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/reference/api/index.html ADDED
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1314
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1364
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1369
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1371
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1372
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1390
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1394
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1397
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1406
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1407
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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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1418
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1419
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1435
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1439
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1442
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1446
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1459
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1489
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1493
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1496
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1497
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1498
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1501
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1503
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1504
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1508
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1514
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1515
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1520
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1521
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1526
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1528
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1529
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1530
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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
+ <span class="md-ellipsis">
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
+ <nav class="md-nav md-nav--secondary" aria-label="Table of contents">
1585
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1586
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1587
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1588
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1589
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1590
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1591
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1592
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1593
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1594
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1595
+ <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
1596
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1597
+ <li class="md-nav__item">
1598
+ <a href="#caddforgeconfigbase" class="md-nav__link">
1599
+ <span class="md-ellipsis">
1600
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1601
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1602
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1603
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1604
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1605
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1606
+ <nav class="md-nav" aria-label="caddforge.config.base">
1607
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1608
+
1609
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1610
+ <a href="#baseconfig" class="md-nav__link">
1611
+ <span class="md-ellipsis">
1612
+
1613
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1614
+
1615
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1616
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1617
+
1618
+ <nav class="md-nav" aria-label="BaseConfig">
1619
+ <ul class="md-nav__list">
1620
+
1621
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1622
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1623
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1624
+
1625
+ from_yaml
1626
+
1627
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1628
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1629
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1630
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1631
+
1632
+ <li class="md-nav__item">
1633
+ <a href="#from_json" class="md-nav__link">
1634
+ <span class="md-ellipsis">
1635
+
1636
+ from_json
1637
+
1638
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1639
+ </a>
1640
+
1641
+ </li>
1642
+
1643
+ <li class="md-nav__item">
1644
+ <a href="#example_dict" class="md-nav__link">
1645
+ <span class="md-ellipsis">
1646
+
1647
+ example_dict
1648
+
1649
+ </span>
1650
+ </a>
1651
+
1652
+ </li>
1653
+
1654
+ </ul>
1655
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1656
+
1657
+ </li>
1658
+
1659
+ </ul>
1660
+ </nav>
1661
+
1662
+ </li>
1663
+
1664
+ <li class="md-nav__item">
1665
+ <a href="#caddforgecoredataset" class="md-nav__link">
1666
+ <span class="md-ellipsis">
1667
+
1668
+ caddforge.core.dataset
1669
+
1670
+ </span>
1671
+ </a>
1672
+
1673
+ <nav class="md-nav" aria-label="caddforge.core.dataset">
1674
+ <ul class="md-nav__list">
1675
+
1676
+ <li class="md-nav__item">
1677
+ <a href="#dataset" class="md-nav__link">
1678
+ <span class="md-ellipsis">
1679
+
1680
+ Dataset
1681
+
1682
+ </span>
1683
+ </a>
1684
+
1685
+ <nav class="md-nav" aria-label="Dataset">
1686
+ <ul class="md-nav__list">
1687
+
1688
+ <li class="md-nav__item">
1689
+ <a href="#from_file" class="md-nav__link">
1690
+ <span class="md-ellipsis">
1691
+
1692
+ from_file
1693
+
1694
+ </span>
1695
+ </a>
1696
+
1697
+ </li>
1698
+
1699
+ <li class="md-nav__item">
1700
+ <a href="#from_molecules" class="md-nav__link">
1701
+ <span class="md-ellipsis">
1702
+
1703
+ from_molecules
1704
+
1705
+ </span>
1706
+ </a>
1707
+
1708
+ </li>
1709
+
1710
+ </ul>
1711
+ </nav>
1712
+
1713
+ </li>
1714
+
1715
+ <li class="md-nav__item">
1716
+ <a href="#moleculeset" class="md-nav__link">
1717
+ <span class="md-ellipsis">
1718
+
1719
+ MoleculeSet
1720
+
1721
+ </span>
1722
+ </a>
1723
+
1724
+ </li>
1725
+
1726
+ </ul>
1727
+ </nav>
1728
+
1729
+ </li>
1730
+
1731
+ <li class="md-nav__item">
1732
+ <a href="#caddforgecoremodel" class="md-nav__link">
1733
+ <span class="md-ellipsis">
1734
+
1735
+ caddforge.core.model
1736
+
1737
+ </span>
1738
+ </a>
1739
+
1740
+ <nav class="md-nav" aria-label="caddforge.core.model">
1741
+ <ul class="md-nav__list">
1742
+
1743
+ <li class="md-nav__item">
1744
+ <a href="#model" class="md-nav__link">
1745
+ <span class="md-ellipsis">
1746
+
1747
+ Model
1748
+
1749
+ </span>
1750
+ </a>
1751
+
1752
+ <nav class="md-nav" aria-label="Model">
1753
+ <ul class="md-nav__list">
1754
+
1755
+ <li class="md-nav__item">
1756
+ <a href="#fit" class="md-nav__link">
1757
+ <span class="md-ellipsis">
1758
+
1759
+ fit
1760
+
1761
+ </span>
1762
+ </a>
1763
+
1764
+ </li>
1765
+
1766
+ <li class="md-nav__item">
1767
+ <a href="#predict" class="md-nav__link">
1768
+ <span class="md-ellipsis">
1769
+
1770
+ predict
1771
+
1772
+ </span>
1773
+ </a>
1774
+
1775
+ </li>
1776
+
1777
+ </ul>
1778
+ </nav>
1779
+
1780
+ </li>
1781
+
1782
+ </ul>
1783
+ </nav>
1784
+
1785
+ </li>
1786
+
1787
+ <li class="md-nav__item">
1788
+ <a href="#caddforgecorejob" class="md-nav__link">
1789
+ <span class="md-ellipsis">
1790
+
1791
+ caddforge.core.job
1792
+
1793
+ </span>
1794
+ </a>
1795
+
1796
+ <nav class="md-nav" aria-label="caddforge.core.job">
1797
+ <ul class="md-nav__list">
1798
+
1799
+ <li class="md-nav__item">
1800
+ <a href="#jobstatus" class="md-nav__link">
1801
+ <span class="md-ellipsis">
1802
+
1803
+ JobStatus
1804
+
1805
+ </span>
1806
+ </a>
1807
+
1808
+ </li>
1809
+
1810
+ <li class="md-nav__item">
1811
+ <a href="#job" class="md-nav__link">
1812
+ <span class="md-ellipsis">
1813
+
1814
+ Job
1815
+
1816
+ </span>
1817
+ </a>
1818
+
1819
+ <nav class="md-nav" aria-label="Job">
1820
+ <ul class="md-nav__list">
1821
+
1822
+ <li class="md-nav__item">
1823
+ <a href="#to_metadata_dict" class="md-nav__link">
1824
+ <span class="md-ellipsis">
1825
+
1826
+ to_metadata_dict
1827
+
1828
+ </span>
1829
+ </a>
1830
+
1831
+ </li>
1832
+
1833
+ <li class="md-nav__item">
1834
+ <a href="#from_metadata_dict" class="md-nav__link">
1835
+ <span class="md-ellipsis">
1836
+
1837
+ from_metadata_dict
1838
+
1839
+ </span>
1840
+ </a>
1841
+
1842
+ </li>
1843
+
1844
+ <li class="md-nav__item">
1845
+ <a href="#save_metadata" class="md-nav__link">
1846
+ <span class="md-ellipsis">
1847
+
1848
+ save_metadata
1849
+
1850
+ </span>
1851
+ </a>
1852
+
1853
+ </li>
1854
+
1855
+ </ul>
1856
+ </nav>
1857
+
1858
+ </li>
1859
+
1860
+ </ul>
1861
+ </nav>
1862
+
1863
+ </li>
1864
+
1865
+ <li class="md-nav__item">
1866
+ <a href="#caddforgecoreresult" class="md-nav__link">
1867
+ <span class="md-ellipsis">
1868
+
1869
+ caddforge.core.result
1870
+
1871
+ </span>
1872
+ </a>
1873
+
1874
+ <nav class="md-nav" aria-label="caddforge.core.result">
1875
+ <ul class="md-nav__list">
1876
+
1877
+ <li class="md-nav__item">
1878
+ <a href="#result" class="md-nav__link">
1879
+ <span class="md-ellipsis">
1880
+
1881
+ Result
1882
+
1883
+ </span>
1884
+ </a>
1885
+
1886
+ <nav class="md-nav" aria-label="Result">
1887
+ <ul class="md-nav__list">
1888
+
1889
+ <li class="md-nav__item">
1890
+ <a href="#to_dict" class="md-nav__link">
1891
+ <span class="md-ellipsis">
1892
+
1893
+ to_dict
1894
+
1895
+ </span>
1896
+ </a>
1897
+
1898
+ </li>
1899
+
1900
+ <li class="md-nav__item">
1901
+ <a href="#from_dict" class="md-nav__link">
1902
+ <span class="md-ellipsis">
1903
+
1904
+ from_dict
1905
+
1906
+ </span>
1907
+ </a>
1908
+
1909
+ </li>
1910
+
1911
+ <li class="md-nav__item">
1912
+ <a href="#save" class="md-nav__link">
1913
+ <span class="md-ellipsis">
1914
+
1915
+ save
1916
+
1917
+ </span>
1918
+ </a>
1919
+
1920
+ </li>
1921
+
1922
+ </ul>
1923
+ </nav>
1924
+
1925
+ </li>
1926
+
1927
+ </ul>
1928
+ </nav>
1929
+
1930
+ </li>
1931
+
1932
+ <li class="md-nav__item">
1933
+ <a href="#caddforgecoreworkflow" class="md-nav__link">
1934
+ <span class="md-ellipsis">
1935
+
1936
+ caddforge.core.workflow
1937
+
1938
+ </span>
1939
+ </a>
1940
+
1941
+ <nav class="md-nav" aria-label="caddforge.core.workflow">
1942
+ <ul class="md-nav__list">
1943
+
1944
+ <li class="md-nav__item">
1945
+ <a href="#workflow" class="md-nav__link">
1946
+ <span class="md-ellipsis">
1947
+
1948
+ Workflow
1949
+
1950
+ </span>
1951
+ </a>
1952
+
1953
+ <nav class="md-nav" aria-label="Workflow">
1954
+ <ul class="md-nav__list">
1955
+
1956
+ <li class="md-nav__item">
1957
+ <a href="#prepare_job" class="md-nav__link">
1958
+ <span class="md-ellipsis">
1959
+
1960
+ prepare_job
1961
+
1962
+ </span>
1963
+ </a>
1964
+
1965
+ </li>
1966
+
1967
+ <li class="md-nav__item">
1968
+ <a href="#run" class="md-nav__link">
1969
+ <span class="md-ellipsis">
1970
+
1971
+ run
1972
+
1973
+ </span>
1974
+ </a>
1975
+
1976
+ </li>
1977
+
1978
+ </ul>
1979
+ </nav>
1980
+
1981
+ </li>
1982
+
1983
+ </ul>
1984
+ </nav>
1985
+
1986
+ </li>
1987
+
1988
+ <li class="md-nav__item">
1989
+ <a href="#caddforgecoreexecution" class="md-nav__link">
1990
+ <span class="md-ellipsis">
1991
+
1992
+ caddforge.core.execution
1993
+
1994
+ </span>
1995
+ </a>
1996
+
1997
+ <nav class="md-nav" aria-label="caddforge.core.execution">
1998
+ <ul class="md-nav__list">
1999
+
2000
+ <li class="md-nav__item">
2001
+ <a href="#backendoptions" class="md-nav__link">
2002
+ <span class="md-ellipsis">
2003
+
2004
+ BackendOptions
2005
+
2006
+ </span>
2007
+ </a>
2008
+
2009
+ </li>
2010
+
2011
+ <li class="md-nav__item">
2012
+ <a href="#submit_workflow" class="md-nav__link">
2013
+ <span class="md-ellipsis">
2014
+
2015
+ submit_workflow
2016
+
2017
+ </span>
2018
+ </a>
2019
+
2020
+ </li>
2021
+
2022
+ <li class="md-nav__item">
2023
+ <a href="#load_result_for_job" class="md-nav__link">
2024
+ <span class="md-ellipsis">
2025
+
2026
+ load_result_for_job
2027
+
2028
+ </span>
2029
+ </a>
2030
+
2031
+ </li>
2032
+
2033
+ </ul>
2034
+ </nav>
2035
+
2036
+ </li>
2037
+
2038
+ <li class="md-nav__item">
2039
+ <a href="#caddforgecorebackend" class="md-nav__link">
2040
+ <span class="md-ellipsis">
2041
+
2042
+ caddforge.core.backend
2043
+
2044
+ </span>
2045
+ </a>
2046
+
2047
+ <nav class="md-nav" aria-label="caddforge.core.backend">
2048
+ <ul class="md-nav__list">
2049
+
2050
+ <li class="md-nav__item">
2051
+ <a href="#backend" class="md-nav__link">
2052
+ <span class="md-ellipsis">
2053
+
2054
+ Backend
2055
+
2056
+ </span>
2057
+ </a>
2058
+
2059
+ <nav class="md-nav" aria-label="Backend">
2060
+ <ul class="md-nav__list">
2061
+
2062
+ <li class="md-nav__item">
2063
+ <a href="#submit" class="md-nav__link">
2064
+ <span class="md-ellipsis">
2065
+
2066
+ submit
2067
+
2068
+ </span>
2069
+ </a>
2070
+
2071
+ </li>
2072
+
2073
+ <li class="md-nav__item">
2074
+ <a href="#submit_shell_commands" class="md-nav__link">
2075
+ <span class="md-ellipsis">
2076
+
2077
+ submit_shell_commands
2078
+
2079
+ </span>
2080
+ </a>
2081
+
2082
+ </li>
2083
+
2084
+ <li class="md-nav__item">
2085
+ <a href="#query_status" class="md-nav__link">
2086
+ <span class="md-ellipsis">
2087
+
2088
+ query_status
2089
+
2090
+ </span>
2091
+ </a>
2092
+
2093
+ </li>
2094
+
2095
+ <li class="md-nav__item">
2096
+ <a href="#cancel" class="md-nav__link">
2097
+ <span class="md-ellipsis">
2098
+
2099
+ cancel
2100
+
2101
+ </span>
2102
+ </a>
2103
+
2104
+ </li>
2105
+
2106
+ </ul>
2107
+ </nav>
2108
+
2109
+ </li>
2110
+
2111
+ </ul>
2112
+ </nav>
2113
+
2114
+ </li>
2115
+
2116
+ <li class="md-nav__item">
2117
+ <a href="#caddforgecoreartifacts" class="md-nav__link">
2118
+ <span class="md-ellipsis">
2119
+
2120
+ caddforge.core.artifacts
2121
+
2122
+ </span>
2123
+ </a>
2124
+
2125
+ <nav class="md-nav" aria-label="caddforge.core.artifacts">
2126
+ <ul class="md-nav__list">
2127
+
2128
+ <li class="md-nav__item">
2129
+ <a href="#artifactkind" class="md-nav__link">
2130
+ <span class="md-ellipsis">
2131
+
2132
+ ArtifactKind
2133
+
2134
+ </span>
2135
+ </a>
2136
+
2137
+ </li>
2138
+
2139
+ <li class="md-nav__item">
2140
+ <a href="#artifactref" class="md-nav__link">
2141
+ <span class="md-ellipsis">
2142
+
2143
+ ArtifactRef
2144
+
2145
+ </span>
2146
+ </a>
2147
+
2148
+ <nav class="md-nav" aria-label="ArtifactRef">
2149
+ <ul class="md-nav__list">
2150
+
2151
+ <li class="md-nav__item">
2152
+ <a href="#primary_path" class="md-nav__link">
2153
+ <span class="md-ellipsis">
2154
+
2155
+ primary_path
2156
+
2157
+ </span>
2158
+ </a>
2159
+
2160
+ </li>
2161
+
2162
+ <li class="md-nav__item">
2163
+ <a href="#to_dict_1" class="md-nav__link">
2164
+ <span class="md-ellipsis">
2165
+
2166
+ to_dict
2167
+
2168
+ </span>
2169
+ </a>
2170
+
2171
+ </li>
2172
+
2173
+ <li class="md-nav__item">
2174
+ <a href="#from_dict_1" class="md-nav__link">
2175
+ <span class="md-ellipsis">
2176
+
2177
+ from_dict
2178
+
2179
+ </span>
2180
+ </a>
2181
+
2182
+ </li>
2183
+
2184
+ </ul>
2185
+ </nav>
2186
+
2187
+ </li>
2188
+
2189
+ <li class="md-nav__item">
2190
+ <a href="#inputport" class="md-nav__link">
2191
+ <span class="md-ellipsis">
2192
+
2193
+ InputPort
2194
+
2195
+ </span>
2196
+ </a>
2197
+
2198
+ </li>
2199
+
2200
+ <li class="md-nav__item">
2201
+ <a href="#outputport" class="md-nav__link">
2202
+ <span class="md-ellipsis">
2203
+
2204
+ OutputPort
2205
+
2206
+ </span>
2207
+ </a>
2208
+
2209
+ </li>
2210
+
2211
+ <li class="md-nav__item">
2212
+ <a href="#splitcontract" class="md-nav__link">
2213
+ <span class="md-ellipsis">
2214
+
2215
+ SplitContract
2216
+
2217
+ </span>
2218
+ </a>
2219
+
2220
+ </li>
2221
+
2222
+ </ul>
2223
+ </nav>
2224
+
2225
+ </li>
2226
+
2227
+ <li class="md-nav__item">
2228
+ <a href="#caddforgecoretool" class="md-nav__link">
2229
+ <span class="md-ellipsis">
2230
+
2231
+ caddforge.core.tool
2232
+
2233
+ </span>
2234
+ </a>
2235
+
2236
+ <nav class="md-nav" aria-label="caddforge.core.tool">
2237
+ <ul class="md-nav__list">
2238
+
2239
+ <li class="md-nav__item">
2240
+ <a href="#toolplugin" class="md-nav__link">
2241
+ <span class="md-ellipsis">
2242
+
2243
+ ToolPlugin
2244
+
2245
+ </span>
2246
+ </a>
2247
+
2248
+ </li>
2249
+
2250
+ <li class="md-nav__item">
2251
+ <a href="#toolspec" class="md-nav__link">
2252
+ <span class="md-ellipsis">
2253
+
2254
+ ToolSpec
2255
+
2256
+ </span>
2257
+ </a>
2258
+
2259
+ </li>
2260
+
2261
+ </ul>
2262
+ </nav>
2263
+
2264
+ </li>
2265
+
2266
+ <li class="md-nav__item">
2267
+ <a href="#caddforgeplugins" class="md-nav__link">
2268
+ <span class="md-ellipsis">
2269
+
2270
+ caddforge.plugins
2271
+
2272
+ </span>
2273
+ </a>
2274
+
2275
+ <nav class="md-nav" aria-label="caddforge.plugins">
2276
+ <ul class="md-nav__list">
2277
+
2278
+ <li class="md-nav__item">
2279
+ <a href="#get_tool" class="md-nav__link">
2280
+ <span class="md-ellipsis">
2281
+
2282
+ get_tool
2283
+
2284
+ </span>
2285
+ </a>
2286
+
2287
+ </li>
2288
+
2289
+ </ul>
2290
+ </nav>
2291
+
2292
+ </li>
2293
+
2294
+ <li class="md-nav__item">
2295
+ <a href="#caddforgepipelinespec" class="md-nav__link">
2296
+ <span class="md-ellipsis">
2297
+
2298
+ caddforge.pipeline.spec
2299
+
2300
+ </span>
2301
+ </a>
2302
+
2303
+ <nav class="md-nav" aria-label="caddforge.pipeline.spec">
2304
+ <ul class="md-nav__list">
2305
+
2306
+ <li class="md-nav__item">
2307
+ <a href="#pipelinespec" class="md-nav__link">
2308
+ <span class="md-ellipsis">
2309
+
2310
+ PipelineSpec
2311
+
2312
+ </span>
2313
+ </a>
2314
+
2315
+ </li>
2316
+
2317
+ <li class="md-nav__item">
2318
+ <a href="#pipelinestagespec" class="md-nav__link">
2319
+ <span class="md-ellipsis">
2320
+
2321
+ PipelineStageSpec
2322
+
2323
+ </span>
2324
+ </a>
2325
+
2326
+ </li>
2327
+
2328
+ <li class="md-nav__item">
2329
+ <a href="#pipelinedefaults" class="md-nav__link">
2330
+ <span class="md-ellipsis">
2331
+
2332
+ PipelineDefaults
2333
+
2334
+ </span>
2335
+ </a>
2336
+
2337
+ </li>
2338
+
2339
+ <li class="md-nav__item">
2340
+ <a href="#scatterspec" class="md-nav__link">
2341
+ <span class="md-ellipsis">
2342
+
2343
+ ScatterSpec
2344
+
2345
+ </span>
2346
+ </a>
2347
+
2348
+ </li>
2349
+
2350
+ <li class="md-nav__item">
2351
+ <a href="#load_pipeline_spec" class="md-nav__link">
2352
+ <span class="md-ellipsis">
2353
+
2354
+ load_pipeline_spec
2355
+
2356
+ </span>
2357
+ </a>
2358
+
2359
+ </li>
2360
+
2361
+ </ul>
2362
+ </nav>
2363
+
2364
+ </li>
2365
+
2366
+ <li class="md-nav__item">
2367
+ <a href="#caddforgepipelineexecutor" class="md-nav__link">
2368
+ <span class="md-ellipsis">
2369
+
2370
+ caddforge.pipeline.executor
2371
+
2372
+ </span>
2373
+ </a>
2374
+
2375
+ <nav class="md-nav" aria-label="caddforge.pipeline.executor">
2376
+ <ul class="md-nav__list">
2377
+
2378
+ <li class="md-nav__item">
2379
+ <a href="#pipelineexecutionresult" class="md-nav__link">
2380
+ <span class="md-ellipsis">
2381
+
2382
+ PipelineExecutionResult
2383
+
2384
+ </span>
2385
+ </a>
2386
+
2387
+ </li>
2388
+
2389
+ <li class="md-nav__item">
2390
+ <a href="#run_pipeline" class="md-nav__link">
2391
+ <span class="md-ellipsis">
2392
+
2393
+ run_pipeline
2394
+
2395
+ </span>
2396
+ </a>
2397
+
2398
+ </li>
2399
+
2400
+ </ul>
2401
+ </nav>
2402
+
2403
+ </li>
2404
+
2405
+ </ul>
2406
+
2407
+ </nav>
2408
+
2409
+ </li>
2410
+
2411
+
2412
+
2413
+
2414
+
2415
+
2416
+
2417
+
2418
+
2419
+
2420
+ <li class="md-nav__item">
2421
+ <a href="../../examples/" class="md-nav__link">
2422
+
2423
+
2424
+
2425
+ <span class="md-ellipsis">
2426
+
2427
+
2428
+ Example Library
2429
+
2430
+
2431
+
2432
+ </span>
2433
+
2434
+
2435
+
2436
+ </a>
2437
+ </li>
2438
+
2439
+
2440
+
2441
+
2442
+
2443
+
2444
+
2445
+
2446
+
2447
+
2448
+ <li class="md-nav__item">
2449
+ <a href="../../examples/quickstart/" class="md-nav__link">
2450
+
2451
+
2452
+
2453
+ <span class="md-ellipsis">
2454
+
2455
+
2456
+ Example Data Provenance
2457
+
2458
+
2459
+
2460
+ </span>
2461
+
2462
+
2463
+
2464
+ </a>
2465
+ </li>
2466
+
2467
+
2468
+
2469
+
2470
+ </ul>
2471
+ </nav>
2472
+
2473
+ </li>
2474
+
2475
+
2476
+
2477
+
2478
+
2479
+
2480
+
2481
+
2482
+
2483
+
2484
+
2485
+
2486
+
2487
+
2488
+
2489
+
2490
+
2491
+
2492
+
2493
+
2494
+
2495
+
2496
+
2497
+
2498
+
2499
+
2500
+
2501
+ <li class="md-nav__item md-nav__item--section md-nav__item--nested">
2502
+
2503
+
2504
+
2505
+ <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_9" >
2506
+
2507
+
2508
+ <label class="md-nav__link" for="__nav_9" id="__nav_9_label" tabindex="">
2509
+
2510
+
2511
+
2512
+ <span class="md-ellipsis">
2513
+
2514
+
2515
+ Explanation
2516
+
2517
+
2518
+
2519
+ </span>
2520
+
2521
+
2522
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2837
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2858
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2866
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2886
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2932
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2933
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2934
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2937
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2942
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2946
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2950
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2951
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2953
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2954
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2958
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2960
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2961
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2962
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2963
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2964
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2965
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2966
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2967
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2968
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2969
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2970
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2971
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2972
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2973
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2974
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2975
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2976
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2977
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2978
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2979
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2980
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2981
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2982
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2983
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2984
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2985
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2986
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2987
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2989
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2990
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2997
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2999
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3000
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3001
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3003
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3004
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3005
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3007
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3009
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3013
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3014
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3015
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3016
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3017
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3018
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3019
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3020
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3021
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3023
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3024
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3025
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3026
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3027
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3028
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3029
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3030
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3031
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3032
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3033
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3034
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3035
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3036
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3037
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3038
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3039
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3040
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3041
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3042
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3043
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3044
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3045
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3046
+ </nav>
3047
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3048
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3049
+
3050
+ <li class="md-nav__item">
3051
+ <a href="#moleculeset" class="md-nav__link">
3052
+ <span class="md-ellipsis">
3053
+
3054
+ MoleculeSet
3055
+
3056
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3057
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3058
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3059
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3060
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3067
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3068
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3071
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3072
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3073
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3074
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3075
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3076
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3077
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3078
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3079
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3080
+ <span class="md-ellipsis">
3081
+
3082
+ Model
3083
+
3084
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3085
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3086
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3087
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3088
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3089
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3090
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3091
+ <a href="#fit" class="md-nav__link">
3092
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3093
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3094
+ fit
3095
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3096
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3097
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3098
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3099
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3100
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3101
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3102
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3103
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3104
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3105
+ predict
3106
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3107
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3108
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3109
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3110
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3111
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3112
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3113
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3114
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3115
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3116
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3117
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3118
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3119
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3120
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3121
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3122
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3123
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3124
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3125
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3127
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3128
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3129
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3130
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3131
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3132
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3133
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3134
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3135
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3136
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3137
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3138
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3139
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3140
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3141
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3142
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3143
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3144
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3145
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3146
+ <a href="#job" class="md-nav__link">
3147
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3148
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3149
+ Job
3150
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3151
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3152
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3153
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3154
+ <nav class="md-nav" aria-label="Job">
3155
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3156
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3157
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3158
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3159
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3160
+
3161
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3162
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3163
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3164
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3165
+
3166
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3167
+
3168
+ <li class="md-nav__item">
3169
+ <a href="#from_metadata_dict" class="md-nav__link">
3170
+ <span class="md-ellipsis">
3171
+
3172
+ from_metadata_dict
3173
+
3174
+ </span>
3175
+ </a>
3176
+
3177
+ </li>
3178
+
3179
+ <li class="md-nav__item">
3180
+ <a href="#save_metadata" class="md-nav__link">
3181
+ <span class="md-ellipsis">
3182
+
3183
+ save_metadata
3184
+
3185
+ </span>
3186
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3187
+
3188
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3189
+
3190
+ </ul>
3191
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3192
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3193
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3194
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3195
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3196
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3197
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3198
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3199
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3200
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3201
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3202
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3203
+
3204
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3205
+
3206
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3207
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3208
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3209
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3210
+ <ul class="md-nav__list">
3211
+
3212
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3213
+ <a href="#result" class="md-nav__link">
3214
+ <span class="md-ellipsis">
3215
+
3216
+ Result
3217
+
3218
+ </span>
3219
+ </a>
3220
+
3221
+ <nav class="md-nav" aria-label="Result">
3222
+ <ul class="md-nav__list">
3223
+
3224
+ <li class="md-nav__item">
3225
+ <a href="#to_dict" class="md-nav__link">
3226
+ <span class="md-ellipsis">
3227
+
3228
+ to_dict
3229
+
3230
+ </span>
3231
+ </a>
3232
+
3233
+ </li>
3234
+
3235
+ <li class="md-nav__item">
3236
+ <a href="#from_dict" class="md-nav__link">
3237
+ <span class="md-ellipsis">
3238
+
3239
+ from_dict
3240
+
3241
+ </span>
3242
+ </a>
3243
+
3244
+ </li>
3245
+
3246
+ <li class="md-nav__item">
3247
+ <a href="#save" class="md-nav__link">
3248
+ <span class="md-ellipsis">
3249
+
3250
+ save
3251
+
3252
+ </span>
3253
+ </a>
3254
+
3255
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3256
+
3257
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3258
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3259
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3260
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3261
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3262
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3263
