caddforge-docs 0.3.0__py3-none-any.whl
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- 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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463
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|
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464
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
|
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|
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467
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|
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468
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<label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="">
|
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469
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|
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470
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<span class="md-ellipsis">
|
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475
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How-to Guides
|
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477
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<span class="md-nav__icon md-icon"></span>
|
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484
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</label>
|
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485
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|
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486
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<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
|
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487
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<label class="md-nav__title" for="__nav_3">
|
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488
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<span class="md-nav__icon md-icon"></span>
|
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|
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491
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How-to Guides
|
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492
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493
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494
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</label>
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<ul class="md-nav__list" data-md-scrollfix>
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<li class="md-nav__item">
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<a href="../../how-to/jobs/" class="md-nav__link">
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<span class="md-ellipsis">
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Jobs and Results
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</span>
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</a>
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530
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531
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<li class="md-nav__item">
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532
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<a href="../../how-to/scatter/" class="md-nav__link">
|
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533
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|
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534
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535
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|
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<span class="md-ellipsis">
|
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537
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|
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538
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|
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539
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Scatter and Reduce
|
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540
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|
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541
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542
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|
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543
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</span>
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</a>
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558
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559
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<li class="md-nav__item">
|
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560
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<a href="../../how-to/troubleshooting/" class="md-nav__link">
|
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561
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|
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562
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|
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563
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|
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<span class="md-ellipsis">
|
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565
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|
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566
|
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|
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567
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Troubleshooting
|
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568
|
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|
|
569
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|
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570
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|
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571
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</span>
|
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|
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</a>
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</li>
|
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578
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|
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579
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|
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580
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|
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581
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</ul>
|
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582
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</nav>
|
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583
|
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|
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584
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</li>
|
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585
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|
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<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
|
619
|
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|
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620
|
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|
|
621
|
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|
|
622
|
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
|
|
623
|
+
|
|
624
|
+
|
|
625
|
+
<div class="md-nav__link md-nav__container">
|
|
626
|
+
<a href="../../core/" class="md-nav__link ">
|
|
627
|
+
|
|
628
|
+
|
|
629
|
+
|
|
630
|
+
<span class="md-ellipsis">
|
|
631
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|
|
632
|
+
|
|
633
