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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<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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<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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How-to Guides
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</label>
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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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Scatter and Reduce
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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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<span class="md-ellipsis">
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Troubleshooting
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</nav>
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<li class="md-nav__item md-nav__item--active md-nav__item--section md-nav__item--nested">
|
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
|
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|
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628
|
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|
|
629
|
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<div class="md-nav__link md-nav__container">
|
|
630
|
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<a href="../" class="md-nav__link ">
|
|
631
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|
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632
|
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|
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<span class="md-ellipsis">
|
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Core
|
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|
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|
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640
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|
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</span>
|
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644
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</a>
|
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646
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|
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647
|
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|
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648
|
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<label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
|
|
649
|
+
<span class="md-nav__icon md-icon"></span>
|
|
650
|
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</label>
|
|
651
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|
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652
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</div>
|
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653
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|
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654
|
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<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
|
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|
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658
|
+
|
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659
|
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Core
|
|
660
|
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|
|
661
|
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|
|
662
|
+
</label>
|
|
663
|
+
<ul class="md-nav__list" data-md-scrollfix>
|
|
664
|
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|
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665
|
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|
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666
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|
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669
|
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|
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670
|
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671
|
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<li class="md-nav__item">
|
|
672
|
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<a href="../concepts/" class="md-nav__link">
|
|
673
|
+
|
|
674
|
+
|
|
675
|
+
|
|
676
|
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<span class="md-ellipsis">
|
|
677
|
+
|
|
678
|
+
|
|
679
|
+
Concepts
|
|
680
|
+
|
|
681
|
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|
|
682
|
+
|
|
683
|
+
</span>
|
|
684
|
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|
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685
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686
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|
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687
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</a>
|
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688
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</li>
|
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689
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|
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698
|
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|
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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
|
+
|
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707
|
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Configuration
|
|
708
|
+
|
|
709
|
+
|
|
710
|
+
|
|
711
|
+
</span>
|
|
712
|
+
|
|
713
|
+
|
|
714
|
+
|
|
715
|
+
</a>
|
|
716
|
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</li>
|
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717
|
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|
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718
|
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|
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719
|
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|
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720
|
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|
|
721
|
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722
|
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|
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723
|
+
|
|
724
|
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|
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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
|
+
|
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746
|
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|
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747
|
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|
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748
|
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|
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749
|
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|
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750
|
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|
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751
|
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|
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752
|
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|
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753
|
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|
|
754
|
+
|
|
755
|
+
<li class="md-nav__item">
|
|
756
|
+
<a href="../jobs-results/" class="md-nav__link">
|
|
757
|
+
|
|
758
|
+
|
|
759
|
+
|
|
760
|
+
<span class="md-ellipsis">
|
|
761
|
+
|
|
762
|
+
|
|
763
|
+
Jobs and Results
|
|
764
|
+
|
|
765
|
+
|
|
766
|
+
|
|
767
|
+
</span>
|
|
768
|
+
|
|
769
|
+
|
|
770
|
+
|
|
771
|
+
</a>
|
|
772
|
+
</li>
|
|
773
|
+
|
|
774
|
+
|
|
775
|
+
|
|
776
|
+
|
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777
|
+
|
|
778
|
+
|
|
779
|
+
|
|
780
|
+
|
|
781
|
+
|
|
782
|
+
|
|
783
|
+
|
|
784
|
+
|
|
785
|
+
<li class="md-nav__item md-nav__item--active">
|
|
786
|
+
|
|
787
|
+
<input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
|
|
788
|
+
|
|
789
|
+
|
|
790
|
+
|
|
791
|
+
|
|
792
|
+
|
|
793
|
+
<label class="md-nav__link md-nav__link--active" for="__toc">
|
|
794
|
+
|
|
795
|
+
|
|
796
|
+
|
|
797
|
+
<span class="md-ellipsis">
|
|
798
|
+
|
|
799
|
+
|
|
800
|
+
Slurm Backend
|
|
801
|
+
|
|
802
|
+
|
|
803
|
+
|
|
804
|
+
</span>
|
|
805
|
+
|
|
806
|
+
|
|
807
|
+
|
|
808
|
+
<span class="md-nav__icon md-icon"></span>
|
|
809
|
+
</label>
|
|
810
|
+
|
|
811
|
+
<a href="./" class="md-nav__link md-nav__link--active">
|
|
812
|
+
|
|
813
|
+
|
|
814
|
+
|
|
815
|
+
<span class="md-ellipsis">
|
|
816
|
+
|
|
817
|
+
|
|
818
|
+
Slurm Backend
|
|
819
|
+
|
|
820
|
+
|
|
821
|
+
|
|
822
|
+
</span>
|
|
823
|
+
|
|
824
|
+
|
|
825
|
+
|
|
826
|
+
</a>
|
|
827
|
+
|
|
828
|
+
|
|
829
|
+
|
|
830
|
+
<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
|
|
831
|
+
|
|
832
|
+
|
|
833
|
+
|
|
834
|
+
|
|
835
|
+
|
|
836
|
+
|
|
837
|
+
<label class="md-nav__title" for="__toc">
|
|
838
|
+
<span class="md-nav__icon md-icon"></span>
|
|
839
|
+
Table of contents
|
|
840
|
+
</label>
|
|
841
|
+
<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
|
|
842
|
+
|
|
843
|
+
<li class="md-nav__item">
|
|
844
|
+
<a href="#basic-usage" class="md-nav__link">
|
|
845
|
+
<span class="md-ellipsis">
|
|
846
|
+
|
|
847
|
+
Basic Usage
|
|
848
|
+
|
|
849
|
+
</span>
|
|
850
|
+
</a>
|
|
851
|
+
|
|
852
|
+
</li>
|
|
853
|
+
|
|
854
|
+
<li class="md-nav__item">
|
|
855
|
+
<a href="#environment-requirement" class="md-nav__link">
|
|
856
|
+
<span class="md-ellipsis">
|
|
857
|
+
|
|
858
|
+
Environment Requirement
|
|
859
|
+
|
|
860
|
+
</span>
|
|
861
|
+
</a>
|
|
862
|
+
|
|
863
|
+
</li>
|
|
864
|
+
|
|
865
|
+
<li class="md-nav__item">
|
|
866
|
+
<a href="#option-a-packed-condamicromamba-environment" class="md-nav__link">
|
|
867
|
+
<span class="md-ellipsis">
|
|
868
|
+
|
|
869
|
+
Option A: Packed Conda/Micromamba Environment
|
|
870
|
+
|
|
871
|
+
</span>
|
|
872
|
+
</a>
|
|
873
|
+
|
|
874
|
+
<nav class="md-nav" aria-label="Option A: Packed Conda/Micromamba Environment">
|
|
875
|
+
<ul class="md-nav__list">
|
|
876
|
+
|
|
877
|
+
<li class="md-nav__item">
|
|
878
|
+
<a href="#sidecar-and-fallback-behavior" class="md-nav__link">
|
|
879
|
+
<span class="md-ellipsis">
|
|
880
|
+
|
|
881
|
+
Sidecar and fallback behavior
|
|
882
|
+
|
|
883
|
+
</span>
|
|
884
|
+
</a>
|
|
885
|
+
|
|
886
|
+
</li>
|
|
887
|
+
|
|
888
|
+
<li class="md-nav__item">
|
|
889
|
+
<a href="#node-local-cache" class="md-nav__link">
|
|
890
|
+
<span class="md-ellipsis">
|
|
891
|
+
|
|
892
|
+
Node-local cache
|
|
893
|
+
|
|
894
|
+
</span>
|
|
895
|
+
</a>
|
|
896
|
+
|
|
897
|
+
</li>
|
|
898
|
+
|
|
899
|
+
<li class="md-nav__item">
|
|
900
|
+
<a href="#replacing-a-managed-pack" class="md-nav__link">
|
|
901
|
+
<span class="md-ellipsis">
|
|
902
|
+
|
|
903
|
+
Replacing a managed pack
|
|
904
|
+
|
|
905
|
+
</span>
|
|
906
|
+
</a>
|
|
907
|
+
|
|
908
|
+
</li>
|
|
909
|
+
|
|
910
|
+
</ul>
|
|
911
|
+
</nav>
|
|
912
|
+
|
|
913
|
+
</li>
|
|
914
|
+
|
|
915
|
+
<li class="md-nav__item">
|
|
916
|
+
<a href="#option-b-wheelhouse-and-per-job-virtualenv" class="md-nav__link">
|
|
917
|
+
<span class="md-ellipsis">
|
|
918
|
+
|
|
919
|
+
Option B: Wheelhouse and Per-Job Virtualenv
|
|
920
|
+
|
|
921
|
+
</span>
|
|
922
|
+
</a>
|
|
923
|
+
|
|
924
|
+
</li>
|
|
925
|
+
|
|
926
|
+
<li class="md-nav__item">
|
|
927
|
+
<a href="#option-c-site-specific-setup-commands" class="md-nav__link">
|
|
928
|
+
<span class="md-ellipsis">
|
|
929
|
+
|
|
930
|
+
Option C: Site-Specific Setup Commands
|
|
931
|
+
|
|
932
|
+
</span>
|
|
933
|
+
</a>
|
|
934
|
+
|
|
935
|
+
</li>
|
|
936
|
+
|
|
937
|
+
<li class="md-nav__item">
|
|
938
|
+
<a href="#practical-rules" class="md-nav__link">
|
|
939
|
+
<span class="md-ellipsis">
|
|
940
|
+
|
|
941
|
+
Practical Rules
|
|
942
|
+
|
|
943
|
+
</span>
|
|
944
|
+
</a>
|
|
945
|
+
|
|
946
|
+
</li>
|
|
947
|
+
|
|
948
|
+
</ul>
|
|
949
|
+
|
|
950
|
+
</nav>
|
|
951
|
+
|
|
952
|
+
</li>
|
|
953
|
+
|
|
954
|
+
|
|
955
|
+
|
|
956
|
+
|
|
957
|
+
|
|
958
|
+
|
|
959
|
+
|
|
960
|
+
|
|
961
|
+
|
|
962
|
+
|
|
963
|
+
<li class="md-nav__item">
|
|
964
|
+
<a href="../plugins/" class="md-nav__link">
|
|
965
|
+
|
|
966
|
+
|
|
967
|
+
|
|
968
|
+
<span class="md-ellipsis">
|
|
969
|
+
|
|
970
|
+
|
|
971
|
+
Plugins
|
|
972
|
+
|
|
973
|
+
|
|
974
|
+
|
|
975
|
+
</span>
|
|
976
|
+
|
|
977
|
+
|
|
978
|
+
|
|
979
|
+
</a>
|
|
980
|
+
</li>
|
|
981
|
+
|
|
982
|
+
|
|
983
|
+
|
|
984
|
+
|
|
985
|
+
</ul>
|
|
986
|
+
</nav>
|
|
987
|
+
|
|
988
|
+
</li>
|
|
989
|
+
|
|
990
|
+
|
|
991
|
+
|
|
992
|
+
|
|
993
|
+
|
|
994
|
+
|
|
995
|
+
|
|
996
|
+
|
|
997
|
+
|
|
998
|
+
|
|
999
|
+
|
|
1000
|
+
|
|
1001
|
+
|
|
1002
|
+
|
|
1003
|
+
|
|
1004
|
+
|
|
1005
|
+
|
|
1006
|
+
|
|
1007
|
+
|
|
1008
|
+
|
|
1009
|
+
|
|
1010
|
+
|
|
1011
|
+
|
|
1012
|
+
|
|
1013
|
+
|
|
1014
|
+
|
|
1015
|
+
|
|
1016
|
+
|
|
1017
|
+
|
|
1018
|
+
<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
|
1019
|
+
|
|
1020
|
+
|
|
1021
|
+
|
|
1022
|
+
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
|
|
1023
|
+
|
|
1024
|
+
|
|
1025
|
+
<div class="md-nav__link md-nav__container">
|
|
1026
|
+
<a href="../../pipelines/" class="md-nav__link ">
|
|
1027
|
+
|
|
1028
|
+
|
|
1029
|
+
|
|
1030
|
+
<span class="md-ellipsis">
|
|
1031
|
+
|
|
1032
|
+
|
|
1033
|
+
Pipelines
|
|
1034
|
+
|
|
1035
|
+
|
|
1036
|
+
|
|
1037
|
+
</span>
|
|
1038
|
+
|
|
1039
|
+
|
|
1040
|
+
|
|
1041
|
+
</a>
|
|
1042
|
+
|
|
1043
|
+
|
|
1044
|
+
<label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
|
|
1045
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1046
|
+
</label>
|
|
1047
|
+
|
|
1048
|
+
</div>
|
|
1049
|
+
|
|
1050
|
+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
|
|
1051
|
+
<label class="md-nav__title" for="__nav_5">
|
|
1052
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1053
|
+
|
|
1054
|
+
|
|
1055
|
+
Pipelines
|
|
1056
|
+
|
|
1057
|
+
|
|
1058
|
+
</label>
|
|
1059
|
+
<ul class="md-nav__list" data-md-scrollfix>
|
|
1060
|
+
|
|
1061
|
+
|
|
1062
|
+
|
|
1063
|
+
|
|
1064
|
+
|
|
1065
|
+
|
|
1066
|
+
|
|
1067
|
+
<li class="md-nav__item">
|
|
1068
|
+
<a href="../../pipelines/specification/" class="md-nav__link">
|
|
1069
|
+
|
|
1070
|
+
|
|
1071
|
+
|
|
1072
|
+
<span class="md-ellipsis">
|
|
1073
|
+
|
|
1074
|
+
|
|
1075
|
+
Specification
|
|
1076
|
+
|
|
1077
|
+
|
|
1078
|
+
|
|
1079
|
+
</span>
|
|
1080
|
+
|
|
1081
|
+
|
|
1082
|
+
|
|
1083
|
+
</a>
|
|
1084
|
+
</li>
|
|
1085
|
+
|
|
1086
|
+
|
|
1087
|
+
|
|
1088
|
+
|
|
1089
|
+
|
|
1090
|
+
|
|
1091
|
+
|
|
1092
|
+
|
|
1093
|
+
|
|
1094
|
+
|
|
1095
|
+
<li class="md-nav__item">
|
|
1096
|
+
<a href="../../pipelines/artifacts/" class="md-nav__link">
|
|
1097
|
+
|
|
1098
|
+
|
|
1099
|
+
|
|
1100
|
+
<span class="md-ellipsis">
|
|
1101
|
+
|
|
1102
|
+
|
|
1103
|
+
Artifacts
|
|
1104
|
+
|
|
1105
|
+
|
|
1106
|
+
|
|
1107
|
+
</span>
|
|
1108
|
+
|
|
1109
|
+
|
|
1110
|
+
|
|
1111
|
+
</a>
|
|
1112
|
+
</li>
|
|
1113
|
+
|
|
1114
|
+
|
|
1115
|
+
|
|
1116
|
+
|
|
1117
|
+
|
|
1118
|
+
|
|
1119
|
+
|
|
1120
|
+
|
|
1121
|
+
|
|
1122
|
+
|
|
1123
|
+
<li class="md-nav__item">
|
|
1124
|
+
<a href="../../pipelines/built-ins/" class="md-nav__link">
|
|
1125
|
+
|
|
1126
|
+
|
|
1127
|
+
|
|
1128
|
+
<span class="md-ellipsis">
|
|
1129
|
+
|
|
1130
|
+
|
|
1131
|
+
Built-in Stages
|
|
1132
|
+
|
|
1133
|
+
|
|
1134
|
+
|
|
1135
|
+
</span>
|
|
1136
|
+
|
|
1137
|
+
|
|
1138
|
+
|
|
1139
|
+
</a>
|
|
1140
|
+
</li>
|
|
1141
|
+
|
|
1142
|
+
|
|
1143
|
+
|
|
1144
|
+
|
|
1145
|
+
|
|
1146
|
+
|
|
1147
|
+
|
|
1148
|
+
|
|
1149
|
+
|
|
1150
|
+
|
|
1151
|
+
<li class="md-nav__item">
|
|
1152
|
+
<a href="../../pipelines/examples/" class="md-nav__link">
|
|
1153
|
+
|
|
1154
|
+
|
|
1155
|
+
|
|
1156
|
+
<span class="md-ellipsis">
|
|
1157
|
+
|
|
1158
|
+
|
|
1159
|
+
Examples
|
|
1160
|
+
|
|
1161
|
+
|
|
1162
|
+
|
|
1163
|
+
</span>
|
|
1164
|
+
|
|
1165
|
+
|
|
1166
|
+
|
|
1167
|
+
</a>
|
|
1168
|
+
</li>
|
|
1169
|
+
|
|
1170
|
+
|
|
1171
|
+
|
|
1172
|
+
|
|
1173
|
+
</ul>
