Merge branch 'interactive-widget' of...

Merge branch 'interactive-widget' of https://github.com/aaristov/napari-segment into interactive-widget

.github/workflows/test_and_deploy.yml

@@ -7,13 +7,13 @@ on:
   push:
     branches:
       - main
-      - npe2
+      - interactive-widget
     tags:
       - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
   pull_request:
     branches:
       - main
-      - npe2
+      - interactive-widget
   workflow_dispatch:
 
 jobs:

setup.cfg

@@ -35,6 +35,9 @@ install_requires =
     numpy
     scikit-image
     zarr
+    matplotlib
+    dask
+    imageio_ffmpeg
 python_requires = >=3.8
 include_package_data = True
 package_dir =

src/napari_segment/_tests/test_dock_widget.py

-from napari_segment import ExampleQWidget, example_magic_widget
-import numpy as np
-
-# make_napari_viewer is a pytest fixture that returns a napari viewer object
-# 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)
-
-    # call our widget method
-    my_widget._on_click()
-
-    # read captured output and check that it's as we expected
-    captured = capsys.readouterr()
-    assert captured.out == "napari has 1 layers\n"
-    
-def test_example_magic_widget(make_napari_viewer, capsys):
-    viewer = make_napari_viewer()
-    layer = viewer.add_image(np.random.random((100, 100)))
-
-    # this time, our widget will be a MagicFactory or FunctionGui instance
-    my_widget = example_magic_widget()
-
-    # if we "call" this object, it'll execute our function
-    my_widget(viewer.layers[0])
-
-    # read captured output and check that it's as we expected
-    captured = capsys.readouterr()
-    assert captured.out == f"you have selected {layer}\n"

src/napari_segment/_tests/test_widget.py

-from napari_segment import ExampleQWidget, example_magic_widget
+from napari_segment import SegmentStack
 import numpy as np
+import dask.array as da
 
 # make_napari_viewer is a pytest fixture that returns a napari viewer object
 # capsys is a pytest fixture that captures stdout and stderr output streams
-def test_example_q_widget(make_napari_viewer, capsys):
+def test_segment_stack(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)))
+    viewer.add_image(np.random.random((5, 100, 100)), name="test_data", metadata={"path": "fakepath.nd2"})
 
     # create our widget, passing in the viewer
-    my_widget = ExampleQWidget(viewer)
+    widget = SegmentStack(viewer)
+    assert widget.input.current_choice == "test_data"
+    assert widget.path == "fakepath.nd2"
+    assert isinstance(widget.ddata, da.Array) 
+    assert widget.ddata.chunks == ((1, 1, 1, 1, 1), (100/widget.binning,), (100/widget.binning,))
 
-    # call our widget method
-    my_widget._on_click()
-
-    # read captured output and check that it's as we expected
-    captured = capsys.readouterr()
-    assert captured.out == "napari has 1 layers\n"
     
-def test_example_magic_widget(make_napari_viewer, capsys):
-    viewer = make_napari_viewer()
-    layer = viewer.add_image(np.random.random((100, 100)))
-
-    # this time, our widget will be a MagicFactory or FunctionGui instance
-    my_widget = example_magic_widget()
-
-    # if we "call" this object, it'll execute our function
-    my_widget(viewer.layers[0])
-
     # read captured output and check that it's as we expected
-    captured = capsys.readouterr()
-    assert captured.out == f"you have selected {layer}\n"
+    # captured = capsys.readouterr()
+    # assert captured.out == "napari has 1 layers\n"