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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947
+ <span class="md-ellipsis">
948
+
949
+
950
+ Specification
951
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952
+
953
+
954
+ </span>
955
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956
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957
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958
+ </a>
959
+
960
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961
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962
+ <nav class="md-nav md-nav--secondary" aria-label="Table of contents">
963
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964
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965
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966
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967
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968
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969
+ <label class="md-nav__title" for="__toc">
970
+ <span class="md-nav__icon md-icon"></span>
971
+ Table of contents
972
+ </label>
973
+ <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
974
+
975
+ <li class="md-nav__item">
976
+ <a href="#rules" class="md-nav__link">
977
+ <span class="md-ellipsis">
978
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979
+ Rules
980
+
981
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982
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983
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984
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985
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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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995
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996
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1003
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1007
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1008
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1009
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1010
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1011
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1012
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1013
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1014
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1015
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1016
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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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1029
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1030
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1031
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1035
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1036
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1037
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1038
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1039
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1040
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1041
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1042
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1043
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1044
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1045
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1046
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1047
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1063
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1066
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1070
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1074
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1075
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1077
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1078
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1080
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1081
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1083
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1120
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1125
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1128
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1129
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1130
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1132
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1133
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1135
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1136
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1137
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1138
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1139
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1140
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1142
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1143
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1144
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1145
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1146
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1147
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1148
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1149
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1150
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1151
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1152
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1161
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1162
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1164
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1167
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1169
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1170
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1171
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1172
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1173
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1174
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1175
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1176
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1177
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1178
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1179
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1180
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1181
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1182
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1183
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1185
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1186
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1187
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1188
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1198
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1199
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1200
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1201
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1202
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1203
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1204
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1205
+ Docking
1206
+
1207
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1208
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1209
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1210
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1211
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1212
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1213
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1214
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1215
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1217
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1225
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1226
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1227
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1230
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1231
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1232
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1233
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1234
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1235
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1236
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1237
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1238
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1239
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1240
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1241
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1242
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1243
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1255
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1259
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1262
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1264
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1265
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1266
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1268
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1269
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1270
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1271
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1282
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1283
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1284
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1285
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1286
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1287
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1288
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1289
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1290
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1291
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1292
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1293
