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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466
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
|
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468
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|
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469
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470
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<label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="">
|
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<span class="md-ellipsis">
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477
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How-to Guides
|
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478
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479
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484
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<span class="md-nav__icon md-icon"></span>
|
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486
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</label>
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487
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|
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488
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<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
|
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489
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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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494
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495
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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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506
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<a href="../../how-to/jobs/" class="md-nav__link">
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508
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509
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<span class="md-ellipsis">
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511
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Jobs and Results
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</span>
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</a>
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532
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<li class="md-nav__item">
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534
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<a href="../../how-to/scatter/" class="md-nav__link">
|
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|
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536
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537
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|
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538
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<span class="md-ellipsis">
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539
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|
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540
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|
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541
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Scatter and Reduce
|
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542
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|
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543
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544
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545
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</span>
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</a>
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560
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<li class="md-nav__item">
|
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562
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<a href="../../how-to/troubleshooting/" class="md-nav__link">
|
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563
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|
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564
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|
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565
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|
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566
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<span class="md-ellipsis">
|
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567
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|
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568
|
+
|
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569
|
+
Troubleshooting
|
|
570
|
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|
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571
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|
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572
|
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|
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573
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</span>
|
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574
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|
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|
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|
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577
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</a>
|
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578
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</li>
|
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580
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|
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581
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|
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582
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|
|
583
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</ul>
|
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584
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</nav>
|
|
585
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|
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586
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</li>
|
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587
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|
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621
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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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624
|
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|
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625
|
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|
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626
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
|
|
627
|
+
|
|
628
|
+
|
|
629
|
+
<div class="md-nav__link md-nav__container">
|
|
630
|
+
<a href="../" class="md-nav__link ">
|
|
631
|
+
|
|
632
|
+
|
|
633
|
+
|
|
634
|
+
<span class="md-ellipsis">
|
|
635
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+
|
|
636
|
+
|
|
637
|
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Core
|
|
638
|
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|
|
639
|
+
|
|
640
|
+
|
|
641
|
+
</span>
|
|
642
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|
|
643
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|
|
644
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+
|
|
645
|
+
</a>
|
|
646
|
+
|
|
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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|
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685
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|
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686
|
+
|
|
687
|
+
</a>
|
|
688
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</li>
|
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689
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691
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696
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697
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|
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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
|
+
|
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707
|
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Configuration
|
|
708
|
+
|
|
709
|
+
|
|
710
|
+
|
|
711
|
+
</span>
|
|
712
|
+
|
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713
|
+
|
|
714
|
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|
|
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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|
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721
|
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722