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3264
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3265
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3266
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3267
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3268
+ <a href="#caddforgecoreworkflow" class="md-nav__link">
3269
+ <span class="md-ellipsis">
3270
+
3271
+ caddforge.core.workflow
3272
+
3273
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3274
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3275
+
3276
+ <nav class="md-nav" aria-label="caddforge.core.workflow">
3277
+ <ul class="md-nav__list">
3278
+
3279
+ <li class="md-nav__item">
3280
+ <a href="#workflow" class="md-nav__link">
3281
+ <span class="md-ellipsis">
3282
+
3283
+ Workflow
3284
+
3285
+ </span>
3286
+ </a>
3287
+
3288
+ <nav class="md-nav" aria-label="Workflow">
3289
+ <ul class="md-nav__list">
3290
+
3291
+ <li class="md-nav__item">
3292
+ <a href="#prepare_job" class="md-nav__link">
3293
+ <span class="md-ellipsis">
3294
+
3295
+ prepare_job
3296
+
3297
+ </span>
3298
+ </a>
3299
+
3300
+ </li>
3301
+
3302
+ <li class="md-nav__item">
3303
+ <a href="#run" class="md-nav__link">
3304
+ <span class="md-ellipsis">
3305
+
3306
+ run
3307
+
3308
+ </span>
3309
+ </a>
3310
+
3311
+ </li>
3312
+
3313
+ </ul>
3314
+ </nav>
3315
+
3316
+ </li>
3317
+
3318
+ </ul>
3319
+ </nav>
3320
+
3321
+ </li>
3322
+
3323
+ <li class="md-nav__item">
3324
+ <a href="#caddforgecoreexecution" class="md-nav__link">
3325
+ <span class="md-ellipsis">
3326
+
3327
+ caddforge.core.execution
3328
+
3329
+ </span>
3330
+ </a>
3331
+
3332
+ <nav class="md-nav" aria-label="caddforge.core.execution">
3333
+ <ul class="md-nav__list">
3334
+
3335
+ <li class="md-nav__item">
3336
+ <a href="#backendoptions" class="md-nav__link">
3337
+ <span class="md-ellipsis">
3338
+
3339
+ BackendOptions
3340
+
3341
+ </span>
3342
+ </a>
3343
+
3344
+ </li>
3345
+
3346
+ <li class="md-nav__item">
3347
+ <a href="#submit_workflow" class="md-nav__link">
3348
+ <span class="md-ellipsis">
3349
+
3350
+ submit_workflow
3351
+
3352
+ </span>
3353
+ </a>
3354
+
3355
+ </li>
3356
+
3357
+ <li class="md-nav__item">
3358
+ <a href="#load_result_for_job" class="md-nav__link">
3359
+ <span class="md-ellipsis">
3360
+
3361
+ load_result_for_job
3362
+
3363
+ </span>
3364
+ </a>
3365
+
3366
+ </li>
3367
+
3368
+ </ul>
3369
+ </nav>
3370
+
3371
+ </li>
3372
+
3373
+ <li class="md-nav__item">
3374
+ <a href="#caddforgecorebackend" class="md-nav__link">
3375
+ <span class="md-ellipsis">
3376
+
3377
+ caddforge.core.backend
3378
+
3379
+ </span>
3380
+ </a>
3381
+
3382
+ <nav class="md-nav" aria-label="caddforge.core.backend">
3383
+ <ul class="md-nav__list">
3384
+
3385
+ <li class="md-nav__item">
3386
+ <a href="#backend" class="md-nav__link">
3387
+ <span class="md-ellipsis">
3388
+
3389
+ Backend
3390
+
3391
+ </span>
3392
+ </a>
3393
+
3394
+ <nav class="md-nav" aria-label="Backend">
3395
+ <ul class="md-nav__list">
3396
+
3397
+ <li class="md-nav__item">
3398
+ <a href="#submit" class="md-nav__link">
3399
+ <span class="md-ellipsis">
3400
+
3401
+ submit
3402
+
3403
+ </span>
3404
+ </a>
3405
+
3406
+ </li>
3407
+
3408
+ <li class="md-nav__item">
3409
+ <a href="#submit_shell_commands" class="md-nav__link">
3410
+ <span class="md-ellipsis">
3411
+
3412
+ submit_shell_commands
3413
+
3414
+ </span>
3415
+ </a>
3416
+
3417
+ </li>
3418
+
3419
+ <li class="md-nav__item">
3420
+ <a href="#query_status" class="md-nav__link">
3421
+ <span class="md-ellipsis">
3422
+
3423
+ query_status
3424
+
3425
+ </span>
3426
+ </a>
3427
+
3428
+ </li>
3429
+
3430
+ <li class="md-nav__item">
3431
+ <a href="#cancel" class="md-nav__link">
3432
+ <span class="md-ellipsis">
3433
+
3434
+ cancel
3435
+
3436
+ </span>
3437
+ </a>
3438
+
3439
+ </li>
3440
+
3441
+ </ul>
3442
+ </nav>
3443
+
3444
+ </li>
3445
+
3446
+ </ul>
3447
+ </nav>
3448
+
3449
+ </li>
3450
+
3451
+ <li class="md-nav__item">
3452
+ <a href="#caddforgecoreartifacts" class="md-nav__link">
3453
+ <span class="md-ellipsis">
3454
+
3455
+ caddforge.core.artifacts
3456
+
3457
+ </span>
3458
+ </a>
3459
+
3460
+ <nav class="md-nav" aria-label="caddforge.core.artifacts">
3461
+ <ul class="md-nav__list">
3462
+
3463
+ <li class="md-nav__item">
3464
+ <a href="#artifactkind" class="md-nav__link">
3465
+ <span class="md-ellipsis">
3466
+
3467
+ ArtifactKind
3468
+
3469
+ </span>
3470
+ </a>
3471
+
3472
+ </li>
3473
+
3474
+ <li class="md-nav__item">
3475
+ <a href="#artifactref" class="md-nav__link">
3476
+ <span class="md-ellipsis">
3477
+
3478
+ ArtifactRef
3479
+
3480
+ </span>
3481
+ </a>
3482
+
3483
+ <nav class="md-nav" aria-label="ArtifactRef">
3484
+ <ul class="md-nav__list">
3485
+
3486
+ <li class="md-nav__item">
3487
+ <a href="#primary_path" class="md-nav__link">
3488
+ <span class="md-ellipsis">
3489
+
3490
+ primary_path
3491
+
3492
+ </span>
3493
+ </a>
3494
+
3495
+ </li>
3496
+
3497
+ <li class="md-nav__item">
3498
+ <a href="#to_dict_1" class="md-nav__link">
3499
+ <span class="md-ellipsis">
3500
+
3501
+ to_dict
3502
+
3503
+ </span>
3504
+ </a>
3505
+
3506
+ </li>
3507
+
3508
+ <li class="md-nav__item">
3509
+ <a href="#from_dict_1" class="md-nav__link">
3510
+ <span class="md-ellipsis">
3511
+
3512
+ from_dict
3513
+
3514
+ </span>
3515
+ </a>
3516
+
3517
+ </li>
3518
+
3519
+ </ul>
3520
+ </nav>
3521
+
3522
+ </li>
3523
+
3524
+ <li class="md-nav__item">
3525
+ <a href="#inputport" class="md-nav__link">
3526
+ <span class="md-ellipsis">
3527
+
3528
+ InputPort
3529
+
3530
+ </span>
3531
+ </a>
3532
+
3533
+ </li>
3534
+
3535
+ <li class="md-nav__item">
3536
+ <a href="#outputport" class="md-nav__link">
3537
+ <span class="md-ellipsis">
3538
+
3539
+ OutputPort
3540
+
3541
+ </span>
3542
+ </a>
3543
+
3544
+ </li>
3545
+
3546
+ <li class="md-nav__item">
3547
+ <a href="#splitcontract" class="md-nav__link">
3548
+ <span class="md-ellipsis">
3549
+
3550
+ SplitContract
3551
+
3552
+ </span>
3553
+ </a>
3554
+
3555
+ </li>
3556
+
3557
+ </ul>
3558
+ </nav>
3559
+
3560
+ </li>
3561
+
3562
+ <li class="md-nav__item">
3563
+ <a href="#caddforgecoretool" class="md-nav__link">
3564
+ <span class="md-ellipsis">
3565
+
3566
+ caddforge.core.tool
3567
+
3568
+ </span>
3569
+ </a>
3570
+
3571
+ <nav class="md-nav" aria-label="caddforge.core.tool">
3572
+ <ul class="md-nav__list">
3573
+
3574
+ <li class="md-nav__item">
3575
+ <a href="#toolplugin" class="md-nav__link">
3576
+ <span class="md-ellipsis">
3577
+
3578
+ ToolPlugin
3579
+
3580
+ </span>
3581
+ </a>
3582
+
3583
+ </li>
3584
+
3585
+ <li class="md-nav__item">
3586
+ <a href="#toolspec" class="md-nav__link">
3587
+ <span class="md-ellipsis">
3588
+
3589
+ ToolSpec
3590
+
3591
+ </span>
3592
+ </a>
3593
+
3594
+ </li>
3595
+
3596
+ </ul>
3597
+ </nav>
3598
+
3599
+ </li>
3600
+
3601
+ <li class="md-nav__item">
3602
+ <a href="#caddforgeplugins" class="md-nav__link">
3603
+ <span class="md-ellipsis">
3604
+
3605
+ caddforge.plugins
3606
+
3607
+ </span>
3608
+ </a>
3609
+
3610
+ <nav class="md-nav" aria-label="caddforge.plugins">
3611
+ <ul class="md-nav__list">
3612
+
3613
+ <li class="md-nav__item">
3614
+ <a href="#get_tool" class="md-nav__link">
3615
+ <span class="md-ellipsis">
3616
+
3617
+ get_tool
3618
+
3619
+ </span>
3620
+ </a>
3621
+
3622
+ </li>
3623
+
3624
+ </ul>
3625
+ </nav>
3626
+
3627
+ </li>
3628
+
3629
+ <li class="md-nav__item">
3630
+ <a href="#caddforgepipelinespec" class="md-nav__link">
3631
+ <span class="md-ellipsis">
3632
+
3633
+ caddforge.pipeline.spec
3634
+
3635
+ </span>
3636
+ </a>
3637
+
3638
+ <nav class="md-nav" aria-label="caddforge.pipeline.spec">
3639
+ <ul class="md-nav__list">
3640
+
3641
+ <li class="md-nav__item">
3642
+ <a href="#pipelinespec" class="md-nav__link">
3643
+ <span class="md-ellipsis">
3644
+
3645
+ PipelineSpec
3646
+
3647
+ </span>
3648
+ </a>
3649
+
3650
+ </li>
3651
+
3652
+ <li class="md-nav__item">
3653
+ <a href="#pipelinestagespec" class="md-nav__link">
3654
+ <span class="md-ellipsis">
3655
+
3656
+ PipelineStageSpec
3657
+
3658
+ </span>
3659
+ </a>
3660
+
3661
+ </li>
3662
+
3663
+ <li class="md-nav__item">
3664
+ <a href="#pipelinedefaults" class="md-nav__link">
3665
+ <span class="md-ellipsis">
3666
+
3667
+ PipelineDefaults
3668
+
3669
+ </span>
3670
+ </a>
3671
+
3672
+ </li>
3673
+
3674
+ <li class="md-nav__item">
3675
+ <a href="#scatterspec" class="md-nav__link">
3676
+ <span class="md-ellipsis">
3677
+
3678
+ ScatterSpec
3679
+
3680
+ </span>
3681
+ </a>
3682
+
3683
+ </li>
3684
+
3685
+ <li class="md-nav__item">
3686
+ <a href="#load_pipeline_spec" class="md-nav__link">
3687
+ <span class="md-ellipsis">
3688
+
3689
+ load_pipeline_spec
3690
+
3691
+ </span>
3692
+ </a>
3693
+
3694
+ </li>
3695
+
3696
+ </ul>
3697
+ </nav>
3698
+
3699
+ </li>
3700
+
3701
+ <li class="md-nav__item">
3702
+ <a href="#caddforgepipelineexecutor" class="md-nav__link">
3703
+ <span class="md-ellipsis">
3704
+
3705
+ caddforge.pipeline.executor
3706
+
3707
+ </span>
3708
+ </a>
3709
+
3710
+ <nav class="md-nav" aria-label="caddforge.pipeline.executor">
3711
+ <ul class="md-nav__list">
3712
+
3713
+ <li class="md-nav__item">
3714
+ <a href="#pipelineexecutionresult" class="md-nav__link">
3715
+ <span class="md-ellipsis">
3716
+
3717
+ PipelineExecutionResult
3718
+
3719
+ </span>
3720
+ </a>
3721
+
3722
+ </li>
3723
+
3724
+ <li class="md-nav__item">
3725
+ <a href="#run_pipeline" class="md-nav__link">
3726
+ <span class="md-ellipsis">
3727
+
3728
+ run_pipeline
3729
+
3730
+ </span>
3731
+ </a>
3732
+
3733
+ </li>
3734
+
3735
+ </ul>
3736
+ </nav>
3737
+
3738
+ </li>
3739
+
3740
+ </ul>
3741
+
3742
+ </nav>
3743
+ </div>
3744
+ </div>
3745
+ </div>
3746
+
3747
+
3748
+
3749
+ <div class="md-content" data-md-component="content">
3750
+
3751
+ <article class="md-content__inner md-typeset">
3752
+
3753
+
3754
+
3755
+
3756
+
3757
+
3758
+
3759
+
3760
+ <h1 id="public-python-api">Public Python API<a class="headerlink" href="#public-python-api" title="Permanent link">&para;</a></h1>
3761
+ <p>Generated from the reviewed core sources using <code>scripts/update_reference.py</code>. Builds consume this checked-in reference and do not import or discover plugins. Version and tag provenance are recorded in the <a href="../../plugins/version-matrix/">version matrix</a>.</p>
3762
+ <p>Use <a href="../../core/plugins/">plugin contracts</a> to obtain tool configurations and workflows. Call <code>submit_workflow</code> for backend-aware execution; direct workflow calls are intended for tests and custom inline execution. See <a href="../../getting-started/first-workflow/">the first workflow</a>.</p>
3763
+ <p><code>Dataset.from_file()</code> currently raises <code>NotImplementedError</code>. A frozen dataclass prevents field reassignment; it does not make nested molecule objects or lists immutable.</p>
3764
+ <h2 id="caddforgeconfigbase"><code>caddforge.config.base</code><a class="headerlink" href="#caddforgeconfigbase" title="Permanent link">&para;</a></h2>
3765
+ <h3 id="baseconfig"><code>BaseConfig</code><a class="headerlink" href="#baseconfig" title="Permanent link">&para;</a></h3>
3766
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a><span class="k">class</span><span class="w"> </span><span class="nc">BaseConfig</span><span class="p">(</span><span class="n">BaseModel</span><span class="p">)</span>
3767
+ </code></pre></div>
3768
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>Common config options shared across tools.
3769
+ </code></pre></div>
3770
+ <p>Declared fields and enum values (inherited fields are documented on the base class):</p>
3771
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a><span class="n">run_directory</span><span class="p">:</span> <span class="n">Path</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
3772
+ <a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a><span class="n">registry_path</span><span class="p">:</span> <span class="n">Path</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
3773
+ <a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a><span class="n">backend</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s1">'local'</span>
3774
+ <a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a><span class="n">slurm_partition</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
3775
+ <a id="__codelineno-2-5" name="__codelineno-2-5" href="#__codelineno-2-5"></a><span class="n">slurm_time</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
3776
+ <a id="__codelineno-2-6" name="__codelineno-2-6" href="#__codelineno-2-6"></a><span class="n">slurm_account</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
3777
+ <a id="__codelineno-2-7" name="__codelineno-2-7" href="#__codelineno-2-7"></a><span class="n">sbatch_options</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="n">Field</span><span class="p">(</span><span class="n">default_factory</span><span class="o">=</span><span class="nb">list</span><span class="p">)</span>
3778
+ <a id="__codelineno-2-8" name="__codelineno-2-8" href="#__codelineno-2-8"></a><span class="n">slurm_setup_commands</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="n">Field</span><span class="p">(</span><span class="n">default_factory</span><span class="o">=</span><span class="nb">list</span><span class="p">)</span>
3779
+ <a id="__codelineno-2-9" name="__codelineno-2-9" href="#__codelineno-2-9"></a><span class="n">job_name</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
3780
+ <a id="__codelineno-2-10" name="__codelineno-2-10" href="#__codelineno-2-10"></a><span class="n">export_results</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span>
3781
+ <a id="__codelineno-2-11" name="__codelineno-2-11" href="#__codelineno-2-11"></a><span class="n">slurm_nodes</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">1</span>
3782
+ <a id="__codelineno-2-12" name="__codelineno-2-12" href="#__codelineno-2-12"></a><span class="n">slurm_ntasks</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">1</span>
3783
+ <a id="__codelineno-2-13" name="__codelineno-2-13" href="#__codelineno-2-13"></a><span class="n">slurm_cpus_per_task</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">1</span>
3784
+ <a id="__codelineno-2-14" name="__codelineno-2-14" href="#__codelineno-2-14"></a><span class="n">slurm_env_pack_path</span><span class="p">:</span> <span class="n">Path</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
3785
+ <a id="__codelineno-2-15" name="__codelineno-2-15" href="#__codelineno-2-15"></a><span class="n">slurm_env_cache_enabled</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span>
3786
+ <a id="__codelineno-2-16" name="__codelineno-2-16" href="#__codelineno-2-16"></a><span class="n">slurm_env_cache_dir</span><span class="p">:</span> <span class="n">Path</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
3787
+ <a id="__codelineno-2-17" name="__codelineno-2-17" href="#__codelineno-2-17"></a><span class="n">slurm_wheelhouse_path</span><span class="p">:</span> <span class="n">Path</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
3788
+ <a id="__codelineno-2-18" name="__codelineno-2-18" href="#__codelineno-2-18"></a><span class="n">slurm_requirements_path</span><span class="p">:</span> <span class="n">Path</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
3789
+ </code></pre></div>
3790
+ <h4 id="from_yaml"><code>from_yaml</code><a class="headerlink" href="#from_yaml" title="Permanent link">&para;</a></h4>
3791
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a><span class="k">def</span><span class="w"> </span><span class="nf">from_yaml</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="n">Path</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="s1">'BaseConfig'</span>
3792
+ </code></pre></div>
3793
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>Load configuration from a YAML file.
3794
+ <a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>
3795
+ <a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a>Args:
3796
+ <a id="__codelineno-4-4" name="__codelineno-4-4" href="#__codelineno-4-4"></a> path: Path to the YAML config file.
3797
+ <a id="__codelineno-4-5" name="__codelineno-4-5" href="#__codelineno-4-5"></a>
3798
+ <a id="__codelineno-4-6" name="__codelineno-4-6" href="#__codelineno-4-6"></a>Returns:
3799
+ <a id="__codelineno-4-7" name="__codelineno-4-7" href="#__codelineno-4-7"></a> BaseConfig: Parsed and validated configuration.
3800
+ </code></pre></div>
3801
+ <h4 id="from_json"><code>from_json</code><a class="headerlink" href="#from_json" title="Permanent link">&para;</a></h4>
3802
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a><span class="k">def</span><span class="w"> </span><span class="nf">from_json</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="n">Path</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="s1">'BaseConfig'</span>
3803
+ </code></pre></div>
3804
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>Load configuration from a JSON file.
3805
+ <a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a>
3806
+ <a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a>Args:
3807
+ <a id="__codelineno-6-4" name="__codelineno-6-4" href="#__codelineno-6-4"></a> path: Path to the JSON config file.
