caddforge-docs 0.3.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- caddforge_docs/__init__.py +1 -0
- caddforge_docs/cli.py +20 -0
- caddforge_docs/server.py +124 -0
- caddforge_docs/site/404.html +2118 -0
- caddforge_docs/site/assets/_mkdocstrings.css +237 -0
- caddforge_docs/site/assets/images/favicon.png +0 -0
- caddforge_docs/site/assets/javascripts/bundle.d7400e89.min.js +16 -0
- caddforge_docs/site/assets/javascripts/bundle.d7400e89.min.js.map +7 -0
- caddforge_docs/site/assets/javascripts/workers/search.2c215733.min.js +42 -0
- caddforge_docs/site/assets/javascripts/workers/search.2c215733.min.js.map +7 -0
- caddforge_docs/site/assets/licenses/W3C-Software-and-Document-2015.txt +15 -0
- caddforge_docs/site/assets/licenses/autogrid-COPYING-GPL-2.txt +339 -0
- caddforge_docs/site/assets/licenses/autogrid-GCC-RUNTIME-COPYING-GPL-3.txt +674 -0
- caddforge_docs/site/assets/licenses/autogrid-GCC-RUNTIME-EXCEPTION.txt +73 -0
- caddforge_docs/site/assets/licenses/autogrid-GCC-RUNTIME-NOTICE.txt +24 -0
- caddforge_docs/site/assets/licenses/caddforge-opencosmors-COPYING.txt +674 -0
- caddforge_docs/site/assets/licenses/caddforge-opencosmors-LICENSE.txt +165 -0
- caddforge_docs/site/assets/licenses/caddforge-unidock-tools-LICENSE.txt +202 -0
- caddforge_docs/site/assets/licenses/clipboard-LICENSE.txt +19 -0
- caddforge_docs/site/assets/licenses/escape-html-LICENSE.txt +2 -0
- caddforge_docs/site/assets/licenses/focus-visible-LICENSE.txt +4 -0
- caddforge_docs/site/assets/licenses/fontawesome-LICENSE.txt +165 -0
- caddforge_docs/site/assets/licenses/fuzzaldrin-plus-LICENSE.txt +21 -0
- caddforge_docs/site/assets/licenses/lunr-LICENSE.txt +17 -0
- caddforge_docs/site/assets/licenses/material-LICENSE.txt +20 -0
- caddforge_docs/site/assets/licenses/material-design-color-LICENSE.txt +31 -0
- caddforge_docs/site/assets/licenses/material-shadows-LICENSE.txt +31 -0
- caddforge_docs/site/assets/licenses/mkdocs-material-LICENSE.txt +19 -0
- caddforge_docs/site/assets/licenses/mkdocs-material-extensions-LICENSE.txt +21 -0
- caddforge_docs/site/assets/licenses/mkdocs-section-index-LICENSE.txt +21 -0
- caddforge_docs/site/assets/licenses/mkdocstrings-LICENSE.txt +15 -0
- caddforge_docs/site/assets/licenses/mkdocstrings-python-LICENSE.txt +15 -0
- caddforge_docs/site/assets/licenses/octicons-LICENSE.txt +21 -0
- caddforge_docs/site/assets/licenses/preact-LICENSE.txt +19 -0
- caddforge_docs/site/assets/licenses/properdocs-LICENSE.txt +26 -0
- caddforge_docs/site/assets/licenses/pymdown-extensions-LICENSE.txt +113 -0
- caddforge_docs/site/assets/licenses/rxjs-LICENSE.txt +180 -0
- caddforge_docs/site/assets/licenses/simple-LICENSE.txt +30 -0
- caddforge_docs/site/assets/licenses/tiny-emitter-LICENSE.txt +19 -0
- caddforge_docs/site/assets/licenses/tslib-LICENSE.txt +12 -0
- caddforge_docs/site/assets/licenses/zeno-rocha-components-LICENSE.txt +22 -0
- caddforge_docs/site/assets/stylesheets/main.ec1eaa64.min.css +1 -0
- caddforge_docs/site/assets/stylesheets/main.ec1eaa64.min.css.map +1 -0
- caddforge_docs/site/assets/stylesheets/palette.ab4e12ef.min.css +1 -0
- caddforge_docs/site/assets/stylesheets/palette.ab4e12ef.min.css.map +1 -0
- caddforge_docs/site/core/cli/index.html +2446 -0
- caddforge_docs/site/core/concepts/index.html +2340 -0
- caddforge_docs/site/core/configuration/index.html +2300 -0
- caddforge_docs/site/core/index.html +2170 -0
- caddforge_docs/site/core/jobs-results/index.html +2315 -0
- caddforge_docs/site/core/plugins/index.html +2200 -0
- caddforge_docs/site/core/slurm/index.html +2562 -0
- caddforge_docs/site/development/ci-publishing/index.html +2345 -0
- caddforge_docs/site/development/contributing/index.html +2311 -0
- caddforge_docs/site/development/documentation/index.html +2380 -0
- caddforge_docs/site/development/index.html +2201 -0
- caddforge_docs/site/development/release-notes/index.html +2504 -0
- caddforge_docs/site/development/release-readiness/index.html +2333 -0
- caddforge_docs/site/development/security/index.html +2181 -0
- caddforge_docs/site/development/tool-authoring/index.html +2435 -0
- caddforge_docs/site/examples/index.html +2465 -0
- caddforge_docs/site/examples/manifest.json +158 -0
- caddforge_docs/site/examples/minimize/component_overrides.yaml +14 -0
- caddforge_docs/site/examples/minimize/ligand_only.yaml +13 -0
- caddforge_docs/site/examples/minimize/pipeline_docking.yaml +84 -0
- caddforge_docs/site/examples/minimize/pipeline_scatter.yaml +49 -0
- caddforge_docs/site/examples/minimize/pocket_free_shell_restrained.yaml +13 -0
- caddforge_docs/site/examples/minimize/pocket_restrained.yaml +13 -0
- caddforge_docs/site/examples/minimize/prepared_metal.yaml +14 -0
- caddforge_docs/site/examples/minimize/sidechains_free_backbone_fixed.yaml +13 -0
- caddforge_docs/site/examples/minimize/sidechains_free_backbone_restrained.yaml +13 -0
- caddforge_docs/site/examples/pipelines/descriptor-model-and-candidate-filter.yaml +44 -0
- caddforge_docs/site/examples/pipelines/dock-extract-and-minimize-poses.yaml +85 -0
- caddforge_docs/site/examples/pipelines/docking-screen-and-rescore.yaml +55 -0
- caddforge_docs/site/examples/pipelines/flexible-gnina-to-openbpmd-to-md-to-abfe.yaml +189 -0
- caddforge_docs/site/examples/pipelines/gnina-flexible-complex-artifacts.yaml +52 -0
- caddforge_docs/site/examples/pipelines/minimize-a-multi-pose-sdf.yaml +46 -0
- caddforge_docs/site/examples/pipelines/pose-level-md-selection.yaml +95 -0
- caddforge_docs/site/examples/pipelines/result-collection-and-diagnostics.yaml +55 -0
- caddforge_docs/site/examples/quickstart/diagnostics.yaml +8 -0
- caddforge_docs/site/examples/quickstart/index.html +2172 -0
- caddforge_docs/site/examples/quickstart/pipeline.yaml +23 -0
- caddforge_docs/site/examples/quickstart/run.py +18 -0
- caddforge_docs/site/examples/quickstart/run_pipeline.py +6 -0
- caddforge_docs/site/examples/quickstart/scores.csv +7 -0
- caddforge_docs/site/examples/quickstart/values.csv +31 -0
- caddforge_docs/site/examples/run_tool.py +40 -0
- caddforge_docs/site/examples/tools/datascience-csv-scatter.yaml +17 -0
- caddforge_docs/site/examples/tools/datascience-distribution-diagnostics.yaml +10 -0
- caddforge_docs/site/examples/tools/descriptors-ani-conformers.yaml +9 -0
- caddforge_docs/site/examples/tools/descriptors-ani-psa.yaml +9 -0
- caddforge_docs/site/examples/tools/descriptors-cluster-molecules.yaml +11 -0
- caddforge_docs/site/examples/tools/descriptors-phesa.yaml +7 -0
- caddforge_docs/site/examples/tools/docking-gnina.yaml +12 -0
- caddforge_docs/site/examples/tools/docking-idockya.yaml +8 -0
- caddforge_docs/site/examples/tools/docking-unidock.yaml +12 -0
- caddforge_docs/site/examples/tools/fep-openfe-abfe.yaml +53 -0
- caddforge_docs/site/examples/tools/fep-openfe-rbfe-septop.yaml +23 -0
- caddforge_docs/site/examples/tools/md-center-and-align.yaml +16 -0
- caddforge_docs/site/examples/tools/md-cluster-representative.yaml +16 -0
- caddforge_docs/site/examples/tools/md-extract-frames.yaml +17 -0
- caddforge_docs/site/examples/tools/md-fix-structure.yaml +20 -0
- caddforge_docs/site/examples/tools/md-grand.yaml +28 -0
- caddforge_docs/site/examples/tools/md-inducia.yaml +29 -0
- caddforge_docs/site/examples/tools/md-minimize.yaml +13 -0
- caddforge_docs/site/examples/tools/md-openbpmd.yaml +11 -0
- caddforge_docs/site/examples/tools/md-plain-md.yaml +28 -0
- caddforge_docs/site/examples/tools/ml-explore-classifier.yaml +5 -0
- caddforge_docs/site/examples/tools/ml-model-factory.yaml +32 -0
- caddforge_docs/site/examples/tools/ml-model-zoo.yaml +16 -0
- caddforge_docs/site/examples/tools/ml-pca.yaml +10 -0
- caddforge_docs/site/examples/tools/ml-simple-gp.yaml +17 -0
- caddforge_docs/site/examples/tools/qm-transfer-free-energy.yaml +11 -0
- caddforge_docs/site/explanation/references/index.html +2218 -0
