Merge branch 'main' into kb-impl

* main: (26 commits)
  Fix some typing in napari.components (napari#6203)
  Use class name for object that does not have qt name (napari#6222)
  test: [Automatic] Constraints upgrades: `hypothesis`, `magicgui`, `psygnal`, `tensorstore`, `tifffile`, `tqdm`, `virtualenv` (napari#6143)
  Replace more np.all( ... = ...) with np.array_equal (napari#6213)
  remove np.all(... == ...) in test_surface.py (napari#6218)
  Ensure pandas Series is initialized with a list as data (napari#6226)
  Stop using temporary directory for store array for paint test (napari#6191)
  Bugfix: ensure thumbnail represents canvas when multiscale (napari#6200)
  cleanup np.all(... == ...) from test_points.py (napari#6217)
  [pre-commit.ci] pre-commit autoupdate (napari#6221)
  use app-model for file menu (napari#4865)
  Add tests to cover slicing behavior when changing layers and data (napari#4819)
  [pre-commit.ci] pre-commit autoupdate (napari#6128)
  Add test coverage for async slicing of labels (napari#5325)
  Add collision check when set colors for labels layer (napari#6193)
  Update "toggle ndview" text (napari#6192)
  Prevent layer controls buttons changing layout while taking screenshots with flash effect on (napari#6194)
  Fix typing in napari.utils.perf (napari#6132)
  Add GUI test coverage for changes to Labels.show_selected_label (napari#5372)
  Fix types in 'napari.utils.colormaps.categorical_colormap' (napari#6154)
  ...

.github/workflows/test_pull_requests.yml

@@ -165,6 +165,7 @@ jobs:
   test_pip_install:
     name: ubuntu-latest 3.9 pip install
     runs-on: ubuntu-latest
+    timeout-minutes: 30
     steps:
       - uses: actions/checkout@v3
         with:
@@ -196,6 +197,7 @@ jobs:
   test_examples:
     name: test examples
     runs-on: ubuntu-latest
+    timeout-minutes: 10
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4

.github/workflows/upgrade_test_constraints.yml

@@ -9,6 +9,10 @@ on:
   issue_comment:
     types: [ created ]
 
+  pull_request:
+    paths:
+      - '.github/workflows/upgrade_test_constraints.yml'
+
 concurrency:
   group: test-${{ github.ref }}
   cancel-in-progress: true

.pre-commit-config.yaml

@@ -1,21 +1,21 @@
 repos:
 -   repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 23.7.0
+    rev: 23.9.1
     hooks:
     - id: black
       pass_filenames: true
       exclude: _vendor|vendored|examples
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.281
+    rev: v0.0.288
     hooks:
       - id: ruff
         exclude: _vendor|vendored
 -   repo: https://github.com/seddonym/import-linter
-    rev: v1.10.0
+    rev: v1.11.1
     hooks:
     - id: import-linter
       stages: [manual]
 -   repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.23.3
+    rev: 0.26.3
     hooks:
       - id: check-github-workflows

examples/dev/slicing/janelia_s3_n5_multiscale.py

@@ -18,7 +18,7 @@
 
 # s0 (highest resolution) through s5 (lowest resolution) are available
 data = []
-for i in range(0, 5):
+for i in range(5):
     zarr_array = group[f'em/fibsem-uint16/s{i}']
     data.append(da.from_zarr(zarr_array, chunks=zarr_array.chunks))
 

napari/_app_model/_submenus.py

@@ -25,6 +25,24 @@
             enablement=LLSCK.active_layer_is_image_3d,
         ),
     ),
+    (
+        MenuId.MENUBAR_FILE,
+        SubmenuItem(
+            submenu=MenuId.FILE_OPEN_WITH_PLUGIN,
+            title=trans._('Open with Plugin'),
+            group=MenuGroup.NAVIGATION,
+            order=99,
+        ),
+    ),
+    (
+        MenuId.MENUBAR_FILE,
+        SubmenuItem(
+            submenu=MenuId.FILE_SAMPLES,
+            title=trans._('Open Sample'),
+            group=MenuGroup.NAVIGATION,
+            order=100,
+        ),
+    ),
     (
         MenuId.MENUBAR_VIEW,
         SubmenuItem(submenu=MenuId.VIEW_AXES, title=trans._('Axes')),

napari/_app_model/actions/_view_actions.py

@@ -10,7 +10,7 @@
 from app_model.types import Action, ToggleRule
 
 from napari._app_model.actions._toggle_action import ViewerToggleAction
-from napari.constants import CommandId, MenuId
+from napari.constants import CommandId, MenuGroup, MenuId
 from napari.settings import get_settings
 
 VIEW_ACTIONS: List[Action] = []
@@ -46,14 +46,22 @@ def _get_current_tooltip_visibility():
     return get_settings().appearance.layer_tooltip_visibility
 
