Merge pull request galaxyproject#18755 from nsoranzo/fix_B039

Fix new flake8-bugbear B039 and mypy type-var errors

lib/galaxy/dependencies/pinned-lint-requirements.txt

@@ -1,7 +1,7 @@
-attrs==23.2.0
-flake8==7.1.0
-flake8-bugbear==24.4.26
+attrs==24.2.0
+flake8==7.1.1
+flake8-bugbear==24.8.19
 mccabe==0.7.0
-pycodestyle==2.12.0
+pycodestyle==2.12.1
 pyflakes==3.2.0
-ruff==0.6.1
+ruff==0.6.3

lib/galaxy/model/base.py

@@ -38,8 +38,7 @@
 # of a request (which run within a threadpool) to see changes to the ContextVar
 # state. See https://github.com/tiangolo/fastapi/issues/953#issuecomment-586006249
 # for details
-_request_state: Dict[str, str] = {}
-REQUEST_ID = ContextVar("request_id", default=_request_state.copy())
+REQUEST_ID: ContextVar[Union[Dict[str, str], None]] = ContextVar("request_id", default=None)
 
 
 @contextlib.contextmanager
@@ -112,12 +111,12 @@ def new_session(self):
 
     def request_scopefunc(self):
         """
-        Return a value that is used as dictionary key for sqlalchemy's ScopedRegistry.
+        Return a value that is used as dictionary key for SQLAlchemy's ScopedRegistry.
 
         This ensures that threads or request contexts will receive a single identical session
         from the ScopedRegistry.
         """
-        return REQUEST_ID.get().get("request") or threading.get_ident()
+        return REQUEST_ID.get({}).get("request") or threading.get_ident()
 
     @staticmethod
     def set_request_id(request_id):

lib/galaxy/tool_util/verify/__init__.py

@@ -471,8 +471,8 @@ def files_contains(file1, file2, attributes=None):
 
 
 def _singleobject_intersection_over_union(
-    mask1: "numpy.typing.NDArray",
-    mask2: "numpy.typing.NDArray",
+    mask1: "numpy.typing.NDArray[numpy.bool_]",
+    mask2: "numpy.typing.NDArray[numpy.bool_]",
 ) -> "numpy.floating":
     return numpy.logical_and(mask1, mask2).sum() / numpy.logical_or(mask1, mask2).sum()
 
@@ -483,7 +483,7 @@ def _multiobject_intersection_over_union(
     pin_labels: Optional[List[int]] = None,
     repeat_reverse: bool = True,
 ) -> List["numpy.floating"]:
-    iou_list = []
+    iou_list: List[numpy.floating] = []
     for label1 in numpy.unique(mask1):
         cc1 = mask1 == label1
 
@@ -494,13 +494,13 @@ def _multiobject_intersection_over_union(
 
         # Otherwise, use the object with the largest IoU value, excluding the pinned labels.
         else:
-            cc1_iou_list = []
+            cc1_iou_list: List[numpy.floating] = []
             for label2 in numpy.unique(mask2[cc1]):
                 if pin_labels is not None and label2 in pin_labels:
                     continue
                 cc2 = mask2 == label2
                 cc1_iou_list.append(_singleobject_intersection_over_union(cc1, cc2))
-            iou_list.append(max(cc1_iou_list))
+            iou_list.append(max(cc1_iou_list))  # type: ignore[type-var, unused-ignore]  # https://github.com/python/typeshed/issues/12562
 
     if repeat_reverse:
         iou_list.extend(_multiobject_intersection_over_union(mask2, mask1, pin_labels, repeat_reverse=False))
@@ -511,7 +511,7 @@ def _multiobject_intersection_over_union(
 def intersection_over_union(
     mask1: "numpy.typing.NDArray", mask2: "numpy.typing.NDArray", pin_labels: Optional[List[int]] = None
 ) -> "numpy.floating":
-    """Compute the intersection over union (IoU) for the objects in two masks containing lables.
+    """Compute the intersection over union (IoU) for the objects in two masks containing labels.
 