- caddforge_docs/site/explanation/reproducibility/index.html +2306 -0
- caddforge_docs/site/explanation/third-party-notices/index.html +2599 -0
- caddforge_docs/site/getting-started/first-pipeline/index.html +2195 -0
- caddforge_docs/site/getting-started/first-workflow/index.html +2329 -0
- caddforge_docs/site/getting-started/index.html +2200 -0
- caddforge_docs/site/getting-started/installation/index.html +2541 -0
- caddforge_docs/site/gui/index.html +2267 -0
- caddforge_docs/site/gui/plugin-authoring/index.html +2280 -0
- caddforge_docs/site/gui/walkthrough/index.html +2181 -0
- caddforge_docs/site/how-to/jobs/index.html +2195 -0
- caddforge_docs/site/how-to/scatter/index.html +2193 -0
- caddforge_docs/site/how-to/troubleshooting/index.html +2429 -0
- caddforge_docs/site/index.html +2359 -0
- caddforge_docs/site/objects.inv +0 -0
- caddforge_docs/site/pipelines/artifacts/index.html +2314 -0
- caddforge_docs/site/pipelines/built-ins/index.html +2670 -0
- caddforge_docs/site/pipelines/examples/index.html +3186 -0
- caddforge_docs/site/pipelines/index.html +2164 -0
- caddforge_docs/site/pipelines/specification/index.html +2278 -0
- caddforge_docs/site/plugins/datascience/index.html +2405 -0
- caddforge_docs/site/plugins/descriptors/index.html +2609 -0
- caddforge_docs/site/plugins/docking/index.html +2480 -0
- caddforge_docs/site/plugins/fep/index.html +2508 -0
- caddforge_docs/site/plugins/index.html +2216 -0
- caddforge_docs/site/plugins/md/index.html +3795 -0
- caddforge_docs/site/plugins/ml/index.html +2815 -0
- caddforge_docs/site/plugins/qm/index.html +2309 -0
- caddforge_docs/site/plugins/version-matrix/index.html +2449 -0
- caddforge_docs/site/reference/api/index.html +4414 -0
- caddforge_docs/site/reference/index.html +2166 -0
- caddforge_docs/site/search/search_index.json +1 -0
- caddforge_docs/site/sitemap.xml +191 -0
- caddforge_docs/site/sitemap.xml.gz +0 -0
- caddforge_docs-0.3.0.dist-info/METADATA +158 -0
- caddforge_docs-0.3.0.dist-info/RECORD +152 -0
- caddforge_docs-0.3.0.dist-info/WHEEL +4 -0
- caddforge_docs-0.3.0.dist-info/entry_points.txt +2 -0
- caddforge_docs-0.3.0.dist-info/licenses/LICENSE +21 -0
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<li class="md-nav__item md-nav__item--section md-nav__item--nested">
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
|
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<label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="">
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How-to Guides
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<span class="md-nav__icon md-icon"></span>
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</label>
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<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
|
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<label class="md-nav__title" for="__nav_3">
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<span class="md-nav__icon md-icon"></span>
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How-to Guides
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</label>
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<ul class="md-nav__list" data-md-scrollfix>
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<li class="md-nav__item">
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<a href="../../how-to/jobs/" class="md-nav__link">
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<span class="md-ellipsis">
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Jobs and Results
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<li class="md-nav__item">
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<a href="../../how-to/scatter/" class="md-nav__link">
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<span class="md-ellipsis">
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|
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541
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Scatter and Reduce
|
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543
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</a>
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<li class="md-nav__item">
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<a href="../../how-to/troubleshooting/" class="md-nav__link">
|
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|
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566
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<span class="md-ellipsis">
|
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|
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568
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|
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569
|
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Troubleshooting
|
|
570
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|
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571
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|
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|
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573
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</span>
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|
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</a>
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|
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581
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|
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582
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|
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</ul>
|
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</nav>
|
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|
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<li class="md-nav__item md-nav__item--active md-nav__item--section md-nav__item--nested">
|
|
623
|
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|
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|
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|
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|
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|
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|
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
|
|
627
|
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|
|
628
|
+
|
|
629
|
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<div class="md-nav__link md-nav__container">
|
|
630
|
+
<a href="../" class="md-nav__link ">
|
|
631
|
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|
|
632
|
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|
|
633
|
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|
|
634
|
+
<span class="md-ellipsis">
|
|
635
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|
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636
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|
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637
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Core
|
|
638
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|
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639
|
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|
|
640
|
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|
|
641
|
+
</span>
|
|
642
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|
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643
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|
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644
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|
|
645
|
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</a>
|
|
646
|
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|
|
647
|
+
|
|
648
|
+
<label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
|
|
649
|
+
<span class="md-nav__icon md-icon"></span>
|
|
650
|
+
</label>
|
|
651
|
+
|
|
652
|
+
</div>
|
|
653
|
+
|
|
654
|
+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
|
|
655
|
+
<label class="md-nav__title" for="__nav_4">
|
|
656
|
+
<span class="md-nav__icon md-icon"></span>
|
|
657
|
+
|
|
658
|
+
|
|
659
|
+
Core
|
|
660
|
+
|
|
661
|
+
|
|
662
|
+
</label>
|
|
663
|
+
<ul class="md-nav__list" data-md-scrollfix>
|
|
664
|
+
|
|
665
|
+
|
|
666
|
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|
|
667
|
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|
|
668
|
+
|
|
669
|
+
|
|
670
|
+
|
|
671
|
+
<li class="md-nav__item">
|
|
672
|
+
<a href="../concepts/" class="md-nav__link">
|
|
673
|
+
|
|
674
|
+
|
|
675
|
+
|
|
676
|
+
<span class="md-ellipsis">
|
|
677
|
+
|
|
678
|
+
|
|
679
|
+
Concepts
|
|
680
|
+
|
|
681
|
+
|
|
682
|
+
|
|
683
|
+
</span>
|
|
684
|
+
|
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685
|
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|
|
686
|
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|
|
687
|
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</a>
|
|
688
|
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</li>
|
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689
|
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|
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691
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696
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697
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|
|
698
|
+
|
|
699
|
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<li class="md-nav__item">
|
|
700
|
+
<a href="../configuration/" class="md-nav__link">
|
|
701
|
+
|
|
702
|
+
|
|
703
|
+
|
|
704
|
+
<span class="md-ellipsis">
|
|
705
|
+
|
|
706
|
+
|
|
707
|
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Configuration
|
|
708
|
+
|
|
709
|
+
|
|
710
|
+
|
|
711
|
+
</span>
|
|
712
|
+
|
|
713
|
+
|
|
714
|
+
|
|
715
|
+
</a>
|
|
716
|
+
</li>
|
|
717
|
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|
|
718
|
+
|
|
719
|
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|
|
720
|
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|
|
721
|
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|
|
722
|
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|
|
723
|
+
|
|
724
|
+
|
|
725
|
+
|
|
726
|
+
|
|
727
|
+
<li class="md-nav__item">
|
|
728
|
+
<a href="../cli/" class="md-nav__link">
|
|
729
|
+
|
|
730
|
+
|
|
731
|
+
|
|
732
|
+
<span class="md-ellipsis">
|
|
733
|
+
|
|
734
|
+
|
|
735
|
+
CLI
|
|
736
|
+
|
|
737
|
+
|
|
738
|
+
|
|
739
|
+
</span>
|
|
740
|
+
|
|
741
|
+
|
|
742
|
+
|
|
743
|
+
</a>
|
|
744
|
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</li>
|
|
745
|
+
|
|
746
|
+
|
|
747
|
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|
|
748
|
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|
|
749
|
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|
|
750
|
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|
|
751
|
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|
|
752
|
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|
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753
|
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|
|
754
|
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|
|
755
|
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|
|
756
|
+
|
|
757
|
+
<li class="md-nav__item md-nav__item--active">
|
|
758
|
+
|
|
759
|
+
<input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
|
|
760
|
+
|
|
761
|
+
|
|
762
|
+
|
|
763
|
+
|
|
764
|
+
|
|
765
|
+
<label class="md-nav__link md-nav__link--active" for="__toc">
|
|
766
|
+
|
|
767
|
+
|
|
768
|
+
|
|
769
|
+
<span class="md-ellipsis">
|
|
770
|
+
|
|
771
|
+
|
|
772
|
+
Jobs and Results
|
|
773
|
+
|
|
774
|
+
|
|
775
|
+
|
|
776
|
+
</span>
|
|
777
|
+
|
|
778
|
+
|
|
779
|
+
|
|
780
|
+
<span class="md-nav__icon md-icon"></span>
|
|
781
|
+
</label>
|
|
782
|
+
|
|
783
|
+
<a href="./" class="md-nav__link md-nav__link--active">
|
|
784
|
+
|
|
785
|
+
|
|
786
|
+
|
|
787
|
+
<span class="md-ellipsis">
|
|
788
|
+
|
|
789
|
+
|
|
790
|
+
Jobs and Results
|
|
791
|
+
|
|
792
|
+
|
|
793
|
+
|
|
794
|
+
</span>
|
|
795
|
+
|
|
796
|
+
|
|
797
|
+
|
|
798
|
+
</a>
|
|
799
|
+
|
|
800
|
+
|
|
801
|
+
|
|
802
|
+
<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
|
|
803
|
+
|
|
804
|
+
|
|
805
|
+
|
|
806
|
+
|
|
807
|
+
|
|
808
|
+
|
|
809
|
+
<label class="md-nav__title" for="__toc">
|
|
810
|
+
<span class="md-nav__icon md-icon"></span>
|
|
811
|
+
Table of contents
|
|
812
|
+
</label>
|
|
813
|
+
<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
|
|
814
|
+
|
|
815
|
+
<li class="md-nav__item">
|
|
816
|
+
<a href="#metadata" class="md-nav__link">
|
|
817
|
+
<span class="md-ellipsis">
|
|
818
|
+
|
|
819
|
+
Metadata
|
|
820
|
+
|
|
821
|
+
</span>
|
|
822
|
+
</a>
|
|
823
|
+
|
|
824
|
+
</li>
|
|
825
|
+
|
|
826
|
+
<li class="md-nav__item">
|
|
827
|
+
<a href="#registry" class="md-nav__link">
|
|
828
|
+
<span class="md-ellipsis">
|
|
829
|
+
|
|
830
|
+
Registry
|
|
831
|
+
|
|
832
|
+
</span>
|
|
833
|
+
</a>
|
|
834
|
+
|
|
835
|
+
</li>
|
|
836
|
+
|
|
837
|
+
<li class="md-nav__item">
|
|
838
|
+
<a href="#loading-results" class="md-nav__link">
|
|
839
|
+
<span class="md-ellipsis">
|
|
840
|
+
|
|
841
|
+
Loading results
|
|
842
|
+
|
|
843
|
+
</span>
|
|
844
|
+
</a>
|
|
845
|
+
|
|
846
|
+
</li>
|
|
847
|
+
|
|
848
|
+
</ul>
|
|
849
|
+
|
|
850
|
+
</nav>
|
|
851
|
+
|
|
852
|
+
</li>
|
|
853
|
+
|
|
854
|
+
|
|
855
|
+
|
|
856
|
+
|
|
857
|
+
|
|
858
|
+
|
|
859
|
+
|
|
860
|
+
|
|
861
|
+
|
|
862
|
+
|
|
863
|
+
<li class="md-nav__item">
|
|
864
|
+
<a href="../slurm/" class="md-nav__link">
|
|
865
|
+
|
|
866
|
+
|
|
867
|
+
|
|
868
|
+
<span class="md-ellipsis">
|
|
869
|
+
|
|
870
|
+
|
|
871
|
+
Slurm Backend
|
|
872
|
+
|
|
873
|
+
|
|
874
|
+
|
|
875
|
+
</span>
|
|
876
|
+
|
|
877
|
+
|
|
878
|
+
|
|
879
|
+
</a>
|
|
880
|
+
</li>
|
|
881
|
+
|
|
882
|
+
|
|
883
|
+
|
|
884
|
+
|
|
885
|
+
|
|
886
|
+
|
|
887
|
+
|
|
888
|
+
|
|
889
|
+
|
|
890
|
+
|
|
891
|
+
<li class="md-nav__item">
|
|
892
|
+
<a href="../plugins/" class="md-nav__link">
|
|
893
|
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894
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895
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<span class="md-ellipsis">
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897
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898
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899
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Plugins
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900
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901
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902
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|
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903
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</span>
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906
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907
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</a>
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908
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</li>
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909
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910
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911
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912
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913
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</ul>
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914
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</nav>
