slide2vec 4.5.2__tar.gz → 4.5.3__tar.gz

{slide2vec-4.5.2 → slide2vec-4.5.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: slide2vec
-Version: 4.5.2
+Version: 4.5.3
 Summary: Embedding of whole slide images with Foundation Models
 Author-email: Clément Grisi <clement.grisi@radboudumc.nl>
 License-Expression: Apache-2.0
@@ -15,7 +15,7 @@ Classifier: Programming Language :: Python :: 3.13
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: hs2p[asap,cucim,openslide,sam2,vips]>=4.0.6
+Requires-Dist: hs2p[asap,cucim,openslide,sam2,vips]>=4.0.7
 Requires-Dist: omegaconf
 Requires-Dist: matplotlib
 Requires-Dist: numpy<2
@@ -65,7 +65,7 @@ Requires-Dist: numpy<2; extra == "fm"
 Requires-Dist: pandas; extra == "fm"
 Requires-Dist: pillow; extra == "fm"
 Requires-Dist: rich; extra == "fm"
-Requires-Dist: hs2p[asap,cucim,openslide,sam2,vips]>=4.0.6; extra == "fm"
+Requires-Dist: hs2p[asap,cucim,openslide,sam2,vips]>=4.0.7; extra == "fm"
 Requires-Dist: wandb; extra == "fm"
 Requires-Dist: torch<2.8,>=2.3; extra == "fm"
 Requires-Dist: torchvision>=0.18.0; extra == "fm"

{slide2vec-4.5.2 → slide2vec-4.5.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "slide2vec"
-version = "4.5.2"
+version = "4.5.3"
 description = "Embedding of whole slide images with Foundation Models"
 readme = "README.md"
 requires-python = ">=3.10"
@@ -21,7 +21,7 @@ classifiers = [
     "Programming Language :: Python :: 3.13",
 ]
 dependencies = [
-    "hs2p[asap,cucim,openslide,sam2,vips]>=4.0.6",
+    "hs2p[asap,cucim,openslide,sam2,vips]>=4.0.7",
     "omegaconf",
     "matplotlib",
     "numpy<2",
@@ -88,7 +88,7 @@ fm = [
     "pandas",
     "pillow",
     "rich",
-    "hs2p[asap,cucim,openslide,sam2,vips]>=4.0.6",
+    "hs2p[asap,cucim,openslide,sam2,vips]>=4.0.7",
     "wandb",
     "torch>=2.3,<2.8",
     "torchvision>=0.18.0",
@@ -164,7 +164,7 @@ no_implicit_reexport = true
 max-line-length = 160
 
 [tool.bumpver]
-current_version = "4.5.2"
+current_version = "4.5.3"
 version_pattern = "MAJOR.MINOR.PATCH"
 commit = false       # We do version bumping in CI, not as a commit
 tag = false          # Git tag already exists — we don't auto-tag

{slide2vec-4.5.2 → slide2vec-4.5.3}/slide2vec/__init__.py

@@ -11,7 +11,7 @@ from slide2vec.api import (
 from slide2vec.artifacts import HierarchicalEmbeddingArtifact, SlideEmbeddingArtifact, TileEmbeddingArtifact
 
 
-__version__ = "4.5.2"
+__version__ = "4.5.3"
 
 __all__ = [
     "Model",

{slide2vec-4.5.2 → slide2vec-4.5.3}/slide2vec/inference.py

@@ -608,7 +608,14 @@ def run_pipeline(
         raise ValueError("At least one slide is required")
     if execution.output_dir is None:
         raise ValueError("ExecutionOptions.output_dir is required for Pipeline.run(...)")
-    if execution.num_gpus > 1:
+    # `validate_multi_gpu_execution` validates the multi-GPU *embedding* setup
+    # and touches `torch.cuda` in the parent process. A tiling-only run has no
+    # embedding stage, so skip it: any GPU work during tiling (e.g. SAM2 mask
+    # generation on cuda) runs inside the spawned tiling workers, which
+    # initialize their own CUDA and do not depend on this parent-side check.
+    # Initializing a CUDA context in the parent here only buys needless fork
+    # risk for the downstream tiling pool with no benefit.
+    if not tiling_only and execution.num_gpus > 1:
         distributed_stage.validate_multi_gpu_execution(model, execution)
 
     output_dir = Path(execution.output_dir)

{slide2vec-4.5.2 → slide2vec-4.5.3}/slide2vec.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: slide2vec
-Version: 4.5.2
+Version: 4.5.3
 Summary: Embedding of whole slide images with Foundation Models
 Author-email: Clément Grisi <clement.grisi@radboudumc.nl>
 License-Expression: Apache-2.0
@@ -15,7 +15,7 @@ Classifier: Programming Language :: Python :: 3.13
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: hs2p[asap,cucim,openslide,sam2,vips]>=4.0.6
+Requires-Dist: hs2p[asap,cucim,openslide,sam2,vips]>=4.0.7
 Requires-Dist: omegaconf
 Requires-Dist: matplotlib
 Requires-Dist: numpy<2
@@ -65,7 +65,7 @@ Requires-Dist: numpy<2; extra == "fm"
 Requires-Dist: pandas; extra == "fm"
 Requires-Dist: pillow; extra == "fm"
 Requires-Dist: rich; extra == "fm"
-Requires-Dist: hs2p[asap,cucim,openslide,sam2,vips]>=4.0.6; extra == "fm"
+Requires-Dist: hs2p[asap,cucim,openslide,sam2,vips]>=4.0.7; extra == "fm"
 Requires-Dist: wandb; extra == "fm"
 Requires-Dist: torch<2.8,>=2.3; extra == "fm"
 Requires-Dist: torchvision>=0.18.0; extra == "fm"

