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/getting-started/first-workflow/index.html ADDED
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940
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941
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942
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943
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944
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945
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946
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947
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948
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950
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951
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952
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953
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954
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955
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956
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957
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958
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959
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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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966
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967
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968
+ <label class="md-nav__title" for="__nav_5">
969
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970
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971
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972
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973
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974
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975
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976
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977
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978
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980
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981
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982
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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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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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1002
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1003
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1009
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1010
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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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1028
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1029
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1030
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1032
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1034
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1037
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1038
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1039
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1042
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1046
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1048
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1049
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1050
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1051
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1053
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1054
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1055
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1056
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1057
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1058
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1060
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1069
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1070
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1074
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1075
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1076
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1077
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1078
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1079
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1080
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1081
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1082
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1083
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1084
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1085
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1086
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1088
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1091
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1092
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1102
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1124
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1126
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1127
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1128
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1129
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1130
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1131
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1132
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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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1141
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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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1153
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1154
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1155
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1156
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1157
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1158
+ <span class="md-nav__icon md-icon"></span>
1159
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1160
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1161
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1162
+
1163
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="false">
1164
+ <label class="md-nav__title" for="__nav_6">
1165
+ <span class="md-nav__icon md-icon"></span>
1166
+
1167
+
1168
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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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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
+
1184
+
1185
+ <span class="md-ellipsis">
1186
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1187
+
1188
+ Version Matrix
1189
+
1190
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1191
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1192
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1193
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1194
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1195
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1196
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1197
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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
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1207
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1208
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1209
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1210
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1211
+
1212
+
1213
+ <span class="md-ellipsis">
1214
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1215
+
1216
+ Docking
1217
+
1218
+
1219
+
1220
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1221
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1222
+
1223
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1224
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1225
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1226
