style: update ruff

.pre-commit-config.yaml

@@ -13,7 +13,7 @@ repos:
   - id: mixed-line-ending
     args: [ --fix=lf ]
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.5.0
+  rev: v0.8.4
   hooks:
     - id: ruff
     - id: ruff-format

pyproject.toml

@@ -42,7 +42,7 @@ etl = [
     "setuptools",  # pinned for 3.12 because yoyo-migrations still uses pkg_resources
 ]
 tests = ["pytest>=6.0", "pytest-cov", "mock", "httpx", "deepdiff"]
-dev = ["pre-commit>=3.7.1", "ruff==0.5.0"]
+dev = ["pre-commit>=3.7.1", "ruff==0.8.4"]
 docs = [
     "sphinx==6.1.3",
     "sphinx-autodoc-typehints==1.22.0",
@@ -121,6 +121,8 @@ 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
     "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
@@ -139,13 +141,13 @@ fixable = [
     "PT",
     "RSE",
     "SIM",
+    "PLC",
+    "PLE",
     "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*
@@ -161,7 +163,7 @@ fixable = [
 # S321 - suspicious-ftp-lib-usage
 # *ignored for compatibility with formatter
 ignore = [
-    "ANN003", "ANN101", "ANN102",
+    "ANN003",
     "D203", "D205", "D206", "D213", "D300", "D400", "D415",
     "E111", "E114", "E117", "E501",
     "W191",
@@ -171,7 +173,6 @@ ignore = [
 [tool.ruff.lint.per-file-ignores]
 # ANN001 - missing-type-function-argument
 # ANN2 - missing-return-type
-# ANN102 - missing-type-cls
 # F401 - unused-import
 # N805 - invalid-first-argument-name-for-method
 # D100 - undocumented-public-module
@@ -186,7 +187,6 @@ ignore = [
 "tests/*" = [
     "ANN001",
     "ANN2",
-    "ANN102",
     "D100",
     "D102",
     "S101",

src/gene/database/postgresql.py

@@ -804,12 +804,12 @@ def load_from_remote(self, url: str | None) -> None:
                     for chunk in r.iter_content(chunk_size=8192):
                         if chunk:
                             h.write(chunk)
-            tar = tarfile.open(temp_tarfile, "r:gz")
-            tar_dump_file = next(
-                f for f in tar.getmembers() if f.name.startswith("gene_norm_")
-            )
-            tar.extractall(path=tempdir_path, members=[tar_dump_file])  # noqa: S202
-            dump_file = tempdir_path / tar_dump_file.name
+            with tarfile.open(temp_tarfile, "r:gz") as tar:
+                tar_dump_file = next(
+                    f for f in tar.getmembers() if f.name.startswith("gene_norm_")
+                )
+                tar.extractall(path=tempdir_path, members=[tar_dump_file])  # noqa: S202
+                dump_file = tempdir_path / tar_dump_file.name
 
             self.drop_db()
             system_call = f"psql {self.conninfo} -f {dump_file.absolute()}"

src/gene/etl/__init__.py

@@ -10,10 +10,10 @@
 from .ncbi import NCBI
 
 __all__ = [
-    "Ensembl",
     "HGNC",
     "NCBI",
-    "GeneNormalizerEtlError",
+    "Ensembl",
     "GeneFileVersionError",
+    "GeneNormalizerEtlError",
     "GeneSourceFetchError",
 ]

src/gene/query.py

@@ -246,10 +246,10 @@ def _get_search_response(self, query: str, sources: set[str]) -> dict:
 
             except DatabaseReadException as e:
                 _logger.error(
-                    "Encountered DatabaseReadException looking up %s %s: ",
+                    "Encountered DatabaseReadException %s looking up %s %s: ",
+                    e,
                     item_type,
                     term,
-                    e,
                 )
                 continue