style: update ruff and precommit

.github/workflows/checks.yaml

@@ -33,7 +33,7 @@ jobs:
         run: python3 -m pip install ".[dev]"
 
       - name: Check style
-        run: python3 -m ruff check . && ruff format --check .
+        run: python3 -m ruff check . && python3 -m ruff format --check .
   rust-test:
     runs-on: ubuntu-latest
     defaults:
@@ -62,3 +62,22 @@ jobs:
         run: rustup component add rustfmt
 
       - run: cargo fmt -- --check
+  precommit_hooks:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        cmd:
+          - "end-of-file-fixer"
+          - "trailing-whitespace"
+          - "mixed-line-ending"
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+
+      - uses: pre-commit/action@v3.0.1
+        with:
+          extra_args: ${{ matrix.cmd }} --all-files

.pre-commit-config.yaml

@@ -9,8 +9,10 @@ repos:
       - 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: v0.5.0  # ruff version
+    rev: v0.8.6  # ruff version
     hooks:
       - id: ruff-format
       - id: ruff
@@ -22,4 +24,4 @@ repos:
         entry: bash -c 'cd rust && cargo fmt'
         args: ['--verbose', '--']
 
-minimum_pre_commit_version: 3.7.1
+minimum_pre_commit_version: 4.0.1

pyproject.toml

@@ -30,8 +30,8 @@ tests = [
 ]
 dev = [
     "maturin",
-    "ruff==0.5.0",
-    "pre-commit>=3.7.1",
+    "ruff==0.8.6",
+    "pre-commit>=4.0.1",
 ]
 
 [project.urls]
@@ -94,6 +94,9 @@ select = [
     "ARG",  # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg
     "PTH",  # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
     "PGH",  # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh
+    "PLC",  # https://docs.astral.sh/ruff/rules/#convention-c
+    "PLE",  # https://docs.astral.sh/ruff/rules/#error-e_1
+    "TRY",  # https://docs.astral.sh/ruff/rules/#tryceratops-try
     "PERF",  # https://docs.astral.sh/ruff/rules/#perflint-perf
     "FURB",  # https://docs.astral.sh/ruff/rules/#refurb-furb
     "RUF",  # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
@@ -112,51 +115,27 @@ fixable = [
     "PT",
     "RSE",
     "SIM",
+    "PLC",
+    "PLE",
+    "TRY",
     "PERF",
     "FURB",
     "RUF"
 ]
-# ANN003 - missing-type-kwargs
-# ANN101 - missing-type-self
-# ANN102 - missing-type-cls
-# D203 - one-blank-line-before-class
-# D205 - blank-line-after-summary
-# D206 - indent-with-spaces*
-# D213 - multi-line-summary-second-line
-# D300 - triple-single-quotes*
-# D400 - ends-in-period
-# D415 - ends-in-punctuation
-# E111 - indentation-with-invalid-multiple*
-# E114 - indentation-with-invalid-multiple-comment*
-# E117 - over-indented*
-# E501 - line-too-long*
-# W191 - tab-indentation*
-# S321 - suspicious-ftp-lib-usage
-# *ignored for compatibility with formatter
 ignore = [
-    "ANN003", "ANN101", "ANN102",
-    "D203", "D205", "D206", "D213", "D300", "D400", "D415",
-    "E111", "E114", "E117", "E501",
-    "W191",
+    # ignored for compatibility with formatter:
+    "D206", "D300", "E111", "E114", "E117", "E501", "W191",
+    # other
+    "ANN003",
+    "D203", "D205", "D213", "D400", "D415",
     "S321",
+    "PLC0206",
 ]
 
 [tool.ruff.lint.per-file-ignores]
-# ANN001 - missing-type-function-argument
-# ANN2 - missing-return-type
-# ANN102 - missing-type-cls
-# D301 - escape-sequence-in-docstring
-# S101 - assert
-# B011 - assert-false
-# D100 - undocumented-public-module
-# D101 - undocumented-public-class
-# D102 - undocumented-public-method
-# D103 - undocumented-public-function
-# INP001 - implicit-namespace-package
 "tests/*" = [
     "ANN001",
     "ANN2",
-    "ANN102",
     "S101",
     "B011",
     "INP001",
@@ -167,5 +146,8 @@ ignore = [
 ]
 "src/vrsix/cli.py" = ["D301"]
 
+[tool.ruff.lint.flake8-annotations]
+mypy-init-return = true
+
 [tool.ruff.format]
 docstring-code-format = true

src/vrsix/load.py

@@ -14,13 +14,13 @@
 from vrsix.sqlite import DEFAULT_SQLITE_LOCATION
 
 __all__ = [
-    "load_vcf",
-    "vcf_to_sqlite",
     "FiletypeError",
     "SqliteFileError",
-    "VrsixError",
     "VcfError",
     "VrsixDbError",
+    "VrsixError",
+    "load_vcf",
+    "vcf_to_sqlite",
 ]
 
 _logger = logging.getLogger(__name__)

tests/test_load.py

@@ -8,7 +8,7 @@
 from vrsix import load
 
 
-@pytest.fixture()
+@pytest.fixture
 def temp_dir() -> Generator:
     with tempfile.TemporaryDirectory() as temp_dir:
         yield Path(temp_dir)