Merge branch 'develop' into multichannel-reading

.github/workflows/mypy-type-check.yml

@@ -40,7 +40,7 @@ jobs:
         mypy --install-types --non-interactive --follow-imports=skip \
           tiatoolbox/__init__.py \
           tiatoolbox/__main__.py \
-          tiatoolbox/typing.py \
+          tiatoolbox/type_hints.py \
           tiatoolbox/tiatoolbox.py \
           tiatoolbox/utils \
           tiatoolbox/tools \

.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==0.8.2 pytest pytest-cov pytest-runner
+        python -m pip install ruff==0.9.4 pytest pytest-cov pytest-runner
         pip install -r requirements/requirements.txt
     - name: Cache tiatoolbox static assets
       uses: actions/cache@v3

.pre-commit-config.yaml

@@ -23,7 +23,7 @@ repos:
         - mdformat-black
         - mdformat-myst
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.21
+    rev: 0.7.22
     hooks:
     - id: mdformat
       # Optionally add plugins
@@ -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: v0.8.6
+    rev: v0.9.4
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

pre-commit/notebook_urls.py

@@ -197,7 +197,9 @@ def check_notebook(
         for line_num, line in enumerate(cell["source"]):
             new_line = replace_line(line, to_ref, replacements)
             if new_line != line:
-                print(f"{path.name}: Changed (cell {cell_num+1}, line {line_num+1})")
+                print(
+                    f"{path.name}: Changed (cell {cell_num + 1}, line {line_num + 1})"
+                )
                 changed = True
                 cell["source"][line_num] = new_line
     return changed, notebook

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==0.8.2  # This will be updated by pre-commit bot to latest version
+ruff==0.9.4  # 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_multi_task_segmentor.py

@@ -128,9 +128,9 @@ def test_functionality_hovernetplus(remote_sample: Callable, tmp_path: Path) ->
 
     assert len(inst_dict) > 0, "Must have some nuclei."
     assert layer_map is not None, "Must have some layers."
-    assert (
-        layer_map.shape == required_dims
-    ), "Output layer map dimensions must be same as the expected output shape"
+    assert layer_map.shape == required_dims, (
+        "Output layer map dimensions must be same as the expected output shape"
+    )
 
 
 def test_functionality_hovernet(remote_sample: Callable, tmp_path: Path) -> None:

tests/test_annotation_stores.py

@@ -40,7 +40,7 @@
 if TYPE_CHECKING:  # pragma: no cover
     from numbers import Number
 
-    from tiatoolbox.typing import Geometry
+    from tiatoolbox.type_hints import Geometry
 
 
 sqlite3.enable_callback_tracebacks(True)  # noqa: FBT003

tests/test_docs.py

@@ -141,7 +141,7 @@ def raise_source_exception(
         for n, line in enumerate(source.splitlines())
     ]
     if source_offset:
-        source_lines.insert(source_lineno, f"{' '*(source_offset+3)}^ {message}")
+        source_lines.insert(source_lineno, f"{' ' * (source_offset + 3)}^ {message}")
     annotated_source = "\n".join(source_lines)
     exception = type(exception) if exception else SyntaxError
     msg = f"{rel_path}:{file_lineno}: {message}\n{annotated_source}"

tests/test_patch_extraction.py

@@ -21,7 +21,7 @@
 )
 
 if TYPE_CHECKING:
-    from tiatoolbox.typing import IntPair, Resolution, Units
+    from tiatoolbox.type_hints import IntPair, Resolution, Units
 
 
 def read_points_patches(

tests/test_tileserver.py

@@ -461,7 +461,7 @@ def test_change_overlay(  # noqa: PLR0915
         assert response.status_code == 200
         assert response.content_type == "text/html; charset=utf-8"
         # check that the overlay has been correctly added
-        lname = f"layer{len(empty_app.pyramids[session_id])-1}"
+        lname = f"layer{len(empty_app.pyramids[session_id]) - 1}"
         layer = empty_app.pyramids[session_id][lname]
         assert layer.wsi.info.file_path == overlay_path
 
@@ -493,7 +493,7 @@ def test_change_overlay(  # noqa: PLR0915
             data={"overlay_path": safe_str(jpg_path)},
         )
         # check that the overlay has been correctly added
-        lname = f"layer{len(empty_app.pyramids[session_id])-1}"
+        lname = f"layer{len(empty_app.pyramids[session_id]) - 1}"
         layer = empty_app.pyramids[session_id][lname]
         assert np.all(layer.wsi.img == imread(jpg_path))
 
