Merge branch 'develop' into add-slide-data

Author: shaneahmed

.github/workflows/python-package.yml

@@ -30,7 +30,7 @@ jobs:
         sudo apt update
         sudo apt-get install -y libopenjp2-7 libopenjp2-tools
         python -m pip install --upgrade pip
-        python -m pip install ruff==0.12.11 pytest pytest-cov pytest-runner
+        python -m pip install ruff==0.13.3 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: v0.12.11
+    rev: v0.13.3
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

examples/04-patch-extraction.ipynb

@@ -762,7 +762,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": null,
    "metadata": {
     "colab": {
      "base_uri": "https://localhost:8080/",
@@ -793,7 +793,7 @@
    "source": [
     "def plot_mask_and_locs(thumb: np.ndarray, mask: np.ndarray, locs: dict) -> None:\n",
     "    \"\"\"Plots slide thumbnail, mask and patch locations side by side.\"\"\"\n",
-    "    fig, axs = plt.subplots(1, 3)\n",
+    "    _, axs = plt.subplots(1, 3)\n",
     "    for ax in axs:\n",
     "        ax.set(xticks=[], yticks=[])\n",
     "\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==0.12.11  # This will be updated by pre-commit bot to latest version
+ruff==0.13.3  # This will be updated by pre-commit bot to latest version
 toml>=0.10.2
 twine>=4.0.1
 wheel>=0.37.1

tests/models/test_patch_predictor.py

@@ -147,7 +147,7 @@ def test_patch_dataset_crash(tmp_path: Path) -> None:
         ],
         dtype=object,
     )
-    with pytest.raises(ValueError, match="Provided input array is non-numerical."):
+    with pytest.raises(ValueError, match=r"Provided input array is non-numerical."):
         _ = PatchDataset(imgs)
 
     # ndarray(s) of NHW images
@@ -160,7 +160,7 @@ def test_patch_dataset_crash(tmp_path: Path) -> None:
         RNG.integers(0, 255, (4, 4, 3)),
         RNG.integers(0, 255, (4, 5, 3)),
     ]
-    with pytest.raises(ValueError, match="Images must have the same dimensions."):
+    with pytest.raises(ValueError, match=r"Images must have the same dimensions."):
         _ = PatchDataset(imgs)
 
     # list of ndarray(s) with HW and HWC mixed up
@@ -170,15 +170,15 @@ def test_patch_dataset_crash(tmp_path: Path) -> None:
     ]
     with pytest.raises(
         ValueError,
-        match="Each sample must be an array of the form HWC.",
+        match=r"Each sample must be an array of the form HWC.",
     ):
         _ = PatchDataset(imgs)
 
     # list of mixed dtype
     imgs = [RNG.integers(0, 255, (4, 4, 3)), "you_should_crash_here", 123, 456]
     with pytest.raises(
         ValueError,
-        match="Input must be either a list/array of images or a list of "
+        match=r"Input must be either a list/array of images or a list of "
         "valid image paths.",
     ):
         _ = PatchDataset(imgs)
@@ -187,7 +187,7 @@ def test_patch_dataset_crash(tmp_path: Path) -> None:
     imgs = ["you_should_crash_here", 123, 456]
     with pytest.raises(
         ValueError,
-        match="Input must be either a list/array of images or a list of "
+        match=r"Input must be either a list/array of images or a list of "
         "valid image paths.",
     ):
         _ = PatchDataset(imgs)
@@ -290,11 +290,11 @@ def __getitem__(self: Proto, idx: int) -> object:
         )
 
     # invalid mode
-    with pytest.raises(ValueError, match="`X` is not supported."):
+    with pytest.raises(ValueError, match=r"`X` is not supported."):
         reuse_init(mode="X")
 
     # invalid patch
-    with pytest.raises(ValueError, match="Invalid `patch_input_shape` value None."):
+    with pytest.raises(ValueError, match=r"Invalid `patch_input_shape` value None."):
         reuse_init()
     with pytest.raises(
         ValueError,
@@ -306,7 +306,7 @@ def __getitem__(self: Proto, idx: int) -> object:
         match=r"Invalid `patch_input_shape` value \['512' 'a'\].",
     ):
         reuse_init_wsi(patch_input_shape=[512, "a"])
-    with pytest.raises(ValueError, match="Invalid `stride_shape` value None."):
+    with pytest.raises(ValueError, match=r"Invalid `stride_shape` value None."):
         reuse_init_wsi(patch_input_shape=512)
     # invalid stride
     with pytest.raises(

tests/test_annotation_stores.py

@@ -569,7 +569,7 @@ def test_sqlite_store_index_version_error(monkeypatch: object) -> None:
     """Test adding an index with SQlite <3.9."""
     store = SQLiteStore()
     monkeypatch.setattr(sqlite3, "sqlite_version_info", (3, 8, 0))
-    with pytest.raises(EnvironmentError, match="Requires sqlite version 3.9.0"):
+    with pytest.raises(EnvironmentError, match=r"Requires sqlite version 3.9.0"):
         store.create_index("foo", lambda _, p: "foo" in p)
 
 

tests/test_dsl.py

@@ -467,7 +467,7 @@ def test_has_key_exception(
         """Test has_key function with exception."""
         eval_globals, eval_locals, _ = extract_variables(scenario_variables)
         query = "has_key(1, 'a')"
-        with pytest.raises(TypeError, match="(not iterable)|(Unsupported type)"):
+        with pytest.raises(TypeError, match=r"(not iterable)|(Unsupported type)"):
             _ = eval(  # skipcq: PYL-W0123
                 query,
                 eval_globals,

tests/test_exceptions.py

@@ -13,6 +13,6 @@ def test_exception_tests() -> None:
 
     with pytest.raises(
         ValueError,
-        match="`stain_matrix` is only defined when using.*custom",
+        match=r"`stain_matrix` is only defined when using.*custom",
     ):
         get_normalizer(method_name="reinhard", stain_matrix="[1, 2]")

tests/test_patch_extraction.py

@@ -470,7 +470,7 @@ def test_filter_coordinates() -> None:
     # Test for bad mask input
     with pytest.raises(
         TypeError,
-        match="`mask_reader` should be wsireader.VirtualWSIReader.",
+        match=r"`mask_reader` should be wsireader.VirtualWSIReader.",
     ):
         PatchExtractor.filter_coordinates(
             mask,
@@ -495,14 +495,14 @@ def test_filter_coordinates() -> None:
         )
 
     # Test for put of range min_mask_ratio
-    with pytest.raises(ValueError, match="`min_mask_ratio` must be between 0 and 1."):
+    with pytest.raises(ValueError, match=r"`min_mask_ratio` must be between 0 and 1."):
         PatchExtractor.filter_coordinates(
             mask_reader,
             bbox_list,
             slide_shape,
             min_mask_ratio=-0.5,
         )
-    with pytest.raises(ValueError, match="`min_mask_ratio` must be between 0 and 1."):
+    with pytest.raises(ValueError, match=r"`min_mask_ratio` must be between 0 and 1."):
         PatchExtractor.filter_coordinates(
             mask_reader,
             bbox_list,

tests/test_tileserver.py

@@ -701,7 +701,7 @@ def test_no_ann_layer(empty_app: TileServer, remote_sample: Callable) -> None:
             "/tileserver/slide",
             data={"slide_path": safe_str(remote_sample("svs-1-small"))},
         )
-        with pytest.raises(ValueError, match="No annotation layer found."):
+        with pytest.raises(ValueError, match=r"No annotation layer found."):
             client.get("/tileserver/prop_names/all")