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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464
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|
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465
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|
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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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471
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|
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472
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|
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<span class="md-ellipsis">
|
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|
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|
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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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480
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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
|
+
<label class="md-nav__title" for="__nav_3">
|
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<span class="md-nav__icon md-icon"></span>
|
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491
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|
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492
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|
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How-to Guides
|
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494
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|
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495
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496
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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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|
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509
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<span class="md-ellipsis">
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511
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512
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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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535
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|
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536
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|
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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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|
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545
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</span>
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</a>
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</li>
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|
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|
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560
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561
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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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568
|
+
|
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569
|
+
Troubleshooting
|
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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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|
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|
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576
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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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579
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|
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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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586
|
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</li>
|
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587
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588
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|
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|
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619
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|
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<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
|
621
|
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|
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622
|
+
|
|
623
|
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|
|
624
|
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
|
|
625
|
+
|
|
626
|
+
|
|
627
|
+
<div class="md-nav__link md-nav__container">
|
|
628
|
+
<a href="../../core/" class="md-nav__link ">
|
|
629
|
+
|
|
630
|
+
|
|
631
|
+
|
|
632
|
+
<span class="md-ellipsis">
|
|
633
|
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|
|
634
|
+
|
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635
|
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Core
|
|
636
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|
|
637
|
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|
|
638
|
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|
|
639
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</span>
|
|
640
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|
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641
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|
|
642
|
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|
|
643
|
+
</a>
|
|
644
|
+
|
|
645
|
+
|
|
646
|
+
<label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
|
|
647
|
+
<span class="md-nav__icon md-icon"></span>
|
|
648
|
+
</label>
|
|
649
|
+
|
|
650
|
+
</div>
|
|
651
|
+
|
|
652
|
+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
|
|
653
|
+
<label class="md-nav__title" for="__nav_4">
|
|
654
|
+
<span class="md-nav__icon md-icon"></span>
|
|
655
|
+
|
|
656
|
+
|
|
657
|
+
Core
|
|
658
|
+
|
|
659
|
+
|
|
660
|
+
</label>
|
|
661
|
+
<ul class="md-nav__list" data-md-scrollfix>
|
|
662
|
+
|
|
663
|
+
|
|
664
|
+
|
|
665
|
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|
|
666
|
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|
|
667
|
+
|
|
668
|
+
|
|
669
|
+
<li class="md-nav__item">
|
|
670
|
+
<a href="../../core/concepts/" class="md-nav__link">
|
|
671
|
+
|
|
672
|
+
|
|
673
|
+
|
|
674
|
+
<span class="md-ellipsis">
|
|
675
|
+
|
|
676
|
+
|
|
677
|
+
Concepts
|
|
678
|
+
|
|
679
|
+
|
|
680
|
+
|
|
681
|
+
</span>
|
|
682
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|
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683
|
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|
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684
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|
|
685
|
+
</a>
|
|
686
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</li>
|
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687
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|
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688
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|
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689
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694
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|
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695
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|
|
696
|
+
|
|
697
|
+
<li class="md-nav__item">
|
|
698
|
+
<a href="../../core/configuration/" class="md-nav__link">
|
|
699
|
+
|
|
700
|
+
|
|
701
|
+
|
|
702
|
+
<span class="md-ellipsis">
|
|
703
|
+
|
|
704
|
+
|
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705
|
+
Configuration
|
|
706
|
+
|
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707
|
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|
|
708
|
+
|
|
709
|
+
</span>
|
|
710
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|
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711
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|
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712
|
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|
|
713
|
+
</a>
|
|
714
|
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</li>
|
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715
|
+
|
|
716
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|
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717
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|
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718
|
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|
|
719
|