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Core
|
|
634
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|
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635
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|
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636
|
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|
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637
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</span>
|
|
638
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|
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639
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|
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640
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|
|
641
|
+
</a>
|
|
642
|
+
|
|
643
|
+
|
|
644
|
+
<label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
|
|
645
|
+
<span class="md-nav__icon md-icon"></span>
|
|
646
|
+
</label>
|
|
647
|
+
|
|
648
|
+
</div>
|
|
649
|
+
|
|
650
|
+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
|
|
651
|
+
<label class="md-nav__title" for="__nav_4">
|
|
652
|
+
<span class="md-nav__icon md-icon"></span>
|
|
653
|
+
|
|
654
|
+
|
|
655
|
+
Core
|
|
656
|
+
|
|
657
|
+
|
|
658
|
+
</label>
|
|
659
|
+
<ul class="md-nav__list" data-md-scrollfix>
|
|
660
|
+
|
|
661
|
+
|
|
662
|
+
|
|
663
|
+
|
|
664
|
+
|
|
665
|
+
|
|
666
|
+
|
|
667
|
+
<li class="md-nav__item">
|
|
668
|
+
<a href="../../core/concepts/" class="md-nav__link">
|
|
669
|
+
|
|
670
|
+
|
|
671
|
+
|
|
672
|
+
<span class="md-ellipsis">
|
|
673
|
+
|
|
674
|
+
|
|
675
|
+
Concepts
|
|
676
|
+
|
|
677
|
+
|
|
678
|
+
|
|
679
|
+
</span>
|
|
680
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|
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681
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682
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|
|
683
|
+
</a>
|
|
684
|
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</li>
|
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685
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|
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686
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692
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|
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693
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|
|
694
|
+
|
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695
|
+
<li class="md-nav__item">
|
|
696
|
+
<a href="../../core/configuration/" class="md-nav__link">
|
|
697
|
+
|
|
698
|
+
|
|
699
|
+
|
|
700
|
+
<span class="md-ellipsis">
|
|
701
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+
|
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702
|
+
|
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703
|
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Configuration
|
|
704
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+
|
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705
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|
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706
|
+
|
|
707
|
+
</span>
|
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708
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|
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709
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|
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710
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|
|
711
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+
</a>
|
|
712
|
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</li>
|
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713
|
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|
|
714
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|
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715
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|
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716
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|
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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
|
+
|
|
722
|
+
|
|
723
|
+
<li class="md-nav__item">
|
|
724
|
+
<a href="../../core/cli/" class="md-nav__link">
|
|
725
|
+
|
|
726
|
+
|
|
727
|
+
|
|
728
|
+
<span class="md-ellipsis">
|
|
729
|
+
|
|
730
|
+
|
|
731
|
+
CLI
|
|
732
|
+
|
|
733
|
+
|
|
734
|
+
|
|
735
|
+
</span>
|
|
736
|
+
|
|
737
|
+
|
|
738
|
+
|
|
739
|
+
</a>
|
|
740
|
+
</li>
|
|
741
|
+
|
|
742
|
+
|
|
743
|
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|
|
744
|
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|
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745
|
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|
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746
|
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|
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747
|
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|
|
748
|
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|
|
749
|
+
|
|
750
|
+
|
|
751
|
+
<li class="md-nav__item">
|
|
752
|
+
<a href="../../core/jobs-results/" class="md-nav__link">
|
|
753
|
+
|
|
754
|
+
|
|
755
|
+
|
|
756
|
+
<span class="md-ellipsis">
|
|
757
|
+
|
|
758
|
+
|
|
759
|
+
Jobs and Results
|
|
760
|
+
|
|
761
|
+
|
|
762
|
+
|
|
763
|
+
</span>
|
|
764
|
+
|
|
765
|
+
|
|
766
|
+
|
|
767
|
+
</a>
|
|
768
|
+
</li>
|
|
769
|
+
|
|
770
|
+
|
|
771
|
+
|
|
772
|
+
|
|
773
|
+
|
|
774
|
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|
|
775
|
+
|
|
776
|
+
|
|
777
|
+
|
|
778
|
+
|
|
779
|
+
<li class="md-nav__item">
|
|
780
|
+
<a href="../../core/slurm/" class="md-nav__link">
|
|
781
|
+
|
|
782
|
+
|
|
783
|
+
|
|
784
|
+
<span class="md-ellipsis">
|
|
785
|
+
|
|
786
|
+
|
|
787
|
+
Slurm Backend
|
|
788
|
+
|
|
789
|
+
|
|
790
|
+
|
|
791
|
+
</span>
|
|
792
|
+
|
|
793
|
+
|
|
794
|
+
|
|
795
|
+
</a>
|
|
796
|
+
</li>
|
|
797
|
+
|
|
798
|
+
|
|
799
|
+
|
|
800
|
+
|
|
801
|
+
|
|
802
|
+
|
|
803
|
+
|
|
804
|
+
|
|
805
|
+
|
|
806
|
+
|
|
807
|
+
<li class="md-nav__item">
|
|
808
|
+
<a href="../../core/plugins/" class="md-nav__link">
|
|
809
|
+
|
|
810
|
+
|
|
811
|
+
|
|
812
|
+
<span class="md-ellipsis">
|
|
813
|
+
|
|
814
|
+
|
|
815
|
+
Plugins
|
|
816
|
+
|
|
817
|
+
|
|
818
|
+
|
|
819
|
+
</span>
|
|
820
|
+
|
|
821
|
+
|
|
822
|
+
|
|
823
|
+
</a>
|
|
824
|
+
</li>
|
|
825
|
+
|
|
826
|
+
|
|
827
|
+
|
|
828
|
+
|
|
829
|
+
</ul>
|
|
830
|
+
</nav>
|
|
831
|
+
|
|
832
|
+
</li>
|
|
833
|
+
|
|
834
|
+
|
|
835
|
+
|
|
836
|
+
|
|
837
|
+
|
|
838
|
+
|
|
839
|
+
|
|
840
|
+
|
|
841
|
+
|
|
842
|
+
|
|
843
|
+
|
|
844
|
+
|
|
845
|
+
|
|
846
|
+
|
|
847
|
+
|
|
848
|
+
|
|
849
|
+
|
|
850
|
+
|
|
851
|
+
|
|
852
|
+
|
|
853
|
+
|
|
854
|
+
|
|
855
|
+
|
|
856
|
+
|
|
857
|
+
|
|
858
|
+
|
|
859
|
+
|
|
860
|
+
|
|
861
|
+
|
|
862
|
+
<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
|
863
|
+
|
|
864
|
+
|
|
865
|
+
|
|
866
|
+
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
|
|
867
|
+
|
|
868
|
+
|
|
869
|
+
<div class="md-nav__link md-nav__container">
|
|
870
|
+
<a href="../../pipelines/" class="md-nav__link ">
|
|
871
|
+
|
|
872
|
+
|
|
873
|
+
|
|
874
|
+
<span class="md-ellipsis">
|
|
875
|
+
|
|
876
|
+
|
|
877
|
+
Pipelines
|
|
878
|
+
|
|
879
|
+
|
|
880
|
+
|
|
881
|
+
</span>
|
|
882
|
+
|
|
883
|
+
|
|
884
|
+
|
|
885
|
+
</a>
|
|
886
|
+
|
|
887
|
+
|
|
888
|
+
<label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
|
|
889
|
+
<span class="md-nav__icon md-icon"></span>
|
|
890
|
+
</label>
|
|
891
|
+
|
|
892
|
+
</div>
|
|
893
|
+
|
|
894
|
+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
|
|
895
|
+
<label class="md-nav__title" for="__nav_5">
|
|
896
|
+
<span class="md-nav__icon md-icon"></span>
|
|
897
