style: update ruff

.pre-commit-config.yaml

@@ -10,7 +10,7 @@ repos:
       - id: detect-aws-credentials
         args: [ --allow-missing-credentials ]
   - 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

analysis/speed_test.ipynb

@@ -15,7 +15,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from pyliftover import LiftOver \n",
+    "from pyliftover import LiftOver\n",
+    "\n",
     "from agct import Converter"
    ]
   },

pyproject.toml

@@ -31,7 +31,7 @@ tests = [
 ]
 dev = [
     "maturin",
-    "ruff==0.5.0",
+    "ruff==0.8.6",
     "pre-commit>=3.7.1",
 ]
 
@@ -88,10 +88,14 @@ select = [
     "RSE",  # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
     "RET",  # https://docs.astral.sh/ruff/rules/#flake8-return-ret
     "SLF",  # https://docs.astral.sh/ruff/rules/#flake8-self-slf
+    "SLOT",  # https://docs.astral.sh/ruff/rules/#flake8-slots-slot
     "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
     "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
@@ -110,6 +114,9 @@ fixable = [
     "PT",
     "RSE",
     "SIM",
+    "PLC",
+    "PLE",
+    "TRY",
     "PERF",
     "FURB",
     "RUF"
@@ -130,23 +137,39 @@ fixable = [
 # E501 - line-too-long*
 # W191 - tab-indentation*
 # S321 - suspicious-ftp-lib-usage
+# PLC0206 - dict-index-missing-items
 # *ignored for compatibility with formatter
 ignore = [
-    "ANN003", "ANN101", "ANN102",
+    "ANN003",
     "D203", "D205", "D206", "D213", "D300", "D400", "D415",
     "E111", "E114", "E117", "E501",
     "W191",
     "S321",
+    "PLC0206",
 ]
 
 [tool.ruff.lint.per-file-ignores]
 # ANN001 - missing-type-function-argument
 # ANN2 - missing-return-type
-# ANN102 - missing-type-cls
+# D100 - undocumented-public-module
+# D102 - undocumented-public-class
+# D103 - undocumented-public-function
 # S101 - assert
 # B011 - assert-false
 # INP001 - implicit-namespace-package
-"tests/*" = ["ANN001", "ANN2", "ANN102", "S101", "B011", "INP001"]
+"tests/*" = [
+    "ANN001",
+    "ANN2",
+    "D100",
+    "D102",
+    "D103",
+    "S101",
+    "B011",
+    "INP001"
+]
+
+[tool.ruff.lint.flake8-annotations]
+mypy-init-return = true
 
 [tool.ruff.format]
 docstring-code-format = true

src/agct/__init__.py

@@ -2,4 +2,4 @@
 
 from agct.converter import Converter, Genome, Strand
 
-__all__ = ["Converter", "Strand", "Genome"]
+__all__ = ["Converter", "Genome", "Strand"]

src/agct/converter.py

@@ -90,12 +90,12 @@ def __init__(
 
         try:
             self._converter = _core.Converter(chainfile)
-        except FileNotFoundError as e:
-            _logger.error("Unable to open chainfile located at %s", chainfile)
-            raise e
-        except _core.ChainfileError as e:
-            _logger.error("Error reading chainfile located at %s", chainfile)
-            raise e
+        except FileNotFoundError:
+            _logger.exception("Unable to open chainfile located at %s", chainfile)
+            raise
+        except _core.ChainfileError:
+            _logger.exception("Error reading chainfile located at %s", chainfile)
+            raise
 
     @staticmethod
     def _download_function_builder(from_db: Genome, to_db: Genome) -> Callable:
@@ -147,7 +147,7 @@ def convert_coordinate(
         except _core.NoLiftoverError:
             results = []
         except _core.ChainfileError:
-            _logger.error(
+            _logger.exception(
                 "Encountered internal error while converting coordinates - is the chainfile invalid? (%s, %s, %s)",
                 chrom,
                 pos,
@@ -159,12 +159,12 @@ def convert_coordinate(
             try:
                 pos = int(result[1])
             except ValueError:
-                _logger.error("Got invalid position value in %s", result)
+                _logger.exception("Got invalid position value in %s", result)
                 continue
             try:
                 strand = Strand(result[2])
             except ValueError:
-                _logger.error("Got invalid Strand value in %s", result)
+                _logger.exception("Got invalid Strand value in %s", result)
                 continue
             formatted_results.append((result[0], pos, strand))
         return formatted_results