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/core/cli/index.html ADDED
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931
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932
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933
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934
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935
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936
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937
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938
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939
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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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949
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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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988
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989
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990
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991
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992
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993
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994
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995
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996
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997
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998
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999
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1000
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1001
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1002
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1003
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1004
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1005
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1006
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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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1028
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1029
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1030
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1031
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1032
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1033
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1034
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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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1048
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1049
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1050
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1051
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1052
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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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1059
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1060
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1061
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1062
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1063
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1064
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1065
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1066
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1067
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1068
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1069
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1070
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1071
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1072
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1073
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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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1087
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1088
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1089
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1090
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1091
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1092
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1093
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1094
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1095
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1096
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1097
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1098
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1099
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1100
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1101
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1102
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1103
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1104
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1105
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1106
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1107
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1108
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1109
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1110
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1111
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1112
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1113
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1114
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1115
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1116
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1117
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1118
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1119
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1120
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1121
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1122
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1123
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1124
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1125
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1126
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1127
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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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1133
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1134
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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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1153
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1155
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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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1184
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1185
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1186
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1187
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1188
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1189
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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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1206
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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
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1212
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1213
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1214
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1215
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1216
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1217
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1218
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1219
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1220
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1221
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1222
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1223
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1224
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1225
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1226
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1227
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1228
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1229
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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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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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1257
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1258
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1259
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1260
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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
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1270
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1271
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1272
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1273
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1274
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1275
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1276
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1277
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1278
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1279
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1280
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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
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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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1302
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1303
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1304
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1305
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1306
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1307
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1308
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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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1315
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1316
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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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1323
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1324
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1325
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1326
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1327
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1328
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1329
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1330
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1331
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1332
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1333
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1334
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1335
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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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1344
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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
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1353
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1354
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1355
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1356
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1357
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1358
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1359