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Pipelines
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901
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</label>
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<ul class="md-nav__list" data-md-scrollfix>
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910
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911
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<li class="md-nav__item">
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912
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<a href="../../pipelines/specification/" class="md-nav__link">
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913
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914
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915
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<span class="md-ellipsis">
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919
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Specification
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921
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926
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<li class="md-nav__item">
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940
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<a href="../../pipelines/artifacts/" class="md-nav__link">
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942
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<span class="md-ellipsis">
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Artifacts
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950
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966
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967
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<li class="md-nav__item">
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968
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<a href="../../pipelines/built-ins/" class="md-nav__link">
|
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969
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970
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971
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<span class="md-ellipsis">
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973
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975
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Built-in Stages
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978
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980
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981
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</a>
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987
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994
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995
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<li class="md-nav__item">
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996
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<a href="../../pipelines/examples/" class="md-nav__link">
|
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997
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998
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999
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1000
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<span class="md-ellipsis">
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1001
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1002
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1003
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Examples
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1004
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1005
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1006
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|
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1007
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</span>
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1008
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1009
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1010
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</a>
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1016
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</ul>
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1018
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</nav>
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1021
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1024
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1038
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1056
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1057
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<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
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1060
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1061
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1062
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" >
|
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1063
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|
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1064
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+
|
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1065
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+
<div class="md-nav__link md-nav__container">
|
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1066
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+
<a href="../../plugins/" class="md-nav__link ">
|
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1067
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+
|
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1068
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|
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1069
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+
|
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1070
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+
<span class="md-ellipsis">
|
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1071
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+
|
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1072
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|
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1073
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+
Plugins
|
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1074
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|
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1075
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|
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1076
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|
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1077
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</span>
|
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1078
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1079
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|
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1080
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|
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1081
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</a>
|
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1082
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+
|
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1083
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+
|
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1084
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+
<label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
|
|
1085
|
+
<span class="md-nav__icon md-icon"></span>
|
