style: update style tooling, run it

Author: jsstevenson

.github/workflows/labels.yml

@@ -26,4 +26,4 @@ jobs:
             https://raw.githubusercontent.com/biocommons/.github/main/etc/labels.yml
             .github/labels.yml
 
-          delete-other-labels: false
+          delete-other-labels: false

pyproject.toml

@@ -23,10 +23,9 @@ dev = [
     "build ~= 0.8",
     "ipython ~= 8.4",
     "mypy-extensions ~= 1.0",
-    "pre-commit ~= 3.4",
+    "pre-commit >= 4.2.0",
     "pyright~=1.1",
     "ruff == 0.12.8",
-    "pre-commit>=4.2.0",
 ]
 tests = [
     "pytest-cov ~= 4.1",
@@ -199,15 +198,17 @@ ignore = [
     "E501",
     "W191",
     "S321",
+    "COM812",
     # other
     "ANN002",
     "ANN003",
     "PLR0913",
     "PLC0206",
     "EM101",
     "D213",
+    "D203",
     "D400",
-    "d415",
+    "D415",
 ]
 
 [tool.ruff.lint.per-file-ignores]

src/biocommons/example/__main__.py

@@ -8,9 +8,9 @@
 _logger = logging.getLogger(__name__)
 
 
-def main():  # pragma: no cover
+def main() -> None:  # pragma: no cover
     """marvin.example main"""
-    import coloredlogs
+    import coloredlogs  # noqa: PLC0415
 
     logging.Formatter.converter = time.gmtime
     coloredlogs.install(
@@ -22,8 +22,8 @@ def main():  # pragma: no cover
     quote = marvin.get_quote()
     _logger.warning("Got quote from Marvin (len=%s)", len(quote))
 
-    print("Marvin says:")
-    print(quote)
+    print("Marvin says:")  # noqa: T201
+    print(quote)  # noqa: T201
 
 
 if __name__ == "__main__":

src/biocommons/example/marvin.py

@@ -18,7 +18,7 @@
 
 
 def is_alive() -> bool:
-    """tests whether Marvin is alive
+    """Test whether Marvin is alive
 
     >>> is_alive() is True
     True
@@ -28,7 +28,7 @@ def is_alive() -> bool:
 
 
 def get_quote() -> str:
-    """return random Marvin quote
+    """Return random Marvin quote
 
     eg> get_quote()
     "There's only one life-form as intelligent..."

src/biocommons/example/marvin_adjacent_test.py

@@ -1,8 +1,8 @@
 """biocommons.example test, adjacent to code"""
 
-from .marvin import get_quote
+from biocommons.example.marvin import get_quote
 
 
-def test_get_quote():
-    """test get_quote"""
+def test_get_quote() -> None:
+    """Test get_quote"""
     assert get_quote() is not None  # noqa: S101

src/biocommons/example/quotes.yaml

@@ -12,15 +12,15 @@ quotes:
     fifty thousand times more intelligent than you and even I don't
     know the answer. It gives me a headache just trying to think down
     to your level.
-           
+
   - >-
     There's only one life-form as intelligent as me within thirty
     parsecs of here and that's me.
-           
+
   - >-
     I wish you'd just tell me rather trying to engage my enthusiasm
     because I haven't got one.
-           
+
   - >-
     And then, of course, I've got this terrible pain in all the diodes
     down my left side.

src/biocommons/example/tests/__init__.py

@@ -0,0 +1 @@
+"""Declare tests internal to src directory"""

src/biocommons/example/tests/conftest.py

@@ -1,10 +1,13 @@
+"""Provide fixtures to tests."""
+
 import importlib.resources
 
 import pytest
 import yaml
 
 
-@pytest.fixture()
-def all_quotes():
+@pytest.fixture
+def all_quotes() -> None:
+    """Provide quotes fixture"""
     quotes_stream = importlib.resources.files("example").joinpath("quotes.yaml").read_text()
     return yaml.load(quotes_stream, Loader=yaml.SafeLoader)["quotes"]

src/biocommons/example/tests/marvin_subdir_test.py

@@ -1,9 +1,9 @@
 """biocommons.example test, within tests directory adjacent to source"""
 
-from ..marvin import get_quote
+from biocommons.example.marvin import get_quote
 
 
-def test_get_quote(all_quotes):
-    """test get_quote"""
+def test_get_quote(all_quotes: list[str]) -> None:
+    """Test get_quote"""
     # NB: all_quotes argument is a test fixture; see ./conftest.py
     assert get_quote() in all_quotes  # noqa: S101