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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
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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
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1392
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1393
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1394
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1395
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1396
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1397
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1398
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1399
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1400
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1401
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1402
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1403
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1404
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1405
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1406
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1407
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1408
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1409
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1410
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1411
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1412
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1413
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1414
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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
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1423
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1424
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1425
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1426
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1427
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1428
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1429
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1430
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1431
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1432
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1433
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1434
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1435
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1436
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1437
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1438
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1439
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1440
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1441
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1442
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1443
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1444
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1445
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1446
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1447
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1448
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1449
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1451
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1452
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1453
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1454
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1471
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1477
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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
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1498
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1499
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1500
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1501
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1502
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1503
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1504
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1505
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1506
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1507
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1508
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1509
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1510
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1511
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1512
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1513
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1514
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1515
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1516
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1517
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1518
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1519
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1520
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1521
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1522
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1523
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1524
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1525
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1526
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1527
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1528
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1529
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1530
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1531
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1532
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1533
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1534
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1535
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1536
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1537
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1538
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1539
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1540
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1541
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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
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1571
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1572
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1573
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1574
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1575
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1576
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1577
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1578
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1579
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1580
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1581
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1582
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1583
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1584
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1585
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1586
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1587
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1588
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1589
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1590
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1591
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1592
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1593
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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
+
1618
+
1619
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1620
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1621
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1622
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1623
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1624
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1625
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1626
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1627
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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
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1635
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1636
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1637
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1638
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1639
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1640
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1641
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1642
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1643
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1644
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1645
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1646
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1647
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1648
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1649
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1650
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1651
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1652
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1653
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1654
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1655
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1656
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1657
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1658
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1659
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1660
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1661
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1662
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1663
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1664
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1665
+
1666
+ <span class="md-ellipsis">
1667
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1668
+
1669
+ Public Python API
1670
+
1671
+
1672
+
1673
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1674
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1675
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1676
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1677
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1678
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1679
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1680
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1681
+
1682
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1683
+
1684
+
1685
+
1686
+
1687
+
1688
+
1689
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1690
+ <a href="../../examples/" class="md-nav__link">
1691
+
1692
+
1693
+
1694
+ <span class="md-ellipsis">
1695
+
1696
+
1697
+ Example Library
1698
+
1699
+
1700
+
1701
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1702
+
1703
+
1704
+
1705
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1706
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1707
+
1708
+
1709
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1710
+
1711
+
1712
+
1713
+
1714
+
1715
+
1716
+
1717
+ <li class="md-nav__item">
1718
+ <a href="../../examples/quickstart/" class="md-nav__link">
1719
+
1720
+
1721
+
1722
+ <span class="md-ellipsis">
1723
+
1724
+
1725
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1726
+
1727
+
1728
+
1729
+ </span>
1730
+
1731
+
1732
+
1733
+ </a>
1734
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1735
+
1736
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1737
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1738
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1739
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1740
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1741
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1742
