Merge branch 'release_24.0' into release_24.1

lib/galaxy/tool_util/verify/__init__.py

@@ -476,7 +476,7 @@ 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
 
@@ -487,13 +487,13 @@ 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))
@@ -522,7 +522,7 @@ 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]: