Merge pull request #26 from danforthcenter/diagnose-test-issues

Debug intermittent testing failures

.github/workflows/continuous-integration.yml

@@ -30,8 +30,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        sudo apt-get update
-        sudo apt-get install --no-install-recommends libyaml-dev libegl1-mesa libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-shape0 libxcb-cursor0 xserver-xephyr xvfb
+        sudo apt-get install --no-install-recommends libyaml-dev libegl1-mesa libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-shape0 libxcb-cursor0 xserver-xephyr
         python -m pip install --upgrade pip
         pip install flake8 pytest pytest-cov pytest-qt pytest-xvfb ipython anyio
     - name: Lint with flake8
@@ -48,8 +47,9 @@ jobs:
         pip uninstall -y opencv-python
         pip install opencv-python-headless
     - name: Tests
-      uses: aganders3/headless-gui@v2
+      uses: aganders3/headless-gui@v2.2
       with:
+        xvfb-screen-size: 1280x720x24
         run: pytest --cov-report=xml --cov=./
     - name: Upload coverage to Deepsource
       uses: deepsourcelabs/test-coverage-action@master

tests/test_annotate_points.py

@@ -11,7 +11,7 @@ def test_points(test_data):
     img = cv2.imread(test_data.small_rgb_img)
 
     # initialize interactive tool
-    drawer_rgb = Points(img, figsize=(12, 6))
+    drawer_rgb = Points(img, figsize=(5, 5))
 
     # simulate mouse clicks
     # event 1, left click to add point
@@ -56,7 +56,7 @@ def test_points_print_coords(test_data, tmpdir):
     img = cv2.imread(test_data.small_rgb_img)
 
     # initialize interactive tool
-    drawer_rgb = Points(img, figsize=(12, 6))
+    drawer_rgb = Points(img, figsize=(5, 5))
 
     # simulate mouse clicks
     # event 1, left click to add point
@@ -82,7 +82,7 @@ def test_points_import_list(test_data):
     # Read in a test image
     img = cv2.imread(test_data.small_rgb_img)
     # initialize interactive tool
-    drawer_rgb = Points(img, figsize=(12, 6), label="default")
+    drawer_rgb = Points(img, figsize=(5, 5), label="default")
     totalpoints1 = [(158, 531), (361, 112), (500, 418), (269.25303806488864, 385.69839981447126),
                     (231.21964288863632, 445.995245825603), (293.37177646934134, 448.778177179963),
                     (240.49608073650273, 277.1640769944342), (279.4571196975417, 240.05832560296852),
@@ -98,7 +98,7 @@ def test_points_import_list_warn(test_data):
     # Read in a test image
     img = cv2.imread(test_data.small_rgb_img)
     # initialize interactive tool
-    drawer_rgb = Points(img, figsize=(12, 6), label="default")
+    drawer_rgb = Points(img, figsize=(5, 5), label="default")
     totalpoints1 = [(158, 531), (361, 112), (500, 418), (445.50535717435065, 138.94515306122452)]
     drawer_rgb.import_list(coords=totalpoints1)
 
@@ -108,7 +108,7 @@ def test_points_import_list_warn(test_data):
 def test_points_import_file(test_data):
     """Test for plantcv-annotate."""
     img = cv2.imread(test_data.small_rgb_img)
-    counter = Points(img, figsize=(8, 6))
+    counter = Points(img, figsize=(5, 5))
     file = test_data.pollen_coords
     counter.import_file(file)
 
@@ -121,7 +121,7 @@ def test_points_view(test_data):
     img = cv2.imread(test_data.small_rgb_img)
 
     # initialize interactive tool
-    drawer_rgb = Points(img, figsize=(12, 6))
+    drawer_rgb = Points(img, figsize=(5, 5))
 
     # simulate mouse clicks
     # event 1, left click to add point
@@ -137,7 +137,7 @@ def test_points_view(test_data):
     drawer_rgb.onclick(e2)
     drawer_rgb.view(view_all=False)
 
-    assert str(drawer_rgb.fig) == "Figure(1200x600)"
+    assert str(drawer_rgb.fig) == "Figure(500x500)"
 
 
 def test_points_view_warn(test_data):
@@ -146,7 +146,7 @@ def test_points_view_warn(test_data):
     img = cv2.imread(test_data.small_rgb_img)
 
     # initialize interactive tool, implied default label and "r" color
-    drawer_rgb = Points(img, figsize=(12, 6))
+    drawer_rgb = Points(img, figsize=(5, 5))
 
     # simulate mouse clicks, event 1=left click to add point
     e1 = matplotlib.backend_bases.MouseEvent(name="button_press_event", canvas=drawer_rgb.fig.canvas,
@@ -156,4 +156,4 @@ def test_points_view_warn(test_data):
     drawer_rgb.onclick(e1)
     drawer_rgb.view(label="new", color='r')
 
-    assert str(drawer_rgb.fig) == "Figure(1200x600)"
+    assert str(drawer_rgb.fig) == "Figure(500x500)"

tests/test_napari_classes.py

@@ -16,3 +16,4 @@ def test_napari_classes(make_napari_viewer):
     keys = napari_classes(viewer)
 
     assert keys == ['total', 'test']
+    viewer.close()

tests/test_napari_join_labels.py

@@ -14,6 +14,7 @@ def test_napari_join_labels(test_data):
     labeled, _ = napari_join_labels(img, viewer)
 
     assert np.shape(labeled) == (576, 537)
+    viewer.close()
 
 
 def test_napari_join_allclass(test_data):
@@ -34,6 +35,7 @@ def test_napari_join_allclass(test_data):
     labeled, _ = napari_join_labels(img, viewer)
 
     assert np.shape(labeled) == (576, 537)
+    viewer.close()
 
 
 def test_napari_join_warn(test_data):
@@ -54,6 +56,7 @@ def test_napari_join_warn(test_data):
     labeled, _ = napari_join_labels(img, viewer)
 
     assert np.shape(labeled) == (576, 537)
+    viewer.close()
 
 
 def test_napari_join_print(test_data, tmpdir):
@@ -77,3 +80,4 @@ def test_napari_join_print(test_data, tmpdir):
     labeled, _ = napari_join_labels(img, viewer)
 
     assert np.shape(labeled) == (576, 537)
+    viewer.close()

tests/test_napari_label_classes.py

@@ -13,3 +13,4 @@ def test_napari_label_classes_gray(test_data):
                       face_color="red", size=1)
 
     assert len(viewer.layers['background'].data) == 1
+    viewer.close()

tests/test_napari_open.py

@@ -13,6 +13,7 @@ def test_napari_open_rgb(test_data):
                       face_color="red", size=1)
 
     assert len(viewer.layers['total'].data) == 2
+    viewer.close()
 
 
 def test_napari_open_gray(test_data):
@@ -25,6 +26,7 @@ def test_napari_open_gray(test_data):
                       face_color="red", size=1)
 
     assert len(viewer.layers['total'].data) == 2
+    viewer.close()
 
 
 def test_napari_open_envi(test_data):
@@ -38,3 +40,4 @@ def test_napari_open_envi(test_data):
                       face_color="red", size=1)
 
     assert len(viewer.layers['total'].data) == 2
+    viewer.close()