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1743
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1744
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1745
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1746
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1747
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1748
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1749
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1750
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1751
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1752
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1753
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1754
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1755
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1756
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1757
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1758
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1759
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1760
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1761
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1762
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1763
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1764
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1765
+
1766
+
1767
+
1768
+
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
+
1777
+ <label class="md-nav__link" for="__nav_9" id="__nav_9_label" tabindex="">
1778
+
1779
+
1780
+
1781
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1782
+
1783
+
1784
+ Explanation
1785
+
1786
+
1787
+
1788
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1789
+
1790
+
1791
+
1792
+ <span class="md-nav__icon md-icon"></span>
1793
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1794
+
1795
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_9_label" aria-expanded="false">
1796
+ <label class="md-nav__title" for="__nav_9">
1797
+ <span class="md-nav__icon md-icon"></span>
1798
+
1799
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1800
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1801
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1802
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1803
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1804
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1805
+
1806
+
1807
+
1808
+
1809
+
1810
+
1811
+
1812
+ <li class="md-nav__item">
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+ <a href="../../explanation/reproducibility/" class="md-nav__link">
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+ <span class="md-ellipsis">
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+ Reproducibility
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+ <span class="md-ellipsis">
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+ </span>
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+ Tool Authoring
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+ </a>
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+ <span class="md-ellipsis">
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+ Contributing
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+ </span>
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+ </a>
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+
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+
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+ <span class="md-ellipsis">
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+
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+
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+ Security Reporting
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+
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+
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+
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+ </span>
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+
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+ </a>
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+ <li class="md-nav__item">
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+ <a href="../../development/release-readiness/" class="md-nav__link">
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+
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+
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+
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+ <span class="md-ellipsis">
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+
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+
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+ Release Readiness
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+
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+ </span>
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+ </a>
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+ <a href="../../development/ci-publishing/" class="md-nav__link">
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+
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+
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+
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+ <span class="md-ellipsis">
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+
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+
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+ CI and Publishing
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+
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+
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+
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+ </span>
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+
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+ </a>
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+ </li>
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+ </ul>
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+ </nav>
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+
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+ </li>
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+
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+
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+ </ul>
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+ </nav>
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+ </div>
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+ </div>
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+ </div>
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+
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+
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+
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+ <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
2184
+ <div class="md-sidebar__scrollwrap">
2185
+ <div class="md-sidebar__inner">
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+
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+
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+ <nav class="md-nav md-nav--secondary" aria-label="Table of contents">
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+
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+
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+
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+
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+
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+
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+ <label class="md-nav__title" for="__toc">
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+ <span class="md-nav__icon md-icon"></span>
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+ Table of contents
2198
+ </label>
2199
+ <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
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+
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+ <li class="md-nav__item">
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+ <a href="#open-documentation" class="md-nav__link">
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+ <span class="md-ellipsis">
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+
2205
+ Open documentation
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+
2207
+ </span>
2208
+ </a>
2209
+
2210
+ </li>
2211
+
2212
+ <li class="md-nav__item">
2213
+ <a href="#discover-tools" class="md-nav__link">
2214
+ <span class="md-ellipsis">
2215
+
2216
+ Discover tools
2217
+
2218
+ </span>
2219
+ </a>
2220
+
2221
+ </li>
2222
+
2223
+ <li class="md-nav__item">
2224
+ <a href="#show-a-config-template" class="md-nav__link">
2225
+ <span class="md-ellipsis">
2226
+
2227
+ Show a config template
2228
+
2229
+ </span>
2230
+ </a>
2231
+
2232
+ </li>
2233
+
2234
+ <li class="md-nav__item">
2235
+ <a href="#run-a-workflow" class="md-nav__link">
2236
+ <span class="md-ellipsis">
2237
+
2238
+ Run a workflow
2239
+
2240
+ </span>
2241
+ </a>
2242
+
2243
+ </li>
2244
+
2245
+ <li class="md-nav__item">
2246
+ <a href="#pack-a-slurm-environment" class="md-nav__link">
2247
+ <span class="md-ellipsis">
2248
+
2249
+ Pack a Slurm environment
2250
+
2251
+ </span>
2252
+ </a>
2253
+
2254
+ </li>
2255
+
2256
+ <li class="md-nav__item">
2257
+ <a href="#jobs" class="md-nav__link">
2258
+ <span class="md-ellipsis">
2259
+
2260
+ Jobs
2261
+
2262
+ </span>
2263
+ </a>
2264
+
2265
+ </li>
2266
+
2267
+ <li class="md-nav__item">
2268
+ <a href="#pipelines" class="md-nav__link">
2269
+ <span class="md-ellipsis">
2270
+
2271
+ Pipelines
2272
+
2273
+ </span>
2274
+ </a>
2275
+
2276
+ </li>
2277
+
2278
+ </ul>
2279
+
2280
+ </nav>
2281
+ </div>
2282
+ </div>
2283
+ </div>
2284
+
2285
+
2286
+
2287
+ <div class="md-content" data-md-component="content">
2288
+
2289
+ <article class="md-content__inner md-typeset">
2290
+
2291
+
2292
+
2293
+
2294
+
2295
+
2296
+
2297
+
2298
+ <h1 id="cli">CLI<a class="headerlink" href="#cli" title="Permanent link">&para;</a></h1>
2299
+ <p>The <code>caddforge</code> CLI is the main user interface for running workflows and inspecting jobs.</p>
2300
+ <h2 id="open-documentation">Open documentation<a class="headerlink" href="#open-documentation" title="Permanent link">&para;</a></h2>
2301
+ <p>Install <code>caddforge-docs</code> to enable the optional documentation command. Version
2302
+ <code>0.3.0</code> is tagged and awaiting package-index publication; install the source checkout with
2303
+ <code>python -m pip install ../caddforge-docs</code> for now. Once that release is available:</p>
2304
+ <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-docs
2305
+ <a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a>caddforge<span class="w"> </span>docs
2306
+ </code></pre></div>
2307
+ <p>The planned public bundle includes this package automatically. Core-only and
2308
+ selective plugin installations add it separately. See the
2309
+ <a href="../../plugins/version-matrix/">version matrix</a> for current availability.</p>
2310
+ <p>The command serves the documentation bundled with the installed docs release, opens the default
2311
+ browser, and runs until Ctrl+C. No source checkout, documentation build tools, or internet connection
2312
+ are needed. It defaults to <code>127.0.0.1</code> with an automatically assigned port:</p>
2313
+ <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>docs<span class="w"> </span>--host<span class="w"> </span><span class="m">0</span>.0.0.0<span class="w"> </span>--port<span class="w"> </span><span class="m">8001</span>
2314
+ <a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>caddforge<span class="w"> </span>docs<span class="w"> </span>--host<span class="w"> </span>localhost<span class="w"> </span>--no-browser
2315
+ <a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a>caddforge<span class="w"> </span>docs<span class="w"> </span>--host<span class="w"> </span>::1
2316
+ </code></pre></div>
2317
+ <p><code>--host</code> accepts hostnames, IPv4, and IPv6 addresses. Wildcard bindings open a loopback browser URL;
2318
+ remote clients should use the server's reachable address and printed port. <code>--no-browser</code> suppresses
2319
+ automatic opening. If no browser can be launched, the server stays available at the printed URL.
