Start removing type:ingore comments from SA2.0 PR

lib/galaxy/managers/notification.py

@@ -275,8 +275,8 @@ def update_broadcasted_notification(self, notification_id: int, request: Notific
     def get_user_notification_preferences(self, user: User) -> UserNotificationPreferences:
         """Gets the user's current notification preferences or the default ones if no preferences are set."""
         current_notification_preferences = (
-            user.preferences[NOTIFICATION_PREFERENCES_SECTION_NAME]  # type:ignore[index]
-            if NOTIFICATION_PREFERENCES_SECTION_NAME in user.preferences  # type:ignore[operator]
+            user.preferences[NOTIFICATION_PREFERENCES_SECTION_NAME]
+            if NOTIFICATION_PREFERENCES_SECTION_NAME in user.preferences
             else None
         )
         try:
@@ -291,9 +291,7 @@ def update_user_notification_preferences(
         """Updates the user's notification preferences with the requested changes."""
         notification_preferences = self.get_user_notification_preferences(user)
         notification_preferences.update(request.preferences)
-        user.preferences[NOTIFICATION_PREFERENCES_SECTION_NAME] = (
-            notification_preferences.model_dump_json()
-        )  # type:ignore[index]
+        user.preferences[NOTIFICATION_PREFERENCES_SECTION_NAME] = notification_preferences.model_dump_json()
         with transaction(self.sa_session):
             self.sa_session.commit()
         return notification_preferences

lib/galaxy/managers/sharable.py

@@ -179,7 +179,7 @@ def share_with(self, item, user: User, flush: bool = True):
         """
         # precondition: user has been validated
         # get or create
-        existing = self.get_share_assocs(item, user=user)  # type:ignore[dict-item]
+        existing = self.get_share_assocs(item, user=user)
         if existing:
             return existing.pop(0)
         return self._create_user_share_assoc(item, user, flush=flush)

lib/galaxy/model/store/__init__.py

@@ -2175,7 +2175,7 @@ def export_history(
         # Write collections' attributes (including datasets list) to file.
         stmt_hdca = (
             select(model.HistoryDatasetCollectionAssociation)
-            .where(model.HistoryDatasetCollectionAssociation.history == history)  # type:ignore[arg-type]
+            .where(model.HistoryDatasetCollectionAssociation.history == history)
             .where(model.HistoryDatasetCollectionAssociation.deleted == expression.false())
         )
         collections = sa_session.scalars(stmt_hdca)

lib/galaxy/workflow/modules.py

@@ -2516,13 +2516,13 @@ def inject(self, step: WorkflowStep, step_args=None, steps=None, **kwargs):
         If step_args is provided from a web form this is applied to generate
         'state' else it is just obtained from the database.
         """
-        step.upgrade_messages = {}  # type: ignore[assignment]
+        step.upgrade_messages = {}
 
         # Make connection information available on each step by input name.
         step.setup_input_connections_by_name()
 
         # Populate module.
-        module = step.module = module_factory.from_workflow_step(self.trans, step, **kwargs)  # type: ignore[assignment]
+        module = step.module = module_factory.from_workflow_step(self.trans, step, **kwargs)
 
         # Any connected input needs to have value DummyDataset (these
         # are not persisted so we need to do it every time)