caddforge-docs 0.3.0__py3-none-any.whl

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  1. caddforge_docs/__init__.py +1 -0
  2. caddforge_docs/cli.py +20 -0
  3. caddforge_docs/server.py +124 -0
  4. caddforge_docs/site/404.html +2118 -0
  5. caddforge_docs/site/assets/_mkdocstrings.css +237 -0
  6. caddforge_docs/site/assets/images/favicon.png +0 -0
  7. caddforge_docs/site/assets/javascripts/bundle.d7400e89.min.js +16 -0
  8. caddforge_docs/site/assets/javascripts/bundle.d7400e89.min.js.map +7 -0
  9. caddforge_docs/site/assets/javascripts/workers/search.2c215733.min.js +42 -0
  10. caddforge_docs/site/assets/javascripts/workers/search.2c215733.min.js.map +7 -0
  11. caddforge_docs/site/assets/licenses/W3C-Software-and-Document-2015.txt +15 -0
  12. caddforge_docs/site/assets/licenses/autogrid-COPYING-GPL-2.txt +339 -0
  13. caddforge_docs/site/assets/licenses/autogrid-GCC-RUNTIME-COPYING-GPL-3.txt +674 -0
  14. caddforge_docs/site/assets/licenses/autogrid-GCC-RUNTIME-EXCEPTION.txt +73 -0
  15. caddforge_docs/site/assets/licenses/autogrid-GCC-RUNTIME-NOTICE.txt +24 -0
  16. caddforge_docs/site/assets/licenses/caddforge-opencosmors-COPYING.txt +674 -0
  17. caddforge_docs/site/assets/licenses/caddforge-opencosmors-LICENSE.txt +165 -0
  18. caddforge_docs/site/assets/licenses/caddforge-unidock-tools-LICENSE.txt +202 -0
  19. caddforge_docs/site/assets/licenses/clipboard-LICENSE.txt +19 -0
  20. caddforge_docs/site/assets/licenses/escape-html-LICENSE.txt +2 -0
  21. caddforge_docs/site/assets/licenses/focus-visible-LICENSE.txt +4 -0
  22. caddforge_docs/site/assets/licenses/fontawesome-LICENSE.txt +165 -0
  23. caddforge_docs/site/assets/licenses/fuzzaldrin-plus-LICENSE.txt +21 -0
  24. caddforge_docs/site/assets/licenses/lunr-LICENSE.txt +17 -0
  25. caddforge_docs/site/assets/licenses/material-LICENSE.txt +20 -0
  26. caddforge_docs/site/assets/licenses/material-design-color-LICENSE.txt +31 -0
  27. caddforge_docs/site/assets/licenses/material-shadows-LICENSE.txt +31 -0
  28. caddforge_docs/site/assets/licenses/mkdocs-material-LICENSE.txt +19 -0
  29. caddforge_docs/site/assets/licenses/mkdocs-material-extensions-LICENSE.txt +21 -0
  30. caddforge_docs/site/assets/licenses/mkdocs-section-index-LICENSE.txt +21 -0
  31. caddforge_docs/site/assets/licenses/mkdocstrings-LICENSE.txt +15 -0
  32. caddforge_docs/site/assets/licenses/mkdocstrings-python-LICENSE.txt +15 -0
  33. caddforge_docs/site/assets/licenses/octicons-LICENSE.txt +21 -0
  34. caddforge_docs/site/assets/licenses/preact-LICENSE.txt +19 -0
  35. caddforge_docs/site/assets/licenses/properdocs-LICENSE.txt +26 -0
  36. caddforge_docs/site/assets/licenses/pymdown-extensions-LICENSE.txt +113 -0
  37. caddforge_docs/site/assets/licenses/rxjs-LICENSE.txt +180 -0
  38. caddforge_docs/site/assets/licenses/simple-LICENSE.txt +30 -0
  39. caddforge_docs/site/assets/licenses/tiny-emitter-LICENSE.txt +19 -0
  40. caddforge_docs/site/assets/licenses/tslib-LICENSE.txt +12 -0
  41. caddforge_docs/site/assets/licenses/zeno-rocha-components-LICENSE.txt +22 -0
  42. caddforge_docs/site/assets/stylesheets/main.ec1eaa64.min.css +1 -0
  43. caddforge_docs/site/assets/stylesheets/main.ec1eaa64.min.css.map +1 -0
  44. caddforge_docs/site/assets/stylesheets/palette.ab4e12ef.min.css +1 -0
  45. caddforge_docs/site/assets/stylesheets/palette.ab4e12ef.min.css.map +1 -0
  46. caddforge_docs/site/core/cli/index.html +2446 -0
  47. caddforge_docs/site/core/concepts/index.html +2340 -0
  48. caddforge_docs/site/core/configuration/index.html +2300 -0
  49. caddforge_docs/site/core/index.html +2170 -0
  50. caddforge_docs/site/core/jobs-results/index.html +2315 -0
  51. caddforge_docs/site/core/plugins/index.html +2200 -0
  52. caddforge_docs/site/core/slurm/index.html +2562 -0
  53. caddforge_docs/site/development/ci-publishing/index.html +2345 -0
  54. caddforge_docs/site/development/contributing/index.html +2311 -0
  55. caddforge_docs/site/development/documentation/index.html +2380 -0
  56. caddforge_docs/site/development/index.html +2201 -0
  57. caddforge_docs/site/development/release-notes/index.html +2504 -0
  58. caddforge_docs/site/development/release-readiness/index.html +2333 -0
  59. caddforge_docs/site/development/security/index.html +2181 -0
  60. caddforge_docs/site/development/tool-authoring/index.html +2435 -0
  61. caddforge_docs/site/examples/index.html +2465 -0
  62. caddforge_docs/site/examples/manifest.json +158 -0
  63. caddforge_docs/site/examples/minimize/component_overrides.yaml +14 -0
  64. caddforge_docs/site/examples/minimize/ligand_only.yaml +13 -0
  65. caddforge_docs/site/examples/minimize/pipeline_docking.yaml +84 -0
  66. caddforge_docs/site/examples/minimize/pipeline_scatter.yaml +49 -0
  67. caddforge_docs/site/examples/minimize/pocket_free_shell_restrained.yaml +13 -0
  68. caddforge_docs/site/examples/minimize/pocket_restrained.yaml +13 -0
  69. caddforge_docs/site/examples/minimize/prepared_metal.yaml +14 -0
  70. caddforge_docs/site/examples/minimize/sidechains_free_backbone_fixed.yaml +13 -0
  71. caddforge_docs/site/examples/minimize/sidechains_free_backbone_restrained.yaml +13 -0
  72. caddforge_docs/site/examples/pipelines/descriptor-model-and-candidate-filter.yaml +44 -0
  73. caddforge_docs/site/examples/pipelines/dock-extract-and-minimize-poses.yaml +85 -0
  74. caddforge_docs/site/examples/pipelines/docking-screen-and-rescore.yaml +55 -0
  75. caddforge_docs/site/examples/pipelines/flexible-gnina-to-openbpmd-to-md-to-abfe.yaml +189 -0
  76. caddforge_docs/site/examples/pipelines/gnina-flexible-complex-artifacts.yaml +52 -0
  77. caddforge_docs/site/examples/pipelines/minimize-a-multi-pose-sdf.yaml +46 -0
  78. caddforge_docs/site/examples/pipelines/pose-level-md-selection.yaml +95 -0
  79. caddforge_docs/site/examples/pipelines/result-collection-and-diagnostics.yaml +55 -0
  80. caddforge_docs/site/examples/quickstart/diagnostics.yaml +8 -0
  81. caddforge_docs/site/examples/quickstart/index.html +2172 -0
  82. caddforge_docs/site/examples/quickstart/pipeline.yaml +23 -0
  83. caddforge_docs/site/examples/quickstart/run.py +18 -0
  84. caddforge_docs/site/examples/quickstart/run_pipeline.py +6 -0
  85. caddforge_docs/site/examples/quickstart/scores.csv +7 -0
  86. caddforge_docs/site/examples/quickstart/values.csv +31 -0
  87. caddforge_docs/site/examples/run_tool.py +40 -0
  88. caddforge_docs/site/examples/tools/datascience-csv-scatter.yaml +17 -0
  89. caddforge_docs/site/examples/tools/datascience-distribution-diagnostics.yaml +10 -0
  90. caddforge_docs/site/examples/tools/descriptors-ani-conformers.yaml +9 -0
  91. caddforge_docs/site/examples/tools/descriptors-ani-psa.yaml +9 -0
  92. caddforge_docs/site/examples/tools/descriptors-cluster-molecules.yaml +11 -0
  93. caddforge_docs/site/examples/tools/descriptors-phesa.yaml +7 -0
  94. caddforge_docs/site/examples/tools/docking-gnina.yaml +12 -0
  95. caddforge_docs/site/examples/tools/docking-idockya.yaml +8 -0
  96. caddforge_docs/site/examples/tools/docking-unidock.yaml +12 -0
  97. caddforge_docs/site/examples/tools/fep-openfe-abfe.yaml +53 -0
  98. caddforge_docs/site/examples/tools/fep-openfe-rbfe-septop.yaml +23 -0
  99. caddforge_docs/site/examples/tools/md-center-and-align.yaml +16 -0
  100. caddforge_docs/site/examples/tools/md-cluster-representative.yaml +16 -0
  101. caddforge_docs/site/examples/tools/md-extract-frames.yaml +17 -0
  102. caddforge_docs/site/examples/tools/md-fix-structure.yaml +20 -0
  103. caddforge_docs/site/examples/tools/md-grand.yaml +28 -0
  104. caddforge_docs/site/examples/tools/md-inducia.yaml +29 -0
  105. caddforge_docs/site/examples/tools/md-minimize.yaml +13 -0
  106. caddforge_docs/site/examples/tools/md-openbpmd.yaml +11 -0
  107. caddforge_docs/site/examples/tools/md-plain-md.yaml +28 -0
  108. caddforge_docs/site/examples/tools/ml-explore-classifier.yaml +5 -0
  109. caddforge_docs/site/examples/tools/ml-model-factory.yaml +32 -0
  110. caddforge_docs/site/examples/tools/ml-model-zoo.yaml +16 -0
  111. caddforge_docs/site/examples/tools/ml-pca.yaml +10 -0
  112. caddforge_docs/site/examples/tools/ml-simple-gp.yaml +17 -0
  113. caddforge_docs/site/examples/tools/qm-transfer-free-energy.yaml +11 -0
  114. caddforge_docs/site/explanation/references/index.html +2218 -0
  115. caddforge_docs/site/explanation/reproducibility/index.html +2306 -0
  116. caddforge_docs/site/explanation/third-party-notices/index.html +2599 -0
  117. caddforge_docs/site/getting-started/first-pipeline/index.html +2195 -0
  118. caddforge_docs/site/getting-started/first-workflow/index.html +2329 -0
  119. caddforge_docs/site/getting-started/index.html +2200 -0
  120. caddforge_docs/site/getting-started/installation/index.html +2541 -0
  121. caddforge_docs/site/gui/index.html +2267 -0
  122. caddforge_docs/site/gui/plugin-authoring/index.html +2280 -0
  123. caddforge_docs/site/gui/walkthrough/index.html +2181 -0
  124. caddforge_docs/site/how-to/jobs/index.html +2195 -0
  125. caddforge_docs/site/how-to/scatter/index.html +2193 -0
  126. caddforge_docs/site/how-to/troubleshooting/index.html +2429 -0
  127. caddforge_docs/site/index.html +2359 -0
  128. caddforge_docs/site/objects.inv +0 -0
  129. caddforge_docs/site/pipelines/artifacts/index.html +2314 -0
  130. caddforge_docs/site/pipelines/built-ins/index.html +2670 -0
  131. caddforge_docs/site/pipelines/examples/index.html +3186 -0
  132. caddforge_docs/site/pipelines/index.html +2164 -0
  133. caddforge_docs/site/pipelines/specification/index.html +2278 -0
  134. caddforge_docs/site/plugins/datascience/index.html +2405 -0
  135. caddforge_docs/site/plugins/descriptors/index.html +2609 -0
  136. caddforge_docs/site/plugins/docking/index.html +2480 -0
  137. caddforge_docs/site/plugins/fep/index.html +2508 -0
  138. caddforge_docs/site/plugins/index.html +2216 -0
  139. caddforge_docs/site/plugins/md/index.html +3795 -0
  140. caddforge_docs/site/plugins/ml/index.html +2815 -0
  141. caddforge_docs/site/plugins/qm/index.html +2309 -0
  142. caddforge_docs/site/plugins/version-matrix/index.html +2449 -0
  143. caddforge_docs/site/reference/api/index.html +4414 -0
  144. caddforge_docs/site/reference/index.html +2166 -0
  145. caddforge_docs/site/search/search_index.json +1 -0
  146. caddforge_docs/site/sitemap.xml +191 -0
  147. caddforge_docs/site/sitemap.xml.gz +0 -0
  148. caddforge_docs-0.3.0.dist-info/METADATA +158 -0
  149. caddforge_docs-0.3.0.dist-info/RECORD +152 -0
  150. caddforge_docs-0.3.0.dist-info/WHEEL +4 -0
  151. caddforge_docs-0.3.0.dist-info/entry_points.txt +2 -0
  152. caddforge_docs-0.3.0.dist-info/licenses/LICENSE +21 -0
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953
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967
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978
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984
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985
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986
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991
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993
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994
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1006
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1007
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1009
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1020
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1021
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1069
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1070
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1076
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1077
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1078
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1079
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1080
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1081