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915
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<li class="md-nav__item md-nav__item--section md-nav__item--nested">
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948
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949
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950
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
|
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951
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+
|
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952
|
+
|
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953
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<div class="md-nav__link md-nav__container">
|
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954
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+
<a href="../../pipelines/" class="md-nav__link ">
|
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955
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+
|
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956
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957
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958
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<span class="md-ellipsis">
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959
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960
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961
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Pipelines
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962
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963
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964
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965
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966
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967
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968
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969
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</a>
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970
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971
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972
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<label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
|
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973
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+
<span class="md-nav__icon md-icon"></span>
|
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974
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</label>
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975
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976
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</div>
|
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977
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|
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978
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<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
|
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979
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+
<label class="md-nav__title" for="__nav_5">
|
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980
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<span class="md-nav__icon md-icon"></span>
|
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981
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+
|
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982
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|
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983
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Pipelines
|
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984
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|
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985
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|
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986
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+
</label>
|
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987
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<ul class="md-nav__list" data-md-scrollfix>
|
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988
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|
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989
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990
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991
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992
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993
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994
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995
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<li class="md-nav__item">
|
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996
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+
<a href="../../pipelines/specification/" class="md-nav__link">
|
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997
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+
|
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998
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|
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999
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|
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1000
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<span class="md-ellipsis">
|
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1001
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|
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1002
|
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|
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1003
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Specification
|
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1004
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1005
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1006
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|
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1007
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</span>
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1008
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1009
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1010
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1011
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</a>
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1012
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</li>
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1013
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1014
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1015
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1016
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1017
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1018
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1019
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1020
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1021
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1022
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|
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1023
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<li class="md-nav__item">
|
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1024
|
+
<a href="../../pipelines/artifacts/" class="md-nav__link">
|
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1025
|
+
|
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1026
|
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|
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1027
|
+
|
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1028
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<span class="md-ellipsis">
