Fix package mypy errors

lib/galaxy/model/store/__init__.py

@@ -2162,7 +2162,7 @@ def export_history(
         # Write collections' attributes (including datasets list) to file.
         stmt_hdca = (
             select(model.HistoryDatasetCollectionAssociation)
-            .where(model.HistoryDatasetCollectionAssociation.history == history)
+            .where(model.HistoryDatasetCollectionAssociation.history == history)  # type:ignore[arg-type]
             .where(model.HistoryDatasetCollectionAssociation.deleted == expression.false())
         )
         collections = sa_session.scalars(stmt_hdca)

lib/galaxy/tool_util/toolbox/watcher.py

@@ -9,9 +9,9 @@
 
     can_watch = True
 except ImportError:
-    Observer = None
-    FileSystemEventHandler = object
-    PollingObserver = None
+    Observer = None  # type:ignore[assignment, misc]
+    FileSystemEventHandler = object  # type:ignore[assignment, misc]
+    PollingObserver = None  # type:ignore[assignment, misc]
     can_watch = False
 
 from galaxy.util.hash_util import md5_hash_file

lib/galaxy/tools/wrappers.py

@@ -384,7 +384,7 @@ def __init__(
             if isinstance(dataset_instance, HasTags):
                 self.groups = {
                     tag.user_value.lower()
-                    for tag in dataset_instance.tags  # type:ignore[attr-defined]
+                    for tag in dataset_instance.tags  # type:ignore[unused-ignore, attr-defined]
                     if tag.user_tname == "group"
                 }
             else:

lib/galaxy/util/watcher.py

@@ -13,9 +13,9 @@
 
     can_watch = True
 except ImportError:
-    Observer = None
-    FileSystemEventHandler = object
-    PollingObserver = None
+    Observer = None  # type:ignore[assignment]
+    FileSystemEventHandler = object  # type:ignore[assignment, misc]
+    PollingObserver = None  # type:ignore[assignment, misc]
     can_watch = False
 
 from galaxy.util.hash_util import md5_hash_file

lib/galaxy_test/selenium/framework.py

@@ -536,7 +536,7 @@ def setup_shared_state(self):
     NavigatesGalaxyMixin = object
 
 
-class UsesLibraryAssertions(NavigatesGalaxyMixin):
+class UsesLibraryAssertions(NavigatesGalaxyMixin):  # type:ignore[valid-type, misc]
     @retry_assertion_during_transitions
     def assert_num_displayed_items_is(self, n):
         num_displayed = self.num_displayed_items()
@@ -546,7 +546,7 @@ def num_displayed_items(self) -> int:
         return len(self.libraries_table_elements())
 
 
-class UsesHistoryItemAssertions(NavigatesGalaxyMixin):
+class UsesHistoryItemAssertions(NavigatesGalaxyMixin):  # type:ignore[valid-type, misc]
     def assert_item_peek_includes(self, hid, expected):
         item_body = self.history_panel_item_component(hid=hid)
         peek_text = item_body.peek.wait_for_text()
@@ -584,7 +584,7 @@ def assert_item_hid_text(self, hid):
 )
 
 
-class UsesWorkflowAssertions(NavigatesGalaxyMixin):
+class UsesWorkflowAssertions(NavigatesGalaxyMixin):  # type:ignore[valid-type, misc]
     @retry_assertion_during_transitions
     def _assert_showing_n_workflows(self, n):
         if (actual_count := len(self.workflow_index_table_elements())) != n:

lib/tool_shed/test/base/playwrightbrowser.py

@@ -132,7 +132,7 @@ def _fill_form_value(self, form: Locator, control_name: str, value: FormValueTyp
         input_s = form.locator(f"select[name='{control_name}']")
         if input_i.count():
             if control_name in ["redirect"]:
-                input_i.input_value = value
+                input_i.input_value = value  # type:ignore[method-assign, assignment]
             else:
                 if isinstance(value, bool):
                     if value and not input_i.is_checked():
@@ -142,9 +142,9 @@ def _fill_form_value(self, form: Locator, control_name: str, value: FormValueTyp
                 else:
                     input_i.fill(value)
         if input_t.count():
-            input_t.fill(value)
+            input_t.fill(value)  # type:ignore[arg-type]
         if input_s.count():
-            input_s.select_option(value)
+            input_s.select_option(value)  # type:ignore[arg-type]
 
     def edit_repository_categories(self, categories_to_add: List[str], categories_to_remove: List[str]) -> None:
         multi_select = "form[name='categories'] select[name='category_id']"

lib/tool_shed/test/base/twillbrowser.py

@@ -5,7 +5,7 @@
 )
 
 import twill.commands as tc
-from twill.browser import FormElement
+from twill.browser import FormElement  # type:ignore[attr-defined]
 
 from galaxy.util import smart_str
 from .browser import (
@@ -19,7 +19,7 @@
 
 
 def visit_url(url: str, allowed_codes: List[int]) -> str:
-    new_url = tc.go(url)
+    new_url = tc.go(url)  # type:ignore[func-returns-value]
     return_code = tc.browser.code
     assert return_code in allowed_codes, "Invalid HTTP return code {}, allowed codes: {}".format(
         return_code,

test/unit/app/managers/test_HistoryManager.py

@@ -85,7 +85,10 @@ def test_base(self):
 
         self.log("should be able to order")
         history3 = self.history_manager.create(name="history3", user=user2)
-        name_first_then_time = (model.History.name, sqlalchemy.desc(model.History.create_time))
+        name_first_then_time = (
+            model.History.name,
+            sqlalchemy.desc(model.History.create_time),
+        )  # type:ignore[var-annotated]
         assert self.history_manager.list(order_by=name_first_then_time) == [history2, history1, history3]
 
     def test_copy(self):