scib-metrics 0.5.2__tar.gz → 0.5.3__tar.gz

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Files changed (78) hide show
  1. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/PKG-INFO +1 -1
  2. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/pyproject.toml +1 -1
  3. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/src/scib_metrics/benchmark/_core.py +0 -4
  4. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/.codecov.yaml +0 -0
  5. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/.cruft.json +0 -0
  6. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/.editorconfig +0 -0
  7. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/.github/ISSUE_TEMPLATE/bug_report.yml +0 -0
  8. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/.github/ISSUE_TEMPLATE/config.yml +0 -0
  9. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/.github/ISSUE_TEMPLATE/feature_request.yml +0 -0
  10. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/.github/workflows/build.yaml +0 -0
  11. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/.github/workflows/release.yaml +0 -0
  12. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/.github/workflows/test_linux.yaml +0 -0
  13. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/.github/workflows/test_linux_cuda.yaml +0 -0
  14. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/.github/workflows/test_linux_pre.yaml +0 -0
  15. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/.github/workflows/test_macos.yaml +0 -0
  16. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/.github/workflows/test_macos_m1.yaml +0 -0
  17. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/.github/workflows/test_windows.yaml +0 -0
  18. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/.gitignore +0 -0
  19. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/.pre-commit-config.yaml +0 -0
  20. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/.readthedocs.yaml +0 -0
  21. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/CHANGELOG.md +0 -0
  22. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/LICENSE +0 -0
  23. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/README.md +0 -0
  24. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/docs/Makefile +0 -0
  25. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/docs/_static/.gitkeep +0 -0
  26. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/docs/_static/css/custom.css +0 -0
  27. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/docs/_templates/.gitkeep +0 -0
  28. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/docs/_templates/autosummary/class.rst +0 -0
  29. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/docs/_templates/class_no_inherited.rst +0 -0
  30. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/docs/api.md +0 -0
  31. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/docs/changelog.md +0 -0
  32. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/docs/conf.py +0 -0
  33. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/docs/contributing.md +0 -0
  34. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/docs/extensions/.gitkeep +0 -0
  35. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/docs/extensions/typed_returns.py +0 -0
  36. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/docs/index.md +0 -0
  37. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/docs/notebooks/large_scale.ipynb +0 -0
  38. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/docs/notebooks/lung_example.ipynb +0 -0
  39. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/docs/references.bib +0 -0
  40. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/docs/references.md +0 -0
  41. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/docs/template_usage.md +0 -0
  42. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/docs/tutorials.md +0 -0
  43. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/setup.py +0 -0
  44. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/src/scib_metrics/__init__.py +0 -0
  45. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/src/scib_metrics/_settings.py +0 -0
  46. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/src/scib_metrics/_types.py +0 -0
  47. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/src/scib_metrics/benchmark/__init__.py +0 -0
  48. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/src/scib_metrics/metrics/__init__.py +0 -0
  49. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/src/scib_metrics/metrics/_graph_connectivity.py +0 -0
  50. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/src/scib_metrics/metrics/_isolated_labels.py +0 -0
  51. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/src/scib_metrics/metrics/_kbet.py +0 -0
  52. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/src/scib_metrics/metrics/_lisi.py +0 -0
  53. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/src/scib_metrics/metrics/_nmi_ari.py +0 -0
  54. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/src/scib_metrics/metrics/_pcr_comparison.py +0 -0
  55. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/src/scib_metrics/metrics/_silhouette.py +0 -0
  56. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/src/scib_metrics/nearest_neighbors/__init__.py +0 -0
  57. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/src/scib_metrics/nearest_neighbors/_dataclass.py +0 -0
  58. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/src/scib_metrics/nearest_neighbors/_jax.py +0 -0