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1294
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1295
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1296
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1297
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1298
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1299
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1300
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1301
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1310
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1311
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1312
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1313
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1314
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1315
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1317
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1318
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1319
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1320
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1321
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1322
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1324
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1325
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1326
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1327
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1338
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1339
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1340
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1342
+ <span class="md-ellipsis">
1343
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1345
+ ML
1346
+
1347
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1348
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1349
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1350
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1351
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1352
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1353
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1354
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1355
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1356
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1366
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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
+ Data Science
1374
+
1375
+
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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1388
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1389
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1415
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1416
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1417
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1418
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1419
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1420
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1421
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1422
+
1423
+ <div class="md-nav__link md-nav__container">
1424
+ <a href="../../gui/" class="md-nav__link ">
1425
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1426
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1427
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1428
+ <span class="md-ellipsis">
1429
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1430
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1431
+ GUI
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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1438
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1439
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1440
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1441
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1442
+ <label class="md-nav__link " for="__nav_7" id="__nav_7_label" tabindex="">
1443
+ <span class="md-nav__icon md-icon"></span>
1444
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1445
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1446
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1447
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1448
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_7_label" aria-expanded="false">
1449
+ <label class="md-nav__title" for="__nav_7">
1450
+ <span class="md-nav__icon md-icon"></span>
1451
+
1452
+
1453
+ GUI
1454
+
1455
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1456
+ </label>
1457
+ <ul class="md-nav__list" data-md-scrollfix>
1458
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1459
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1460
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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
+
1468
+
1469
+
1470
+ <span class="md-ellipsis">
1471
+
1472
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1473
+ Walkthrough
1474
+
1475
+
1476
+
1477
+ </span>
1478
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1479
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1480
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1481
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1482
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1483
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1484
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1485
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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
+
1498
+ <span class="md-ellipsis">
1499
+
1500
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1501
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1502
+
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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1513
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1516
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1517
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1519
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1532
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1537
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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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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
+
1571
+
1572
+ <label class="md-nav__link " for="__nav_8" id="__nav_8_label" tabindex="">
1573
+ <span class="md-nav__icon md-icon"></span>
1574
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1575
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1576
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1577
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1578
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_8_label" aria-expanded="false">
1579
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1580
+ <span class="md-nav__icon md-icon"></span>
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
+
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
+
1599
+
1600
+ <span class="md-ellipsis">
1601
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1602
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1603
+ Public Python API
1604
+
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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1616
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1617
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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
+
1626
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1627
+
1628
+ <span class="md-ellipsis">
1629
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1630
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1631
+ Example Library
1632
+
1633
+
1634
+
1635
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1636
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1637
+
1638
+
1639
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1640
+ </li>
1641
+
1642
+
1643
+
1644
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1645
+
1646
+
1647
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1648
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1649
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1650
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1651
+ <li class="md-nav__item">
1652
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1653
+
1654
+
1655
+
1656
+ <span class="md-ellipsis">
1657
+
1658
+
1659
+ Example Data Provenance
1660
+
1661
+
1662
+
1663
+ </span>
1664
+
1665
+
1666
+
1667
+ </a>
1668
+ </li>
1669
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1670
+
1671
+
1672
+
1673
+ </ul>
1674
+ </nav>
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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1680
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1681
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1682
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1683
+
1684
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1685
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1686
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1687
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1688
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1689
+
1690
+
1691
+
1692
+
1693
+
1694
+
1695
+
1696
+
1697
+
1698
+
1699
+
1700
+
1701
+
1702
+
1703
+
1704
+ <li class="md-nav__item md-nav__item--section md-nav__item--nested">
1705
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1706
+
1707
+
1708
+ <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_9" >
1709
+
1710
+
1711
+ <label class="md-nav__link" for="__nav_9" id="__nav_9_label" tabindex="">
1712
+
1713
+
1714
+
1715
+ <span class="md-ellipsis">
1716
+
1717
+
1718
+ Explanation
1719
+
1720
+
1721
+
1722
+ </span>
1723
+
1724
+
1725
+
1726
+ <span class="md-nav__icon md-icon"></span>
1727
+ </label>
1728
+
1729
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_9_label" aria-expanded="false">
1730
+ <label class="md-nav__title" for="__nav_9">
1731
+ <span class="md-nav__icon md-icon"></span>
1732
+
1733
+
1734