|
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1029
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+
|
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1030
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+
|
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1031
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+
Artifacts
|
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1032
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|
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1033
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1034
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|
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1035
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</span>
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1036
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1037
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|
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1038
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|
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1039
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</a>
|
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1040
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</li>
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1049
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1050
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|
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1051
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<li class="md-nav__item">
|
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1052
|
+
<a href="../../pipelines/built-ins/" class="md-nav__link">
|
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1053
|
+
|
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1054
|
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|
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1055
|
+
|
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1056
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+
<span class="md-ellipsis">
|
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1057
|
+
|
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1058
|
+
|
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1059
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+
Built-in Stages
|
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1060
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|
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1061
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|
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1062
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+
|
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1063
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</span>
|
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1064
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1065
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1066
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|
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1067
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</a>
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1068
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1069
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1071
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1078
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|
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1079
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<li class="md-nav__item">
|
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1080
|
+
<a href="../../pipelines/examples/" class="md-nav__link">
|
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1081
|
+
|
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1082
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+
|
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1083
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+
|
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1084
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+
<span class="md-ellipsis">
|
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1085
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+
|
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1086
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+
|
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1087
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+
Examples
|
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1088
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|
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1089
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|
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1090
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+
|
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1091
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</span>
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1092
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1093
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1094
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1095
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</a>
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1096
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</li>
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1097
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1098
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1099
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|
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1100
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+
|
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1101
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+
</ul>
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1102
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+
</nav>
|
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1103
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+
|
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1104
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+
</li>
|
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1105
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1106
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1107
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1108
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1109
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1110
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1111
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1112
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1113
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1120
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1123
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1124
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1125
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1126
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1127
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1128
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1129
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1130
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1132
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1140
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1141
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<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
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1144
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1145
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1146
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" >
|