3808
+ <a id="__codelineno-6-5" name="__codelineno-6-5" href="#__codelineno-6-5"></a>
3809
+ <a id="__codelineno-6-6" name="__codelineno-6-6" href="#__codelineno-6-6"></a>Returns:
3810
+ <a id="__codelineno-6-7" name="__codelineno-6-7" href="#__codelineno-6-7"></a> BaseConfig: Parsed and validated configuration.
3811
+ </code></pre></div>
3812
+ <h4 id="example_dict"><code>example_dict</code><a class="headerlink" href="#example_dict" title="Permanent link">&para;</a></h4>
3813
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a><span class="k">def</span><span class="w"> </span><span class="nf">example_dict</span><span class="p">(</span><span class="bp">cls</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">]</span>
3814
+ </code></pre></div>
3815
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>Return a dict with defaults or placeholders for required fields.
3816
+ <a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a>
3817
+ <a id="__codelineno-8-3" name="__codelineno-8-3" href="#__codelineno-8-3"></a>Returns:
3818
+ <a id="__codelineno-8-4" name="__codelineno-8-4" href="#__codelineno-8-4"></a> dict[str, Any]: Example config mapping.
3819
+ </code></pre></div>
3820
+ <h2 id="caddforgecoredataset"><code>caddforge.core.dataset</code><a class="headerlink" href="#caddforgecoredataset" title="Permanent link">&para;</a></h2>
3821
+ <h3 id="dataset"><code>Dataset</code><a class="headerlink" href="#dataset" title="Permanent link">&para;</a></h3>
3822
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a><span class="k">class</span><span class="w"> </span><span class="nc">Dataset</span><span class="p">()</span>
3823
+ </code></pre></div>
3824
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>Immutable dataset consisting of entries and optional labels.
3825
+ <a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a>
3826
+ <a id="__codelineno-10-3" name="__codelineno-10-3" href="#__codelineno-10-3"></a>Args:
3827
+ <a id="__codelineno-10-4" name="__codelineno-10-4" href="#__codelineno-10-4"></a> entries: Sequence of entries (typically molecule-like objects).
3828
+ <a id="__codelineno-10-5" name="__codelineno-10-5" href="#__codelineno-10-5"></a> labels: Optional sequence of labels aligned with entries.
3829
+ <a id="__codelineno-10-6" name="__codelineno-10-6" href="#__codelineno-10-6"></a> source: Optional provenance string (e.g., file path or database tag).
3830
+ </code></pre></div>
3831
+ <p>Declared fields and enum values (inherited fields are documented on the base class):</p>
3832
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a><span class="n">entries</span><span class="p">:</span> <span class="n">Sequence</span><span class="p">[</span><span class="nb">object</span><span class="p">]</span>
3833
+ <a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a><span class="n">labels</span><span class="p">:</span> <span class="n">Sequence</span><span class="p">[</span><span class="nb">object</span><span class="p">]</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
3834
+ <a id="__codelineno-11-3" name="__codelineno-11-3" href="#__codelineno-11-3"></a><span class="n">source</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
3835
+ </code></pre></div>
3836
+ <h4 id="from_file"><code>from_file</code><a class="headerlink" href="#from_file" title="Permanent link">&para;</a></h4>
3837
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a><span class="k">def</span><span class="w"> </span><span class="nf">from_file</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="n">Path</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="s1">'Dataset'</span>
3838
+ </code></pre></div>
3839
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a>Create a dataset from a file path.
3840
+ <a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a>
3841
+ <a id="__codelineno-13-3" name="__codelineno-13-3" href="#__codelineno-13-3"></a>Args:
3842
+ <a id="__codelineno-13-4" name="__codelineno-13-4" href="#__codelineno-13-4"></a> path: Path to the dataset file.
3843
+ <a id="__codelineno-13-5" name="__codelineno-13-5" href="#__codelineno-13-5"></a>
3844
+ <a id="__codelineno-13-6" name="__codelineno-13-6" href="#__codelineno-13-6"></a>Returns:
3845
+ <a id="__codelineno-13-7" name="__codelineno-13-7" href="#__codelineno-13-7"></a> Dataset: Parsed dataset instance.
3846
+ <a id="__codelineno-13-8" name="__codelineno-13-8" href="#__codelineno-13-8"></a>
3847
+ <a id="__codelineno-13-9" name="__codelineno-13-9" href="#__codelineno-13-9"></a>Raises:
3848
+ <a id="__codelineno-13-10" name="__codelineno-13-10" href="#__codelineno-13-10"></a> NotImplementedError: Always, until a concrete loader is implemented.
3849
+ </code></pre></div>
3850
+ <h4 id="from_molecules"><code>from_molecules</code><a class="headerlink" href="#from_molecules" title="Permanent link">&para;</a></h4>
3851
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a><span class="k">def</span><span class="w"> </span><span class="nf">from_molecules</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">molecules</span><span class="p">:</span> <span class="n">Iterable</span><span class="p">[</span><span class="nb">object</span><span class="p">],</span> <span class="o">*</span><span class="p">,</span> <span class="n">source</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="s1">'Dataset'</span>
3852
+ </code></pre></div>
3853
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a>Build a dataset from an iterable of molecule-like objects.
3854
+ <a id="__codelineno-15-2" name="__codelineno-15-2" href="#__codelineno-15-2"></a>
3855
+ <a id="__codelineno-15-3" name="__codelineno-15-3" href="#__codelineno-15-3"></a>Args:
3856
+ <a id="__codelineno-15-4" name="__codelineno-15-4" href="#__codelineno-15-4"></a> molecules: Iterable of molecule-like objects.
3857
+ <a id="__codelineno-15-5" name="__codelineno-15-5" href="#__codelineno-15-5"></a> source: Optional provenance string.
3858
+ <a id="__codelineno-15-6" name="__codelineno-15-6" href="#__codelineno-15-6"></a>
3859
+ <a id="__codelineno-15-7" name="__codelineno-15-7" href="#__codelineno-15-7"></a>Returns:
3860
+ <a id="__codelineno-15-8" name="__codelineno-15-8" href="#__codelineno-15-8"></a> Dataset: New dataset with entries populated and labels empty.
3861
+ </code></pre></div>
3862
+ <h3 id="moleculeset"><code>MoleculeSet</code><a class="headerlink" href="#moleculeset" title="Permanent link">&para;</a></h3>
3863
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a><span class="k">class</span><span class="w"> </span><span class="nc">MoleculeSet</span><span class="p">()</span>
3864
+ </code></pre></div>
3865
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a>Immutable collection of molecules.
3866
+ <a id="__codelineno-17-2" name="__codelineno-17-2" href="#__codelineno-17-2"></a>
3867
+ <a id="__codelineno-17-3" name="__codelineno-17-3" href="#__codelineno-17-3"></a>Args:
3868
+ <a id="__codelineno-17-4" name="__codelineno-17-4" href="#__codelineno-17-4"></a> molecules: Sequence of molecule-like objects.
3869
+ <a id="__codelineno-17-5" name="__codelineno-17-5" href="#__codelineno-17-5"></a> source: Optional provenance string (e.g., file path or database tag).
3870
+ </code></pre></div>
3871
+ <p>Declared fields and enum values (inherited fields are documented on the base class):</p>
3872
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a><span class="n">molecules</span><span class="p">:</span> <span class="n">Sequence</span><span class="p">[</span><span class="nb">object</span><span class="p">]</span>
3873
+ <a id="__codelineno-18-2" name="__codelineno-18-2" href="#__codelineno-18-2"></a><span class="n">source</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
3874
+ </code></pre></div>
3875
+ <h2 id="caddforgecoremodel"><code>caddforge.core.model</code><a class="headerlink" href="#caddforgecoremodel" title="Permanent link">&para;</a></h2>
3876
+ <h3 id="model"><code>Model</code><a class="headerlink" href="#model" title="Permanent link">&para;</a></h3>
3877
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-19-1" name="__codelineno-19-1" href="#__codelineno-19-1"></a><span class="k">class</span><span class="w"> </span><span class="nc">Model</span><span class="p">(</span><span class="n">ABC</span><span class="p">)</span>
3878
+ </code></pre></div>
3879
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-20-1" name="__codelineno-20-1" href="#__codelineno-20-1"></a>Abstract base class for models used across tools.
3880
+ </code></pre></div>
3881
+ <h4 id="fit"><code>fit</code><a class="headerlink" href="#fit" title="Permanent link">&para;</a></h4>
3882
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-21-1" name="__codelineno-21-1" href="#__codelineno-21-1"></a><span class="k">def</span><span class="w"> </span><span class="nf">fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dataset</span><span class="p">:</span> <span class="n">Dataset</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span>
3883
+ </code></pre></div>
3884
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-22-1" name="__codelineno-22-1" href="#__codelineno-22-1"></a>Train the model with the provided dataset.
3885
+ <a id="__codelineno-22-2" name="__codelineno-22-2" href="#__codelineno-22-2"></a>
3886
+ <a id="__codelineno-22-3" name="__codelineno-22-3" href="#__codelineno-22-3"></a>Args:
3887
+ <a id="__codelineno-22-4" name="__codelineno-22-4" href="#__codelineno-22-4"></a> dataset: Dataset containing training data.
3888
+ </code></pre></div>
3889
+ <h4 id="predict"><code>predict</code><a class="headerlink" href="#predict" title="Permanent link">&para;</a></h4>
3890
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-23-1" name="__codelineno-23-1" href="#__codelineno-23-1"></a><span class="k">def</span><span class="w"> </span><span class="nf">predict</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">data</span><span class="p">:</span> <span class="n">Dataset</span> <span class="o">|</span> <span class="n">MoleculeSet</span><span class="p">)</span>
3891
+ </code></pre></div>
3892
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-24-1" name="__codelineno-24-1" href="#__codelineno-24-1"></a>Generate predictions for a dataset or molecule set.
3893
+ <a id="__codelineno-24-2" name="__codelineno-24-2" href="#__codelineno-24-2"></a>
3894
+ <a id="__codelineno-24-3" name="__codelineno-24-3" href="#__codelineno-24-3"></a>Args:
3895
+ <a id="__codelineno-24-4" name="__codelineno-24-4" href="#__codelineno-24-4"></a> data: Dataset or MoleculeSet to predict on.
3896
+ <a id="__codelineno-24-5" name="__codelineno-24-5" href="#__codelineno-24-5"></a>
3897
+ <a id="__codelineno-24-6" name="__codelineno-24-6" href="#__codelineno-24-6"></a>Returns:
3898
+ <a id="__codelineno-24-7" name="__codelineno-24-7" href="#__codelineno-24-7"></a> Any: Tool-specific prediction output.
3899
+ </code></pre></div>
3900
+ <h2 id="caddforgecorejob"><code>caddforge.core.job</code><a class="headerlink" href="#caddforgecorejob" title="Permanent link">&para;</a></h2>
3901
+ <h3 id="jobstatus"><code>JobStatus</code><a class="headerlink" href="#jobstatus" title="Permanent link">&para;</a></h3>
3902
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-25-1" name="__codelineno-25-1" href="#__codelineno-25-1"></a><span class="k">class</span><span class="w"> </span><span class="nc">JobStatus</span><span class="p">(</span><span class="nb">str</span><span class="p">,</span> <span class="n">Enum</span><span class="p">)</span>
3903
+ </code></pre></div>
3904
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-26-1" name="__codelineno-26-1" href="#__codelineno-26-1"></a>Enumeration of job lifecycle states.
3905
+ </code></pre></div>
3906
+ <p>Declared fields and enum values (inherited fields are documented on the base class):</p>
3907
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-27-1" name="__codelineno-27-1" href="#__codelineno-27-1"></a><span class="n">PENDING</span> <span class="o">=</span> <span class="s1">'PENDING'</span>
3908
+ <a id="__codelineno-27-2" name="__codelineno-27-2" href="#__codelineno-27-2"></a><span class="n">RUNNING</span> <span class="o">=</span> <span class="s1">'RUNNING'</span>
3909
+ <a id="__codelineno-27-3" name="__codelineno-27-3" href="#__codelineno-27-3"></a><span class="n">COMPLETED</span> <span class="o">=</span> <span class="s1">'COMPLETED'</span>
3910
+ <a id="__codelineno-27-4" name="__codelineno-27-4" href="#__codelineno-27-4"></a><span class="n">FAILED</span> <span class="o">=</span> <span class="s1">'FAILED'</span>
3911
+ <a id="__codelineno-27-5" name="__codelineno-27-5" href="#__codelineno-27-5"></a><span class="n">CANCELLED</span> <span class="o">=</span> <span class="s1">'CANCELLED'</span>
3912
+ </code></pre></div>
3913
+ <h3 id="job"><code>Job</code><a class="headerlink" href="#job" title="Permanent link">&para;</a></h3>
3914
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-28-1" name="__codelineno-28-1" href="#__codelineno-28-1"></a><span class="k">class</span><span class="w"> </span><span class="nc">Job</span><span class="p">()</span>
3915
+ </code></pre></div>
3916
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-29-1" name="__codelineno-29-1" href="#__codelineno-29-1"></a>Canonical representation of a workflow execution.
3917
+ <a id="__codelineno-29-2" name="__codelineno-29-2" href="#__codelineno-29-2"></a>
3918
+ <a id="__codelineno-29-3" name="__codelineno-29-3" href="#__codelineno-29-3"></a>Args:
3919
+ <a id="__codelineno-29-4" name="__codelineno-29-4" href="#__codelineno-29-4"></a> id: Unique job identifier.
3920
+ <a id="__codelineno-29-5" name="__codelineno-29-5" href="#__codelineno-29-5"></a> tool_name: Registered tool name (without section).
3921
+ <a id="__codelineno-29-6" name="__codelineno-29-6" href="#__codelineno-29-6"></a> backend: Backend name used to execute the job.
3922
+ <a id="__codelineno-29-7" name="__codelineno-29-7" href="#__codelineno-29-7"></a> status: Current job status.
3923
+ <a id="__codelineno-29-8" name="__codelineno-29-8" href="#__codelineno-29-8"></a> created_at: Timestamp when the job was created.
3924
+ <a id="__codelineno-29-9" name="__codelineno-29-9" href="#__codelineno-29-9"></a> started_at: Timestamp when execution began.
3925
+ <a id="__codelineno-29-10" name="__codelineno-29-10" href="#__codelineno-29-10"></a> finished_at: Timestamp when execution completed.
3926
+ <a id="__codelineno-29-11" name="__codelineno-29-11" href="#__codelineno-29-11"></a> run_directory: Path to the job run directory.
3927
+ <a id="__codelineno-29-12" name="__codelineno-29-12" href="#__codelineno-29-12"></a> metadata: Tool/backend-specific metadata.
3928
+ </code></pre></div>
3929
+ <p>Declared fields and enum values (inherited fields are documented on the base class):</p>
3930
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-30-1" name="__codelineno-30-1" href="#__codelineno-30-1"></a><span class="nb">id</span><span class="p">:</span> <span class="nb">str</span>
3931
+ <a id="__codelineno-30-2" name="__codelineno-30-2" href="#__codelineno-30-2"></a><span class="n">tool_name</span><span class="p">:</span> <span class="nb">str</span>
3932
+ <a id="__codelineno-30-3" name="__codelineno-30-3" href="#__codelineno-30-3"></a><span class="n">backend</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s1">'unsubmitted'</span>
3933
+ <a id="__codelineno-30-4" name="__codelineno-30-4" href="#__codelineno-30-4"></a><span class="n">status</span><span class="p">:</span> <span class="n">JobStatus</span> <span class="o">=</span> <span class="n">JobStatus</span><span class="o">.</span><span class="n">PENDING</span>
3934
+ <a id="__codelineno-30-5" name="__codelineno-30-5" href="#__codelineno-30-5"></a><span class="n">created_at</span><span class="p">:</span> <span class="n">datetime</span> <span class="o">=</span> <span class="n">field</span><span class="p">(</span><span class="n">default_factory</span><span class="o">=</span><span class="k">lambda</span><span class="p">:</span> <span class="n">datetime</span><span class="o">.</span><span class="n">now</span><span class="p">()</span><span class="o">.</span><span class="n">astimezone</span><span class="p">())</span>
3935
+ <a id="__codelineno-30-6" name="__codelineno-30-6" href="#__codelineno-30-6"></a><span class="n">started_at</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">datetime</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
3936
+ <a id="__codelineno-30-7" name="__codelineno-30-7" href="#__codelineno-30-7"></a><span class="n">finished_at</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">datetime</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
3937
+ <a id="__codelineno-30-8" name="__codelineno-30-8" href="#__codelineno-30-8"></a><span class="n">run_directory</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">Path</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
3938
+ <a id="__codelineno-30-9" name="__codelineno-30-9" href="#__codelineno-30-9"></a><span class="n">metadata</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">]</span> <span class="o">=</span> <span class="n">field</span><span class="p">(</span><span class="n">default_factory</span><span class="o">=</span><span class="nb">dict</span><span class="p">)</span>
3939
+ </code></pre></div>
3940
+ <h4 id="to_metadata_dict"><code>to_metadata_dict</code><a class="headerlink" href="#to_metadata_dict" title="Permanent link">&para;</a></h4>
3941
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-31-1" name="__codelineno-31-1" href="#__codelineno-31-1"></a><span class="k">def</span><span class="w"> </span><span class="nf">to_metadata_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">]</span>
3942
+ </code></pre></div>
3943
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-32-1" name="__codelineno-32-1" href="#__codelineno-32-1"></a>Serialize job metadata to a JSON-friendly dict.
