Fix incorrect type in tool_util.deps and fix package structure.

lib/galaxy/tool_util/deps/__init__.py

@@ -11,9 +11,10 @@
     Dict,
     List,
     Optional,
-    TYPE_CHECKING,
 )
 
+from typing_extensions import Protocol
+
 from galaxy.util import (
     hash_util,
     plugin_config,
@@ -33,9 +34,6 @@
 )
 from .resolvers.tool_shed_packages import ToolShedPackageDependencyResolver
 
-if TYPE_CHECKING:
-    from galaxy.jobs import JobDestination
-
 log = logging.getLogger(__name__)
 
 CONFIG_VAL_NOT_FOUND = object()
@@ -106,6 +104,16 @@ def build_dependency_manager(
     return NullDependencyManager()
 
 
+ContainerType = str
+DestinationId = str
+DestinationParametersType = Dict[str, Any]
+
+
+class DestinationProtocol(Protocol):
+    id: Optional[DestinationId]
+    params: DestinationParametersType
+
+
 class DependencyManager:
     """
     A DependencyManager attempts to resolve named and versioned dependencies by
@@ -118,6 +126,7 @@ class DependencyManager:
     dependency available in the current shell environment.
     """
 
+    _destination_for_container_type: Dict[ContainerType, List[DestinationProtocol]]
     cached = False
 
     def __init__(
@@ -145,21 +154,26 @@ def __init__(
             plugin_source = self.__build_dependency_resolvers_plugin_source(conf_file)
         self.dependency_resolvers = self.__parse_resolver_conf_plugins(plugin_source)
         self._enabled_container_types: List[str] = []
-        self._destination_for_container_type: Dict[str, Dict[str, JobDestination]] = {}
+        self._destination_for_container_type = {}
 
-    def set_enabled_container_types(self, container_types_to_destinations):
+    def set_enabled_container_types(
+        self, container_types_to_destinations: Dict[ContainerType, List[DestinationProtocol]]
+    ):
         """Set the union of all enabled container types."""
         self._enabled_container_types = list(container_types_to_destinations.keys())
         # Just pick first enabled destination for a container type, probably covers the most common deployment scenarios
         self._destination_for_container_type = container_types_to_destinations
 
-    def get_destination_info_for_container_type(self, container_type, destination_id=None):
+    def get_destination_info_for_container_type(
+        self, container_type: ContainerType, destination_id: Optional[DestinationId] = None
+    ) -> Optional[DestinationParametersType]:
         if destination_id is None:
             return next(iter(self._destination_for_container_type[container_type])).params
         else:
             for destination in self._destination_for_container_type[container_type]:
                 if destination.id == destination_id:
                     return destination.params
+        return None
 
     @property
     def enabled_container_types(self):