|
|
1174
|
+
</nav>
|
|
1175
|
+
|
|
1176
|
+
</li>
|
|
1177
|
+
|
|
1178
|
+
|
|
1179
|
+
|
|
1180
|
+
|
|
1181
|
+
|
|
1182
|
+
|
|
1183
|
+
|
|
1184
|
+
|
|
1185
|
+
|
|
1186
|
+
|
|
1187
|
+
|
|
1188
|
+
|
|
1189
|
+
|
|
1190
|
+
|
|
1191
|
+
|
|
1192
|
+
|
|
1193
|
+
|
|
1194
|
+
|
|
1195
|
+
|
|
1196
|
+
|
|
1197
|
+
|
|
1198
|
+
|
|
1199
|
+
|
|
1200
|
+
|
|
1201
|
+
|
|
1202
|
+
|
|
1203
|
+
|
|
1204
|
+
|
|
1205
|
+
|
|
1206
|
+
|
|
1207
|
+
|
|
1208
|
+
|
|
1209
|
+
|
|
1210
|
+
|
|
1211
|
+
|
|
1212
|
+
|
|
1213
|
+
|
|
1214
|
+
<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
|
1215
|
+
|
|
1216
|
+
|
|
1217
|
+
|
|
1218
|
+
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" >
|
|
1219
|
+
|
|
1220
|
+
|
|
1221
|
+
<div class="md-nav__link md-nav__container">
|
|
1222
|
+
<a href="../../plugins/" class="md-nav__link ">
|
|
1223
|
+
|
|
1224
|
+
|
|
1225
|
+
|
|
1226
|
+
<span class="md-ellipsis">
|
|
1227
|
+
|
|
1228
|
+
|
|
1229
|
+
Plugins
|
|
1230
|
+
|
|
1231
|
+
|
|
1232
|
+
|
|
1233
|
+
</span>
|
|
1234
|
+
|
|
1235
|
+
|
|
1236
|
+
|
|
1237
|
+
</a>
|
|
1238
|
+
|
|
1239
|
+
|
|
1240
|
+
<label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
|
|
1241
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1242
|
+
</label>
|
|
1243
|
+
|
|
1244
|
+
</div>
|
|
1245
|
+
|
|
1246
|
+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="false">
|
|
1247
|
+
<label class="md-nav__title" for="__nav_6">
|
|
1248
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1249
|
+
|
|
1250
|
+
|
|
1251
|
+
Plugins
|
|
1252
|
+
|
|
1253
|
+
|
|
1254
|
+
</label>
|
|
1255
|
+
<ul class="md-nav__list" data-md-scrollfix>
|
|
1256
|
+
|
|
1257
|
+
|
|
1258
|
+
|
|
1259
|
+
|
|
1260
|
+
|
|
1261
|
+
|
|
1262
|
+
|
|
1263
|
+
<li class="md-nav__item">
|
|
1264
|
+
<a href="../../plugins/version-matrix/" class="md-nav__link">
|
|
1265
|
+
|
|
1266
|
+
|
|
1267
|
+
|
|
1268
|
+
<span class="md-ellipsis">
|
|
1269
|
+
|
|
1270
|
+
|
|
1271
|
+
Version Matrix
|
|
1272
|
+
|
|
1273
|
+
|
|
1274
|
+
|
|
1275
|
+
</span>
|
|
1276
|
+
|
|
1277
|
+
|
|
1278
|
+
|
|
1279
|
+
</a>
|
|
1280
|
+
</li>
|
|
1281
|
+
|
|
1282
|
+
|
|
1283
|
+
|
|
1284
|
+
|
|
1285
|
+
|
|
1286
|
+
|
|
1287
|
+
|
|
1288
|
+
|
|
1289
|
+
|
|
1290
|
+
|
|
1291
|
+
<li class="md-nav__item">
|
|
1292
|
+
<a href="../../plugins/docking/" class="md-nav__link">
|
|
1293
|
+
|
|
1294
|
+
|
|
1295
|
+
|
|
1296
|
+
<span class="md-ellipsis">
|
|
1297
|
+
|
|
1298
|
+
|
|
1299
|
+
Docking
|
|
1300
|
+
|
|
1301
|
+
|
|
1302
|
+
|
|
1303
|
+
</span>
|
|
1304
|
+
|
|
1305
|
+
|
|
1306
|
+
|
|
1307
|
+
</a>
|
|
1308
|
+
</li>
|
|
1309
|
+
|
|
1310
|
+
|
|
1311
|
+
|
|
1312
|
+
|
|
1313
|
+
|
|
1314
|
+
|
|
1315
|
+
|
|
1316
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<a href="../../plugins/qm/" class="md-nav__link">
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QM
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<a href="../../plugins/ml/" class="md-nav__link">
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ML
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<a href="../../plugins/datascience/" class="md-nav__link">
|
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Data Science
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|
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1471
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|
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</nav>
|
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|
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|
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1513
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|
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|
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<div class="md-nav__link md-nav__container">
|
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1518
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<a href="../../gui/" class="md-nav__link ">
|
|
1519
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|
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1520
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1521
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1523
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1524
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1525
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GUI
|
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1527
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1529
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|
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1532
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1533
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|
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1535
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|
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1536
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+
<label class="md-nav__link " for="__nav_7" id="__nav_7_label" tabindex="">
|
|
1537
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1538
|
+
</label>
|
|
1539
|
+
|
|
1540
|
+
</div>
|
|
1541
|
+
|
|
1542
|
+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_7_label" aria-expanded="false">
|
|
1543
|
+
<label class="md-nav__title" for="__nav_7">
|
|
1544
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+
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|
|
1545
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1546
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|
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1547
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+
GUI
|
|
1548
|
+
|
|
1549
|
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|
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1550
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+
</label>
|
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1551
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|
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|
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|
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|
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1562
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1563
|
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<span class="md-ellipsis">
|
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1565
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|
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1566
|
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|
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1567
|
+
Walkthrough
|
|
1568
|
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|
|
1569
|
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|
|
1570
|
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|
|
1571
|
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|
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1573
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|
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1588
|
+
<a href="../../gui/plugin-authoring/" class="md-nav__link">
|
|
1589
|
+
|
|
1590
|
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|
|
1591
|
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|
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<span class="md-ellipsis">
|
|
1593
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|
|
1594
|
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|
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1595
|
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Plugin GUI Authoring
|
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1596
|
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|
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1597
|
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|
|
1598
|
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|
|
1599
|
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</span>
|
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1600
|
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|
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|