|
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|
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723
|
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|
|
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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|
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746
|
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747
|
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748
|
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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
|
+
|
|
777
|
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|
|
778
|
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|
|
779
|
+
|
|
780
|
+
|
|
781
|
+
|
|
782
|
+
|
|
783
|
+
<li class="md-nav__item">
|
|
784
|
+
<a href="../slurm/" class="md-nav__link">
|
|
785
|
+
|
|
786
|
+
|
|
787
|
+
|
|
788
|
+
<span class="md-ellipsis">
|
|
789
|
+
|
|
790
|
+
|
|
791
|
+
Slurm Backend
|
|
792
|
+
|
|
793
|
+
|
|
794
|
+
|
|
795
|
+
</span>
|
|
796
|
+
|
|
797
|
+
|
|
798
|
+
|
|
799
|
+
</a>
|
|
800
|
+
</li>
|
|
801
|
+
|
|
802
|
+
|
|
803
|
+
|
|
804
|
+
|
|
805
|
+
|
|
806
|
+
|
|
807
|
+
|
|
808
|
+
|
|
809
|
+
|
|
810
|
+
|
|
811
|
+
|
|
812
|
+
|
|
813
|
+
<li class="md-nav__item md-nav__item--active">
|
|
814
|
+
|
|
815
|
+
<input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
|
|
816
|
+
|
|
817
|
+
|
|
818
|
+
|
|
819
|
+
|
|
820
|
+
|
|
821
|
+
<a href="./" class="md-nav__link md-nav__link--active">
|
|
822
|
+
|
|
823
|
+
|
|
824
|
+
|
|
825
|
+
<span class="md-ellipsis">
|
|
826
|
+
|
|
827
|
+
|
|
828
|
+
Plugins
|
|
829
|
+
|
|
830
|
+
|
|
831
|
+
|
|
832
|
+
</span>
|
|
833
|
+
|
|
834
|
+
|
|
835
|
+
|
|
836
|
+
</a>
|
|
837
|
+
|
|
838
|
+
</li>
|
|
839
|
+
|
|
840
|
+
|
|
841
|
+
|
|
842
|
+
|
|
843
|
+
</ul>
|
|
844
|
+
</nav>
|
|
845
|
+
|
|
846
|
+
</li>
|
|
847
|
+
|
|
848
|
+
|
|
849
|
+
|
|
850
|
+
|
|
851
|
+
|
|
852
|
+
|
|
853
|
+
|
|
854
|
+
|
|
855
|
+
|
|
856
|
+
|
|
857
|
+
|
|
858
|
+
|
|
859
|
+
|
|
860
|
+
|
|
861
|
+
|
|
862
|
+
|
|
863
|
+
|
|
864
|
+
|
|
865
|
+
|
|
866
|
+
|
|
867
|
+
|
|
868
|
+
|
|
869
|
+
|
|
870
|
+
|
|
871
|
+
|
|
872
|
+
|
|
873
|
+
|
|
874
|
+
|
|
875
|
+
|
|
876
|
+
<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
|
877
|
+
|
|
878
|
+
|
|
879
|
+
|
|
880
|
+
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
|
|
881
|
+
|
|
882
|
+
|
|
883
|
+
<div class="md-nav__link md-nav__container">
|
|
884
|
+
<a href="../../pipelines/" class="md-nav__link ">
|
|
885
|
+
|
|
886
|
+
|
|
887
|
+
|
|
888
|
+
<span class="md-ellipsis">
|
|
889
|
+
|
|
890
|
+
|
|
891
|
+
Pipelines
|
|
892
|
+
|
|
893
|
+
|
|
894
|
+
|
|
895
|
+
</span>
|
|
896
|
+
|
|
897
|
+
|
|
898
|
+
|
|
899
|
+
</a>
|
|
900
|
+
|
|
901
|
+
|
|
902
|
+
<label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
|
|
903
|
+
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<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
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909
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<label class="md-nav__title" for="__nav_5">
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Pipelines
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Specification
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Artifacts
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<span class="md-ellipsis">
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987
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Built-in Stages
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992
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</a>
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1008
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<li class="md-nav__item">
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1010
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<a href="../../pipelines/examples/" class="md-nav__link">
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1016
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Examples
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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_6" >
|
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1078
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1079
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<div class="md-nav__link md-nav__container">
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1080
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<a href="../../plugins/" class="md-nav__link ">
|
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1081
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1082
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1083
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<span class="md-ellipsis">
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1085
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1086
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1087
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Plugins
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1088
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1089
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1090
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1091
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1092
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1093
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1095
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</a>
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1096
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1097
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1098
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<label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
|
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1099
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+
<span class="md-nav__icon md-icon"></span>
|
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1100
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+
</label>
|
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1101
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+
|
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1102
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+
</div>
|
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1103
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+
|
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1104
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+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="false">
|
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1105
|
+
<label class="md-nav__title" for="__nav_6">
|
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1106
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+
<span class="md-nav__icon md-icon"></span>
|
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1107
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+
|
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1108
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+
|
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1109
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+
Plugins
|
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1110
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+
|
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1111
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+
|
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1112
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+
</label>
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1113
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+
<ul class="md-nav__list" data-md-scrollfix>
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1114
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1115
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|
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1120
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|
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1121
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+
<li class="md-nav__item">
|
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1122
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<a href="../../plugins/version-matrix/" class="md-nav__link">
|
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1123
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+
|
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1124
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+
|
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1125
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+
|
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1126
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+
<span class="md-ellipsis">
|
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1127
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+
