Ruff update

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 default_install_hook_types: [pre-commit, pre-push]
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.4  # if you update this, also update pyproject.toml
+    rev: v0.5.5  # if you update this, also update pyproject.toml
     hooks:
       - name: Ruff formatting
         id: ruff-format

cumulus_library/actions/builder.py

@@ -94,9 +94,7 @@ def _load_and_execute_builder(
     table_builder_class = table_builder_subclasses[0]
     table_builder = table_builder_class()
     if write_reference_sql:
-        table_builder.prepare_queries(
-            config=config, manifest=manifest, parser=db_parser
-        )
+        table_builder.prepare_queries(config=config, manifest=manifest, parser=db_parser)
         table_builder.comment_queries(doc_str=doc_str)
         new_filename = pathlib.Path(f"{filename}").stem + ".sql"
         table_builder.write_queries(
@@ -191,7 +189,7 @@ def run_statistics_builders(
         existing_stats = (
             config.db.cursor()
             .execute(
-                "SELECT view_name FROM "
+                "SELECT view_name FROM "  # noqa: S608
                 f"{manifest.get_study_prefix()}__{enums.ProtectedTables.STATISTICS.value}"
             )
             .fetchall()
@@ -273,9 +271,7 @@ def build_study(
     """
     queries = []
     for file in manifest.get_sql_file_list(continue_from):
-        for query in base_utils.parse_sql(
-            base_utils.load_text(f"{manifest._study_path}/{file}")
-        ):
+        for query in base_utils.parse_sql(base_utils.load_text(f"{manifest._study_path}/{file}")):
             queries.append([query, file])
     if len(queries) == 0:
         return []
@@ -377,9 +373,7 @@ def _execute_build_queries(
                 "start with a string like `study_prefix__`.",
             )
         try:
-            with base_utils.query_console_output(
-                config.verbose, query[0], progress, task
-            ):
+            with base_utils.query_console_output(config.verbose, query[0], progress, task):
                 cursor.execute(query[0])
         except Exception as e:  # pylint: disable=broad-exception-caught
             _query_error(

cumulus_library/actions/cleaner.py

@@ -57,7 +57,7 @@ def get_unprotected_stats_view_table(
         protected_list = cursor.execute(
             f"""SELECT {artifact_type.lower()}_name 
             FROM {drop_prefix}{enums.ProtectedTables.STATISTICS.value}
-            WHERE study_name = '{display_prefix}'"""
+            WHERE study_name = '{display_prefix}'"""  # noqa: S608
         ).fetchall()
         for protected_tuple in protected_list:
             if protected_tuple in db_contents:
@@ -66,9 +66,7 @@ def get_unprotected_stats_view_table(
         # this check handles athena reporting views as also being tables,
         # so we don't waste time dropping things that don't exist
         if artifact_type == "TABLE":
-            if not any(
-                db_row_tuple[0] in iter_q_and_t for iter_q_and_t in unprotected_list
-            ):
+            if not any(db_row_tuple[0] in iter_q_and_t for iter_q_and_t in unprotected_list):
                 unprotected_list.append([db_row_tuple[0], artifact_type])
         else:
             unprotected_list.append([db_row_tuple[0], artifact_type])

cumulus_library/actions/exporter.py

@@ -27,9 +27,7 @@ def reset_counts_exports(
 def _write_chunk(writer, chunk, arrow_schema):
     writer.write(
         pyarrow.Table.from_pandas(
-            chunk.sort_values(
-                by=list(chunk.columns), ascending=False, na_position="first"
-            ),
+            chunk.sort_values(by=list(chunk.columns), ascending=False, na_position="first"),
             preserve_index=False,
             schema=arrow_schema,
         )
@@ -70,11 +68,9 @@ def export_study(
         table_list,
         description=f"Exporting {manifest.get_study_prefix()} data...",
     ):
-        query = f"SELECT * FROM {table}"
+        query = f"SELECT * FROM {table}"  # noqa: S608
         query = base_utils.update_query_if_schema_specified(query, manifest)
-        dataframe_chunks, db_schema = config.db.execute_as_pandas(
-            query, chunksize=chunksize
-        )
+        dataframe_chunks, db_schema = config.db.execute_as_pandas(query, chunksize=chunksize)
         path.mkdir(parents=True, exist_ok=True)
         arrow_schema = pyarrow.schema(config.db.col_pyarrow_types_from_sql(db_schema))
         with parquet.ParquetWriter(f"{path}/{table}.parquet", arrow_schema) as p_writer:

cumulus_library/apis/umls.py

@@ -99,9 +99,7 @@ def get_vsac_valuesets(
             included_records = all_responses[0].get("compose", {}).get("include", [])
             for record in included_records:
                 if "valueSet" in record:
-                    valueset = self.get_vsac_valuesets(
-                        action=action, url=record["valueSet"][0]
-                    )
+                    valueset = self.get_vsac_valuesets(action=action, url=record["valueSet"][0])
                     all_responses.append(valueset[0])
         return all_responses
 