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1085
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1087
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1101
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1110
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1111
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1117
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1118
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1121
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1123
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1126
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1146
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1166
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1167
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1174
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1175
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1176
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1177
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1179
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1181
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1202
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1230
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1234
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1238
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1258
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1286
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1290
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1294
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1295
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1314
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1364
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1365
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1367
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1368
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1369
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1370
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1371
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1372
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1373
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1374
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1387
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1388
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1389
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1390
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1391
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1392
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1394
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1396
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1397
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1407
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1409
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1411
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1412
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1413
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1414
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1434
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1435
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1438
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1439
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1440
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1441
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1442
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1443
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1455
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1456
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1459
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1486
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1487
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1488
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1489
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1490
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1491
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1492
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1493
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1494
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1495
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1496
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1497
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1498
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1499
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1500
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1501
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1502
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1504
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1505
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1511
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1512
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1513
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1514
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1516
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1518
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1520
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1522
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1523
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1524
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1525
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1526
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1527
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1533
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1536
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1537
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1538
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1539
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1540
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1541
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1542
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1543
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1544
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1545
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1546
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1547
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1548
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1549
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1550
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1551
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1552
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1553
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1554
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1555
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1556
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1560
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1564
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1565
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1566
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1567
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1568
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1569
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1570
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1571
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1572
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1573
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1574
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1575
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1576
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1577
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1578
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1579
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1580
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1581
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1582
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1583
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1584
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1585
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1586
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1587
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1588
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1589
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1590
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1591
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1592
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1593
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1594
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1595
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1596
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1597
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1598
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1599
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1600
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1601
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1602
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1603
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1604
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1605
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1606
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1607
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1608
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1609
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1610
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1611
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1612
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1613
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1614
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1615
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1617
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1624
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1636
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1637
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1638
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1639
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1640
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1641
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1642
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1643
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1644
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1645
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1646
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1647
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1648
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1649
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1650
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1651
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1652
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1653
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1654
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1655
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1656
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1657
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1658
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1659
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1660
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1661
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1662
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1663
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1664
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1665
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1666
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1667
