added the dependencies

pyproject.toml

@@ -29,6 +29,10 @@ dependencies = [
     "magicgui",
     "qtpy",
     "scikit-image",
+    "cellpose",
+    "czifile",
+    "big-fish",
+    "scikit-image"
 ]
 
 [project.optional-dependencies]

src/segment_embryo/_tests/test_widget.py

@@ -1,62 +1,18 @@
 import numpy as np
 
 from segment_embryo._widget import (
-    ExampleQWidget,
-    ImageThreshold,
-    threshold_autogenerate_widget,
-    threshold_magic_widget,
+    EmbryoSegmentationWidget
 )
 
 
-def test_threshold_autogenerate_widget():
-    # because our "widget" is a pure function, we can call it and
-    # test it independently of napari
-    im_data = np.random.random((100, 100))
-    thresholded = threshold_autogenerate_widget(im_data, 0.5)
-    assert thresholded.shape == im_data.shape
-    # etc.
-
-
-# make_napari_viewer is a pytest fixture that returns a napari viewer object
-# you don't need to import it, as long as napari is installed
-# in your testing environment
-def test_threshold_magic_widget(make_napari_viewer):
-    viewer = make_napari_viewer()
-    layer = viewer.add_image(np.random.random((100, 100)))
-
-    # our widget will be a MagicFactory or FunctionGui instance
-    my_widget = threshold_magic_widget()
-
-    # if we "call" this object, it'll execute our function
-    thresholded = my_widget(viewer.layers[0], 0.5)
-    assert thresholded.shape == layer.data.shape
-    # etc.
-
-
-def test_image_threshold_widget(make_napari_viewer):
-    viewer = make_napari_viewer()
-    layer = viewer.add_image(np.random.random((100, 100)))
-    my_widget = ImageThreshold(viewer)
-
-    # because we saved our widgets as attributes of the container
-    # we can set their values without having to "interact" with the viewer
-    my_widget._image_layer_combo.value = layer
-    my_widget._threshold_slider.value = 0.5
-
-    # this allows us to run our functions directly and ensure
-    # correct results
-    my_widget._threshold_im()
-    assert len(viewer.layers) == 2
-
-
 # capsys is a pytest fixture that captures stdout and stderr output streams
 def test_example_q_widget(make_napari_viewer, capsys):
     # make viewer and add an image layer using our fixture
     viewer = make_napari_viewer()
     viewer.add_image(np.random.random((100, 100)))
 
     # create our widget, passing in the viewer
-    my_widget = ExampleQWidget(viewer)
+    my_widget = EmbryoSegmentationWidget(viewer)
 
     # call our widget method
     my_widget._on_click()