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|
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</ul>
|
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</nav>
|
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|
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|
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<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
|
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|
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|
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|
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|
|
1643
|
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|
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|
+
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_8" >
|
|
1645
|
+
|
|
1646
|
+
|
|
1647
|
+
<div class="md-nav__link md-nav__container">
|
|
1648
|
+
<a href="../../reference/" class="md-nav__link ">
|
|
1649
|
+
|
|
1650
|
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|
|
1651
|
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|
|
1652
|
+
<span class="md-ellipsis">
|
|
1653
|
+
|
|
1654
|
+
|
|
1655
|
+
Reference
|
|
1656
|
+
|
|
1657
|
+
|
|
1658
|
+
|
|
1659
|
+
</span>
|
|
1660
|
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|
|
1661
|
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|
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1662
|
+
|
|
1663
|
+
</a>
|
|
1664
|
+
|
|
1665
|
+
|
|
1666
|
+
<label class="md-nav__link " for="__nav_8" id="__nav_8_label" tabindex="">
|
|
1667
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1668
|
+
</label>
|
|
1669
|
+
|
|
1670
|
+
</div>
|
|
1671
|
+
|
|
1672
|
+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_8_label" aria-expanded="false">
|
|
1673
|
+
<label class="md-nav__title" for="__nav_8">
|
|
1674
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1675
|
+
|
|
1676
|
+
|
|
1677
|
+
Reference
|
|
1678
|
+
|
|
1679
|
+
|
|
1680
|
+
</label>
|
|
1681
|
+
<ul class="md-nav__list" data-md-scrollfix>
|
|
1682
|
+
|
|
1683
|
+
|
|
1684
|
+
|
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1685
|
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|
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|
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|
|
1687
|
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|
|
1688
|
+
|
|
1689
|
+
<li class="md-nav__item">
|
|
1690
|
+
<a href="../../reference/api/" class="md-nav__link">
|
|
1691
|
+
|
|
1692
|
+
|
|
1693
|
+
|
|
1694
|
+
<span class="md-ellipsis">
|
|
1695
|
+
|
|
1696
|
+
|
|
1697
|
+
Public Python API
|
|
1698
|
+
|
|
1699
|
+
|
|
1700
|
+
|
|
1701
|
+
</span>
|
|
1702
|
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|
|
1703
|
+
|
|
1704
|
+
|
|
1705
|
+
</a>
|
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1706
|
+
</li>
|
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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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|
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1715
|
+
|
|
1716
|
+
|
|
1717
|
+
<li class="md-nav__item">
|
|
1718
|
+
<a href="../../examples/" class="md-nav__link">
|
|
1719
|
+
|
|
1720
|
+
|
|
1721
|
+
|
|
1722
|
+
<span class="md-ellipsis">
|
|
1723
|
+
|
|
1724
|
+
|
|
1725
|
+
Example Library
|
|
1726
|
+
|
|
1727
|
+
|
|
1728
|
+
|
|
1729
|
+
</span>
|
|
1730
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|
|
1731
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|
|
1732
|
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|
|
1733
|
+
</a>
|
|
1734
|
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</li>
|
|
1735
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|
|
1736
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|
|
1737
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|
|
1738
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|
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1739
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|
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1740
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|
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1741
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|
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1742
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|
|
1743
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|
|
1744
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|
|
1745
|
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<li class="md-nav__item">
|
|
1746
|
+
<a href="../../examples/quickstart/" class="md-nav__link">
|
|
1747
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|
|
1748
|
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|
|
1749
|
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|
|
1750
|
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<span class="md-ellipsis">
|
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Example Data Provenance
|
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_9" >
|
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<label class="md-nav__link" for="__nav_9" id="__nav_9_label" tabindex="">
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Explanation
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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_9_label" aria-expanded="false">
|
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<label class="md-nav__title" for="__nav_9">
|
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<span class="md-nav__icon md-icon"></span>
|
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Explanation
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|
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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="../../explanation/reproducibility/" class="md-nav__link">
|
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1843
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1844
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<span class="md-ellipsis">
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1848
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Reproducibility
|
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1849
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1850
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1851
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1852
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<li class="md-nav__item">
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1869
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<a href="../../explanation/references/" class="md-nav__link">
|
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1872
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<span class="md-ellipsis">
|
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1874
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|
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1875
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|
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1876
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Method References
|
|
1877
|
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|
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1878
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|
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1879
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|
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1880
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1881
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1883
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1895
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<li class="md-nav__item">
|
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1897
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<a href="../../explanation/third-party-notices/" class="md-nav__link">
|
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1898
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|
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1899
