[pre-commit.ci] pre-commit autoupdate + fix qt tests (#360)

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

updates:
- [github.com/pre-commit/mirrors-mypy: v1.15.0 → v1.17.1](pre-commit/mirrors-mypy@v1.15.0...v1.17.1)
- [github.com/pre-commit/pre-commit-hooks: v5.0.0 → v6.0.0](pre-commit/pre-commit-hooks@v5.0.0...v6.0.0)
- [github.com/astral-sh/ruff-pre-commit: v0.11.6 → v0.12.8](astral-sh/ruff-pre-commit@v0.11.6...v0.12.8)

* workaround qt test (command double registration)

* fix pre-commit

---------

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

Author: pre-commit-ci[bot]

.mypy.ini

@@ -1,7 +1,6 @@
 [mypy]
 mypy_path = napari-spatialdata
 python_version = 3.10
-plugins = numpy.typing.mypy_plugin
 
 ignore_errors = False
 warn_redundant_casts = True

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ default_stages:
 minimum_pre_commit_version: 2.9.3
 repos:
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.15.0
+    rev: v1.17.1
     hooks:
       - id: mypy
         additional_dependencies: [numpy>=1.23]
@@ -22,16 +22,16 @@ repos:
     hooks:
       - id: prettier
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: detect-private-key
       - id: check-merge-conflict
       - id: check-ast
       - id: check-symlinks
       - id: check-added-large-files
       - id: check-executables-have-shebangs
-      - id: fix-encoding-pragma
-        args: [--remove]
+      #      - id: fix-encoding-pragma
+      #        args: [--remove]
       - id: end-of-file-fixer
       - id: mixed-line-ending
         args: [--fix=lf]
@@ -49,7 +49,11 @@ repos:
     hooks:
       - id: blacken-docs
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.6
+    rev: v0.12.8
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.20.0
+    hooks:
+      - id: pyupgrade

src/napari_spatialdata/_model.py

@@ -246,7 +246,7 @@ def adata_layer(self) -> str | None:  # noqa: D102
         return self._adata_layer
 
     @adata_layer.setter
-    def adata_layer(self, adata_layer: str) -> None:
+    def adata_layer(self, adata_layer: str | None) -> None:
         self._adata_layer = adata_layer
 
     @property

src/napari_spatialdata/_scatterwidgets.py

@@ -114,7 +114,7 @@ def setComponent(self, text: int | str | None) -> None:
         elif self.getAttribute() == "obsm":
             if TYPE_CHECKING:
                 assert isinstance(text, int | str)
-            self.text = text  # type: ignore[assignment]
+            self.text = text
             super().setIndex(text)
 
     @property

src/napari_spatialdata/utils/_utils.py

@@ -487,7 +487,7 @@ def get_napari_version() -> packaging.version.Version:
 
 
 @contextmanager
-def block_signals(widget: QObject) -> Generator[None, None, None]:
+def block_signals(widget: QObject) -> Generator[None]:
     try:
         widget.blockSignals(True)
         yield

tests/test_cli.py

@@ -1,5 +1,6 @@
 from pathlib import Path
 
+import pytest
 from click.testing import CliRunner
 from napari.viewer import Viewer
 from spatialdata.datasets import blobs
@@ -14,6 +15,7 @@ def test_view_exists():
     Viewer.close_all()
 
 
+@pytest.mark.usefixtures("mock_app_model")
 def test_view_path_not_exists():
     runner = CliRunner()
     with runner.isolated_filesystem():
@@ -26,6 +28,7 @@ def test_view_path_not_exists():
         Viewer.close_all()
 
 
+@pytest.mark.usefixtures("mock_app_model")
 def test_view_path_is_dir():
     runner = CliRunner()
     with runner.isolated_filesystem():

tests/test_interactive.py

@@ -18,6 +18,7 @@
 )
 
 
+@pytest.mark.usefixtures("mock_app_model")
 class TestImages(PlotTester, metaclass=PlotTesterMeta):
     def test_plot_can_add_element_image(self, sdata_blobs: SpatialData):
         blobs_image = Image2DModel.parse(sdata_blobs["blobs_image"], c_coords=("r", "g", "b"))
@@ -51,6 +52,7 @@ def test_switch_coordinate_system(self, sdata_blobs: SpatialData):
         Viewer.close_all()
 
 
+@pytest.mark.usefixtures("mock_app_model")
 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)
@@ -59,6 +61,7 @@ def test_plot_can_add_element_switch_cs(sdata_blobs: SpatialData):
     Viewer.close_all()
 
 
+@pytest.mark.usefixtures("mock_app_model")
 class TestInteractive(PlotTester, metaclass=PlotTesterMeta):
     def test_get_layer_existing(self, sdata_blobs: SpatialData):
         i = Interactive(sdata=sdata_blobs, headless=True)

tests/test_scatterwidgets.py

@@ -7,6 +7,9 @@
 from napari_spatialdata._model import DataModel
 from napari_spatialdata._scatterwidgets import PlotWidget
 
+pytestmark = pytest.mark.usefixtures("mock_app_model")
+
+
 DATA_LEN = 100
 
 

tests/test_widgets.py

@@ -267,6 +267,7 @@ def test_layer_selection(make_napari_viewer: Any, image: ArrayLike, widget: Any,
     assert widget.model.adata.n_obs == 0
 
 
+@pytest.mark.usefixtures("mock_app_model")
 def test_export_no_rois(adata_labels):
     """Test export for no rois situation."""
 
@@ -277,6 +278,7 @@ def test_export_no_rois(adata_labels):
     assert scatter_widget.status_label.text() == "Status: No rois selected."
 
 
+@pytest.mark.usefixtures("mock_app_model")
 def test_export_no_name(adata_labels, mocker):
     """Test export - no column name provided."""
 
@@ -290,6 +292,7 @@ def test_export_no_name(adata_labels, mocker):
     assert scatter_widget._model.adata.obs.equals(adata_labels.obs)
 
 
+@pytest.mark.usefixtures("mock_app_model")
 def test_new_annotation(adata_labels, annotation_values, mocker):
     """Test export - adding a new annotation."""
 
@@ -304,6 +307,7 @@ def test_new_annotation(adata_labels, annotation_values, mocker):
     assert np.array_equal(scatter_widget._model.adata.obs.test, annotation_values)
 
 
+@pytest.mark.usefixtures("mock_app_model")
 def test_old_annotation(adata_labels, annotation_values, mocker):
     """Test updating existing annotation."""