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1147
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|
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1148
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|
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1149
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<div class="md-nav__link md-nav__container">
|
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1150
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<a href="../../plugins/" class="md-nav__link ">
|
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1151
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|
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1152
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1153
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1154
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<span class="md-ellipsis">
|
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1155
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|
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1156
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|
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1157
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Plugins
|
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1158
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|
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1159
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|
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1160
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1161
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1162
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1163
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1164
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1165
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</a>
|
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1166
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|
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1167
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|
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1168
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+
<label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
|
|
1169
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1170
|
+
</label>
|
|
1171
|
+
|
|
1172
|
+
</div>
|
|
1173
|
+
|
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1174
|
+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="false">
|
|
1175
|
+
<label class="md-nav__title" for="__nav_6">
|
|
1176
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1177
|
+
|
|
1178
|
+
|
|
1179
|
+
Plugins
|
|
1180
|
+
|
|
1181
|
+
|
|
1182
|
+
</label>
|
|
1183
|
+
<ul class="md-nav__list" data-md-scrollfix>
|
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1184
|
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|
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1185
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1186
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1187
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1189
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|
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1190
|
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|
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1191
|
+
<li class="md-nav__item">
|
|
1192
|
+
<a href="../../plugins/version-matrix/" class="md-nav__link">
|
|
1193
|
+
|
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1194
|
+
|
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1195
|
+
|
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1196
|
+
<span class="md-ellipsis">
|
|
1197
|
+
|
|
1198
|
+
|
|
1199
|
+
Version Matrix
|
|
1200
|
+
|
|
1201
|
+
|
|
1202
|
+
|
|
1203
|
+
</span>
|
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1204
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|
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1205
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|
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1206
|
+
|
|
1207
|
+
</a>
|
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1208
|
+
</li>
|
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1209
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|
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1210
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|
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1211
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1212
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1213
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1214
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1215
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|
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1217
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|
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1218
|
+
|
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1219
|
+
<li class="md-nav__item">
|
|
1220
|
+
<a href="../../plugins/docking/" class="md-nav__link">
|
|
1221
|
+
|
|
1222
|
+
|
|
1223
|
+
|
|
1224
|
+
<span class="md-ellipsis">
|
|
1225
|
+
|
|
1226
|
+
|
|
1227
|
+
Docking
|
|
1228
|
+
|
|
1229
|
+
|
|
1230
|
+
|
|
1231
|
+
</span>
|
|
1232
|
+
|
|
1233
|
+
|
|
1234
|
+
|
|
1235
|
+
</a>
|
|
1236
|
+
</li>
|
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1237
|
+
|
|
1238
|
+
|
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1239
|
+
|
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1240
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|
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1241
|
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1242
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1243
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1244
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|
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1245
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|
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1246
|
+
|
|
1247
|
+
<li class="md-nav__item">
|
|
1248
|
+
<a href="../../plugins/descriptors/" class="md-nav__link">
|
|
1249
|
+
|
|
1250
|
+
|
|
1251
|
+
|
|
1252
|
+
<span class="md-ellipsis">
|
|
1253
|
+
|
|
1254
|
+
|
|
1255
|
+
Descriptors
|
|
1256
|
+
|
|
1257
|
+
|
|
1258
|
+
|
|
1259
|
+
</span>
|
|
1260
|
+
|
|
1261
|
+
|
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1262
|
+
|
|
1263
|
+
</a>
|
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1264
|
+
</li>
|
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1265
|
+
|
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1266
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+
|
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1267
|
+
|
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1268
|
+
|
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1269
|
+
|
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1270
|
+
|
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1271
|
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|
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1272
|
+
|
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1273
|
+
|
|
1274
|
+
|
|
1275
|
+
<li class="md-nav__item">
|
|
1276
|
+
<a href="../../plugins/md/" class="md-nav__link">
|
|
1277
|
+
|
|
1278
|
+
|
|
1279
|
+
|
|
1280
|
+
<span class="md-ellipsis">
|
|
1281
|
+
|
|
1282
|
+
|
|
1283
|
+
MD
|
|
1284
|
+
|
|
1285
|
+
|
|
1286
|
+
|
|
1287
|
+
</span>
|
|
1288
|
+
|
|
1289
|
+
|
|
1290
|
+
|
|
1291
|
+
</a>
|
|
1292
|
+
</li>
|
|
1293
|
+
|
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1294
|
+
|
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1295
|
+
|
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1296