 
-VIEW_ACTIONS.append(
-    # TODO: this could be made into a toggle setting Action subclass
-    # using a similar pattern to the above ViewerToggleAction classes
-    Action(
-        id=CommandId.TOGGLE_LAYER_TOOLTIPS,
-        title=CommandId.TOGGLE_LAYER_TOOLTIPS.title,
-        menus=[{'id': MenuId.MENUBAR_VIEW, 'group': '1_render', 'order': 10}],
-        callback=_tooltip_visibility_toggle,
-        toggled=ToggleRule(get_current=_get_current_tooltip_visibility),
-    ),
+VIEW_ACTIONS.extend(
+    [
+        # TODO: this could be made into a toggle setting Action subclass
+        # using a similar pattern to the above ViewerToggleAction classes
+        Action(
+            id=CommandId.TOGGLE_LAYER_TOOLTIPS,
+            title=CommandId.TOGGLE_LAYER_TOOLTIPS.title,
+            menus=[
+                {
+                    'id': MenuId.MENUBAR_VIEW,
+                    'group': MenuGroup.RENDER,
+                    'order': 10,
+                }
+            ],
+            callback=_tooltip_visibility_toggle,
+            toggled=ToggleRule(get_current=_get_current_tooltip_visibility),
+        ),
+    ]
 )

napari/_qt/_qapp_model/_tests/test_qapp_model_menus.py

@@ -1,28 +1,65 @@
-from unittest.mock import MagicMock
-
+import numpy as np
 import pytest
+from app_model.types import Action
 
-from napari import viewer
-from napari._app_model import constants, get_app
+from napari._app_model import get_app
+from napari._app_model.constants import MenuId
+from napari._app_model.context import LayerListContextKeys as LLCK
 from napari._qt._qapp_model import build_qmodel_menu
-from napari._qt._qapp_model.qactions import init_qactions
-from napari._qt.qt_main_window import Window
+from napari.layers import Image
 
 
-@pytest.mark.parametrize('menu_id', list(constants.MenuId))
-def test_build_qmodel_menu(qtbot, menu_id):
-    """Test that we can build qmenus for all registered menu IDs"""
+# `builtins` required so there are samples registered, so samples menu exists
+@pytest.mark.parametrize('menu_id', list(MenuId))
+def test_build_qmodel_menu(builtins, make_napari_viewer, qtbot, menu_id):
+    """Test that we can build qmenus for all registered menu IDs."""
     app = get_app()
 
-    mock = MagicMock()
-    with app.injection_store.register(
-        providers={viewer.Viewer: lambda: mock, Window: lambda: mock}
-    ):
-        init_qactions.cache_clear()
-        init_qactions()
+    # Configures `app`, registers actions and initializes plugins
+    make_napari_viewer()
+
+    menu = build_qmodel_menu(menu_id)
+    qtbot.addWidget(menu)
+
+    # `>=` because separator bars count as actions
+    assert len(menu.actions()) >= len(app.menus.get_menu(menu_id))
+
+
+def test_update_menu_state_context(make_napari_viewer):
+    """Test `_update_menu_state` correctly updates enabled/visible state."""
+    app = get_app()
+    viewer = make_napari_viewer()
+
+    action = Action(
+        id='dummy_id',
+        title='dummy title',
+        callback=lambda: None,
+        menus=[{'id': MenuId.MENUBAR_FILE, 'when': (LLCK.num_layers > 0)}],
+        enablement=(LLCK.num_layers == 2),
+    )
+    app.register_action(action)
+
+    dummy_action = viewer.window.file_menu.findAction('dummy_id')
+
+    assert 'dummy_id' in app.commands
+    assert len(viewer.layers) == 0
+    # `dummy_action` should be disabled & not visible as num layers == 0
+    viewer.window._update_menu_state('file_menu')
+    assert not dummy_action.isVisible()
+    assert not dummy_action.isEnabled()
 
-        menu = build_qmodel_menu(menu_id)
-        qtbot.addWidget(menu)
+    layer_a = Image(np.random.random((10, 10)))
+    viewer.layers.append(layer_a)
+    assert len(viewer.layers) == 1
+    viewer.window._update_menu_state('file_menu')
+    # `dummy_action` should be visible but not enabled after adding layer
+    assert dummy_action.isVisible()
+    assert not dummy_action.isEnabled()
 
-        # `>=` because separator bars count as actions
-        assert len(menu.actions()) >= len(app.menus.get_menu(menu_id))
+    layer_b = Image(np.random.random((10, 10)))
+    viewer.layers.append(layer_b)
+    assert len(viewer.layers) == 2
+    # `dummy_action` should be enabled and visible after adding second layer
+    viewer.window._update_menu_state('file_menu')
+    assert dummy_action.isVisible()
+    assert dummy_action.isEnabled()

napari/_qt/_qapp_model/qactions/__init__.py

@@ -23,6 +23,7 @@ def init_qactions() -> None:
     """
 
     from napari._app_model import get_app
+    from napari._qt._qapp_model.qactions._file import Q_FILE_ACTIONS
     from napari._qt._qapp_model.qactions._help import Q_HELP_ACTIONS
     from napari._qt._qapp_model.qactions._view import Q_VIEW_ACTIONS
     from napari._qt.qt_main_window import Window, _QtMainWindow
@@ -51,5 +52,4 @@ def _provide_qt_viewer() -> Optional[QtViewer]:
         return None
 
     # register actions
-    for action in chain(Q_VIEW_ACTIONS, Q_HELP_ACTIONS):
-        app.register_action(action)
+    app.register_actions(chain(Q_FILE_ACTIONS, Q_HELP_ACTIONS, Q_VIEW_ACTIONS))