Merge pull request #372 from smart-on-fhir/dependabot/pip/ruff-lt-0.10

build(deps): update ruff requirement from <0.9 to <0.10

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.0  # keep in rough sync with pyproject.toml
+    rev: v0.9.1  # keep in rough sync with pyproject.toml
     hooks:
       - name: Ruff formatting
         id: ruff-format

cumulus_etl/loaders/fhir/bulk_export.py

@@ -397,7 +397,7 @@ async def _download_all_ndjson_files(self, resource_json: dict, item_type: str)
         for file in files:
             count = resource_counts.get(file["type"], -1) + 1
             resource_counts[file["type"]] = count
-            filename = f'{file["type"]}.{count:03}.ndjson'
+            filename = f"{file['type']}.{count:03}.ndjson"
             coroutines.append(
                 self._download_ndjson_file(
                     file["url"],

cumulus_etl/loaders/i2b2/oracle/query.py

@@ -39,7 +39,7 @@ def sql_visit() -> str:
     import_date = format_date("IMPORT_DATE")
 
     cols_dates = f"{start_date}, {end_date}, {import_date}, LENGTH_OF_STAY"
-    cols = "ENCOUNTER_NUM, PATIENT_NUM, LOCATION_CD, INOUT_CD, " f"{cols_dates}"
+    cols = f"ENCOUNTER_NUM, PATIENT_NUM, LOCATION_CD, INOUT_CD, {cols_dates}"
     return f"select {cols} \n from {Table.visit.value}"  # noqa: S608
 
 
@@ -97,7 +97,7 @@ def sql_observation_fact(categories: list[str]) -> str:
         f"O.CONCEPT_CD, O.INSTANCE_NUM, {import_date}, O.TVAL_CHAR, "
         f"O.VALTYPE_CD, O.VALUEFLAG_CD, O.NVAL_NUM, O.UNITS_CD, O.OBSERVATION_BLOB"
     )
-    cols = f"{cols_patient_dim}, {cols_provider_dim}, {cols_visit_dim}, " f"{cols_obs_fact}"
+    cols = f"{cols_patient_dim}, {cols_provider_dim}, {cols_visit_dim}, {cols_obs_fact}"
 
     matchers = [f"(concept_cd like '{category}:%')" for category in categories]
 

pyproject.toml

@@ -53,7 +53,7 @@ dev = [
     "pre-commit",
     # Ruff is using minor versions for breaking changes until their 1.0 release.
     # See https://docs.astral.sh/ruff/versioning/
-    "ruff < 0.9",  # keep in rough sync with pre-commit-config.yaml
+    "ruff < 0.10",  # keep in rough sync with pre-commit-config.yaml
 ]
 
 [project.urls]

tests/etl/base.py

@@ -81,9 +81,9 @@ async def run_etl(
         if batch_size:
             args.append(f"--batch-size={batch_size}")
         if tasks:
-            args.append(f'--task={",".join(tasks)}')
+            args.append(f"--task={','.join(tasks)}")
         if tags:
-            args.append(f'--task-filter={",".join(tags)}')
+            args.append(f"--task-filter={','.join(tags)}")
         if philter:
             args.append("--philter")
         if export_to:

tests/etl/test_tasks.py

@@ -389,7 +389,7 @@ async def test_contained_medications(self):
         self.assertEqual(1, med_req_format.write_records.call_count)
         batch = med_req_format.write_records.call_args[0][0]
         self.assertEqual(
-            f'#{self.codebook.db.resource_hash("123")}',
+            f"#{self.codebook.db.resource_hash('123')}",
             batch.rows[0]["medicationReference"]["reference"],
         )
 
@@ -440,7 +440,7 @@ async def test_external_medications(self, mock_download):
         batch = med_req_format.write_records.call_args[0][0]
         self.assertEqual([self.codebook.db.resource_hash("A")], [row["id"] for row in batch.rows])
         self.assertEqual(
-            f'Medication/{self.codebook.db.resource_hash("123")}',
+            f"Medication/{self.codebook.db.resource_hash('123')}",
             batch.rows[0]["medicationReference"]["reference"],
         )
 

tests/loaders/i2b2/test_i2b2_loader.py

@@ -34,7 +34,7 @@ async def test_duplicate_ids(self):
 
             common.write_text(
                 f"{tmpdir}/patient_dimension.csv",
-                "PATIENT_NUM,BIRTH_DATE\n" "123,1982-10-16\n" "123,1983-11-17\n" "456,2000-01-13\n",
+                "PATIENT_NUM,BIRTH_DATE\n123,1982-10-16\n123,1983-11-17\n456,2000-01-13\n",
             )
 
             results = await i2b2_loader.load_resources({"Patient"})

tests/loaders/i2b2/test_i2b2_oracle_query.py

@@ -28,7 +28,7 @@ def shorten(sql: str) -> str:
 def count_by_date_group(table: schema.Table, column_date="import_date") -> str:
     return shorten(
         f"""
-                    select {count_by_date(column_date, f'{column_date}_cnt')}
+                    select {count_by_date(column_date, f"{column_date}_cnt")}
                     from {table.value}
                     group by {query.cast_date(column_date)}
                     order by {query.cast_date(column_date)} desc