  59. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/src/scib_metrics/nearest_neighbors/_pynndescent.py +0 -0
  60. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/src/scib_metrics/utils/__init__.py +0 -0
  61. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/src/scib_metrics/utils/_diffusion_nn.py +0 -0
  62. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/src/scib_metrics/utils/_dist.py +0 -0
  63. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/src/scib_metrics/utils/_kmeans.py +0 -0
  64. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/src/scib_metrics/utils/_lisi.py +0 -0
  65. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/src/scib_metrics/utils/_pca.py +0 -0
  66. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/src/scib_metrics/utils/_pcr.py +0 -0
  67. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/src/scib_metrics/utils/_silhouette.py +0 -0
  68. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/src/scib_metrics/utils/_utils.py +0 -0
  69. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/tests/__init__.py +0 -0
  70. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/tests/test_benchmarker.py +0 -0
  71. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/tests/test_metrics.py +0 -0
  72. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/tests/test_neighbors.py +0 -0
  73. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/tests/test_pcr_comparison.py +0 -0
  74. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/tests/utils/__init__.py +0 -0
  75. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/tests/utils/data.py +0 -0
  76. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/tests/utils/sampling.py +0 -0
  77. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/tests/utils/test_pca.py +0 -0
  78. {scib_metrics-0.5.2 → scib_metrics-0.5.3}/tests/utils/test_pcr.py +0 -0
{scib_metrics-0.5.2 → scib_metrics-0.5.3}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: scib-metrics
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- Version: 0.5.2
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+ Version: 0.5.3
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  Summary: Accelerated and Python-only scIB metrics
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  Project-URL: Documentation, https://scib-metrics.readthedocs.io/
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  Project-URL: Source, https://github.com/yoseflab/scib-metrics
{scib_metrics-0.5.2 → scib_metrics-0.5.3}/pyproject.toml RENAMED
@@ -5,7 +5,7 @@ requires = ["hatchling"]
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  [project]
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  name = "scib-metrics"
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- version = "0.5.2"
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+ version = "0.5.3"
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  description = "Accelerated and Python-only scIB metrics"
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  readme = "README.md"
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  requires-python = ">=3.10"
{scib_metrics-0.5.2 → scib_metrics-0.5.3}/src/scib_metrics/benchmark/_core.py RENAMED
@@ -282,10 +282,6 @@ class Benchmarker:
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  # Compute scores
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  per_class_score = df.groupby(_METRIC_TYPE).mean().transpose()
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- if "Batch correction" not in per_class_score.columns:
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- per_class_score["Batch correction"] = 0.5
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- if "Bio conservation" not in per_class_score.columns:
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- per_class_score["Bio conservation"] = 0.5
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  # This is the default scIB weighting from the manuscript
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  if self._batch_correction_metrics is not None and self._bio_conservation_metrics is not None:
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  per_class_score["Total"] = (
{scib_metrics-0.5.2 → scib_metrics-0.5.3}/.codecov.yaml RENAMED
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{scib_metrics-0.5.2 → scib_metrics-0.5.3}/.cruft.json RENAMED
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{scib_metrics-0.5.2 → scib_metrics-0.5.3}/.editorconfig RENAMED
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{scib_metrics-0.5.2 → scib_metrics-0.5.3}/.gitignore RENAMED
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{scib_metrics-0.5.2 → scib_metrics-0.5.3}/CHANGELOG.md RENAMED
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{scib_metrics-0.5.2 → scib_metrics-0.5.3}/LICENSE RENAMED
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{scib_metrics-0.5.2 → scib_metrics-0.5.3}/README.md RENAMED
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{scib_metrics-0.5.2 → scib_metrics-0.5.3}/docs/Makefile RENAMED
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{scib_metrics-0.5.2 → scib_metrics-0.5.3}/docs/api.md RENAMED
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{scib_metrics-0.5.2 → scib_metrics-0.5.3}/docs/conf.py RENAMED
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{scib_metrics-0.5.2 → scib_metrics-0.5.3}/docs/index.md RENAMED
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{scib_metrics-0.5.2 → scib_metrics-0.5.3}/setup.py RENAMED
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