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1227
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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
+
1241
+ <span class="md-ellipsis">
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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1252
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1253
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1254
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1255
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1256
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1261
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1262
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1263
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1264
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1265
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1266
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1267
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1268
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1269
+ <span class="md-ellipsis">
1270
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1271
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1272
+ MD
1273
+
1274
+
1275
+
1276
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1277
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1278
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1279
+
1280
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1281
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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
+
1296
+
1297
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1298
+
1299
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1300
+ FEP
1301
+
1302
+
1303
+
1304
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1305
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1306
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1307
+
1308
+ </a>
1309
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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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1317
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1320
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1321
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1322
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1323
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1324
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1325
+ <span class="md-ellipsis">
1326
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1327
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1328
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1329
+
1330
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1331
+
1332
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1333
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1334
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1335
+
1336
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1337
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1338
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1339
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1340
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1341
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1342
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1343
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1345
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1346
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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
+
1353
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1354
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1355
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1356
+ ML
1357
+
1358
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1359
+
1360
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1361
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1362
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1363
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1364
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1365
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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
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1374
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1375
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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
+
1386
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1387
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1388
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1389
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1390
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1391
+
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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1402
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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
+
1430
+
1431
+ <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_7" >
1432
+
1433
+
1434
+ <div class="md-nav__link md-nav__container">
1435
+ <a href="../../gui/" class="md-nav__link ">
1436
+
1437
+
1438
+
1439
+ <span class="md-ellipsis">
1440
+
1441
+
1442
+ GUI
1443
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1444
+
1445
+
1446
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1447
+
1448
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1449
+
1450
+ </a>
1451
+
1452
+
1453
+ <label class="md-nav__link " for="__nav_7" id="__nav_7_label" tabindex="">
1454
+ <span class="md-nav__icon md-icon"></span>
1455
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1456
+
1457
+ </div>
1458
+
1459
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_7_label" aria-expanded="false">
1460
+ <label class="md-nav__title" for="__nav_7">
1461
+ <span class="md-nav__icon md-icon"></span>
1462
+
1463
+
1464
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1465
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1466
+
1467
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1468
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1469
+
1470
+
1471
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1472
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1473
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1474
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1475
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1476
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1477
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1478
+
1479
+
1480
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1481
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1482
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1483
+
1484
+ Walkthrough
1485
+
1486
+
1487
+
1488
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1489
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1490
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1491
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1492
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1493
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1494
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1495
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1496
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1497
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1498
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1499
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1500
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1501
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1502
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1503
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1504
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1505
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1506
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1507
+
1508
+
1509
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1510
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1511
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1512
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1513
+
1514
+
1515
+
1516