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1086
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+
</label>
|
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1087
|
+
|
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1088
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+
</div>
|
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1089
|
+
|
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1090
|
+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="false">
|
|
1091
|
+
<label class="md-nav__title" for="__nav_6">
|
|
1092
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1093
|
+
|
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1094
|
+
|
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1095
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+
Plugins
|
|
1096
|
+
|
|
1097
|
+
|
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1098
|
+
</label>
|
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1099
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+
<ul class="md-nav__list" data-md-scrollfix>
|
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1100
|
+
|
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1101
|
+
|
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1102
|
+
|
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1103
|
+
|
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1104
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1105
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|
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1106
|
+
|
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1107
|
+
<li class="md-nav__item">
|
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1108
|
+
<a href="../../plugins/version-matrix/" class="md-nav__link">
|
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1109
|
+
|
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1110
|
+
|
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1111
|
+
|
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1112
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+
<span class="md-ellipsis">
|
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1113
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+
|
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1114
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+
|
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1115
|
+
Version Matrix
|
|
1116
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+
|
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1117
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+
|
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1118
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+
|
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1119
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+
</span>
|
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1120
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|
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1121
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1122
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+
|
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1123
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+
</a>
|
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1124
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</li>
|
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1125
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1126
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1127
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1128
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1129
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1130
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1133
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1134
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1135
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<li class="md-nav__item">
|
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1136
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<a href="../../plugins/docking/" class="md-nav__link">
|
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1137
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|
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1138
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|
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1139
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1140
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<span class="md-ellipsis">
|
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1141
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1142
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1143
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Docking
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1144
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|
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1145
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1146
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|
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1147
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</span>
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1148
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1149
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1150
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|
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1151
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</a>
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1152
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</li>
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1155
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1161
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1162
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|
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1163
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<li class="md-nav__item">
|
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1164
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<a href="../../plugins/descriptors/" class="md-nav__link">
|
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1165
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+
|
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1166
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|
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1167
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|
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1168
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+
<span class="md-ellipsis">
|
|
1169
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|
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1170
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+
|
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1171
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+
Descriptors
|
|
1172
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|
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1173
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+
|
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1174
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+
|
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1175
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+
</span>
|
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1176
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|
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1177
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+
|
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1178
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|
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1179
