patchworks 0.11.20__tar.gz → 0.11.21__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (77) hide show
  1. {patchworks-0.11.20 → patchworks-0.11.21}/.github/workflows/release.yml +0 -14
  2. {patchworks-0.11.20 → patchworks-0.11.21}/PKG-INFO +2 -2
  3. {patchworks-0.11.20 → patchworks-0.11.21}/pyproject.toml +1 -1
  4. {patchworks-0.11.20 → patchworks-0.11.21}/tests/test_relations.py +6 -2
  5. {patchworks-0.11.20 → patchworks-0.11.21}/.github/workflows/docs.yml +0 -0
  6. {patchworks-0.11.20 → patchworks-0.11.21}/.github/workflows/lint.yml +0 -0
  7. {patchworks-0.11.20 → patchworks-0.11.21}/.gitignore +0 -0
  8. {patchworks-0.11.20 → patchworks-0.11.21}/.markdownlint-cli2.yaml +0 -0
  9. {patchworks-0.11.20 → patchworks-0.11.21}/LICENSE +0 -0
  10. {patchworks-0.11.20 → patchworks-0.11.21}/README.md +0 -0
  11. {patchworks-0.11.20 → patchworks-0.11.21}/cliff.toml +0 -0
  12. {patchworks-0.11.20 → patchworks-0.11.21}/docs/api/chunks.md +0 -0
  13. {patchworks-0.11.20 → patchworks-0.11.21}/docs/api/cluster.md +0 -0
  14. {patchworks-0.11.20 → patchworks-0.11.21}/docs/api/io.md +0 -0
  15. {patchworks-0.11.20 → patchworks-0.11.21}/docs/api/merge_tile_labels.md +0 -0
  16. {patchworks-0.11.20 → patchworks-0.11.21}/docs/api/plugins/cellpose.md +0 -0
  17. {patchworks-0.11.20 → patchworks-0.11.21}/docs/api/plugins/napari.md +0 -0
  18. {patchworks-0.11.20 → patchworks-0.11.21}/docs/api/plugins/ome_zarr.md +0 -0
  19. {patchworks-0.11.20 → patchworks-0.11.21}/docs/api/relabel.md +0 -0
  20. {patchworks-0.11.20 → patchworks-0.11.21}/docs/api/tile_process.md +0 -0
  21. {patchworks-0.11.20 → patchworks-0.11.21}/docs/assets/logo.png +0 -0
  22. {patchworks-0.11.20 → patchworks-0.11.21}/docs/examples/cellpose_2d.md +0 -0
  23. {patchworks-0.11.20 → patchworks-0.11.21}/docs/examples/cellpose_2d.py +0 -0
  24. {patchworks-0.11.20 → patchworks-0.11.21}/docs/examples/cellpose_3d.md +0 -0
  25. {patchworks-0.11.20 → patchworks-0.11.21}/docs/examples/cellpose_3d.py +0 -0
  26. {patchworks-0.11.20 → patchworks-0.11.21}/docs/examples/custom.md +0 -0
  27. {patchworks-0.11.20 → patchworks-0.11.21}/docs/examples/custom_method.py +0 -0
  28. {patchworks-0.11.20 → patchworks-0.11.21}/docs/examples/standalone_merge.md +0 -0
  29. {patchworks-0.11.20 → patchworks-0.11.21}/docs/examples/stardist.md +0 -0
  30. {patchworks-0.11.20 → patchworks-0.11.21}/docs/examples/stardist_2d.py +0 -0
  31. {patchworks-0.11.20 → patchworks-0.11.21}/docs/getting_started.md +0 -0
  32. {patchworks-0.11.20 → patchworks-0.11.21}/docs/guide/gpu_distributed.md +0 -0
  33. {patchworks-0.11.20 → patchworks-0.11.21}/docs/guide/merging.md +0 -0
  34. {patchworks-0.11.20 → patchworks-0.11.21}/docs/guide/ome_zarr_napari.md +0 -0
  35. {patchworks-0.11.20 → patchworks-0.11.21}/docs/guide/performance.md +0 -0
  36. {patchworks-0.11.20 → patchworks-0.11.21}/docs/guide/pitfalls.md +0 -0
  37. {patchworks-0.11.20 → patchworks-0.11.21}/docs/guide/skip_empty.md +0 -0
  38. {patchworks-0.11.20 → patchworks-0.11.21}/docs/guide/snakemake.md +0 -0
  39. {patchworks-0.11.20 → patchworks-0.11.21}/docs/guide/tiling.md +0 -0
  40. {patchworks-0.11.20 → patchworks-0.11.21}/docs/index.md +0 -0
  41. {patchworks-0.11.20 → patchworks-0.11.21}/mkdocs.yml +0 -0
  42. {patchworks-0.11.20 → patchworks-0.11.21}/src/patchworks/__init__.py +0 -0
  43. {patchworks-0.11.20 → patchworks-0.11.21}/src/patchworks/_chunks.py +0 -0
  44. {patchworks-0.11.20 → patchworks-0.11.21}/src/patchworks/_cluster.py +0 -0
  45. {patchworks-0.11.20 → patchworks-0.11.21}/src/patchworks/_core.py +0 -0
  46. {patchworks-0.11.20 → patchworks-0.11.21}/src/patchworks/_distributed.py +0 -0
  47. {patchworks-0.11.20 → patchworks-0.11.21}/src/patchworks/_io.py +0 -0
  48. {patchworks-0.11.20 → patchworks-0.11.21}/src/patchworks/_merge.py +0 -0
  49. {patchworks-0.11.20 → patchworks-0.11.21}/src/patchworks/_relabel.py +0 -0
  50. {patchworks-0.11.20 → patchworks-0.11.21}/src/patchworks/_relations.py +0 -0
  51. {patchworks-0.11.20 → patchworks-0.11.21}/src/patchworks/plugins/__init__.py +0 -0
  52. {patchworks-0.11.20 → patchworks-0.11.21}/src/patchworks/plugins/cellpose.py +0 -0
  53. {patchworks-0.11.20 → patchworks-0.11.21}/src/patchworks/plugins/napari.py +0 -0
  54. {patchworks-0.11.20 → patchworks-0.11.21}/src/patchworks/plugins/ome_zarr.py +0 -0
  55. {patchworks-0.11.20 → patchworks-0.11.21}/tests/test_core.py +0 -0
  56. {patchworks-0.11.20 → patchworks-0.11.21}/tests/test_distributed.py +0 -0
  57. {patchworks-0.11.20 → patchworks-0.11.21}/tests/test_napari.py +0 -0
  58. {patchworks-0.11.20 → patchworks-0.11.21}/tests/test_ome_zarr.py +0 -0
  59. {patchworks-0.11.20 → patchworks-0.11.21}/workflow/README.md +0 -0
  60. {patchworks-0.11.20 → patchworks-0.11.21}/workflow/Snakefile +0 -0
  61. {patchworks-0.11.20 → patchworks-0.11.21}/workflow/config/config.yaml +0 -0
  62. {patchworks-0.11.20 → patchworks-0.11.21}/workflow/config/config_cyto.yaml +0 -0
  63. {patchworks-0.11.20 → patchworks-0.11.21}/workflow/config/config_nuclei.yaml +0 -0
  64. {patchworks-0.11.20 → patchworks-0.11.21}/workflow/config/multi.yaml +0 -0
  65. {patchworks-0.11.20 → patchworks-0.11.21}/workflow/pixi.toml +0 -0
  66. {patchworks-0.11.20 → patchworks-0.11.21}/workflow/profile/slurm/config.yaml +0 -0
  67. {patchworks-0.11.20 → patchworks-0.11.21}/workflow/rules/common.smk +0 -0
  68. {patchworks-0.11.20 → patchworks-0.11.21}/workflow/rules/convert.smk +0 -0
  69. {patchworks-0.11.20 → patchworks-0.11.21}/workflow/rules/merge.smk +0 -0
  70. {patchworks-0.11.20 → patchworks-0.11.21}/workflow/rules/segment.smk +0 -0
  71. {patchworks-0.11.20 → patchworks-0.11.21}/workflow/scripts/_pw.py +0 -0
  72. {patchworks-0.11.20 → patchworks-0.11.21}/workflow/scripts/convert.py +0 -0
  73. {patchworks-0.11.20 → patchworks-0.11.21}/workflow/scripts/fetch_model.py +0 -0
  74. {patchworks-0.11.20 → patchworks-0.11.21}/workflow/scripts/merge.py +0 -0
  75. {patchworks-0.11.20 → patchworks-0.11.21}/workflow/scripts/prepare_tiles.py +0 -0
  76. {patchworks-0.11.20 → patchworks-0.11.21}/workflow/scripts/run_multi.py +0 -0
  77. {patchworks-0.11.20 → patchworks-0.11.21}/workflow/scripts/segment_tile.py +0 -0
@@ -48,17 +48,3 @@ jobs:
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  - name: Publish to PyPI
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  uses: pypa/gh-action-pypi-publish@release/v1
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-
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- # Rebuild the org-wide pdoc apidocs site so it picks up the new version.