@@ -517,7 +517,7 @@ def test_change_overlay(  # noqa: PLR0915
             data={"overlay_path": safe_str(tiff_path)},
         )
         # check that the overlay has been correctly added
-        lname = f"layer{len(empty_app.pyramids[session_id])-1}"
+        lname = f"layer{len(empty_app.pyramids[session_id]) - 1}"
         layer = empty_app.pyramids[session_id][lname]
         assert layer.wsi.info.file_path == tiff_path
 

tests/test_utils.py

@@ -28,7 +28,7 @@
 from tiatoolbox.utils.transforms import locsize2bounds
 
 if TYPE_CHECKING:
-    from tiatoolbox.typing import IntBounds
+    from tiatoolbox.type_hints import IntBounds
 
 RNG = np.random.default_rng()  # Numpy Random Generator
 

tests/test_wsireader.py

@@ -52,7 +52,7 @@
     import requests
     from openslide import OpenSlide
 
-    from tiatoolbox.typing import IntBounds, IntPair
+    from tiatoolbox.type_hints import IntBounds, IntPair
     from tiatoolbox.wsicore.wsimeta import WSIMeta
 
 # -------------------------------------------------------------------------------------

tiatoolbox/annotation/storage.py

@@ -83,10 +83,10 @@
     py_regexp,
 )
 from tiatoolbox.enums import GeometryType
-from tiatoolbox.typing import CallablePredicate, CallableSelect, Geometry
+from tiatoolbox.type_hints import CallablePredicate, CallableSelect, Geometry
 
 if TYPE_CHECKING:  # pragma: no cover
-    from tiatoolbox.typing import (
+    from tiatoolbox.type_hints import (
         Predicate,
         Properties,
         QueryGeometry,

tiatoolbox/models/architecture/hovernet.py

@@ -338,8 +338,7 @@ def __init__(
 
         if mode not in ["original", "fast"]:
             msg = (
-                f"Invalid mode {mode} for HoVerNet. "
-                f"Only support `original` or `fast`."
+                f"Invalid mode {mode} for HoVerNet. Only support `original` or `fast`."
             )
             raise ValueError(
                 msg,

tiatoolbox/models/architecture/nuclick.py

@@ -24,7 +24,7 @@
 from tiatoolbox.models.models_abc import ModelABC
 
 if TYPE_CHECKING:  # pragma: no cover
-    from tiatoolbox.typing import IntPair
+    from tiatoolbox.type_hints import IntPair
 
 bn_axis = 1
 

tiatoolbox/models/architecture/utils.py

@@ -88,14 +88,6 @@ def compile_model(
         logger.warning(msg=msg)
         return model
 
-    # This check will be removed when torch.compile is supported in Python 3.12+
-    if sys.version_info > (3, 12):  # pragma: no cover
-        msg = "torch-compile is currently not supported in Python 3.12+."
-        logger.warning(
-            msg=msg,
-        )
-        return model
-
     if isinstance(  # pragma: no cover
         model,
         torch._dynamo.eval_frame.OptimizedModule,  # skipcq: PYL-W0212 # noqa: SLF001

tiatoolbox/models/dataset/classification.py

@@ -20,7 +20,7 @@
     import torch
     from PIL.Image import Image
 
-    from tiatoolbox.typing import IntPair, Resolution, Units
+    from tiatoolbox.type_hints import IntPair, Resolution, Units
 
 
 class _TorchPreprocCaller:

tiatoolbox/models/engine/multi_task_segmentor.py

@@ -43,7 +43,7 @@
 if TYPE_CHECKING:  # pragma: no cover
     import torch
 
-    from tiatoolbox.typing import IntBounds
+    from tiatoolbox.type_hints import IntBounds
 
 
 # Python is yet to be able to natively pickle Object method/static method.

tiatoolbox/models/engine/patch_predictor.py

@@ -21,7 +21,7 @@
 from tiatoolbox.wsicore.wsireader import VirtualWSIReader, WSIReader
 
 if TYPE_CHECKING:  # pragma: no cover
-    from tiatoolbox.typing import IntPair, Resolution, Units
+    from tiatoolbox.type_hints import IntPair, Resolution, Units
 
 
 class IOPatchPredictorConfig(IOSegmentorConfig):

tiatoolbox/models/engine/semantic_segmentor.py

@@ -28,7 +28,7 @@
 if TYPE_CHECKING:  # pragma: no cover
     from multiprocessing.managers import Namespace
 