@@ -143,24 +141,21 @@ def download_umls_files(
             "url": file_meta["downloadUrl"],
             "apiKey": self.api_key,
         }
-        download_res = requests.get(
+        download_res = requests.get(  # noqa: S113
             "https://uts-ws.nlm.nih.gov/download", params=download_payload, stream=True
         )
 
         with open(path / file_meta["fileName"], "wb") as f:
             chunks_read = 0
             with base_utils.get_progress_bar() as progress:
-                task = progress.add_task(
-                    f"Downloading {file_meta['fileName']}", total=None
-                )
+                task = progress.add_task(f"Downloading {file_meta['fileName']}", total=None)
                 for chunk in download_res.iter_content(chunk_size=1024):
                     f.write(chunk)
                     chunks_read += 1
                     progress.update(
                         task,
                         description=(
-                            f"Downloading {file_meta['fileName']}: "
-                            f"{chunks_read/1000} MB"
+                            f"Downloading {file_meta['fileName']}: " f"{chunks_read/1000} MB"
                         ),
                     )
         if unzip:

cumulus_library/base_table_builder.py

@@ -56,17 +56,13 @@ def execute_queries(
             table_names = []
             for query in self.queries:
                 # Get the first non-whitespace word after create table
-                table_name = re.search(
-                    '(?i)(?<=create table )(([a-zA-Z0-9_".-]+))', query
-                )
+                table_name = re.search('(?i)(?<=create table )(([a-zA-Z0-9_".-]+))', query)
 
                 if table_name:
                     if table_name[0] == "IF":
                         # Edge case - if we're doing an empty conditional CTAS creation,
                         # we need to run a slightly different regex
-                        table_name = re.search(
-                            '(?i)(?<=not exists )(([a-zA-Z0-9_".-]+))', query
-                        )
+                        table_name = re.search('(?i)(?<=not exists )(([a-zA-Z0-9_".-]+))', query)
 
                     table_name = table_name[0]
                     table_names.append(table_name)
@@ -81,20 +77,16 @@ def execute_queries(
             for query in self.queries:
                 try:
                     query = base_utils.update_query_if_schema_specified(query, manifest)
-                    with base_utils.query_console_output(
-                        config.verbose, query, progress, task
-                    ):
+                    with base_utils.query_console_output(config.verbose, query, progress, task):
                         cursor.execute(query)
                 except Exception as e:  # pylint: disable=broad-exception-caught
                     sys.exit(
-                        "An error occured executing this query:\n----\n"
-                        f"{query}\n----\n"
-                        f"{e}"
+                        "An error occured executing this query:\n----\n" f"{query}\n----\n" f"{e}"
                     )
 
         self.post_execution(config, *args, **kwargs)
 
-    def post_execution(  # noqa: B027 - this looks like, but is not, an abstract method
+    def post_execution(
         self,
         config: base_utils.StudyConfig,
         *args,

cumulus_library/log_utils.py

@@ -94,7 +94,7 @@ def _log_table(
         # Migrating logging tables
         if "lib_transactions" in table_name:
             cols = cursor.execute(
-                "SELECT column_name FROM information_schema.columns "
+                "SELECT column_name FROM information_schema.columns "  # noqa: S608
                 f"WHERE table_name ='{table_name}' "
                 f"AND table_schema ='{db_schema}'"
             ).fetchall()
@@ -109,13 +109,11 @@ def _log_table(
                 alter_query = ""
                 if isinstance(config.db, databases.AthenaDatabaseBackend):
                     alter_query = (
-                        f"ALTER TABLE {db_schema}.{table_name} "
-                        "ADD COLUMNS(message string)"
+                        f"ALTER TABLE {db_schema}.{table_name} " "ADD COLUMNS(message string)"
                     )
                 elif isinstance(config.db, databases.DuckDatabaseBackend):
                     alter_query = (
-                        f"ALTER TABLE {db_schema}.{table_name} "
-                        "ADD COLUMN message varchar"
+                        f"ALTER TABLE {db_schema}.{table_name} " "ADD COLUMN message varchar"
                     )
                 cursor.execute(alter_query)
                 cursor.execute(query)

