curie}\t{get_name_by_curie(curie, version)}")
+        click.echo(f"{curie}\t{get_name_by_curie(curie, version=version)}")
 
 
 @lookup.command()
@@ -295,7 +295,7 @@ def descendants(prefix: str, identifier: str, force: bool, version: Optional[str
     """Look up descendants."""
     curies = get_descendants(prefix=prefix, identifier=identifier, force=force, version=version)
     for curie in sorted(curies or []):
-        click.echo(f"{curie}\t{get_name_by_curie(curie, version)}")
+        click.echo(f"{curie}\t{get_name_by_curie(curie, version=version)}")
 
 
 @lookup.command()

src/pyobo/sources/mesh.py

@@ -333,6 +333,7 @@ def get_mesh_category_curies(
     """
     if version is None:
         version = get_version("mesh")
+        assert version is not None
     tree_to_mesh = get_tree_to_mesh_id(version=version)
     rv = []
     for i in range(1, 100):

src/pyobo/utils/path.py

@@ -25,7 +25,7 @@
 
 logger = logging.getLogger(__name__)
 
-VersionHint = Union[None, str, Callable[[], str]]
+VersionHint = Union[None, str, Callable[[], Optional[str]]]
 
 requests_ftp.monkeypatch_session()
 
@@ -46,6 +46,7 @@ def prefix_directory_join(
         logger.info("[%s] got version %s", prefix, version)
     elif not isinstance(version, str):
         raise TypeError(f"Invalid type: {version} ({type(version)})")
+    assert version is not None
     version = cleanup_version(version, prefix=prefix)
     if version is not None and "/" in version:
         raise ValueError(f"[{prefix}] Can not have slash in version: {version}")

src/pyobo/xrefdb/sources/pubchem.py

@@ -19,6 +19,7 @@ def get_pubchem_mesh_df(version: Optional[str] = None) -> pd.DataFrame:
     """Get PubChem Compound-MeSH xrefs."""
     if version is None:
         version = get_version("pubchem")
+        assert version is not None
     cid_mesh_url = _get_pubchem_extras_url(version, "CID-MeSH")
     return pd.DataFrame(
         [