fix: Fix napari 0.5.0 compatybility (#1116)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **New Features**
- Enhanced compatibility with Napari version 5.0, including conditional
logic for colormap and layer viewing.

- **Bug Fixes**
- Improved color handling logic for label highlighting in various
widgets.
- Corrected rendering image logic in tests to ensure accurate
assertions.

- **Dependencies**
  - Updated `numpy` dependency to version >= 1.18.5 but < 2.

- **Tests**
- Introduced version-based conditional logic in tests for better Napari
compatibility.
- Adjusted test assertions for image rendering and colormap type
validations.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

package/PartSeg/_roi_mask/image_view.py

@@ -1,9 +1,14 @@
+from importlib.metadata import version
+
+from packaging.version import parse as parse_version
 from vispy.app import MouseEvent
 
 from PartSeg._roi_mask.stack_settings import StackSettings
 from PartSeg.common_gui.channel_control import ChannelProperty
 from PartSeg.common_gui.napari_image_view import ImageInfo, ImageView, LabelEnum
 
+_napari_ge_0_5_0 = parse_version(version("napari")) >= parse_version("0.5.0a1")
+
 
 class StackImageView(ImageView):
     """
@@ -14,7 +19,10 @@ class StackImageView(ImageView):
 
     def __init__(self, settings: StackSettings, channel_property: ChannelProperty, name: str):
         super().__init__(settings, channel_property, name)
-        self.viewer_widget.canvas.events.mouse_press.connect(self.component_click)
+        if _napari_ge_0_5_0:
+            self.viewer_widget.canvas._scene_canvas.events.mouse_press.connect(self.component_click)
+        else:
+            self.viewer_widget.canvas.events.mouse_press.connect(self.component_click)
 
     def refresh_selected(self):
         if (

package/PartSeg/common_backend/base_settings.py

@@ -17,6 +17,7 @@
 from napari.utils import Colormap
 from napari.utils.theme import get_theme
 from napari.utils.theme import template as napari_template
+from packaging.version import parse as parse_version
 from qtpy.QtCore import QObject, Signal
 from qtpy.QtWidgets import QMessageBox, QWidget
 
@@ -37,6 +38,8 @@
     from napari.settings import NapariSettings
 logger = logging.getLogger(__name__)
 
+_napari_ge_5 = parse_version(napari.__version__) >= parse_version("0.5.0a1")
+
 DIR_HISTORY = "io.dir_location_history"
 FILE_HISTORY = "io.files_open_history"
 MULTIPLE_FILES_OPEN_HISTORY = "io.multiple_files_open_history"
@@ -268,6 +271,8 @@ def theme_name(self) -> str:
     @property
     def theme(self):
         """Theme as structure."""
+        if _napari_ge_5:
+            return get_theme(self.theme_name)
         try:
             return get_theme(self.theme_name, as_dict=False)
         except TypeError:  # pragma: no cover

package/PartSeg/common_gui/error_report.py

@@ -12,12 +12,14 @@
 import traceback
 import typing
 from contextlib import suppress
+from importlib.metadata import version
 
 import numpy as np
 import requests
 import sentry_sdk
 from napari.settings import get_settings
 from napari.utils.theme import get_theme
+from packaging.version import parse as parse_version
 from qtpy.QtGui import QIcon
 from qtpy.QtWidgets import (
     QApplication,
@@ -53,6 +55,7 @@
 _FEEDBACK_URL = "https://sentry.io/api/0/projects/{organization_slug}/{project_slug}/user-feedback/".format(
     organization_slug="cent", project_slug="partseg"
 )
+_napari_ge_5 = parse_version(version("napari")) >= parse_version("0.5.0a1")
 
