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==0.4.9 pytest pytest-cov pytest-runner
+        python -m pip install ruff==0.4.10 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: v0.4.9
+    rev: v0.4.10
     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==0.4.9  # This will be updated by pre-commit bot to latest version
+ruff==0.4.10  # This will be updated by pre-commit bot to latest version
 toml>=0.10.2
 twine>=4.0.1
 wheel>=0.37.1

tests/test_annotation_stores.py

@@ -27,6 +27,7 @@
     Polygon,
 )
 
+from tiatoolbox import logger
 from tiatoolbox.annotation import (
     Annotation,
     AnnotationStore,
@@ -52,6 +53,14 @@
 FILLED_LEN = 2 * (GRID_SIZE[0] * GRID_SIZE[1])
 RNG = np.random.default_rng(0)  # Numpy Random Generator
 
+# ----------------------------------------------------------------------
+# Resets
+# ----------------------------------------------------------------------
+
+# Reset filters in logger.
+for filter_ in logger.filters:
+    logger.removeFilter(filter_)
+
 # ----------------------------------------------------------------------
 # Helper Functions
 # ----------------------------------------------------------------------

tests/test_init.py

@@ -109,6 +109,14 @@ def test_logger_output() -> None:
 
 def test_duplicate_filter(caplog: pytest.LogCaptureFixture) -> None:
     """Test DuplicateFilter for warnings."""
+    # Test logger reset after applying duplicate filter.
+    duplicate_filter = DuplicateFilter()
+    logger.addFilter(duplicate_filter)
+
+    # Reset filters in logger.
+    for filter_ in logger.filters:
+        logger.removeFilter(filter_)
+
     for _ in range(2):
         logger.warning("Test duplicate filter warnings.")
     assert "Test duplicate filter warnings." in caplog.text

tiatoolbox/annotation/storage.py

@@ -814,7 +814,7 @@ def patch_many(
         geometries = geometries or (None for _ in keys)  # pragma: no branch
         # Update the store
         for key, geometry, properties in zip(keys, geometries, properties_iter):
-            properties_ = copy.deepcopy(properties)
+            properties_ = cast(dict[str, Any], copy.deepcopy(properties))
             self.patch(key, geometry, properties_)
 
     def remove(self: AnnotationStore, key: str) -> None: