lavlab-shell 0.3.1__tar.gz → 0.3.2__tar.gz

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Files changed (38) hide show
  1. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/PKG-INFO +1 -1
  2. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/src/shell/__about__.py +1 -1
  3. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/src/shell/infer_omero_wsi.py +3 -0
  4. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/src/shell/inference.py +1 -1
  5. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/.devcontainer/Dockerfile +0 -0
  6. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/.editorconfig +0 -0
  7. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/.github/dependabot.yml +0 -0
  8. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/.github/workflows/build.yml +0 -0
  9. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/.github/workflows/lint.yml +0 -0
  10. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/.github/workflows/publish.yml +0 -0
  11. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/.github/workflows/pytest.yml +0 -0
  12. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/.gitignore +0 -0
  13. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/.pre-commit-config.yaml +0 -0
  14. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/CONTRIBUTING.md +0 -0
  15. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/Dockerfile +0 -0
  16. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/LICENSE.txt +0 -0
  17. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/Makefile +0 -0
  18. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/README.md +0 -0
  19. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/docs/api.md +0 -0
  20. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/docs/index.md +0 -0
  21. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/mkdocs.yml +0 -0
  22. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/pyproject.toml +0 -0
  23. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/requirements/requirements-docs.txt +0 -0
  24. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/requirements/requirements-lint.txt +0 -0
  25. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/requirements/requirements-test.txt +0 -0
  26. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/requirements/requirements-types.txt +0 -0
  27. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/requirements.txt +0 -0
  28. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/src/shell/__init__.py +0 -0
  29. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/src/shell/benchmark.py +0 -0
  30. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/src/shell/cli.py +0 -0
  31. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/src/shell/infer_wsi.py +0 -0
  32. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/src/shell/model.py +0 -0
  33. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/src/shell/py.typed +0 -0
  34. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/src/shell/transforms.py +0 -0
  35. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/src/shell/weights/model_v1.pth +0 -0
  36. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/tests/__init__.py +0 -0
  37. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/tests/conftest.py +0 -0
  38. {lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/tests/test_shell.py +0 -0
{lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: lavlab-shell
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- Version: 0.3.1
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+ Version: 0.3.2
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  Summary: SHELL Highlights Epithelium and Lumen Locations — whole-slide H&E segmentation
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  Project-URL: Documentation, https://github.com/laviolette-lab/shell#readme
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  Project-URL: Issues, https://github.com/laviolette-lab/shell/issues
{lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/src/shell/__about__.py RENAMED
@@ -3,4 +3,4 @@
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  # SPDX-License-Identifier: MIT
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  """Version information for shell."""
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- __version__ = "0.3.1"
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+ __version__ = "0.3.2"
{lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/src/shell/infer_omero_wsi.py RENAMED
@@ -1689,6 +1689,7 @@ def infer_omero_wsi(
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  save_eho=save_eho,
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  output_path=output_path,
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  tile_overlap=tile_overlap,
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+ roi_size=inference_tile_size,
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  sw_overlap=sw_overlap,
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  num_fetch_workers=num_fetch_workers,
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  )
@@ -1736,6 +1737,7 @@ def _run_pipeline(
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  save_eho: str | None,
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  output_path: str,
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  tile_overlap: int,
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+ roi_size: int,
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  sw_overlap: float,
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  num_fetch_workers: int = 4,
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  ) -> np.ndarray:
@@ -1842,6 +1844,7 @@ def _run_pipeline(
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  tile_eho,
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  model,
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  device,
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+ roi_size=(roi_size, roi_size),
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  overlap=sw_overlap,
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  )
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  del tile_eho
{lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/src/shell/inference.py RENAMED
@@ -40,7 +40,7 @@ from torch.amp import autocast
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  # ---------------------------------------------------------------------------
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  # Default inference parameters
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  # ---------------------------------------------------------------------------
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- VAL_ROI_SIZE: tuple[int, int] = (512, 512)
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+ VAL_ROI_SIZE: tuple[int, int] = (2048, 2048)
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  VAL_SW_BATCH: int = 16
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  VAL_SW_OVERLAP: float = 0.25
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{lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/.editorconfig RENAMED
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{lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/.gitignore RENAMED
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{lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/Dockerfile RENAMED
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{lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/LICENSE.txt RENAMED
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{lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/Makefile RENAMED
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{lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/README.md RENAMED
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{lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/docs/api.md RENAMED
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{lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/docs/index.md RENAMED
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{lavlab_shell-0.3.1 → lavlab_shell-0.3.2}/mkdocs.yml RENAMED
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