Merge branch 'develop' into add-registered-slide-vis

Author: shaneahmed

.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