-    from tiatoolbox.typing import IntPair, Resolution, Units
+    from tiatoolbox.type_hints import IntPair, Resolution, Units
 
 
 def _estimate_canvas_parameters(

tiatoolbox/tools/patchextraction.py

@@ -20,7 +20,7 @@
     from pandas import DataFrame
 
     from tiatoolbox.annotation.storage import AnnotationStore
-    from tiatoolbox.typing import Resolution, Units
+    from tiatoolbox.type_hints import Resolution, Units
 
 
 def validate_shape(shape: np.ndarray) -> bool:

tiatoolbox/tools/registration/wsi_registration.py

@@ -24,7 +24,7 @@
 from tiatoolbox.wsicore.wsireader import VirtualWSIReader, WSIReader
 
 if TYPE_CHECKING:  # pragma: no cover
-    from tiatoolbox.typing import IntBounds, Resolution, Units
+    from tiatoolbox.type_hints import IntBounds, Resolution, Units
 
 RGB_IMAGE_DIM = 3
 BIN_MASK_DIM = 2

tiatoolbox/utils/image.py

@@ -18,7 +18,7 @@
 )
 
 if TYPE_CHECKING:  # pragma: no cover
-    from tiatoolbox.typing import IntBounds, NumpyPadLiteral
+    from tiatoolbox.type_hints import IntBounds, NumpyPadLiteral
 
 PADDING_TO_BOUNDS = np.array([-1, -1, 1, 1])
 """

tiatoolbox/utils/misc.py

@@ -220,8 +220,7 @@ def load_stain_matrix(stain_matrix_input: np.ndarray | PathLike) -> np.ndarray:
         _, __, suffixes = split_path_name_ext(stain_matrix_input)
         if suffixes[-1] not in [".csv", ".npy"]:
             msg = (
-                "If supplying a path to a stain matrix, "
-                "use either a npy or a csv file"
+                "If supplying a path to a stain matrix, use either a npy or a csv file"
             )
             raise FileNotSupportedError(
                 msg,

tiatoolbox/visualization/bokeh_app/main.py

@@ -1411,7 +1411,7 @@ def segment_on_box() -> None:
     # Make a mask defining the box
     thumb = UI["vstate"].wsi.slide_thumbnail()
     conv_mpp = UI["vstate"].dims[0] / thumb.shape[1]
-    msg = f'box tl: {UI["box_source"].data["x"][0]}, {UI["box_source"].data["y"][0]}'
+    msg = f"box tl: {UI['box_source'].data['x'][0]}, {UI['box_source'].data['y'][0]}"
     logger.info(msg)
     x = round(
         (UI["box_source"].data["x"][0] - 0.5 * UI["box_source"].data["width"][0])

tiatoolbox/visualization/tileserver.py

@@ -103,7 +103,7 @@ def __init__(  # noqa: PLR0915
         if isinstance(layers, list):
             layers_dict = {"slide": layers[0]}
             for i, p in enumerate(layers[1:]):
-                layers_dict[f"layer-{i+1}"] = p
+                layers_dict[f"layer-{i + 1}"] = p
             layers = layers_dict
         # Set up the layer dict.
         meta = None

tiatoolbox/wsicore/wsimeta.py

@@ -20,7 +20,7 @@
 if TYPE_CHECKING:  # pragma: no cover
     from collections.abc import Mapping, Sequence
 
-    from tiatoolbox.typing import Resolution, Units
+    from tiatoolbox.type_hints import Resolution, Units
 
 
 class WSIMeta:

tiatoolbox/wsicore/wsireader.py

@@ -36,7 +36,14 @@
 
     import glymur
 
-    from tiatoolbox.typing import Bounds, IntBounds, IntPair, NumPair, Resolution, Units
+    from tiatoolbox.type_hints import (
+        Bounds,
+        IntBounds,
+        IntPair,
+        NumPair,
+        Resolution,
+        Units,
+    )
     from tiatoolbox.wsicore.metadata.ngff import Multiscales
 
 pixman_warning()