Strict typing

Author: cthoyt

src/bioontologies/cli.py

@@ -29,7 +29,7 @@
 
 @click.group()
 @click.version_option()
-def main():
+def main() -> None:
     """CLI for bioontologies."""
 
 
@@ -42,7 +42,7 @@ def main():
     is_flag=True,
     help="Save intermediate OBO Graph JSON file if conversion from OWL is required",
 )
-def index(prefix: str, graph_id: str | None, directory: Path | None, save_obograph: bool):
+def index(prefix: str, graph_id: str | None, directory: Path | None, save_obograph: bool) -> None:
     """Generate a node index file."""
     from .robot import get_obograph_by_prefix
 

src/bioontologies/ner.py

@@ -97,7 +97,7 @@ def get_literal_mappings_subset(
     ancestors: curies.Reference | Sequence[curies.Reference],
     *,
     check: bool = False,
-    **kwargs,
+    **kwargs: Any,
 ) -> list[ssslm.LiteralMapping]:
     """Get a subset of literal mappings for terms under the ancestors."""
     if isinstance(ancestors, curies.Reference):

src/bioontologies/relations/api.py

@@ -111,7 +111,7 @@ def get_curie_to_norm_name() -> Mapping[str, str]:
 HEADER = ["prefix", "identifier", "label", "synonyms"]
 
 
-def main():
+def main() -> None:
     """Download and process the relation ontology data."""
     from bioontologies import get_obograph_by_prefix
     from bioontologies.obograph import GraphDocument

src/bioontologies/upgrade/import_debio.py

@@ -8,7 +8,7 @@
 OBO_PURL = "http://purl.obolibrary.org/obo/"
 
 
-def main():
+def main() -> None:
     """Import rewrites from DeBiO."""
     for node in requests.get(URL, timeout=5).json()["graphs"][0]["nodes"]:
         if node.get("type") != "PROPERTY":

tox.ini

@@ -115,8 +115,7 @@ deps =
     mypy
     pydantic
     types-requests
-skip_install = true
-commands = mypy --install-types --non-interactive --ignore-missing-imports src/
+commands = mypy --ignore-missing-imports --strict src/
 
 [testenv:doc8]
 skip_install = true