style: update ruff

.pre-commit-config.yaml

@@ -12,7 +12,7 @@ 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-format
       - id: ruff

pyproject.toml

@@ -36,7 +36,7 @@ dynamic=["version"]
 
 [project.optional-dependencies]
 tests = ["pytest", "pytest-cov", "pytest-asyncio"]
-dev = ["pre-commit>=3.7.1", "pytest", "pytest-cov", "pytest-asyncio", "ruff==0.5.0"]
+dev = ["pre-commit>=3.7.1", "pytest", "pytest-cov", "pytest-asyncio", "ruff==0.8.4"]
 docs = [
     "sphinx==6.1.3",
     "sphinx-autodoc-typehints==1.22.0",
@@ -104,10 +104,14 @@ 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
@@ -131,8 +135,6 @@ fixable = [
     "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*
@@ -146,18 +148,19 @@ 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
-# ANN102 - missing-type-cls
 # ANN2 - missing-return-type
 # ANN201 - missing-return-type-undocumented-public-function
 # D100 - undocumented-public-module
@@ -172,15 +175,14 @@ ignore = [
 "tests/*" = [
     "ANN001",
     "ANN2",
-    "ANN102",
     "D100",
     "D102",
     "S101",
     "B011",
     "INP001",
     "SLF001"
 ]
-"src/fusor/models.py" = ["ANN201", "N803", "N805", "N815", "ANN001", "ANN2", "ANN102"]
+"src/fusor/models.py" = ["ANN201", "N803", "N805", "N815", "ANN001", "ANN2"]
 "scripts/*" = ["INP001"]
 
 [tool.ruff.lint.flake8-annotations]

src/fusor/__init__.py

@@ -4,7 +4,7 @@
 
 from fusor.fusor import FUSOR
 
-__all__ = ["__version__", "FUSOR"]
+__all__ = ["FUSOR", "__version__"]
 
 
 try:

src/fusor/models.py

@@ -436,7 +436,7 @@ def _access_object_attr(
             return obj.get(attr_name)
         else:
             msg = "Unrecognized type, should only pass entities with properties"
-            raise ValueError(msg)
+            raise ValueError(msg)  # noqa: TRY004
 
     @classmethod
     def _fetch_gene_id(

src/fusor/nomenclature.py

@@ -175,7 +175,7 @@ def generate_nomenclature(fusion: Fusion, sr: SeqRepo) -> str:
             ):
                 parts.append(gene_nomenclature(element))
         else:
-            raise ValueError
+            raise ValueError  # noqa: TRY004
     if (
         isinstance(fusion, AssayedFusion)
         and fusion.assay

src/fusor/tools.py

@@ -85,8 +85,8 @@ async def check_data_resources(
                 _logger.error("Health check failed: gene DB is incompletely populated")
             else:
                 gene_status = True
-    except Exception as e:
-        _logger.error("Encountered error while creating gene DB: %s", e)
+    except Exception:
+        _logger.exception("Encountered error while initializing gene DB")
     return FusorDataResourceStatus(
         cool_seq_tool=all(cst_status), gene_normalizer=gene_status
     )

tests/conftest.py

@@ -836,7 +836,7 @@ def exhaustive_example(alk_gene, braf_gene, tpm3_gene):
     }
 
 
-@pytest.fixture()
+@pytest.fixture
 def fusion_example():
     """Create test fixture for a fake fusion without additional property expansion."""
     return {

tests/test_fusor.py

@@ -251,7 +251,7 @@ def mane_transcript_segment_element():
     return TranscriptSegmentElement(**params)
 
 
-@pytest.fixture()
+@pytest.fixture
 def fusion_ensg_sequence_id(templated_sequence_element_ensg):
     """Create fixture using Ensemble gene ID."""
     params = {
@@ -451,7 +451,7 @@ def test_fusion(
     assert msg in str(excinfo.value)
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_transcript_segment_element(
     fusor_instance, transcript_segment_element, mane_transcript_segment_element
 ):

tests/test_translators.py

@@ -124,7 +124,7 @@ def test_valid_fusion_partners(translator_instance):
     assert not partners_check
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_jaffa(
     fusion_data_example, fusion_data_example_nonexonic, translator_instance
 ):
@@ -176,7 +176,7 @@ async def test_jaffa(
     assert jaffa_fusor_nonexonic.structure == fusion_data_example_nonexonic.structure
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_star_fusion(
     fusion_data_example, fusion_data_example_nonexonic, translator_instance
 ):
@@ -218,7 +218,7 @@ async def test_star_fusion(
     )
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_fusion_catcher(
     fusion_data_example, fusion_data_example_nonexonic, translator_instance
 ):
@@ -261,7 +261,7 @@ async def test_fusion_catcher(
     )
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_fusion_map(
     fusion_data_example, fusion_data_example_nonexonic, translator_instance
 ):
@@ -307,7 +307,7 @@ async def test_fusion_map(
     )
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_arriba(
     fusion_data_example, fusion_data_example_nonexonic, translator_instance
 ):
@@ -371,7 +371,7 @@ async def test_arriba(
     assert arriba_fusor_nonexonic.structure == fusion_data_example_nonexonic.structure
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_cicero(
     fusion_data_example, fusion_data_example_nonexonic, translator_instance
 ):
@@ -475,7 +475,7 @@ async def test_cicero(
     )
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_enfusion(
     fusion_data_example, fusion_data_example_nonexonic, translator_instance
 ):
@@ -519,7 +519,7 @@ async def test_enfusion(
     assert enfusion_fusor_nonexonic.structure == fusion_data_example_nonexonic.structure
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_genie(
     fusion_data_example, fusion_data_example_nonexonic, translator_instance
 ):