slide2vec 5.5.0__tar.gz → 5.7.0__tar.gz

{slide2vec-5.5.0 → slide2vec-5.7.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: slide2vec
-Version: 5.5.0
+Version: 5.7.0
 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]>=4.3.0
+Requires-Dist: hs2p[asap,cucim,openslide,sam2,vips]>=4.4.1
 Requires-Dist: omegaconf
 Requires-Dist: matplotlib
 Requires-Dist: numpy<2
@@ -47,6 +47,12 @@ Requires-Dist: einops==0.8.0; extra == "prism"
 Requires-Dist: environs==11.0.0; extra == "prism"
 Requires-Dist: sacremoses==0.1.1; extra == "prism"
 Requires-Dist: xformers==0.0.31; extra == "prism"
+Provides-Extra: prism2
+Requires-Dist: torch>=2.3; extra == "prism2"
+Requires-Dist: transformers==4.51.3; extra == "prism2"
+Requires-Dist: safetensors; extra == "prism2"
+Requires-Dist: einops; extra == "prism2"
+Requires-Dist: flash-attn>=2.6.3; extra == "prism2"
 Provides-Extra: hibou
 Requires-Dist: scipy~=1.8.1; extra == "hibou"
 Requires-Dist: scikit-image~=0.19.3; extra == "hibou"
@@ -58,6 +64,10 @@ Requires-Dist: timm==1.0.3; extra == "titan"
 Requires-Dist: einops==0.6.1; extra == "titan"
 Requires-Dist: einops-exts==0.0.4; extra == "titan"
 Requires-Dist: transformers==4.46.0; extra == "titan"
+Provides-Extra: waiv
+Requires-Dist: transformers<6,>=5.14; extra == "waiv"
+Requires-Dist: safetensors>=0.8; extra == "waiv"
+Requires-Dist: huggingface_hub==1.25.1; extra == "waiv"
 Provides-Extra: fm
 Requires-Dist: omegaconf>=2.3.0; extra == "fm"
 Requires-Dist: matplotlib; extra == "fm"
@@ -65,7 +75,7 @@ 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]>=4.3.0; extra == "fm"
+Requires-Dist: hs2p[asap,cucim,openslide,sam2,vips]>=4.4.1; extra == "fm"
 Requires-Dist: wandb; extra == "fm"
 Requires-Dist: torch<2.8,>=2.3; extra == "fm"
 Requires-Dist: torchvision>=0.18.0; extra == "fm"
@@ -132,6 +142,10 @@ pip install git+https://github.com/prov-gigapath/prov-gigapath.git
 
 AtlasPatch-backed tissue segmentation is available through hs2p's `sam2` path in the bundled install.
 
+Waiv encoders use a separately tested Transformers 5 runtime. Install them in
+their own environment with `pip install "slide2vec[waiv]"`; the `waiv` extra is
+incompatible with the existing `fm`, `prism`, and `titan` dependency pins.
+
 ## Python API
 
 ```python
@@ -225,7 +239,8 @@ The package writes explicit artifact directories:
 
 ### Supported Models
 
-`slide2vec` currently ships preset configs for 22 tile-level models and 3 slide-level models.  
+`slide2vec` currently ships presets for 28 tile-level models, 4 slide-level models,
+and 1 patient-level model.
 For the full catalog and preset names, see [`docs/models.md`](docs/models.md).
 
 ## CLI

{slide2vec-5.5.0 → slide2vec-5.7.0}/README.md

@@ -26,6 +26,10 @@ pip install git+https://github.com/prov-gigapath/prov-gigapath.git
 
 AtlasPatch-backed tissue segmentation is available through hs2p's `sam2` path in the bundled install.
 
+Waiv encoders use a separately tested Transformers 5 runtime. Install them in
+their own environment with `pip install "slide2vec[waiv]"`; the `waiv` extra is
+incompatible with the existing `fm`, `prism`, and `titan` dependency pins.
+
 ## Python API
 
 ```python
@@ -119,7 +123,8 @@ The package writes explicit artifact directories:
 
 ### Supported Models
 
-`slide2vec` currently ships preset configs for 22 tile-level models and 3 slide-level models.  
+`slide2vec` currently ships presets for 28 tile-level models, 4 slide-level models,
+and 1 patient-level model.
 For the full catalog and preset names, see [`docs/models.md`](docs/models.md).
 
 ## CLI

{slide2vec-5.5.0 → slide2vec-5.7.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "slide2vec"
-version = "5.5.0"
+version = "5.7.0"
 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]>=4.3.0",
+    "hs2p[asap,cucim,openslide,sam2,vips]>=4.4.1",
     "omegaconf",
     "matplotlib",
     "numpy<2",
@@ -67,6 +67,13 @@ prism = [
     "sacremoses==0.1.1",
     "xformers==0.0.31",
 ]
+prism2 = [
+    "torch>=2.3",
+    "transformers==4.51.3",
+    "safetensors",
+    "einops",
+    "flash-attn>=2.6.3",
+]
 hibou = [
     "scipy~=1.8.1",
     "scikit-image~=0.19.3",
@@ -81,6 +88,11 @@ titan = [
     "einops-exts==0.0.4",
     "transformers==4.46.0",
 ]
+waiv = [
+    "transformers>=5.14,<6",
+    "safetensors>=0.8",
+    "huggingface_hub==1.25.1",
+]
 fm = [
     "omegaconf>=2.3.0",
     "matplotlib",
@@ -88,7 +100,7 @@ fm = [
     "pandas",
     "pillow",
     "rich",
-    "hs2p[asap,cucim,openslide,sam2,vips]>=4.3.0",
+    "hs2p[asap,cucim,openslide,sam2,vips]>=4.4.1",
     "wandb",
     "torch>=2.3,<2.8",
     "torchvision>=0.18.0",
@@ -141,12 +153,13 @@ slide2vec = ["py.typed"]
 "slide2vec.configs" = ["*.yaml", "models/*.yaml", "preprocessing/*.yaml"]
 
 [tool.pytest.ini_options]
-addopts = "--cov=slide2vec"
+addopts = "--cov=slide2vec -m 'not gpu_integration'"
 testpaths = [
     "tests",
 ]
 markers = [
     "heavy: real-weight foundation-model inference on CPU; minutes per test. Excluded from the PR suite via `-m 'not heavy'`; run on the scheduled/manual heavy workflow (.github/workflows/nightly-heavy.yaml).",
+    "gpu_integration: real one-GPU versus multi-GPU parity; requires at least two visible CUDA devices. Run explicitly with `CUDA_VISIBLE_DEVICES=0,1 python -m pytest -m gpu_integration --no-cov`.",
 ]
 
 [tool.mypy]
@@ -167,7 +180,7 @@ no_implicit_reexport = true
 max-line-length = 160
 
 [tool.bumpver]
-current_version = "5.5.0"
+current_version = "5.7.0"
 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-5.5.0 → slide2vec-5.7.0}/slide2vec/__init__.py

@@ -20,9 +20,10 @@ from slide2vec.artifacts import (
     SlideEmbeddingArtifact,
     TileEmbeddingArtifact,
 )
+from slide2vec.runtime.dense_encode import DenseEncodeGeometry, DenseEncodeKit
 
 
-__version__ = "5.5.0"
+__version__ = "5.7.0"
 
 __all__ = [
     "Model",
@@ -31,6 +32,8 @@ __all__ = [
     "PreprocessingConfig",
     "DenseOptions",
     "DenseImageOptions",
+    "DenseEncodeGeometry",
+    "DenseEncodeKit",
     "SlideRegions",
     "ImageSpec",
     "ExecutionOptions",