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: v0.8.6
     hooks:
       - id: ruff-format
       - id: ruff

pyproject.toml

@@ -44,7 +44,7 @@ dev = [
     "ipython",
     "ipykernel",
     "psycopg2-binary",
-    "ruff==0.5.0"
+    "ruff==0.8.6"
 ]
 tests = ["pytest", "pytest-cov", "pytest-asyncio==0.18.3", "mock"]
 docs = [
@@ -116,10 +116,14 @@ lint.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
@@ -138,14 +142,15 @@ lint.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*
@@ -159,26 +164,40 @@ lint.fixable = [
 # E501 - line-too-long*
 # W191 - tab-indentation*
 # S321 - suspicious-ftp-lib-usage
+# PLC0206 - dict-index-missing-items
 # *ignored for compatibility with formatter
 lint.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
 # N805 - invalid-first-argument-name-for-method
 # F821 - undefined-name
 # F401 - unused-import
 # INP001 - implicit-namespace-package
 # SLF001 - private-member-access
 # ARG001 - unused-function-argument
-"tests/*" = ["ANN001", "ANN2", "ANN102", "S101", "INP001", "SLF001", "ARG001"]
+"tests/*" = [
+    "ANN001",
+    "ANN2",
+    "D100",
+    "D102",
+    "D103",
+    "S101",
+    "INP001",
+    "SLF001",
+    "ARG001"
+]
 "*__init__.py" = ["F401"]
 "src/cool_seq_tool/schemas.py" = ["ANN201", "N805", "ANN001"]
 

src/cool_seq_tool/mappers/__init__.py

@@ -6,4 +6,4 @@
 from .exon_genomic_coords import ExonGenomicCoordsMapper
 
 
-__all__ = ["AlignmentMapper", "LiftOver", "ManeTranscript", "ExonGenomicCoordsMapper"]
+__all__ = ["AlignmentMapper", "ExonGenomicCoordsMapper", "LiftOver", "ManeTranscript"]

src/cool_seq_tool/mappers/exon_genomic_coords.py

@@ -1022,11 +1022,8 @@ def _use_alt_start_i(is_seg_start: bool, strand: Strand) -> bool:
         :return ``True`` if alt_start_i should be used, ``False`` if alt_end_i should
         be used
         """
-        return (
-            is_seg_start
-            and strand == Strand.POSITIVE
-            or not is_seg_start
-            and strand == Strand.NEGATIVE
+        return (is_seg_start and strand == Strand.POSITIVE) or (
+            not is_seg_start and strand == Strand.NEGATIVE
         )
 
     @staticmethod

src/cool_seq_tool/resources/status.py

@@ -88,11 +88,11 @@ async def check_status(
         try:
             get_data_file(r)
         except FileNotFoundError:
-            _logger.error(
+            _logger.exception(
                 "%s does not exist at configured location %s", name_lower, declared_path
             )
         except ValueError:
-            _logger.error(
+            _logger.exception(
                 "%s configured at %s is not a valid file.", name_lower, declared_path
             )
         except Exception as e:
@@ -107,19 +107,17 @@ async def check_status(
             chain_file_37_to_38=chain_file_37_to_38,
             chain_file_38_to_37=chain_file_38_to_37,
         )
-    except (FileNotFoundError, ChainfileError) as e:
-        _logger.error("agct converter setup failed: %s", e)
+    except (FileNotFoundError, ChainfileError):
+        _logger.exception("agct converter setup failed")
     except Exception as e:
         _logger.critical("Encountered unexpected error setting up agct: %s", e)
     else:
         status["liftover"] = True
 
     try:
         await UtaDatabase.create(db_url)
-    except (OSError, InvalidCatalogNameError, UndefinedTableError) as e:
-        _logger.error(
-            "Encountered error instantiating UTA at URI %s: %s", UTA_DB_URL, e
-        )
+    except (OSError, InvalidCatalogNameError, UndefinedTableError):
+        _logger.exception("Encountered error instantiating UTA at URI %s", UTA_DB_URL)
     except Exception as e:
         _logger.critical(
             "Encountered unexpected error instantiating UTA from URI %s: %s",
@@ -134,10 +132,10 @@ async def check_status(
             sr = SeqRepo(root_dir=SEQREPO_ROOT_DIR)
         sra = SeqRepoAccess(sr)
         sra.sr["NC_000001.11"][1000:1001]
-    except OSError as e:
-        _logger.error("Encountered error while instantiating SeqRepo: %s", e)
+    except OSError:
+        _logger.exception("Encountered error while instantiating SeqRepo")
     except KeyError:
-        _logger.error("SeqRepo data fetch test failed -- is it populated?")
+        _logger.exception("SeqRepo data fetch test failed -- is it populated?")
     except Exception as e:
         _logger.critical("Encountered unexpected error setting up SeqRepo: %s", e)
     else:

src/cool_seq_tool/sources/uta_database.py

@@ -162,11 +162,11 @@ async def create_pool(self) -> None:
                     database=self.args.database,
                 )
             except InterfaceError as e:
-                _logger.error(
-                    "While creating connection pool, encountered exception %s", e
+                _logger.exception(
+                    "While creating connection pool, encountered exception"
                 )
                 msg = "Could not create connection pool"
-                raise Exception(msg) from e
+                raise Exception(msg) from e  # noqa: TRY002
 
