style: update ruff (#392)

per GenomicMedLab/software-templates#80

Author: jsstevenson

.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: v0.8.6
   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==0.8.6"]
 docs = [
     "sphinx==6.1.3",
     "sphinx-autodoc-typehints==1.22.0",
@@ -117,10 +117,14 @@ 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
@@ -139,13 +143,14 @@ 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*
@@ -159,19 +164,20 @@ 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
 # F401 - unused-import
 # N805 - invalid-first-argument-name-for-method
 # D100 - undocumented-public-module
@@ -186,7 +192,6 @@ ignore = [
 "tests/*" = [
     "ANN001",
     "ANN2",
-    "ANN102",
     "D100",
     "D102",
     "S101",

src/gene/cli.py

@@ -206,7 +206,7 @@ def _load_source(
     try:
         processed_ids += source.perform_etl(use_existing)
     except GeneNormalizerEtlError as e:
-        _logger.error(e)
+        _logger.exception("ETL error while loading %s", n)
         click.echo(f"Encountered error while loading {n}: {e}.")
         click.get_current_context().exit()
     end_load = timer()
@@ -322,13 +322,13 @@ def update_normalizer_db(
 
         if len(sources_split) == 0:
             err_msg = "Must enter 1 or more source names to update"
-            raise Exception(err_msg)
+            raise ValueError(err_msg)
 
         non_sources = set(sources_split) - set(SOURCES)
 
         if len(non_sources) != 0:
             err_msg = f"Not valid source(s): {non_sources}"
-            raise Exception(err_msg)
+            raise ValueError(err_msg)
 
         parsed_source_names = {SourceName(SOURCES[s]) for s in sources_split}
         _update_normalizer(parsed_source_names, db, update_merged, use_existing)

src/gene/database/dynamodb.py

@@ -105,8 +105,8 @@ def drop_db(self) -> None:
         try:
             if not self._check_delete_okay():
                 return
-        except DatabaseWriteException as e:
-            raise e
+        except DatabaseWriteException:  # noqa: TRY203
+            raise
 
         if self.gene_table in self.list_tables():
             self.dynamodb.Table(self.gene_table).delete()
@@ -250,9 +250,9 @@ def get_record_by_id(
             response = self.genes.query(KeyConditionExpression=exp)
             record = response["Items"][0]
             del record["label_and_type"]
-            return record
+            return record  # noqa: TRY300
         except ClientError as e:
-            _logger.error(
+            _logger.exception(
                 "boto3 client error on get_records_by_id for search term %s: %s",
                 concept_id,
                 e.response["Error"]["Message"],
@@ -275,7 +275,7 @@ def get_refs_by_type(self, search_term: str, ref_type: RefType) -> list[str]:
             matches = self.genes.query(KeyConditionExpression=filter_exp)
             return [m["concept_id"] for m in matches.get("Items", None)]
         except ClientError as e:
-            _logger.error(
+            _logger.exception(
                 "boto3 client error on get_refs_by_type for search term %s: %s",
                 search_term,
                 e.response["Error"]["Message"],
@@ -378,7 +378,7 @@ def add_record(self, record: dict, src_name: SourceName) -> None:
         try:
             self.batch.put_item(Item=record)
         except ClientError as e:
-            _logger.error(
+            _logger.exception(
                 "boto3 client error on add_record for %s: %s",
                 concept_id,
                 e.response["Error"]["Message"],
@@ -411,7 +411,7 @@ def add_merged_record(self, record: dict) -> None:
         try:
             self.batch.put_item(Item=record)
         except ClientError as e:
-            _logger.error(
+            _logger.exception(
                 "boto3 client error on add_record for " "%s: %s",
                 concept_id,
                 e.response["Error"]["Message"],
@@ -438,7 +438,7 @@ def _add_ref_record(
         try:
             self.batch.put_item(Item=record)
         except ClientError as e:
-            _logger.error(
+            _logger.exception(
                 "boto3 client error adding reference %s for %s with match type %s: %s",
                 term,
                 concept_id,
@@ -473,7 +473,7 @@ def update_merge_ref(self, concept_id: str, merge_ref: Any) -> None:  # noqa: AN
                 )
                 raise DatabaseWriteException(err_msg) from e
 
-            _logger.error(
+            _logger.exception(
                 "boto3 client error in `database.update_record()`: %s",
                 e.response["Error"]["Message"],
             )

src/gene/database/postgresql.py

@@ -121,8 +121,8 @@ def drop_db(self) -> None:
         try:
             if not self._check_delete_okay():
                 return
-        except DatabaseWriteException as e:
-            raise e
+        except DatabaseWriteException:  # noqa: TRY203
+            raise
 
         with self.conn.cursor() as cur:
             cur.execute(self._drop_db_query)
@@ -601,7 +601,7 @@ def add_record(self, record: dict, src_name: SourceName) -> None:  # noqa: ARG00
                     cur.execute(self._ins_symbol_query, [record["symbol"], concept_id])
                 self.conn.commit()
             except UniqueViolation:
-                _logger.error("Record with ID %s already exists", concept_id)
+                _logger.exception("Record with ID %s already exists", concept_id)
                 self.conn.rollback()
 
     _add_merged_record_query = b"""
@@ -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/etl/merge.py

@@ -57,13 +57,13 @@ def create_merged_concepts(self, record_ids: set[str]) -> None:
                     self._database.update_merge_ref(concept_id, merge_ref)
                 except DatabaseWriteException as dw:
                     if str(dw).startswith("No such record exists"):
-                        _logger.error(
+                        _logger.exception(
                             "Updating nonexistent record: %s for merge ref to %s",
                             concept_id,
                             merge_ref,
                         )
                     else:
-                        _logger.error(str(dw))
+                        _logger.exception("Encountered unknown DB write exception")
             uploaded_ids |= group
         self._database.complete_write_transaction()
         _logger.info("Merged concept generation successful.")
@@ -135,9 +135,9 @@ def record_order(record: dict) -> tuple:
                 source_rank = SourcePriority[src].value
             else:
                 err_msg = (
-                    f"Prohibited source: {src} in concept_id " f"{record['concept_id']}"
+                    f"Prohibited source: {src} in concept_id {record['concept_id']}"
                 )
-                raise Exception(err_msg)
+                raise ValueError(err_msg)
             return source_rank, record["concept_id"]
 
         records.sort(key=record_order)

src/gene/query.py

@@ -167,9 +167,9 @@ def _fetch_record(
         """
         try:
             match = self.db.get_record_by_id(concept_id, case_sensitive=False)
-        except DatabaseReadException as e:
-            _logger.error(
-                "Encountered DatabaseReadException looking up %s: %s", concept_id, e
+        except DatabaseReadException:
+            _logger.exception(
+                "Encountered DatabaseReadException looking up %s", concept_id
             )
         else:
             if match:
@@ -243,12 +243,11 @@ def _get_search_response(self, query: str, sources: set[str]) -> dict:
                             self._fetch_record(resp, ref, MatchType[item_type.upper()])
                             matched_concept_ids.append(ref)
 
-            except DatabaseReadException as e:
-                _logger.error(
+            except DatabaseReadException:
+                _logger.exception(
                     "Encountered DatabaseReadException looking up %s %s: ",
                     item_type,
                     term,
-                    e,
                 )
                 continue