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+
</a>
|
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1180
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</li>
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1181
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1182
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1189
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|
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1190
|
+
|
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1191
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+
<li class="md-nav__item">
|
|
1192
|
+
<a href="../../plugins/md/" class="md-nav__link">
|
|
1193
|
+
|
|
1194
|
+
|
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1195
|
+
|
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1196
|
+
<span class="md-ellipsis">
|
|
1197
|
+
|
|
1198
|
+
|
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1199
|
+
MD
|
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1200
|
+
|
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1201
|
+
|
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1202
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+
|
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1203
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+
</span>
|
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1204
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1205
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1206
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|
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1207
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+
</a>
|
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1208
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+
</li>
|
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1209
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1210
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1211
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1212
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1213
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1214
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1215
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1216
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1217
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|
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1218
|
+
|
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1219
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+
<li class="md-nav__item">
|
|
1220
|
+
<a href="../../plugins/fep/" class="md-nav__link">
|
|
1221
|
+
|
|
1222
|
+
|
|
1223
|
+
|
|
1224
|
+
<span class="md-ellipsis">
|
|
1225
|
+
|
|
1226
|
+
|
|
1227
|
+
FEP
|
|
1228
|
+
|
|
1229
|
+
|
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1230
|
+
|
|
1231
|
+
</span>
|
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1232
|
+
|
|
1233
|
+
|
|
1234
|
+
|
|
1235
|
+
</a>
|
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1236
|
+
</li>
|
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1237
|
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1238
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1239
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1240
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1241
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1242
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1243
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1244
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|
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1245
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|
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1246
|
+
|
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1247
|
+
<li class="md-nav__item">
|
|
1248
|
+
<a href="../../plugins/qm/" class="md-nav__link">
|
|
1249
|
+
|
|
1250
|
+
|
|
1251
|
+
|
|
1252
|
+
<span class="md-ellipsis">
|
|
1253
|
+
|
|
1254
|
+
|
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1255
|
+
QM
|
|
1256
|
+
|
|
1257
|
+
|
|
1258
|
+
|
|
1259
|
+
</span>
|
|
1260
|
+
|
|
1261
|
+
|
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1262
|
+
|
|
1263
|
+
</a>
|
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1264
|
+
</li>
|
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1265
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1266
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1267
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1268
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1269
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1270
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1271
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1272
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1273
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|
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1274
|
+
|
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1275
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+
<li class="md-nav__item">
|
|
1276
|
+
<a href="../../plugins/ml/" class="md-nav__link">
|
|
1277
|
+
|
|
1278
|
+
|
|
1279
|
+
|
|
1280
|
+
<span class="md-ellipsis">
|
|
1281
|
+
|
|
1282
|
+
|
|
1283
|
+
ML
|
|
1284
|
+
|
|
1285
|
+
|
|
1286
|
+
|
|
1287
|
+
</span>
|
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1288
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|
|
1289
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+
|
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1290
|
+
|
|
1291
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</a>
|
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1292
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</li>
|
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1293
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1294
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1295
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1296
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1297
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1298
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|
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1299
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|
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1300
|
+
|
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1301
|
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|
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1302
|
+
|
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1303
|
+
<li class="md-nav__item">
|
|
1304
|
+
<a href="../../plugins/datascience/" class="md-nav__link">
|
|
1305
|
+
|
|
1306
|
+
|
|
1307
|
+
|
|
1308
|
+
<span class="md-ellipsis">
|
|
1309
|
+
|
|
1310
|
+
|
|
1311
|
+
Data Science
|
|
1312
|
+
|
|
1313
|
+
|
|
1314
|
+
|
|
1315
|
+
</span>
|
|
1316
|
+
|
|
1317
|
+
|
|
1318
|
+
|
|
1319
|
+
</a>
|
|
1320
|
+
</li>
|
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1321
|
+
|
|
1322
|
+
|
|
1323
|
+
|
|
1324
|
+
|
|
1325
|
+
</ul>
|
|
1326
|
+
</nav>
|
|
1327
|
+
|
|
1328
|
+
</li>
|
|
1329
|
+
|
|
1330
|
+
|
|
1331
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+
|
|
1332
|
+
|
|
1333
|
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|
1334
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|
|
1335
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|
|
1336
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+
|
|
1337
|
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|
|
1338
|
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|
|
1339
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|
|
1340
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|
|
1341
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|
|
1342
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|
