Fix failing tox tests (#87)

* Disable the tutorial

* Clean up tutorial after completion

* Hide tutorial during testing

* Break down tests into smaller units

* Run black

Author: jeylau

src/napari_deeplabcut/_tests/conftest.py

@@ -1,12 +1,15 @@
 import cv2
 import numpy as np
+import os
+
+os.environ["hide_tutorial"] = "True"
 import pandas as pd
 import pytest
 from napari_deeplabcut import keypoints, _writer
 from skimage.io import imsave
 
 
-@pytest.fixture  # TODO Hack to make this fixture session-scoped
+@pytest.fixture
 def viewer(make_napari_viewer):
     viewer = make_napari_viewer()
     for action in viewer.window.plugins_menu.actions():
@@ -22,12 +25,15 @@ def fake_keypoints():
     n_animals = 2
     n_kpts = 3
     data = np.random.rand(n_rows, n_animals * n_kpts * 2)
-    cols = pd.MultiIndex.from_product([
-        ["me"],
-        [f"animal_{i}" for i in range(n_animals)],
-        [f"kpt_{i}" for i in range(n_kpts)],
-        ["x", "y"]
-    ], names=["scorer", "individuals", "bodyparts", "coords"])
+    cols = pd.MultiIndex.from_product(
+        [
+            ["me"],
+            [f"animal_{i}" for i in range(n_animals)],
+            [f"kpt_{i}" for i in range(n_kpts)],
+            ["x", "y"],
+        ],
+        names=["scorer", "individuals", "bodyparts", "coords"],
+    )
     df = pd.DataFrame(data, columns=cols, index=range(n_rows))
     return df
 
@@ -68,11 +74,12 @@ def config_path(tmp_path_factory):
         "colormap": "viridis",
         "video_sets": {
             "fake_video": [],
-        }
+        },
     }
     path = str(tmp_path_factory.mktemp("configs") / "config.yaml")
     _writer._write_config(
-        path, params=cfg,
+        path,
+        params=cfg,
     )
     return path
 
@@ -83,7 +90,7 @@ def video_path(tmp_path_factory):
     h = w = 50
     writer = cv2.VideoWriter(
         output_path,
-        cv2.VideoWriter_fourcc(*'MJPG'),
+        cv2.VideoWriter_fourcc(*"MJPG"),
         2,
         (w, h),
     )

src/napari_deeplabcut/_tests/test_keypoints.py

@@ -2,16 +2,31 @@
 from napari_deeplabcut import keypoints
 
 
-def test_store(store, fake_keypoints):
+def test_store_advance_step(store):
     assert store.current_step == 0
     store._advance_step(event=None)
     assert store.current_step == 1
 
+
+def test_store_labels(store, fake_keypoints):
     assert store.n_steps == fake_keypoints.shape[0]
     assert store.labels == list(
         fake_keypoints.columns.get_level_values("bodyparts").unique()
     )
 
+
+def test_store_find_first_unlabeled_frame(store, fake_keypoints):
+    store._find_first_unlabeled_frame(event=None)
+    assert store.current_step == store.n_steps - 1
+    # Remove a frame to test whether it is correctly found
+    ind_to_remove = 2
+    data = store.layer.data
+    store.layer.data = data[data[:, 0] != ind_to_remove]
+    store._find_first_unlabeled_frame(event=None)
+    assert store.current_step == ind_to_remove
+
+
+def test_store_keypoints(store, fake_keypoints):
     annotated_keypoints = store.annotated_keypoints
     assert len(annotated_keypoints) == fake_keypoints.shape[1] // 2
     assert annotated_keypoints[0].id == "animal_0"
@@ -26,15 +41,6 @@ def test_store(store, fake_keypoints):
     assert store.current_keypoint == kpt
     store.next_keypoint()
 
-    store._find_first_unlabeled_frame(event=None)
-    assert store.current_step == store.n_steps - 1
-    # Remove a frame to test whether it is correctly found
-    ind_to_remove = 2
-    data = store.layer.data
-    store.layer.data = data[data[:, 0] != ind_to_remove]
-    store._find_first_unlabeled_frame(event=None)
-    assert store.current_step == ind_to_remove
-
 
 def test_point_resize(viewer, points):
     viewer.layers.selection.add(points)
@@ -46,7 +52,7 @@ def test_point_resize(viewer, points):
 
 
 def test_add_unnanotated(store):
-    store.layer.metadata["controls"].label_mode = 'loop'
+    store.layer.metadata["controls"].label_mode = "loop"
     ind_to_remove = 0
     data = store.layer.data
     store.layer.data = data[data[:, 0] != ind_to_remove]
@@ -59,10 +65,11 @@ def test_add_unnanotated(store):
 
 
 def test_add_quick(store):
-    store.layer.metadata["controls"].label_mode = 'quick'
+    store.layer.metadata["controls"].label_mode = "quick"
     store.current_keypoint = store._keypoints[0]
     coord = store.current_step, -1, -1
     keypoints._add(store, coord=coord)
     np.testing.assert_array_equal(
-        store.layer.data[store.current_step], coord,
+        store.layer.data[store.current_step],
+        coord,
     )

src/napari_deeplabcut/_tests/test_misc.py

@@ -40,8 +40,7 @@ def test_to_os_dir_sep_invalid():
 
