fix tests (#20)

* fix those tests

src/arcos_gui/_tests/test_helper_functions.py

@@ -16,10 +16,11 @@
 from arcos_gui._main_widget import MainWindow
 
 
-def test_open_plugin(make_napari_viewer):
+def test_open_plugin(make_napari_viewer, qtbot):
     viewer = make_napari_viewer()
 
     plugin = open_plugin(viewer)
+    qtbot.addWidget(plugin)
 
     assert isinstance(plugin, MainWindow)
 
@@ -64,9 +65,10 @@ def test_load_sample_data_invalid_data(make_napari_viewer):
 )
 
 
-def test_load_dataframe(make_napari_viewer):
+def test_load_dataframe(make_napari_viewer, qtbot):
     viewer = make_napari_viewer()
     plugin = open_plugin(viewer)
+    qtbot.addWidget(plugin)
     load_dataframe(
         df=sample_df,
         frame_column="frame",
@@ -84,17 +86,19 @@ def test_load_dataframe(make_napari_viewer):
     assert plugin.data.original_data.value.empty is False
 
 
-def test_load_dataframe_with_columnpicker(make_napari_viewer):
+def test_load_dataframe_with_columnpicker(make_napari_viewer, qtbot):
     viewer = make_napari_viewer()
     plugin = open_plugin(viewer)
+    qtbot.addWidget(plugin)
     load_dataframe_with_columnpicker(df=sample_df, plugin=plugin)
     assert plugin._input_controller.picker.isVisibleTo(plugin)
     plugin._input_controller.picker.close()
 
 
-def test_filter_data(make_napari_viewer, capsys):
+def test_filter_data(make_napari_viewer, capsys, qtbot):
     viewer = make_napari_viewer()
     plugin = open_plugin(viewer)
+    qtbot.addWidget(plugin)
     plugin.data.columns.value.frame_column = "t"
     plugin.data.columns.value.x_column = "x"
     plugin.data.columns.value.y_column = "y"
@@ -114,6 +118,7 @@ def test_filter_data(make_napari_viewer, capsys):
 def test_run_binarization_only(make_napari_viewer, qtbot):
     viewer = make_napari_viewer()
     plugin = open_plugin(viewer)
+    qtbot.addWidget(plugin)
     plugin.data.columns.value.frame_column = "t"
     plugin.data.columns.value.x_column = "x"
     plugin.data.columns.value.y_column = "y"
@@ -143,6 +148,7 @@ def test_run_binarization_only(make_napari_viewer, qtbot):
 def test_run_arcos(make_napari_viewer, qtbot):
     viewer = make_napari_viewer()
     plugin = open_plugin(viewer)
+    qtbot.addWidget(plugin)
     plugin.data.columns.value.frame_column = "t"
     plugin.data.columns.value.x_column = "x"
     plugin.data.columns.value.y_column = "y"
@@ -172,9 +178,10 @@ def test_run_arcos(make_napari_viewer, qtbot):
     assert len(viewer.layers) == 4
 
 
-def test_get_arcos_output(make_napari_viewer):
+def test_get_arcos_output(make_napari_viewer, qtbot):
     viewer = make_napari_viewer()
     plugin = open_plugin(viewer)
+    qtbot.addWidget(plugin)
     # Mocking output and stats for the plugin. Replace with suitable mock data.
     mock_output = MagicMock(spec=pd.DataFrame)
     mock_stats = MagicMock(spec=pd.DataFrame)
@@ -186,8 +193,9 @@ def test_get_arcos_output(make_napari_viewer):
     assert stats == mock_stats
 
 
-def test_get_current_arcos_plugin(make_napari_viewer):
+def test_get_current_arcos_plugin(make_napari_viewer, qtbot):
     viewer = make_napari_viewer()
     plugin = open_plugin(viewer)
+    qtbot.addWidget(plugin)
     retrieved_plugin = get_current_arcos_plugin()
     assert retrieved_plugin == plugin

src/arcos_gui/_tests/test_main_widget.py

@@ -1,6 +1,5 @@
 from __future__ import annotations
 
-import gc
 from typing import TYPE_CHECKING
 from unittest.mock import patch
 
@@ -9,23 +8,20 @@
 from arcos_gui._main_widget import MainWindow
 from arcos_gui.processing._arcos_wrapper import calculate_arcos_stats
 from arcos_gui.tools._config import ARCOS_LAYERS
-from pytestqt.qtbot import QtBot
 
 if TYPE_CHECKING:
     import napari.viewer
+    from pytestqt.qtbot import QtBot
 
 
 @pytest.fixture()
-def dock_arcos_widget(make_napari_viewer, qtbot):
+def dock_arcos_widget(make_napari_viewer, qtbot: QtBot):
     from arcos_gui._main_widget import MainWindow
 
     viewer = make_napari_viewer()
     mywidget = MainWindow(viewer=viewer)
     qtbot.addWidget(mywidget)
-    yield viewer, mywidget, qtbot
-    mywidget.deleteLater()
-    viewer.close()
-    gc.collect()
+    return viewer, mywidget, qtbot
 
 
 @pytest.fixture()
@@ -214,8 +210,9 @@ def test_load_data_with_measurement_math(
     mywidget._input_controller.picker.additional_filter.setCurrentText("None")
     mywidget._input_controller.picker.measurement_math.setCurrentText("Add")
     # user clicks ok
-    with qtbot.waitSignal(mywidget._input_controller.loading_worker.finished):
-        mywidget._input_controller.picker.ok_button.click()
+    mywidget._input_controller.picker.ok_button.click()
+    qtbot.waitSignal(mywidget._input_controller.loading_worker.finished)
+    qtbot.waitUntil(lambda: mywidget.data.original_data.value.empty is False)
 
     columnames_list = mywidget.data.columns.value.pickablepickable_columns_names
     assert columnames_list == [
@@ -285,6 +282,7 @@ def test_add_all_layers_with_data(
     assert viewer.layers[1].name == ARCOS_LAYERS["active_cells"]
     assert viewer.layers[2].name == ARCOS_LAYERS["collective_events_cells"]
     assert viewer.layers[3].name == ARCOS_LAYERS["event_hulls"]
+    qtbot.wait(1000)
 
 
 def test_first_all_then_bin(

src/arcos_gui/_tests/test_widgets/test_input_data_widget.py

@@ -647,6 +647,7 @@ def test_load_data_from_multiple_label_properties_with_tracks_fail(
 
     controller.picker.ok_button.click()
     qtbot.waitSignal(controller.matching_worker.finished)
+    qtbot.wait(500)
 
     capture_output = capsys.readouterr()
     assert (