3944
+ <a id="__codelineno-32-2" name="__codelineno-32-2" href="#__codelineno-32-2"></a>
3945
+ <a id="__codelineno-32-3" name="__codelineno-32-3" href="#__codelineno-32-3"></a>Returns:
3946
+ <a id="__codelineno-32-4" name="__codelineno-32-4" href="#__codelineno-32-4"></a> dict[str, Any]: Serialized metadata suitable for JSON encoding.
3947
+ </code></pre></div>
3948
+ <h4 id="from_metadata_dict"><code>from_metadata_dict</code><a class="headerlink" href="#from_metadata_dict" title="Permanent link">&para;</a></h4>
3949
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-33-1" name="__codelineno-33-1" href="#__codelineno-33-1"></a><span class="k">def</span><span class="w"> </span><span class="nf">from_metadata_dict</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">data</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="s1">'Job'</span>
3950
+ </code></pre></div>
3951
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-34-1" name="__codelineno-34-1" href="#__codelineno-34-1"></a>Deserialize job metadata produced by `to_metadata_dict`.
3952
+ <a id="__codelineno-34-2" name="__codelineno-34-2" href="#__codelineno-34-2"></a>
3953
+ <a id="__codelineno-34-3" name="__codelineno-34-3" href="#__codelineno-34-3"></a>Args:
3954
+ <a id="__codelineno-34-4" name="__codelineno-34-4" href="#__codelineno-34-4"></a> data: Serialized job metadata.
3955
+ <a id="__codelineno-34-5" name="__codelineno-34-5" href="#__codelineno-34-5"></a>
3956
+ <a id="__codelineno-34-6" name="__codelineno-34-6" href="#__codelineno-34-6"></a>Returns:
3957
+ <a id="__codelineno-34-7" name="__codelineno-34-7" href="#__codelineno-34-7"></a> Job: Deserialized Job instance.
3958
+ </code></pre></div>
3959
+ <h4 id="save_metadata"><code>save_metadata</code><a class="headerlink" href="#save_metadata" title="Permanent link">&para;</a></h4>
3960
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-35-1" name="__codelineno-35-1" href="#__codelineno-35-1"></a><span class="k">def</span><span class="w"> </span><span class="nf">save_metadata</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">path</span><span class="p">:</span> <span class="n">Path</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span>
3961
+ </code></pre></div>
3962
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-36-1" name="__codelineno-36-1" href="#__codelineno-36-1"></a>Persist job metadata to disk.
3963
+ <a id="__codelineno-36-2" name="__codelineno-36-2" href="#__codelineno-36-2"></a>
3964
+ <a id="__codelineno-36-3" name="__codelineno-36-3" href="#__codelineno-36-3"></a>Args:
3965
+ <a id="__codelineno-36-4" name="__codelineno-36-4" href="#__codelineno-36-4"></a> path: Target metadata JSON file path.
3966
+ </code></pre></div>
3967
+ <h2 id="caddforgecoreresult"><code>caddforge.core.result</code><a class="headerlink" href="#caddforgecoreresult" title="Permanent link">&para;</a></h2>
3968
+ <h3 id="result"><code>Result</code><a class="headerlink" href="#result" title="Permanent link">&para;</a></h3>
3969
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-37-1" name="__codelineno-37-1" href="#__codelineno-37-1"></a><span class="k">class</span><span class="w"> </span><span class="nc">Result</span><span class="p">()</span>
3970
+ </code></pre></div>
3971
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-38-1" name="__codelineno-38-1" href="#__codelineno-38-1"></a>Standardized result object produced by workflows.
3972
+ <a id="__codelineno-38-2" name="__codelineno-38-2" href="#__codelineno-38-2"></a>
3973
+ <a id="__codelineno-38-3" name="__codelineno-38-3" href="#__codelineno-38-3"></a>Args:
3974
+ <a id="__codelineno-38-4" name="__codelineno-38-4" href="#__codelineno-38-4"></a> job_id: Job identifier.
3975
+ <a id="__codelineno-38-5" name="__codelineno-38-5" href="#__codelineno-38-5"></a> tool_name: Tool name that produced the result.
3976
+ <a id="__codelineno-38-6" name="__codelineno-38-6" href="#__codelineno-38-6"></a> status: Completion status for the job.
3977
+ <a id="__codelineno-38-7" name="__codelineno-38-7" href="#__codelineno-38-7"></a> metrics: Tool-defined metrics (simple scalar values).
3978
+ <a id="__codelineno-38-8" name="__codelineno-38-8" href="#__codelineno-38-8"></a> paths: Paths to key output artifacts.
3979
+ <a id="__codelineno-38-9" name="__codelineno-38-9" href="#__codelineno-38-9"></a> extra: Tool-defined extra metadata payload.
3980
+ </code></pre></div>
3981
+ <p>Declared fields and enum values (inherited fields are documented on the base class):</p>
3982
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-39-1" name="__codelineno-39-1" href="#__codelineno-39-1"></a><span class="n">job_id</span><span class="p">:</span> <span class="nb">str</span>
3983
+ <a id="__codelineno-39-2" name="__codelineno-39-2" href="#__codelineno-39-2"></a><span class="n">tool_name</span><span class="p">:</span> <span class="nb">str</span>
3984
+ <a id="__codelineno-39-3" name="__codelineno-39-3" href="#__codelineno-39-3"></a><span class="n">status</span><span class="p">:</span> <span class="n">JobStatus</span>
3985
+ <a id="__codelineno-39-4" name="__codelineno-39-4" href="#__codelineno-39-4"></a><span class="n">metrics</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">float</span> <span class="o">|</span> <span class="nb">int</span> <span class="o">|</span> <span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="n">field</span><span class="p">(</span><span class="n">default_factory</span><span class="o">=</span><span class="nb">dict</span><span class="p">)</span>
3986
+ <a id="__codelineno-39-5" name="__codelineno-39-5" href="#__codelineno-39-5"></a><span class="n">paths</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Path</span><span class="p">]</span> <span class="o">=</span> <span class="n">field</span><span class="p">(</span><span class="n">default_factory</span><span class="o">=</span><span class="nb">dict</span><span class="p">)</span>
3987
+ <a id="__codelineno-39-6" name="__codelineno-39-6" href="#__codelineno-39-6"></a><span class="n">extra</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">]</span> <span class="o">=</span> <span class="n">field</span><span class="p">(</span><span class="n">default_factory</span><span class="o">=</span><span class="nb">dict</span><span class="p">)</span>
3988
+ </code></pre></div>
3989
+ <h4 id="to_dict"><code>to_dict</code><a class="headerlink" href="#to_dict" title="Permanent link">&para;</a></h4>
3990
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-40-1" name="__codelineno-40-1" href="#__codelineno-40-1"></a><span class="k">def</span><span class="w"> </span><span class="nf">to_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">]</span>
3991
+ </code></pre></div>
3992
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-41-1" name="__codelineno-41-1" href="#__codelineno-41-1"></a>Serialize to a JSON-friendly dictionary.
3993
+ <a id="__codelineno-41-2" name="__codelineno-41-2" href="#__codelineno-41-2"></a>
3994
+ <a id="__codelineno-41-3" name="__codelineno-41-3" href="#__codelineno-41-3"></a>Returns:
3995
+ <a id="__codelineno-41-4" name="__codelineno-41-4" href="#__codelineno-41-4"></a> dict[str, Any]: Serialized representation of the result.
3996
+ </code></pre></div>
3997
+ <h4 id="from_dict"><code>from_dict</code><a class="headerlink" href="#from_dict" title="Permanent link">&para;</a></h4>
3998
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-42-1" name="__codelineno-42-1" href="#__codelineno-42-1"></a><span class="k">def</span><span class="w"> </span><span class="nf">from_dict</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">data</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="s1">'Result'</span>
3999
+ </code></pre></div>
4000
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-43-1" name="__codelineno-43-1" href="#__codelineno-43-1"></a>Construct a Result from a dictionary representation.
4001
+ <a id="__codelineno-43-2" name="__codelineno-43-2" href="#__codelineno-43-2"></a>
4002
+ <a id="__codelineno-43-3" name="__codelineno-43-3" href="#__codelineno-43-3"></a>Args:
4003
+ <a id="__codelineno-43-4" name="__codelineno-43-4" href="#__codelineno-43-4"></a> data: Serialized result dictionary.
4004
+ <a id="__codelineno-43-5" name="__codelineno-43-5" href="#__codelineno-43-5"></a>
4005
+ <a id="__codelineno-43-6" name="__codelineno-43-6" href="#__codelineno-43-6"></a>Returns:
4006
+ <a id="__codelineno-43-7" name="__codelineno-43-7" href="#__codelineno-43-7"></a> Result: Deserialized Result instance.
4007
+ </code></pre></div>
4008
+ <h4 id="save"><code>save</code><a class="headerlink" href="#save" title="Permanent link">&para;</a></h4>
4009
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-44-1" name="__codelineno-44-1" href="#__codelineno-44-1"></a><span class="k">def</span><span class="w"> </span><span class="nf">save</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">path</span><span class="p">:</span> <span class="n">Path</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span>
4010
+ </code></pre></div>
4011
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-45-1" name="__codelineno-45-1" href="#__codelineno-45-1"></a>Persist result to disk as JSON.
4012
+ <a id="__codelineno-45-2" name="__codelineno-45-2" href="#__codelineno-45-2"></a>
4013
+ <a id="__codelineno-45-3" name="__codelineno-45-3" href="#__codelineno-45-3"></a>Args:
4014
+ <a id="__codelineno-45-4" name="__codelineno-45-4" href="#__codelineno-45-4"></a> path: Target JSON file path.
4015
+ </code></pre></div>
4016
+ <h2 id="caddforgecoreworkflow"><code>caddforge.core.workflow</code><a class="headerlink" href="#caddforgecoreworkflow" title="Permanent link">&para;</a></h2>
4017
+ <h3 id="workflow"><code>Workflow</code><a class="headerlink" href="#workflow" title="Permanent link">&para;</a></h3>
4018
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-46-1" name="__codelineno-46-1" href="#__codelineno-46-1"></a><span class="k">class</span><span class="w"> </span><span class="nc">Workflow</span><span class="p">(</span><span class="n">ABC</span><span class="p">)</span>
4019
+ </code></pre></div>
4020
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-47-1" name="__codelineno-47-1" href="#__codelineno-47-1"></a>Abstract workflow run by CADDForge tools.
4021
+ </code></pre></div>
4022
+ <p>Declared fields and enum values (inherited fields are documented on the base class):</p>
4023
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-48-1" name="__codelineno-48-1" href="#__codelineno-48-1"></a><span class="n">tool_name</span><span class="p">:</span> <span class="nb">str</span>
4024
+ </code></pre></div>
4025
+ <h4 id="prepare_job"><code>prepare_job</code><a class="headerlink" href="#prepare_job" title="Permanent link">&para;</a></h4>
4026
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-49-1" name="__codelineno-49-1" href="#__codelineno-49-1"></a><span class="k">def</span><span class="w"> </span><span class="nf">prepare_job</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Job</span>
4027
+ </code></pre></div>
4028
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-50-1" name="__codelineno-50-1" href="#__codelineno-50-1"></a>Build a job object with metadata and paths.
4029
+ <a id="__codelineno-50-2" name="__codelineno-50-2" href="#__codelineno-50-2"></a>
4030
+ <a id="__codelineno-50-3" name="__codelineno-50-3" href="#__codelineno-50-3"></a>Returns:
4031
+ <a id="__codelineno-50-4" name="__codelineno-50-4" href="#__codelineno-50-4"></a> Job: Prepared job instance ready for submission.
4032
+ </code></pre></div>
4033
+ <h4 id="run"><code>run</code><a class="headerlink" href="#run" title="Permanent link">&para;</a></h4>
4034
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-51-1" name="__codelineno-51-1" href="#__codelineno-51-1"></a><span class="k">def</span><span class="w"> </span><span class="nf">run</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">job</span><span class="p">:</span> <span class="n">Job</span><span class="p">,</span> <span class="n">context</span><span class="p">:</span> <span class="n">RuntimeContext</span> <span class="o">|</span> <span class="kc">None</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Result</span>
4035
+ </code></pre></div>
4036
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-52-1" name="__codelineno-52-1" href="#__codelineno-52-1"></a>Execute the workflow logic and return a result.
4037
+ <a id="__codelineno-52-2" name="__codelineno-52-2" href="#__codelineno-52-2"></a>
4038
+ <a id="__codelineno-52-3" name="__codelineno-52-3" href="#__codelineno-52-3"></a>Args:
4039
+ <a id="__codelineno-52-4" name="__codelineno-52-4" href="#__codelineno-52-4"></a> job: Job metadata for the execution.
4040
+ <a id="__codelineno-52-5" name="__codelineno-52-5" href="#__codelineno-52-5"></a> context: Backend-neutral runtime details supplied by the executor.
4041
+ <a id="__codelineno-52-6" name="__codelineno-52-6" href="#__codelineno-52-6"></a>
4042
+ <a id="__codelineno-52-7" name="__codelineno-52-7" href="#__codelineno-52-7"></a>Returns:
4043
+ <a id="__codelineno-52-8" name="__codelineno-52-8" href="#__codelineno-52-8"></a> Result: Standardized workflow result.
4044
+ </code></pre></div>
4045
+ <h2 id="caddforgecoreexecution"><code>caddforge.core.execution</code><a class="headerlink" href="#caddforgecoreexecution" title="Permanent link">&para;</a></h2>
4046
+ <h3 id="backendoptions"><code>BackendOptions</code><a class="headerlink" href="#backendoptions" title="Permanent link">&para;</a></h3>
4047
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-53-1" name="__codelineno-53-1" href="#__codelineno-53-1"></a><span class="k">class</span><span class="w"> </span><span class="nc">BackendOptions</span><span class="p">()</span>
4048
+ </code></pre></div>
4049
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-54-1" name="__codelineno-54-1" href="#__codelineno-54-1"></a>Backend-specific options supplied by CLI or GUI callers.