 def test_guarantee_multiindex_rows():
     fake_index = [
-        f"labeled-data/subfolder_{i}/image_{j}"
-        for i in range(3) for j in range(10)
+        f"labeled-data/subfolder_{i}/image_{j}" for i in range(3) for j in range(10)
     ]
     df = pd.DataFrame(index=fake_index)
     misc.guarantee_multiindex_rows(df)
@@ -68,9 +67,15 @@ def test_dlc_header():
     scorer = "me"
     animals = [f"animal_{n}" for n in range(n_animals)]
     keypoints = [f"kpt_{n}" for n in range(n_keypoints)]
-    fake_columns = pd.MultiIndex.from_product([
-        [scorer], animals, keypoints, ["x", "y", "likelihood"],
-    ], names=["scorer", "individuals", "bodyparts", "coords"])
+    fake_columns = pd.MultiIndex.from_product(
+        [
+            [scorer],
+            animals,
+            keypoints,
+            ["x", "y", "likelihood"],
+        ],
+        names=["scorer", "individuals", "bodyparts", "coords"],
+    )
     header = misc.DLCHeader(fake_columns)
     assert header.scorer == scorer
     header.scorer = "you"

src/napari_deeplabcut/_tests/test_reader.py

@@ -64,8 +64,7 @@ def test_read_config(config_path):
 def test_read_hdf_old_index(tmp_path_factory, fake_keypoints):
     path = str(tmp_path_factory.mktemp("folder") / "data.h5")
     old_index = [
-        f"labeled-data/video/img{i}.png"
-        for i in range(fake_keypoints.shape[0])
+        f"labeled-data/video/img{i}.png" for i in range(fake_keypoints.shape[0])
     ]
     fake_keypoints.index = old_index
     fake_keypoints.to_hdf(path, key="data")
@@ -79,11 +78,13 @@ def test_read_hdf_old_index(tmp_path_factory, fake_keypoints):
 
 def test_read_hdf_new_index(tmp_path_factory, fake_keypoints):
     path = str(tmp_path_factory.mktemp("folder") / "data.h5")
-    new_index = pd.MultiIndex.from_product([
-        ["labeled-data"],
-        ["video"],
-        [f"img{i}.png" for i in range(fake_keypoints.shape[0])]
-    ])
+    new_index = pd.MultiIndex.from_product(
+        [
+            ["labeled-data"],
+            ["video"],
+            [f"img{i}.png" for i in range(fake_keypoints.shape[0])],
+        ]
+    )
     fake_keypoints.index = new_index
     fake_keypoints.to_hdf(path, key="data")
     layers = _reader.read_hdf(path)

src/napari_deeplabcut/_tests/test_widgets.py

@@ -5,7 +5,7 @@
 
 
 def test_guess_continuous():
-    assert _widgets.guess_continuous(np.array([0.]))
+    assert _widgets.guess_continuous(np.array([0.0]))
     assert not _widgets.guess_continuous(np.array(list("abc")))
 
 
@@ -40,7 +40,7 @@ def test_store_crop_coordinates(viewer, images, config_path):
     viewer.layers.selection.add(images)
     _ = viewer.add_shapes(
         np.random.random((4, 3)),
-        shape_type='rectangle',
+        shape_type="rectangle",
     )
     controls = _widgets.KeypointControls(viewer)
     controls._images_meta = {
@@ -55,17 +55,17 @@ def test_toggle_face_color(viewer, points):
     view = viewer.window._qt_viewer
     # By default, points are colored by individual with multi-animal data
     assert points._face.color_properties.name == "id"
-    view.canvas.events.key_press(key=keys.Key('F'))
+    view.canvas.events.key_press(key=keys.Key("F"))
     assert points._face.color_properties.name == "label"
-    view.canvas.events.key_press(key=keys.Key('F'))
+    view.canvas.events.key_press(key=keys.Key("F"))
     assert points._face.color_properties.name == "id"
 
 
 def test_toggle_edge_color(viewer, points):
     viewer.layers.selection.add(points)
     view = viewer.window._qt_viewer
     np.testing.assert_array_equal(points.edge_width, 0)
-    view.canvas.events.key_press(key=keys.Key('E'))
+    view.canvas.events.key_press(key=keys.Key("E"))
     np.testing.assert_array_equal(points.edge_width, 2)
 
 
@@ -82,7 +82,7 @@ def test_keypoints_dropdown_menu(store):
     widget = _widgets.KeypointsDropdownMenu(store)
     assert "id" in widget.menus
     assert "label" in widget.menus
-    label_menu = widget.menus['label']
+    label_menu = widget.menus["label"]
     label_menu.currentText() == "kpt_0"
     widget.update_menus(event=None)
     label_menu.currentText() == "kpt_2"
@@ -92,7 +92,7 @@ def test_keypoints_dropdown_menu(store):
 
 def test_keypoints_dropdown_menu_smart_reset(store):
     widget = _widgets.KeypointsDropdownMenu(store)
-    label_menu = widget.menus['label']
+    label_menu = widget.menus["label"]
     label_menu.update_to("kpt_2")
     widget._locked = True
     widget.smart_reset(event=None)
@@ -119,4 +119,4 @@ def test_color_scheme_display(qtbot):
     widget.add_entry("keypoint", "red")
     assert widget.scheme_dict["keypoint"] == "red"
     assert widget._container.layout().count() == 1
-    qtbot.add_widget(widget)
+    qtbot.add_widget(widget)