protcross 0.2.0__tar.gz → 0.2.2__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 (113) hide show
  1. {protcross-0.2.0 → protcross-0.2.2}/MANIFEST.in +2 -3
  2. protcross-0.2.2/PKG-INFO +954 -0
  3. protcross-0.2.2/README.md +905 -0
  4. {protcross-0.2.0 → protcross-0.2.2}/constraints/py310-ci.txt +4 -4
  5. {protcross-0.2.0 → protcross-0.2.2}/pyproject.toml +11 -7
  6. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/__init__.py +1 -1
  7. protcross-0.2.2/src/protcross/__main__.py +7 -0
  8. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/assets.py +513 -36
  9. protcross-0.2.2/src/protcross/cli/inspect.py +48 -0
  10. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/cli/main.py +15 -5
  11. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/cli/predict.py +206 -44
  12. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/cli/setup_assets.py +16 -3
  13. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/data/__init__.py +3 -0
  14. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/data/af2.py +62 -18
  15. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/data/dataset.py +92 -18
  16. protcross-0.2.2/src/protcross/data/esm.py +178 -0
  17. protcross-0.2.2/src/protcross/data/inspection.py +307 -0
  18. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/data/label_mapping.py +100 -30
  19. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/data/pca.py +9 -2
  20. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/data/preprocess.py +114 -11
  21. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/data/structure.py +139 -16
  22. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/inference/pdb.py +94 -5
  23. protcross-0.2.2/src/protcross/inference/predictor.py +2193 -0
  24. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/models/backbones/pointnet2.py +74 -42
  25. {protcross-0.2.0 → protcross-0.2.2}/src/protcross.egg-info/SOURCES.txt +7 -3
  26. protcross-0.2.2/tests/test_assets.py +885 -0
  27. {protcross-0.2.0 → protcross-0.2.2}/tests/test_checkpoint_smoke.py +38 -0
  28. {protcross-0.2.0 → protcross-0.2.2}/tests/test_cli.py +233 -4
  29. protcross-0.2.2/tests/test_docs_drift.py +134 -0
  30. {protcross-0.2.0 → protcross-0.2.2}/tests/test_inference_result.py +687 -15
  31. {protcross-0.2.0 → protcross-0.2.2}/tests/test_label_mapping.py +59 -0
  32. {protcross-0.2.0 → protcross-0.2.2}/tests/test_legacy_archive.py +3 -1
  33. {protcross-0.2.0 → protcross-0.2.2}/tests/test_packaging_and_compat.py +3 -13
  34. protcross-0.2.2/tests/test_pca_and_dataset.py +463 -0
  35. protcross-0.2.2/tests/test_pdb_output_preservation.py +99 -0
  36. protcross-0.2.2/tests/test_pointnet2_fallback.py +245 -0
  37. {protcross-0.2.0 → protcross-0.2.2}/tests/test_structure_and_pdb.py +194 -1
  38. protcross-0.2.2/tests/test_structure_inspection.py +215 -0
  39. protcross-0.2.0/PKG-INFO +0 -680
  40. protcross-0.2.0/README.md +0 -635
  41. protcross-0.2.0/examples/README.md +0 -46
  42. protcross-0.2.0/reproduction/legacy/README.md +0 -105
  43. protcross-0.2.0/src/protcross/data/esm.py +0 -94
  44. protcross-0.2.0/src/protcross/inference/predictor.py +0 -1127
  45. protcross-0.2.0/tests/test_assets.py +0 -285
  46. protcross-0.2.0/tests/test_docs_drift.py +0 -42
  47. protcross-0.2.0/tests/test_pca_and_dataset.py +0 -73
  48. {protcross-0.2.0 → protcross-0.2.2}/LICENSE +0 -0
  49. {protcross-0.2.0 → protcross-0.2.2}/configs/data/protein_seg.yaml +0 -0
  50. {protcross-0.2.0 → protcross-0.2.2}/configs/model/da_module.yaml +0 -0
  51. {protcross-0.2.0 → protcross-0.2.2}/configs/train.yaml +0 -0
  52. {protcross-0.2.0 → protcross-0.2.2}/configs/trainer/default.yaml +0 -0
  53. {protcross-0.2.0 → protcross-0.2.2}/environment.yml +0 -0
  54. {protcross-0.2.0 → protcross-0.2.2}/examples/6fhu.pdb +0 -0
  55. {protcross-0.2.0 → protcross-0.2.2}/reproduction/legacy/analyze_geometric.py +0 -0
  56. {protcross-0.2.0 → protcross-0.2.2}/reproduction/legacy/eval_dataset.py +0 -0
  57. {protcross-0.2.0 → protcross-0.2.2}/reproduction/legacy/eval_run.py +0 -0
  58. {protcross-0.2.0 → protcross-0.2.2}/reproduction/legacy/eval_utils.py +0 -0
  59. {protcross-0.2.0 → protcross-0.2.2}/reproduction/legacy/get_af2.py +0 -0
  60. {protcross-0.2.0 → protcross-0.2.2}/reproduction/legacy/map_labels-o.py +0 -0
  61. {protcross-0.2.0 → protcross-0.2.2}/reproduction/legacy/map_labels.py +0 -0
  62. {protcross-0.2.0 → protcross-0.2.2}/reproduction/legacy/pdb_uniprot_mapping.json +0 -0
  63. {protcross-0.2.0 → protcross-0.2.2}/reproduction/legacy/preprocess_esm.py +0 -0
  64. {protcross-0.2.0 → protcross-0.2.2}/reproduction/legacy/run_Predict_ProtCross.py +0 -0
  65. {protcross-0.2.0 → protcross-0.2.2}/reproduction/legacy/run_Strategy.py +0 -0
  66. {protcross-0.2.0 → protcross-0.2.2}/reproduction/legacy/run_multiseed_benchmark.py +0 -0
  67. {protcross-0.2.0 → protcross-0.2.2}/reproduction/legacy/sensitivity-cutoff.py +0 -0
  68. {protcross-0.2.0 → protcross-0.2.2}/reproduction/legacy/setup_assets.py +0 -0
  69. {protcross-0.2.0 → protcross-0.2.2}/reproduction/legacy/test_adaptive.py +0 -0