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|
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1900
|
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1901
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<span class="md-ellipsis">
|
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1902
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|
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1903
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|
|
1904
|
+
Third-party Notices
|
|
1905
|
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|
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1906
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|
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1907
|
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|
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1908
|
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</span>
|
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1909
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|
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1910
|
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|
|
1911
|
+
|
|
1912
|
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</a>
|
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1913
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</li>
|
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1914
|
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|
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1915
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1916
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|
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1917
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|
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1918
|
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</ul>
|
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1919
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</nav>
|
|
1920
|
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|
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1921
|
+
</li>
|
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1922
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1923
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1924
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1925
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1926
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1930
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1931
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1932
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1933
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1934
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1939
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1940
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1941
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1942
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1943
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1944
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1945
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1946
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1947
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1948
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1949
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1950
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1951
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1952
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1953
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1954
|
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1955
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1956
|
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|
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1957
|
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<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
|
1958
|
+
|
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1959
|
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|
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1960
|
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|
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1961
|
+
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_10" >
|
|
1962
|
+
|
|
1963
|
+
|
|
1964
|
+
<div class="md-nav__link md-nav__container">
|
|
1965
|
+
<a href="../../development/" class="md-nav__link ">
|
|
1966
|
+
|
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1967
|
+
|
|
1968
|
+
|
|
1969
|
+
<span class="md-ellipsis">
|
|
1970
|
+
|
|
1971
|
+
|
|
1972
|
+
Development
|
|
1973
|
+
|
|
1974
|
+
|
|
1975
|
+
|
|
1976
|
+
</span>
|
|
1977
|
+
|
|
1978
|
+
|
|
1979
|
+
|
|
1980
|
+
</a>
|
|
1981
|
+
|
|
1982
|
+
|
|
1983
|
+
<label class="md-nav__link " for="__nav_10" id="__nav_10_label" tabindex="">
|
|
1984
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1985
|
+
</label>
|
|
1986
|
+
|
|
1987
|
+
</div>
|
|
1988
|
+
|
|
1989
|
+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_10_label" aria-expanded="false">
|
|
1990
|
+
<label class="md-nav__title" for="__nav_10">
|
|
1991
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1992
|
+
|
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1993
|
+
|
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1994
|
+
Development
|
|
1995
|
+
|
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1996
|
+
|
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1997
|
+
</label>
|
|
1998
|
+
<ul class="md-nav__list" data-md-scrollfix>
|
|
1999
|
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2000
|
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2001
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2002
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2003
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2004
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2005
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2006
|
+
<li class="md-nav__item">
|
|
2007
|
+
<a href="../../development/release-notes/" class="md-nav__link">
|
|
2008
|
+
|
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2009
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+
|
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2010
|
+
|
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2011
|
+
<span class="md-ellipsis">
|
|
2012
|
+
|
|
2013
|
+
|
|
2014
|
+
Release Notes
|
|
2015
|
+
|
|
2016
|
+
|
|
2017
|
+
|
|
2018
|
+
</span>
|
|
2019
|
+
|
|
2020
|
+
|
|
2021
|
+
|
|
2022
|
+
</a>
|
|
2023
|
+
</li>
|
|
2024
|
+
|
|
2025
|
+
|
|
2026
|
+
|
|
2027
|
+
|
|
2028
|
+
|
|
2029
|
+
|
|
2030
|
+
|
|
2031
|
+
|
|
2032
|
+
|
|
2033
|
+
|
|
2034
|
+
<li class="md-nav__item">
|
|
2035
|
+
<a href="../../development/tool-authoring/" class="md-nav__link">
|
|
2036
|
+
|
|
2037
|
+
|
|
2038
|
+
|
|
2039
|
+
<span class="md-ellipsis">
|
|
2040
|
+
|
|
2041
|
+
|
|
2042
|
+
Tool Authoring
|
|
2043
|
+
|
|
2044
|
+
|
|
2045
|
+
|
|
2046
|
+
</span>
|
|
2047
|
+
|
|
2048
|
+
|
|
2049
|
+
|
|
2050
|
+
</a>
|
|
2051
|
+
</li>
|
|
2052
|
+
|
|
2053
|
+
|
|
2054
|
+
|
|
2055
|
+
|
|
2056
|
+
|
|
2057
|
+
|
|
2058
|
+
|
|
2059
|
+
|
|
2060
|
+
|
|
2061
|
+
|
|
2062
|
+
<li class="md-nav__item">
|
|
2063
|
+
<a href="../../development/documentation/" class="md-nav__link">
|
|
2064
|
+
|
|
2065
|
+
|
|
2066
|
+
|
|
2067
|
+
<span class="md-ellipsis">
|
|
2068
|
+
|
|
2069
|
+
|
|
2070
|
+
Documentation
|
|
2071
|
+
|
|
2072
|
+
|
|
2073
|
+
|
|
2074
|
+
</span>
|
|
2075
|
+
|
|
2076
|
+
|
|
2077
|
+
|
|
2078
|
+
</a>
|
|
2079
|
+
</li>
|
|
2080
|
+
|
|
2081
|
+
|
|
2082
|
+
|
|
2083
|
+
|
|
2084
|
+
|
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2085
|
+
|
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2086
|
+
|
|
2087
|
+
|
|
2088
|
+
|
|
2089
|
+
|
|
2090
|
+
<li class="md-nav__item">
|
|
2091
|
+
<a href="../../development/contributing/" class="md-nav__link">
|
|
2092
|
+
|
|
2093
|
+
|
|
2094
|
+
|
|
2095
|
+
<span class="md-ellipsis">
|
|
2096
|
+
|
|
2097
|
+
|
|
2098
|
+
Contributing
|
|
2099
|
+
|
|
