slide2vec 4.6.0__tar.gz → 4.6.2__tar.gz

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Files changed (98) hide show
  1. {slide2vec-4.6.0 → slide2vec-4.6.2}/PKG-INFO +3 -3
  2. {slide2vec-4.6.0 → slide2vec-4.6.2}/pyproject.toml +4 -4
  3. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/__init__.py +1 -1
  4. slide2vec-4.6.2/slide2vec/encoders/base.py +653 -0
  5. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/encoders/models/conch.py +33 -0
  6. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/encoders/models/hibou.py +40 -0
  7. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/encoders/models/midnight.py +40 -0
  8. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/encoders/models/phikon.py +42 -0
  9. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/runtime/hierarchical.py +25 -7
  10. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec.egg-info/PKG-INFO +3 -3
  11. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec.egg-info/SOURCES.txt +1 -0
  12. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec.egg-info/requires.txt +2 -2
  13. slide2vec-4.6.2/tests/test_attention_extraction.py +427 -0
  14. {slide2vec-4.6.0 → slide2vec-4.6.2}/tests/test_regression_inference.py +41 -0
  15. slide2vec-4.6.0/slide2vec/encoders/base.py +0 -335
  16. {slide2vec-4.6.0 → slide2vec-4.6.2}/LICENSE +0 -0
  17. {slide2vec-4.6.0 → slide2vec-4.6.2}/README.md +0 -0
  18. {slide2vec-4.6.0 → slide2vec-4.6.2}/setup.cfg +0 -0
  19. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/__main__.py +0 -0
  20. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/api.py +0 -0
  21. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/artifacts.py +0 -0
  22. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/cli.py +0 -0
  23. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/configs/__init__.py +0 -0
  24. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/configs/default.yaml +0 -0
  25. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/configs/resources.py +0 -0
  26. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/data/__init__.py +0 -0
  27. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/data/dataset.py +0 -0
  28. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/data/tile_reader.py +0 -0
  29. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/data/tile_store.py +0 -0
  30. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/distributed/__init__.py +0 -0
  31. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/distributed/direct_embed_worker.py +0 -0
  32. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/distributed/pipeline_worker.py +0 -0
  33. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/encoders/__init__.py +0 -0
  34. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/encoders/models/__init__.py +0 -0
  35. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/encoders/models/gigapath.py +0 -0
  36. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/encoders/models/hoptimus.py +0 -0
  37. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/encoders/models/lunit.py +0 -0
  38. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/encoders/models/moozy/__init__.py +0 -0
  39. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/encoders/models/moozy/blocks.py +0 -0
  40. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/encoders/models/moozy/case.py +0 -0
  41. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/encoders/models/moozy/loading.py +0 -0
  42. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/encoders/models/moozy/slide.py +0 -0
  43. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/encoders/models/moozy/types.py +0 -0
  44. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/encoders/models/musk.py +0 -0
  45. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/encoders/models/prism.py +0 -0
  46. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/encoders/models/prost40m.py +0 -0
  47. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/encoders/models/titan.py +0 -0
  48. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/encoders/models/uni.py +0 -0
  49. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/encoders/models/virchow.py +0 -0
  50. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/encoders/registry.py +0 -0
  51. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/encoders/validation.py +0 -0
  52. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/inference.py +0 -0
  53. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/progress.py +0 -0
  54. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/runtime/__init__.py +0 -0
  55. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/runtime/artifacts_collect.py +0 -0
  56. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/runtime/batching.py +0 -0
  57. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/runtime/cpu_budget.py +0 -0
  58. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/runtime/distributed.py +0 -0
  59. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/runtime/distributed_stage.py +0 -0
  60. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/runtime/embedding.py +0 -0
  61. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/runtime/embedding_persist.py +0 -0
  62. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/runtime/embedding_pipeline.py +0 -0
  63. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/runtime/manifest.py +0 -0
  64. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/runtime/model_settings.py +0 -0
  65. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/runtime/patient_pipeline.py +0 -0
  66. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/runtime/persist_callbacks.py +0 -0
  67. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/runtime/persistence.py +0 -0
  68. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/runtime/process_list.py +0 -0
  69. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/runtime/progress_bridge.py +0 -0
  70. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/runtime/registry.py +0 -0
  71. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/runtime/serialization.py +0 -0
  72. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/runtime/slide_encode.py +0 -0
  73. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/runtime/tiling.py +0 -0
  74. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/runtime/tiling_pipeline.py +0 -0
  75. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/runtime/types.py +0 -0
  76. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/runtime/worker_io.py +0 -0
  77. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/utils/__init__.py +0 -0
  78. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/utils/config.py +0 -0
  79. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/utils/coordinates.py +0 -0
