fix(tests): fix tests for napari widgets, fix #374 (#376)

* Fix: Refactor test_widget_open_file to use qtbot for consistent GUI testing

* style(pre-commit.ci): auto fixes

* fix(tests): fix tests for napari widgets, fix #374

Napari widget tests hang before

---------

Co-authored-by: adambasha0 <readam@adbasha>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Qin Yu <[email protected]>

tests/widgets/test_widget_nuc_fix.py

@@ -1,26 +1,18 @@
-import os
-
-import napari
-import pytest
 from magicgui import magicgui
 from napari.types import LayerDataTuple
 
 from plantseg.core.image import PlantSegImage
 from plantseg.viewer_napari.widgets.dataprocessing import widget_fix_over_under_segmentation_from_nuclei
 from tests.tasks.dataprocessing.test_advanced_dataprocessing_tasks import complex_test_PlantSegImages
 
-IN_GITHUB_ACTIONS = os.getenv("GITHUB_ACTIONS") == "true"  # set to true in GitHub Actions by default to skip CUDA tests
-
 
 @magicgui
 def widget_add_image(image: PlantSegImage) -> LayerDataTuple:
     """Add a plantseg.core.image.PlantSegImage to napari viewer as a napari.layers.Layer."""
     return image.to_napari_layer_tuple()
 
 
-@pytest.mark.skip(reason="Test hangs even if scheduled task completes.")
-@pytest.mark.skipif(IN_GITHUB_ACTIONS, reason="GUI tests hang in GitHub Actions.")
-def test_widget_fix_over_under_segmentation_from_nuclei(make_napari_viewer_proxy, complex_test_PlantSegImages):
+def test_widget_fix_over_under_segmentation_from_nuclei(qtbot, make_napari_viewer_proxy, complex_test_PlantSegImages):
     """
     Test the widget_fix_over_under_segmentation_from_nuclei function in a napari viewer environment.
 
@@ -47,16 +39,16 @@ def test_widget_fix_over_under_segmentation_from_nuclei(make_napari_viewer_proxy
         widget_add_image(boundary_pmap)
 
     # Run the widget for correcting segmentation
+    count_layers = len(viewer.layers)
     widget_fix_over_under_segmentation_from_nuclei(
         segmentation_cells=viewer.layers[cell_seg.name],
         segmentation_nuclei=viewer.layers[nuclei_seg.name],
         boundary_pmaps=viewer.layers[boundary_pmap.name] if boundary_pmap is not None else None,
         threshold=(30, 60),  # Threshold range as percentages (30% merge, 60% split)
         quantile=(10, 90),  # Quantile range as percentages (10%-90%)
     )
-    napari.run()
+    qtbot.waitUntil(lambda: count_layers < len(viewer.layers), timeout=20000)
 
-    # Validate the corrected segmentation layer properties
-    corrected_layer = viewer.layers[f"{cell_seg.name}_nuc_fix"]
-    assert corrected_layer.data.shape == cell_seg.data.shape, "Corrected layer shape is incorrect."
-    assert corrected_layer.data.dtype == cell_seg.data.dtype, "Corrected layer data type is incorrect."
+    corrected_layer = viewer.layers[f"{cell_seg.name}_nuc_fixed"]
+    assert corrected_layer.data.shape == cell_seg.shape, "Corrected layer shape is incorrect."
+    assert corrected_layer.data.dtype == cell_seg._data.dtype, "Corrected layer data type is incorrect."

tests/widgets/test_widget_open_file.py

@@ -1,25 +1,19 @@
-import os
-
-import napari
 import numpy as np
-import pytest
 
 from plantseg.io.h5 import create_h5
 from plantseg.io.voxelsize import VoxelSize
 from plantseg.viewer_napari.widgets.io import PathMode, widget_open_file
 
-IN_GITHUB_ACTIONS = os.getenv("GITHUB_ACTIONS") == "true"  # set to true in GitHub Actions by default to skip CUDA tests
-
 
-@pytest.mark.skipif(IN_GITHUB_ACTIONS, reason="GUI tests hangs in GitHub Actions.")
-def test_widget_open_file(make_napari_viewer_proxy, path_h5):
+def test_widget_open_file(qtbot, make_napari_viewer_proxy, path_h5):
     viewer = make_napari_viewer_proxy()
     shape = (10, 10, 10)
     data = np.random.rand(*shape).astype(np.float32)
     voxel_size = VoxelSize(voxels_size=(0.235, 0.15, 0.15))
     create_h5(path_h5, data, "raw", voxel_size=voxel_size)
     create_h5(path_h5, data, "prob", voxel_size=voxel_size)
 
