Merge branch 'develop' into feature-extractor-example

.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

.pre-commit-config.yaml

@@ -60,7 +60,7 @@ repos:
       - id: rst-inline-touching-normal # Detect mistake of inline code touching normal text in rst.
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.7.4
+    rev: v0.8.1
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

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/annotation/__init__.py

@@ -8,4 +8,4 @@
     SQLiteStore,
 )
 
-__all__ = ["AnnotationStore", "SQLiteStore", "DictionaryStore", "Annotation"]
+__all__ = ["Annotation", "AnnotationStore", "DictionaryStore", "SQLiteStore"]

tiatoolbox/annotation/storage.py

@@ -1371,11 +1371,13 @@ def bquery(
             for key, annotation in self.items()
             if (
                 query_geometry is None
-                or isinstance(query_geometry, (Polygon, Point, LineString))
-                and Polygon.from_bounds(*annotation.geometry.bounds).intersects(
-                    Polygon.from_bounds(*query_geometry.bounds),
+                or (
+                    isinstance(query_geometry, (Polygon, Point, LineString))
+                    and Polygon.from_bounds(*annotation.geometry.bounds).intersects(
+                        Polygon.from_bounds(*query_geometry.bounds),
+                    )
+                    and self._eval_where(where, annotation.properties)
                 )
-                and self._eval_where(where, annotation.properties)
             )
         }
 

tiatoolbox/models/__init__.py

@@ -25,14 +25,14 @@
 )
 
 __all__ = [
+    "SCCNN",
     "HoVerNet",
     "HoVerNetPlus",
     "IDaRS",
     "MapDe",
     "MicroNet",
-    "NuClick",
-    "SCCNN",
     "MultiTaskSegmentor",
+    "NuClick",
     "NucleusInstanceSegmentor",
     "PatchPredictor",
     "SemanticSegmentor",

tiatoolbox/models/architecture/__init__.py

@@ -18,7 +18,7 @@
     from tiatoolbox.models.models_abc import IOConfigABC
 
 
-__all__ = ["get_pretrained_model", "fetch_pretrained_weights"]
+__all__ = ["fetch_pretrained_weights", "get_pretrained_model"]
 PRETRAINED_INFO = rcParam["pretrained_model_info"]
 
 

tiatoolbox/utils/__init__.py

@@ -20,10 +20,10 @@
 )
 
 __all__ = [
+    "download_data",
     "imread",
     "imwrite",
-    "save_yaml",
     "save_as_json",
-    "download_data",
+    "save_yaml",
     "unzip_data",
 ]

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

@@ -308,10 +308,8 @@ def get_mapper_for_prop(prop: str, mapper_type: str = "auto") -> str | dict[str,
     prop_vals = json.loads(resp.text)
     # If auto, guess what cmap should be
     if (
-        (len(prop_vals) > MAX_CAT or len(prop_vals) == 0)
-        and mapper_type == "auto"
-        or mapper_type == "continuous"
-    ):
+        (len(prop_vals) > MAX_CAT or len(prop_vals) == 0) and mapper_type == "auto"
+    ) or mapper_type == "continuous":
         cmap = (
             "viridis" if UI["cmap_select"].value == "dict" else UI["cmap_select"].value
         )
@@ -647,24 +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

tiatoolbox/wsicore/__init__.py

@@ -7,6 +7,6 @@
 
 # Top level imports
 __all__ = [
-    "WSIReader",
     "WSIMeta",
+    "WSIReader",
 ]