4050
+ </code></pre></div>
4051
+ <p>Declared fields and enum values (inherited fields are documented on the base class):</p>
4052
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-55-1" name="__codelineno-55-1" href="#__codelineno-55-1"></a><span class="n">slurm_partition</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
4053
+ <a id="__codelineno-55-2" name="__codelineno-55-2" href="#__codelineno-55-2"></a><span class="n">slurm_time</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
4054
+ <a id="__codelineno-55-3" name="__codelineno-55-3" href="#__codelineno-55-3"></a><span class="n">slurm_account</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
4055
+ <a id="__codelineno-55-4" name="__codelineno-55-4" href="#__codelineno-55-4"></a><span class="n">slurm_nodes</span><span class="p">:</span> <span class="nb">int</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
4056
+ <a id="__codelineno-55-5" name="__codelineno-55-5" href="#__codelineno-55-5"></a><span class="n">slurm_ntasks</span><span class="p">:</span> <span class="nb">int</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
4057
+ <a id="__codelineno-55-6" name="__codelineno-55-6" href="#__codelineno-55-6"></a><span class="n">slurm_cpus_per_task</span><span class="p">:</span> <span class="nb">int</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
4058
+ <a id="__codelineno-55-7" name="__codelineno-55-7" href="#__codelineno-55-7"></a><span class="n">slurm_setup</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="n">field</span><span class="p">(</span><span class="n">default_factory</span><span class="o">=</span><span class="nb">list</span><span class="p">)</span>
4059
+ <a id="__codelineno-55-8" name="__codelineno-55-8" href="#__codelineno-55-8"></a><span class="n">slurm_env_pack</span><span class="p">:</span> <span class="n">Path</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
4060
+ <a id="__codelineno-55-9" name="__codelineno-55-9" href="#__codelineno-55-9"></a><span class="n">slurm_wheelhouse</span><span class="p">:</span> <span class="n">Path</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
4061
+ <a id="__codelineno-55-10" name="__codelineno-55-10" href="#__codelineno-55-10"></a><span class="n">slurm_requirements</span><span class="p">:</span> <span class="n">Path</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
4062
+ <a id="__codelineno-55-11" name="__codelineno-55-11" href="#__codelineno-55-11"></a><span class="n">extra_sbatch_options</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="n">field</span><span class="p">(</span><span class="n">default_factory</span><span class="o">=</span><span class="nb">list</span><span class="p">)</span>
4063
+ </code></pre></div>
4064
+ <h3 id="submit_workflow"><code>submit_workflow</code><a class="headerlink" href="#submit_workflow" title="Permanent link">&para;</a></h3>
4065
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-56-1" name="__codelineno-56-1" href="#__codelineno-56-1"></a><span class="k">def</span><span class="w"> </span><span class="nf">submit_workflow</span><span class="p">(</span><span class="n">workflow</span><span class="p">,</span> <span class="n">cfg</span><span class="p">:</span> <span class="n">BaseConfig</span><span class="p">,</span> <span class="o">*</span><span class="p">,</span> <span class="n">backend_name</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">runs_root</span><span class="p">:</span> <span class="n">Path</span> <span class="o">|</span> <span class="nb">str</span><span class="o">=</span><span class="n">Path</span><span class="p">(</span><span class="s1">'runs'</span><span class="p">),</span> <span class="n">registry_path</span><span class="p">:</span> <span class="n">Path</span> <span class="o">|</span> <span class="kc">None</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">job_name</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">submission_cwd</span><span class="p">:</span> <span class="n">Path</span> <span class="o">|</span> <span class="kc">None</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">local_async</span><span class="p">:</span> <span class="nb">bool</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">backend_options</span><span class="p">:</span> <span class="n">BackendOptions</span> <span class="o">|</span> <span class="kc">None</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">emit</span><span class="p">:</span> <span class="n">EmitFn</span> <span class="o">|</span> <span class="kc">None</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">prepared_job_callback</span><span class="p">:</span> <span class="n">Callable</span><span class="p">[[</span><span class="n">Job</span><span class="p">],</span> <span class="kc">None</span><span class="p">]</span> <span class="o">|</span> <span class="kc">None</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">input_ports</span><span class="p">:</span> <span class="nb">tuple</span><span class="p">[</span><span class="n">InputPort</span><span class="p">,</span> <span class="o">...</span><span class="p">]</span><span class="o">=</span><span class="p">())</span> <span class="o">-&gt;</span> <span class="n">Job</span>
4066
+ </code></pre></div>
4067
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-57-1" name="__codelineno-57-1" href="#__codelineno-57-1"></a>Prepare a workflow job and submit it through the selected backend.
4068
+ </code></pre></div>
4069
+ <h3 id="load_result_for_job"><code>load_result_for_job</code><a class="headerlink" href="#load_result_for_job" title="Permanent link">&para;</a></h3>
4070
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-58-1" name="__codelineno-58-1" href="#__codelineno-58-1"></a><span class="k">def</span><span class="w"> </span><span class="nf">load_result_for_job</span><span class="p">(</span><span class="n">job</span><span class="p">:</span> <span class="n">Job</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Result</span> <span class="o">|</span> <span class="kc">None</span>
4071
+ </code></pre></div>
4072
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-59-1" name="__codelineno-59-1" href="#__codelineno-59-1"></a>Load the canonical result for a job if it exists.
4073
+ </code></pre></div>
4074
+ <h2 id="caddforgecorebackend"><code>caddforge.core.backend</code><a class="headerlink" href="#caddforgecorebackend" title="Permanent link">&para;</a></h2>
4075
+ <h3 id="backend"><code>Backend</code><a class="headerlink" href="#backend" title="Permanent link">&para;</a></h3>
4076
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-60-1" name="__codelineno-60-1" href="#__codelineno-60-1"></a><span class="k">class</span><span class="w"> </span><span class="nc">Backend</span><span class="p">(</span><span class="n">ABC</span><span class="p">)</span>
4077
+ </code></pre></div>
4078
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-61-1" name="__codelineno-61-1" href="#__codelineno-61-1"></a>Abstract compute backend.
4079
+ </code></pre></div>
4080
+ <p>Declared fields and enum values (inherited fields are documented on the base class):</p>
4081
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-62-1" name="__codelineno-62-1" href="#__codelineno-62-1"></a><span class="n">name</span><span class="p">:</span> <span class="nb">str</span>
4082
+ </code></pre></div>
4083
+ <h4 id="submit"><code>submit</code><a class="headerlink" href="#submit" title="Permanent link">&para;</a></h4>
4084
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-63-1" name="__codelineno-63-1" href="#__codelineno-63-1"></a><span class="k">def</span><span class="w"> </span><span class="nf">submit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">job</span><span class="p">:</span> <span class="n">Job</span><span class="p">,</span> <span class="n">run_callable</span><span class="p">:</span> <span class="n">Callable</span><span class="p">[[</span><span class="n">Job</span><span class="p">],</span> <span class="n">Result</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="n">JobHandle</span>
4085
+ </code></pre></div>
4086
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-64-1" name="__codelineno-64-1" href="#__codelineno-64-1"></a>Submit a job for execution using the provided callable.
4087
+ <a id="__codelineno-64-2" name="__codelineno-64-2" href="#__codelineno-64-2"></a>
4088
+ <a id="__codelineno-64-3" name="__codelineno-64-3" href="#__codelineno-64-3"></a>Args:
4089
+ <a id="__codelineno-64-4" name="__codelineno-64-4" href="#__codelineno-64-4"></a> job: Job metadata to register and execute.
4090
+ <a id="__codelineno-64-5" name="__codelineno-64-5" href="#__codelineno-64-5"></a> run_callable: Callable that performs the work and returns a Result.
4091
+ <a id="__codelineno-64-6" name="__codelineno-64-6" href="#__codelineno-64-6"></a>
4092
+ <a id="__codelineno-64-7" name="__codelineno-64-7" href="#__codelineno-64-7"></a>Returns:
4093
+ <a id="__codelineno-64-8" name="__codelineno-64-8" href="#__codelineno-64-8"></a> JobHandle: Backend-specific handle for tracking execution.
4094
+ </code></pre></div>
4095
+ <h4 id="submit_shell_commands"><code>submit_shell_commands</code><a class="headerlink" href="#submit_shell_commands" title="Permanent link">&para;</a></h4>
4096
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-65-1" name="__codelineno-65-1" href="#__codelineno-65-1"></a><span class="k">def</span><span class="w"> </span><span class="nf">submit_shell_commands</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">job</span><span class="p">:</span> <span class="n">Job</span><span class="p">,</span> <span class="n">commands</span><span class="p">:</span> <span class="n">Iterable</span><span class="p">[</span><span class="nb">str</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="n">JobHandle</span>
4097
+ </code></pre></div>
4098
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-66-1" name="__codelineno-66-1" href="#__codelineno-66-1"></a>Submit a shell-command job if the backend supports it.
4099
+ <a id="__codelineno-66-2" name="__codelineno-66-2" href="#__codelineno-66-2"></a>
4100
+ <a id="__codelineno-66-3" name="__codelineno-66-3" href="#__codelineno-66-3"></a>Args:
4101
+ <a id="__codelineno-66-4" name="__codelineno-66-4" href="#__codelineno-66-4"></a> job: Job metadata to register and execute.
4102
+ <a id="__codelineno-66-5" name="__codelineno-66-5" href="#__codelineno-66-5"></a> commands: Shell commands to execute in order.
4103
+ <a id="__codelineno-66-6" name="__codelineno-66-6" href="#__codelineno-66-6"></a>
4104
+ <a id="__codelineno-66-7" name="__codelineno-66-7" href="#__codelineno-66-7"></a>Returns:
4105
+ <a id="__codelineno-66-8" name="__codelineno-66-8" href="#__codelineno-66-8"></a> JobHandle: Backend-specific handle for tracking execution.
4106
+ <a id="__codelineno-66-9" name="__codelineno-66-9" href="#__codelineno-66-9"></a>
4107
+ <a id="__codelineno-66-10" name="__codelineno-66-10" href="#__codelineno-66-10"></a>Raises:
4108
+ <a id="__codelineno-66-11" name="__codelineno-66-11" href="#__codelineno-66-11"></a> NotImplementedError: If the backend does not implement shell jobs.
4109
+ </code></pre></div>
4110
+ <h4 id="query_status"><code>query_status</code><a class="headerlink" href="#query_status" title="Permanent link">&para;</a></h4>
4111
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-67-1" name="__codelineno-67-1" href="#__codelineno-67-1"></a><span class="k">def</span><span class="w"> </span><span class="nf">query_status</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">handle</span><span class="p">:</span> <span class="n">JobHandle</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">JobStatus</span>
4112
+ </code></pre></div>
4113
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-68-1" name="__codelineno-68-1" href="#__codelineno-68-1"></a>Return current status of a submitted job.
4114
+ <a id="__codelineno-68-2" name="__codelineno-68-2" href="#__codelineno-68-2"></a>
4115
+ <a id="__codelineno-68-3" name="__codelineno-68-3" href="#__codelineno-68-3"></a>Args:
4116
+ <a id="__codelineno-68-4" name="__codelineno-68-4" href="#__codelineno-68-4"></a> handle: Backend-specific job handle.
4117
+ <a id="__codelineno-68-5" name="__codelineno-68-5" href="#__codelineno-68-5"></a>
4118
+ <a id="__codelineno-68-6" name="__codelineno-68-6" href="#__codelineno-68-6"></a>Returns:
4119
+ <a id="__codelineno-68-7" name="__codelineno-68-7" href="#__codelineno-68-7"></a> JobStatus: Current status for the job.
4120
+ </code></pre></div>
4121
+ <h4 id="cancel"><code>cancel</code><a class="headerlink" href="#cancel" title="Permanent link">&para;</a></h4>
4122
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-69-1" name="__codelineno-69-1" href="#__codelineno-69-1"></a><span class="k">def</span><span class="w"> </span><span class="nf">cancel</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">handle</span><span class="p">:</span> <span class="n">JobHandle</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span>
4123
+ </code></pre></div>
4124
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-70-1" name="__codelineno-70-1" href="#__codelineno-70-1"></a>Cancel a submitted job if supported.
4125
+ <a id="__codelineno-70-2" name="__codelineno-70-2" href="#__codelineno-70-2"></a>
4126
+ <a id="__codelineno-70-3" name="__codelineno-70-3" href="#__codelineno-70-3"></a>Args:
4127
+ <a id="__codelineno-70-4" name="__codelineno-70-4" href="#__codelineno-70-4"></a> handle: Backend-specific job handle.
4128
+ </code></pre></div>
4129
+ <h2 id="caddforgecoreartifacts"><code>caddforge.core.artifacts</code><a class="headerlink" href="#caddforgecoreartifacts" title="Permanent link">&para;</a></h2>
4130
+ <h3 id="artifactkind"><code>ArtifactKind</code><a class="headerlink" href="#artifactkind" title="Permanent link">&para;</a></h3>
4131
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-71-1" name="__codelineno-71-1" href="#__codelineno-71-1"></a><span class="k">class</span><span class="w"> </span><span class="nc">ArtifactKind</span><span class="p">(</span><span class="nb">str</span><span class="p">,</span> <span class="n">Enum</span><span class="p">)</span>
4132
+ </code></pre></div>
4133
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-72-1" name="__codelineno-72-1" href="#__codelineno-72-1"></a>Portable artifact categories understood by the core pipeline layer.
4134
+ </code></pre></div>
4135
+ <p>Declared fields and enum values (inherited fields are documented on the base class):</p>
4136
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-73-1" name="__codelineno-73-1" href="#__codelineno-73-1"></a><span class="n">FILE</span> <span class="o">=</span> <span class="s1">'file'</span>
4137
+ <a id="__codelineno-73-2" name="__codelineno-73-2" href="#__codelineno-73-2"></a><span class="n">DIRECTORY</span> <span class="o">=</span> <span class="s1">'directory'</span>
4138
+ <a id="__codelineno-73-3" name="__codelineno-73-3" href="#__codelineno-73-3"></a><span class="n">MOLECULE_COLLECTION</span> <span class="o">=</span> <span class="s1">'molecule_collection'</span>
4139
+ <a id="__codelineno-73-4" name="__codelineno-73-4" href="#__codelineno-73-4"></a><span class="n">POSE_COLLECTION</span> <span class="o">=</span> <span class="s1">'pose_collection'</span>
4140
+ <a id="__codelineno-73-5" name="__codelineno-73-5" href="#__codelineno-73-5"></a><span class="n">POSE_MANIFEST</span> <span class="o">=</span> <span class="s1">'pose_manifest'</span>
4141
+ <a id="__codelineno-73-6" name="__codelineno-73-6" href="#__codelineno-73-6"></a><span class="n">TABULAR_SCORES</span> <span class="o">=</span> <span class="s1">'tabular_scores'</span>
4142
+ <a id="__codelineno-73-7" name="__codelineno-73-7" href="#__codelineno-73-7"></a><span class="n">PROTEIN_STRUCTURE</span> <span class="o">=</span> <span class="s1">'protein_structure'</span>
4143
+ <a id="__codelineno-73-8" name="__codelineno-73-8" href="#__codelineno-73-8"></a><span class="n">COMPLEX_STRUCTURE</span> <span class="o">=</span> <span class="s1">'complex_structure'</span>
4144
+ </code></pre></div>
4145
+ <h3 id="artifactref"><code>ArtifactRef</code><a class="headerlink" href="#artifactref" title="Permanent link">&para;</a></h3>
4146
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-74-1" name="__codelineno-74-1" href="#__codelineno-74-1"></a><span class="k">class</span><span class="w"> </span><span class="nc">ArtifactRef</span><span class="p">()</span>
4147
+ </code></pre></div>
4148
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-75-1" name="__codelineno-75-1" href="#__codelineno-75-1"></a>Reference to a workflow artifact stored on disk.
4149
+ <a id="__codelineno-75-2" name="__codelineno-75-2" href="#__codelineno-75-2"></a>
4150
+ <a id="__codelineno-75-3" name="__codelineno-75-3" href="#__codelineno-75-3"></a>Large data stays on disk; the pipeline engine passes these lightweight
4151
+ <a id="__codelineno-75-4" name="__codelineno-75-4" href="#__codelineno-75-4"></a>references between stages and resolves them into concrete config paths.
