Merge branch 'main' into keybind-contribution

* main: (38 commits)
  Fix `test_worker_with_progress` by wait on worker end (napari#5548)
  Un-set unified title and tool bar on mac (Qt property) (napari#5533)
  Set PYTHONEXECUTABLE as part of macos fixes on (re)startup (napari#5531)
  Fix key error issue of action manager (napari#5539)
  Clean dangling widget in test (napari#5544)
  Use pytest-pretty for better log readability (napari#5525)
  Update vendoring tool to check on matplotlib colormap (napari#5181)
  MAINT: add time limit for CI. (napari#5495)
  Add show_debug notification (napari#5101)
  Overlays 2.0 (napari#4894)
  Clarify layer's editable property and separate interaction with visible property (napari#5413)
  ci(dependabot): bump docker/build-push-action from 3 to 4 (napari#5523)
  Fix opening file dialogs in PySide (napari#5492)
  [pre-commit.ci] pre-commit autoupdate (napari#5518)
  Replace flake8, isort and pyupgrade by ruff, enable additional usefull rules (napari#5513)
  MAINT: Don't format logs in log call (napari#5504)
  Fix conda avaliability check (napari#5496)
  Handle case when QtDims play thread is partially deleted (napari#5499)
  Bugfix: Add missing Enums and Flags required by PySide6 > 6.4 (napari#5480)
  Refactor Main Window status bar to improve information presentation (napari#5451)
  ...

.devcontainer/devcontainer.json

@@ -31,7 +31,7 @@
 	"forwardPorts": [5900, 5901, 6080],
 
 	// Use 'postCreateCommand' to run commands after the container is created.
-	"postCreateCommand": "pip install -U pip && pip install -e .[dev] && pre-commit install",
+	"postCreateCommand": "pip install -U pip && pip install -e .[pyqt, dev] && pre-commit install",
 
 	// Comment out to connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
 	"remoteUser": "vscode",

.github/workflows/build_docs.yml

@@ -49,7 +49,7 @@ jobs:
           python -c 'import napari.layers; print(napari.layers.__doc__)'
 
       - name: Build Docs
-        uses: GabrielBB/xvfb-action@v1
+        uses: aganders3/headless-gui@v1
         env:
           GOOGLE_CALENDAR_ID: ${{ secrets.GOOGLE_CALENDAR_ID }}
           GOOGLE_CALENDAR_API_KEY: ${{ secrets.GOOGLE_CALENDAR_API_KEY }}

.github/workflows/docker-singularity-publish.yml

@@ -77,7 +77,7 @@ jobs:
       # Build and push Docker image with Buildx (don't push on PR)
       # https://github.com/docker/build-push-action
       - name: Build and push Docker image
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v4
         with:
           context: .
           push: ${{ github.event_name != 'pull_request' }}

.github/workflows/test_comprehensive.yml

@@ -12,6 +12,9 @@ on:
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
+env:
+  COLUMNS: 120
+
 concurrency:
   group: comprehensive-test
 
@@ -100,7 +103,7 @@ jobs:
       # in which case we are declaring one specific tox environment to run.
       # see tox.ini for more
       - name: Test with tox
-        uses: GabrielBB/xvfb-action@v1
+        uses: aganders3/headless-gui@v1
         with:
           run: python -m tox
         env:
@@ -151,7 +154,7 @@ jobs:
           pip install ./napari-from-github[all,testing]
 
       - name: Test
-        uses: GabrielBB/xvfb-action@v1
+        uses: aganders3/headless-gui@v1
         with:
           run: python -m pytest --pyargs napari --color=yes
 
@@ -170,6 +173,6 @@ jobs:
           pip install setuptools tox tox-gh-actions
 
       - name: Test
-        uses: GabrielBB/xvfb-action@v1
+        uses: aganders3/headless-gui@v1
         with:
           run: tox -e py39-linux-pyside2-examples

.github/workflows/test_prereleases.yml

@@ -9,6 +9,9 @@ on:
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
+env:
+  COLUMNS: 120
+
 jobs:
   test:
     name: ${{ matrix.platform }} py${{ matrix.python }} ${{ matrix.backend }} --pre
@@ -46,7 +49,7 @@ jobs:
 
       - name: Test with tox
         # run tests using pip install --pre
-        uses: GabrielBB/xvfb-action@v1
+        uses: aganders3/headless-gui@v1
         with:
           run: python -m tox -v --pre
         env:

.github/workflows/test_pull_requests.yml

@@ -11,28 +11,36 @@ concurrency:
   group: test-${{ github.ref }}
   cancel-in-progress: true
 
