Merge branch 'dev-define-engines-abc' into dev-update-engine-abc-wsi

.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==0.0.286 pytest pytest-cov pytest-runner
+        python -m pip install ruff==0.1.13 pytest pytest-cov pytest-runner
         pip install -r requirements/requirements.txt
     - name: Cache tiatoolbox static assets
       uses: actions/cache@v3

.pre-commit-config.yaml

@@ -68,7 +68,7 @@ repos:
         language: python
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.1.11
+    rev: v0.1.13
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

requirements/requirements.txt

@@ -32,5 +32,5 @@ torch>=2.1.0
 torchvision>=0.15.0
 tqdm>=4.64.1
 umap-learn>=0.5.3
-wsidicom>=0.7.0
+wsidicom>=0.7.0, <0.18.0 # newly released version is causing tests to fail for now
 zarr>=2.13.3

requirements/requirements_dev.txt

@@ -12,7 +12,7 @@ pytest>=7.2.0
 pytest-cov>=4.0.0
 pytest-runner>=6.0
 pytest-xdist[psutil]
-ruff==0.0.286  # This will be updated by pre-commit bot to latest version
+ruff==0.1.13  # This will be updated by pre-commit bot to latest version
 toml>=0.10.2
 twine>=4.0.1
 wheel>=0.37.1

tiatoolbox/wsicore/metadata/ngff.py

@@ -100,7 +100,7 @@ class CoordinateTransform:
 
     """
 
-    type: str = "identity"  # noqa: A003
+    type: str = "identity"
     scale: list[float] | None = None
 
 
@@ -140,7 +140,7 @@ class Axis:
     """
 
     name: TCZYX
-    type: Literal["time", "space", "channel"]  # noqa: A003
+    type: Literal["time", "space", "channel"]
     unit: SpaceUnits | TimeUnits | None = None
 
 
@@ -186,8 +186,8 @@ class Window:
     """
 
     end: Number = 255
-    max: Number = 255  # noqa: A003
-    min: Number = 0  # noqa: A003
+    max: Number = 255
+    min: Number = 0
     start: Number = 0
 
 
@@ -257,7 +257,7 @@ class Omero:
     """
 
     name: str | None = None
-    id: int = 1  # noqa: A003
+    id: int = 1
     channels: list = field(
         default_factory=lambda: [
             Channel(label="Red", color="FF0000"),

tiatoolbox/wsicore/wsireader.py

@@ -225,7 +225,7 @@ class WSIReader:
     """
 
     @staticmethod
-    def open(  # noqa: A003, PLR0911
+    def open(  # noqa: PLR0911
         input_img: str | Path | np.ndarray | WSIReader,
         mpp: tuple[Number, Number] | None = None,
         power: Number | None = None,