Merge branch 'develop' into mypy-tiatoolbox-cli

.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==0.6.1 pytest pytest-cov pytest-runner
+        python -m pip install ruff==0.6.2 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: v0.6.1
+    rev: v0.6.2
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

requirements/requirements_dev.txt

@@ -11,7 +11,7 @@ pytest>=7.2.0
 pytest-cov>=4.0.0
 pytest-runner>=6.0
 pytest-xdist[psutil]
-ruff==0.6.1  # This will be updated by pre-commit bot to latest version
+ruff==0.6.2  # 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/transforms.py

@@ -53,9 +53,9 @@ def background_composite(
     )
     composite.alpha_composite(image)
     if not alpha:
-        return np.asarray(composite.convert("RGB"))
+        return np.array(composite.convert("RGB"))
 
-    return np.asarray(composite)
+    return np.array(composite)
 
 
 def _convert_scalar_to_width_height(array: np.ndarray) -> np.ndarray:

tiatoolbox/visualization/bokeh_app/main.py

@@ -689,7 +689,7 @@ def slide_toggle_cb(attr: str) -> None:  # noqa: ARG001
         UI["p"].renderers[0].alpha = 0.0
 
 
-def node_select_cb(attr: str, old: int, new: int) -> None:  # noqa: ARG001
+def node_select_cb(attr: str, old: int, new: int) -> None:
     """Placeholder callback to do something on node selection."""
     # Do something on node select if desired