Merge branch 'main' into screenshot_without_margins

.github/workflows/test_prereleases.yml

@@ -11,6 +11,7 @@ on:
   pull_request:
     paths:
       - '.github/workflows/test_prereleases.yml'
+      - 'resources/constraints/version_denylist.txt'
 
 env:
   COLUMNS: 120
@@ -42,6 +43,10 @@ jobs:
 
       - uses: tlambert03/setup-qt-libs@v1
 
+      - name: Setup Graphviz
+        uses: ts-graphviz/setup-graphviz@v2
+        continue-on-error: true
+
       - name: Install Windows OpenGL
         if: runner.os == 'Windows'
         run: |
@@ -64,6 +69,7 @@ jobs:
           BACKEND: ${{ matrix.backend }}
           COVERAGE: "no_cov"
           PYVISTA_OFF_SCREEN: True  # required for opengl on windows
+          PIP_CONSTRAINT: resources/constraints/version_denylist.txt
 
       # If something goes wrong, we can open an issue in the repo
       - name: Report Failures

.github/workflows/upgrade_test_constraints.yml

@@ -165,7 +165,7 @@ jobs:
           #
           # --extra pyqt5 etc - names of extra sections from pyproject.toml that should be checked for the dependencies list (maybe we could create a super extra section to collect them all in)
           flags+=" --extra pyqt5"
-          flags+=" --extra pyqt6_experimental"
+          flags+=" --extra pyqt6"
           flags+=" --extra pyside2"
           flags+=" --extra pyside6_experimental"
           flags+=" --extra testing"

CITATION.cff

@@ -103,6 +103,11 @@ authors:
   affiliation: Chan Zuckerberg Initiative
   orcid: https://orcid.org/0000-0002-3841-8344
   alias: aganders3
+- given-names: Andrew
+  family-names: Annex
+  affiliation: SETI Institute/NASA ARC
+  orcid: https://orcid.org/0000-0002-0253-2313
+  alias:  AndrewAnnex
 - given-names: Peter
   family-names: Boone
   alias: boonepeter
@@ -121,6 +126,16 @@ authors:
     CNRS, Palaiseau, France
   orcid: https://orcid.org/0000-0002-9441-9173
   alias: ClementCaporal
+- given-names: Jan
+  family-names: Eglinger
+  affiliation: Friedrich Miescher Institute for Biomedical Research (FMI), Basel (Switzerland)
+  orcid: https://orcid.org/0000-0001-7234-1435
+  alias: imagejan
+- given-names: Andreas
+  family-names: Eisenbarth
+  affiliation: EMBL Heidelberg, Germany
+  orcid: https://orcid.org/0000-0002-1113-9556
+  alias: aeisenbarth
 - given-names: Jeremy
   family-names: Freeman
   affiliation: Chan Zuckerberg Initiative
@@ -209,11 +224,21 @@ authors:
   family-names: Nauroth-Kreß
   affiliation: University Hospital Würzburg - Institute of Neuroradiology
   alias: Chris-N-K
+- given-names: David
+  family-names: Palecek
+  affiliation: Algarve Centre of Marine Sciences (CCMAR)
+  orcid: https://orcid.org/0009-0003-9328-8540
+  alias: palec87
 - given-names: Constantin
   family-names: Pape
   affiliation: Georg-August-Universität Göttingen
   orcid: https://orcid.org/0000-0001-6562-7187
   alias: constantinpape
+- given-names: Eric
+  family-names: Perlman
+  affiliation: Yikes LLC
+  orcid: https://orcid.org/0000-0001-5542-1302
+  alias: perlman
 - given-names: Kim
   family-names: Pevey
   alias: kcpevey
@@ -227,6 +252,9 @@ authors:
   affiliation: Brown University
   orcid: https://orcid.org/0000-0003-4501-5428
   alias: kir0ul
+- given-names: David
+  family-names: Pinto
+  alias: MarchisLost
 - given-names: Jaime
   family-names: Rodríguez-Guerra
   affiliation: Quansight Labs
@@ -242,11 +270,19 @@ authors:
   affiliation: European Bioinformatics Institute - European Molecular Biology Laboratory
   orcid: https://orcid.org/0000-0002-2447-5911
   alias: ctr26
+- given-names: James
+  family-names: Ryan
+  alias: jamesyan-git
 - given-names: Gabriel
   family-names: Selzer
   affiliation: University of Wisconsin-Madison
   orcid: https://orcid.org/0009-0002-2400-1940
   alias: gselzer
+- given-names: MB
+  family-names: Smith
+  affiliation: AI lab for Living Technologies, University Medical Centre Utrecht (The Netherlands)
+  orcid: https://orcid.org/0000-0002-1405-0100
+  alias: odinsbane
 - given-names: Paul
   family-names: Smith
   affiliation: University College London
@@ -255,6 +291,11 @@ authors:
 - given-names: Konstantin
   family-names: Sofiiuk
   alias: ksofiyuk
+- given-names: Johannes
+  family-names: Soltwedel
+  affiliation: DFG cluster of excellence 'Physics of Life', TU Dresden
+  orcid: https://orcid.org/0000-0003-1273-2412
+  alias: jo-mueller
 - given-names: David
   family-names: Stansby
   affiliation: University College London
@@ -269,6 +310,11 @@ authors:
   family-names: Wadhwa
   affiliation: Quansight Labs
   alias: ppwadhwa
+- given-names: Martin
+  family-names: Weigert
+  affiliation: TU-Dresden / EPFL
+  orcid: https://orcid.org/0000-0002-7780-9057
+  alias: maweigert
 - given-names: Jonas
   family-names: Windhager
   affiliation: ETH Zurich / University of Zurich

