Update napari to 0.6.2 and add bermuda (#368)

melonora · web-flow · commit 0429cf1ab2dc · 2025-07-04T11:22:01.000+02:00
* simplify conditional

* bump version, change to ctrl+l

* add bermuda

* add blog post

* correct doc reference

* use export_figure

* remove argument

* match type hint

* verify path

* update artefact path

* revert viewer theme change

* check readthedocs with pydanticv2

* constrain dask

* constrain dask

* attempt fix mac

* add warning

* change caplog index

* change access of deprecated _dock_widgets access
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -69,7 +69,7 @@ jobs:
         uses: actions/upload-artifact@v4
         with:
           name: plotting-results-${{ matrix.python-version }}-${{ matrix.platform }}
-          path: /home/runner/work/napari-spatialdata/napari-spatialdata/tests/plots/*
+          path: /Users/runner/work/napari-spatialdata/napari-spatialdata/tests/plots/generated/*
 
   test_benchmarks:
     name: test benchmarks
diff --git a/README.md b/README.md
@@ -17,8 +17,7 @@
 [link-pypi]: https://pypi.org/project/napari-spatialdata/
 
 This repository contains a napari plugin for interactively exploring and annotating
-SpatialData objects. Here you can find the [napari-spatialdata documentation]
-(https://spatialdata.scverse.org/projects/napari/en/stable/notebooks/spatialdata.html). `napari-spatialdata` is part of the `SpatialData` ecosystem. To learn more about SpatialData, please see the [spatialdata documentation](https://spatialdata.scverse.org/).
+SpatialData objects. Here you can find the [napari-spatialdata documentation](https://spatialdata.scverse.org/projects/napari/en/stable/notebooks/spatialdata.html). `napari-spatialdata` is part of the `SpatialData` ecosystem. To learn more about SpatialData, please see the [spatialdata documentation](https://spatialdata.scverse.org/).
 
 ## Installation
 
@@ -28,6 +27,13 @@ You can install `napari-spatialdata` via [pip]:
 
 The `all` command will install the qt bindings `PyQt5`.
 
+Napari now also includes multiple triangulation backends. These improve the speed by which a napari 'Shapes' layer gets
+loaded (this does not improve the speed of editing large numbers of shapes yet!). See also the napari
+[documentation](https://napari.org/stable/guides/triangulation.html) and already slightly older [blog post](https://napari.org/island-dispatch/blog/triangles_speedup_beta.html). For installation via
+pip:
+
+    pip install napari-spatialdata[all, bermuda]
+
 You can find more details on this in the [installation instructions](https://spatialdata.scverse.org/en/stable/installation.html).
 
 ## Using napari-spatialdata as default zarr reader
diff --git a/setup.cfg b/setup.cfg
@@ -37,11 +37,11 @@ install_requires =
     anndata
     click
     cycler
-    dask>=2024.4.1
+    dask>=2024.4.1,<=2024.11.2
     geopandas
     loguru
     matplotlib
-    napari>=0.4.19.post1,<0.5.6
+    napari>=0.6.2
     napari-matplotlib
     numba
     numpy
@@ -66,6 +66,9 @@ package_dir =
 
 
 [options.extras_require]
+bermuda =
+    bermuda
+
 test =
     loguru
     pytest
@@ -92,7 +95,7 @@ doc =
     squidpy
 
 readthedocs =
-	pydantic<2
+	pydantic>2
 
 # this is just to trigger pip to check for pre-releases as well
 pre =
diff --git a/src/napari_spatialdata/_view.py b/src/napari_spatialdata/_view.py
@@ -426,7 +426,7 @@ def __init__(self, napari_viewer: Viewer, model: DataModel | None = None) -> Non
         super().__init__()
 
         self._viewer = napari_viewer
-        self._model = model if model else napari_viewer.window._dock_widgets["SpatialData"].widget().viewer_model._model
+        self._model = model if model else napari_viewer.window.dock_widgets["SpatialData"].viewer_model.model
 
