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

.github/workflows/test_prereleases.yml

@@ -79,13 +79,14 @@ jobs:
         uses: aganders3/headless-gui@v2
         timeout-minutes: 60
         with:
-          run: python -m tox -v --pre
+          run: python -m tox run -v -- -v
         env:
           PLATFORM: ${{ matrix.platform }}
           PYVISTA_OFF_SCREEN: True  # required for opengl on windows
           NAPARI: latest
           BACKEND: PyQt5
           PIP_CONSTRAINT: requirements/pre_test_problematic_version.txt
+          PIP_PRE: 1
 
       # If something goes wrong, we can open an issue in the repo
       - name: Report Failures

.pre-commit-config.yaml

@@ -20,7 +20,7 @@ repos:
     - id: debug-statements
     - id: mixed-line-ending
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.7
+    rev: v0.6.3
     hooks:
       - id: ruff
 -   repo: https://github.com/pre-commit/pygrep-hooks
@@ -39,7 +39,7 @@ repos:
           - mdformat-toc
 
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: 'v1.11.1'  # Use the sha / tag you want to point at
+    rev: 'v1.11.2'  # Use the sha / tag you want to point at
     hooks:
     -   id: mypy
         files: ^package/PartSegImage/.+\.py

package/PartSegImage/tifffile_fixes.py

@@ -19,7 +19,7 @@ def asarray(self, *args, **kwargs):
         self.parent.report_func()
         return res
 
-    def _dummy_report_func(self):  # noqa: ARG001
+    def _dummy_report_func(self):
         """dummy function for report_func"""
 
     TiffFile.report_func = _dummy_report_func

package/tests/conftest.py

@@ -45,7 +45,7 @@ def bundle_test_dir():
     return Path(os.path.join(os.path.dirname(__file__), "test_data"))
 
 
-@pytest.fixture()
+@pytest.fixture
 def image(tmp_path):
     data = np.zeros([20, 20, 20, 2], dtype=np.uint16)
     data[10:-1, 1:-1, 1:-1, 0] = 20
@@ -56,7 +56,7 @@ def image(tmp_path):
     return Image(data, (10**-3, 10**-3, 10**-3), axes_order="ZYXC", file_path=str(tmp_path / "test.tiff"))
 
 
-@pytest.fixture()
+@pytest.fixture
 def image2(image, tmp_path):
     data = np.zeros([20, 20, 20, 1], dtype=np.uint8)
     data[10:-1, 1:-1, 1:-1, 0] = 20
@@ -65,14 +65,14 @@ def image2(image, tmp_path):
     return img
 
 
-@pytest.fixture()
+@pytest.fixture
 def image2d(tmp_path):
     data = np.zeros([20, 20], dtype=np.uint8)
     data[10:-1, 1:-1] = 20
     return Image(data, (10**-3, 10**-3), axes_order="YX", file_path=str(tmp_path / "test.tiff"))
 
 
-@pytest.fixture()
+@pytest.fixture
 def stack_image():
     data = np.zeros([20, 40, 40, 2], dtype=np.uint8)
     for x, y in itertools.product([0, 20], repeat=2):
@@ -85,7 +85,7 @@ def stack_image():
     return MaskProjectTuple("test_path", Image(data, (2, 1, 1), axes_order="ZYXC", file_path="test_path"))
 
 
-@pytest.fixture()
+@pytest.fixture
 def algorithm_parameters():
     algorithm_parameters = {
         "algorithm_name": "Lower threshold",
@@ -100,7 +100,7 @@ def algorithm_parameters():
     return deepcopy(algorithm_parameters)
 
 
-@pytest.fixture()
+@pytest.fixture
 def roi_extraction_profile():
     return ROIExtractionProfile(
         name="test",
@@ -109,7 +109,7 @@ def roi_extraction_profile():
     )
 
 
-@pytest.fixture()
+@pytest.fixture
 def mask_segmentation_parameters():
     return ROIExtractionProfile(
         name="",
@@ -128,7 +128,7 @@ def mask_segmentation_parameters():
     )
 
