Enable warn_unused_ignores mypy option

lib/galaxy/__init__.py

@@ -4,4 +4,4 @@
 
 from pkgutil import extend_path
 
-__path__ = extend_path(__path__, __name__)  # type: ignore[has-type]
+__path__ = extend_path(__path__, __name__)

lib/galaxy/app.py

@@ -687,7 +687,7 @@ def __init__(self, **kwargs) -> None:
         self.watchers = self._register_singleton(ConfigWatchers)
         self._configure_toolbox()
         # Load Data Manager
-        self.data_managers = self._register_singleton(DataManagers)  # type: ignore[type-abstract]
+        self.data_managers = self._register_singleton(DataManagers)
         # Load the update repository manager.
         self.update_repository_manager = self._register_singleton(
             UpdateRepositoryManager, UpdateRepositoryManager(self)

lib/galaxy/app_unittest_utils/toolbox_support.py

@@ -81,7 +81,7 @@ def setUp(self):
         install_model = mapping.init("sqlite:///:memory:", create_tables=True)
         self.app.tool_cache = ToolCache()
         self.app.install_model = install_model
-        self.app.reindex_tool_search = self.__reindex  # type: ignore[assignment]
+        self.app.reindex_tool_search = self.__reindex  # type: ignore[method-assign]
         itp_config = os.path.join(self.test_directory, "integrated_tool_panel.xml")
         self.app.config.integrated_tool_panel_config = itp_config
         self.app.watchers = ConfigWatchers(self.app)

lib/galaxy/authnz/custos_authnz.py

@@ -35,7 +35,7 @@
 try:
     import pkce
 except ImportError:
-    pkce = None  # type: ignore[assignment]
+    pkce = None  # type: ignore[assignment, unused-ignore]
 
 log = logging.getLogger(__name__)
 STATE_COOKIE_NAME = "galaxy-oidc-state"

lib/galaxy/datatypes/constructive_solid_geometry.py

@@ -142,7 +142,7 @@ def display_peek(self, dataset: DatasetProtocol) -> str:
             return f"Ply file ({nice_size(dataset.get_size())})"
 
 
-class PlyAscii(Ply, data.Text):  # type: ignore[misc]
+class PlyAscii(Ply, data.Text):
     """
     >>> from galaxy.datatypes.sniff import get_test_fname
     >>> fname = get_test_fname('test.plyascii')
@@ -160,7 +160,7 @@ def __init__(self, **kwd):
         data.Text.__init__(self, **kwd)
 
 
-class PlyBinary(Ply, Binary):  # type: ignore[misc]
+class PlyBinary(Ply, Binary):
     file_ext = "plybinary"
     subtype = "binary"
 
@@ -477,7 +477,7 @@ def display_peek(self, dataset: DatasetProtocol) -> str:
             return f"Vtk file ({nice_size(dataset.get_size())})"
 
 
-class VtkAscii(Vtk, data.Text):  # type: ignore[misc]
+class VtkAscii(Vtk, data.Text):
     """
     >>> from galaxy.datatypes.sniff import get_test_fname
     >>> fname = get_test_fname('test.vtkascii')
@@ -495,7 +495,7 @@ def __init__(self, **kwd):
         data.Text.__init__(self, **kwd)
 
 
-class VtkBinary(Vtk, Binary):  # type: ignore[misc]
+class VtkBinary(Vtk, Binary):
     """
     >>> from galaxy.datatypes.sniff import get_test_fname
     >>> fname = get_test_fname('test.vtkbinary')

lib/galaxy/jobs/runners/aws.py

@@ -521,10 +521,10 @@ def parse_destination_params(self, params):
         check_required = []
         parsed_params = {}
         for k, spec in self.DESTINATION_PARAMS_SPEC.items():
-            value = params.get(k, spec.get("default"))  # type: ignore[attr-defined]
-            if spec.get("required") and not value:  # type: ignore[attr-defined]
+            value = params.get(k, spec.get("default"))
+            if spec.get("required") and not value:
                 check_required.append(k)
-            mapper = spec.get("map")    # type: ignore[attr-defined]
+            mapper = spec.get("map")
             parsed_params[k] = mapper(value)  # type: ignore[operator]
         if check_required:
             raise AWSBatchRunnerException(

lib/galaxy/jobs/runners/util/kill.py

@@ -11,7 +11,7 @@
     )
 except ImportError:
     """Don't make psutil a strict requirement, but use if available."""
-    Process = None  # type: ignore
+    Process = None
 
 
 def kill_pid(pid: int, use_psutil: bool = True):

lib/galaxy/managers/history_contents.py

@@ -413,7 +413,7 @@ def _contained_id_map(self, id_list):
         component_class = self.contained_class
         stmt = (
             select(component_class)
-            .where(component_class.id.in_(id_list))  # type: ignore[attr-defined]
+            .where(component_class.id.in_(id_list))
             .options(undefer(component_class._metadata))
             .options(joinedload(component_class.dataset).joinedload(model.Dataset.actions))
             .options(joinedload(component_class.tags))  # type: ignore[attr-defined]

lib/galaxy/managers/users.py

@@ -313,7 +313,7 @@ def by_api_key(self, api_key: str, sa_session=None):
 
     def by_oidc_access_token(self, access_token: str):
         if hasattr(self.app, "authnz_manager") and self.app.authnz_manager:
-            user = self.app.authnz_manager.match_access_token_to_user(self.app.model.session, access_token)  # type: ignore[attr-defined]
+            user = self.app.authnz_manager.match_access_token_to_user(self.app.model.session, access_token)
             return user
         else:
             return None

lib/galaxy/managers/workflows.py

@@ -538,7 +538,7 @@ def build_invocations_query(
             for inv in trans.sa_session.scalars(stmt)
             if self.check_security(trans, inv, check_ownership=True, check_accessible=False)
         ]
-        return invocations, total_matches  # type:ignore[return-value]
+        return invocations, total_matches
 
 
 MissingToolsT = List[Tuple[str, str, Optional[str], str]]