cumulus_library/statistics/psm.py

@@ -133,9 +133,7 @@ def _create_covariate_table(
         """Creates a covariate table from the loaded toml config"""
         # checks for primary & link ref being the same
         source_refs = list({self.config.primary_ref, self.config.count_ref} - {None})
-        pos_query = psm_templates.get_distinct_ids(
-            source_refs, self.config.pos_source_table
-        )
+        pos_query = psm_templates.get_distinct_ids(source_refs, self.config.pos_source_table)
         pos = self._get_sampled_ids(
             cursor,
             schema,
@@ -187,8 +185,8 @@ def psm_plot_match(
         Title="Side by side matched controls",
         Ylabel="Number of patients",
         Xlabel="propensity logit",
-        names=["positive_cohort", "negative_cohort"],  # noqa: B006
-        colors=["#E69F00", "#56B4E9"],  # noqa: B006
+        names=None,
+        colors=None,
         save=True,
         filename="propensity_match.png",
     ):
@@ -199,6 +197,8 @@ def psm_plot_match(
         and passing in the psm object instead of assuming a call from inside
         the PsmPy class.
         """
+        names = names or ["positive_cohort", "negative_cohort"]
+        colors = colors or ["#E69F00", "#56B4E9"]
         dftreat = psm.df_matched[psm.df_matched[psm.treatment] == 1]
         dfcontrol = psm.df_matched[psm.df_matched[psm.treatment] == 0]
         x1 = dftreat[matched_entity]
@@ -217,7 +217,7 @@ def psm_plot_match(
     def psm_effect_size_plot(
         self,
         psm,
-        title="Standardized Mean differences accross covariates before and after matching",  # noqa: E501
+        title="Standardized Mean differences accross covariates before and after matching",
         before_color="#FCB754",
         after_color="#3EC8FB",
         save=False,
@@ -239,9 +239,7 @@ def psm_effect_size_plot(
         for cl in psm.xvars:
             data.append([cl, "before", cohenD(df_preds_b4_float, psm.treatment, cl)])
             data.append([cl, "after", cohenD(df_preds_after_float, psm.treatment, cl)])
-        psm.effect_size = pandas.DataFrame(
-            data, columns=["Variable", "matching", "Effect Size"]
-        )
+        psm.effect_size = pandas.DataFrame(data, columns=["Variable", "matching", "Effect Size"])
         sns.set_style("white")
         sns_plot = sns.barplot(
             data=psm.effect_size,
@@ -260,17 +258,13 @@ def generate_psm_analysis(
     ):
         stats_table = f"{self.config.target_table}_{table_suffix}"
         """Runs PSM statistics on generated tables"""
-        cursor.execute(
-            base_templates.get_alias_table_query(stats_table, self.config.target_table)
-        )
+        cursor.execute(base_templates.get_alias_table_query(stats_table, self.config.target_table))
         df = cursor.execute(
             base_templates.get_select_all_query(self.config.target_table)
         ).as_pandas()
         symptoms_dict = self._get_symptoms_dict(self.config.classification_json)
         for dependent_variable, codes in symptoms_dict.items():
-            df[dependent_variable] = df["code"].apply(
-                lambda x, codes=codes: 1 if x in codes else 0
-            )
+            df[dependent_variable] = df["code"].apply(lambda x, codes=codes: 1 if x in codes else 0)
         df = df.drop(columns="code")
         # instance_count present but unused for PSM if table contains a count_ref input
         # (it's intended for manual review)
@@ -342,13 +336,10 @@ def generate_psm_analysis(
             )
         except ValueError:
             sys.exit(
-                "Encountered a value error during KNN matching. Try increasing "
-                "your sample size."
+                "Encountered a value error during KNN matching. Try increasing " "your sample size."
             )
 
-    def prepare_queries(
-        self, config: base_utils.StudyConfig, *args, table_suffix: str, **kwargs
-    ):
+    def prepare_queries(self, config: base_utils.StudyConfig, *args, table_suffix: str, **kwargs):
         self._create_covariate_table(config.db.cursor(), config.schema, table_suffix)
 
     def post_execution(

cumulus_library/studies/discovery/discovery_templates/discovery_templates.py

@@ -21,7 +21,7 @@ def get_system_pairs(output_table_name: str, code_system_tables: list) -> str:
         for column in table["column_hierarchy"]:
             unnest_layer = ".".join(x for x in [unnest_layer, column[0]] if x)
             display_col = ".".join(x for x in [display_col, column[0]] if x)
-            if column[1] == list:
+            if column[1] is list:
                 squashed_hierarchy.append((unnest_layer, list))
                 unnest_layer = ""
         if unnest_layer != "":