 
-@pytest.fixture()
+@pytest.fixture
 def stack_segmentation1(stack_image: MaskProjectTuple, mask_segmentation_parameters):
     data = np.zeros([20, 40, 40], dtype=np.uint8)
     for i, (x, y) in enumerate(itertools.product([0, 20], repeat=2), start=1):
@@ -140,7 +140,7 @@ def stack_segmentation1(stack_image: MaskProjectTuple, mask_segmentation_paramet
     )
 
 
-@pytest.fixture()
+@pytest.fixture
 def analysis_segmentation(stack_image: MaskProjectTuple):
     data = np.zeros([20, 40, 40], dtype=np.uint8)
     for i, (x, y) in enumerate(itertools.product([0, 20], repeat=2), start=1):
@@ -149,13 +149,13 @@ def analysis_segmentation(stack_image: MaskProjectTuple):
     return ProjectTuple(file_path=stack_image.file_path, image=stack_image.image, roi_info=data)
 
 
-@pytest.fixture()
+@pytest.fixture
 def analysis_segmentation2(analysis_segmentation: ProjectTuple):
     mask = (analysis_segmentation.roi_info.roi > 0).astype(np.uint8)
     return dataclasses.replace(analysis_segmentation, mask=mask)
 
 
-@pytest.fixture()
+@pytest.fixture
 def stack_segmentation2(stack_image: MaskProjectTuple, mask_segmentation_parameters):
     data = np.zeros([20, 40, 40], dtype=np.uint8)
     for i, (x, y) in enumerate(itertools.product([0, 20], repeat=2), start=1):
@@ -168,12 +168,12 @@ def stack_segmentation2(stack_image: MaskProjectTuple, mask_segmentation_paramet
     )
 
 
-@pytest.fixture()
+@pytest.fixture
 def mask_property():
     return MaskProperty.simple_mask()
 
 
-@pytest.fixture()
+@pytest.fixture
 def mask_property_non_default():
     return MaskProperty(
         dilate=RadiusType.R2D,
@@ -186,7 +186,7 @@ def mask_property_non_default():
     )
 
 
-@pytest.fixture()
+@pytest.fixture
 def measurement_profiles():
     statistics = [
         MeasurementEntry(
@@ -221,14 +221,14 @@ def measurement_profiles():
     )
 
 
-@pytest.fixture()
+@pytest.fixture
 def border_rim_profile():
     return ROIExtractionProfile(
         name="border_profile", algorithm=BorderRim.get_name(), values=BorderRim.get_default_values()
     )
 
 
-@pytest.fixture()
+@pytest.fixture
 def lower_threshold_profile():
     return ROIExtractionProfile(
         name="lower_profile",
@@ -237,7 +237,7 @@ def lower_threshold_profile():
     )
 
 
-@pytest.fixture()
+@pytest.fixture
 def mask_threshold_profile():
     return ROIExtractionProfile(
         name="mask_profile",
@@ -246,7 +246,7 @@ def mask_threshold_profile():
     )
 
 
-@pytest.fixture()
+@pytest.fixture
 def sample_pipeline(border_rim_profile, lower_threshold_profile, mask_property):
     return SegmentationPipeline(
         name="sample_pipeline",
@@ -255,7 +255,7 @@ def sample_pipeline(border_rim_profile, lower_threshold_profile, mask_property):
     )
 
 
-@pytest.fixture()
+@pytest.fixture
 def sample_pipeline2(border_rim_profile, lower_threshold_profile, mask_property):
     return SegmentationPipeline(
         name="sample_pipeline2",
@@ -264,7 +264,7 @@ def sample_pipeline2(border_rim_profile, lower_threshold_profile, mask_property)
     )
 