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1668
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1669
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1670
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1671
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1672
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1673
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1674
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1675
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1676
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1677
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1678
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1679
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1681
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1683
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1684
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1686
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1687
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1688
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1689
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1690
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1691
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1692
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1693
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1694
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1695
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1696
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1697
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1698
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1699
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1700
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1701
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1702
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1703
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1704
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1705
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1706
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1707
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1708
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1709
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1710
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1711
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1712
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1713
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1714
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1715
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1716
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1717
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1718
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1719
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1720
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1721
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1722
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1723
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1724
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1725
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1726
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1727
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1728
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1729
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1730
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1731
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1732
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1733
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1734
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1735
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1736
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1738
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1739
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1740
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1741
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1742
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1743
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1744
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1745
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1746
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1747
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1748
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1749
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1750
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1751
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1752
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1753
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1754
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1755
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1756
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1757
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1758
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1759
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1760
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1761
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1762
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1763
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1765
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1766
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1768
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1773
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1800
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1801
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1806
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1810
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1813
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1814
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1817
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1818
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1819
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1820
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1821
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1822
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1823
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1824
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1825
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1826
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1827
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1828
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1829
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1830
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1831
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1832
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1833
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1834
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1835
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1836
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1837
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_10_label" aria-expanded="true">
1838
+ <label class="md-nav__title" for="__nav_10">
1839
+ <span class="md-nav__icon md-icon"></span>
1840
+
1841
+
1842
+ Development
1843
+
1844
+
1845
+ </label>
1846
+ <ul class="md-nav__list" data-md-scrollfix>
1847
+
1848
+
1849
+
1850
+
1851
+
1852
+
1853
+
1854
+
1855
+
1856
+ <li class="md-nav__item md-nav__item--active">
1857
+
1858
+ <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
1859
+
1860
+
1861
+
1862
+
1863
+
1864
+ <label class="md-nav__link md-nav__link--active" for="__toc">
1865
+
1866
+
1867
+
1868
+ <span class="md-ellipsis">
1869
+
1870
+
1871
+ Release Notes
1872
+
1873
+
1874
+
1875
+ </span>
1876
+
1877
+
1878
+
1879
+ <span class="md-nav__icon md-icon"></span>
1880
+ </label>
1881
+
1882
+ <a href="./" class="md-nav__link md-nav__link--active">
1883
+
1884
+
1885
+
1886
+ <span class="md-ellipsis">
1887
+
1888
+
1889
+ Release Notes
1890
+
1891
+
1892
+
1893
+ </span>
1894
+
1895
+
1896
+
1897
+ </a>
1898
+
1899
+
1900
+
1901
+ <nav class="md-nav md-nav--secondary" aria-label="Table of contents">
1902
+
1903
+
1904
+
1905
+
1906
+
1907
+
1908
+ <label class="md-nav__title" for="__toc">
1909
+ <span class="md-nav__icon md-icon"></span>
1910
+ Table of contents
1911
+ </label>
1912
+ <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
1913
+
1914
+ <li class="md-nav__item">
1915
+ <a href="#030" class="md-nav__link">
1916
+ <span class="md-ellipsis">
1917
+
1918
+ 0.3.0
1919
+
1920
+ </span>
1921
+ </a>
1922
+
1923
+ <nav class="md-nav" aria-label="0.3.0">
1924
+ <ul class="md-nav__list">
1925
+
1926
+ <li class="md-nav__item">
1927
+ <a href="#public-component-source-tags" class="md-nav__link">
1928
+ <span class="md-ellipsis">
1929
+
1930
+ Public component source tags
1931
+
1932
+ </span>
1933
+ </a>
1934
+
1935
+ </li>
1936
+
1937
+ <li class="md-nav__item">
1938
+ <a href="#documentation-and-packaging" class="md-nav__link">
1939
+ <span class="md-ellipsis">
1940
+
1941
+ Documentation and packaging
1942
+
1943
+ </span>
1944
+ </a>
1945
+
1946
+ </li>
1947
+
1948
+ </ul>
1949
+ </nav>
1950
+
1951
+ </li>
1952
+
1953
+ <li class="md-nav__item">
1954
+ <a href="#021" class="md-nav__link">
1955
+ <span class="md-ellipsis">
1956
+
1957
+ 0.2.1
1958
+
1959
+ </span>
1960
+ </a>
1961
+
1962
+ </li>
1963
+
1964
+ <li class="md-nav__item">
1965
+ <a href="#020" class="md-nav__link">
1966
+ <span class="md-ellipsis">
1967
+
1968
+ 0.2.0
1969
+
1970
+ </span>
1971
+ </a>
1972
+
1973
+ <nav class="md-nav" aria-label="0.2.0">
1974
+ <ul class="md-nav__list">
1975
+
1976
+ <li class="md-nav__item">
1977
+ <a href="#installed-documentation" class="md-nav__link">
1978
+ <span class="md-ellipsis">
1979
+
1980
+ Installed documentation
1981
+
1982
+ </span>
1983
+ </a>
1984
+
1985
+ </li>
1986
+
1987
+ <li class="md-nav__item">
1988
+ <a href="#guides-and-reference" class="md-nav__link">
1989
+ <span class="md-ellipsis">
1990
+
1991
+ Guides and reference
1992
+
1993
+ </span>
1994
+ </a>
1995
+
1996
+ </li>
1997
+
1998
+ <li class="md-nav__item">
1999
+ <a href="#validation-and-publication" class="md-nav__link">
2000
+ <span class="md-ellipsis">
2001
+
2002
+ Validation and publication
2003
+
2004
+ </span>
2005
+ </a>
2006
+
2007
+ </li>
2008
+
2009
+ </ul>
2010
+ </nav>
2011
+
2012
+ </li>
2013
+
2014
+ </ul>
2015
+
2016
+ </nav>
2017
+
2018
+ </li>
2019
+
2020
+
2021
+
2022
+
2023
+
2024
+
2025
+
2026
+
2027
+
2028
+
2029
+ <li class="md-nav__item">
2030
+ <a href="../tool-authoring/" class="md-nav__link">
2031
+
2032
+
2033
+
2034
+ <span class="md-ellipsis">
2035
+
2036
+
2037
+ Tool Authoring
2038
+
2039
+
2040
+
2041
+ </span>
2042
+
2043
+
2044
+
2045
+ </a>
2046
+ </li>
2047
+
2048
+
2049
+
2050
+
2051
+
2052
+
2053
+
2054
+
2055
+
2056
+
2057
+ <li class="md-nav__item">
2058
+ <a href="../documentation/" class="md-nav__link">
2059
+
2060
+
2061
+
2062
+ <span class="md-ellipsis">
2063
+
2064
+
2065
+ Documentation
2066
+
2067
+
2068
+
2069
+ </span>
2070
+
2071
+
2072
+
2073
+ </a>
2074
+ </li>
2075
+
2076
+
2077
+
2078
+
2079
+
2080
+
2081
+
2082
+
2083
+
2084
+
2085
+ <li class="md-nav__item">
2086
+ <a href="../contributing/" class="md-nav__link">
2087
+
2088
+
2089
+
2090
+ <span class="md-ellipsis">
2091
+
2092
+
2093
+ Contributing
2094
+
2095
+
2096
+
2097
+ </span>
2098
+
2099
+
2100
+
2101
+ </a>
2102
+ </li>
2103
+
2104
+
2105
+
2106
+
2107
+
2108
+
2109
+
2110
+
2111
+
2112
+
2113
+ <li class="md-nav__item">
2114
+ <a href="../security/" class="md-nav__link">
2115
+
2116
+
2117
+
2118
+ <span class="md-ellipsis">
2119
+
2120
+
2121
+ Security Reporting
2122
+
2123
+
2124
+
2125
+ </span>
2126
+
2127
+
2128
+
2129
+ </a>
2130
+ </li>
2131
+
2132
+
2133
+
2134
+
2135
+
2136
