Remove deprecated code from Labels layer (napari#6641)

# References and relevant issues

This completes the deprecations started in napari#6542. All it does is remove
the things we warned we would remove. 😂

---------

Co-authored-by: Grzegorz Bokota <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

napari/benchmarks/benchmark_labels_layer.py

@@ -10,6 +10,7 @@
 import napari
 from napari.components.dims import Dims
 from napari.layers import Labels
+from napari.utils.colormaps import DirectLabelColormap
 
 from .utils import Skip, labeled_particles
 
@@ -95,12 +96,13 @@ def setup(self, n, brush_size, color_mode, contour):
             (n, n), dtype=np.int32, n=int(np.log2(n) ** 2), seed=1
         )
 
-        colors = None
+        self.layer = Labels(self.data)
+
         if color_mode == 'direct':
             random_label_ids = np.random.randint(64, size=50)
             colors = {i + 1: np.random.random(4) for i in random_label_ids}
-
-        self.layer = Labels(self.data, color=colors)
+            colors[None] = np.array([0, 0, 0, 0.3])
+            self.layer.colormap = DirectLabelColormap(color_dict=colors)
 
         self.layer.brush_size = brush_size
         self.layer.contour = contour
@@ -132,9 +134,10 @@ def setup(self, n, dtype):
         random_label_ids = np.random.randint(
             low=max(-10000, info.min), high=min(10000, info.max), size=20
         )
+        colors = {i + 1: np.random.random(4) for i in random_label_ids}
+        colors[None] = np.array([0, 0, 0, 0.3])
         self.layer = Labels(
-            self.data,
-            color={i + 1: np.random.random(4) for i in random_label_ids},
+            self.data, colormap=DirectLabelColormap(color_dict=colors)
         )
         self.layer._raw_to_displayed(
             self.layer._slice.image.raw, (slice(0, n), slice(0, n))

napari/benchmarks/benchmark_qt_viewer_labels.py

@@ -16,6 +16,7 @@
 import napari
 from napari.components.viewer_model import ViewerModel
 from napari.qt import QtViewer
+from napari.utils.colormaps import DirectLabelColormap
 
 from .utils import Skip
 
@@ -150,7 +151,7 @@ def setup(self, radius, dtype, label_mode):
             )
             colors[None] = 'yellow'
             colors[0] = 'transparent'
-            self.layer.color = colors
+            self.layer.colormap = DirectLabelColormap(color_dict=colors)
         self.qt_viewr.show()
 
     @staticmethod

napari/components/_tests/test_viewer_model.py

@@ -138,16 +138,6 @@ def test_add_labels():
     assert viewer.dims.ndim == 2
 
 
-def test_add_labels_warnings():
-    """Test adding labels image."""
-    viewer = ViewerModel()
-    np.random.seed(0)
-    with pytest.warns(
-        FutureWarning, match='Setting Labels.num_colors is deprecated since'
-    ):
-        viewer.add_labels(np.zeros((10, 15), dtype=np.uint8), num_colors=20)
-
-
 def test_add_points():
     """Test adding points."""
     viewer = ViewerModel()

napari/layers/labels/_tests/test_labels.py

@@ -1,6 +1,7 @@
 import copy
 import itertools
 import time
+from collections import defaultdict
 from dataclasses import dataclass
 from tempfile import TemporaryDirectory
 from typing import List
@@ -12,7 +13,6 @@
 import xarray as xr
 import zarr
 from numpy.core.numerictypes import issubdtype
-from numpy.testing import assert_array_almost_equal, assert_raises
 from skimage import data as sk_data
 
 from napari._tests.utils import check_layer_world_data_extent
@@ -261,56 +261,6 @@ def test_blending():
 
