caddforge-docs 0.3.0__py3-none-any.whl

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Files changed (152) hide show
  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
caddforge_docs/site/how-to/jobs/index.html ADDED
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941
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942
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960
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961
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962
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963
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964
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965
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967
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968
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969
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970
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971
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976
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977
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978
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979
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980
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981
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982
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983
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984
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986
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987
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988
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989
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990
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991
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992
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993
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994
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995
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996
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997
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998
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999
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1000
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1001
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1003
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1017
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1018
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1019
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1020
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1021
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1022
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1023
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1024
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1025
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1026
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1027
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1032
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1033
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1038
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1077
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1080
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1081
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1082
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1083
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1085
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1088
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1089
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1090
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1091
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1092
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1095
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1099
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1101
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1102
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1103
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1106
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1110
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1113
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1122
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1123
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1124
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1125
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1126
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1127
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1129
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1130
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1134
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1135
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1138
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1139
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1151
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1155
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1158
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1159
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1160
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1161
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1162
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1163
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1164
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1165
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1166
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1167
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1178
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1179
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1183
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1186
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1190
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1192
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1193
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1194
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1195
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1211
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1214
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1218
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1219
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1220
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1221
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1222
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1223
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1234
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1235
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1239
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1241
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1242
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1243
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1244
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1245
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1246
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1247
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1248
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1249
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1250
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1251
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1263
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1267
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1269
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1270
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1271
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1272
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1273
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1274
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1275
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1276
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1277
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1278
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1279
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1280
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1298
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1300
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1301
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1302
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1306
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1307
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1323
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1326
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1328
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1330
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1333
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1334
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1369
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1370
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1371
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1373
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1376
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1377
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1378
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1379
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1380
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1381
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1382
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1383
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1384
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1385
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1386
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1387
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1388
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1391
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1392
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1393
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1394
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1395
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1396
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1397
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1398
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1399
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1400
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1401
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1402
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1403
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1404
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1405
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1406
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1407
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1408
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1409
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1410
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1418
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1419
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1420
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1421
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1423
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1424
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1425
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1426
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1427
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1428
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1429
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1430
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1431
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1432
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1433
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1434
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1435
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1436
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1446
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1447
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1449
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1450
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1451
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1452
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1453
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1454
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1455
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1456
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1457
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1458
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1459
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1460
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1461
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1462
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1463
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1464
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1465
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1466
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1467
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1468
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1469
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1470
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1471
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1472
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1473
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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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1503
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1504
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1505
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1506
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1507
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1508
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1509
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1510
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1511
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1512
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1513
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1514
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1515
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1516
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1517
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1518
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1519
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1520
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1521
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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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1528
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1529
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1530
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1531
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1532
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1533
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1534
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1535
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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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1544
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1545
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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
+
1557
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1558
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1559
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1560
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1561
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1562
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1563
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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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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
+ Example Library
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
+
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
+
1615
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1616
+
1617
+
1618
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1619
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1620
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1621
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1622
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1623
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1624
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1625
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1626
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1627
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1629
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1632
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1633
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1634
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1636
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1637
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1638
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1646
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1648
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1649
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1650
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1651
+
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
+
1659
+
1660
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1661
+
1662
+
1663
+ <label class="md-nav__link" for="__nav_9" id="__nav_9_label" tabindex="">
1664
+
1665
+
1666
+
1667
+ <span class="md-ellipsis">
1668
+
1669
+
1670
+ Explanation
1671
+
1672
+
1673
+
1674
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1675
+
1676
+
1677
+
1678
+ <span class="md-nav__icon md-icon"></span>
1679
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1680
+
1681
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_9_label" aria-expanded="false">
1682
+ <label class="md-nav__title" for="__nav_9">
1683
+ <span class="md-nav__icon md-icon"></span>
1684
+
1685
+
1686
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1687
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1688
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1689
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1690
+ <ul class="md-nav__list" data-md-scrollfix>
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
+
1702
+
1703
+ <span class="md-ellipsis">
1704
+
1705
+
1706
+ Reproducibility
1707
+
1708
+
1709
+
1710
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1711
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1712
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1713
+
1714
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1715
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1716
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1717
+
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
+ Method References
1735
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1736
+
1737
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1738
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1739
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1740
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1741
+
1742
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1743
+ </li>
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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1764
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1765
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1766
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1767
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1768
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1769
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1770
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1771
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1772
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1773
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1774
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1775
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1777
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1778
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1780
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1809
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1810
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1811
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1812
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1813
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1814
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1815
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1816
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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
+
1826
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1827
+ <span class="md-ellipsis">
1828
+
1829
+
1830
+ Development
1831
+
1832
+
1833
+
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+
2099
+ <h1 id="manage-jobs-and-results">Manage Jobs and Results<a class="headerlink" href="#manage-jobs-and-results" title="Permanent link">&para;</a></h1>
2100
+ <p>Run these commands from the submission directory so they share the default registry:</p>
2101
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>caddforge<span class="w"> </span>list-jobs
2102
+ <a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a>caddforge<span class="w"> </span>status<span class="w"> </span>&lt;job-id&gt;
2103
+ <a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a>caddforge<span class="w"> </span>logs<span class="w"> </span>&lt;job-id&gt;
2104
+ <a id="__codelineno-0-4" name="__codelineno-0-4" href="#__codelineno-0-4"></a>caddforge<span class="w"> </span>logs<span class="w"> </span>&lt;job-id&gt;<span class="w"> </span>--follow
2105
+ </code></pre></div>
2106
+ <p>Status refresh reconciles scheduler information with recorded results. Log following
2107
+ is useful during long runs; Ctrl+C stops following without cancelling the job.