+    count_layers = len(viewer.layers)
     widget_open_file(
         path_mode=PathMode.FILE.value,
         path=path_h5,
@@ -29,7 +23,7 @@ def test_widget_open_file(make_napari_viewer_proxy, path_h5):
         stack_layout="ZYX",
         update_other_widgets=False,
     )
-    napari.run()
+    qtbot.waitUntil(lambda: count_layers < len(viewer.layers), timeout=20000)
 
     assert viewer.layers[0].name == "test_raw"
     assert viewer.layers[0].data.shape == shape

tests/widgets/test_widget_preprocessing.py

@@ -1,6 +1,3 @@
-import os
-
-import napari
 import numpy as np
 import pytest
 from magicgui import magicgui
@@ -10,8 +7,6 @@
 from plantseg.io.voxelsize import VoxelSize
 from plantseg.viewer_napari.widgets.dataprocessing import RescaleModes, widget_rescaling
 
-IN_GITHUB_ACTIONS = os.getenv("GITHUB_ACTIONS") == "true"  # set to true in GitHub Actions by default to skip CUDA tests
-
 
 def create_layer_name(name: str, suffix: str):
     return f"{name}_{suffix}"
@@ -51,56 +46,58 @@ def widget_add_image(image: PlantSegImage) -> LayerDataTuple:
     return image.to_napari_layer_tuple()
 
 
-@pytest.mark.skipif(IN_GITHUB_ACTIONS, reason="GUI tests hangs in GitHub Actions.")
 class TestWidgetRescaling:
-    def test_rescaling_from_factor(self, make_napari_viewer_proxy, sample_image):
+    def test_rescaling_from_factor(self, qtbot, make_napari_viewer_proxy, sample_image):
         viewer = make_napari_viewer_proxy()
         widget_add_image(sample_image)
 
         factor = 0.5
+        count_layers = len(viewer.layers)
         widget_rescaling(
             image=viewer.layers[sample_image.name],
             mode=RescaleModes.FROM_FACTOR,
             rescaling_factor=(factor, factor, factor),
             update_other_widgets=False,
         )
-        napari.run()
+        qtbot.waitUntil(lambda: count_layers < len(viewer.layers), timeout=20000)
 
         old_layer = viewer.layers[sample_image.name]
         new_layer = viewer.layers[sample_image.name + '_rescaled']
         np.testing.assert_allclose(new_layer.data.shape, np.multiply(old_layer.data.shape, factor), rtol=1e-5)
         np.testing.assert_allclose(np.multiply(new_layer.scale, factor), old_layer.scale, rtol=1e-5)
 
-    def test_rescaling_to_layer_voxel_size(self, make_napari_viewer_proxy, sample_image, sample_label):
+    def test_rescaling_to_layer_voxel_size(self, qtbot, make_napari_viewer_proxy, sample_image, sample_label):
         viewer = make_napari_viewer_proxy()
         widget_add_image(sample_image)
         widget_add_image(sample_label)
 
+        count_layers = len(viewer.layers)
         widget_rescaling(
             image=viewer.layers[sample_image.name],
             mode=RescaleModes.TO_LAYER_VOXEL_SIZE,
             reference_layer=viewer.layers[sample_label.name],
             update_other_widgets=False,
         )
-        napari.run()
+        qtbot.waitUntil(lambda: count_layers < len(viewer.layers), timeout=20000)
 
         reference_layer = viewer.layers[sample_label.name]
         new_layer = viewer.layers[sample_image.name + '_rescaled']
 
         np.testing.assert_allclose(new_layer.data.shape, reference_layer.data.shape, rtol=1e-5)
         np.testing.assert_allclose(new_layer.scale, reference_layer.scale, rtol=1e-5)
 
-    def test_rescaling_to_model_voxel_size(self, make_napari_viewer_proxy, sample_image):
+    def test_rescaling_to_model_voxel_size(self, qtbot, make_napari_viewer_proxy, sample_image):
         viewer = make_napari_viewer_proxy()
         widget_add_image(sample_image)
 
+        count_layers = len(viewer.layers)
         widget_rescaling(
             image=viewer.layers[sample_image.name],
             mode=RescaleModes.TO_MODEL_VOXEL_SIZE,
             reference_model='PlantSeg_3Dnuc_platinum',  # voxel size: (0.2837, 0.1268, 0.1268)
             update_other_widgets=False,
         )
-        napari.run()
+        qtbot.waitUntil(lambda: count_layers < len(viewer.layers), timeout=20000)
 
         old_layer = viewer.layers[sample_image.name]
         new_layer = viewer.layers[sample_image.name + '_rescaled']
@@ -116,18 +113,19 @@ def test_rescaling_to_model_voxel_size(self, make_napari_viewer_proxy, sample_im
 
         np.testing.assert_allclose(new_shape * new_scale, old_shape * old_scale, atol=0.1)
 