     The IoU is computed for each uniquely labeled image region (object), and the overall minimum value is returned (i.e. the worst value).
     To compute the IoU for each object, the corresponding object in the other mask needs to be determined.
@@ -529,7 +529,7 @@ def intersection_over_union(
         count = sum(label in mask for mask in (mask1, mask2))
         count_str = {1: "one", 2: "both"}
         assert count == 2, f"Label {label} is pinned but missing in {count_str[2 - count]} of the images."
-    return min(_multiobject_intersection_over_union(mask1, mask2, pin_labels))
+    return min(_multiobject_intersection_over_union(mask1, mask2, pin_labels))  # type: ignore[type-var, unused-ignore]  # https://github.com/python/typeshed/issues/12562
 
 
 def _parse_label_list(label_list_str: Optional[str]) -> List[int]:

test/unit/webapps/test_request_scoped_sqlalchemy_sessions.py

@@ -8,14 +8,18 @@
 import pytest
 from fastapi import FastAPI
 from fastapi.param_functions import Depends
-from httpx import AsyncClient
+from httpx import (
+    ASGITransport,
+    AsyncClient,
+)
 from starlette_context import context as request_context
 
 from galaxy.app_unittest_utils.galaxy_mock import MockApp
 from galaxy.webapps.base.api import add_request_id_middleware
 
 app = FastAPI()
 add_request_id_middleware(app)
+transport = ASGITransport(app=app)
 GX_APP = None
 
 
@@ -96,7 +100,7 @@ def assert_scoped_session_is_thread_local(gx_app):
 
 @pytest.mark.asyncio
 async def test_request_scoped_sa_session_single_request():
-    async with AsyncClient(app=app, base_url="http://test") as client:
+    async with AsyncClient(base_url="http://test", transport=transport) as client:
         response = await client.get("/")
         assert response.status_code == 200
         assert response.json() == {"msg": "Hello World"}
@@ -106,7 +110,7 @@ async def test_request_scoped_sa_session_single_request():
 
 @pytest.mark.asyncio
 async def test_request_scoped_sa_session_exception():
-    async with AsyncClient(app=app, base_url="http://test") as client:
+    async with AsyncClient(base_url="http://test", transport=transport) as client:
         with pytest.raises(UnexpectedException):
             await client.get("/internal_server_error")
         assert GX_APP
@@ -115,7 +119,7 @@ async def test_request_scoped_sa_session_exception():
 
 @pytest.mark.asyncio
 async def test_request_scoped_sa_session_concurrent_requests_sync():
-    async with AsyncClient(app=app, base_url="http://test") as client:
+    async with AsyncClient(base_url="http://test", transport=transport) as client:
         awaitables = (client.get("/sync_wait") for _ in range(10))
         result = await asyncio.gather(*awaitables)
         uuids = []
@@ -129,7 +133,7 @@ async def test_request_scoped_sa_session_concurrent_requests_sync():
 
 @pytest.mark.asyncio
 async def test_request_scoped_sa_session_concurrent_requests_async():
-    async with AsyncClient(app=app, base_url="http://test") as client:
+    async with AsyncClient(base_url="http://test", transport=transport) as client:
         awaitables = (client.get("/async_wait") for _ in range(10))
         result = await asyncio.gather(*awaitables)
         uuids = []
@@ -147,7 +151,7 @@ async def test_request_scoped_sa_session_concurrent_requests_and_background_thre
     target = functools.partial(assert_scoped_session_is_thread_local, GX_APP)
     with concurrent.futures.ThreadPoolExecutor() as pool:
         background_pool = loop.run_in_executor(pool, target)
-        async with AsyncClient(app=app, base_url="http://test") as client:
+        async with AsyncClient(base_url="http://test", transport=transport) as client:
             awaitables = (client.get("/async_wait") for _ in range(10))
             result = await asyncio.gather(*awaitables)
             uuids = []