+
2137
+
2138
+
2139
+
2140
+
2141
+ <li class="md-nav__item">
2142
+ <a href="../release-readiness/" class="md-nav__link">
2143
+
2144
+
2145
+
2146
+ <span class="md-ellipsis">
2147
+
2148
+
2149
+ Release Readiness
2150
+
2151
+
2152
+
2153
+ </span>
2154
+
2155
+
2156
+
2157
+ </a>
2158
+ </li>
2159
+
2160
+
2161
+
2162
+
2163
+
2164
+
2165
+
2166
+
2167
+
2168
+
2169
+ <li class="md-nav__item">
2170
+ <a href="../ci-publishing/" class="md-nav__link">
2171
+
2172
+
2173
+
2174
+ <span class="md-ellipsis">
2175
+
2176
+
2177
+ CI and Publishing
2178
+
2179
+
2180
+
2181
+ </span>
2182
+
2183
+
2184
+
2185
+ </a>
2186
+ </li>
2187
+
2188
+
2189
+
2190
+
2191
+ </ul>
2192
+ </nav>
2193
+
2194
+ </li>
2195
+
2196
+
2197
+
2198
+ </ul>
2199
+ </nav>
2200
+ </div>
2201
+ </div>
2202
+ </div>
2203
+
2204
+
2205
+
2206
+ <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
2207
+ <div class="md-sidebar__scrollwrap">
2208
+ <div class="md-sidebar__inner">
2209
+
2210
+
2211
+ <nav class="md-nav md-nav--secondary" aria-label="Table of contents">
2212
+
2213
+
2214
+
2215
+
2216
+
2217
+
2218
+ <label class="md-nav__title" for="__toc">
2219
+ <span class="md-nav__icon md-icon"></span>
2220
+ Table of contents
2221
+ </label>
2222
+ <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
2223
+
2224
+ <li class="md-nav__item">
2225
+ <a href="#030" class="md-nav__link">
2226
+ <span class="md-ellipsis">
2227
+
2228
+ 0.3.0
2229
+
2230
+ </span>
2231
+ </a>
2232
+
2233
+ <nav class="md-nav" aria-label="0.3.0">
2234
+ <ul class="md-nav__list">
2235
+
2236
+ <li class="md-nav__item">
2237
+ <a href="#public-component-source-tags" class="md-nav__link">
2238
+ <span class="md-ellipsis">
2239
+
2240
+ Public component source tags
2241
+
2242
+ </span>
2243
+ </a>
2244
+
2245
+ </li>
2246
+
2247
+ <li class="md-nav__item">
2248
+ <a href="#documentation-and-packaging" class="md-nav__link">
2249
+ <span class="md-ellipsis">
2250
+
2251
+ Documentation and packaging
2252
+
2253
+ </span>
2254
+ </a>
2255
+
2256
+ </li>
2257
+
2258
+ </ul>
2259
+ </nav>
2260
+
2261
+ </li>
2262
+
2263
+ <li class="md-nav__item">
2264
+ <a href="#021" class="md-nav__link">
2265
+ <span class="md-ellipsis">
2266
+
2267
+ 0.2.1
2268
+
2269
+ </span>
2270
+ </a>
2271
+
2272
+ </li>
2273
+
2274
+ <li class="md-nav__item">
2275
+ <a href="#020" class="md-nav__link">
2276
+ <span class="md-ellipsis">
2277
+
2278
+ 0.2.0
2279
+
2280
+ </span>
2281
+ </a>
2282
+
2283
+ <nav class="md-nav" aria-label="0.2.0">
2284
+ <ul class="md-nav__list">
2285
+
2286
+ <li class="md-nav__item">
2287
+ <a href="#installed-documentation" class="md-nav__link">
2288
+ <span class="md-ellipsis">
2289
+
2290
+ Installed documentation
2291
+
2292
+ </span>
2293
+ </a>
2294
+
2295
+ </li>
2296
+
2297
+ <li class="md-nav__item">
2298
+ <a href="#guides-and-reference" class="md-nav__link">
2299
+ <span class="md-ellipsis">
2300
+
2301
+ Guides and reference
2302
+
2303
+ </span>
2304
+ </a>
2305
+
2306
+ </li>
2307
+
2308
+ <li class="md-nav__item">
2309
+ <a href="#validation-and-publication" class="md-nav__link">
2310
+ <span class="md-ellipsis">
2311
+
2312
+ Validation and publication
2313
+
2314
+ </span>
2315
+ </a>
2316
+
2317
+ </li>
2318
+
2319
+ </ul>
2320
+ </nav>
2321
+
2322
+ </li>
2323
+
2324
+ </ul>
2325
+
2326
+ </nav>
2327
+ </div>
2328
+ </div>
2329
+ </div>
2330
+
2331
+
2332
+
2333
+ <div class="md-content" data-md-component="content">
2334
+
2335
+ <article class="md-content__inner md-typeset">
2336
+
2337
+
2338
+
2339
+
2340
+
2341
+
2342
+
2343
+
2344
+ <h1 id="documentation-release-notes">Documentation Release Notes<a class="headerlink" href="#documentation-release-notes" title="Permanent link">&para;</a></h1>
2345
+ <h2 id="030">0.3.0<a class="headerlink" href="#030" title="Permanent link">&para;</a></h2>
2346
+ <p>Documentation source tag: <code>v0.3.0</code>. Package-index publication is pending.</p>
2347
+ <h3 id="public-component-source-tags">Public component source tags<a class="headerlink" href="#public-component-source-tags" title="Permanent link">&para;</a></h3>
2348
+ <ul>
2349
+ <li>
2350
+ <p>Core <code>v0.22.0</code>, QM <code>v0.3.0</code>, ML <code>v0.4.0</code>, GUI <code>v0.6.0</code>, data science
2351
+ <code>v0.5.0</code>, descriptors <code>v0.11.0</code>, FEP <code>v0.7.0</code>, docking <code>v0.7.0</code>, and
2352
+ MD <code>v0.13.0</code> identify the reviewed public source commits recorded in the
2353
+ <a href="../../plugins/version-matrix/">version matrix</a>.
2354
+ Publication was checked on 2026-10-15: all listed component versions
2355
+ except MD <code>0.13.0</code> are published on PyPI. MD is tagged and awaiting
2356
+ publication. Documentation <code>0.3.0</code> is tagged and awaiting publication;
2357
+ the updated bundle release remains pending.</p>
2358
+ </li>
2359
+ <li>
2360
+ <p>Core CI installs the <code>[test]</code> extra, including RDKit for hydrogenation
2361
+ coverage, and its help assertions handle plain and styled terminal output.
2362
+ QM uses the published <code>caddforge-opencosmors==0.0.1</code> dependency and
2363
+ <code>pyocl-idor&gt;=0.8.3</code> with Java 21 or newer.</p>
2364
+ </li>
2365
+ <li>
2366
+ <p>MD tests support Python 3.10 through the conditional <code>tomli</code> backport.
2367
+ Its installed-wheel runner preserves declared pytest markers while excluding
2368
+ checkout runtime sources.</p>
2369
+ </li>
2370
+ </ul>
2371
+ <h3 id="documentation-and-packaging">Documentation and packaging<a class="headerlink" href="#documentation-and-packaging" title="Permanent link">&para;</a></h3>
2372
+ <ul>
2373
+ <li>Record verified package-index availability, update current installation and
2374
+ migration examples, and generate API provenance from the version matrix.</li>
2375
+ <li>
2376
+ <p>Normalize ANSI formatting in CLI error assertions and cover plain and styled
2377
+ output. The wheel CI job installs the declared <code>[test]</code> extra.</p>