napari/_qt/_qapp_model/_tests/test_view_menu.py

@@ -49,22 +49,28 @@ def test_toggle_axes_scale_bar_attr(
 
 
 @skip_local_popups
-def test_toggle_fullscreen(make_napari_viewer):
+def test_toggle_fullscreen(make_napari_viewer, qtbot):
     """Test toggle fullscreen action."""
     action_id = 'napari.window.view.toggle_fullscreen'
     app = get_app()
     viewer = make_napari_viewer(show=True)
 
     # Check initial default state (no fullscreen)
-    assert not viewer.window._qt_window._fullscreen_flag
+    assert not viewer.window._qt_window.isFullScreen()
 
     # Check fullscreen state change
     app.commands.execute_command(action_id)
-    assert viewer.window._qt_window._fullscreen_flag
+    if sys.platform == 'darwin':
+        # On macOS, wait for the animation to complete
+        qtbot.wait(250)
+    assert viewer.window._qt_window.isFullScreen()
 
     # Check return to non fullscreen state
     app.commands.execute_command(action_id)
-    assert not viewer.window._qt_window._fullscreen_flag
+    if sys.platform == 'darwin':
+        # On macOS, wait for the animation to complete
+        qtbot.wait(250)
+    assert not viewer.window._qt_window.isFullScreen()
 
 
 @skip_local_focus

napari/_qt/_tests/test_qt_viewer.py

@@ -1116,3 +1116,100 @@ def test_points_2d_to_3d(make_napari_viewer):
     QApplication.processEvents()
     viewer.dims.ndisplay = 3
     QApplication.processEvents()
+
+
+@skip_local_popups
+def test_scale_bar_colored(qt_viewer, qtbot):
+    viewer = qt_viewer.viewer
+    scale_bar = viewer.scale_bar
+
+    # Add black image
+    data = np.zeros((2, 2))
+    viewer.add_image(data)
+
+    # Check scale bar is not visible (all the canvas is black - `[0, 0, 0, 255]`)
+    def check_all_black():
+        screenshot = qt_viewer.screenshot(flash=False)
+        assert np.all(screenshot == [0, 0, 0, 255], axis=-1).all()
+
+    qtbot.waitUntil(check_all_black)
+
+    # Check scale bar is visible (canvas has white `[1, 1, 1, 255]` in it)
+    def check_white_scale_bar():
+        screenshot = qt_viewer.screenshot(flash=False)
+        assert not np.all(screenshot == [0, 0, 0, 255], axis=-1).all()
+        assert np.all(screenshot == [1, 1, 1, 255], axis=-1).any()
+
+    scale_bar.visible = True
+    qtbot.waitUntil(check_white_scale_bar)
+
+    # Check scale bar is colored (canvas has fuchsia `[1, 0, 1, 255]` and not white in it)
+    def check_colored_scale_bar():
+        screenshot = qt_viewer.screenshot(flash=False)
+        assert not np.all(screenshot == [1, 1, 1, 255], axis=-1).any()
+        assert np.all(screenshot == [1, 0, 1, 255], axis=-1).any()
+
+    scale_bar.colored = True
+    qtbot.waitUntil(check_colored_scale_bar)
+
+    # Check scale bar is still visible but not colored (canvas has white again but not fuchsia in it)
+    def check_only_white_scale_bar():
+        screenshot = qt_viewer.screenshot(flash=False)
+        assert np.all(screenshot == [1, 1, 1, 255], axis=-1).any()
+        assert not np.all(screenshot == [1, 0, 1, 255], axis=-1).any()
+
+    scale_bar.colored = False
+    qtbot.waitUntil(check_only_white_scale_bar)
+
+
+@skip_local_popups
+def test_scale_bar_ticks(qt_viewer, qtbot):
+    viewer = qt_viewer.viewer
+    scale_bar = viewer.scale_bar
+
+    # Add black image
+    data = np.zeros((2, 2))
+    viewer.add_image(data)
+
+    # Check scale bar is not visible (all the canvas is black - `[0, 0, 0, 255]`)
+    def check_all_black():
+        screenshot = qt_viewer.screenshot(flash=False)
+        assert np.all(screenshot == [0, 0, 0, 255], axis=-1).all()
+
+    qtbot.waitUntil(check_all_black)
+
+    # Check scale bar is visible (canvas has white `[1, 1, 1, 255]` in it)
+    def check_white_scale_bar():
+        screenshot = qt_viewer.screenshot(flash=False)
+        assert not np.all(screenshot == [0, 0, 0, 255], axis=-1).all()
+        assert np.all(screenshot == [1, 1, 1, 255], axis=-1).any()
+
+    scale_bar.visible = True
+    qtbot.waitUntil(check_white_scale_bar)
+
+    # Check scale bar has ticks active and take screenshot for later comparison
+    assert scale_bar.ticks
+    screenshot_with_ticks = qt_viewer.screenshot(flash=False)
+
+    # Check scale bar without ticks (still white present but new screenshot differs from ticks one)
+    def check_no_ticks_scale_bar():
+        screenshot = qt_viewer.screenshot(flash=False)
+        assert np.all(screenshot == [1, 1, 1, 255], axis=-1).any()
+        npt.assert_raises(
+            AssertionError,
+            npt.assert_array_equal,
+            screenshot,
+            screenshot_with_ticks,
+        )
+
+    scale_bar.ticks = False
+    qtbot.waitUntil(check_no_ticks_scale_bar)
+
+    # Check scale bar again has ticks (still white present and new screenshot corresponds with ticks one)
+    def check_ticks_scale_bar():
+        screenshot = qt_viewer.screenshot(flash=False)
+        assert np.all(screenshot == [1, 1, 1, 255], axis=-1).any()
+        npt.assert_array_equal(screenshot, screenshot_with_ticks)
+
+    scale_bar.ticks = True
+    qtbot.waitUntil(check_ticks_scale_bar)