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|
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720
|
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|
|
721
|
+
|
|
722
|
+
|
|
723
|
+
|
|
724
|
+
|
|
725
|
+
<li class="md-nav__item">
|
|
726
|
+
<a href="../../core/cli/" class="md-nav__link">
|
|
727
|
+
|
|
728
|
+
|
|
729
|
+
|
|
730
|
+
<span class="md-ellipsis">
|
|
731
|
+
|
|
732
|
+
|
|
733
|
+
CLI
|
|
734
|
+
|
|
735
|
+
|
|
736
|
+
|
|
737
|
+
</span>
|
|
738
|
+
|
|
739
|
+
|
|
740
|
+
|
|
741
|
+
</a>
|
|
742
|
+
</li>
|
|
743
|
+
|
|
744
|
+
|
|
745
|
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|
|
746
|
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|
|
747
|
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|
|
748
|
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|
|
749
|
+
|
|
750
|
+
|
|
751
|
+
|
|
752
|
+
|
|
753
|
+
<li class="md-nav__item">
|
|
754
|
+
<a href="../../core/jobs-results/" class="md-nav__link">
|
|
755
|
+
|
|
756
|
+
|
|
757
|
+
|
|
758
|
+
<span class="md-ellipsis">
|
|
759
|
+
|
|
760
|
+
|
|
761
|
+
Jobs and Results
|
|
762
|
+
|
|
763
|
+
|
|
764
|
+
|
|
765
|
+
</span>
|
|
766
|
+
|
|
767
|
+
|
|
768
|
+
|
|
769
|
+
</a>
|
|
770
|
+
</li>
|
|
771
|
+
|
|
772
|
+
|
|
773
|
+
|
|
774
|
+
|
|
775
|
+
|
|
776
|
+
|
|
777
|
+
|
|
778
|
+
|
|
779
|
+
|
|
780
|
+
|
|
781
|
+
<li class="md-nav__item">
|
|
782
|
+
<a href="../../core/slurm/" class="md-nav__link">
|
|
783
|
+
|
|
784
|
+
|
|
785
|
+
|
|
786
|
+
<span class="md-ellipsis">
|
|
787
|
+
|
|
788
|
+
|
|
789
|
+
Slurm Backend
|
|
790
|
+
|
|
791
|
+
|
|
792
|
+
|
|
793
|
+
</span>
|
|
794
|
+
|
|
795
|
+
|
|
796
|
+
|
|
797
|
+
</a>
|
|
798
|
+
</li>
|
|
799
|
+
|
|
800
|
+
|
|
801
|
+
|
|
802
|
+
|
|
803
|
+
|
|
804
|
+
|
|
805
|
+
|
|
806
|
+
|
|
807
|
+
|
|
808
|
+
|
|
809
|
+
<li class="md-nav__item">
|
|
810
|
+
<a href="../../core/plugins/" class="md-nav__link">
|
|
811
|
+
|
|
812
|
+
|
|
813
|
+
|
|
814
|
+
<span class="md-ellipsis">
|
|
815
|
+
|
|
816
|
+
|
|
817
|
+
Plugins
|
|
818
|
+
|
|
819
|
+
|
|
820
|
+
|
|
821
|
+
</span>
|
|
822
|
+
|
|
823
|
+
|
|
824
|
+
|
|
825
|
+
</a>
|
|
826
|
+
</li>
|
|
827
|
+
|
|
828
|
+
|
|
829
|
+
|
|
830
|
+
|
|
831
|
+
</ul>
|
|
832
|
+
</nav>
|
|
833
|
+
|
|
834
|
+
</li>
|
|
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
|
+
|
|
863
|
+
|
|
864
|
+
<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
|
865
|
+
|
|
866
|
+
|
|
867
|
+
|
|
868
|
+
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
|
|
869
|
+
|
|
870
|
+
|
|
871
|
+
<div class="md-nav__link md-nav__container">
|
|
872
|
+
<a href="../../pipelines/" class="md-nav__link ">
|
|
873
|
+
|
|
874
|
+
|
|
875
|
+
|
|
876
|
+
<span class="md-ellipsis">
|
|
877
|
+
|
|
878
|
+
|
|
879
|
+
Pipelines
|
|
880
|
+
|
|
881
|
+
|
|
882
|
+
|
|
883
|
+
</span>
|
|
884
|
+
|
|
885
|
+
|
|
886
|
+
|
|
887
|
+
</a>
|
|
888
|
+
|
|
889
|
+
|
|
890
|
+
<label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
|
|
891
|
+
<span class="md-nav__icon md-icon"></span>
|
|
892
|
+
</label>
|
|
893
|
+
|
|
894
|
+
</div>
|
|
895
|
+
|
|
896
|
+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
|
|
897
|
+
<label class="md-nav__title" for="__nav_5">
|
|
898
|
+
<span class="md-nav__icon md-icon"></span>
|
|
899
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Pipelines
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903
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912
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<li class="md-nav__item">
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915
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920
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921
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Specification
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924
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925
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<span class="md-ellipsis">
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Artifacts
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</span>
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968
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969
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<li class="md-nav__item">
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970
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<a href="../../pipelines/built-ins/" class="md-nav__link">
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971
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972
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<span class="md-ellipsis">
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975
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976
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977
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Built-in Stages
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978
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979
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980
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981
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</a>
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996
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997
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<li class="md-nav__item">
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998
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<a href="../../pipelines/examples/" class="md-nav__link">
|
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999
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1000
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1001
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1002
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<span class="md-ellipsis">
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1003
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1004
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1005
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Examples
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1006
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1007
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1008
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1009
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</span>
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</a>
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1016
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</ul>
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1020
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</nav>
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1021
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1024
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1059
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<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
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1062
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1063
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" >
|
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1065
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|
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1066
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+
|
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1067
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<div class="md-nav__link md-nav__container">
|
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1068
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+
<a href="../../plugins/" class="md-nav__link ">
|
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1069
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|
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1070
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1071
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|
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1072
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+
<span class="md-ellipsis">
|
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1073
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|
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1074
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1075
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Plugins
|
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1076
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|
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1077
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|
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1078
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1079
