Merge branch 'develop' into add-slide-data

Author: shaneahmed

.github/workflows/python-package.yml

@@ -20,9 +20,9 @@ jobs:
         python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
@@ -33,7 +33,7 @@ jobs:
         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
+      uses: actions/cache@v4
       with:
         key: tiatoolbox-home-static
         path: ~/.tiatoolbox
@@ -76,6 +76,17 @@ jobs:
         coverage-file: coverage.xml
         dsn: ${{ secrets.DEEPSOURCE_DSN }}
         fail-ci-on-error: false
+    - name: List tiatoolbox contents
+      run: ls -lahR ~/.tiatoolbox
+    - name: Delete Hugging Face cache for large models
+      run: |
+        find ~/.tiatoolbox/models -type f -size +250M -exec bash -c '
+          for model_path; do
+            model_name=$(basename "$model_path")
+            cache_dir="$HOME/.tiatoolbox/models/.cache/huggingface/download"
+            rm -vf "$cache_dir/${model_name}.lock" "$cache_dir/${model_name}.metadata"
+          done
+          ' bash {} +
 
   release:
     runs-on: ubuntu-24.04
@@ -84,10 +95,10 @@ jobs:
     if: github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' || github.ref == 'refs/heads/pre-release' || startsWith(github.ref, 'refs/tags/v')
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Set up Python 3.10
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: '3.10'
         cache: 'pip'

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

@@ -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_mapde.py

@@ -1,6 +1,7 @@
 """Unit test package for SCCNN."""
 
 from collections.abc import Callable
+from pathlib import Path
 
 import numpy as np
 import torch
@@ -14,15 +15,15 @@
 ON_GPU = toolbox_env.has_gpu()
 
 
-def _load_mapde(name: str) -> MapDe:
+def _load_mapde(name: str) -> tuple[MapDe, str]:
     """Loads MapDe model with specified weights."""
     model = MapDe()
     weights_path = fetch_pretrained_weights(name)
     map_location = select_device(on_gpu=ON_GPU)
     pretrained = torch.load(weights_path, map_location=map_location)
     model.load_state_dict(pretrained)
     model.to(map_location)
-    return model
+    return model, weights_path
 
 
 def test_functionality(remote_sample: Callable) -> None:
@@ -42,12 +43,13 @@ def test_functionality(remote_sample: Callable) -> None:
         coord_space="resolution",
     )
 
-    model = _load_mapde(name="mapde-conic")
+    model, weights_path = _load_mapde(name="mapde-conic")
     patch = model.preproc(patch)
     batch = torch.from_numpy(patch)[None]
     output = model.infer_batch(model, batch, device=select_device(on_gpu=ON_GPU))
     output = model.postproc(output[0])
     assert np.all(output[0:2] == [[19, 171], [53, 89]])
+    Path(weights_path).unlink()
 
 
 def test_multiclass_output() -> None:

tests/models/test_arch_micronet.py

@@ -42,6 +42,7 @@ def test_functionality(
     output = model.infer_batch(model, batch, device=map_location)
     output, _ = model.postproc(output[0])
     assert np.max(np.unique(output)) == 46
+    Path(weights_path).unlink()
 
 
 def test_value_error() -> None:
@@ -54,7 +55,7 @@ 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 +75,7 @@ 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

@@ -86,9 +86,9 @@ 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