 
-@pytest.fixture()
+@pytest.fixture
 def history_element(image, lower_threshold_profile):
     roi = np.zeros(image.shape, dtype=np.uint8)
     roi[0, 2:10] = 1

package/tests/test_PartSeg/conftest.py

@@ -11,14 +11,14 @@
 from PartSeg.common_gui import napari_image_view
 
 
-@pytest.fixture()
+@pytest.fixture
 def base_settings(image, tmp_path, measurement_profiles):
     settings = BaseSettings(tmp_path)
     settings.image = image
     return settings
 
 
-@pytest.fixture()
+@pytest.fixture
 def part_settings(image, tmp_path, measurement_profiles):
     settings = PartSettings(tmp_path)
     settings.image = image
@@ -27,7 +27,7 @@ def part_settings(image, tmp_path, measurement_profiles):
     return settings
 
 
-@pytest.fixture()
+@pytest.fixture
 def stack_settings(tmp_path, image):
     settings = StackSettings(tmp_path)
     settings.image = image
@@ -37,7 +37,7 @@ def stack_settings(tmp_path, image):
     chose.deleteLater()
 
 
-@pytest.fixture()
+@pytest.fixture
 def part_settings_with_project(image, analysis_segmentation2, tmp_path):
     settings = PartSettings(tmp_path)
     settings.image = image

package/tests/test_PartSeg/roi_analysis/test_batch.py

@@ -5,7 +5,7 @@
 from PartSegCore.analysis.calculation_plan import CalculationPlan, CalculationTree, MaskSuffix, RootType
 
 
-@pytest.fixture()
+@pytest.fixture
 def calculation_prepare(tmp_path, part_settings, qtbot):
     def _constructor(file_list, calculation_plan=None):
         if calculation_plan is None:

package/tests/test_PartSeg/roi_analysis/test_export_batch.py

@@ -18,7 +18,7 @@
 )
 
 
-@pytest.fixture()
+@pytest.fixture
 def _dummy_tiffs(tmp_path):
     for i in range(1, 11):
         (tmp_path / f"stack1_component{i}.tif").touch()
@@ -74,7 +74,7 @@ def test_fail_export_empty_excel(tmp_path):
         list(export_to_archive(tmp_path / "empty.xlsx", tmp_path, tmp_path / "arch.tar.gz"))
 
 
-@pytest.fixture()
+@pytest.fixture
 def zenodo_kwargs():
     return {
         "zenodo_token": "sample_token",

package/tests/test_PartSeg/roi_analysis/test_image_view.py

@@ -7,7 +7,7 @@
 from PartSegCore.roi_info import ROIInfo
 
 
-@pytest.mark.windows_ci_skip()
+@pytest.mark.windows_ci_skip
 def test_synchronize(part_settings, image2, qtbot):
     prop = ChannelProperty(part_settings, "test1")
     view1 = ResultImageView(part_settings, prop, "test1")
@@ -36,7 +36,7 @@ def test_synchronize(part_settings, image2, qtbot):
     view2.hide()
 
 
-@pytest.mark.windows_ci_skip()
+@pytest.mark.windows_ci_skip
 def test_synchronize_change_image_dim(part_settings, image2, image2d, qtbot):
     part_settings.image = image2d
     prop = ChannelProperty(part_settings, "test1")
@@ -101,7 +101,7 @@ def test_setting_properties(self, part_settings, image2, qtbot):
         part_settings.set_in_profile("test.image_state.only_border", False)
         assert not view.only_border.isChecked()
 
-    @pytest.mark.windows_ci_skip()
+    @pytest.mark.windows_ci_skip
     def test_resize(self, part_settings, image2, qtbot):
         prop = ChannelProperty(part_settings, "test")
         view = ResultImageView(part_settings, prop, "test")
@@ -118,7 +118,7 @@ def test_resize(self, part_settings, image2, qtbot):
         assert view.btn_layout2.count() == 2
         view.hide()
 