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</span>
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1080
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1081
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1082
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1083
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</a>
|
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1084
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1085
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1086
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+
<label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
|
|
1087
|
+
<span class="md-nav__icon md-icon"></span>
|
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1088
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+
</label>
|
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1089
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+
|
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1090
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+
</div>
|
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1091
|
+
|
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1092
|
+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="false">
|
|
1093
|
+
<label class="md-nav__title" for="__nav_6">
|
|
1094
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1095
|
+
|
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1096
|
+
|
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1097
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+
Plugins
|
|
1098
|
+
|
|
1099
|
+
|
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1100
|
+
</label>
|
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1101
|
+
<ul class="md-nav__list" data-md-scrollfix>
|
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1102
|
+
|
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1103
|
+
|
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1104
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1105
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1106
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1108
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|
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1109
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+
<li class="md-nav__item">
|
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1110
|
+
<a href="../../plugins/version-matrix/" class="md-nav__link">
|
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1111
|
+
|
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1112
|
+
|
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1113
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+
|
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1114
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+
<span class="md-ellipsis">
|
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1115
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+
|
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1116
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+
|
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1117
|
+
Version Matrix
|
|
1118
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+
|
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1119
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+
|
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1120
|
+
|
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1121
|
+
</span>
|
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1122
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|
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1123
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1124
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|
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1125
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</a>
|
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1126
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</li>
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1128
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1129
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1136
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1137
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<li class="md-nav__item">
|
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1138
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<a href="../../plugins/docking/" class="md-nav__link">
|
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1139
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|
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1140
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1141
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1142
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<span class="md-ellipsis">
|
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1143
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1144
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1145
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Docking
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1146
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1147
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1148
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1149
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</span>
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1150
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1151
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1152
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1153
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</a>
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1154
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1164
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1165
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<li class="md-nav__item">
|
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1166
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<a href="../../plugins/descriptors/" class="md-nav__link">
|
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1167
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|
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1168
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1169
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|
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1170
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<span class="md-ellipsis">
|
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1171
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|
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1172
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|
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1173
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+
Descriptors
|
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1174
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1175
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1176
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|
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1177
|
+
</span>
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1178
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1179
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1180
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1181
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</a>
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1182
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1190
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1191
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1192
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+
|
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1193
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+
<li class="md-nav__item">
|
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1194
|
+
<a href="../../plugins/md/" class="md-nav__link">
|
|
1195
|
+
|
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1196
|
+
|
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1197
|
+
|
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1198
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+
<span class="md-ellipsis">
|
|
1199
|
+
|
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1200
|
+
|
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1201
|
+
MD
|
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1202
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1203
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1204
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|
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1205
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+