 
 def _print_traceback(exception, file_):
@@ -82,7 +85,10 @@ def __init__(self, exception: Exception, description: str, additional_notes: str
         self.create_issue_btn = QPushButton("Create issue")
         self.cancel_btn = QPushButton("Cancel")
         self.error_description = QTextEdit()
-        theme = get_theme(get_settings().appearance.theme, as_dict=False)
+        if _napari_ge_5:
+            theme = get_theme(get_settings().appearance.theme)
+        else:
+            theme = get_theme(get_settings().appearance.theme, as_dict=False)
         self._highlight = Pylighter(self.error_description.document(), "python", theme.syntax_style)
         self.traceback_summary = additional_info
         if additional_info is None:

package/PartSeg/common_gui/napari_image_view.py

@@ -42,6 +42,17 @@
     from napari._qt.widgets.qt_viewer_buttons import QtViewerPushButton as QtViewerPushButton_
 _napari_ge_4_13 = parse_version(napari.__version__) >= parse_version("0.4.13a1")
 _napari_ge_4_17 = parse_version(napari.__version__) >= parse_version("0.4.17a1")
+_napari_ge_5 = parse_version(napari.__version__) >= parse_version("0.5.0a1")
+
+
+def get_highlight_colormap():
+    cmap_dict = {0: (0, 0, 0, 0), 1: "white", None: (0, 0, 0, 0)}
+    if _napari_ge_5:
+        from napari.utils.colormaps import DirectLabelColormap
+
+        return {"colormap": DirectLabelColormap(color_dict=cmap_dict)}
+
+    return {"color": cmap_dict}
 
 
 class QtViewerPushButton(QtViewerPushButton_):
@@ -838,8 +849,8 @@ def _mark_layer(self, num: int, flash: bool, image_info: ImageInfo):
                 component_mark,
                 scale=image_info.roi.scale,
                 blending="translucent",
-                color={0: (0, 0, 0, 0), 1: "white"},
                 opacity=0.7,
+                **get_highlight_colormap(),
             )
             self.viewer.layers.selection.active = active_layer
         else:
@@ -965,6 +976,17 @@ def closeEvent(self, event):
         self.close()
         super().closeEvent(event)
 
+    def _render(self):
+        if _napari_ge_5:
+            return self.canvas._scene_canvas.render()
+        return self.canvas.render()
+
+    if _napari_ge_5:
+
+        @property
+        def view(self):
+            return self.canvas.view
+
 
 class SearchComponentModal(QtPopup):
     def __init__(self, image_view: ImageView, search_type: SearchType, component_num: int, max_components):

package/PartSeg/plugins/napari_widgets/lables_control.py

@@ -1,13 +1,17 @@
+from importlib.metadata import version
 from typing import List, Sequence
 
 from napari import Viewer
 from napari.layers import Labels
+from packaging.version import parse as parse_version
 from qtpy.QtWidgets import QHBoxLayout, QPushButton, QTabWidget
 
 from PartSeg.common_backend.base_settings import BaseSettings
 from PartSeg.common_gui.label_create import LabelChoose, LabelEditor, LabelShow
 from PartSeg.plugins.napari_widgets._settings import get_settings
 
+NAPARI_GE_5_0 = parse_version(version("napari")) >= parse_version("0.5.0a1")
+
 
 class NapariLabelShow(LabelShow):
     def __init__(self, viewer: Viewer, name: str, label: List[Sequence[float]], removable, parent=None):
@@ -36,7 +40,11 @@ def apply_label(self):
         ):
             max_val = layer.data.max()
             labels = {i + 1: [x / 255 for x in self.label[i % len(self.label)]] for i in range(max_val + 5)}
-            layer.color = labels
+            labels[None] = [0, 0, 0, 0]
+            if NAPARI_GE_5_0:
+                layer.colormap = labels
+            else:
+                layer.color = labels
 
 
 class NaparliLabelChoose(LabelChoose):

package/PartSeg/plugins/napari_widgets/search_label_widget.py

@@ -8,7 +8,7 @@
 from qtpy.QtCore import QTimer
 from vispy.geometry import Rect
 
-from PartSeg.common_gui.napari_image_view import SearchType
+from PartSeg.common_gui.napari_image_view import SearchType, get_highlight_colormap
 from PartSegCore.roi_info import ROIInfo
 