|
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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<label class="md-nav__title" for="__nav_8">
|
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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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Example Data Provenance
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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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1645
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_9" >
|
|
1647
|
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|
|
1648
|
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|
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1649
|
+
<label class="md-nav__link" for="__nav_9" id="__nav_9_label" tabindex="">
|
|
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|
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<span class="md-ellipsis">
|
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|
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|
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|
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1656
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Explanation
|
|
1657
|
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|
|
1658
|
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|
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1659
|
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|
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1660
|
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|
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|
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1663
|
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|
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1664
|
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<span class="md-nav__icon md-icon"></span>
|
|
1665
|
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</label>
|
|
1666
|
+
|
|
1667
|
+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_9_label" aria-expanded="false">
|
|
1668
|
+
<label class="md-nav__title" for="__nav_9">
|
|
1669
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1670
|
+
|
|
1671
|
+
|
|
1672
|
+
Explanation
|
|
1673
|
+
|
|
1674
|
+
|
|
1675
|
+
</label>
|
|
1676
|
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<ul class="md-nav__list" data-md-scrollfix>
|
|
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|
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1678
|
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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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|
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<a href="../../explanation/reproducibility/" class="md-nav__link">
|
|
1686
|
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|
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1687
|
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|
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1688
|
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+
<span class="md-ellipsis">
|
|
1690
|
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|
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1691
|
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|
|
1692
|
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Reproducibility
|
|
1693
|
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|
|
1694
|
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|
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1695
|
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|
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1696
|
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</span>
|
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1699
|
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|
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|
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<li class="md-nav__item">
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<a href="../../explanation/references/" class="md-nav__link">
|
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|
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|
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<span class="md-ellipsis">
|
|
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|
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|
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1719
|
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|
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1720
|
+
Method References
|
|
1721
|
+
|
|
1722
|
+
|
|
1723
|
+
|
|
1724
|
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</span>
|
|
1725
|
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|
|
1726
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|
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1727
|
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|
|
1728
|
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</a>
|
|
1729
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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">
|
|
1742
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1743
|
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|
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1744
|
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|
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1745
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+
<span class="md-ellipsis">
|
|
1746
|
+
|
|
1747
|
+
|
|
1748
|
+
Third-party Notices
|
|
1749
|
+
|
|
1750
|
+
|
|
1751
|
+
|
|
1752
|
+
</span>
|
|
1753
|
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|
|
1754
|
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|
|
1755
|
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|
|
1756
|
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</a>
|
|
1757
|
+
</li>
|
|
1758
|
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|
|
1759
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|
|
1760
|
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|
|
1761
|
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|
|
1762
|
+
</ul>
|
|
1763
|
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</nav>
|
|
1764
|
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|
|
1765
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</li>
|
|
1766
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|
1767
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|
|
1768
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|
|
1769
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1770
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1771
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1772
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1773
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|
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Validate a change
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Python distribution releases
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|
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2157
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<span class="md-ellipsis">
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|
2158
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|
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2159
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Validate a change
|
|
2160
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|
|
2161
|
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|
|
2162
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</a>
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2167