</span>
|
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1206
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1207
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1208
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1209
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</a>
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1210
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</li>
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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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1218
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1219
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|
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1220
|
+
|
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1221
|
+
<li class="md-nav__item">
|
|
1222
|
+
<a href="../../plugins/fep/" class="md-nav__link">
|
|
1223
|
+
|
|
1224
|
+
|
|
1225
|
+
|
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1226
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+
<span class="md-ellipsis">
|
|
1227
|
+
|
|
1228
|
+
|
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1229
|
+
FEP
|
|
1230
|
+
|
|
1231
|
+
|
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1232
|
+
|
|
1233
|
+
</span>
|
|
1234
|
+
|
|
1235
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|
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1236
|
+
|
|
1237
|
+
</a>
|
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1238
|
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</li>
|
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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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1245
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1246
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1247
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|
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1248
|
+
|
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1249
|
+
<li class="md-nav__item">
|
|
1250
|
+
<a href="../../plugins/qm/" class="md-nav__link">
|
|
1251
|
+
|
|
1252
|
+
|
|
1253
|
+
|
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1254
|
+
<span class="md-ellipsis">
|
|
1255
|
+
|
|
1256
|
+
|
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1257
|
+
QM
|
|
1258
|
+
|
|
1259
|
+
|
|
1260
|
+
|
|
1261
|
+
</span>
|
|
1262
|
+
|
|
1263
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|
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1264
|
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|
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1265
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+
</a>
|
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1266
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</li>
|
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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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1274
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1275
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1276
|
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|
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1277
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+
<li class="md-nav__item">
|
|
1278
|
+
<a href="../../plugins/ml/" class="md-nav__link">
|
|
1279
|
+
|
|
1280
|
+
|
|
1281
|
+
|
|
1282
|
+
<span class="md-ellipsis">
|
|
1283
|
+
|
|
1284
|
+
|
|
1285
|
+
ML
|
|
1286
|
+
|
|
1287
|
+
|
|
1288
|
+
|
|
1289
|
+
</span>
|
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1290
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|
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1291
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+
|
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1292
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|
|
1293
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</a>
|
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1294
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</li>
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1295
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1296
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1297
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1298
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1299
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1300
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|
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1301
|
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1302
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|
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1303
|
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|
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1304
|
+
|
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1305
|
+
<li class="md-nav__item">
|
|
1306
|
+
<a href="../../plugins/datascience/" class="md-nav__link">
|
|
1307
|
+
|
|
1308
|
+
|
|
1309
|
+
|
|
1310
|
+
<span class="md-ellipsis">
|
|
1311
|
+
|
|
1312
|
+
|
|
1313
|
+
Data Science
|
|
1314
|
+
|
|
1315
|
+
|
|
1316
|
+
|
|
1317
|
+
</span>
|
|
1318
|
+
|
|
1319
|
+
|
|
1320
|
+
|
|
1321
|
+
</a>
|
|
1322
|
+
</li>
|
|
1323
|
+
|
|
1324
|
+
|
|
1325
|
+
|
|
1326
|
+
|
|
1327
|
+
</ul>
|
|
1328
|
+
</nav>
|
|
1329
|
+
|
|
1330
|
+
</li>
|
|
1331
|
+
|
|
1332
|
+
|
|
1333
|
+
|
|
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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|
|
1345
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|
|
1346
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+
|
|
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Plugin GUI Authoring
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Reference
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|
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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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|
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1647
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|
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_9" >
|
|
1649
|
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|
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1650
|
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|
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1651
|
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<label class="md-nav__link" for="__nav_9" id="__nav_9_label" tabindex="">
|
|
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<span class="md-ellipsis">
|
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|
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|
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|
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1658
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Explanation
|
|
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|
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|
|
1660
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|
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|
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|
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|
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1665
|
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|
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1666
|
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<span class="md-nav__icon md-icon"></span>
|
|
1667
|
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</label>
|
|
1668
|
+
|
|
1669
|
+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_9_label" aria-expanded="false">
|
|
1670
|
+
<label class="md-nav__title" for="__nav_9">
|
|
1671
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1672
|
+
|
|
1673
|
+
|
|
1674
|
+
Explanation
|
|
1675
|
+
|
|
1676
|
+
|
|
1677
|
+
</label>
|
|
1678
|
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<ul class="md-nav__list" data-md-scrollfix>
|
|
1679
|
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|
1680
|
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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">
|
|
1688
|
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|
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1689
|
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|
|
1690
|
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<span class="md-ellipsis">
|
|
1692
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|
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1693
|
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|
|
1694
|