 HIGHLIGHT_LABEL_NAME = ".Highlight"
@@ -77,8 +77,8 @@ def _highlight(self):
                 name=HIGHLIGHT_LABEL_NAME,
                 scale=labels.scale,
                 blending="translucent",
-                color={0: (0, 0, 0, 0), 1: "white"},
                 opacity=0.7,
+                **get_highlight_colormap(),
             )
 
             def flash_fun(layer_=layer):

package/tests/test_PartSeg/test_channel_control.py

@@ -309,12 +309,12 @@ def check_parameters(name, index):
     @pytest.mark.windows_ci_skip()
     def test_image_view_integration(self, qtbot, tmp_path, ch_property, image_view):
         image_view.viewer_widget.screenshot(flash=False)
-        image1 = image_view.viewer_widget.canvas.render()
+        image1 = image_view.viewer_widget._render()
         assert np.any(image1 != 255)
         ch_property.minimum_value.setValue(100)
         ch_property.maximum_value.setValue(10000)
         ch_property.filter_radius.setValue(0.5)
-        image2 = image_view.viewer_widget.canvas.render()
+        image2 = image_view.viewer_widget._render()
         assert np.any(image2 != 255)
 
         assert np.all(image1 == image2)
@@ -328,13 +328,13 @@ def check_parameters(name, index):
         ):
             ch_property.fixed.setChecked(True)
 
-        image1 = image_view.viewer_widget.canvas.render()
+        image1 = image_view.viewer_widget._render()
         assert np.any(image1 != 255)
         with qtbot.waitSignal(image_view.channel_control.coloring_update), qtbot.waitSignal(
             image_view.channel_control.change_channel, check_params_cb=check_parameters
         ):
             ch_property.minimum_value.setValue(20)
-        image2 = image_view.viewer_widget.canvas.render()
+        image2 = image_view.viewer_widget._render()
         assert np.any(image2 != 255)
         assert np.any(image1 != image2)
 
@@ -392,7 +392,7 @@ def check_parameters(name, index):
         ):
             ch_property.fixed.setChecked(True)
         image_view.viewer_widget.screenshot(flash=False)
-        image1 = image_view.viewer_widget.canvas.render()
+        image1 = image_view.viewer_widget._render()
         with qtbot.waitSignal(image_view.channel_control.coloring_update), qtbot.waitSignal(
             image_view.channel_control.change_channel, check_params_cb=check_parameters
         ):

package/tests/test_PartSeg/test_common_backend.py

@@ -193,10 +193,8 @@ def test_safe_repr(self):
         assert PartSegCore.utils.safe_repr(np.arange(3)) == "array([0, 1, 2])"
 
     def test_safe_repr_napari_image(self):
-        assert (
-            PartSegCore.utils.safe_repr(napari.layers.Image(np.zeros((10, 10, 5))))
-            == "<Image of shape: (10, 10, 5), dtype: float64, slice"
-            " (0, slice(None, None, None), slice(None, None, None))>"
+        assert PartSegCore.utils.safe_repr(napari.layers.Image(np.zeros((10, 10, 5)))).startswith(
+            "<Image of shape: (10, 10, 5), dtype: float64, slice"
         )
 
 

package/tests/test_PartSeg/test_napari_image_view.py

@@ -1,12 +1,14 @@
 # pylint: disable=no-self-use
 import gc
 from functools import partial
+from importlib.metadata import version
 from unittest.mock import MagicMock
 
 import numpy as np
 import pytest
 from napari.layers import Image as NapariImage
 from napari.qt import QtViewer
+from packaging.version import parse as parse_version
 from qtpy.QtCore import QPoint
 from vispy.geometry import Rect
 