-    @pytest.mark.windows_ci_skip()
+    @pytest.mark.windows_ci_skip
     def test_with_roi_alternatives(self, part_settings, image2, qtbot):
         prop = ChannelProperty(part_settings, "test")
         view = ResultImageView(part_settings, prop, "test")

package/tests/test_PartSeg/roi_analysis/test_main_window.py

@@ -12,7 +12,7 @@
 
 class TestAnalysisMainWindow:
     # @pytest.mark.skipif((platform.system() == "Linux") and CI_BUILD, reason="debug test fail")
-    @pytest.mark.pyside_skip()
+    @pytest.mark.pyside_skip
     def test_opening(self, qtbot, tmpdir):
         main_window = MainWindow(tmpdir, initial_image=False)
         qtbot.addWidget(main_window)
@@ -22,15 +22,15 @@ def test_opening(self, qtbot, tmpdir):
         main_window.advanced_window.close()
         qtbot.wait(50)
 
-    @pytest.mark.pyside_skip()
+    @pytest.mark.pyside_skip
     def test_change_theme(self, qtbot, tmpdir):
         main_window = MainWindow(tmpdir, initial_image=False)
         qtbot.addWidget(main_window)
         assert main_window.raw_image.viewer.theme == "light"
         main_window.settings.theme_name = "dark"
         assert main_window.raw_image.viewer.theme == "dark"
 
-    @pytest.mark.pyside_skip()
+    @pytest.mark.pyside_skip
     def test_scale_bar(self, qtbot, tmpdir):
         main_window = MainWindow(tmpdir, initial_image=False)
         qtbot.addWidget(main_window)
@@ -51,7 +51,7 @@ def test_get_project_info(self, image, tmp_path):
         assert set(res.roi_info.bound_info) == {1}
 
 
-@pytest.fixture()
+@pytest.fixture
 def analysis_options(qtbot, part_settings):
     ch_property = ChannelProperty(part_settings, "test")
     qtbot.addWidget(ch_property)

package/tests/test_PartSeg/roi_mask/test_batch.py

@@ -4,7 +4,7 @@
 from PartSegCore.mask.io_functions import SaveROIOptions
 
 
-@pytest.fixture()
+@pytest.fixture
 def batch_task(stack_image, mask_threshold_profile):
     return BatchTask(stack_image, mask_threshold_profile, None)
 

package/tests/test_PartSeg/roi_mask/test_main_window.py

@@ -9,21 +9,21 @@
 
 class TestMaskMainWindow:
     # @pytest.mark.skipif((platform.system() == "Linux") and CI_BUILD, reason="vispy problem")
-    @pytest.mark.pyside_skip()
+    @pytest.mark.pyside_skip
     def test_opening(self, qtbot, tmpdir):
         main_window = MainWindow(tmpdir, initial_image=False)
         qtbot.addWidget(main_window)
         qtbot.wait(50)
 
-    @pytest.mark.pyside_skip()
+    @pytest.mark.pyside_skip
     def test_change_theme(self, qtbot, tmpdir):
         main_window = MainWindow(tmpdir, initial_image=False)
         qtbot.addWidget(main_window)
         assert main_window.image_view.viewer.theme == "light"
         main_window.settings.theme_name = "dark"
         assert main_window.image_view.viewer.theme == "dark"
 
-    @pytest.mark.pyside_skip()
+    @pytest.mark.pyside_skip
     def test_scale_bar(self, qtbot, tmpdir):
         main_window = MainWindow(tmpdir, initial_image=False)
         qtbot.addWidget(main_window)
@@ -43,7 +43,7 @@ def test_get_project_info(self, image, tmp_path):
         res = MainWindow.get_project_info(str(tmp_path / "test.tiff"), image, ROIInfo(roi))
         assert res.roi_extraction_parameters == {1: None}
 
-    @pytest.mark.pyside_skip()
+    @pytest.mark.pyside_skip
     def test_window_title(self, tmpdir, image, image2, qtbot):
         main_window = MainWindow(tmpdir, initial_image=False)
         qtbot.addWidget(main_window)