2320
+ The command is absent when the docs package is not installed.</p>
2321
+ <h2 id="discover-tools">Discover tools<a class="headerlink" href="#discover-tools" title="Permanent link">&para;</a></h2>
2322
+ <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>list-tools
2323
+ </code></pre></div>
2324
+ <h2 id="show-a-config-template">Show a config template<a class="headerlink" href="#show-a-config-template" title="Permanent link">&para;</a></h2>
2325
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>caddforge<span class="w"> </span>show-config<span class="w"> </span>&lt;section&gt;<span class="w"> </span>&lt;tool&gt;
2326
+ </code></pre></div>
2327
+ <p>Example:</p>
2328
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>caddforge<span class="w"> </span>show-config<span class="w"> </span>docking<span class="w"> </span>unidock
2329
+ </code></pre></div>
2330
+ <h2 id="run-a-workflow">Run a workflow<a class="headerlink" href="#run-a-workflow" title="Permanent link">&para;</a></h2>
2331
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>caddforge<span class="w"> </span>run<span class="w"> </span>&lt;section&gt;<span class="w"> </span>&lt;tool&gt;<span class="w"> </span>--config<span class="w"> </span>config.yaml
2332
+ </code></pre></div>
2333
+ <p>Examples:</p>
2334
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>caddforge<span class="w"> </span>run<span class="w"> </span>docking<span class="w"> </span>unidock<span class="w"> </span>--config<span class="w"> </span>unidock.yaml
2335
+ <a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a>caddforge<span class="w"> </span>run<span class="w"> </span>md<span class="w"> </span>openbpmd<span class="w"> </span>--config<span class="w"> </span>openbpmd.yaml
2336
+ <a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a>caddforge<span class="w"> </span>run<span class="w"> </span>fep<span class="w"> </span>openfe-abfe<span class="w"> </span>--config<span class="w"> </span>abfe.yaml
2337
+ </code></pre></div>
2338
+ <h2 id="pack-a-slurm-environment">Pack a Slurm environment<a class="headerlink" href="#pack-a-slurm-environment" title="Permanent link">&para;</a></h2>
2339
+ <p>Create a relocatable Conda environment archive and its managed SHA-256 sidecar:</p>
2340
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a><span class="c1"># Pack the active environment.</span>
2341
+ <a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>caddforge<span class="w"> </span>pack-env<span class="w"> </span>--output<span class="w"> </span>/shared/envs/caddforge-dev.tar.gz
2342
+ <a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a>
2343
+ <a id="__codelineno-7-4" name="__codelineno-7-4" href="#__codelineno-7-4"></a><span class="c1"># Pack a named environment.</span>
2344
+ <a id="__codelineno-7-5" name="__codelineno-7-5" href="#__codelineno-7-5"></a>caddforge<span class="w"> </span>pack-env<span class="w"> </span>--name<span class="w"> </span>caddforge<span class="w"> </span>--output<span class="w"> </span>/shared/envs/caddforge.tar.gz
2345
+ <a id="__codelineno-7-6" name="__codelineno-7-6" href="#__codelineno-7-6"></a>
2346
+ <a id="__codelineno-7-7" name="__codelineno-7-7" href="#__codelineno-7-7"></a><span class="c1"># Pack an explicit environment prefix.</span>
2347
+ <a id="__codelineno-7-8" name="__codelineno-7-8" href="#__codelineno-7-8"></a>caddforge<span class="w"> </span>pack-env<span class="w"> </span>--prefix<span class="w"> </span>/scratch/<span class="nv">$USER</span>/envs/caddforge<span class="w"> </span><span class="se">\</span>
2348
+ <a id="__codelineno-7-9" name="__codelineno-7-9" href="#__codelineno-7-9"></a><span class="w"> </span>--output<span class="w"> </span>/shared/envs/caddforge.tar.gz
2349
+ </code></pre></div>
2350
+ <p><code>--name</code> and <code>--prefix</code> are mutually exclusive. The output must end in <code>.tar.gz</code>. Existing archive
2351
+ or sidecar files are protected unless <code>--force</code> is supplied:</p>
2352
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>caddforge<span class="w"> </span>pack-env<span class="w"> </span>--output<span class="w"> </span>/shared/envs/caddforge-dev.tar.gz<span class="w"> </span>--force
2353
+ </code></pre></div>
2354
