Merge pull request #45 from bento-platform/lint/black

lint: add black auto-formatter

.github/workflows/lint.yml

@@ -17,6 +17,8 @@ jobs:
         run: python -m pip install poetry
       - name: Install dependencies
         run: python -m poetry install --only dev
+      - name: Run black
+        run: python -m poetry run black --check bento_service_registry tests
       - name: Run linter
         run: python -m poetry run flake8 ./bento_service_registry ./tests
       - name: Run type checker

bento_service_registry/app.py

@@ -37,7 +37,8 @@ def create_app(config_override: Callable[[], Config] | None = None) -> FastAPI:
     authz_middleware.attach(app)
 
     app.exception_handler(StarletteHTTPException)(
-        http_exception_handler_factory(get_logger(config_for_setup), authz_middleware))
+        http_exception_handler_factory(get_logger(config_for_setup), authz_middleware)
+    )
     app.exception_handler(RequestValidationError)(validation_exception_handler_factory(authz_middleware))
 
     return app

bento_service_registry/bento_services_json.py

@@ -54,7 +54,7 @@ async def get_bento_services_by_compose_id(config: ConfigDependency) -> BentoSer
 
 
 async def get_bento_services_by_kind(
-    bento_services_by_compose_id: BentoServicesByComposeIDDependency
+    bento_services_by_compose_id: BentoServicesByComposeIDDependency,
 ) -> BentoServicesByKind:
     services_by_kind: BentoServicesByKind = {}
 

bento_service_registry/data_types.py

@@ -41,7 +41,8 @@ async def get_data_types_from_service(
     async with http_session.get(urljoin(service_url_norm, "data-types"), headers=authz_header) as res:
         if res.status != status.HTTP_200_OK:
             logger.error(
-                f"Got non-200 response from data type service ({service_url=}): {res.status=}; body={await res.json()}")
+                f"Got non-200 response from data type service ({service_url=}): {res.status=}; body={await res.json()}"
+            )
             return ()
 
         dts: list[DataTypeWithServiceURL] = []

bento_service_registry/routes.py

@@ -65,7 +65,8 @@ async def get_service_by_id(
     if service_data is None:
         raise HTTPException(
             status.HTTP_500_INTERNAL_SERVER_ERROR,
-            f"An internal error was encountered with service with ID {service_id}")
+            f"An internal error was encountered with service with ID {service_id}",
+        )
 
     return service_data
 

bento_service_registry/services.py

@@ -91,7 +91,8 @@ async def get_service(
                     # TypeError can happen if None is received
                     self._logger.error(
                         f"{service_info_url}: Encountered invalid response ({str(e)}) - {await r.text()} "
-                        f"(Took {(datetime.now() - dt).total_seconds():.1f}s)")
+                        f"(Took {(datetime.now() - dt).total_seconds():.1f}s)"
+                    )
 
         except asyncio.TimeoutError:
             self._logger.error(f"Encountered timeout with {service_info_url}")
@@ -109,10 +110,12 @@ async def get_services(
         service_info: GA4GHServiceInfo,
     ) -> tuple[dict, ...]:
         if not self._co:
-            self._co = asyncio.gather(*(
-                self.get_service(authz_header, http_session, service_info, s)
-                for s in bento_services_by_kind.values()
-            ))
+            self._co = asyncio.gather(
+                *(
+                    self.get_service(authz_header, http_session, service_info, s)
+                    for s in bento_services_by_kind.values()
+                )
+            )
 
         service_list: list[dict | None] = await self._co
         self._co = None

bento_service_registry/types.py

@@ -3,6 +3,7 @@
 
 # TODO: py3.11(?): optional TypedDict props
 
+
 # required props for chord_services.json entries
 class BaseBentoService(TypedDict):
     url_template: str

bento_service_registry/workflows.py

@@ -45,7 +45,8 @@ async def get_workflows_from_service(
         if res.status != status.HTTP_200_OK:
             logger.error(
                 f"Got non-200 response from data type service ({service_url=}): {res.status=}; body={data}; "
-                f"took {time_taken:.1f}s")
+                f"took {time_taken:.1f}s"
+            )
             return {}
 
         logger.debug(f"{workflows_url}: took {time_taken:.1f}s")
@@ -70,7 +71,8 @@ async def get_workflows(
     logger.debug("Collecting workflows from workflow-providing services")
 
     workflow_services = [
-        s for s in services_tuple
+        s
+        for s in services_tuple
         if (b := s.get("bento", {})).get("dataService", False) or b.get("workflowProvider", False)
     ]
 

pyproject.toml

@@ -40,3 +40,7 @@ pytest-asyncio = "^0.23.6"
 pytest-cov = "^4.1.0"
 tox = "^4.15.0"
 types-aiofiles = "^23.2.0"
+black = "^24.4.2"
+
+[tool.black]
+line_length = 120

tests/conftest.py

@@ -35,6 +35,7 @@ def get_config_inner():
 def client():
     tgc = test_get_config(debug_mode=False)
     from bento_service_registry.app import create_app
+
     app = create_app(tgc)
     yield TestClient(app)
 
@@ -43,12 +44,14 @@ def client():
 def client_debug_mode():
     tgc = test_get_config(debug_mode=True)
     from bento_service_registry.app import create_app
+
     app = create_app(tgc)
     yield TestClient(app)
 
 
 async def _service_info_fixt(config: Config):
     from bento_service_registry.service_info import get_service_info
+
     return await get_service_info(config, test_logger)
 
 

tox.ini

@@ -9,5 +9,6 @@ allowlist_externals =
 commands =
     poetry install --sync
     poetry run pytest -svv --cov=bento_service_registry --cov-branch {posargs}
+    poetry run black --check bento_service_registry tests
     poetry run flake8 ./bento_service_registry ./tests
     poetry run mypy bento_service_registry