  70. {protcross-0.2.0 → protcross-0.2.2}/reproduction/legacy/train.py +0 -0
  71. {protcross-0.2.0 → protcross-0.2.2}/setup.cfg +0 -0
  72. {protcross-0.2.0 → protcross-0.2.2}/src/evopoint_da/__init__.py +0 -0
  73. {protcross-0.2.0 → protcross-0.2.2}/src/evopoint_da/_compat.py +0 -0
  74. {protcross-0.2.0 → protcross-0.2.2}/src/evopoint_da/assets.py +0 -0
  75. {protcross-0.2.0 → protcross-0.2.2}/src/evopoint_da/cli/__init__.py +0 -0
  76. {protcross-0.2.0 → protcross-0.2.2}/src/evopoint_da/data/__init__.py +0 -0
  77. {protcross-0.2.0 → protcross-0.2.2}/src/evopoint_da/evaluation/__init__.py +0 -0
  78. {protcross-0.2.0 → protcross-0.2.2}/src/evopoint_da/experiments/__init__.py +0 -0
  79. {protcross-0.2.0 → protcross-0.2.2}/src/evopoint_da/inference/__init__.py +0 -0
  80. {protcross-0.2.0 → protcross-0.2.2}/src/evopoint_da/models/__init__.py +0 -0
  81. {protcross-0.2.0 → protcross-0.2.2}/src/evopoint_da/models/backbones/__init__.py +0 -0
  82. {protcross-0.2.0 → protcross-0.2.2}/src/evopoint_da/models/heads/__init__.py +0 -0
  83. {protcross-0.2.0 → protcross-0.2.2}/src/evopoint_da/training/__init__.py +0 -0
  84. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/cli/__init__.py +0 -0
  85. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/cli/download_af2.py +0 -0
  86. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/cli/map_labels.py +0 -0
  87. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/cli/preprocess.py +0 -0
  88. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/cli/train.py +0 -0
  89. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/configs/__init__.py +0 -0
  90. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/configs/data/protein_seg.yaml +0 -0
  91. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/configs/model/da_module.yaml +0 -0
  92. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/configs/train.yaml +0 -0
  93. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/configs/trainer/default.yaml +0 -0
  94. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/data/components.py +0 -0
  95. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/data/datamodule.py +0 -0
  96. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/evaluation/__init__.py +0 -0
  97. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/evaluation/adaptive.py +0 -0
  98. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/evaluation/metrics.py +0 -0
  99. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/experiments/__init__.py +0 -0
  100. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/experiments/multiseed_benchmark.py +0 -0
  101. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/experiments/strategy_search.py +0 -0
  102. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/inference/__init__.py +0 -0
  103. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/models/__init__.py +0 -0
  104. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/models/backbones/__init__.py +0 -0
  105. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/models/domain_weights.py +0 -0
  106. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/models/heads/__init__.py +0 -0
  107. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/models/heads/classifier.py +0 -0
  108. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/models/module.py +0 -0
  109. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/training/__init__.py +0 -0
  110. {protcross-0.2.0 → protcross-0.2.2}/src/protcross/training/run.py +0 -0
  111. {protcross-0.2.0 → protcross-0.2.2}/tests/conftest.py +0 -0
  112. {protcross-0.2.0 → protcross-0.2.2}/tests/test_metrics.py +0 -0
  113. {protcross-0.2.0 → protcross-0.2.2}/tests/test_strategy_search.py +0 -0
{protcross-0.2.0 → protcross-0.2.2}/MANIFEST.in RENAMED
@@ -5,11 +5,10 @@ include environment.yml
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  recursive-include constraints *.txt
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  recursive-include configs *.yaml
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  recursive-include src/protcross/configs *.yaml
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- recursive-include examples *.pdb *.md
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- recursive-include reproduction/legacy *.py *.md *.json
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+ recursive-include examples *.pdb
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+ recursive-include reproduction/legacy *.py *.json
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  recursive-include tests *.py
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  recursive-exclude tests/desktop *
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- exclude RELEASE_NOTES_0.1.2.md
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  recursive-exclude data *
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  recursive-exclude checkpoint *
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  recursive-exclude checkpoints *