2378
+ </li>
2379
+ <li>
2380
+ <p>Standardize package CI on tested wheels, Python 3.10/3.12, release metadata
2381
+ checks, and tag-triggered PyPI Trusted Publishing. Add docs package releases
2382
+ alongside opt-in Pages, run bundle migration tests with core sources, and
2383
+ derive packaging expectations from current metadata instead of inherited pins.</p>
2384
+ </li>
2385
+ <li>
2386
+ <p>Install PyOCL using the public <code>pyocl-idor&gt;=0.8.3</code> distribution; Python imports
2387
+ remain <code>pyocl</code>. Provision Java 21 in affected CI workflows and document the
2388
+ Java 21 or newer runtime requirement.</p>
2389
+ </li>
2390
+ <li>
2391
+ <p>Start new public repositories without earlier development history. New public
2392
+ component tags and verified publication status are recorded above. Documentation
2393
+ continues its version sequence at <code>0.3.0</code>; the bundle version awaits assignment.</p>
2394
+ </li>
2395
+ <li>Declare MIT licensing and ship project and third-party licence texts.</li>
2396
+ <li>Remove ESOL and Glide / Glide WS integrations from the public component sources.</li>
2397
+ <li>Pin the documentation theme to the reviewed assets and reject unreviewed theme
2398
+ versions or non-English search assets.</li>
2399
+ </ul>
2400
+ <p>The notes below describe inherited development milestones, not tags or releases
2401
+ in the new public repositories. See the <a href="../../plugins/version-matrix/">version matrix</a>.</p>
2402
+ <h2 id="021">0.2.1<a class="headerlink" href="#021" title="Permanent link">&para;</a></h2>
2403
+ <ul>
2404
+ <li>Document bundle <code>0.22.0</code>, which includes <code>caddforge-docs==0.2.1</code> and the
2405
+ <code>caddforge docs</code> command by default.</li>
2406
+ <li>Keep documentation authoring and test extras outside the runtime bundle.</li>
2407
+ <li>Update installation examples, CLI guidance, the version matrix, and release ordering.</li>
2408
+ <li>Retain separate docs installation instructions for bundle <code>0.21.0</code>, core-only,
2409
+ and selective plugin environments.</li>
2410
+ </ul>
2411
+ <p>This inherited milestone does not establish a new public release or publication.</p>
2412
+ <h2 id="020">0.2.0<a class="headerlink" href="#020" title="Permanent link">&para;</a></h2>
2413
+ <p>This inherited milestone introduced the packaged documentation. New public
2414
+ package releases and public site deployment remain separate actions.</p>
2415
+ <h3 id="installed-documentation">Installed documentation<a class="headerlink" href="#installed-documentation" title="Permanent link">&para;</a></h3>
2416
+ <ul>
2417
+ <li>Added the optional <code>caddforge docs</code> command, registered only when this package is installed.</li>
2418
+ <li>Ship a complete static site with search, assets, and downloadable examples for offline viewing.</li>
2419
+ <li>Support <code>--host</code>, <code>--port</code>, and <code>--no-browser</code>, including IPv4, IPv6, and hostnames.</li>
2420
+ <li>Build the site into wheels and editable installations; source distributions contain everything
2421
+ needed to rebuild it. Reinstall after source edits to refresh the installed view.</li>
2422
+ </ul>
2423
+ <h3 id="guides-and-reference">Guides and reference<a class="headerlink" href="#guides-and-reference" title="Permanent link">&para;</a></h3>
2424
+ <ul>
2425
+ <li>Added runnable CLI and Python tutorials using synthetic table data and a two-stage core pipeline.</li>
2426
+ <li>Added configurations for 26 documented scientific workflows and eight advanced pipeline templates.</li>
2427
+ <li>Added job, scatter, troubleshooting, GUI, reproducibility, contributor, and security guidance.</li>
2428
+ <li>Generate the public core API reference from an explicit source allowlist without importing plugins.</li>
2429
+ <li>Document core <code>0.21.0</code>, bundle <code>0.21.0</code>, and the latest tagged public plugins, including MD terminal
2430
+ policies and encoded PheSA references.</li>
2431
+ <li>Forward declared runtime inputs in Python submission examples so compressed inputs use core staging.</li>
2432
+ </ul>
2433
+ <h3 id="validation-and-publication">Validation and publication<a class="headerlink" href="#validation-and-publication" title="Permanent link">&para;</a></h3>
2434
+ <ul>
2435
+ <li>Check local links and anchors, example syntax and schemas, and packaged artifacts.</li>
2436
+ <li>Validate GitHub branch/tag pushes; Pages deployment remains opt-in and
2437
+ limited to the default branch after validation.</li>
2438
+ <li>Keep scientific engine validation distinct from template schema checks and lightweight tutorials.</li>
2439
+ <li>Record outstanding licensing, public-index dependency, hosting, and reporting-route prerequisites
2440
+ in the <a href="../release-readiness/">release checklist</a>.</li>
2441
+ </ul>
2442
+
2443
+
2444
+
2445
+
2446
+
2447
+
2448
+
2449
+
2450
+
2451
+
2452
+
2453
+
2454
+
2455
+ </article>
2456
+ </div>
2457
+
2458
+
2459
+ <script>var target=document.getElementById(location.hash.slice(1));target&&target.name&&(target.checked=target.name.startsWith("__tabbed_"))</script>
2460
+ </div>
2461
+
2462
+ <button type="button" class="md-top md-icon" data-md-component="top" hidden>
2463
+
2464
+ <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M13 20h-2V8l-5.5 5.5-1.42-1.42L12 4.16l7.92 7.92-1.42 1.42L13 8z"/></svg>
2465
+ Back to top
2466
+ </button>
2467
+
2468
+ </main>
2469
+
2470
+ <footer class="md-footer">
2471
+
2472
+ <div class="md-footer-meta md-typeset">
2473
+ <div class="md-footer-meta__inner md-grid">
2474
+ <div class="md-copyright">
2475
+
2476
+
2477
+ Made with
2478
+ <a href="https://squidfunk.github.io/mkdocs-material/" target="_blank" rel="noopener">
2479
+ Material for MkDocs
2480
+ </a>
2481
+
2482
+ </div>
2483
+
2484
+ </div>
2485
+ </div>
2486
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