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|
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2168
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|
|
2169
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|
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2170
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Host the generated site
|
|
2171
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|
|
2172
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|
|
2173
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</a>
|
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2178
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|
|
2179
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<span class="md-ellipsis">
|
|
2180
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|
|
2181
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Python distribution releases
|
|
2182
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2183
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<div class="md-content" data-md-component="content">
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<article class="md-content__inner md-typeset">
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<h1 id="ci-and-publishing">CI and Publishing<a class="headerlink" href="#ci-and-publishing" title="Permanent link">¶</a></h1>
|
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<p>Documentation validation is separate from deployment and Python package upload.</p>
|
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|
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<h2 id="validate-a-change">Validate a change<a class="headerlink" href="#validate-a-change" title="Permanent link">¶</a></h2>
|
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|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>python<span class="w"> </span>-m<span class="w"> </span>pip<span class="w"> </span>install<span class="w"> </span>-r<span class="w"> </span>requirements.txt<span class="w"> </span>-r<span class="w"> </span>requirements-test.txt
|
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2212
|
+
<a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a>properdocs<span class="w"> </span>build<span class="w"> </span>--strict<span class="w"> </span>--site-dir<span class="w"> </span>site
|
|
2213
|
+
<a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a>python<span class="w"> </span>scripts/check_links.py<span class="w"> </span>site
|
|
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|
+
<a id="__codelineno-0-4" name="__codelineno-0-4" href="#__codelineno-0-4"></a>python<span class="w"> </span>-m<span class="w"> </span>pytest<span class="w"> </span>-q
|
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|
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</code></pre></div>
|
|
2216
|
+
<p>The tests build wheels and rebuild from a source distribution, check packaged
|
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|
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assets, and test the installed-docs CLI and server. Tutorial
|
|
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|
+
integration tests require compatible core and data-science installations; they
|
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|
+
report skips when those packages are absent. Run them explicitly in a compatible
|
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|
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public-component environment before release.</p>
|
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|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>python<span class="w"> </span>-m<span class="w"> </span>pytest<span class="w"> </span>tests/test_examples.py<span class="w"> </span>-q<span class="w"> </span>--require-examples
|
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|
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</code></pre></div>
|
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|
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<p>GitHub branch and tag pushes and pull requests run documentation checks without
|
|
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|
+
requiring deployment. Publication jobs depend
|
|
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|
+
on successful validation. Optional scientific
|
|
2226
|
+
template schema checks use an explicit list of public configuration classes;
|
|
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|
+
they do not discover arbitrary installed plugins.</p>
|
|
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|
+
<h2 id="host-the-generated-site">Host the generated site<a class="headerlink" href="#host-the-generated-site" title="Permanent link">¶</a></h2>
|
|
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|
+
<p>GitHub Pages uses <code>.github/workflows/pages.yml</code>. Enable Pages with the GitHub
|
|
2230
|
+
Actions source, then opt in with repository variable <code>DOCS_PUBLISH_ENABLED=true</code>.
|
|
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|
+
Builds produce static artifacts on ordinary changes, but deployments run only for an
|
|
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|
+
enabled default branch, including a manual workflow on that branch. Release tags
|
|
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|
+
run validation without deploying Pages.</p>
|
|
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|
+
<p>Configure the public site and repository URLs in <code>properdocs.yml</code> after hosting
|
|
2235
|
+
is established. The source is platform-neutral. The installed docs package ships
|
|
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|
+
its own site; hosting is not required to use <code>caddforge docs</code>.</p>
|
|
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|
+
<h2 id="python-distribution-releases">Python distribution releases<a class="headerlink" href="#python-distribution-releases" title="Permanent link">¶</a></h2>
|
|
2238
|
+
<p><code>caddforge-core</code> owns Python modules and the CLI. The metadata-only bundle publishes
|
|
2239
|
+
the <code>caddforge</code> distribution and pins the reviewed component set. See
|
|
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|
+
<a href="../release-readiness/">release prerequisites</a> before any release.</p>
|
|
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|
+
<p>Every public component uses <code>.github/workflows/release.yml</code> for branch/PR
|
|
2242
|
+
validation and publication on pushed <code>v*</code> tags, matching PyOCL and the
|
|
2243
|
+
maintained third-party tools. A single Python 3.12 build produces the wheel
|
|
2244
|
+
and source archive; tests install that exact wheel on Linux with Python
|
|
2245
|
+
3.10 and 3.12. Publication depends on all required checks. Manual runs and
|
|
2246
|
+
branch pushes do not publish. No <code>PYPI_PUBLISH_ENABLED</code> variable is used.</p>
|
|
2247
|
+
<p>Metadata checks run on ordinary builds as well as tags. They reject private
|
|
2248
|
+
dependencies and direct Git requirements, compare wheel/source metadata, and
|
|
2249
|
+
require a release tag to match the built version. Release tags must have
|
|
2250
|
+
public versions without local or <code>.dev</code> suffixes; a <code>0.x</code> version still
|
|
2251
|
+
represents the project's initial development series. Core and plugin versions
|
|
2252
|
+
come from Git tags. Docs and bundle versions are explicit in <code>pyproject.toml</code>
|
|
2253
|
+
and must be updated before tagging.</p>
|
|
2254
|
+
<p>The tests run from temporary fixture copies without checkout <code>src</code> directories.
|
|
2255
|
+
Core, data-science, GUI, ML, QM and docking run their regression suites.