  80. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/utils/log_utils.py +0 -0
  81. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/utils/tiling_io.py +0 -0
  82. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec/utils/utils.py +0 -0
  83. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec.egg-info/dependency_links.txt +0 -0
  84. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec.egg-info/entry_points.txt +0 -0
  85. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec.egg-info/not-zip-safe +0 -0
  86. {slide2vec-4.6.0 → slide2vec-4.6.2}/slide2vec.egg-info/top_level.txt +0 -0
  87. {slide2vec-4.6.0 → slide2vec-4.6.2}/tests/test_architecture_runtime_split.py +0 -0
  88. {slide2vec-4.6.0 → slide2vec-4.6.2}/tests/test_dense_extraction.py +0 -0
  89. {slide2vec-4.6.0 → slide2vec-4.6.2}/tests/test_dense_locality_gated.py +0 -0
  90. {slide2vec-4.6.0 → slide2vec-4.6.2}/tests/test_encoder_registry.py +0 -0
  91. {slide2vec-4.6.0 → slide2vec-4.6.2}/tests/test_hs2p_package_cutover.py +0 -0
  92. {slide2vec-4.6.0 → slide2vec-4.6.2}/tests/test_output_consistency.py +0 -0
  93. {slide2vec-4.6.0 → slide2vec-4.6.2}/tests/test_progress.py +0 -0
  94. {slide2vec-4.6.0 → slide2vec-4.6.2}/tests/test_regression_core.py +0 -0
  95. {slide2vec-4.6.0 → slide2vec-4.6.2}/tests/test_regression_models.py +0 -0
  96. {slide2vec-4.6.0 → slide2vec-4.6.2}/tests/test_runtime_batching.py +0 -0
  97. {slide2vec-4.6.0 → slide2vec-4.6.2}/tests/test_tile_store.py +0 -0
  98. {slide2vec-4.6.0 → slide2vec-4.6.2}/tests/test_tiling_pipeline.py +0 -0
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: slide2vec
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- Version: 4.6.0
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+ Version: 4.6.2
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  Summary: Embedding of whole slide images with Foundation Models
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  Author-email: Clément Grisi <clement.grisi@radboudumc.nl>
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  License-Expression: Apache-2.0
@@ -15,7 +15,7 @@ Classifier: Programming Language :: Python :: 3.13
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  Requires-Python: >=3.10
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  Description-Content-Type: text/markdown
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  License-File: LICENSE
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- Requires-Dist: hs2p[asap,cucim,openslide,sam2,vips]>=4.0.7
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+ Requires-Dist: hs2p[asap,cucim,openslide,sam2,vips]>=4.0.8
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  Requires-Dist: omegaconf
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  Requires-Dist: matplotlib
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  Requires-Dist: numpy<2
@@ -65,7 +65,7 @@ Requires-Dist: numpy<2; extra == "fm"
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  Requires-Dist: pandas; extra == "fm"
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  Requires-Dist: pillow; extra == "fm"
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  Requires-Dist: rich; extra == "fm"
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- Requires-Dist: hs2p[asap,cucim,openslide,sam2,vips]>=4.0.7; extra == "fm"
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+ Requires-Dist: hs2p[asap,cucim,openslide,sam2,vips]>=4.0.8; extra == "fm"
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  Requires-Dist: wandb; extra == "fm"
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  Requires-Dist: torch<2.8,>=2.3; extra == "fm"
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  Requires-Dist: torchvision>=0.18.0; extra == "fm"
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
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  [project]
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  name = "slide2vec"
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- version = "4.6.0"
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+ version = "4.6.2"
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  description = "Embedding of whole slide images with Foundation Models"
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  readme = "README.md"
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  requires-python = ">=3.10"
@@ -21,7 +21,7 @@ classifiers = [
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  "Programming Language :: Python :: 3.13",
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  ]
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  dependencies = [
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- "hs2p[asap,cucim,openslide,sam2,vips]>=4.0.7",
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+ "hs2p[asap,cucim,openslide,sam2,vips]>=4.0.8",
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  "omegaconf",
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  "matplotlib",
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  "numpy<2",
@@ -88,7 +88,7 @@ fm = [
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  "pandas",
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  "pillow",
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  "rich",
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- "hs2p[asap,cucim,openslide,sam2,vips]>=4.0.7",
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+ "hs2p[asap,cucim,openslide,sam2,vips]>=4.0.8",
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  "wandb",
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  "torch>=2.3,<2.8",
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  "torchvision>=0.18.0",
@@ -164,7 +164,7 @@ no_implicit_reexport = true
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  max-line-length = 160
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  [tool.bumpver]
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- current_version = "4.6.0"
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+ current_version = "4.6.2"
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  version_pattern = "MAJOR.MINOR.PATCH"
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  commit = false # We do version bumping in CI, not as a commit
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  tag = false # Git tag already exists — we don't auto-tag
@@ -11,7 +11,7 @@ from slide2vec.api import (
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  from slide2vec.artifacts import HierarchicalEmbeddingArtifact, SlideEmbeddingArtifact, TileEmbeddingArtifact
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- __version__ = "4.6.0"
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+ __version__ = "4.6.2"
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  __all__ = [
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  "Model",