{slide2vec-4.5.2 → slide2vec-4.5.3}/slide2vec.egg-info/requires.txt

@@ -1,4 +1,4 @@
-hs2p[asap,cucim,openslide,sam2,vips]>=4.0.6
+hs2p[asap,cucim,openslide,sam2,vips]>=4.0.7
 omegaconf
 matplotlib
 numpy<2
@@ -27,7 +27,7 @@ numpy<2
 pandas
 pillow
 rich
-hs2p[asap,cucim,openslide,sam2,vips]>=4.0.6
+hs2p[asap,cucim,openslide,sam2,vips]>=4.0.7
 wandb
 torch<2.8,>=2.3
 torchvision>=0.18.0

{slide2vec-4.5.2 → slide2vec-4.5.3}/tests/test_regression_inference.py

@@ -125,6 +125,91 @@ def test_pipeline_run_uses_distributed_embedding_path_when_num_gpus_is_greater_t
     assert result.tile_artifacts == ["tile-artifact"]
     assert result.slide_artifacts == ["slide-artifact"]
 
+
+def test_run_pipeline_tiling_only_skips_multi_gpu_validation(monkeypatch, tmp_path: Path):
+    """Tiling is CPU-only; it must not initialize CUDA in the parent.
+
+    ``validate_multi_gpu_execution`` calls ``torch.cuda`` in the parent process,
+    which (combined with forking the tiling pool) caused deadlocks. For a
+    tiling-only run there is no GPU stage, so the validation must be skipped even
+    when ``num_gpus > 1``.
+    """
+    import slide2vec.inference as inference
+
+    slide = make_slide("slide-a")
+    tiling_result = SimpleNamespace(x=np.array([0, 1]), y=np.array([2, 3]), tile_size_lv0=224)
+
+    monkeypatch.setattr(
+        tiling_pipeline,
+        "prepare_tiled_slides",
+        lambda *args, **kwargs: ([slide], [tiling_result], tmp_path / "process_list.csv"),
+    )
+
+    validate_calls = []
+    monkeypatch.setattr(
+        distributed_stage,
+        "validate_multi_gpu_execution",
+        lambda *args, **kwargs: validate_calls.append(True),
+    )
+
+    result = inference.run_pipeline(
+        Model.from_preset("virchow2"),
+        slides=[slide],
+        preprocessing=DEFAULT_PREPROCESSING,
+        tiling_only=True,
+        execution=ExecutionOptions(output_dir=tmp_path, num_gpus=2),
+    )
+
+    assert validate_calls == []
+    assert result.tile_artifacts == []
+    assert result.slide_artifacts == []
+    assert result.process_list_path == tmp_path / "process_list.csv"
+
+
+def test_run_pipeline_validates_multi_gpu_when_not_tiling_only(monkeypatch, tmp_path: Path):
+    """The multi-GPU fast-fail check must still run for full embedding runs."""
+    import slide2vec.inference as inference
+
+    slide = make_slide("slide-a")
+    tiling_result = SimpleNamespace(x=np.array([0, 1]), y=np.array([2, 3]), tile_size_lv0=224)
+
+    monkeypatch.setattr(
+        tiling_pipeline,
+        "prepare_tiled_slides",
+        lambda *args, **kwargs: ([slide], [tiling_result], tmp_path / "process_list.csv"),
+    )
+    monkeypatch.setattr(
+        artifacts_collect,
+        "run_distributed_embedding_stage",
+        lambda *args, **kwargs: None,
+    )
+    monkeypatch.setattr(
+        artifacts_collect,
+        "collect_pipeline_artifacts",
+        lambda *args, **kwargs: (["tile-artifact"], [], ["slide-artifact"]),
+    )
+    monkeypatch.setattr(
+        artifacts_collect, "update_process_list_after_embedding", lambda *args, **kwargs: None
+    )
+
+    validate_calls = []
+    monkeypatch.setattr(
+        distributed_stage,
+        "validate_multi_gpu_execution",
+        lambda *args, **kwargs: validate_calls.append(True),
+    )
+
+    inference.run_pipeline(
+        Model.from_preset("virchow2"),
+        slides=[slide],
+        preprocessing=DEFAULT_PREPROCESSING,
+        tiling_only=False,
+        execution=ExecutionOptions(output_dir=tmp_path, num_gpus=2),
+    )
+
+    assert validate_calls == [True]
+
+
 def test_run_pipeline_distributed_branch_delegates_to_distributed_collection_helper(monkeypatch, tmp_path: Path):
     import slide2vec.inference as inference