+env:
+  COLUMNS: 120
+
 jobs:
   manifest:
     # make sure all necessary files will be bundled in the release
     name: Check Manifest
+    timeout-minutes: 15
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
           python-version: "3.x"
           cache-dependency-path: setup.cfg
+          cache: 'pip'
+      - name: Install Dependencies
+        run: pip install --upgrade pip
+      - name: Install Napari dev
+        run: pip install -e .[build]
       - name: Check Manifest
         run: |
-          pip install --upgrade pip
-          pip install -e .[build]
           make typestubs
           make check-manifest
 
   localization_syntax:
     # make sure all necessary files will be bundled in the release
     name: Check l18n syntax
     runs-on: ubuntu-latest
+    timeout-minutes: 2
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
@@ -48,6 +56,7 @@ jobs:
   test:
     name: ${{ matrix.platform }} ${{ matrix.python }} ${{ matrix.toxenv || matrix.backend }} ${{ matrix.MIN_REQ && 'min_req' }}
     runs-on: ${{ matrix.platform }}
+    timeout-minutes: 40
     strategy:
       fail-fast: false
       matrix:
@@ -84,10 +93,9 @@ jobs:
           - python: 3.9
             platform: ubuntu-latest
             backend: pyside6
-# uncoment when new qtpy is released
-#          - python: '3.10'
-#            platform: ubuntu-latest
-#            backend: pyside6
+          - python: '3.10'
+            platform: ubuntu-latest
+            backend: pyside6
 
     steps:
       - name: Cancel Previous Runs
@@ -134,7 +142,9 @@ jobs:
       # `tox -e py38-linux-pyqt,py38-linux-pyside`
       # see tox.ini for more
       - name: Test with tox
-        uses: GabrielBB/xvfb-action@v1
+        # the longest is macos-latest 3.9 pyqt5 at ~30 minutes.
+        timeout-minutes: 35
+        uses: aganders3/headless-gui@v1
         with:
           run: python -m tox
         env:
@@ -144,6 +154,7 @@ jobs:
           NUMPY_EXPERIMENTAL_ARRAY_FUNCTION: ${{ matrix.MIN_REQ || 1 }}
           PYVISTA_OFF_SCREEN: True
           MIN_REQ: ${{ matrix.MIN_REQ }}
+          FORCE_COLOR: 1
       - uses: actions/upload-artifact@v3
         with:
           name: upload pytest timing reports as json
@@ -176,7 +187,7 @@ jobs:
           pip install ./napari-from-github[all,testing]
 
       - name: Test
-        uses: GabrielBB/xvfb-action@v1
+        uses: aganders3/headless-gui@v1
         with:
           run: |
             python -m pytest --pyargs napari --color=yes
@@ -198,6 +209,6 @@ jobs:
           pip install setuptools tox tox-gh-actions
 
       - name: Test
-        uses: GabrielBB/xvfb-action@v1
+        uses: aganders3/headless-gui@v1
         with:
           run: tox -e py39-linux-pyside2-examples

.pre-commit-config.yaml

@@ -5,43 +5,26 @@ repos:
     -   id: absolufy-imports
         exclude: _vendor|vendored|examples
 -   repo: https://github.com/hadialqattan/pycln
-    rev: v2.1.2
+    rev: v2.1.3
     hooks:
     - id: pycln
--   repo: https://github.com/pycqa/isort
-    rev: 5.11.4
-    hooks:
-    - id: isort
-      exclude: _vendor|vendored|examples
 -   repo: https://github.com/psf/black
     rev: 22.12.0
     hooks:
     - id: black
       pass_filenames: true
       exclude: _vendor|vendored|examples
 -   repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.206
+    rev: v0.0.237
     hooks:
       - id: ruff
         exclude: _vendor|vendored
--   repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
-    hooks:
-    - id: flake8
-      additional_dependencies: [flake8-typing-imports]
-      pass_filenames: true
-      # this seems to need to be here in addition to setup.cfg
-      exclude: _vendor|vendored|__init__.py|examples
--   repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.1
-    hooks:
-    - id: pyupgrade
-      args: ["--py38-plus", "--keep-runtime-typing"]
-      exclude: _vendor|vendored|examples
 -   repo: https://github.com/seddonym/import-linter
-    rev: v1.6.0
+    rev: v1.7.0
     hooks:
     - id: import-linter
       stages: [manual]
-
-
+-   repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: 0.21.0
+    hooks:
+      - id: check-github-workflows