|
+
|
|
1297
|
+
|
|
1298
|
+
|
|
1299
|
+
|
|
1300
|
+
|
|
1301
|
+
|
|
1302
|
+
|
|
1303
|
+
<li class="md-nav__item">
|
|
1304
|
+
<a href="../../plugins/fep/" class="md-nav__link">
|
|
1305
|
+
|
|
1306
|
+
|
|
1307
|
+
|
|
1308
|
+
<span class="md-ellipsis">
|
|
1309
|
+
|
|
1310
|
+
|
|
1311
|
+
FEP
|
|
1312
|
+
|
|
1313
|
+
|
|
1314
|
+
|
|
1315
|
+
</span>
|
|
1316
|
+
|
|
1317
|
+
|
|
1318
|
+
|
|
1319
|
+
</a>
|
|
1320
|
+
</li>
|
|
1321
|
+
|
|
1322
|
+
|
|
1323
|
+
|
|
1324
|
+
|
|
1325
|
+
|
|
1326
|
+
|
|
1327
|
+
|
|
1328
|
+
|
|
1329
|
+
|
|
1330
|
+
|
|
1331
|
+
<li class="md-nav__item">
|
|
1332
|
+
<a href="../../plugins/qm/" class="md-nav__link">
|
|
1333
|
+
|
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Plugin GUI Authoring
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<label class="md-nav__title" for="__nav_8">
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Reference
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Public Python API
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Example Library
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|
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<span class="md-ellipsis">
|
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1681
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Example Data Provenance
|
|
1682
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1683
|
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|
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1684
|
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|
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1685
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|
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|
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1729
|
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|
+
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_9" >
|
|
1731
|
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|
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1732
|
+
|
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1733
|
+
<label class="md-nav__link" for="__nav_9" id="__nav_9_label" tabindex="">
|
|
1734
|
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|
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1735
|
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|
|
1736
|
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|
|
1737
|
+
<span class="md-ellipsis">
|
|
1738
|
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|
|
1739
|
+
|
|
1740
|
+
Explanation
|
|
1741
|
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|
|
1742
|
+
|
|
1743
|
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|
|
1744
|
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</span>
|
|
1745
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|
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1746
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|
|
1747
|
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|
|
1748
|
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<span class="md-nav__icon md-icon"></span>
|
|
1749
|
+
</label>
|
|
1750
|
+
|
|
1751
|
+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_9_label" aria-expanded="false">
|
|
1752
|
+
<label class="md-nav__title" for="__nav_9">
|
|
1753
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1754
|
+
|
|
1755
|
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|
|
1756
|
+
Explanation
|
|
1757
|
+
|
|
1758
|
+
|
|
1759
|
+
</label>
|
|
1760
|
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<ul class="md-nav__list" data-md-scrollfix>
|
|
1761
|
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|
|
1762
|
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|
|
1763
|
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|
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1764
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1765
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Release Readiness
|
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|
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2106
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<span class="md-ellipsis">
|
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2108
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|
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2109
|
+
|
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2110
|
+
CI and Publishing
|
|
2111
|
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|
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2112
|
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2113
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+
|
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2114
|
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2118
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|
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2119
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|
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2120
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2121
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2122
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2123
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2124
|
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|
|
2125
|
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</nav>
|
|
2126
|
+
|
|
2127
|
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|
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2130
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2131
|
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</ul>
|
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2132
|
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</nav>
|
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|
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|
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2135
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</div>
|
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|
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+
|
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2138
|
+
|
|
2139
|
+
<div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
|
|
2140
|
+
<div class="md-sidebar__scrollwrap">
|
|
2141
|
+
<div class="md-sidebar__inner">
|
|
2142
|
+
|
|
2143
|
+
|
|
2144
|
+
<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
|
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2145
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+
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2146
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2147
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2148
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<label class="md-nav__title" for="__toc">
|
|
2152
|
+
<span class="md-nav__icon md-icon"></span>
|
|
2153
|
+
Table of contents
|
|
2154
|
+
</label>
|
|
2155
|
+
<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
|
|
2156
|
+
|
|
2157
|
+
<li class="md-nav__item">
|
|
2158
|
+
<a href="#metadata" class="md-nav__link">
|
|
2159
|
+
<span class="md-ellipsis">
|
|
2160
|
+
|
|
2161
|
+
Metadata
|
|
2162
|
+
|
|
2163
|
+
</span>
|
|
2164
|
+
</a>
|
|
2165
|
+
|
|
2166
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|
|
2167
|
+
|
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2168
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<li class="md-nav__item">
|
|
2169
|
+
<a href="#registry" class="md-nav__link">
|
|
2170
|
+
<span class="md-ellipsis">
|
|
2171
|
+
|
|
2172
|
+
Registry
|
|
2173
|
+
|
|
2174
|
+
</span>
|
|
2175
|
+
</a>
|
|
2176
|
+
|
|
2177
|
+
</li>
|
|
2178
|
+
|
|
2179
|
+
<li class="md-nav__item">
|
|
2180
|
+