napari/_qt/containers/qt_layer_list.py

@@ -73,6 +73,7 @@ def keyPressEvent(self, e: Optional[QKeyEvent]) -> None:
             e.modifiers() & Qt.KeyboardModifier.AltModifier
             or e.modifiers() & Qt.KeyboardModifier.ControlModifier
             or e.modifiers() & Qt.KeyboardModifier.MetaModifier
+            or e.modifiers() & Qt.KeyboardModifier.ShiftModifier
         ):
             e.ignore()
         elif e.key() != Qt.Key.Key_Space:

napari/_qt/dialogs/_tests/test_reader_dialog.py

@@ -42,7 +42,7 @@ def test_reader_defaults(reader_dialog, tmpdir):
 
     assert widg.findChild(QLabel).text().startswith('Choose reader')
     assert widg._get_plugin_choice() == 'p1'
-    assert widg.persist_checkbox.isChecked()
+    assert not widg.persist_checkbox.isChecked()
 
 
 def test_reader_with_error_message(reader_dialog):
@@ -84,10 +84,10 @@ def test_get_plugin_choice(tmpdir, reader_dialog):
 def test_get_persist_choice(tmpdir, reader_dialog):
     file_pth = tmpdir.join('my_file.tif')
     widg = reader_dialog(pth=file_pth, readers={'p1': 'p1', 'p2': 'p2'})
-    assert widg._get_persist_choice()
+    assert not widg._get_persist_choice()
 
     widg.persist_checkbox.toggle()
-    assert not widg._get_persist_choice()
+    assert widg._get_persist_choice()
 
 
 def test_prepare_dialog_options_no_readers():

napari/_qt/dialogs/qt_reader_dialog.py

@@ -27,7 +27,7 @@ def __init__(
         parent: QWidget = None,
         readers: Optional[dict[str, str]] = None,
         error_message: str = '',
-        persist_checked: bool = True,
+        persist_checked: bool = False,
     ) -> None:
         if readers is None:
             readers = {}
@@ -194,7 +194,7 @@ def handle_gui_reading(
         pth=_path,
         error_message=error_message,
         readers=readers,
-        persist_checked=not plugin_override,
+        persist_checked=plugin_override,
     )
     display_name, persist = readerDialog.get_user_choices()
     if display_name:

napari/_qt/qt_resources/styles/01_buttons.qss

@@ -126,7 +126,7 @@ QtModeRadioButton[mode="polygon"]::indicator {
 }
 
 QtModeRadioButton[mode="labels_polygon"]::indicator {
-  image: url("theme_{{ id }}:/polygon_lasso.svg");
+  image: url("theme_{{ id }}:/polygon.svg");
 }
 
 QtModeRadioButton[mode="polygon_lasso"]::indicator {