Merge branch 'dev-define-engines-abc' into dev-define-semantic-segmentor

# Conflicts:
#	tests/test_utils.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

@@ -10,6 +10,7 @@ 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

@@ -659,3 +659,39 @@ 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

@@ -98,9 +98,9 @@ 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
@@ -162,9 +162,9 @@ def test_patch_dataset_path_imgs(
         assert sampled_img_shape[2] == size[2]
 
 
-def test_patch_dataset_list_imgs(tmp_path: Path) -> None:
+def test_patch_dataset_list_imgs(track_tmp_path: Path) -> None:
     """Test for patch dataset with a list of images as input."""
-    save_dir_path = tmp_path
+    save_dir_path = track_tmp_path
 
     size = (5, 5, 3)
     img = RNG.integers(low=0, high=255, size=size)
@@ -229,10 +229,10 @@ def test_patch_datasetarray_imgs() -> None:
         assert sampled_img_shape[2] == size[2]
 
 
-def test_patch_dataset_crash(tmp_path: Path) -> None:
+def test_patch_dataset_crash(track_tmp_path: Path) -> None:
     """Test to make sure patch dataset crashes with incorrect input."""
     # all below examples should fail when input to PatchDataset
-    save_dir_path = tmp_path
+    save_dir_path = track_tmp_path
 
     # not supported input type
     imgs = {"a": RNG.integers(0, 255, (4, 4, 4))}
@@ -341,7 +341,7 @@ def test_patch_dataset_crash(tmp_path: Path) -> None:
 
 def test_wsi_patch_dataset(  # noqa: PLR0915
     sample_wsi_dict: dict,
-    tmp_path: Path,
+    track_tmp_path: Path,
 ) -> None:
     """A test for creation and bare output."""
     # convert to pathlib Path to prevent wsireader complaint
@@ -488,7 +488,7 @@ def __getitem__(self: Proto, idx: int) -> object:
     )
     negative_mask = imread(mini_wsi_msk)
     negative_mask = np.zeros_like(negative_mask)
-    negative_mask_path = tmp_path / "negative_mask.png"
+    negative_mask_path = track_tmp_path / "negative_mask.png"
     imwrite(negative_mask_path, negative_mask)
     with pytest.raises(ValueError, match="No patch coordinates remain after filtering"):
         _ = WSIPatchDataset(