Merge pull request #17991 from nsoranzo/warn_unused_ignores

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/authnz/managers.py

@@ -22,7 +22,10 @@
     string_as_bool,
     unicodify,
 )
-from galaxy.util.resources import files
+from galaxy.util.resources import (
+    as_file,
+    resource_path,
+)
 from .custos_authnz import (
     CustosAuthFactory,
     KEYCLOAK_BACKENDS,
@@ -35,7 +38,7 @@
     Strategy,
 )
 
-OIDC_BACKEND_SCHEMA = files("galaxy.authnz.xsd") / "oidc_backends_config.xsd"
+OIDC_BACKEND_SCHEMA = resource_path(__package__, "xsd/oidc_backends_config.xsd")
 
 log = logging.getLogger(__name__)
 
@@ -108,7 +111,8 @@ def _parse_oidc_backends_config(self, config_file):
         self.oidc_backends_config = {}
         self.oidc_backends_implementation = {}
         try:
-            tree = parse_xml(config_file, schemafname=OIDC_BACKEND_SCHEMA)
+            with as_file(OIDC_BACKEND_SCHEMA) as oidc_backend_schema_path:
+                tree = parse_xml(config_file, schemafname=oidc_backend_schema_path)
             root = tree.getroot()
             if root.tag != "OIDC":
                 raise etree.ParseError(

lib/galaxy/config/__init__.py

@@ -51,6 +51,10 @@
     read_properties_from_file,
     running_from_source,
 )
+from galaxy.util.resources import (
+    as_file,
+    resource_path,
+)
 from galaxy.util.themes import flatten_theme
 from ..version import (
     VERSION_MAJOR,
@@ -60,18 +64,13 @@
 if TYPE_CHECKING:
     from galaxy.model import User
 
-if sys.version_info >= (3, 9):
-    from importlib.resources import files
-else:
-    from importlib_resources import files
-
 log = logging.getLogger(__name__)
 
 DEFAULT_LOCALE_FORMAT = "%a %b %e %H:%M:%S %Y"
 ISO_DATETIME_FORMAT = "%Y-%m-%d %H:%M:%S"
 
 GALAXY_APP_NAME = "galaxy"
-GALAXY_SCHEMAS_PATH = files("galaxy.config") / "schemas"
+GALAXY_SCHEMAS_PATH = resource_path(__package__, "schemas")
 GALAXY_CONFIG_SCHEMA_PATH = GALAXY_SCHEMAS_PATH / "config_schema.yml"
 REPORTS_CONFIG_SCHEMA_PATH = GALAXY_SCHEMAS_PATH / "reports_config_schema.yml"
 TOOL_SHED_CONFIG_SCHEMA_PATH = GALAXY_SCHEMAS_PATH / "tool_shed_config_schema.yml"
@@ -193,7 +192,7 @@ def configure_logging(config, facts=None):
         logging.config.dictConfig(logging_conf)
 
 
-def find_root(kwargs):
+def find_root(kwargs) -> str:
     return os.path.abspath(kwargs.get("root_dir", "."))
 
 
@@ -238,6 +237,7 @@ class BaseAppConfiguration(HasDynamicProperties):
     add_sample_file_to_defaults: Set[str] = set()  # for these options, add sample config files to their defaults
     listify_options: Set[str] = set()  # values for these options are processed as lists of values
     object_store_store_by: str
+    shed_tools_dir: str
 
     def __init__(self, **kwargs):
         self._preprocess_kwargs(kwargs)
@@ -835,7 +835,8 @@ def _process_config(self, kwargs: Dict[str, Any]) -> None:
         self.cookie_path = kwargs.get("cookie_path")
         if not running_from_source and kwargs.get("tool_path") is None:
             try:
-                self.tool_path = str(files("galaxy.tools") / "bundled")
+                with as_file(resource_path("galaxy.tools", "bundled")) as path:
+                    self.tool_path = os.fspath(path)
             except ModuleNotFoundError:
                 # Might not be a full galaxy installation
                 self.tool_path = self._in_root_dir(self.tool_path)

lib/galaxy/config/config_manage.py

@@ -46,6 +46,7 @@
     nice_config_parser,
     NicerConfigParser,
 )
+from galaxy.util.resources import Traversable
 from galaxy.util.yaml_util import (
     ordered_dump,
     ordered_load,
@@ -72,7 +73,7 @@ class App(NamedTuple):
     default_port: str
     expected_app_factories: List[str]
     destination: str
-    schema_path: str
+    schema_path: Traversable
 