|
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1128
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+
|
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1129
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+
Version Matrix
|
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1130
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+
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1131
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+
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1132
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+
|
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1133
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</span>
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1134
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1135
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1136
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1137
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1138
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1148
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1149
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<li class="md-nav__item">
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1150
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<a href="../../plugins/docking/" class="md-nav__link">
|
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1151
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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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1156
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1157
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Docking
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1158
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1159
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1160
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1161
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1162
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1163
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1164
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1165
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1166
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1176
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1177
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<li class="md-nav__item">
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1178
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<a href="../../plugins/descriptors/" class="md-nav__link">
|
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1179
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1180
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1181
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1182
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<span class="md-ellipsis">
|
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1183
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1184
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1185
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+
Descriptors
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1186
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1187
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1188
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1189
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</span>
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1190
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1191
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1192
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1193
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</a>
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1194
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1196
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1199
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1200
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1201
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1204
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1205
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<li class="md-nav__item">
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1206
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<a href="../../plugins/md/" class="md-nav__link">
|
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1207
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|
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1208
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|
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1209
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1210
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<span class="md-ellipsis">
|
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1211
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1212
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1213
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MD
|
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1214
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1215
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1216
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1217
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</span>
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1218
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1219
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1220
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1221
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</a>
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1222
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1223
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1224
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1225
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1226
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1227
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1228
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1229
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1230
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1231
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1232
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|
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1233
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<li class="md-nav__item">
|
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1234
|
+
<a href="../../plugins/fep/" class="md-nav__link">
|
|
1235
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+
|
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1236
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|
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1237
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|
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1238
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<span class="md-ellipsis">
|
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1239
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|
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1240
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|
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1241
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FEP
|
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1242
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1243
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1244
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1245
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</span>
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1246
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1247
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1248
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1249
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</a>
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1250
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1255
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1257
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1259
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1260
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1261
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<li class="md-nav__item">
|
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1262
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<a href="../../plugins/qm/" class="md-nav__link">
|
|
1263
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+
|
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1264
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|
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1265
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|
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1266
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<span class="md-ellipsis">
|
|
1267