|
|
2256
|
+
Descriptors run plugin, clustering and PheSA tests without downloading ANI
|
|
2257
|
+
weights. MD runs configuration, trajectory and workflow contract tests;
|
|
2258
|
+
external engines and long simulations remain separate. FEP tests orchestration
|
|
2259
|
+
and settings without requiring an OpenFE runtime. FEP and docking install
|
|
2260
|
+
the candidate wheel with its <code>[gui]</code> extra so GUI regression tests exercise
|
|
2261
|
+
the declared dependencies, including the published <code>caddforge-gui</code> package.
|
|
2262
|
+
Each selection is recorded
|
|
2263
|
+
in <code>scripts/ci_tests.json</code>. These profiles do not claim GPU or complete
|
|
2264
|
+
scientific-engine validation.</p>
|
|
2265
|
+
<p>Docs additionally validates source examples, assets, links and distribution
|
|
2266
|
+
rebuilding, tests the installed viewer, and requires successful execution of
|
|
2267
|
+
the CLI/Python tutorials using published core and data science. The docs wheel
|
|
2268
|
+
is installed with its <code>[test]</code> extra, including Rich for terminal-output
|
|
2269
|
+
assertions. The bundle runs the ownership migration with an
|
|
2270
|
+
explicit core source checkout, and requires a clean full installation from
|
|
2271
|
+
public PyPI before publishing. Its release must follow its pinned components.</p>
|
|
2272
|
+
<p>For each PyPI project, configure a Trusted Publisher with GitHub owner
|
|
2273
|
+
<code>idorsia</code>, the corresponding repository, workflow filename <code>release.yml</code>,
|
|
2274
|
+
and environment <code>pypi</code>. For the bundle the PyPI project is <code>caddforge</code>,
|
|
2275
|
+
while the repository is <code>caddforge-bundle</code>. GitHub environments may require
|
|
2276
|
+
reviewer approval if desired. Repository workflows cannot configure these
|
|
2277
|
+
PyPI account settings for you. Publish core first, then GUI before FEP and
|
|
2278
|
+
docking. Publish docking and descriptors before MD, and data-science before
|
|
2279
|
+
docs. Publish the bundle last.</p>
|
|
2280
|
+
<p>Pushing a release tag is the publication action once the Trusted Publisher
|
|
2281
|
+
is configured. <code>.github/workflows/pages.yml</code> handles site deployment independently
|
|
2282
|
+
and retains the explicit <code>DOCS_PUBLISH_ENABLED=true</code> opt-in.</p>
|
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2283
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+
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2284
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</article>
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</div>
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<script>var target=document.getElementById(location.hash.slice(1));target&&target.name&&(target.checked=target.name.startsWith("__tabbed_"))</script>
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</div>
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<button type="button" class="md-top md-icon" data-md-component="top" hidden>
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M13 20h-2V8l-5.5 5.5-1.42-1.42L12 4.16l7.92 7.92-1.42 1.42L13 8z"/></svg>
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Back to top
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</button>
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</main>
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<footer class="md-footer">
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<div class="md-footer-meta md-typeset">
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<div class="md-footer-meta__inner md-grid">
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<div class="md-copyright">
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Made with
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<a href="https://squidfunk.github.io/mkdocs-material/" target="_blank" rel="noopener">
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Material for MkDocs
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</a>
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<div class="md-dialog" data-md-component="dialog">
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<div class="md-dialog__inner md-typeset"></div>
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<script id="__config" type="application/json">{"annotate": null, "base": "../..", "features": ["navigation.instant", "navigation.sections", "navigation.indexes", "navigation.top", "search.highlight", "search.suggest", "content.code.copy"], "search": "../../assets/javascripts/workers/search.2c215733.min.js", "tags": null, "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}, "version": null}</script>
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<script src="../../assets/javascripts/bundle.d7400e89.min.js"></script>
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