Replace Pydantic .dict() with .model_dump()

The .dict() method is deprecated in Pydantic V2 (PydanticDeprecatedSince20)
and slated for removal in V3. The identically-behaving replacement is
.model_dump() — all existing keyword arguments (exclude_unset,
exclude, by_alias) are supported unchanged.

Galaxy has already completed the bulk of the Pydantic v2 migration; these
are the straggling call sites still emitting deprecation warnings in CI.

lib/galaxy/model/__init__.py

@@ -10230,7 +10230,7 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, Serializabl
 
     def add_message(self, message: "InvocationMessageUnion"):
 
-        message_dict = message.dict(
+        message_dict = message.model_dump(
             exclude_unset=True,
             exclude={"history_id"},  # history_id comes in through workflow_invocation and isn't persisted in database
         )

lib/galaxy/tool_util/parser/output_objects.py

@@ -472,7 +472,7 @@ class ToolOutputCollectionStructure:
         return collection_prototype
 
     def to_dict(self):
-        return self.to_model().dict()
+        return self.to_model().model_dump()
 
     def to_model(self) -> ToolOutputCollectionStructureModel:
         discover_datasets = []

lib/galaxy/tool_util/verify/parse.py

@@ -145,7 +145,7 @@ def _description_from_tool_source(
     request_schema: Optional[Dict[str, Any]] = None
     if request_and_schema:
         request = request_and_schema.request.input_state
-        request_schema = request_and_schema.request_schema.dict()
+        request_schema = request_and_schema.request_schema.model_dump()
 
     value_state_representation = raw_test_dict.get("value_state_representation", "test_case_xml")
     tool_id, tool_version = _tool_id_and_version(tool_source, tool_guid)

lib/galaxy/tools/parameters/basic.py

@@ -2052,12 +2052,12 @@ def src_id_to_item(
             for item in adapting:
                 element = TransientCollectionAdapterDatasetInstanceElement(
                     item.name,
-                    cast(HistoryDatasetAssociation, src_id_to_item(sa_session, item.dict(), security)),
+                    cast(HistoryDatasetAssociation, src_id_to_item(sa_session, item.model_dump(), security)),
                 )
                 elements.append(element)
             return recover_adapter(elements, adapter_model)
         else:
-            value = adapting.dict()
+            value = adapting.model_dump()
     src_to_class = {
         "hda": HistoryDatasetAssociation,
         "ldda": LibraryDatasetDatasetAssociation,
@@ -2994,7 +2994,7 @@ def history_item_to_json(value, app, use_security):
     collection_adapter: Optional[CollectionAdapter] = None
     if isinstance(value, CollectionAdapter):
         collection_adapter = value
-        return collection_adapter.to_adapter_model().dict()
+        return collection_adapter.to_adapter_model().model_dump()
     if isinstance(value, MutableMapping) and "src" in value and "id" in value:
         return value
     elif isinstance(value, DatasetCollectionElement):

lib/galaxy/webapps/galaxy/services/dataset_collections.py

@@ -182,7 +182,7 @@ class DatasetCollectionsService(ServiceBase, UsesLibraryMixinItems):
         :returns:   element view of new dataset collection
         """
         # TODO: Error handling...
-        create_params = api_payload_to_create_params(payload.dict(exclude_unset=True, by_alias=True))
+        create_params = api_payload_to_create_params(payload.model_dump(exclude_unset=True, by_alias=True))
         if payload.instance_type == "history":
             if payload.history_id is None:
                 raise exceptions.RequestParameterInvalidException("Parameter history_id is required.")

lib/galaxy/webapps/galaxy/services/histories.py

@@ -395,7 +395,7 @@ class HistoriesService(ServiceBase, ConsumesModelStores, ServesExportStores):
             duration=short_term_storage_target.duration,
             user=trans.async_request_user,
             export_association_id=export_association.id,
-            **payload.dict(),
+            **payload.model_dump(),
         )
         result = prepare_history_download.delay(request=request, task_user_id=getattr(trans.user, "id", None))
         task_summary = async_task_summary(result)
@@ -412,7 +412,7 @@ class HistoriesService(ServiceBase, ConsumesModelStores, ServesExportStores):
             user=trans.async_request_user,
             history_id=history.id,
             export_association_id=export_association.id,
-            **payload.dict(),
+            **payload.model_dump(),
         )
         result = write_history_to.delay(request=request, task_user_id=getattr(trans.user, "id", None))
         task_summary = async_task_summary(result)

lib/tool_shed/managers/model_cache.py

@@ -59,4 +59,4 @@ class ModelCache:
         if not os.path.exists(parent_directory):
             os.makedirs(parent_directory)
         with open(cache_target, "w") as f:
-            json.dump(model_object.dict(), f)
+            json.dump(model_object.model_dump(), f)