Merge branch 'develop' into pre-commit-ci-update-config

.github/workflows/python-package.yml

@@ -30,7 +30,7 @@ jobs:
         sudo apt update
         sudo apt-get install -y libopenslide-dev openslide-tools libopenjp2-7 libopenjp2-tools
         python -m pip install --upgrade pip
-        python -m pip install ruff==0.7.4 pytest pytest-cov pytest-runner
+        python -m pip install ruff==0.8.1 pytest pytest-cov pytest-runner
         pip install -r requirements/requirements.txt
     - name: Cache tiatoolbox static assets
       uses: actions/cache@v3

benchmarks/annotation_store.ipynb

@@ -195,7 +195,7 @@
     "from typing import TYPE_CHECKING, Any\n",
     "\n",
     "import numpy as np\n",
-    "from IPython.display import display\n",
+    "from IPython.display import display_svg\n",
     "from matplotlib import patheffects\n",
     "from matplotlib import pyplot as plt\n",
     "from shapely import affinity\n",
@@ -444,7 +444,7 @@
    ],
    "source": [
     "for n in range(4):\n",
-    "    display(cell_polygon(xy=(0, 0), n_points=20, repeat_first=False, seed=n))"
+    "    display_svg(cell_polygon(xy=(0, 0), n_points=20, repeat_first=False, seed=n))"
    ]
   },
   {

requirements/requirements_dev.txt

@@ -10,7 +10,7 @@ pytest>=7.2.0
 pytest-cov>=4.0.0
 pytest-runner>=6.0
 pytest-xdist[psutil]
-ruff==0.7.4  # This will be updated by pre-commit bot to latest version
+ruff==0.8.1  # This will be updated by pre-commit bot to latest version
 toml>=0.10.2
 twine>=4.0.1
 wheel>=0.37.1

tiatoolbox/utils/visualization.py

@@ -914,26 +914,27 @@ def _set_mapper(
 
     def __setattr__(
         self: AnnotationRenderer,
-        __name: str,
-        __value: str | list | dict | None,
+        name: str,
+        value: str | list | dict | None,
+        /,
     ) -> None:
         """Set attribute each time an attribute is set."""
-        if __name == "mapper":
+        if name == "mapper":
             # save a more readable version of the mapper too
-            _ = self._set_mapper(__value)
+            _ = self._set_mapper(value)
             return
-        if __name == "blur_radius" and isinstance(__value, int):
+        if name == "blur_radius" and isinstance(value, int):
             # need to change additional settings
-            if __value > 0:
-                self.__dict__["blur"] = ImageFilter.GaussianBlur(__value)
+            if value > 0:
+                self.__dict__["blur"] = ImageFilter.GaussianBlur(value)
                 self.__dict__["edge_thickness"] = 0
             else:
                 self.__dict__["blur"] = None
                 self.__dict__["edge_thickness"] = self.__dict__["edge_thickness_old"]
-        elif __name == "edge_thickness":
-            self.__dict__["edge_thickness_old"] = __value
+        elif name == "edge_thickness":
+            self.__dict__["edge_thickness_old"] = value
 
-        self.__dict__[__name] = __value
+        self.__dict__[name] = value
 
     def render_annotations(
         self: AnnotationRenderer,

tiatoolbox/visualization/bokeh_app/main.py

@@ -645,24 +645,25 @@ def __init__(self: ViewerState, slide_path: str | Path) -> None:
 
     def __setattr__(
         self: ViewerState,
-        __name: str,
-        __value: Any,  # noqa: ANN401
+        name: str,
+        value: Any,  # noqa: ANN401
+        /,
     ) -> None:
         """Set an attribute of the viewer state."""
-        if __name == "types":
-            self.__dict__["mapper"] = make_color_dict(__value)
+        if name == "types":
+            self.__dict__["mapper"] = make_color_dict(value)
             self.__dict__["colors"] = list(self.mapper.values())
             if self.cprop == "type":
                 update_mapper()
             # We will standardise the types to strings, keep dict of originals
-            self.__dict__["orig_types"] = {str(x): x for x in __value}
-            __value = [str(x) for x in __value]
+            self.__dict__["orig_types"] = {str(x): x for x in value}
+            value = [str(x) for x in value]
 
-        if __name == "wsi":
-            z = ZoomifyGenerator(__value, tile_size=256)
+        if name == "wsi":
+            z = ZoomifyGenerator(value, tile_size=256)
             self.__dict__["num_zoom_levels"] = z.level_count
 
-        self.__dict__[__name] = __value
+        self.__dict__[name] = value
 
 
 # endregion