@@ -25,6 +27,14 @@
 from PartSegCore.roi_info import ROIInfo
 from PartSegImage import Image
 
+NAPARI_GE_5_0 = parse_version(version("napari")) >= parse_version("0.5.0a1")
+
+
+if NAPARI_GE_5_0:
+    EXPECTED_RANGE = (0, 0, 1)
+else:
+    EXPECTED_RANGE = (0, 1, 1)
+
 
 def test_image_info():
     image_info = ImageInfo(Image(np.zeros((10, 10)), image_spacing=(1, 1), axes_order="XY"), [])
@@ -246,7 +256,7 @@ def test_marking_component_flash(self, base_settings, image_view, tmp_path, qtbo
         assert "timer" in image_view.image_info[str(tmp_path / "test2.tiff")].highlight.metadata
         timer = image_view.image_info[str(tmp_path / "test2.tiff")].highlight.metadata["timer"]
         assert timer.isActive()
-        assert image_view.viewer.dims.range[0] == (0, 1, 1)
+        assert image_view.viewer.dims.range[0] == EXPECTED_RANGE
         qtbot.wait(800)
         image_view.component_unmark(0)
         assert not image_view.image_info[str(tmp_path / "test2.tiff")].highlight.visible

package/tests/test_PartSeg/test_napari_widgets.py

@@ -1,6 +1,7 @@
 import contextlib
 import gc
 import json
+from importlib.metadata import version
 from unittest.mock import patch
 
 import numpy as np
@@ -10,6 +11,7 @@
 from napari.layers import Image as NapariImage
 from napari.layers import Labels
 from napari.utils import Colormap
+from packaging.version import parse as parse_version
 from qtpy.QtCore import QObject, QTimer, Signal
 
 from PartSeg._roi_analysis.partseg_settings import PartSettings
@@ -55,6 +57,28 @@
 from PartSegCore.segmentation.threshold import DoubleThresholdSelection, ThresholdSelection
 from PartSegCore.segmentation.watershed import WatershedSelection
 
+NAPARI_GE_5_0 = parse_version(version("napari")) >= parse_version("0.5.0a1")
+
+if NAPARI_GE_5_0:
+
+    def check_auto_mode(layer):
+        from napari.utils.colormaps import CyclicLabelColormap
+
+        assert isinstance(layer.colormap, CyclicLabelColormap)
+
+    def check_direct_mode(layer):
+        from napari.utils.colormaps import DirectLabelColormap
+
+        assert isinstance(layer.colormap, DirectLabelColormap)
+
+else:
+
+    def check_auto_mode(layer):
+        assert layer.color_mode == "auto"
+
+    def check_direct_mode(layer):
+        assert layer.color_mode == "direct"
+
 
 @pytest.fixture(autouse=True)
 def _clean_settings(tmp_path):
@@ -351,9 +375,9 @@ def test_napari_label_show(viewer_with_data, qtbot):
     assert not widget.apply_label_btn.isEnabled()
     viewer_with_data.layers.selection.remove(viewer_with_data.layers["image"])
     assert widget.apply_label_btn.isEnabled()
-    assert viewer_with_data.layers["label"].color_mode == "auto"
+    check_auto_mode(viewer_with_data.layers["label"])
     widget.apply_label_btn.click()
-    assert viewer_with_data.layers["label"].color_mode == "direct"
+    check_direct_mode(viewer_with_data.layers["label"])
 
 
 def test_napari_colormap_control(viewer_with_data, qtbot):

pyproject.toml

@@ -54,7 +54,7 @@ dependencies = [
     "mahotas>=1.4.10",
     "napari>=0.4.14",
     "nme>=0.1.7",
-    "numpy>=1.18.5",
+    "numpy>=1.18.5,<2", # mahotas requires rebuild for numpy 2.
     "oiffile>=2020.1.18",
     "openpyxl>=2.5.7",
     "packaging>=20.0",