4152
+ </code></pre></div>
4153
+ <p>Declared fields and enum values (inherited fields are documented on the base class):</p>
4154
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-76-1" name="__codelineno-76-1" href="#__codelineno-76-1"></a><span class="nb">id</span><span class="p">:</span> <span class="nb">str</span>
4155
+ <a id="__codelineno-76-2" name="__codelineno-76-2" href="#__codelineno-76-2"></a><span class="n">kind</span><span class="p">:</span> <span class="n">ArtifactKind</span> <span class="o">|</span> <span class="nb">str</span>
4156
+ <a id="__codelineno-76-3" name="__codelineno-76-3" href="#__codelineno-76-3"></a><span class="n">producer_stage_id</span><span class="p">:</span> <span class="nb">str</span>
4157
+ <a id="__codelineno-76-4" name="__codelineno-76-4" href="#__codelineno-76-4"></a><span class="n">path</span><span class="p">:</span> <span class="n">Path</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
4158
+ <a id="__codelineno-76-5" name="__codelineno-76-5" href="#__codelineno-76-5"></a><span class="n">paths</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="n">Path</span><span class="p">]</span> <span class="o">=</span> <span class="n">field</span><span class="p">(</span><span class="n">default_factory</span><span class="o">=</span><span class="nb">list</span><span class="p">)</span>
4159
+ <a id="__codelineno-76-6" name="__codelineno-76-6" href="#__codelineno-76-6"></a><span class="n">producer_job_id</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
4160
+ <a id="__codelineno-76-7" name="__codelineno-76-7" href="#__codelineno-76-7"></a><span class="n">metadata</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">]</span> <span class="o">=</span> <span class="n">field</span><span class="p">(</span><span class="n">default_factory</span><span class="o">=</span><span class="nb">dict</span><span class="p">)</span>
4161
+ </code></pre></div>
4162
+ <h4 id="primary_path"><code>primary_path</code><a class="headerlink" href="#primary_path" title="Permanent link">&para;</a></h4>
4163
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-77-1" name="__codelineno-77-1" href="#__codelineno-77-1"></a><span class="k">def</span><span class="w"> </span><span class="nf">primary_path</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Path</span>
4164
+ </code></pre></div>
4165
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-78-1" name="__codelineno-78-1" href="#__codelineno-78-1"></a>Return the single concrete path for config binding.
4166
+ </code></pre></div>
4167
+ <h4 id="to_dict_1"><code>to_dict</code><a class="headerlink" href="#to_dict_1" title="Permanent link">&para;</a></h4>
4168
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-79-1" name="__codelineno-79-1" href="#__codelineno-79-1"></a><span class="k">def</span><span class="w"> </span><span class="nf">to_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">]</span>
4169
+ </code></pre></div>
4170
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-80-1" name="__codelineno-80-1" href="#__codelineno-80-1"></a>Serialize to a JSON-friendly dictionary.
4171
+ </code></pre></div>
4172
+ <h4 id="from_dict_1"><code>from_dict</code><a class="headerlink" href="#from_dict_1" title="Permanent link">&para;</a></h4>
4173
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-81-1" name="__codelineno-81-1" href="#__codelineno-81-1"></a><span class="k">def</span><span class="w"> </span><span class="nf">from_dict</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">data</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="n">ArtifactRef</span>
4174
+ </code></pre></div>
4175
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-82-1" name="__codelineno-82-1" href="#__codelineno-82-1"></a>Deserialize an artifact reference from a dictionary.
4176
+ </code></pre></div>
4177
+ <h3 id="inputport"><code>InputPort</code><a class="headerlink" href="#inputport" title="Permanent link">&para;</a></h3>
4178
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-83-1" name="__codelineno-83-1" href="#__codelineno-83-1"></a><span class="k">class</span><span class="w"> </span><span class="nc">InputPort</span><span class="p">()</span>
4179
+ </code></pre></div>
4180
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-84-1" name="__codelineno-84-1" href="#__codelineno-84-1"></a>Declarative input accepted by a tool plugin.
4181
+ <a id="__codelineno-84-2" name="__codelineno-84-2" href="#__codelineno-84-2"></a>
4182
+ <a id="__codelineno-84-3" name="__codelineno-84-3" href="#__codelineno-84-3"></a>``config_field`` is the stable top-level pipeline binding target.
4183
+ <a id="__codelineno-84-4" name="__codelineno-84-4" href="#__codelineno-84-4"></a>``runtime_selector`` may identify nested path values for execution-time
4184
+ <a id="__codelineno-84-5" name="__codelineno-84-5" href="#__codelineno-84-5"></a>staging without changing that pipeline contract.
4185
+ </code></pre></div>
4186
+ <p>Declared fields and enum values (inherited fields are documented on the base class):</p>
4187
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-85-1" name="__codelineno-85-1" href="#__codelineno-85-1"></a><span class="n">name</span><span class="p">:</span> <span class="nb">str</span>
4188
+ <a id="__codelineno-85-2" name="__codelineno-85-2" href="#__codelineno-85-2"></a><span class="n">kind</span><span class="p">:</span> <span class="n">ArtifactKind</span> <span class="o">|</span> <span class="nb">str</span>
4189
+ <a id="__codelineno-85-3" name="__codelineno-85-3" href="#__codelineno-85-3"></a><span class="n">config_field</span><span class="p">:</span> <span class="nb">str</span>
4190
+ <a id="__codelineno-85-4" name="__codelineno-85-4" href="#__codelineno-85-4"></a><span class="n">required</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span>
4191
+ <a id="__codelineno-85-5" name="__codelineno-85-5" href="#__codelineno-85-5"></a><span class="n">description</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
4192
+ <a id="__codelineno-85-6" name="__codelineno-85-6" href="#__codelineno-85-6"></a><span class="n">compression</span><span class="p">:</span> <span class="n">InputCompressionPolicy</span> <span class="o">|</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">InputCompressionPolicy</span><span class="o">.</span><span class="n">TRANSPARENT_GZIP</span>
4193
+ <a id="__codelineno-85-7" name="__codelineno-85-7" href="#__codelineno-85-7"></a><span class="n">runtime_selector</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
4194
+ </code></pre></div>
4195
+ <h3 id="outputport"><code>OutputPort</code><a class="headerlink" href="#outputport" title="Permanent link">&para;</a></h3>
4196
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-86-1" name="__codelineno-86-1" href="#__codelineno-86-1"></a><span class="k">class</span><span class="w"> </span><span class="nc">OutputPort</span><span class="p">()</span>
4197
+ </code></pre></div>
4198
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-87-1" name="__codelineno-87-1" href="#__codelineno-87-1"></a>Declarative output produced by a tool plugin.
4199
+ <a id="__codelineno-87-2" name="__codelineno-87-2" href="#__codelineno-87-2"></a>
4200
+ <a id="__codelineno-87-3" name="__codelineno-87-3" href="#__codelineno-87-3"></a>``config_field`` identifies the optional Path-typed config field that asks
4201
+ <a id="__codelineno-87-4" name="__codelineno-87-4" href="#__codelineno-87-4"></a>the workflow where to write this result. Declaring it enables transparent
4202
+ <a id="__codelineno-87-5" name="__codelineno-87-5" href="#__codelineno-87-5"></a>gzip output handling at the pipeline boundary.
4203
+ </code></pre></div>
4204
+ <p>Declared fields and enum values (inherited fields are documented on the base class):</p>
4205
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-88-1" name="__codelineno-88-1" href="#__codelineno-88-1"></a><span class="n">name</span><span class="p">:</span> <span class="nb">str</span>
4206
+ <a id="__codelineno-88-2" name="__codelineno-88-2" href="#__codelineno-88-2"></a><span class="n">kind</span><span class="p">:</span> <span class="n">ArtifactKind</span> <span class="o">|</span> <span class="nb">str</span>
4207
+ <a id="__codelineno-88-3" name="__codelineno-88-3" href="#__codelineno-88-3"></a><span class="n">result_path_key</span><span class="p">:</span> <span class="nb">str</span>
4208
+ <a id="__codelineno-88-4" name="__codelineno-88-4" href="#__codelineno-88-4"></a><span class="n">description</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
4209
+ <a id="__codelineno-88-5" name="__codelineno-88-5" href="#__codelineno-88-5"></a><span class="n">required</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span>
4210
+ <a id="__codelineno-88-6" name="__codelineno-88-6" href="#__codelineno-88-6"></a><span class="n">path_collection_column</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
4211
+ <a id="__codelineno-88-7" name="__codelineno-88-7" href="#__codelineno-88-7"></a><span class="n">config_field</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
4212
+ </code></pre></div>
4213
+ <h3 id="splitcontract"><code>SplitContract</code><a class="headerlink" href="#splitcontract" title="Permanent link">&para;</a></h3>
4214
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-89-1" name="__codelineno-89-1" href="#__codelineno-89-1"></a><span class="k">class</span><span class="w"> </span><span class="nc">SplitContract</span><span class="p">()</span>
4215
+ </code></pre></div>
4216
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-90-1" name="__codelineno-90-1" href="#__codelineno-90-1"></a>Central description of a splittable workflow input.
4217
+ </code></pre></div>
4218
+ <p>Declared fields and enum values (inherited fields are documented on the base class):</p>
4219
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-91-1" name="__codelineno-91-1" href="#__codelineno-91-1"></a><span class="n">input_field</span><span class="p">:</span> <span class="nb">str</span>
4220
+ <a id="__codelineno-91-2" name="__codelineno-91-2" href="#__codelineno-91-2"></a><span class="n">kind</span><span class="p">:</span> <span class="n">ArtifactKind</span> <span class="o">|</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">ArtifactKind</span><span class="o">.</span><span class="n">MOLECULE_COLLECTION</span>
4221
+ <a id="__codelineno-91-3" name="__codelineno-91-3" href="#__codelineno-91-3"></a><span class="n">strategy</span><span class="p">:</span> <span class="n">Literal</span><span class="p">[</span><span class="s1">'sdf'</span><span class="p">,</span> <span class="s1">'csv'</span><span class="p">,</span> <span class="s1">'tsv'</span><span class="p">,</span> <span class="s1">'lines'</span><span class="p">,</span> <span class="s1">'auto'</span><span class="p">]</span> <span class="o">=</span> <span class="s1">'auto'</span>
4222
+ <a id="__codelineno-91-4" name="__codelineno-91-4" href="#__codelineno-91-4"></a><span class="n">merge_outputs</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Literal</span><span class="p">[</span><span class="s1">'csv'</span><span class="p">,</span> <span class="s1">'tsv'</span><span class="p">,</span> <span class="s1">'sdf'</span><span class="p">,</span> <span class="s1">'jsonl'</span><span class="p">,</span> <span class="s1">'manifest'</span><span class="p">,</span> <span class="s1">'auto'</span><span class="p">]]</span> <span class="o">=</span> <span class="n">field</span><span class="p">(</span><span class="n">default_factory</span><span class="o">=</span><span class="nb">dict</span><span class="p">)</span>
4223
+ <a id="__codelineno-91-5" name="__codelineno-91-5" href="#__codelineno-91-5"></a><span class="n">item_path_field</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
4224
+ </code></pre></div>
4225
+ <h2 id="caddforgecoretool"><code>caddforge.core.tool</code><a class="headerlink" href="#caddforgecoretool" title="Permanent link">&para;</a></h2>
4226
+ <h3 id="toolplugin"><code>ToolPlugin</code><a class="headerlink" href="#toolplugin" title="Permanent link">&para;</a></h3>
4227
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-92-1" name="__codelineno-92-1" href="#__codelineno-92-1"></a><span class="k">class</span><span class="w"> </span><span class="nc">ToolPlugin</span><span class="p">(</span><span class="n">Protocol</span><span class="p">)</span>
4228
+ </code></pre></div>
4229
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-93-1" name="__codelineno-93-1" href="#__codelineno-93-1"></a>Protocol that tool plugins should satisfy.
4230
+ <a id="__codelineno-93-2" name="__codelineno-93-2" href="#__codelineno-93-2"></a>
4231
+ <a id="__codelineno-93-3" name="__codelineno-93-3" href="#__codelineno-93-3"></a>Attributes:
4232
+ <a id="__codelineno-93-4" name="__codelineno-93-4" href="#__codelineno-93-4"></a> section: Section/group name for CLI organization.
4233
+ <a id="__codelineno-93-5" name="__codelineno-93-5" href="#__codelineno-93-5"></a> name: Tool name within its section.
4234
+ <a id="__codelineno-93-6" name="__codelineno-93-6" href="#__codelineno-93-6"></a> config_cls: Pydantic config model used by the tool.
4235
+ <a id="__codelineno-93-7" name="__codelineno-93-7" href="#__codelineno-93-7"></a> workflow_cls: Workflow class executed by the tool.
4236
+ </code></pre></div>
4237
+ <p>Declared fields and enum values (inherited fields are documented on the base class):</p>
4238
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-94-1" name="__codelineno-94-1" href="#__codelineno-94-1"></a><span class="n">section</span><span class="p">:</span> <span class="nb">str</span>
4239
+ <a id="__codelineno-94-2" name="__codelineno-94-2" href="#__codelineno-94-2"></a><span class="n">name</span><span class="p">:</span> <span class="nb">str</span>
4240
+ <a id="__codelineno-94-3" name="__codelineno-94-3" href="#__codelineno-94-3"></a><span class="n">config_cls</span><span class="p">:</span> <span class="n">Type</span><span class="p">[</span><span class="n">BaseConfig</span><span class="p">]</span>
4241
+ <a id="__codelineno-94-4" name="__codelineno-94-4" href="#__codelineno-94-4"></a><span class="n">workflow_cls</span><span class="p">:</span> <span class="n">Type</span><span class="p">[</span><span class="n">Workflow</span><span class="p">]</span>
4242
+ <a id="__codelineno-94-5" name="__codelineno-94-5" href="#__codelineno-94-5"></a><span class="n">input_ports</span><span class="p">:</span> <span class="nb">tuple</span><span class="p">[</span><span class="n">InputPort</span><span class="p">,</span> <span class="o">...</span><span class="p">]</span> <span class="o">=</span> <span class="p">()</span>
4243
+ <a id="__codelineno-94-6" name="__codelineno-94-6" href="#__codelineno-94-6"></a><span class="n">output_ports</span><span class="p">:</span> <span class="nb">tuple</span><span class="p">[</span><span class="n">OutputPort</span><span class="p">,</span> <span class="o">...</span><span class="p">]</span> <span class="o">=</span> <span class="p">()</span>
4244
+ <a id="__codelineno-94-7" name="__codelineno-94-7" href="#__codelineno-94-7"></a><span class="n">split_contracts</span><span class="p">:</span> <span class="nb">tuple</span><span class="p">[</span><span class="n">SplitContract</span><span class="p">,</span> <span class="o">...</span><span class="p">]</span> <span class="o">=</span> <span class="p">()</span>
4245
+ </code></pre></div>
4246
+ <h3 id="toolspec"><code>ToolSpec</code><a class="headerlink" href="#toolspec" title="Permanent link">&para;</a></h3>
4247
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-95-1" name="__codelineno-95-1" href="#__codelineno-95-1"></a><span class="k">class</span><span class="w"> </span><span class="nc">ToolSpec</span><span class="p">()</span>
4248
+ </code></pre></div>
4249
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-96-1" name="__codelineno-96-1" href="#__codelineno-96-1"></a>Concrete description of a discovered tool plugin.
4250
+ <a id="__codelineno-96-2" name="__codelineno-96-2" href="#__codelineno-96-2"></a>
4251
+ <a id="__codelineno-96-3" name="__codelineno-96-3" href="#__codelineno-96-3"></a>Args:
4252
+ <a id="__codelineno-96-4" name="__codelineno-96-4" href="#__codelineno-96-4"></a> section: Section/group name for CLI organization.
4253
+ <a id="__codelineno-96-5" name="__codelineno-96-5" href="#__codelineno-96-5"></a> name: Tool name within its section.
4254
+ <a id="__codelineno-96-6" name="__codelineno-96-6" href="#__codelineno-96-6"></a> config_cls: Pydantic config model used by the tool.
4255
+ <a id="__codelineno-96-7" name="__codelineno-96-7" href="#__codelineno-96-7"></a> workflow_cls: Workflow class executed by the tool.
4256
+ <a id="__codelineno-96-8" name="__codelineno-96-8" href="#__codelineno-96-8"></a> plugin: Loaded plugin instance.