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- apidocs:
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- needs: release
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- runs-on: ubuntu-latest
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- steps:
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- - name: Trigger imcf.github.io apidocs rebuild
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- uses: peter-evans/repository-dispatch@v3
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- with:
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- # Fine-grained PAT with "Contents: write" on imcf/imcf.github.io,
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- # stored as the APIDOCS_DISPATCH_TOKEN secret in this repo.
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- token: ${{ secrets.APIDOCS_DISPATCH_TOKEN }}
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- repository: imcf/imcf.github.io
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- event-type: dispatch-event
@@ -1,10 +1,10 @@
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  Metadata-Version: 2.4
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  Name: patchworks
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- Version: 0.11.20
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+ Version: 0.11.21
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  Summary: Tiled processing of arbitrarily large images with globally consistent labels
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  Project-URL: Homepage, https://github.com/imcf/patchworks
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  Project-URL: Issues, https://github.com/imcf/patchworks/issues
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- Author: IMCF Basel
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+ Author-email: Laurent Guerard <laurent.guerard@unibas.ch>
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  License: GPL-3.0-only
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  License-File: LICENSE
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  Keywords: bioimage,chunked,dask,image processing,segmentation,tiling,zarr
@@ -8,7 +8,7 @@ dynamic = ["version"]
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  description = "Tiled processing of arbitrarily large images with globally consistent labels"
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  readme = "README.md"
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  license = { text = "GPL-3.0-only" }
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- authors = [{ name = "IMCF Basel" }]
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+ authors = [{ name = "Laurent Guerard", email = "laurent.guerard@unibas.ch" }]
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  keywords = [
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  "image processing",
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  "tiling",
@@ -17,7 +17,9 @@ def test_label_relations_majority_overlap():
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  b[0:2, 6:8] = 21 # 4 voxels overlap with label 2 -> tie, but let's skew it
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  b[0:2, 6:7] = 20 # tip the tie: label 20 now has 6 voxels vs 21's 2
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- table = label_relations(da.from_array(a, chunks=(2, 5)), da.from_array(b, chunks=(2, 5)))
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+ table = label_relations(
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+ da.from_array(a, chunks=(2, 5)), da.from_array(b, chunks=(2, 5))
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+ )
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  assert table[1]["match"] == 10
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  assert table[1]["overlap_voxels"] == 4
@@ -32,7 +34,9 @@ def test_label_relations_no_overlap_omitted():
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  a[0, 0] = 1
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  b = np.zeros((2, 2), dtype=np.int32) # all background, no overlap anywhere
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- table = label_relations(da.from_array(a, chunks=(2, 2)), da.from_array(b, chunks=(2, 2)))
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+ table = label_relations(
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+ da.from_array(a, chunks=(2, 2)), da.from_array(b, chunks=(2, 2))
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+ )
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  assert table == {}
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