2100
|
+
|
|
2101
|
+
|
|
2102
|
+
</span>
|
|
2103
|
+
|
|
2104
|
+
|
|
2105
|
+
|
|
2106
|
+
</a>
|
|
2107
|
+
</li>
|
|
2108
|
+
|
|
2109
|
+
|
|
2110
|
+
|
|
2111
|
+
|
|
2112
|
+
|
|
2113
|
+
|
|
2114
|
+
|
|
2115
|
+
|
|
2116
|
+
|
|
2117
|
+
|
|
2118
|
+
<li class="md-nav__item">
|
|
2119
|
+
<a href="../../development/security/" class="md-nav__link">
|
|
2120
|
+
|
|
2121
|
+
|
|
2122
|
+
|
|
2123
|
+
<span class="md-ellipsis">
|
|
2124
|
+
|
|
2125
|
+
|
|
2126
|
+
Security Reporting
|
|
2127
|
+
|
|
2128
|
+
|
|
2129
|
+
|
|
2130
|
+
</span>
|
|
2131
|
+
|
|
2132
|
+
|
|
2133
|
+
|
|
2134
|
+
</a>
|
|
2135
|
+
</li>
|
|
2136
|
+
|
|
2137
|
+
|
|
2138
|
+
|
|
2139
|
+
|
|
2140
|
+
|
|
2141
|
+
|
|
2142
|
+
|
|
2143
|
+
|
|
2144
|
+
|
|
2145
|
+
|
|
2146
|
+
<li class="md-nav__item">
|
|
2147
|
+
<a href="../../development/release-readiness/" class="md-nav__link">
|
|
2148
|
+
|
|
2149
|
+
|
|
2150
|
+
|
|
2151
|
+
<span class="md-ellipsis">
|
|
2152
|
+
|
|
2153
|
+
|
|
2154
|
+
Release Readiness
|
|
2155
|
+
|
|
2156
|
+
|
|
2157
|
+
|
|
2158
|
+
</span>
|
|
2159
|
+
|
|
2160
|
+
|
|
2161
|
+
|
|
2162
|
+
</a>
|
|
2163
|
+
</li>
|
|
2164
|
+
|
|
2165
|
+
|
|
2166
|
+
|
|
2167
|
+
|
|
2168
|
+
|
|
2169
|
+
|
|
2170
|
+
|
|
2171
|
+
|
|
2172
|
+
|
|
2173
|
+
|
|
2174
|
+
<li class="md-nav__item">
|
|
2175
|
+
<a href="../../development/ci-publishing/" class="md-nav__link">
|
|
2176
|
+
|
|
2177
|
+
|
|
2178
|
+
|
|
2179
|
+
<span class="md-ellipsis">
|
|
2180
|
+
|
|
2181
|
+
|
|
2182
|
+
CI and Publishing
|
|
2183
|
+
|
|
2184
|
+
|
|
2185
|
+
|
|
2186
|
+
</span>
|
|
2187
|
+
|
|
2188
|
+
|
|
2189
|
+
|
|
2190
|
+
</a>
|
|
2191
|
+
</li>
|
|
2192
|
+
|
|
2193
|
+
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Basic Usage
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Environment Requirement
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Option A: Packed Conda/Micromamba Environment
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<a href="#sidecar-and-fallback-behavior" class="md-nav__link">
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Sidecar and fallback behavior
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<a href="#node-local-cache" class="md-nav__link">
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Node-local cache
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Replacing a managed pack
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<a href="#option-b-wheelhouse-and-per-job-virtualenv" class="md-nav__link">
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<span class="md-ellipsis">
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Option B: Wheelhouse and Per-Job Virtualenv
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<span class="md-ellipsis">
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Option C: Site-Specific Setup Commands
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Practical Rules
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</div>
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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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2352
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2353
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+
|
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2354
|
+
<h1 id="slurm-backend">Slurm Backend<a class="headerlink" href="#slurm-backend" title="Permanent link">¶</a></h1>
|
|
2355
|
+
<p>CADDForge can submit workflows to Slurm through the core <code>SlurmBackend</code>. The backend writes a
|
|
2356
|
+
payload, submits an <code>sbatch</code> script, and uses CADDForge's Slurm runner on the compute node to execute
|
|
2357
|
+
the workflow.</p>
|
|
2358
|
+
<p>Use Slurm for CADDForge-native workflows that can run in a normal Python environment on a compute
|
|
2359
|
+
node. Check each public tool's runtime requirements before selecting a backend.</p>
|
|
2360
|
+
<h2 id="basic-usage">Basic Usage<a class="headerlink" href="#basic-usage" title="Permanent link">¶</a></h2>
|
|
2361
|
+
<p>Replace the partition and account placeholders with values from your cluster administrator.</p>
|
|
2362
|
+
<p>Set <code>backend: slurm</code> in the tool config or pass <code>--backend slurm</code> from the CLI:</p>
|
|
2363
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>caddforge<span class="w"> </span>run<span class="w"> </span>md<span class="w"> </span>plain-md<span class="w"> </span>--config<span class="w"> </span>plain_md.yaml<span class="w"> </span>--backend<span class="w"> </span>slurm<span class="w"> </span>--slurm-time<span class="w"> </span><span class="m">24</span>:00:00
|
|
2364
|
+
</code></pre></div>
|
|
2365
|
+
<p>Common Slurm config fields:</p>
|
|
2366
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a><span class="nt">backend</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">slurm</span>
|
|
2367
|
+
<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a><span class="nt">slurm_partition</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">your-partition</span>
|
|
2368
|
+
<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a><span class="nt">slurm_time</span><span class="p">:</span><span class="w"> </span><span class="s">"24:00:00"</span>
|
|
2369
|
+
<a id="__codelineno-1-4" name="__codelineno-1-4" href="#__codelineno-1-4"></a><span class="nt">slurm_account</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">your-account</span>
|
|
2370
|
+
<a id="__codelineno-1-5" name="__codelineno-1-5" href="#__codelineno-1-5"></a><span class="nt">slurm_nodes</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">1</span>
|
|
2371
|
+
<a id="__codelineno-1-6" name="__codelineno-1-6" href="#__codelineno-1-6"></a><span class="nt">slurm_ntasks</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">1</span>
|
|
2372
|
+
<a id="__codelineno-1-7" name="__codelineno-1-7" href="#__codelineno-1-7"></a><span class="nt">slurm_cpus_per_task</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">8</span>
|
|
2373
|
+
<a id="__codelineno-1-8" name="__codelineno-1-8" href="#__codelineno-1-8"></a><span class="nt">sbatch_options</span><span class="p">:</span>
|
|
2374
|
+
<a id="__codelineno-1-9" name="__codelineno-1-9" href="#__codelineno-1-9"></a><span class="w"> </span><span class="nt">gres</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">gpu:1</span>
|
|
2375
|
+
</code></pre></div>
|
|
2376
|
+
<p>Environment-related shared fields include <code>slurm_env_pack_path</code>, <code>slurm_env_cache_enabled</code>,
|
|
2377
|
+
<code>slurm_env_cache_dir</code>, <code>slurm_wheelhouse_path</code>, <code>slurm_requirements_path</code>, and
|
|
2378
|
+
<code>slurm_setup_commands</code>.</p>
|
|
2379
|
+
<h2 id="environment-requirement">Environment Requirement<a class="headerlink" href="#environment-requirement" title="Permanent link">¶</a></h2>
|
|
2380
|
+
<p>Slurm jobs run on compute nodes, not in the interactive shell where <code>caddforge</code> was launched. The
|
|
2381
|
+
compute node must have access to a compatible Python environment containing:</p>
|
|
2382
|
+
<ul>
|
|
2383
|
+
<li><code>caddforge</code></li>
|
|
2384
|
+
<li>the plugin package being run</li>
|
|
2385
|
+
<li>all Python dependencies</li>
|
|
2386
|
+
<li>all scientific runtime dependencies needed by the workflow</li>
|
|
2387
|
+
</ul>
|
|
2388
|
+
<p>For heavy scientific stacks, install conda-managed packages first, then install CADDForge packages
|
|
2389
|
+
with pip.</p>
|
|
2390
|
+
<h2 id="option-a-packed-condamicromamba-environment">Option A: Packed Conda/Micromamba Environment<a class="headerlink" href="#option-a-packed-condamicromamba-environment" title="Permanent link">¶</a></h2>
|
|
2391
|
+
<p>Use this when the workflow depends on conda-managed scientific packages such as OpenMM, RDKit,
|
|
2392
|
+
OpenFE, or OpenFF. Dependency resolution happens once before submission, and compute nodes reuse a
|
|
2393
|
+
checksum-addressed unpacked environment cache by default.</p>
|
|
2394
|
+
<p>Create the environment, install CADDForge and the required plugins, then use <code>caddforge pack-env</code>.