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Reproducibility
|
|
1695
|
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|
|
1696
|
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|
|
1697
|
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|
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1698
|
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</span>
|
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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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<span class="md-ellipsis">
|
|
1720
|
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|
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1721
|
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|
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1722
|
+
Method References
|
|
1723
|
+
|
|
1724
|
+
|
|
1725
|
+
|
|
1726
|
+
</span>
|
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1727
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1728
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1729
|
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|
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1730
|
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</a>
|
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1731
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</li>
|
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<li class="md-nav__item">
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<a href="../../explanation/third-party-notices/" class="md-nav__link">
|
|
1744
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1745
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|
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1746
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1747
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<span class="md-ellipsis">
|
|
1748
|
+
|
|
1749
|
+
|
|
1750
|
+
Third-party Notices
|
|
1751
|
+
|
|
1752
|
+
|
|
1753
|
+
|
|
1754
|
+
</span>
|
|
1755
|
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|
|
1756
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|
|
1757
|
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|
|
1758
|
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</a>
|
|
1759
|
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</li>
|
|
1760
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|
|
1761
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|
|
1762
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|
|
1763
|
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|
|
1764
|
+
</ul>
|
|
1765
|
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</nav>
|
|
1766
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|
1767
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</li>
|
|
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1769
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1772
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Development
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Development
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Release Notes
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Tool Authoring
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1900
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1901
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<a href="./" class="md-nav__link md-nav__link--active">
|
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1911
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<span class="md-ellipsis">
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Tool Authoring
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1918
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<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
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<label class="md-nav__title" for="__toc">
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<span class="md-nav__icon md-icon"></span>
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Table of contents
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1939
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</label>
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1940
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<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
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1942
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<li class="md-nav__item">
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1943
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<a href="#distribution-dependencies" class="md-nav__link">
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1944
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<span class="md-ellipsis">
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1945
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|
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1946
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Distribution dependencies
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1947
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1948
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</span>
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1949
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</a>
|
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1950
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1951
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</li>
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1952
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1953
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<li class="md-nav__item">
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1954
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<a href="#optional-cli-commands" class="md-nav__link">
|
|
1955
|
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<span class="md-ellipsis">
|
|
1956
|
+
|
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1957
|
+
Optional CLI commands
|
|
1958
|
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|
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1959
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</span>
|
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1960
|
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</a>
|
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1961
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1962
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</li>
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1963
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1964
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<li class="md-nav__item">
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1965
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<a href="#required-pieces" class="md-nav__link">
|
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1966
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<span class="md-ellipsis">
|
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1967
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|
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1968
|
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Required pieces
|
|
1969
|
+
|
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1970
|
+
</span>
|
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1971
|
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</a>
|
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1972
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1973
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1974
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1975
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<li class="md-nav__item">
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1976
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<a href="#pipeline-contracts" class="md-nav__link">
|
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1977
|
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<span class="md-ellipsis">
|
|
1978
|
+
|
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1979
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+
Pipeline contracts
|
|
1980
|
+
|
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1981
|
+
</span>
|
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1982
|
+
</a>
|
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1983
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+
|
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1984
|
+
<nav class="md-nav" aria-label="Pipeline contracts">
|
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1985
|
+
<ul class="md-nav__list">
|
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1986
