Merge branch 'develop' into dev-define-engines-abc

Author: shaneahmed

.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==0.5.2 pytest pytest-cov pytest-runner
+        python -m pip install ruff==0.5.6 "pytest<8.3.0" 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: v0.5.2
+    rev: v0.5.6
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

requirements/requirements_dev.txt

@@ -7,11 +7,11 @@ mypy>=1.6.1
 pip>=22.3
 poetry-bumpversion>=0.3.1
 pre-commit>=2.20.0
-pytest>=7.2.0
+pytest>=7.2.0, <8.3.0
 pytest-cov>=4.0.0
 pytest-runner>=6.0
 pytest-xdist[psutil]
-ruff==0.5.2  # This will be updated by pre-commit bot to latest version
+ruff==0.5.6  # 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/storage.py

@@ -1841,10 +1841,10 @@ def _dump_cases(
             # It is a file-like object, write to it
             if hasattr(fp, "write"):
                 file_handle = cast(IO, fp)
-                return file_fn(file_handle)
+                return file_fn(file_handle)  # type: ignore[func-returns-value]
             # Turn a path into a file handle, then write to it
             with Path(fp).open("w", encoding="utf-8") as file_handle:
-                return file_fn(file_handle)
+                return file_fn(file_handle)  # type: ignore[func-returns-value]
         # Return as str or bytes if no handle/path is given
         return none_fn()
 
@@ -2840,7 +2840,7 @@ def _initialize_query_string_parameters(
 
         return query_string, query_parameters
 
-    def _query(  # noqa: PLR0913
+    def _query(
         self: SQLiteStore,
         columns: str,
         geometry: Geometry | None = None,

tiatoolbox/models/engine/multi_task_segmentor.py

@@ -242,7 +242,7 @@ class MultiTaskSegmentor(NucleusInstanceSegmentor):
 
     """
 
-    def __init__(  # noqa: PLR0913
+    def __init__(
         self: MultiTaskSegmentor,
         batch_size: int = 8,
         num_loader_workers: int = 0,

tiatoolbox/tools/patchextraction.py

@@ -623,7 +623,7 @@ class SlidingWindowPatchExtractor(PatchExtractor):
 
     """
 
-    def __init__(  # noqa: PLR0913
+    def __init__(
         self: SlidingWindowPatchExtractor,
         input_img: str | Path | np.ndarray,
         patch_size: int | tuple[int, int],

tiatoolbox/utils/misc.py

@@ -1171,9 +1171,7 @@ def add_from_dat(
         anns = []
         for subcat in data:
             if (
-                subcat == "resolution"
-                or subcat == "proc_dimensions"
-                or subcat == "base_dimensions"
+                subcat in {"resolution", "proc_dimensions", "base_dimensions"}
                 or "resolution" in subcat
             ):
                 continue

tiatoolbox/wsicore/wsimeta.py

@@ -96,7 +96,7 @@ class WSIMeta:
 
     _valid_axes_characters = "YXSTZ"
 
-    def __init__(  # noqa: PLR0913
+    def __init__(
         self: WSIMeta,
         slide_dimensions: tuple[int, int],
         axes: str,