|
|
2395
|
+
The core package already depends on <code>conda-pack</code>:</p>
|
|
2396
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>micromamba<span class="w"> </span>create<span class="w"> </span>-n<span class="w"> </span>caddforge<span class="w"> </span>-c<span class="w"> </span>conda-forge<span class="w"> </span><span class="nv">python</span><span class="o">=</span><span class="m">3</span>.10
|
|
2397
|
+
<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>micromamba<span class="w"> </span>activate<span class="w"> </span>caddforge
|
|
2398
|
+
<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>micromamba<span class="w"> </span>install<span class="w"> </span>-c<span class="w"> </span>conda-forge<span class="w"> </span>openmm<span class="w"> </span>rdkit
|
|
2399
|
+
<a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a><span class="c1"># Requires the selected MD version to be published; see the version matrix.</span>
|
|
2400
|
+
<a id="__codelineno-2-5" name="__codelineno-2-5" href="#__codelineno-2-5"></a>python<span class="w"> </span>-m<span class="w"> </span>pip<span class="w"> </span>install<span class="w"> </span>caddforge-core<span class="w"> </span>caddforge-md
|
|
2401
|
+
<a id="__codelineno-2-6" name="__codelineno-2-6" href="#__codelineno-2-6"></a>
|
|
2402
|
+
<a id="__codelineno-2-7" name="__codelineno-2-7" href="#__codelineno-2-7"></a><span class="c1"># Pack the active environment.</span>
|
|
2403
|
+
<a id="__codelineno-2-8" name="__codelineno-2-8" href="#__codelineno-2-8"></a>caddforge<span class="w"> </span>pack-env<span class="w"> </span>--output<span class="w"> </span>/shared/envs/caddforge.tar.gz
|
|
2404
|
+
<a id="__codelineno-2-9" name="__codelineno-2-9" href="#__codelineno-2-9"></a>
|
|
2405
|
+
<a id="__codelineno-2-10" name="__codelineno-2-10" href="#__codelineno-2-10"></a><span class="c1"># Alternatively, select a named environment or explicit prefix.</span>
|
|
2406
|
+
<a id="__codelineno-2-11" name="__codelineno-2-11" href="#__codelineno-2-11"></a>caddforge<span class="w"> </span>pack-env<span class="w"> </span>--name<span class="w"> </span>caddforge<span class="w"> </span>--output<span class="w"> </span>/shared/envs/caddforge.tar.gz
|
|
2407
|
+
<a id="__codelineno-2-12" name="__codelineno-2-12" href="#__codelineno-2-12"></a>caddforge<span class="w"> </span>pack-env<span class="w"> </span>--prefix<span class="w"> </span>/path/to/caddforge<span class="w"> </span><span class="se">\</span>
|
|
2408
|
+
<a id="__codelineno-2-13" name="__codelineno-2-13" href="#__codelineno-2-13"></a><span class="w"> </span>--output<span class="w"> </span>/shared/envs/caddforge.tar.gz
|
|
2409
|
+
</code></pre></div>
|
|
2410
|
+
<p>The command creates:</p>
|
|
2411
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>/shared/envs/caddforge.tar.gz
|
|
2412
|
+
<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>/shared/envs/caddforge.tar.gz.sha256
|
|
2413
|
+
</code></pre></div>
|
|
2414
|
+
<p>The sidecar is written in standard <code>sha256sum</code> format. During a long build, <code>pack-env</code> keeps the
|
|
2415
|
+
<code>conda-pack</code> percentage bar on one updating terminal line, streams normal messages, reports elapsed
|
|
2416
|
+
time and the growing archive size during quiet periods, and displays hashing progress.</p>
|
|
2417
|
+
<p>Existing output is protected by default. Use <code>--force</code> for a deliberate fixed-name replacement:</p>
|
|
2418
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>caddforge<span class="w"> </span>pack-env<span class="w"> </span>--output<span class="w"> </span>/shared/envs/caddforge-dev.tar.gz<span class="w"> </span>--force
|
|
2419
|
+
</code></pre></div>
|
|
2420
|
+
<p>Use the packed environment in the workflow config:</p>
|
|
2421
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a><span class="nt">backend</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">slurm</span>
|
|
2422
|
+
<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a><span class="nt">slurm_env_pack_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">/shared/envs/caddforge.tar.gz</span>
|
|
2423
|
+
</code></pre></div>
|
|
2424
|
+
<p>No sidecar path is configured. CADDForge discovers <code><slurm_env_pack_path>.sha256</code> automatically.</p>
|
|
2425
|
+
<h3 id="sidecar-and-fallback-behavior">Sidecar and fallback behavior<a class="headerlink" href="#sidecar-and-fallback-behavior" title="Permanent link">¶</a></h3>
|
|
2426
|
+
<p>With caching enabled, submission uses the following compatibility order:</p>
|
|
2427
|
+
<ol>
|
|
2428
|
+
<li>A valid sidecar supplies the trusted SHA-256 immediately, so the large archive is not hashed by
|
|
2429
|
+
the submission command.</li>
|
|
2430
|
+
<li>If the sidecar is missing, malformed, or names another archive, CADDForge warns and falls back to
|
|
2431
|
+
computing the full archive SHA-256. Manually created packs therefore remain supported.</li>
|
|
2432
|
+
<li>If <code>slurm_env_cache_enabled: false</code>, CADDForge skips sidecar lookup and submission-time hashing,
|
|
2433
|
+
then unpacks the environment separately in each job's private scratch directory. This preserves
|
|
2434
|
+
the behavior used before environment caching was introduced.</li>
|
|
2435
|
+
</ol>
|
|
2436
|
+
<p>The first job requiring a digest on a compute node copies the archive to job-private scratch,
|
|
2437
|
+
verifies it against the selected SHA-256, and installs it into the node-local cache. Later jobs on
|
|
2438
|
+
that node reuse the completed cache entry without copying or unpacking the archive again.</p>
|
|
2439
|
+
<h3 id="node-local-cache">Node-local cache<a class="headerlink" href="#node-local-cache" title="Permanent link">¶</a></h3>
|
|
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|
+
<p>The default per-user cache root is:</p>
|
|
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|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>$SCRATCH_BASE/caddforge_environments/$USER
|
|
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|
+
</code></pre></div>
|
|
2443
|
+
<p>It contains separate environment, lock, and staging directories. Cache locks are node-local and
|
|
2444
|
+
never lock or modify the source archive. Jobs retain a shared usage lock while running, preventing
|
|
2445
|
+
cleanup from deleting an active environment. Entries idle for more than 14 days are removed
|
|
2446
|
+