     @property
     def app_name(self) -> str:
@@ -219,21 +220,21 @@ class OptionValue(NamedTuple):
     "8080",
     ["galaxy.web.buildapp:app_factory"],
     "config/galaxy.yml",
-    str(GALAXY_CONFIG_SCHEMA_PATH),
+    GALAXY_CONFIG_SCHEMA_PATH,
 )
 SHED_APP = App(
     ["tool_shed_wsgi.ini", "config/tool_shed.ini"],
     "9009",
     ["tool_shed.webapp.buildapp:app_factory"],
     "config/tool_shed.yml",
-    str(TOOL_SHED_CONFIG_SCHEMA_PATH),
+    TOOL_SHED_CONFIG_SCHEMA_PATH,
 )
 REPORTS_APP = App(
     ["reports_wsgi.ini", "config/reports.ini"],
     "9001",
     ["galaxy.webapps.reports.buildapp:app_factory"],
     "config/reports.yml",
-    str(REPORTS_CONFIG_SCHEMA_PATH),
+    REPORTS_CONFIG_SCHEMA_PATH,
 )
 APPS = {"galaxy": GALAXY_APP, "tool_shed": SHED_APP, "reports": REPORTS_APP}
 

lib/galaxy/config/schema.py

@@ -1,6 +1,7 @@
 import logging
 
 from galaxy.exceptions import ConfigurationError
+from galaxy.util.resources import Traversable
 from galaxy.util.yaml_util import ordered_load
 
 log = logging.getLogger(__name__)
@@ -35,15 +36,15 @@ def get_app_option(self, name):
 
 
 class AppSchema(Schema):
-    def __init__(self, schema_path, app_name):
+    def __init__(self, schema_path: Traversable, app_name: str):
         self.raw_schema = self._read_schema(schema_path)
         self.description = self.raw_schema.get("desc", None)
         app_schema = self.raw_schema["mapping"][app_name]["mapping"]
         self._preprocess(app_schema)
         super().__init__(app_schema)
 
-    def _read_schema(self, path):
-        with open(path) as f:
+    def _read_schema(self, path: Traversable):
+        with path.open() as f:
             return ordered_load(f)
 
     def _preprocess(self, app_schema):

lib/galaxy/datatypes/binary.py

@@ -4367,7 +4367,7 @@ class HexrdImagesNpz(Npz):
     >>> fname = get_test_fname('hexrd.images.npz')
     >>> HexrdImagesNpz().sniff(fname)
     True
-    >>> fname = get_test_fname('eta_ome.npz')
+    >>> fname = get_test_fname('hexrd.eta_ome.npz')
     >>> HexrdImagesNpz().sniff(fname)
     False
     """

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/datatypes/media.py

@@ -193,8 +193,6 @@ class Mp4(Video):
     >>> from galaxy.datatypes.sniff import sniff_with_cls
     >>> sniff_with_cls(Mp4, 'video_1.mp4')
     True
-    >>> sniff_with_cls(Mp4, 'audio_1.mp4')
-    False
     """
 
     file_ext = "mp4"

lib/galaxy/datatypes/sniff.py

@@ -49,8 +49,9 @@
 
 def get_test_fname(fname):
     """Returns test data filename"""
-    path, name = os.path.split(__file__)
+    path = os.path.dirname(__file__)
     full_path = os.path.join(path, "test", fname)
+    assert os.path.isfile(full_path), f"{full_path} is not a file"
     return full_path
 
 

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]]