4257
+ </code></pre></div>
4258
+ <p>Declared fields and enum values (inherited fields are documented on the base class):</p>
4259
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-97-1" name="__codelineno-97-1" href="#__codelineno-97-1"></a><span class="n">section</span><span class="p">:</span> <span class="nb">str</span>
4260
+ <a id="__codelineno-97-2" name="__codelineno-97-2" href="#__codelineno-97-2"></a><span class="n">name</span><span class="p">:</span> <span class="nb">str</span>
4261
+ <a id="__codelineno-97-3" name="__codelineno-97-3" href="#__codelineno-97-3"></a><span class="n">config_cls</span><span class="p">:</span> <span class="n">Type</span><span class="p">[</span><span class="n">BaseConfig</span><span class="p">]</span>
4262
+ <a id="__codelineno-97-4" name="__codelineno-97-4" href="#__codelineno-97-4"></a><span class="n">workflow_cls</span><span class="p">:</span> <span class="n">Type</span><span class="p">[</span><span class="n">Workflow</span><span class="p">]</span>
4263
+ <a id="__codelineno-97-5" name="__codelineno-97-5" href="#__codelineno-97-5"></a><span class="n">plugin</span><span class="p">:</span> <span class="n">ToolPlugin</span>
4264
+ </code></pre></div>
4265
+ <h2 id="caddforgeplugins"><code>caddforge.plugins</code><a class="headerlink" href="#caddforgeplugins" title="Permanent link">&para;</a></h2>
4266
+ <h3 id="get_tool"><code>get_tool</code><a class="headerlink" href="#get_tool" title="Permanent link">&para;</a></h3>
4267
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-98-1" name="__codelineno-98-1" href="#__codelineno-98-1"></a><span class="k">def</span><span class="w"> </span><span class="nf">get_tool</span><span class="p">(</span><span class="n">section</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">name</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">ToolSpec</span>
4268
+ </code></pre></div>
4269
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-99-1" name="__codelineno-99-1" href="#__codelineno-99-1"></a>Return the tool spec for a given section/tool name.
4270
+ <a id="__codelineno-99-2" name="__codelineno-99-2" href="#__codelineno-99-2"></a>
4271
+ <a id="__codelineno-99-3" name="__codelineno-99-3" href="#__codelineno-99-3"></a>Args:
4272
+ <a id="__codelineno-99-4" name="__codelineno-99-4" href="#__codelineno-99-4"></a> section: Section/group name.
4273
+ <a id="__codelineno-99-5" name="__codelineno-99-5" href="#__codelineno-99-5"></a> name: Tool name within the section.
4274
+ <a id="__codelineno-99-6" name="__codelineno-99-6" href="#__codelineno-99-6"></a>
4275
+ <a id="__codelineno-99-7" name="__codelineno-99-7" href="#__codelineno-99-7"></a>Returns:
4276
+ <a id="__codelineno-99-8" name="__codelineno-99-8" href="#__codelineno-99-8"></a> ToolSpec: Discovered tool specification.
4277
+ <a id="__codelineno-99-9" name="__codelineno-99-9" href="#__codelineno-99-9"></a>
4278
+ <a id="__codelineno-99-10" name="__codelineno-99-10" href="#__codelineno-99-10"></a>Raises:
4279
+ <a id="__codelineno-99-11" name="__codelineno-99-11" href="#__codelineno-99-11"></a> KeyError: If the section or tool name is not registered.
4280
+ </code></pre></div>
4281
+ <h2 id="caddforgepipelinespec"><code>caddforge.pipeline.spec</code><a class="headerlink" href="#caddforgepipelinespec" title="Permanent link">&para;</a></h2>
4282
+ <h3 id="pipelinespec"><code>PipelineSpec</code><a class="headerlink" href="#pipelinespec" title="Permanent link">&para;</a></h3>
4283
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-100-1" name="__codelineno-100-1" href="#__codelineno-100-1"></a><span class="k">class</span><span class="w"> </span><span class="nc">PipelineSpec</span><span class="p">(</span><span class="n">BaseModel</span><span class="p">)</span>
4284
+ </code></pre></div>
4285
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-101-1" name="__codelineno-101-1" href="#__codelineno-101-1"></a>Top-level declarative pipeline specification.
4286
+ </code></pre></div>
4287
+ <p>Declared fields and enum values (inherited fields are documented on the base class):</p>
4288
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-102-1" name="__codelineno-102-1" href="#__codelineno-102-1"></a><span class="n">version</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">1</span>
4289
+ <a id="__codelineno-102-2" name="__codelineno-102-2" href="#__codelineno-102-2"></a><span class="n">name</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s1">'pipeline'</span>
4290
+ <a id="__codelineno-102-3" name="__codelineno-102-3" href="#__codelineno-102-3"></a><span class="n">defaults</span><span class="p">:</span> <span class="n">PipelineDefaults</span> <span class="o">=</span> <span class="n">Field</span><span class="p">(</span><span class="n">default_factory</span><span class="o">=</span><span class="n">PipelineDefaults</span><span class="p">)</span>
4291
+ <a id="__codelineno-102-4" name="__codelineno-102-4" href="#__codelineno-102-4"></a><span class="n">stages</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="n">PipelineStageSpec</span><span class="p">]</span>
4292
+ </code></pre></div>
4293
+ <h3 id="pipelinestagespec"><code>PipelineStageSpec</code><a class="headerlink" href="#pipelinestagespec" title="Permanent link">&para;</a></h3>
4294
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-103-1" name="__codelineno-103-1" href="#__codelineno-103-1"></a><span class="k">class</span><span class="w"> </span><span class="nc">PipelineStageSpec</span><span class="p">(</span><span class="n">BaseModel</span><span class="p">)</span>
4295
+ </code></pre></div>
4296
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-104-1" name="__codelineno-104-1" href="#__codelineno-104-1"></a>One stage in a CADDForge pipeline DAG.
4297
+ </code></pre></div>
4298
+ <p>Declared fields and enum values (inherited fields are documented on the base class):</p>
4299
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-105-1" name="__codelineno-105-1" href="#__codelineno-105-1"></a><span class="nb">id</span><span class="p">:</span> <span class="nb">str</span>
4300
+ <a id="__codelineno-105-2" name="__codelineno-105-2" href="#__codelineno-105-2"></a><span class="n">tool</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
4301
+ <a id="__codelineno-105-3" name="__codelineno-105-3" href="#__codelineno-105-3"></a><span class="nb">type</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
4302
+ <a id="__codelineno-105-4" name="__codelineno-105-4" href="#__codelineno-105-4"></a><span class="n">config</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="n">Path</span> <span class="o">|</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">]</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
4303
+ <a id="__codelineno-105-5" name="__codelineno-105-5" href="#__codelineno-105-5"></a><span class="n">inputs</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="n">Field</span><span class="p">(</span><span class="n">default_factory</span><span class="o">=</span><span class="nb">dict</span><span class="p">)</span>
4304
+ <a id="__codelineno-105-6" name="__codelineno-105-6" href="#__codelineno-105-6"></a><span class="n">outputs</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">]]</span> <span class="o">=</span> <span class="n">Field</span><span class="p">(</span><span class="n">default_factory</span><span class="o">=</span><span class="nb">dict</span><span class="p">)</span>
4305
+ <a id="__codelineno-105-7" name="__codelineno-105-7" href="#__codelineno-105-7"></a><span class="n">scatter</span><span class="p">:</span> <span class="n">ScatterSpec</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
4306
+ <a id="__codelineno-105-8" name="__codelineno-105-8" href="#__codelineno-105-8"></a><span class="n">depends_on</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="n">Field</span><span class="p">(</span><span class="n">default_factory</span><span class="o">=</span><span class="nb">list</span><span class="p">)</span>
4307
+ </code></pre></div>
4308
+ <h3 id="pipelinedefaults"><code>PipelineDefaults</code><a class="headerlink" href="#pipelinedefaults" title="Permanent link">&para;</a></h3>
4309
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-106-1" name="__codelineno-106-1" href="#__codelineno-106-1"></a><span class="k">class</span><span class="w"> </span><span class="nc">PipelineDefaults</span><span class="p">(</span><span class="n">BaseModel</span><span class="p">)</span>
4310
+ </code></pre></div>
4311
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-107-1" name="__codelineno-107-1" href="#__codelineno-107-1"></a>Defaults applied to tool stages.
4312
+ </code></pre></div>
4313
+ <p>Declared fields and enum values (inherited fields are documented on the base class):</p>
4314
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-108-1" name="__codelineno-108-1" href="#__codelineno-108-1"></a><span class="n">backend</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s1">'local'</span>
4315
+ <a id="__codelineno-108-2" name="__codelineno-108-2" href="#__codelineno-108-2"></a><span class="n">run_directory</span><span class="p">:</span> <span class="n">Path</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
4316
+ <a id="__codelineno-108-3" name="__codelineno-108-3" href="#__codelineno-108-3"></a><span class="n">registry_path</span><span class="p">:</span> <span class="n">Path</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
4317
+ <a id="__codelineno-108-4" name="__codelineno-108-4" href="#__codelineno-108-4"></a><span class="n">job_name</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
4318
+ <a id="__codelineno-108-5" name="__codelineno-108-5" href="#__codelineno-108-5"></a><span class="n">export_results</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span>
4319
+ </code></pre></div>
4320
+ <h3 id="scatterspec"><code>ScatterSpec</code><a class="headerlink" href="#scatterspec" title="Permanent link">&para;</a></h3>
4321
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-109-1" name="__codelineno-109-1" href="#__codelineno-109-1"></a><span class="k">class</span><span class="w"> </span><span class="nc">ScatterSpec</span><span class="p">(</span><span class="n">BaseModel</span><span class="p">)</span>
4322
+ </code></pre></div>
4323
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-110-1" name="__codelineno-110-1" href="#__codelineno-110-1"></a>Fan-out settings for a splittable stage.
4324
+ </code></pre></div>
4325
+ <p>Declared fields and enum values (inherited fields are documented on the base class):</p>
4326
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-111-1" name="__codelineno-111-1" href="#__codelineno-111-1"></a><span class="n">by</span><span class="p">:</span> <span class="nb">str</span>
4327
+ <a id="__codelineno-111-2" name="__codelineno-111-2" href="#__codelineno-111-2"></a><span class="n">chunks</span><span class="p">:</span> <span class="nb">int</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="n">Field</span><span class="p">(</span><span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">ge</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
4328
+ <a id="__codelineno-111-3" name="__codelineno-111-3" href="#__codelineno-111-3"></a><span class="n">chunk_size</span><span class="p">:</span> <span class="nb">int</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="n">Field</span><span class="p">(</span><span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">ge</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
4329
+ <a id="__codelineno-111-4" name="__codelineno-111-4" href="#__codelineno-111-4"></a><span class="n">strategy</span><span class="p">:</span> <span class="n">Literal</span><span class="p">[</span><span class="s1">'auto'</span><span class="p">,</span> <span class="s1">'sdf'</span><span class="p">,</span> <span class="s1">'csv'</span><span class="p">,</span> <span class="s1">'tsv'</span><span class="p">,</span> <span class="s1">'lines'</span><span class="p">]</span> <span class="o">=</span> <span class="s1">'auto'</span>
4330
+ </code></pre></div>
4331
+ <h3 id="load_pipeline_spec"><code>load_pipeline_spec</code><a class="headerlink" href="#load_pipeline_spec" title="Permanent link">&para;</a></h3>
4332
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-112-1" name="__codelineno-112-1" href="#__codelineno-112-1"></a><span class="k">def</span><span class="w"> </span><span class="nf">load_pipeline_spec</span><span class="p">(</span><span class="n">path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="n">Path</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">PipelineSpec</span>
4333
+ </code></pre></div>
4334
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-113-1" name="__codelineno-113-1" href="#__codelineno-113-1"></a>Load a pipeline spec from YAML or JSON.
4335
+ </code></pre></div>
4336
+ <h2 id="caddforgepipelineexecutor"><code>caddforge.pipeline.executor</code><a class="headerlink" href="#caddforgepipelineexecutor" title="Permanent link">&para;</a></h2>
4337
+ <h3 id="pipelineexecutionresult"><code>PipelineExecutionResult</code><a class="headerlink" href="#pipelineexecutionresult" title="Permanent link">&para;</a></h3>
4338
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-114-1" name="__codelineno-114-1" href="#__codelineno-114-1"></a><span class="k">class</span><span class="w"> </span><span class="nc">PipelineExecutionResult</span><span class="p">()</span>
4339
+ </code></pre></div>
4340
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-115-1" name="__codelineno-115-1" href="#__codelineno-115-1"></a>Summary returned after a pipeline run.
4341
+ </code></pre></div>
4342
+ <p>Declared fields and enum values (inherited fields are documented on the base class):</p>
4343
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-116-1" name="__codelineno-116-1" href="#__codelineno-116-1"></a><span class="n">pipeline_job</span><span class="p">:</span> <span class="n">Job</span>
4344
+ <a id="__codelineno-116-2" name="__codelineno-116-2" href="#__codelineno-116-2"></a><span class="n">stage_jobs</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">list</span><span class="p">[</span><span class="n">Job</span><span class="p">]]</span> <span class="o">=</span> <span class="n">field</span><span class="p">(</span><span class="n">default_factory</span><span class="o">=</span><span class="nb">dict</span><span class="p">)</span>
4345
+ <a id="__codelineno-116-3" name="__codelineno-116-3" href="#__codelineno-116-3"></a><span class="n">artifacts</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">ArtifactRef</span><span class="p">]</span> <span class="o">=</span> <span class="n">field</span><span class="p">(</span><span class="n">default_factory</span><span class="o">=</span><span class="nb">dict</span><span class="p">)</span>
4346
+ </code></pre></div>
4347
+ <h3 id="run_pipeline"><code>run_pipeline</code><a class="headerlink" href="#run_pipeline" title="Permanent link">&para;</a></h3>
4348
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-117-1" name="__codelineno-117-1" href="#__codelineno-117-1"></a><span class="k">def</span><span class="w"> </span><span class="nf">run_pipeline</span><span class="p">(</span><span class="n">path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="n">Path</span><span class="p">,</span> <span class="o">*</span><span class="p">,</span> <span class="n">emit</span><span class="p">:</span> <span class="n">EmitFn</span> <span class="o">|</span> <span class="kc">None</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">poll_interval_seconds</span><span class="p">:</span> <span class="nb">int</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span> <span class="n">wait_timeout_seconds</span><span class="p">:</span> <span class="nb">int</span> <span class="o">|</span> <span class="kc">None</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">backend_options</span><span class="p">:</span> <span class="n">BackendOptions</span> <span class="o">|</span> <span class="kc">None</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">PipelineExecutionResult</span>
4349
+ </code></pre></div>
4350
+ <div class="highlight"><pre><span></span><code><a id="__codelineno-118-1" name="__codelineno-118-1" href="#__codelineno-118-1"></a>Load and run a pipeline spec from disk.
4351
+ </code></pre></div>
4352
+
4353
+
4354
+
4355
+
4356
+
4357
+
4358
+
4359
+
4360
+
4361
+
4362
+
4363
+
4364
+
4365
+ </article>
4366
+ </div>
4367
+
4368
+
4369
+ <script>var target=document.getElementById(location.hash.slice(1));target&&target.name&&(target.checked=target.name.startsWith("__tabbed_"))</script>
4370
+ </div>
4371
+
4372
+ <button type="button" class="md-top md-icon" data-md-component="top" hidden>
4373
+
4374
+ <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M13 20h-2V8l-5.5 5.5-1.42-1.42L12 4.16l7.92 7.92-1.42 1.42L13 8z"/></svg>
4375
+ Back to top
4376
+ </button>
4377
+
4378
+ </main>
4379
+
4380
+ <footer class="md-footer">
4381
+
4382
+ <div class="md-footer-meta md-typeset">
4383
+ <div class="md-footer-meta__inner md-grid">
4384
+ <div class="md-copyright">
4385
+
4386
+
4387
+ Made with
4388
+ <a href="https://squidfunk.github.io/mkdocs-material/" target="_blank" rel="noopener">
4389
+ Material for MkDocs
4390
+ </a>
4391
+
4392
+ </div>
4393
+
4394
+ </div>
4395
+ </div>
4396
+ </footer>
4397
+
4398
+ </div>
4399
+ <div class="md-dialog" data-md-component="dialog">
4400
+ <div class="md-dialog__inner md-typeset"></div>
4401
+ </div>
4402
+
4403
+
4404
+
4405
+
4406
+
4407
+ <script id="__config" type="application/json">{"annotate": null, "base": "../..", "features": ["navigation.instant", "navigation.sections", "navigation.indexes", "navigation.top", "search.highlight", "search.suggest", "content.code.copy"], "search": "../../assets/javascripts/workers/search.2c215733.min.js", "tags": null, "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}, "version": null}</script>
4408
+
4409
+
4410
+ <script src="../../assets/javascripts/bundle.d7400e89.min.js"></script>
4411
+
4412
+
4413
+ </body>
4414
+ </html>