opportunistically; the lock timeout is 30 minutes. These are core policies, not per-job options.</p>
|
|
2447
|
+
<p>Sites can override the root with an absolute compute-node path:</p>
|
|
2448
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a><span class="nt">slurm_env_cache_dir</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">/scratch/caddforge-environments/my-user</span>
|
|
2449
|
+
</code></pre></div>
|
|
2450
|
+
<p>Node-local caches may disappear during node cleanup or replacement. CADDForge rebuilds missing
|
|
2451
|
+
entries from the shared archive.</p>
|
|
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|
+
<h3 id="replacing-a-managed-pack">Replacing a managed pack<a class="headerlink" href="#replacing-a-managed-pack" title="Permanent link">¶</a></h3>
|
|
2453
|
+
<p><code>pack-env --force</code> creates and hashes the replacement before briefly acquiring a hidden advisory
|
|
2454
|
+
publication lock next to the archive. CADDForge submissions coordinate with this lock when it is
|
|
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|
+
present. The source archive itself is never locked.</p>
|
|
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|
+
<p>An archive and sidecar are separate files, so direct external replacement bypasses this coordination
|
|
2457
|
+
and is unsupported for managed packs. If sidecar publication fails, CADDForge removes the old
|
|
2458
|
+
sidecar when possible, causing submissions to use the safe full-hash fallback.</p>
|
|
2459
|
+
<p>A job records the digest selected at submission. If a fixed-name archive is replaced before an
|
|
2460
|
+
uncached queued job starts, that job fails checksum verification rather than running a different
|
|
2461
|
+
environment. A job whose matching digest is already cached on its compute node can still use that
|
|
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|
+
cache entry.</p>
|
|
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|
+
<h2 id="option-b-wheelhouse-and-per-job-virtualenv">Option B: Wheelhouse and Per-Job Virtualenv<a class="headerlink" href="#option-b-wheelhouse-and-per-job-virtualenv" title="Permanent link">¶</a></h2>
|
|
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|
+
<p>Use this when all required packages are available as wheels from a package index or a prepared
|
|
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|
+
wheelhouse.</p>
|
|
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|
+
<p>Build a wheelhouse:</p>
|
|
2467
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a>python<span class="w"> </span>-m<span class="w"> </span>pip<span class="w"> </span>freeze<span class="w"> </span>><span class="w"> </span>requirements.txt
|
|
2468
|
+
<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a>python<span class="w"> </span>-m<span class="w"> </span>pip<span class="w"> </span>download<span class="w"> </span>-r<span class="w"> </span>requirements.txt<span class="w"> </span>-d<span class="w"> </span>/shared/wheelhouse
|
|
2469
|
+
</code></pre></div>
|
|
2470
|
+
<p>Use it in the workflow config:</p>
|
|
2471
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a><span class="nt">backend</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">slurm</span>
|
|
2472
|
+
<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a><span class="nt">slurm_wheelhouse_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">/shared/wheelhouse</span>
|
|
2473
|
+
<a id="__codelineno-9-3" name="__codelineno-9-3" href="#__codelineno-9-3"></a><span class="nt">slurm_requirements_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">/shared/requirements.txt</span>
|
|
2474
|
+
</code></pre></div>
|
|
2475
|
+
<p>The Slurm job creates a temporary virtualenv, installs from the wheelhouse, and runs the workflow.</p>
|
|
2476
|
+
<h2 id="option-c-site-specific-setup-commands">Option C: Site-Specific Setup Commands<a class="headerlink" href="#option-c-site-specific-setup-commands" title="Permanent link">¶</a></h2>
|
|
2477
|
+
<p>Use <code>slurm_setup_commands</code> only when your cluster already provides a supported module or activation
|
|
2478
|
+
workflow:</p>
|
|
2479
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a><span class="nt">backend</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">slurm</span>
|
|
2480
|
+
<a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a><span class="nt">slurm_setup_commands</span><span class="p">:</span>
|
|
2481
|
+
<a id="__codelineno-10-3" name="__codelineno-10-3" href="#__codelineno-10-3"></a><span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">module purge</span>
|
|
2482
|
+
<a id="__codelineno-10-4" name="__codelineno-10-4" href="#__codelineno-10-4"></a><span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">module load caddforge/0.2</span>
|
|
2483
|
+
<a id="__codelineno-10-5" name="__codelineno-10-5" href="#__codelineno-10-5"></a><span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">source /shared/envs/caddforge/bin/activate</span>
|
|
2484
|
+
</code></pre></div>
|
|
2485
|
+
<p>If you use setup commands, do not also set <code>slurm_env_pack_path</code>,
|
|
2486
|
+
<code>slurm_wheelhouse_path</code>, or <code>slurm_requirements_path</code>. The setup commands are then fully responsible
|
|
2487
|
+
for making the correct Python executable available.</p>
|
|
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|
+
<h2 id="practical-rules">Practical Rules<a class="headerlink" href="#practical-rules" title="Permanent link">¶</a></h2>
|
|
2489
|
+
<ul>
|
|
2490
|
+
<li>Ensure all referenced environment paths are readable from compute nodes.</li>
|
|
2491
|
+
<li>Use exactly one environment strategy per job.</li>
|
|
2492
|
+
<li>Keep packed environments on shared storage, not in a login-node-only path.</li>
|
|
2493
|
+
<li>Prefer <code>caddforge pack-env</code> so submission can use its managed SHA-256 sidecar.</li>
|
|
2494
|
+
<li>Use <code>--force</code> only when replacing a fixed-name archive is intentional, and avoid replacement while
|
|
2495
|
+
uncached jobs using that archive are queued.</li>
|
|
2496
|
+
<li>Rebuild the environment when plugin versions or scientific dependencies change.</li>
|
|
2497
|
+
<li>Prefer packed conda environments for workflows with compiled scientific dependencies.</li>
|
|
2498
|
+
<li>Prefer wheelhouses for pure Python or locally packaged stacks.</li>
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