diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py index 502cc5a3c563..b329db864d3e 100644 --- a/lib/galaxy/model/store/__init__.py +++ b/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) diff --git a/lib/galaxy/tool_util/toolbox/watcher.py b/lib/galaxy/tool_util/toolbox/watcher.py index e570bb58198d..b885ea964e27 100644 --- a/lib/galaxy/tool_util/toolbox/watcher.py +++ b/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 diff --git a/lib/galaxy/tools/wrappers.py b/lib/galaxy/tools/wrappers.py index 3a6a6ff6c2cc..d2594ac95581 100644 --- a/lib/galaxy/tools/wrappers.py +++ b/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: diff --git a/lib/galaxy/util/watcher.py b/lib/galaxy/util/watcher.py index dd4f0110299a..501a2212201c 100644 --- a/lib/galaxy/util/watcher.py +++ b/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 diff --git a/lib/galaxy_test/selenium/framework.py b/lib/galaxy_test/selenium/framework.py index 7fc13f447204..59cf726f73f4 100644 --- a/lib/galaxy_test/selenium/framework.py +++ b/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: diff --git a/lib/tool_shed/test/base/playwrightbrowser.py b/lib/tool_shed/test/base/playwrightbrowser.py index d493e97aa990..4c82a0d7183c 100644 --- a/lib/tool_shed/test/base/playwrightbrowser.py +++ b/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']" diff --git a/lib/tool_shed/test/base/twillbrowser.py b/lib/tool_shed/test/base/twillbrowser.py index 1f4af8791678..a73cdf85b299 100644 --- a/lib/tool_shed/test/base/twillbrowser.py +++ b/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, diff --git a/test/unit/app/managers/test_HistoryManager.py b/test/unit/app/managers/test_HistoryManager.py index ba1710740540..c3627c87d166 100644 --- a/test/unit/app/managers/test_HistoryManager.py +++ b/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):