-    def test_rescaling_to_voxel_size(self, make_napari_viewer_proxy, sample_image):
+    def test_rescaling_to_voxel_size(self, qtbot, make_napari_viewer_proxy, sample_image):
         viewer = make_napari_viewer_proxy()
         widget_add_image(sample_image)
 
         expected_scale = (0.5, 0.5, 0.5)  # target voxel size
+        count_layers = len(viewer.layers)
         widget_rescaling(
             image=viewer.layers[sample_image.name],
             mode=RescaleModes.TO_VOXEL_SIZE,
             out_voxel_size=expected_scale,
             update_other_widgets=False,
         )
-        napari.run()
+        qtbot.waitUntil(lambda: count_layers < len(viewer.layers), timeout=20000)
 
         old_layer = viewer.layers[sample_image.name]
         new_layer = viewer.layers[sample_image.name + '_rescaled']
@@ -138,18 +136,19 @@ def test_rescaling_to_voxel_size(self, make_napari_viewer_proxy, sample_image):
         np.testing.assert_allclose(new_layer.data.shape, expected_shape, rtol=1e-5)
         np.testing.assert_allclose(new_layer.scale, expected_scale, rtol=1e-5)
 
-    def test_rescaling_to_layer_shape(self, make_napari_viewer_proxy, sample_image, sample_label):
+    def test_rescaling_to_layer_shape(self, qtbot, make_napari_viewer_proxy, sample_image, sample_label):
         viewer = make_napari_viewer_proxy()
         widget_add_image(sample_image)
         widget_add_image(sample_label)
 
+        count_layers = len(viewer.layers)
         widget_rescaling(
             image=viewer.layers[sample_image.name],
             mode=RescaleModes.TO_LAYER_SHAPE,
             reference_layer=viewer.layers[sample_label.name],
             update_other_widgets=False,
         )
-        napari.run()
+        qtbot.waitUntil(lambda: count_layers < len(viewer.layers), timeout=20000)
 
         reference_layer = viewer.layers[sample_label.name]
         new_layer = viewer.layers[sample_image.name + '_reshaped']
@@ -159,18 +158,19 @@ def test_rescaling_to_layer_shape(self, make_napari_viewer_proxy, sample_image,
         # In our special case in this test, yes, the scale should be the same
         np.testing.assert_allclose(new_layer.scale, reference_layer.scale, rtol=1e-5)
 
-    def test_rescaling_set_shape(self, make_napari_viewer_proxy, sample_image):
+    def test_rescaling_set_shape(self, qtbot, make_napari_viewer_proxy, sample_image):
         viewer = make_napari_viewer_proxy()
         widget_add_image(sample_image)
 
         target_shape = (20, 50, 50)
+        count_layers = len(viewer.layers)
         widget_rescaling(
             image=viewer.layers[sample_image.name],
             mode=RescaleModes.TO_SHAPE,
             reference_shape=target_shape,
             update_other_widgets=False,
         )
-        napari.run()
+        qtbot.waitUntil(lambda: count_layers < len(viewer.layers), timeout=20000)
 
         old_layer = viewer.layers[sample_image.name]
         new_layer = viewer.layers[sample_image.name + '_reshaped']
@@ -182,18 +182,19 @@ def test_rescaling_set_shape(self, make_napari_viewer_proxy, sample_image):
 
         np.testing.assert_allclose(new_layer.scale, expected_scale, rtol=1e-5)
 
-    def test_rescaling_set_voxel_size(self, make_napari_viewer_proxy, sample_image):
+    def test_rescaling_set_voxel_size(self, qtbot, make_napari_viewer_proxy, sample_image):
         viewer = make_napari_viewer_proxy()
         widget_add_image(sample_image)
 
         target_voxel_size = (2.0, 2.0, 2.0)
+        count_layers = len(viewer.layers)
         widget_rescaling(
             image=viewer.layers[sample_image.name],
             mode=RescaleModes.SET_VOXEL_SIZE,
             out_voxel_size=target_voxel_size,
             update_other_widgets=False,
         )
-        napari.run()
+        qtbot.waitUntil(lambda: count_layers < len(viewer.layers), timeout=20000)
 
         new_layer = viewer.layers[sample_image.name + '_set_voxel_size']
         np.testing.assert_allclose(new_layer.scale, target_voxel_size, rtol=1e-5)