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

# Conflicts:
#	tests/models/test_feature_extractor.py
#	tests/models/test_multi_task_segmentor.py
#	tests/models/test_nucleus_instance_segmentor.py
#	tests/models/test_patch_predictor.py
#	tests/models/test_semantic_segmentation.py
#	tiatoolbox/models/architecture/__init__.py

Author: shaneahmed

requirements/requirements.conda.yml

@@ -9,6 +9,6 @@ dependencies:
   - openslide
   - pip>=20.0.2
   - pixman>=0.39.0
-  - python>=3.9, <=3.12
+  - python>=3.10, <=3.13
   - pip:
     - -r requirements.txt

requirements/requirements.dev.conda.yml

@@ -9,6 +9,6 @@ dependencies:
   - openslide
   - pip>=20.0.2
   - pixman>=0.39.0
-  - python>=3.9, <=3.12
+  - python>=3.10, <=3.13
   - pip:
       - -r requirements_dev.txt

requirements/requirements.txt

@@ -9,6 +9,7 @@ filelock>=3.9.0
 flask>=2.2.2
 flask-cors>=4.0.0
 glymur>=0.12.7
+huggingface_hub>=0.33.3
 imagecodecs>=2022.9.26
 joblib>=1.1.1
 jupyterlab>=3.5.2

requirements/requirements.win64.conda.yml

@@ -9,6 +9,6 @@ dependencies:
   - openjpeg>=2.4.0
   - pip>=20.0.2
   - pixman>=0.39.0
-  - python>=3.9, <=3.12
+  - python>=3.10, <=3.13
   - pip:
       - -r requirements.txt

requirements/requirements.win64.dev.conda.yml

@@ -9,6 +9,6 @@ dependencies:
   - openjpeg>=2.4.0
   - pip>=20.0.2
   - pixman>=0.39.0
-  - python>=3.9, <=3.12
+  - python>=3.10, <=3.13
   - pip:
       - -r requirements_dev.txt

tests/conftest.py

@@ -658,3 +658,39 @@ def timed(fn: Callable, *args: object) -> (Callable, float):
         end = time.time()
         compile_time = end - start
     return result, compile_time
+
+
+_tmp_paths: list[Path] = []
+
+
+@pytest.fixture
+def track_tmp_path(tmp_path: Path) -> Path:
+    """This fixture tracks `tmp_path` for clean up.
+
+    Fixture that wraps pytest's built-in `tmp_path` and tracks each temporary path
+    for later cleanup at the module level.
+
+    Returns:
+        Path: The temporary directory path for the current test function.
+
+    """
+    _tmp_paths.append(tmp_path)
+    return tmp_path
+
+
+@pytest.fixture(scope="module", autouse=True)
+def module_teardown() -> None:
+    """This module tears down temporary data directories.
+
+    Module-scoped fixture that automatically runs after all tests in a module.
+    It cleans up all temporary paths tracked during the module's execution.
+
+    Yields:
+        None: Allows pytest to run tests before executing the teardown logic.
+
+    """
+    yield
+    for path in _tmp_paths:
+        if path.exists():
+            shutil.rmtree(path)
+            print(f"Cleaned up: {path}")

tests/models/test_arch_micronet.py

@@ -54,7 +54,7 @@ def test_value_error() -> None:
     toolbox_env.running_on_ci() or not ON_GPU,
     reason="Local test on machine with GPU.",
 )
-def test_micronet_output(remote_sample: Callable, tmp_path: Path) -> None:
+def test_micronet_output(remote_sample: Callable, track_tmp_path: Path) -> None:
     """Test the output of MicroNet."""
     svs_1_small = Path(remote_sample("svs-1-small"))
     micronet_output = Path(remote_sample("micronet-output"))
@@ -74,7 +74,7 @@ def test_micronet_output(remote_sample: Callable, tmp_path: Path) -> None:
         imgs=[
             svs_1_small,
         ],
-        save_dir=tmp_path / "output",
+        save_dir=track_tmp_path / "output",
     )
 
     output = np.load(output[0][1] + ".raw.0.npy")

tests/models/test_dataset.py

@@ -97,9 +97,9 @@ def test_kather_nonexisting_dir() -> None:
         _ = KatherPatchDataset(save_dir_path="non-existing-path")
 
 
-def test_kather_dataset(tmp_path: Path) -> None:
+def test_kather_dataset(track_tmp_path: Path) -> None:
     """Test for kather patch dataset."""
-    save_dir_path = tmp_path
+    save_dir_path = track_tmp_path
 
     # save to temporary location
     # remove previously generated data