<a href="#loading-results" class="md-nav__link">
|
|
2181
|
+
<span class="md-ellipsis">
|
|
2182
|
+
|
|
2183
|
+
Loading results
|
|
2184
|
+
|
|
2185
|
+
</span>
|
|
2186
|
+
</a>
|
|
2187
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+
|
|
2188
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+
</li>
|
|
2189
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+
|
|
2190
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+
</ul>
|
|
2191
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+
|
|
2192
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</nav>
|
|
2193
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+
</div>
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|
2194
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</div>
|
|
2195
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</div>
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|
2196
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|
|
2197
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|
|
2198
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+
|
|
2199
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+
<div class="md-content" data-md-component="content">
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<article class="md-content__inner md-typeset">
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<h1 id="jobs-and-results">Jobs and Results<a class="headerlink" href="#jobs-and-results" title="Permanent link">¶</a></h1>
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<p>CADDForge writes each workflow execution into a standardized run directory.</p>
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<p>Example layout:</p>
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<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>runs/
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<a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a> 2026-05-05/
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<a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a> <job-id>/
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<a id="__codelineno-0-4" name="__codelineno-0-4" href="#__codelineno-0-4"></a> config.json
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<a id="__codelineno-0-5" name="__codelineno-0-5" href="#__codelineno-0-5"></a> config.yaml # optional tool-specific copy
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<a id="__codelineno-0-6" name="__codelineno-0-6" href="#__codelineno-0-6"></a> metadata.json
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<a id="__codelineno-0-7" name="__codelineno-0-7" href="#__codelineno-0-7"></a> stdout.log
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<a id="__codelineno-0-8" name="__codelineno-0-8" href="#__codelineno-0-8"></a> stderr.log
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<a id="__codelineno-0-9" name="__codelineno-0-9" href="#__codelineno-0-9"></a> results/
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<a id="__codelineno-0-10" name="__codelineno-0-10" href="#__codelineno-0-10"></a> results.json
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<a id="__codelineno-0-11" name="__codelineno-0-11" href="#__codelineno-0-11"></a> result_record.json
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<a id="__codelineno-0-12" name="__codelineno-0-12" href="#__codelineno-0-12"></a> tool_specific/
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</code></pre></div>
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<h2 id="metadata">Metadata<a class="headerlink" href="#metadata" title="Permanent link">¶</a></h2>
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<p>Core saves <code>config.json</code> as the canonical restart configuration. A tool may also
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write a YAML copy; preserve the original submitted YAML alongside the run for
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provenance.</p>
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<p><code>metadata.json</code> should capture job identity, tool name, user, timestamps, backend, versions, and key
|
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runtime parameters when available.</p>
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<h2 id="registry">Registry<a class="headerlink" href="#registry" title="Permanent link">¶</a></h2>
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<p>The job registry maps job IDs to status and paths. CLI commands such as <code>status</code> and <code>logs</code> should
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use the shared registry helpers rather than plugin-specific lookup code.</p>
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<p>Registry access is serialized with a filesystem lock so controller-side updates remain consistent
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under multiprocess fan-out and shared filesystems. Slurm worker payloads do not write to the shared
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registry; status refresh reconciles scheduler state with the job-local metadata and canonical result
|
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records. A completed scientific result is therefore not overwritten by a conflicting terminal
|
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scheduler state.</p>
|
|
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<p>Composite and repeat workflows may record parent-child relationships. Repeat parents are refreshed
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|
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through their children and publish <code>replicas_manifest.json</code> plus aggregate completion metrics once
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all children become terminal.</p>
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<h2 id="loading-results">Loading results<a class="headerlink" href="#loading-results" title="Permanent link">¶</a></h2>
|
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<p>Use the core execution helpers to load canonical results:</p>
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|
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<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a><span class="kn">from</span><span class="w"> </span><span class="nn">caddforge.core.execution</span><span class="w"> </span><span class="kn">import</span> <span class="n">load_result_for_job</span>
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<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>
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<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a><span class="n">result</span> <span class="o">=</span> <span class="n">load_result_for_job</span><span class="p">(</span><span class="n">job</span><span class="p">)</span>
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</code></pre></div>
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<p>Tool-specific summaries may exist. <code>result_record.json</code> takes precedence when
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present; the loader also accepts a canonical <code>results.json</code> from older or simpler
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workflows. Use <code>load_result_for_job</code> to select the record instead of loading a
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tool-specific summary as though it were a CADDForge result.</p>
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</article>
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<button type="button" class="md-top md-icon" data-md-component="top" hidden>
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</main>
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