Minor typing improvements (#482)

Author: cthoyt

pyproject.toml

@@ -68,7 +68,7 @@ dependencies = [
     "humanize",
     "tabulate",
     "cachier",
-    "pystow>=0.7.5",
+    "pystow<=0.7.23",
     "bioversions>=0.8.243",
     "bioregistry>=0.12.30",
     "ssslm>=0.0.13",

src/pyobo/cli/cli.py

@@ -21,13 +21,13 @@
 
 @click.group()
 @click.version_option()
-def main():
+def main() -> None:
     """CLI for PyOBO."""
 
 
 @main.command()
 @click.option("--remove-obo", is_flag=True)
-def clean(remove_obo: bool):
+def clean(remove_obo: bool) -> None:
     """Delete all cached files."""
     suffixes = [
         "_mappings.tsv",
@@ -55,15 +55,15 @@ def clean(remove_obo: bool):
 
 
 @main.command()
-def ls():
+def ls() -> None:
     """List how big all of the OBO files are."""
     import humanize
     from tabulate import tabulate
 
-    entries = [(prefix, os.path.getsize(path)) for prefix, path in _iter_cached_obo()]
+    entries_init = [(prefix, os.path.getsize(path)) for prefix, path in _iter_cached_obo()]
     entries = [
         (prefix, humanize.naturalsize(size), "✅" if not has_nomenclature_plugin(prefix) else "❌")
-        for prefix, size in sorted(entries, key=itemgetter(1), reverse=True)
+        for prefix, size in sorted(entries_init, key=itemgetter(1), reverse=True)
     ]
     click.echo(tabulate(entries, headers=["Source", "Size", "OBO"]))
 

src/pyobo/cli/database.py

@@ -39,7 +39,7 @@
 
 
 @click.group(name="database")
-def main():
+def main() -> None:
     """Build the PyOBO Database."""
 
 
@@ -126,8 +126,7 @@ def build(ctx: click.Context, eager_versions: bool, **kwargs: Unpack[DatabaseKwa
 @database_annotate
 def cache(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Cache all things."""
-    from .database_utils import iter_helper_helper
-    from ..getters import get_ontology
+    from ..getters import get_ontology, iter_helper_helper
 
     if zenodo:
         click.echo("no zenodo for caching")
@@ -144,9 +143,9 @@ def metadata(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) ->
     """Make the prefix-metadata dump."""
     import bioregistry
 
-    from .database_utils import IterHelperHelperDict, iter_helper_helper
+    from .database_utils import IterHelperHelperDict
     from ..api import get_metadata
-    from ..getters import db_output_helper
+    from ..getters import db_output_helper, iter_helper_helper
 
     def _iter_metadata_internal(
         **kwargs: Unpack[IterHelperHelperDict],

src/pyobo/cli/lookup.py

@@ -32,7 +32,7 @@
 
 
 @click.group()
-def lookup():
+def lookup() -> None:
     """Lookup resources."""