[pre-commit.ci] pre-commit autoupdate (#349)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.9.6 → v0.11.5](astral-sh/ruff-pre-commit@v0.9.6...v0.11.5)

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* add viewer close

* second attempt

* attempt fix asv benchmark

* revert

* attempt fix qt leak

* close viewer in interactive test

* close viewer in cli tests

* reattempt

* don't close viewer with plot

* attempt handling widget closing better

* add git log for debug

* remove git log

* additional close viewer

* ensure fetching main

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Wouter-Michiel Vierdag <[email protected]>

Author: pre-commit-ci[bot]

.github/workflows/test.yml

@@ -123,6 +123,9 @@ jobs:
           PR: 1 # prevents asv from running very compute-intensive benchmarks
           PIP_CONSTRAINT: ${{ github.workspace }}/benchmarks/benchmark.txt
 
+      - name: Fetch main branch
+        run: git fetch origin main:main
+
       - name: Run benchmarks latest release
         # here we check if the benchmark on the latest release is not broken
         uses: aganders3/headless-gui@v2

.pre-commit-config.yaml

@@ -49,7 +49,7 @@ repos:
     hooks:
       - id: blacken-docs
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.6
+    rev: v0.11.5
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

README.md

@@ -81,8 +81,7 @@ Marconato, L., Palla, G., Yamauchi, K.A. et al. SpatialData: an open and univers
 [pip]: https://pypi.org/project/pip/
 [pypi]: https://pypi.org/
 [issue]: https://github.com/scverse/napari-spatialdata/issues
-
-[//]: # (numfocus-fiscal-sponsor-attribution)
+[//]: # "numfocus-fiscal-sponsor-attribution"
 
 napari-spatialdata is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).
 If you like scverse® and want to support our mission, please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.

tests/test_aaa.py

@@ -1,4 +1,5 @@
 import pytest
+from napari.viewer import Viewer
 
 from napari_spatialdata._model import DataModel
 from napari_spatialdata._scatterwidgets import PlotWidget
@@ -21,3 +22,4 @@ def test_initialization(plot_widget):
 def test_elementwidget(make_napari_viewer):
     _ = make_napari_viewer()
     assert 1 == 1
+    Viewer.close_all()

tests/test_cli.py

@@ -11,6 +11,7 @@ def test_view_exists():
     runner = CliRunner()
     result = runner.invoke(cli, ["view"])
     assert result.exit_code == 2  # Error because of missing argument
+    Viewer.close_all()
 
 
 def test_view_path_not_exists():
@@ -22,6 +23,8 @@ def test_view_path_not_exists():
         )
         assert result.exit_code == 1
 
+        Viewer.close_all()
+
 
 def test_view_path_is_dir():
     runner = CliRunner()

tests/test_interactive.py

@@ -48,15 +48,15 @@ def test_switch_coordinate_system(self, sdata_blobs: SpatialData):
         i.switch_coordinate_system("global")
         assert i._sdata_widget.coordinate_system_widget._system == "global"
         assert i._sdata_widget.elements_widget._elements
-        i._viewer.close()
+        Viewer.close_all()
 
 
 def test_plot_can_add_element_switch_cs(sdata_blobs: SpatialData):
     i = Interactive(sdata=sdata_blobs, headless=True)
     i.add_element(element="blobs_image", element_coordinate_system="global", view_element_system=True)
     assert i._sdata_widget.coordinate_system_widget._system == "global"
     assert i._viewer.layers[-1].visible
-    i._viewer.close()
+    Viewer.close_all()
 
 
 class TestInteractive(PlotTester, metaclass=PlotTesterMeta):
@@ -66,13 +66,13 @@ def test_get_layer_existing(self, sdata_blobs: SpatialData):
         layer = i.get_layer("blobs_image")
         assert layer is not None, "Expected to retrieve the blobs_image layer, but got None"
         assert layer.name == "blobs_image", f"Expected layer name 'blobs_image', got {layer.name}"
-        i._viewer.close()
+        Viewer.close_all()
 
     def test_get_layer_non_existing(self, sdata_blobs: SpatialData):
         i = Interactive(sdata=sdata_blobs, headless=True)
         layer = i.get_layer("non_existing_layer")
         assert layer is None, "Expected None for a non-existing layer, but got a layer"
-        i._viewer.close()
+        Viewer.close_all()
 
     def test_add_text_to_polygons(self, sdata_blobs: SpatialData):
         i = Interactive(sdata=sdata_blobs, headless=True)
@@ -85,7 +85,7 @@ def test_add_text_to_polygons(self, sdata_blobs: SpatialData):
         # Verify that text is added
         i.add_text_to_polygons(layer_name="blobs_polygons", text_annotations=text_annotations)
         assert polygon_layer.text is not None, "Text annotations were not added to the polygon layer"
-        i._viewer.close()
+        Viewer.close_all()
 
 
 @pytest.mark.skipif(ARM_PROBLEM, reason="Test will segfault on ARM with numpy < 2")
@@ -96,3 +96,4 @@ def test_load_data_in_thread(make_napari_viewer: Callable[[], Viewer], sdata_blo
     with qtbot.waitSignal(i._sdata_widget.worker_thread.finished):
         i.add_element(element="blobs_image", element_coordinate_system="global")
     assert "blobs_image" in viewer.layers
+    Viewer.close_all()

tests/test_scatterwidgets.py

@@ -25,12 +25,19 @@ def coordinates_are_equal(coords1, coords2, tol=1e-6):
 
 
 @pytest.fixture
-def plot_widget(qtbot):
+def plot_widget(qtbot, request):
     """Fixture for creating a PlotWidget instance."""
     model = DataModel()
     widget = PlotWidget(None, model)
     qtbot.addWidget(widget)
-    yield widget
+
+    def cleanup():
+        widget.close()
+        QtWidgets.QApplication.processEvents()  # flush events
+
+    request.addfinalizer(cleanup)
+
+    return widget
 
 
 def test_initialization(plot_widget):