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1517
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1518
+
1519
+
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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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
+
1559
+
1560
+
1561
+ <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_8" >
1562
+
1563
+
1564
+ <div class="md-nav__link md-nav__container">
1565
+ <a href="../../reference/" class="md-nav__link ">
1566
+
1567
+
1568
+
1569
+ <span class="md-ellipsis">
1570
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1571
+
1572
+ Reference
1573
+
1574
+
1575
+
1576
+ </span>
1577
+
1578
+
1579
+
1580
+ </a>
1581
+
1582
+
1583
+ <label class="md-nav__link " for="__nav_8" id="__nav_8_label" tabindex="">
1584
+ <span class="md-nav__icon md-icon"></span>
1585
+ </label>
1586
+
1587
+ </div>
1588
+
1589
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_8_label" aria-expanded="false">
1590
+ <label class="md-nav__title" for="__nav_8">
1591
+ <span class="md-nav__icon md-icon"></span>
1592
+
1593
+
1594
+ Reference
1595
+
1596
+
1597
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1598
+ <ul class="md-nav__list" data-md-scrollfix>
1599
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1600
+
1601
+
1602
+
1603
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1604
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1605
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1606
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1607
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1608
+
1609
+
1610
+
1611
+ <span class="md-ellipsis">
1612
+
1613
+
1614
+ Public Python API
1615
+
1616
+
1617
+
1618
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1619
+
1620
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1621
+
1622
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1623
+ </li>
1624
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1625
+
1626
+
1627
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1628
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1629
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1630
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1631
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1632
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1633
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1634
+ <li class="md-nav__item">
1635
+ <a href="../../examples/" class="md-nav__link">
1636
+
1637
+
1638
+
1639
+ <span class="md-ellipsis">
1640
+
1641
+
1642
+ Example Library
1643
+
1644
+
1645
+
1646
+ </span>
1647
+
1648
+
1649
+
1650
+ </a>
1651
+ </li>
1652
+
1653
+
1654
+
1655
+
1656
+
1657
+
1658
+
1659
+
1660
+
1661
+
1662
+ <li class="md-nav__item">
1663
+ <a href="../../examples/quickstart/" class="md-nav__link">
1664
+
1665
+
1666
+
1667
+ <span class="md-ellipsis">
1668
+
1669
+
1670
+ Example Data Provenance
1671
+
1672
+
1673
+
1674
+ </span>
1675
+
1676
+
1677
+
1678
+ </a>
1679
+ </li>
1680
+
1681
+
1682
+
1683
+
1684
+ </ul>
1685
+ </nav>
1686
+
1687
+ </li>
1688
+
1689
+
1690
+
1691
+
1692
+
1693
+
1694
+
1695
+
1696
+
1697
+
1698
+
1699
+
1700
+
1701
+
1702
+
1703
+
1704
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1705
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1706
+
1707
+
1708
+
1709
+
1710
+
1711
+
1712
+
1713
+
1714
+
1715
+ <li class="md-nav__item md-nav__item--section md-nav__item--nested">
1716
+
1717
+
1718
+
1719
+ <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_9" >
1720
+
1721
+
1722
+ <label class="md-nav__link" for="__nav_9" id="__nav_9_label" tabindex="">
1723
+
1724
+
1725
+
1726
+ <span class="md-ellipsis">
1727
+
1728
+
1729
+ Explanation
1730
+
1731
+
1732
+
1733
+ </span>
1734
+
1735
+
1736
+
1737
+ <span class="md-nav__icon md-icon"></span>
1738
+ </label>
1739
+
1740
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_9_label" aria-expanded="false">
1741
+ <label class="md-nav__title" for="__nav_9">
1742
+ <span class="md-nav__icon md-icon"></span>
1743
+
1744
+
1745
+ Explanation
1746
+
1747
+
1748
+ </label>
1749
+ <ul class="md-nav__list" data-md-scrollfix>
1750
+
1751
+
1752
+
1753
+
1754
+
1755
+
1756
+
1757
+ <li class="md-nav__item">
1758
+ <a href="../../explanation/reproducibility/" class="md-nav__link">
1759
+
1760
+
1761
+
1762
+ <span class="md-ellipsis">
1763
+
1764
+
1765
+ Reproducibility
1766
+
1767
+
1768
+
1769
+ </span>
1770
+
1771
+
1772
+
1773
+ </a>
1774
+ </li>
1775
+
1776
+
1777
+
1778
+
1779
+
1780
+
1781
+
1782
+
1783
+
1784
+
1785
+ <li class="md-nav__item">
1786
+ <a href="../../explanation/references/" class="md-nav__link">
1787
+
1788
+
1789
+
1790
+ <span class="md-ellipsis">
1791
+
1792
+
1793
+ Method References
1794
+
1795
+
1796
+
1797
+ </span>
1798
+
1799
+
1800
+
1801
+ </a>
1802
+ </li>
1803
+
1804
+
1805
+
1806
+
1807
+
1808
+
1809
+
1810
+
1811
+
1812
+
1813
+ <li class="md-nav__item">
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2141
+ <span class="md-nav__icon md-icon"></span>
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+ Table of contents
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+ <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
2145
+
2146
+ <li class="md-nav__item">
2147
+ <a href="#prepare-the-environment-and-files" class="md-nav__link">
2148
+ <span class="md-ellipsis">
2149
+
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+ Prepare the environment and files
2151
+
2152
+ </span>
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+ </a>
2154
+
2155
+ </li>
2156
+
2157
+ <li class="md-nav__item">
2158
+ <a href="#run-from-python" class="md-nav__link">
2159
+ <span class="md-ellipsis">
2160
+
2161
+ Run from Python
2162
+
2163
+ </span>
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+ </a>
2165
+
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+ </li>
2167
+
2168
+ </ul>
2169
+
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+ </nav>
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2174
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2178
+
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+ <article class="md-content__inner md-typeset">
2180
+
2181
+
2182
+
2183
+
2184
+
2185
+
2186
+
2187
+
2188
+ <h1 id="first-workflow-analyze-a-small-table">First Workflow: Analyze a Small Table<a class="headerlink" href="#first-workflow-analyze-a-small-table" title="Permanent link">&para;</a></h1>
2189
+ <p>Run a local job, inspect its outputs, and repeat the same execution from Python.
2190
+ This example uses 30 invented numeric values. It needs no GPU, external engine,
2191
+ downloaded model, or molecular structures.</p>
2192
+ <h2 id="prepare-the-environment-and-files">Prepare the environment and files<a class="headerlink" href="#prepare-the-environment-and-files" title="Permanent link">&para;</a></h2>
2193
+ <p>See <a href="../installation/">installation</a> for release availability and source installation.
2194
+ In a compatible environment, install <code>caddforge-datascience</code>; it installs core automatically:</p>
2195
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>python<span class="w"> </span>-m<span class="w"> </span>pip<span class="w"> </span>install<span class="w"> </span>caddforge-datascience
2196
+ <a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a>caddforge<span class="w"> </span>list-tools
2197
+ <a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a>caddforge<span class="w"> </span>show-config<span class="w"> </span>datascience<span class="w"> </span>distribution-diagnostics
2198
+ </code></pre></div>
2199
+ <p>Download <a href="../../examples/quickstart/values.csv">values.csv</a>,
2200
+ <a href="../../examples/quickstart/diagnostics.yaml">diagnostics.yaml</a>, and
2201
+ <a href="../../examples/quickstart/run.py">run.py</a> into one new directory. Run commands from
2202
+ that directory. Keep CSV and YAML filenames unchanged. Downloaded <code>.py</code> and <code>.yaml</code>
2203
+ links may open as text; save them using the browser's save command.</p>
2204
+ <p>The configuration selects <code>backend: local</code>, a fixed seed, and ten histogram bins.
