style: update ruff and precommit (#409)

Author: jsstevenson

.pre-commit-config.yaml

@@ -12,9 +12,9 @@ repos:
       - id: mixed-line-ending
         args: [ --fix=lf ]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.6
+    rev: v0.12.1
     hooks:
       - id: ruff-format
       - id: ruff
         args: [ --fix, --exit-non-zero-on-fix ]
-minimum_pre_commit_version: 4.0.1
+minimum_pre_commit_version: 4.2.0

pyproject.toml

@@ -40,11 +40,11 @@ dynamic = ["version"]
 
 [project.optional-dependencies]
 dev = [
-    "pre-commit>=4.0.1",
+    "pre-commit>=4.2.0",
     "ipython",
     "ipykernel",
     "psycopg2-binary",
-    "ruff==0.8.6"
+    "ruff==0.12.1",
 ]
 tests = ["pytest", "pytest-cov", "pytest-asyncio==0.18.3", "mock"]
 docs = [

src/cool_seq_tool/handlers/seqrepo_access.py

@@ -75,9 +75,7 @@ def get_reference_sequence(
                     f"Start inter-residue coordinate ({start}) is out of index on {ac}"
                 )
             elif error.startswith("stop out of range"):
-                msg = (
-                    f"End inter-residue coordinate ({end}) is out of " f"index on {ac}"
-                )
+                msg = f"End inter-residue coordinate ({end}) is out of index on {ac}"
             else:
                 msg = f"{e}"
             _logger.warning(msg)

src/cool_seq_tool/mappers/exon_genomic_coords.py

@@ -776,7 +776,7 @@ async def _genomic_to_tx_segment(
             GRCh38 by default. Will attempt to liftover if starting assembly is GRCh37
         :return: Data for a transcript segment boundary (inter-residue coordinates)
         """
-        params = {key: None for key in GenomicTxSeg.model_fields}
+        params = dict.fromkeys(GenomicTxSeg.model_fields)
 
         # Validate inputs exist in UTA
         if gene:

src/cool_seq_tool/mappers/mane_transcript.py

@@ -268,7 +268,7 @@ async def _liftover_to_38(self, genomic_tx_data: GenomicTxMetadata) -> None:
         query = f"""
             SELECT alt_ac
             FROM {self.uta_db.schema}.genomic
-            WHERE alt_ac LIKE '{genomic_tx_data.alt_ac.split('.')[0]}%'
+            WHERE alt_ac LIKE '{genomic_tx_data.alt_ac.split(".")[0]}%'
             {order_by_cond}
             """  # noqa: S608
         nc_acs = await self.uta_db.execute_query(query)

src/cool_seq_tool/sources/uta_database.py

@@ -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 = [
@@ -325,13 +325,13 @@ async def get_cds_start_end(self, tx_ac: str) -> tuple[int, int] | None:
         cds_start_end = await self.execute_query(query)
         if cds_start_end:
             cds_start_end = cds_start_end[0]
-            if cds_start_end[0] is not None and cds_start_end[1] is not None:  # noqa: RET503
+            if cds_start_end[0] is not None and cds_start_end[1] is not None:
                 return cds_start_end[0], cds_start_end[1]
         else:
             _logger.warning(
                 "Unable to get coding start/end site for accession: %s", tx_ac
             )
-            return None
+        return None
 
     async def get_newest_assembly_ac(self, ac: str) -> list[str]:
         """Find accession associated to latest genomic assembly
@@ -352,7 +352,7 @@ async def get_newest_assembly_ac(self, ac: str) -> list[str]:
         query = f"""
             SELECT ac
             FROM {self.schema}._seq_anno_most_recent
-            WHERE ac LIKE '{ac.split('.')[0]}%'
+            WHERE ac LIKE '{ac.split(".")[0]}%'
             AND ((descr IS NULL) OR (descr = ''))
             {order_by_cond}
             """  # noqa: S608
@@ -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)

tests/handlers/test_seqrepo_access.py

@@ -89,7 +89,7 @@ def test_translate_identifier(test_seqrepo_access):
     resp = test_seqrepo_access.translate_identifier("refseq_152263.3")
     assert resp == (
         [],
-        "SeqRepo unable to get translated identifiers for" " refseq_152263.3",
+        "SeqRepo unable to get translated identifiers for refseq_152263.3",
     )