     @classmethod
     async def create(
@@ -221,7 +221,7 @@ async def _create_genomic_table(self) -> None:
                WHERE table_schema = '{self.schema}'
                AND table_name = 'genomic'
             );
-            """  # noqa: S608
+            """
         genomic_table_exists = await self.execute_query(check_table_exists)
         genomic_table_exists = genomic_table_exists[0].get("exists")
         if genomic_table_exists is None:
@@ -250,7 +250,7 @@ async def _create_genomic_table(self) -> None:
                         LEFT JOIN {self.schema}.exon_aln ea ON
                             (((te.exon_id = ea.tx_exon_id) AND
                             (ae.exon_id = ea.alt_exon_id))));
-                """  # noqa: S608
+                """
             await self.execute_query(create_genomic_table)
 
             indexes = [
@@ -499,7 +499,7 @@ async def get_tx_exon_aln_v_data(
             AND {start_pos} BETWEEN {pos_q}
             AND {end_pos} BETWEEN {pos_q}
             {order_by_cond}
-            """  # noqa: S608
+            """
         result = await self.execute_query(query)
         if not result:
             _logger.warning("Unable to find transcript alignment for query: %s", query)
@@ -852,8 +852,8 @@ async def get_chr_assembly(self, ac: str) -> tuple[str, Assembly] | None:
 
         try:
             assembly = Assembly(assembly)
-        except ValueError as e:
-            _logger.error(e)
+        except ValueError:
+            _logger.exception("Unable to parse %s as an Assembly", assembly)
             return None
 
         return chromosome, assembly
@@ -924,11 +924,11 @@ def get_secret() -> str:
 
         try:
             get_secret_value_response = client.get_secret_value(SecretId=secret_name)
-        except ClientError as e:
+        except ClientError:
             # For a list of exceptions thrown, see
             # https://docs.aws.amazon.com/secretsmanager/latest/apireference/API_GetSecretValue.html
-            _logger.error(e)
-            raise e
+            _logger.exception("Encountered AWS client error fetching UTA DB secret")
+            raise
         else:
             return get_secret_value_response["SecretString"]
 

tests/mappers/test_alignment.py

@@ -111,7 +111,7 @@ def _expected(assembly):
     return _expected
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_get_cds_start(test_alignment_mapper):
     """Test that _get_cds_start method works correctly"""
     # Valid
@@ -125,7 +125,7 @@ async def test_get_cds_start(test_alignment_mapper):
     assert w == "Accession NM_004333.6293702 not found in UTA db"
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_p_to_c(test_alignment_mapper, braf_v600e_c, egfr_l858r_c):
     """Test that p_to_c works as expected"""
     # BRAF V600E
@@ -164,7 +164,7 @@ async def test_p_to_c(test_alignment_mapper, braf_v600e_c, egfr_l858r_c):
     }
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_p_to_c_invalid(test_alignment_mapper):
     """Test invalid queries for p_to_c method"""
     # Invalid protein accession
@@ -175,7 +175,7 @@ async def test_p_to_c_invalid(test_alignment_mapper):
     assert resp is None
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_c_to_g(
     test_alignment_mapper,
     braf_v600e_grch37,
@@ -227,7 +227,7 @@ async def test_c_to_g(
         assert resp == expected, params
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_c_to_g_invalid(test_alignment_mapper):
     """Test invalid queries for c_to_g method"""
     # Should not expect to find anything given these two positions
@@ -262,7 +262,7 @@ async def test_c_to_g_invalid(test_alignment_mapper):
     assert w == "c_start_pos and c_end_pos are not a valid range for the codon(s)"
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_p_to_g(
     test_alignment_mapper,
     braf_v600e_grch37,
@@ -350,7 +350,7 @@ async def test_p_to_g(
         assert resp == hras_t2a(assembly), params
 
 
-@pytest.mark.asyncio()
+@pytest.mark.asyncio
 async def test_p_to_g_invalid(test_alignment_mapper):
     """Test invalid queries for p_to_g method"""
     # Invalid protein accession