2205
+ Relative workflow input paths resolve from the submission working directory.</p>
2206
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>caddforge<span class="w"> </span>run<span class="w"> </span>datascience<span class="w"> </span>distribution-diagnostics<span class="w"> </span>--config<span class="w"> </span>diagnostics.yaml
2207
+ </code></pre></div>
2208
+ <p>The terminal prints a job ID. Substitute that ID in:</p>
2209
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>caddforge<span class="w"> </span>status<span class="w"> </span>&lt;job-id&gt;
2210
+ <a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>caddforge<span class="w"> </span>logs<span class="w"> </span>&lt;job-id&gt;
2211
+ <a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>caddforge<span class="w"> </span>list-jobs
2212
+ </code></pre></div>
2213
+ <p>Keep the same working directory for these commands so they use the same default registry.
2214
+ Job status should be <code>COMPLETED</code>. Under the job's <code>runs/&lt;date&gt;/&lt;job-id&gt;/results/</code>, expect:</p>
2215
+ <table>
2216
+ <thead>
2217
+ <tr>
2218
+ <th>File</th>
2219
+ <th>Meaning</th>
2220
+ </tr>
2221
+ </thead>
2222
+ <tbody>
2223
+ <tr>
2224
+ <td><code>distribution_report.json</code></td>
2225
+ <td>Distribution report; <code>counts.n_total</code> is <code>30</code></td>
2226
+ </tr>
2227
+ <tr>
2228
+ <td><code>distribution_diagnostics.png</code></td>
2229
+ <td>Histogram and Q–Q plot</td>
2230
+ </tr>
2231
+ <tr>
2232
+ <td><code>result_record.json</code></td>
2233
+ <td>Canonical job result and named output paths</td>
2234
+ </tr>
2235
+ </tbody>
2236
+ </table>
2237
+ <p>The configuration gives the scientific report its own filename, separate from
2238
+ canonical result records. Load reports through their named result paths.
2239
+ Normality p-values and recommendations describe this toy sample; they do not validate
2240
+ an assay or establish a scientific distribution. The values are dimensionless.</p>
2241
+ <h2 id="run-from-python">Run from Python<a class="headerlink" href="#run-from-python" title="Permanent link">&para;</a></h2>
2242
+ <p>The supplied script uses the same configuration and core submission helpers:</p>
2243
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>python<span class="w"> </span>run.py
2244
+ </code></pre></div>
2245
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></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><span class="p">,</span> <span class="n">submit_workflow</span>
2246
+ <a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a><span class="kn">from</span><span class="w"> </span><span class="nn">caddforge.core.job</span><span class="w"> </span><span class="kn">import</span> <span class="n">JobStatus</span>
2247
+ <a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a><span class="kn">from</span><span class="w"> </span><span class="nn">caddforge.plugins</span><span class="w"> </span><span class="kn">import</span> <span class="n">get_tool</span>
2248
+ <a id="__codelineno-4-4" name="__codelineno-4-4" href="#__codelineno-4-4"></a>
2249
+ <a id="__codelineno-4-5" name="__codelineno-4-5" href="#__codelineno-4-5"></a><span class="n">spec</span> <span class="o">=</span> <span class="n">get_tool</span><span class="p">(</span><span class="s2">"datascience"</span><span class="p">,</span> <span class="s2">"distribution-diagnostics"</span><span class="p">)</span>
2250
+ <a id="__codelineno-4-6" name="__codelineno-4-6" href="#__codelineno-4-6"></a><span class="n">cfg</span> <span class="o">=</span> <span class="n">spec</span><span class="o">.</span><span class="n">config_cls</span><span class="o">.</span><span class="n">from_yaml</span><span class="p">(</span><span class="s2">"diagnostics.yaml"</span><span class="p">)</span>
2251