 
 @pytest.mark.filterwarnings('ignore:.*seed is deprecated.*')
-def test_seed():
-    """Test setting seed."""
-    np.random.seed(0)
-    data = np.random.randint(20, size=(10, 15))
-    layer = Labels(data)
-    assert layer.seed == 0.5
-
-    layer.seed = 0.9
-    assert layer.seed == 0.9
-
-    layer = Labels(data, seed=0.7)
-    assert layer.seed == 0.7
-
-    # ensure setting seed updates the random colormap
-    mapped_07 = layer.colormap.map(layer.data)
-    layer.seed = 0.4
-    mapped_04 = layer.colormap.map(layer.data)
-    assert_raises(
-        AssertionError, assert_array_almost_equal, mapped_07, mapped_04
-    )
-
-
-def test_num_colors():
-    """Test setting number of colors in colormap with deprecated API."""
-    np.random.seed(0)
-    data = np.random.randint(20, size=(10, 15))
-    layer = Labels(data)
-
-    with pytest.warns(FutureWarning, match='num_colors is deprecated'):
-        assert layer.num_colors == 50
-
-    with pytest.warns(FutureWarning, match='num_colors is deprecated'):
-        layer.num_colors = 80
-
-    assert len(layer.colormap) == 80
-
-    with pytest.warns(FutureWarning, match='num_colors is deprecated'):
-        layer = Labels(data, num_colors=60)
-
-    assert len(layer.colormap) == 60
-
-    with pytest.raises(ValueError, match=r'.*Only up to 2\*\*16=65535 colors'):
-        with pytest.warns(FutureWarning, match='num_colors is deprecated'):
-            layer.num_colors = 2**17
-
-    with pytest.raises(ValueError, match=r'.*Only up to 2\*\*16=65535 colors'):
-        with pytest.warns(FutureWarning, match='num_colors is deprecated'):
-            Labels(data, num_colors=2**17)
-
-
 def test_properties():
     """Test adding labels with properties."""
     np.random.seed(0)
@@ -447,11 +397,13 @@ def test_custom_color_dict():
     """Test custom color dict."""
     np.random.seed(0)
     data = np.random.randint(20, size=(10, 15))
-    with pytest.warns(FutureWarning, match='Labels.color is deprecated'):
-        layer = Labels(
-            data,
-            color={2: 'white', 4: 'red', 8: 'blue', 16: 'red', 32: 'blue'},
+    cmap = DirectLabelColormap(
+        color_dict=defaultdict(
+            lambda: 'black',
+            {2: 'white', 4: 'red', 8: 'blue', 16: 'red', 32: 'blue'},
         )
+    )
+    layer = Labels(data, colormap=cmap)
 
     # test with custom color dict
     assert isinstance(layer.get_color(2), np.ndarray)
@@ -462,8 +414,6 @@ def test_custom_color_dict():
 
     # test disable custom color dict
     # should not initialize as white since we are using random.seed
-    with pytest.warns(FutureWarning, match='Labels.color_mode is deprecated'):
-        layer.color_mode = 'auto'
     assert not (layer.get_color(1) == np.array([1.0, 1.0, 1.0, 1.0])).all()
 
 
@@ -1511,30 +1461,26 @@ def test_is_default_color():
     # setting color to default colors doesn't update color mode
     layer.colormap = DirectLabelColormap(color_dict=current_color)
     assert isinstance(layer.colormap, CyclicLabelColormap)
-    with pytest.warns(FutureWarning, match='Labels.color_mode is deprecated'):
-        assert layer.color_mode == 'auto'
 
     # new colors are not default
     new_color = {0: 'white', 1: 'red', 3: 'green', None: 'blue'}
     assert not layer._is_default_colors(new_color)
     # setting the color with non-default colors updates color mode
     layer.colormap = DirectLabelColormap(color_dict=new_color)
     assert isinstance(layer.colormap, DirectLabelColormap)
-    with pytest.warns(FutureWarning, match='Labels.color_mode is deprecated'):
-        assert layer.color_mode == 'direct'
 
 
 def test_large_labels_direct_color():
     """Make sure direct color works with large label ranges"""
     pytest.importorskip('numba')
     data = np.array([[0, 1], [2**16, 2**20]], dtype=np.uint32)
     colors = {1: 'white', 2**16: 'green', 2**20: 'magenta'}
-    layer = Labels(data)
-    with pytest.warns(FutureWarning, match='Labels.color is deprecated'):
-        layer.color = colors
-
-    with pytest.warns(FutureWarning, match='Labels.color_mode is deprecated'):
-        assert layer.color_mode == 'direct'
+    layer = Labels(
+        data,
+        colormap=DirectLabelColormap(
+            color_dict=defaultdict(lambda: 'black', colors)
+        ),
+    )
     np.testing.assert_allclose(layer.get_color(2**20), [1.0, 0.0, 1.0, 1.0])