+ Explanation
1735
+
1736
+
1737
+ </label>
1738
+ <ul class="md-nav__list" data-md-scrollfix>
1739
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1740
+
1741
+
1742
+
1743
+
1744
+
1745
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1746
+ <li class="md-nav__item">
1747
+ <a href="../../explanation/reproducibility/" class="md-nav__link">
1748
+
1749
+
1750
+
1751
+ <span class="md-ellipsis">
1752
+
1753
+
1754
+ Reproducibility
1755
+
1756
+
1757
+
1758
+ </span>
1759
+
1760
+
1761
+
1762
+ </a>
1763
+ </li>
1764
+
1765
+
1766
+
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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1776
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1777
+
1778
+
1779
+ <span class="md-ellipsis">
1780
+
1781
+
1782
+ Method References
1783
+
1784
+
1785
+
1786
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1787
+
1788
+
1789
+
1790
+ </a>
1791
+ </li>
1792
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1793
+
1794
+
1795
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1796
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1797
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1798
+
1799
+
1800
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1801
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1802
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1803
+ <a href="../../explanation/third-party-notices/" class="md-nav__link">
1804
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1805
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1806
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1807
+ <span class="md-ellipsis">
1808
+
1809
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1810
+ Third-party Notices
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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1825
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1826
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1828
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1830
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1831
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1832
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1833
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2130
+ <span class="md-nav__icon md-icon"></span>
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+ Table of contents
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+ </label>
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+ <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
2134
+
2135
+ <li class="md-nav__item">
2136
+ <a href="#rules" class="md-nav__link">
2137
+ <span class="md-ellipsis">
2138
+
2139
+ Rules
2140
+
2141
+ </span>
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+ </a>
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+
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+ </li>
2145
+
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+ </ul>
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2158
+
2159
+
2160
+
2161
+
2162
+
2163
+
2164
+
2165
+
2166
+ <h1 id="pipeline-specification">Pipeline Specification<a class="headerlink" href="#pipeline-specification" title="Permanent link">&para;</a></h1>
2167
+ <p>Pipeline YAML uses stages. A stage is either a tool plugin stage or a generic built-in stage.</p>
2168
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a><span class="nt">version</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">1</span>
2169
+ <a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a><span class="nt">name</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">docking-screen</span>
2170
+ <a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a>
2171
+ <a id="__codelineno-0-4" name="__codelineno-0-4" href="#__codelineno-0-4"></a><span class="nt">defaults</span><span class="p">:</span>
2172
+ <a id="__codelineno-0-5" name="__codelineno-0-5" href="#__codelineno-0-5"></a><span class="w"> </span><span class="nt">backend</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">local</span>
2173
+ <a id="__codelineno-0-6" name="__codelineno-0-6" href="#__codelineno-0-6"></a><span class="w"> </span><span class="nt">registry_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">runs/job_registry.sqlite</span>
2174
+ <a id="__codelineno-0-7" name="__codelineno-0-7" href="#__codelineno-0-7"></a>
2175
+ <a id="__codelineno-0-8" name="__codelineno-0-8" href="#__codelineno-0-8"></a><span class="nt">stages</span><span class="p">:</span>
2176
+ <a id="__codelineno-0-9" name="__codelineno-0-9" href="#__codelineno-0-9"></a><span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="nt">id</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">unidock_screen</span>
2177
+ <a id="__codelineno-0-10" name="__codelineno-0-10" href="#__codelineno-0-10"></a><span class="w"> </span><span class="nt">tool</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">docking/unidock</span>
2178
+ <a id="__codelineno-0-11" name="__codelineno-0-11" href="#__codelineno-0-11"></a><span class="w"> </span><span class="nt">config</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">unidock.yaml</span>
2179
+ <a id="__codelineno-0-12" name="__codelineno-0-12" href="#__codelineno-0-12"></a><span class="w"> </span><span class="nt">scatter</span><span class="p">:</span>
2180
+ <a id="__codelineno-0-13" name="__codelineno-0-13" href="#__codelineno-0-13"></a><span class="w"> </span><span class="nt">by</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">ligand_multisdf_path</span>
2181
+ <a id="__codelineno-0-14" name="__codelineno-0-14" href="#__codelineno-0-14"></a><span class="w"> </span><span class="nt">chunk_size</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">50000</span>
2182
+ <a id="__codelineno-0-15" name="__codelineno-0-15" href="#__codelineno-0-15"></a><span class="w"> </span><span class="nt">outputs</span><span class="p">:</span>
2183
+ <a id="__codelineno-0-16" name="__codelineno-0-16" href="#__codelineno-0-16"></a><span class="w"> </span><span class="nt">scores</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">best_scores_csv</span>
2184
+ <a id="__codelineno-0-17" name="__codelineno-0-17" href="#__codelineno-0-17"></a><span class="w"> </span><span class="nt">poses</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">poses_dir</span>
2185
+ <a id="__codelineno-0-18" name="__codelineno-0-18" href="#__codelineno-0-18"></a>
2186
+ <a id="__codelineno-0-19" name="__codelineno-0-19" href="#__codelineno-0-19"></a><span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="nt">id</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">top_score_filter</span>
2187
+ <a id="__codelineno-0-20" name="__codelineno-0-20" href="#__codelineno-0-20"></a><span class="w"> </span><span class="nt">type</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">filter.tabular</span>
2188
+ <a id="__codelineno-0-21" name="__codelineno-0-21" href="#__codelineno-0-21"></a><span class="w"> </span><span class="nt">inputs</span><span class="p">:</span>
2189
+ <a id="__codelineno-0-22" name="__codelineno-0-22" href="#__codelineno-0-22"></a><span class="w"> </span><span class="nt">table</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">unidock_screen.scores</span>
2190
+ <a id="__codelineno-0-23" name="__codelineno-0-23" href="#__codelineno-0-23"></a><span class="w"> </span><span class="nt">config</span><span class="p">:</span>
2191
+ <a id="__codelineno-0-24" name="__codelineno-0-24" href="#__codelineno-0-24"></a><span class="w"> </span><span class="nt">sort_by</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">best_score</span>
2192
+ <a id="__codelineno-0-25" name="__codelineno-0-25" href="#__codelineno-0-25"></a><span class="w"> </span><span class="nt">ascending</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">true</span>
2193
+ <a id="__codelineno-0-26" name="__codelineno-0-26" href="#__codelineno-0-26"></a><span class="w"> </span><span class="nt">top_n</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">1000</span>
2194
+ </code></pre></div>
2195
+ <h2 id="rules">Rules<a class="headerlink" href="#rules" title="Permanent link">&para;</a></h2>
2196
+ <ul>
2197
+ <li><code>tool</code> stages resolve installed plugins through the registry.</li>
2198
+ <li><code>type</code> stages call generic built-ins from core.</li>
2199
+ <li><code>inputs</code> reference upstream artifacts as <code>stage_id.artifact_name</code>.</li>
2200
+ <li><code>outputs</code> map pipeline artifact names to workflow result path keys. If omitted, CADDForge uses the
2201
+ tool plugin's declared output ports.</li>
2202
+ <li>Optional plugin output ports are skipped when a workflow configuration does not produce the
2203
+ corresponding result path. Manifest-backed output ports can expose a CSV path column as a
2204
+ multi-path artifact for downstream scatter or filtering.</li>
2205
+ <li>If a scattered stage receives additional path-collection inputs with the same length as the
2206
+ scatter input, those paths are bound by row order for each shard. Use this only for paired
2207
+ artifacts selected from the same provenance table, such as ligand SDF and protein PDB files for
2208
+ the same pose. For paired <code>list[Path]</code> config fields, each shard receives a one-item list with its
2209
+ matching path.</li>
2210
+ <li>Scatter strategies include <code>sdf</code>, <code>csv</code>, <code>tsv</code>, <code>lines</code>, and <code>auto</code>. Plugin split contracts can
2211
+ apply these strategies to path members inside structured collection fields and declare
2212
+ deterministic output reducers.</li>
2213
+ <li>Stage IDs are part of the artifact API and should remain stable in examples.</li>
2214
+ <li>Defaults are applied centrally by the executor.</li>
2215
+ </ul>
2216
+
2217
+
2218
+
2219
+
2220
+
2221
+
2222
+
2223
+
2224
+
2225
+
2226
+
2227
+
2228
+
2229
+ </article>
2230
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2231
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