style: update style tooling and linting + run on codebase

.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

.github/workflows/python-package.yml

@@ -44,6 +44,21 @@ jobs:
       run: |
         ruff format --check .
 
+    - name: Ensure EOF line
+      uses: pre-commit/action@v3.0.1
+      with:
+        extra_args: end-of-file-fixer --all-files
+
+    - name: Fix trailing whitespace
+      uses: pre-commit/action@v3.0.1
+      with:
+        extra_args: trailing-whitespace --all-files
+
+    - name: Fix mixed line endings
+      uses: pre-commit/action@v3.0.1
+      with:
+        extra_args: mixed-line-ending --all-files
+
   test:
     runs-on: ubuntu-latest
 

.pre-commit-config.yaml

@@ -1,7 +1,20 @@
 repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0
+  hooks:
+    - id: check-added-large-files
+    - id: detect-private-key
+    - id: trailing-whitespace
+    - id: end-of-file-fixer
+    - id: check-merge-conflict
+    - id: detect-aws-credentials
+      args: [ --allow-missing-credentials ]
+    - id: mixed-line-ending
+      args: [ --fix=lf ]
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.4.4
+  rev: v0.12.8
   hooks:
-    - id: ruff
     - id: ruff-format
-      args: [ --check ]
+    - id: ruff
+      args: [ --fix, --exit-non-zero-on-fix ]
+minimum_pre_commit_version: 4.2.0

Makefile

@@ -65,7 +65,7 @@ build: %:
 
 ############################################################################
 #= TESTING
-# see test configuration in setup.cfg
+# see test configuration in pyproject.toml
 
 #=> test: execute tests
 #=> test-code: test code (including embedded doctests)
@@ -126,6 +126,7 @@ cleaner: clean
 	rm -frv **/*.pyc
 	rm -frv **/*.orig
 	rm -frv **/*.rej
+	rm -fvr .ruff_cache
 
 #=> cleanest: remove files and directories that require more time/network fetches to rebuild
 .PHONY: cleanest

pyproject.toml

@@ -22,8 +22,8 @@ dependencies = ["coloredlogs ~= 15.0", "pyyaml ~= 6.0"]
 dev = [
     "build ~= 0.8",
     "ipython ~= 8.4",
-    "pre-commit ~= 3.4",
-    "ruff == 0.4.4",
+    "pre-commit >= 4.2.0",
+    "ruff == 0.12.8",
 ]
 tests = [
     "pytest-cov ~= 4.1",
@@ -104,63 +104,96 @@ exclude_lines = [
 [tool.ruff]
 src = ["src", "tests"]
 line-length = 100
+exclude = [
+    "bin",
+    "sbin",
+    "docs",
+]
 
 [tool.ruff.lint]
-select = [
-    "F",    # https://docs.astral.sh/ruff/rules/#pyflakes-f
-    "E",
-    "W",    # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w
-    "I",    # https://docs.astral.sh/ruff/rules/#isort-i
-    "N",    # https://docs.astral.sh/ruff/rules/#pep8-naming-n
-    "UP",   # https://docs.astral.sh/ruff/rules/#pyupgrade-up
-    "YTT",  # https://docs.astral.sh/ruff/rules/#flake8-2020-ytt
-    "S",    # https://docs.astral.sh/ruff/rules/#flake8-bandit-s
-    "B",    # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
-    "A",    # https://docs.astral.sh/ruff/rules/#flake8-builtins-a
-    "C4",   # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
-    "DTZ",  # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
-    "EM",   # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
-    "LOG",  # https://docs.astral.sh/ruff/rules/#flake8-logging-log
-    "G",    # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
-    "PIE",  # https://docs.astral.sh/ruff/rules/#flake8-pie-pie
-    "PT",   # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt
-    "RSE",  # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
-    "RET",  # https://docs.astral.sh/ruff/rules/#flake8-return-ret
-    "SIM",  # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
-    "ARG",  # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg
-    "PTH",  # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
-    "PL",   # https://docs.astral.sh/ruff/rules/#pylint-pl
-    "TRY",  # https://docs.astral.sh/ruff/rules/#tryceratops-try
-    "PERF", # https://docs.astral.sh/ruff/rules/#perflint-perf
-    "RUF",  # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
-]
-fixable = [
-    "F401",
-    "F541",
-    "I",
-    "D",
-    "UP",
-    "B",
-    "C4",
-    "EM",
-    "PIE",
-    "PT",
-    "RSE",
-    "RET",
-    "SIM",
-    "PERF",
-    "RUF",
-]
+select = ["ALL"]
 ignore = [
+    # not used
+    "AIR",
+    "ERA",
+    "FAST",
+    "YTT",
+    "FBT",
+    "CPY",
+    "DJ",
+    "EM",
+    "EXE",
+    "FIX",
+    "FA",
+    "INT",
+    "PYI",
+    "TID",
+    "TD",
+    "TC",
+    "C90",
+    "NPY",
+    "PD",
     # ignore for compatibility with formatter
+    "D206",
+    "D300",
     "W191",
     "E111",
     "E114",
     "E117",
+    "E501",
+    "W191",
     "S321",
-    # other
-    "PLR0913",
+    "COM812",
+    # don't require types on *args, **kwargs
+    "ANN002",
+    "ANN003",
+    # subjective pylint thresholds
+    "PLR0904",
+    "PLR091",
+    "PLR1702",
+    # excessive docstring requirements
+    "D105",
+    "D205",
+    "D203",
+    "D213",  # conflicts with D212
+    "D400",
+    "D401",
+    "D403",
+    "D415",
+    # excessive exception message requirements
+    "TRY003",
+    # excessive type ignore requirements
+    "PGH003",
+    # misc unnecessary readability requirements
+    "RET504",
 ]
 
 [tool.ruff.lint.per-file-ignores]
-"tests/*" = ["S101"]
+# ANN001 - missing-type-function-argument
+# ANN2 - missing-return-type
+# D100 - undocumented-public-module
+# D101 - undocumented-public-class
+# D102 - undocumented-public-method
+# D103 - undocumented-public-function
+# S101 - assert
+# B011 - assert-false
+# INP001 - implicit-namespace-package
+# SLF001 - private-member-access
+# BLE001 - blind-except
+"tests/*" = [
+    "ANN001",
+    "ANN2",
+    "D100",
+    "D10",
+    "S101",
+    "B011",
+    "INP001",
+    "SLF001",
+    "BLE001",
+]
+
+[tool.ruff.lint.flake8-annotations]
+mypy-init-return = true
+
+[tool.ruff.format]
+docstring-code-format = true

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
+    """Tests 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():
+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 @@
+# noqa: D104

src/biocommons/example/tests/conftest.py

@@ -1,10 +1,11 @@
+# noqa: D100
 import importlib.resources
 
 import pytest
 import yaml
 
 
-@pytest.fixture()
-def all_quotes():
+@pytest.fixture
+def all_quotes() -> dict:  # noqa: D103
     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):
+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