+ <p>For an intentionally modified Conda environment whose package metadata references missing files,
2355
+ <code>--ignore-missing-files</code> forwards the corresponding <code>conda-pack</code> option. The resulting archive may
2356
+ be incomplete, so use this only when those omissions are understood:</p>
2357
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>caddforge<span class="w"> </span>pack-env<span class="w"> </span>--output<span class="w"> </span>/shared/envs/caddforge-dev.tar.gz<span class="w"> </span>--ignore-missing-files
2358
+ </code></pre></div>
2359
+ <p>The command keeps the <code>conda-pack</code> percentage bar on one updating terminal line, streams normal
2360
+ messages, prints periodic elapsed-time and archive-size heartbeats during quiet periods, and reports
2361
+ hashing progress. On success it prints the archive path, sidecar path, digest, size, elapsed time,
2362
+ and the <code>slurm_env_pack_path</code> config entry.</p>
2363
+ <p>The generated sidecar is named <code>&lt;archive&gt;.sha256</code> and uses standard <code>sha256sum</code> format. See the
2364
+ <a href="../slurm/">Slurm backend guide</a> for cache and compatibility behavior.</p>
2365
+ <h2 id="jobs">Jobs<a class="headerlink" href="#jobs" title="Permanent link">&para;</a></h2>
2366
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>caddforge<span class="w"> </span>status<span class="w"> </span>&lt;job-id&gt;
2367
+ <a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a>caddforge<span class="w"> </span>logs<span class="w"> </span>&lt;job-id&gt;
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+ <a id="__codelineno-10-3" name="__codelineno-10-3" href="#__codelineno-10-3"></a>caddforge<span class="w"> </span>logs<span class="w"> </span>&lt;job-id&gt;<span class="w"> </span>--follow
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+ <a id="__codelineno-10-4" name="__codelineno-10-4" href="#__codelineno-10-4"></a>caddforge<span class="w"> </span><span class="nb">export</span><span class="w"> </span>&lt;job-id&gt;
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+ </code></pre></div>
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+ <p><code>logs --follow</code> prints newly synchronized stdout until the job reaches a terminal state. Use
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+ <code>--poll-interval &lt;seconds&gt;</code> to change the default one-second check interval. Follow mode tolerates
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+ temporary log-file and registry outages, handles scratch-synchronized snapshot replacement, and
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+ suppresses duplicate lines carrying the same <code>event=&lt;sequence&gt;</code> identifier. Press Ctrl+C to stop
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+ following without cancelling the job.</p>
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+ <p>Workflow results are stored in the job run directory by default. Use <code>caddforge export &lt;job-id&gt;</code> to
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+ copy <code>results/</code> back to the submission directory, or set <code>export_results: true</code> in the workflow
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+ config to do that automatically when the job finishes.</p>
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+ <h2 id="pipelines">Pipelines<a class="headerlink" href="#pipelines" title="Permanent link">&para;</a></h2>
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+ <div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a>caddforge<span class="w"> </span>pipeline<span class="w"> </span>run<span class="w"> </span>--config<span class="w"> </span>pipeline.yaml
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+ <a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a>caddforge<span class="w"> </span>pipeline<span class="w"> </span>status<span class="w"> </span>&lt;pipeline-id&gt;
2382
+ <a id="__codelineno-11-3" name="__codelineno-11-3" href="#__codelineno-11-3"></a>caddforge<span class="w"> </span>pipeline<span class="w"> </span>show-artifacts<span class="w"> </span>&lt;pipeline-id&gt;
2383
+ </code></pre></div>
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