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/index.html ADDED
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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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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
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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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979
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980
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981
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982
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983
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984
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985
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986
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987
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988
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989
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990
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991
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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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1032
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1033
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1037
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1038
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1042
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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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1067
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1068
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1069
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1070
+ <a href="../plugins/" class="md-nav__link ">
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
+
1094
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="false">
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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1106
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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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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
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1159
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1160
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1161
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1162
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1163
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1164
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1165
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1166
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1167
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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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1176
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1177
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1178
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1179
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1180
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1181
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1182
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1183
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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
+ FEP
1232
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1233
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1234
+
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
+ ML
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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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
+
1388
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1389
+
1390
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1391
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1392
+ <span class="md-nav__icon md-icon"></span>
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
+
1438
+
1439
+
1440
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1441
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1442
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1443
+ Plugin GUI Authoring
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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1450
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1451
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1452
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1453
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1454
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1455
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1456
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1457
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1458
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1459
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1460
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1461
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1462
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1463
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1464
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1465
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1466
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1467
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1468
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1469
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1471
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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
+
1494
+
1495
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1496
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1497
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1498
+
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
+ Public Python API
1546
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1547
+
1548
+
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
+ <span class="md-ellipsis">
1571
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1572
+
1573
+ Example Library
1574
+
1575
+
1576
+
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
+
1584
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1585
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1586
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1587
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1588
+
1589
+
1590
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1591
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1592
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1593
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1594
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1595
+
1596
+
1597
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1598
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1599
+
1600
+
1601
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1602
+
1603
+
1604
+
1605
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1606
+
1607
+
1608
+
1609
+ </a>
1610
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1611
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1612
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1613
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1614
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1615
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1616
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1617
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1618
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1619
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1620
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1621
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1622
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1623
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1624
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1625
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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
+
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
+
1648
+
1649
+
1650
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1651
+
1652
+
1653
+ <label class="md-nav__link" for="__nav_9" id="__nav_9_label" tabindex="">
1654
+
1655
+
1656
+
1657
+ <span class="md-ellipsis">
1658
+
1659
+
1660
+ Explanation
1661
+
1662
+
1663
+
1664
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1665
+
1666
+
1667
+
1668
+ <span class="md-nav__icon md-icon"></span>
1669
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1670
+
1671
+ <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_9_label" aria-expanded="false">
1672
+ <label class="md-nav__title" for="__nav_9">
1673
+ <span class="md-nav__icon md-icon"></span>
1674
+
1675
+
1676
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1677
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1678
+
1679
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1680
+ <ul class="md-nav__list" data-md-scrollfix>
1681
+
1682
+
1683
+
1684
+
1685
+
1686
+
1687
+
1688
+ <li class="md-nav__item">
1689
+ <a href="../explanation/reproducibility/" class="md-nav__link">
1690
+
1691
+
1692
+
1693
+ <span class="md-ellipsis">
1694
+
1695
+
1696
+ Reproducibility
1697
+
1698
+
1699
+
1700
+ </span>
1701
+
1702
+
1703
+
1704
+ </a>
1705
+ </li>
1706
+
1707
+
1708
+
1709
+
1710
+
1711
+
1712
+
1713
+
1714
+
1715
+
1716
+ <li class="md-nav__item">
1717
+ <a href="../explanation/references/" class="md-nav__link">
1718
+
1719
+
1720
+
1721
+ <span class="md-ellipsis">
1722
+
1723
+
1724
+ Method References
1725
+
1726
+
1727
+
1728
+ </span>
1729
+
1730
+
1731
+
1732
+ </a>
1733
+ </li>
1734
+
1735
+
1736
+
1737
+
1738
+
1739
+
1740
+
1741
+
1742
+
1743
+
1744
+ <li class="md-nav__item">
1745
+ <a href="../explanation/third-party-notices/" class="md-nav__link">
1746
+
1747
+
1748
+
1749
+ <span class="md-ellipsis">
1750
+
1751
+
1752
+ Third-party Notices
1753
+
1754
+
1755
+
1756
+ </span>
1757
+
1758
+
1759
+
1760
+ </a>
1761
+ </li>
1762
+
1763
+
1764
+
1765
+
1766
+ </ul>
1767
+ </nav>
1768
+
1769
+ </li>
1770
+
1771
+
1772
+
1773
+
1774
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1775
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1776
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1777
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1778
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1779
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1782
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1788
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1792
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1794
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1796
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1797
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1798
+
1799
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1800
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1801
+
1802
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1803
+
1804
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1805
+ <li class="md-nav__item md-nav__item--section md-nav__item--nested">
1806
+
1807
+
1808
+
1809
+ <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_10" >
1810
+
1811
+
1812
+ <div class="md-nav__link md-nav__container">
1813
+ <a href="../development/" class="md-nav__link ">
1814
+
1815
+
1816
+
1817
+ <span class="md-ellipsis">
1818
+
1819
+
1820
+ Development
1821
+
1822
+
1823
+
1824
+ </span>
1825
+
1826
+
1827
+
1828
+ </a>
1829
+
1830
+
1831
+ <label class="md-nav__link " for="__nav_10" id="__nav_10_label" tabindex="">
1832
+ <span class="md-nav__icon md-icon"></span>
1833
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1834
+
1835
+ </div>
1836
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+ <p class="admonition-title">Public source tag</p>
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+ <p>This page describes <code>caddforge-core</code> <code>0.22.0</code>, tagged as <code>v0.22.0</code>.
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+ Published on PyPI; see the <a href="../plugins/version-matrix/">version matrix</a>.</p>
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+ <p><code>caddforge-core</code> provides the shared runtime that all tool plugins build on:</p>
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+ <li>base abstractions for data, workflows, jobs, backends, and results</li>
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+ <li>pipeline specification and execution</li>
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+ </ul>
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+ <p>The core package must stay independent of specific scientific tools. Tool-specific behavior belongs
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+ in plugin packages.</p>
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+ <p>For HPC usage, see the <a href="slurm/">Slurm backend guide</a>.</p>
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