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1268
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1269
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QM
|
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1270
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1271
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1272
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|
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1273
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</span>
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1274
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1275
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1276
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1277
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1278
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1287
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1288
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1289
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<li class="md-nav__item">
|
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1290
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<a href="../../plugins/ml/" class="md-nav__link">
|
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1291
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+
|
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1292
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|
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1293
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|
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1294
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<span class="md-ellipsis">
|
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1295
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|
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1296
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|
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1297
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ML
|
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1298
|
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|
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1299
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|
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1300
|
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|
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1301
|
+
</span>
|
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1302
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1303
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1304
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1305
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</a>
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1306
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1307
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1308
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1309
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1310
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1311
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1312
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1313
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1314
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1315
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1316
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|
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1317
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<li class="md-nav__item">
|
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1318
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<a href="../../plugins/datascience/" class="md-nav__link">
|
|
1319
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+
|
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1320
|
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|
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1321
|
+
|
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1322
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<span class="md-ellipsis">
|
|
1323
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+
|
|
1324
|
+
|
|
1325
|
+
Data Science
|
|
1326
|
+
|
|
1327
|
+
|
|
1328
|
+
|
|
1329
|
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</span>
|
|
1330
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|
|
1331
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+
|
|
1332
|
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|
|
1333
|
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</a>
|
|
1334
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</li>
|
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1335
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|
|
1336
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|
|
1337
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|
|
1338
|
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|
|
1339
|
+
</ul>
|
|
1340
|
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</nav>
|
|
1341
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|
|
1342
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</li>
|
|
1343
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|
|
1344
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|
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Plugin GUI Authoring
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Reference
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<label class="md-nav__link " for="__nav_8" id="__nav_8_label" tabindex="">
|
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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_8_label" aria-expanded="false">
|
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<label class="md-nav__title" for="__nav_8">
|
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<span class="md-nav__icon md-icon"></span>
|
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Reference
|
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<a href="../../reference/api/" class="md-nav__link">
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Public Python API
|
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Example Library
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|
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Example Data Provenance
|
|
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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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|
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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">
|
|
1657
|
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|
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1658
|
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|
|
1659
|
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|
|
1660
|
+
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_9" >
|
|
1661
|
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|
|
1662
|
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|
|
1663
|
+
<label class="md-nav__link" for="__nav_9" id="__nav_9_label" tabindex="">
|
|
1664
|
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|
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|
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|
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|
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|
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|
+
<span class="md-ellipsis">
|
|
1668
|
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|
|
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|
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|
|
1670
|
+
Explanation
|
|
1671
|
+
|
|
1672
|
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|
|
1673
|
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|
|
1674
|
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|
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|
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|
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1676
|
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|
|
1677
|
+
|
|
1678
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1679
|
+
</label>
|
|
1680
|
+
|
|
1681
|
+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_9_label" aria-expanded="false">
|
|
1682
|
+
<label class="md-nav__title" for="__nav_9">
|
|
1683
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1684
|
+
|
|
1685
|
+
|
|
1686
|
+
Explanation
|
|
1687
|
+
|
|
1688
|
+
|
|
1689
|
+
</label>
|
|
1690
|
+
<ul class="md-nav__list" data-md-scrollfix>
|
|
1691
|
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|
|
1692
|
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|
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|
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|
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|
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|