README.md

@@ -47,7 +47,8 @@ import napari
 viewer = napari.view_image(data.cells3d(), channel_axis=1, ndisplay=3)
 ```
 
-![napari viewer showing an image of an astronaut.](https://github.com/napari/docs/blob/main/docs/images/screenshot-add-image.png)
+![napari viewer with a multichannel image of cells displayed as two image layers: nuclei and membrane.](https://github.com/napari/docs/blob/main/docs/images/multichannel_cells.png)
+
 
 To use napari from inside a script, use `napari.run()`:
 

examples/3D_paths.py

@@ -12,8 +12,8 @@
 
 import numpy as np
 from skimage import data
-import napari
 
+import napari
 
 blobs = data.binary_blobs(
             length=128, blob_size_fraction=0.05, n_dim=3, volume_fraction=0.05

examples/3Dimage_plane_rendering.py

@@ -7,11 +7,12 @@
 
 .. tags:: visualization-advanced, gui, layers
 """
-import napari
 import numpy as np
-from napari.utils.translations import trans
 from skimage import data
 
+import napari
+from napari.utils.translations import trans
+
 viewer = napari.Viewer(ndisplay=3)
 
 # add a 3D image

examples/3d_kymograph_.py

@@ -7,10 +7,12 @@
 
 .. tags:: experimental
 """
+from itertools import product
+
 import numpy as np
-import napari
 from tqdm import tqdm
-from itertools import product
+
+import napari
 
 try:
     from omero.gateway import BlitzGateway
@@ -157,4 +159,4 @@ def IDR_fetch_image(image_id: int, progressbar: bool = True) -> np.ndarray:
 v.camera.angles = (-20, 23, -50)
 v.camera.zoom = 0.17
 
-napari.run()
+napari.run()

examples/README.rst

@@ -1,6 +1 @@
-Examples of napari usage.
 
-.. toctree::
-    :maxdepth: 1
-
-    ../_tags/tagsindex

examples/add-points-3d.py

@@ -8,10 +8,10 @@
 .. tags:: visualization-nD
 """
 
-from skimage import data
 from scipy import ndimage as ndi
-import napari
+from skimage import data
 
+import napari
 
 blobs = data.binary_blobs(
         length=128, volume_fraction=0.1, n_dim=3

examples/add_3D_image.py

@@ -8,8 +8,8 @@
 """
 
 from skimage import data
-import napari
 
+import napari
 
 blobs = data.binary_blobs(length=64, volume_fraction=0.1, n_dim=3).astype(
     float

examples/add_grayscale_image.py

@@ -7,10 +7,10 @@
 .. tags:: visualization-basic
 """
 
-from skimage import data
-import napari
 import numpy as np
+from skimage import data
 
+import napari
 
 # simulating a grayscale image here for testing contrast limits adjustments
 image = data.astronaut().mean(-1) * 100 + 100

examples/add_image.py

@@ -8,6 +8,7 @@
 """
 
 from skimage import data
+
 import napari
 
 # create the viewer with an image

examples/add_image_transformed.py

@@ -8,6 +8,7 @@
 """
 
 from skimage import data
+
 import napari
 
 # create the viewer with an image and transform (rotate) it

examples/add_labels.py

@@ -10,11 +10,11 @@
 
 from skimage import data
 from skimage.filters import threshold_otsu
-from skimage.segmentation import clear_border
 from skimage.measure import label
-from skimage.morphology import closing, square, remove_small_objects
-import napari
+from skimage.morphology import closing, remove_small_objects, square
+from skimage.segmentation import clear_border
 
+import napari
 
 image = data.coins()[50:-50, 50:-50]
 

examples/add_labels_with_features.py

@@ -8,14 +8,14 @@
 """
 
 
+import numpy as np
 from skimage import data
 from skimage.filters import threshold_otsu
-from skimage.segmentation import clear_border
 from skimage.measure import label
-from skimage.morphology import closing, square, remove_small_objects
-import numpy as np
-import napari
+from skimage.morphology import closing, remove_small_objects, square
+from skimage.segmentation import clear_border
 
+import napari
 
 image = data.coins()[50:-50, 50:-50]
 

examples/add_multiscale_image.py

@@ -7,11 +7,11 @@
 .. tags:: visualization-advanced
 """
 
+import numpy as np
 from skimage import data
 from skimage.transform import pyramid_gaussian
-import napari
-import numpy as np
 
+import napari
 
 # create multiscale from astronaut image
 base = np.tile(data.astronaut(), (8, 8, 1))