2108
+ <code>logs</code> prints stdout; inspect <code>stderr.log</code> directly in the recorded run directory
2109
+ when needed. Core currently has no general CLI <code>cancel</code> command. Use your scheduler's cancellation
2110
+ mechanism when appropriate, then refresh status.</p>
2111
+ <p>After completion, use named result paths rather than assuming output directory names:</p>
2112
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a><span class="kn">from</span><span class="w"> </span><span class="nn">caddforge.core.execution</span><span class="w"> </span><span class="kn">import</span> <span class="n">load_result_for_job</span>
2113
+ <a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a><span class="kn">from</span><span class="w"> </span><span class="nn">caddforge.core.job_registry</span><span class="w"> </span><span class="kn">import</span> <span class="n">get_job</span>
2114
+ <a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a>
2115
+ <a id="__codelineno-1-4" name="__codelineno-1-4" href="#__codelineno-1-4"></a><span class="n">job</span> <span class="o">=</span> <span class="n">get_job</span><span class="p">(</span><span class="s2">"replace-with-your-job-id"</span><span class="p">)</span>
2116
+ <a id="__codelineno-1-5" name="__codelineno-1-5" href="#__codelineno-1-5"></a><span class="k">if</span> <span class="n">job</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
2117
+ <a id="__codelineno-1-6" name="__codelineno-1-6" href="#__codelineno-1-6"></a> <span class="k">raise</span> <span class="ne">LookupError</span><span class="p">(</span><span class="s2">"Job not found in this registry"</span><span class="p">)</span>
2118
+ <a id="__codelineno-1-7" name="__codelineno-1-7" href="#__codelineno-1-7"></a><span class="n">result</span> <span class="o">=</span> <span class="n">load_result_for_job</span><span class="p">(</span><span class="n">job</span><span class="p">)</span>
2119
+ <a id="__codelineno-1-8" name="__codelineno-1-8" href="#__codelineno-1-8"></a><span class="k">if</span> <span class="n">result</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
2120
+ <a id="__codelineno-1-9" name="__codelineno-1-9" href="#__codelineno-1-9"></a> <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s2">"No canonical result yet; check status and logs"</span><span class="p">)</span>
2121
+ <a id="__codelineno-1-10" name="__codelineno-1-10" href="#__codelineno-1-10"></a><span class="nb">print</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">status</span><span class="o">.</span><span class="n">value</span><span class="p">)</span>
2122
+ <a id="__codelineno-1-11" name="__codelineno-1-11" href="#__codelineno-1-11"></a><span class="nb">print</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">paths</span><span class="p">)</span>
2123
+ </code></pre></div>
2124
+ <p><code>caddforge export &lt;job-id&gt;</code> uses recorded submission metadata to copy completed
2125
+ outputs when an export is applicable. Do not remove scratch or original runs until
2126
+ outputs have been verified. <code>caddforge restart &lt;job-id&gt;</code> creates a new recorded
2127
+ execution from the saved tool configuration; it does not guarantee engine-specific
2128
+ checkpoint continuation. Check <code>restart --help</code> and the tool's checkpoint inputs.</p>
2129
+ <p>For an isolated registry in Python, pass <code>registry_path</code> to submission and lookup
2130
+ helpers. CLI <code>status</code> and <code>logs</code> use the default registry; not every CLI command
2131
+ accepts an override. See the <a href="../../core/cli/">CLI reference</a> and
2132
+ <a href="../../core/jobs-results/">canonical result layout</a>.</p>
2133
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