+ <a id="__codelineno-4-7" name="__codelineno-4-7" href="#__codelineno-4-7"></a><span class="n">workflow</span> <span class="o">=</span> <span class="n">spec</span><span class="o">.</span><span class="n">workflow_cls</span><span class="p">(</span><span class="n">cfg</span><span class="p">)</span>
2252
+ <a id="__codelineno-4-8" name="__codelineno-4-8" href="#__codelineno-4-8"></a><span class="n">job</span> <span class="o">=</span> <span class="n">submit_workflow</span><span class="p">(</span>
2253
+ <a id="__codelineno-4-9" name="__codelineno-4-9" href="#__codelineno-4-9"></a> <span class="n">workflow</span><span class="p">,</span> <span class="n">cfg</span><span class="p">,</span> <span class="n">backend_name</span><span class="o">=</span><span class="n">cfg</span><span class="o">.</span><span class="n">backend</span><span class="p">,</span>
2254
+ <a id="__codelineno-4-10" name="__codelineno-4-10" href="#__codelineno-4-10"></a> <span class="n">input_ports</span><span class="o">=</span><span class="nb">tuple</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="n">spec</span><span class="o">.</span><span class="n">plugin</span><span class="p">,</span> <span class="s2">"input_ports"</span><span class="p">,</span> <span class="p">())),</span>
2255
+ <a id="__codelineno-4-11" name="__codelineno-4-11" href="#__codelineno-4-11"></a><span class="p">)</span>
2256
+ <a id="__codelineno-4-12" name="__codelineno-4-12" href="#__codelineno-4-12"></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>
2257
+ <a id="__codelineno-4-13" name="__codelineno-4-13" href="#__codelineno-4-13"></a><span class="k">if</span> <span class="n">result</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">result</span><span class="o">.</span><span class="n">status</span> <span class="o">!=</span> <span class="n">JobStatus</span><span class="o">.</span><span class="n">COMPLETED</span><span class="p">:</span>
2258
+ <a id="__codelineno-4-14" name="__codelineno-4-14" href="#__codelineno-4-14"></a> <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Job </span><span class="si">{</span><span class="n">job</span><span class="o">.</span><span class="n">id</span><span class="si">}</span><span class="s2"> failed; inspect its logs"</span><span class="p">)</span>
2259
+ <a id="__codelineno-4-15" name="__codelineno-4-15" href="#__codelineno-4-15"></a><span class="nb">print</span><span class="p">(</span><span class="n">job</span><span class="o">.</span><span class="n">id</span><span class="p">)</span>
2260
+ <a id="__codelineno-4-16" name="__codelineno-4-16" href="#__codelineno-4-16"></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><span class="s2">"report_json"</span><span class="p">])</span>
2261
+ <a id="__codelineno-4-17" name="__codelineno-4-17" href="#__codelineno-4-17"></a><span class="nb">print</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">metrics</span><span class="p">[</span><span class="s2">"n_total"</span><span class="p">])</span>
2262
+ </code></pre></div>
2263
+ <p>This creates a second job. Local submission waits for the workflow by default;
2264
+ asynchronous or Slurm submission requires checking completion before loading results.
2265
+ Continue with <a href="../first-pipeline/">a small pipeline</a>, or consult
2266
+ <a href="../../how-to/troubleshooting/">troubleshooting</a> if a step fails.</p>
2267
+
2268
+
2269
+
2270
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2271
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2272
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2274
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2275
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2277
+
2278
+
2279
+
2280
+ </article>
2281
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2282
+
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+
2284
+ <script>var target=document.getElementById(location.hash.slice(1));target&&target.name&&(target.checked=target.name.startsWith("__tabbed_"))</script>
2285
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+
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