         self._select_layer()
         self._viewer.layers.selection.events.changed.connect(self._select_layer)
diff --git a/src/napari_spatialdata/_viewer.py b/src/napari_spatialdata/_viewer.py
@@ -52,6 +52,12 @@ def __init__(self, viewer: Viewer, sdata: EventedList) -> None:
         self.sdata = sdata
         self._model = DataModel()
         self._layer_event_caches: dict[str, list[dict[str, Any]]] = {}
+        self.viewer.bind_key("Ctrl-L", self._inherit_metadata, overwrite=True)
+
+        logger.warning(
+            "Due to Shift-L being used as shortcut in napari, it is being deprecated and might not link a new layer"
+            " to an existing SpatialData object in the viewer. Please use ⌘-L on MacOS or else Ctrl-L.",
+        )
         self.viewer.bind_key("Shift-L", self._inherit_metadata, overwrite=True)
         self.viewer.bind_key("Shift-E", self._save_to_sdata, overwrite=True)
         self.viewer.layers.events.inserted.connect(self._on_layer_insert)
diff --git a/src/napari_spatialdata/utils/_test_utils.py b/src/napari_spatialdata/utils/_test_utils.py
@@ -71,26 +71,22 @@ def click_list_widget_item(
             raise ValueError(f"{click} is not a valid click")
 
 
-def take_screenshot(viewer: napari.Viewer, canvas_only: bool = False) -> ArrayLike | Any:
-    """Take screenshot of the Napari viewer.
+def export_figure(viewer: napari.Viewer) -> ArrayLike | Any:
+    """Export figure from the data displayed in the Napari viewer.
 
     Parameters
     ----------
     viewer
         Instance of napari Viewer.
-    canvas_only
-        If True, only the canvas is saved, not the viewer window.
 
     Returns
     -------
-    The screenshot as an array.
+    The exported figure as an array.
     """
-    logger.info("Taking screenshot of viewer")
-    # to distinguish between the black of the image background and the black of the napari background (now white)
-    # TODO (melonora): remove when napari allows for getting rid of margins.
+    logger.info("Export figure of data in viewer canvas")
     old_theme = viewer.theme
     viewer.theme = "light"
-    interactive_screenshot = viewer.screenshot(canvas_only=canvas_only, size=(202, 284))
+    interactive_screenshot = viewer.export_figure()
     viewer.theme = old_theme
     viewer.close()
 
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -22,7 +22,7 @@
 from spatialdata.datasets import blobs
 from spatialdata.models import TableModel
 
-from napari_spatialdata.utils._test_utils import save_image, take_screenshot
+from napari_spatialdata.utils._test_utils import export_figure, save_image
 
 HERE: Path = Path(__file__).parent
 
@@ -214,7 +214,7 @@ def compare(cls, basename: str, tolerance: float | None = None):
         out_path = ACTUAL / f"{basename}.png"
 
         viewer = napari.current_viewer()
-        save_image(take_screenshot(viewer, canvas_only=True), out_path)
+        save_image(export_figure(viewer), str(out_path))
 
         if tolerance is None:
             # see https://github.com/theislab/squidpy/pull/302
diff --git a/tests/plots/groundtruth/Images_can_add_element_image.png b/tests/plots/groundtruth/Images_can_add_element_image.png
diff --git a/tests/plots/groundtruth/Images_can_add_element_label.png b/tests/plots/groundtruth/Images_can_add_element_label.png
diff --git a/tests/plots/groundtruth/Images_can_add_element_multiple.png b/tests/plots/groundtruth/Images_can_add_element_multiple.png
diff --git a/tests/test_spatialdata.py b/tests/test_spatialdata.py
@@ -133,7 +133,7 @@ def test_sdatawidget_points(caplog, make_napari_viewer: Any, blobs_extra_cs: Spa
     with caplog.at_level(logging.INFO):
         assert (
             "Subsampling points because the number of points exceeds the currently supported 400."
-            in caplog.records[0].message
+            in caplog.records[1].message
         )
     assert widget.viewer_model.viewer.layers[1].metadata.get("adata").n_obs == 400
     del blobs_extra_cs.points["many_points"]
diff --git a/tests/test_viewer.py b/tests/test_viewer.py
@@ -1,4 +1,5 @@
 import re
+import sys
 from pathlib import Path
 
 import numpy as np
@@ -32,7 +33,10 @@ def test_metadata_inheritance(qtbot, make_napari_viewer: any):
     layers = widget.viewer_model.viewer.layers
     sdatas = [layer.metadata["sdata"] for layer in layers if "sdata" in layer.metadata]
     assert all(sdatas[0] is sdata for sdata in sdatas[1:])
-    qtbot.keyPress(viewer.window._qt_viewer, Qt.Key_L, Qt.ShiftModifier)
+    if sys.platform == "darwin":
+        qtbot.keyPress(viewer.window._qt_viewer, Qt.Key_L, Qt.MetaModifier)
+    else:
+        qtbot.keyPress(viewer.window._qt_viewer, Qt.Key_L, Qt.ControlModifier)
 
     # Now we did let the shapes layer inherit sdata from another layer. The number of unique spatialdata objects
     # should still be one.
