Merge branch 'release_24.1' into release_24.2

.github/workflows/mulled.yaml

@@ -41,6 +41,8 @@ jobs:
           key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-mulled
       - name: Install Apptainer's singularity
         uses: eWaterCycle/setup-apptainer@v2
+        with:
+          apptainer-version: 1.3.6  # https://github.com/eWaterCycle/setup-apptainer/pull/68
       - name: Install tox
         run: pip install tox
       - name: Run tests

client/src/components/History/CurrentHistory/HistoryOperations/SelectionChangeWarning.vue

@@ -31,7 +31,7 @@ function onDoNotShowAgain() {
 watch(
     () => props.querySelectionBreak,
     () => {
-        dismissCountDown.value = showSelectionQueryBreakWarning ? dismissSecs.value : 0;
+        dismissCountDown.value = showSelectionQueryBreakWarning.value ? dismissSecs.value : 0;
     }
 );
 </script>

lib/galaxy/model/__init__.py

@@ -7736,7 +7736,7 @@ class StoredWorkflow(Base, HasTags, Dictifiable, RepresentById, UsesCreateAndUpd
         order_by=lambda: -Workflow.id,
         cascade_backrefs=False,
     )
-    latest_workflow = relationship(
+    latest_workflow: Mapped["Workflow"] = relationship(
         "Workflow",
         post_update=True,
         primaryjoin=(lambda: StoredWorkflow.latest_workflow_id == Workflow.id),
@@ -7854,7 +7854,7 @@ class StoredWorkflow(Base, HasTags, Dictifiable, RepresentById, UsesCreateAndUpd
         )
         return bool(sa_session.scalar(stmt))
 
-    def copy_tags_from(self, target_user, source_workflow):
+    def copy_tags_from(self, target_user, source_workflow: "StoredWorkflow"):
         # Override to only copy owner tags.
         for src_swta in source_workflow.owner_tags:
             new_swta = src_swta.copy()
@@ -8027,7 +8027,7 @@ class Workflow(Base, Dictifiable, RepresentById):
         """
         return self.top_level_workflow.stored_workflow
 
-    def copy(self, user=None):
+    def copy(self, user: User):
         """Copy a workflow for a new StoredWorkflow object.
 
         Pass user if user-specific information needed.
@@ -8336,7 +8336,7 @@ class WorkflowStep(Base, RepresentById, UsesCreateAndUpdateTime):
                 break
         return target_output
 
-    def copy_to(self, copied_step, step_mapping, user=None):
+    def copy_to(self, copied_step: "WorkflowStep", step_mapping: Dict[int, "WorkflowStep"], user: User):
         copied_step.order_index = self.order_index
         copied_step.type = self.type
         copied_step.tool_id = self.tool_id
@@ -8368,10 +8368,10 @@ class WorkflowStep(Base, RepresentById, UsesCreateAndUpdateTime):
                 copied_step.subworkflow = subworkflow
                 copied_subworkflow = subworkflow
             else:
-                # Can this even happen, building a workflow with a subworkflow you don't own ?
-                copied_subworkflow = subworkflow.copy()
+                # Importing a shared workflow with a subworkflow step
+                copied_subworkflow = subworkflow.copy(user=user)
                 stored_workflow = StoredWorkflow(
-                    user, name=copied_subworkflow.name, workflow=copied_subworkflow, hidden=True
+                    user=user, name=copied_subworkflow.name, workflow=copied_subworkflow, hidden=True
                 )
                 copied_subworkflow.stored_workflow = stored_workflow
                 copied_step.subworkflow = copied_subworkflow

lib/galaxy/webapps/base/controller.py

@@ -973,7 +973,7 @@ class UsesStoredWorkflowMixin(SharableItemSecurityMixin, UsesAnnotations):
             except exceptions.ToolMissingException:
                 pass
 
-    def _import_shared_workflow(self, trans, stored):
+    def _import_shared_workflow(self, trans, stored: model.StoredWorkflow):
         """Imports a shared workflow"""
         # Copy workflow.
         imported_stored = model.StoredWorkflow()

pytest.ini

@@ -1,5 +1,5 @@
 [pytest]
-addopts = --doctest-continue-on-failure --verbosity=1
+addopts = --doctest-continue-on-failure --verbosity=1 --showlocals
 asyncio_mode = auto
 log_level = DEBUG
 # Install pytest-memray and set memray to true here to enable memory profiling of tests

test/unit/tool_util/mulled/test_mulled_update_singularity_containers.py

@@ -46,6 +46,6 @@ def test_singularity_container_test(tmp_path) -> None:
         "singularity",
         tmp_path,
     )
-    assert "samtools:1.0--1" in results["passed"]
-    assert "pybigwig:0.3.22--py36h54a71a5_0" in results["passed"]
-    assert "yasm:1.3.0--0" in results["notest"]
+    assert "samtools:1.0--1" in results["passed"], results
+    assert "pybigwig:0.3.22--py36h54a71a5_0" in results["passed"], results
+    assert "yasm:1.3.0--0" in results["notest"], results