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1697
|
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|
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|
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<li class="md-nav__item">
|
|
1699
|
+
<a href="../../explanation/reproducibility/" class="md-nav__link">
|
|
1700
|
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|
|
1701
|
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|
|
1702
|
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|
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|
+
<span class="md-ellipsis">
|
|
1704
|
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|
|
1705
|
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|
|
1706
|
+
Reproducibility
|
|
1707
|
+
|
|
1708
|
+
|
|
1709
|
+
|
|
1710
|
+
</span>
|
|
1711
|
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|
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1712
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|
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1713
|
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|
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1714
|
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</a>
|
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1715
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|
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|
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|
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<li class="md-nav__item">
|
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1727
|
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<a href="../../explanation/references/" class="md-nav__link">
|
|
1728
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|
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1729
|
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|
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1730
|
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|
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1731
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+
<span class="md-ellipsis">
|
|
1732
|
+
|
|
1733
|
+
|
|
1734
|
+
Method References
|
|
1735
|
+
|
|
1736
|
+
|
|
1737
|
+
|
|
1738
|
+
</span>
|
|
1739
|
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|
|
1740
|
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|
|
1741
|
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|
|
1742
|
+
</a>
|
|
1743
|
+
</li>
|
|
1744
|
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|
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1745
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|
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1746
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1748
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1749
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1753
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|
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<li class="md-nav__item">
|
|
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<a href="../../explanation/third-party-notices/" class="md-nav__link">
|
|
1756
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1757
|
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|
|
1758
|
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|
|
1759
|
+
<span class="md-ellipsis">
|
|
1760
|
+
|
|
1761
|
+
|
|
1762
|
+
Third-party Notices
|
|
1763
|
+
|
|
1764
|
+
|
|
1765
|
+
|
|
1766
|
+
</span>
|
|
1767
|
+
|
|
1768
|
+
|
|
1769
|
+
|
|
1770
|
+
</a>
|
|
1771
|
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</li>
|
|
1772
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|
|
1773
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|
|
1774
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<h1 id="plugins">Plugins<a class="headerlink" href="#plugins" title="Permanent link">¶</a></h1>
|
|
2100
|
+
<p>CADDForge tools are discovered as plugins. The core package defines the interfaces; tool packages
|
|
2101
|
+
register implementations.</p>
|
|
2102
|
+
<p>Plugin packages typically provide:</p>
|
|
2103
|
+
<ul>
|
|
2104
|
+
<li>a validated config class</li>
|
|
2105
|
+
<li>a workflow class</li>
|
|
2106
|
+
<li>a <code>Tool</code> implementation</li>
|
|
2107
|
+
<li>Python entry points under <code>caddforge.tools</code></li>
|
|
2108
|
+
<li>optional GUI extensions</li>
|
|
2109
|
+
<li>optional pipeline input and output ports</li>
|
|
2110
|
+
</ul>
|
|
2111
|
+
<p>Example entry point group:</p>
|
|
2112
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a><span class="k">[project.entry-points.</span><span class="s2">"caddforge.tools"</span><span class="k">]</span>
|
|
2113
|
+
<a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a><span class="n">docking-unidock</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">"cadd_docking.tool:UniDockTool"</span>
|
|
2114
|
+
</code></pre></div>
|
|
2115
|
+
<p>The core CLI uses these entry points to resolve commands such as:</p>
|
|
2116
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>caddforge<span class="w"> </span>run<span class="w"> </span>docking<span class="w"> </span>unidock<span class="w"> </span>--config<span class="w"> </span>unidock.yaml
|
|
2117
|
+
</code></pre></div>
|
|
2118
|
+
<p>Python automation should use the same plugin contract instead of importing tool-internal config and
|
|
2119
|
+
workflow classes directly:</p>
|
|
2120
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></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><span class="p">,</span> <span class="n">submit_workflow</span>
|
|
2121
|
+
<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a><span class="kn">from</span><span class="w"> </span><span class="nn">caddforge.plugins</span><span class="w"> </span><span class="kn">import</span> <span class="n">get_tool</span>
|
|
2122
|
+
<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>
|
|
2123
|
+
<a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a><span class="n">spec</span> <span class="o">=</span> <span class="n">get_tool</span><span class="p">(</span><span class="s2">"docking"</span><span class="p">,</span> <span class="s2">"unidock"</span><span class="p">)</span>
|
|
2124
|
+
<a id="__codelineno-2-5" name="__codelineno-2-5" href="#__codelineno-2-5"></a><span class="n">cfg</span> <span class="o">=</span> <span class="n">spec</span><span class="o">.</span><span class="n">config_cls</span><span class="o">.</span><span class="n">from_yaml</span><span class="p">(</span><span class="s2">"unidock.yaml"</span><span class="p">)</span>
|
|
2125
|
+
<a id="__codelineno-2-6" name="__codelineno-2-6" href="#__codelineno-2-6"></a><span class="n">workflow</span> <span class="o">=</span> <span class="n">spec</span><span class="o">.</span><span class="n">workflow_cls</span><span class="p">(</span><span class="n">cfg</span><span class="p">)</span>
|
|
2126
|
+
<a id="__codelineno-2-7" name="__codelineno-2-7" href="#__codelineno-2-7"></a>
|
|
2127
|
+
<a id="__codelineno-2-8" name="__codelineno-2-8" href="#__codelineno-2-8"></a><span class="n">job</span> <span class="o">=</span> <span class="n">submit_workflow</span><span class="p">(</span>
|
|
2128
|
+
<a id="__codelineno-2-9" name="__codelineno-2-9" href="#__codelineno-2-9"></a> <span class="n">workflow</span><span class="p">,</span> <span class="n">cfg</span><span class="p">,</span> <span class="n">backend_name</span><span class="o">=</span><span class="n">cfg</span><span class="o">.</span><span class="n">backend</span><span class="p">,</span>
|
|
2129
|
+
<a id="__codelineno-2-10" name="__codelineno-2-10" href="#__codelineno-2-10"></a> <span class="n">input_ports</span><span class="o">=</span><span class="nb">tuple</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="n">spec</span><span class="o">.</span><span class="n">plugin</span><span class="p">,</span> <span class="s2">"input_ports"</span><span class="p">,</span> <span class="p">())),</span>
|
|
2130
|
+
<a id="__codelineno-2-11" name="__codelineno-2-11" href="#__codelineno-2-11"></a><span class="p">)</span>
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<a id="__codelineno-2-12" name="__codelineno-2-12" href="#__codelineno-2-12"></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>Forward <code>spec.plugin.input_ports</code> to submission so core can stage declared compressed
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inputs before the scientific workflow runs. The CLI and pipeline executor already
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forward these contracts. Keep original compressed paths in the submitted configuration;
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core manages temporary expanded files.</p>
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<p>Core code must not hardcode specific tool names.</p>
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