|
+
|
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1987
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+
<li class="md-nav__item">
|
|
1988
|
+
<a href="#runtime-input-and-compression-contracts" class="md-nav__link">
|
|
1989
|
+
<span class="md-ellipsis">
|
|
1990
|
+
|
|
1991
|
+
Runtime input and compression contracts
|
|
1992
|
+
|
|
1993
|
+
</span>
|
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1994
|
+
</a>
|
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1995
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+
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1996
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</li>
|
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1997
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+
|
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1998
|
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</ul>
|
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1999
|
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</nav>
|
|
2000
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2001
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</li>
|
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2002
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2003
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<li class="md-nav__item">
|
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2004
|
+
<a href="#scratch-publication-helpers" class="md-nav__link">
|
|
2005
|
+
<span class="md-ellipsis">
|
|
2006
|
+
|
|
2007
|
+
Scratch publication helpers
|
|
2008
|
+
|
|
2009
|
+
</span>
|
|
2010
|
+
</a>
|
|
2011
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|
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2012
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</li>
|
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2013
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2014
|
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<li class="md-nav__item">
|
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2015
|
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<a href="#backends" class="md-nav__link">
|
|
2016
|
+
<span class="md-ellipsis">
|
|
2017
|
+
|
|
2018
|
+
Backends
|
|
2019
|
+
|
|
2020
|
+
</span>
|
|
2021
|
+
</a>
|
|
2022
|
+
|
|
2023
|
+
</li>
|
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2024
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2025
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</ul>
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2026
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2027
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</nav>
|
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2028
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2029
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2031
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2039
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2040
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<li class="md-nav__item">
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2041
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<a href="../documentation/" class="md-nav__link">
|
|
2042
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|
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2043
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2044
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<span class="md-ellipsis">
|
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2046
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|
2047
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|
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2048
|
+
Documentation
|
|
2049
|
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|
|
2050
|
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|
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2051
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|
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2052
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2055
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2056
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|
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2057
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2066
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2067
|
+
|
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2068
|
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<li class="md-nav__item">
|
|
2069
|
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<a href="../contributing/" class="md-nav__link">
|
|
2070
|
+
|
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2071
|
+
|
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2072
|
+
|
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2073
|
+
<span class="md-ellipsis">
|
|
2074
|
+
|
|
2075
|
+
|
|
2076
|
+
Contributing
|
|
2077
|
+
|
|
2078
|
+
|
|
2079
|
+
|
|
2080
|
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2081
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|
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2082
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2083
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|
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2084
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|
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2085
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2086
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2088
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2095
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2096
|
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<li class="md-nav__item">
|
|
2097
|
+
<a href="../security/" class="md-nav__link">
|
|
2098
|
+
|
|
2099
|
+
|
|
2100
|
+
|
|
2101
|
+
<span class="md-ellipsis">
|
|
2102
|
+
|
|
2103
|
+
|
|
2104
|
+
Security Reporting
|
|
2105
|
+
|
|
2106
|
+
|
|
2107
|
+
|
|
2108
|
+
</span>
|
|
2109
|
+
|
|
2110
|
+
|
|
2111
|
+
|
|
2112
|
+
</a>
|
|
2113
|
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</li>
|
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2114
|
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2115
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2116
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2117
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2118
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2119
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2120
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|
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2123
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|
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2124
|
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<li class="md-nav__item">
|
|
2125
|
+
<a href="../release-readiness/" class="md-nav__link">
|
|
2126
|
+
|
|
2127
|
+
|
|
2128
|
+
|
|
2129
|
+
<span class="md-ellipsis">
|
|
2130
|
+
|
|
2131
|
+
|
|
2132
|
+
Release Readiness
|
|
2133
|
+
|
|
2134
|
+
|
|
2135
|
+
|
|
2136
|
+
</span>
|
|
2137
|
+
|
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2138
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+
|
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2139
|
+
|
|
2140
|
+
</a>
|
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2141
|
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</li>
|
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2142
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|
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2143
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2144
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2145
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2146
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2147
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2148
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|
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2149
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|
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2150
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|
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2151
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+
|
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2152
|
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<li class="md-nav__item">
|
|
2153
|
+
<a href="../ci-publishing/" class="md-nav__link">
|
|
2154
|
+
|
|
2155
|
+
|
|
2156
|
+
|
|
2157
|
+
<span class="md-ellipsis">
|
|
2158
|
+
|
|
2159
|
+
|
|
2160
|
+
CI and Publishing
|
|
2161
|
+
|
|
2162
|
+
|
|
2163
|
+
|
|
2164
|
+
</span>
|
|
2165
|
+
|
|
2166
|
+
|
|
2167
|
+
|
|
2168
|
+
</a>
|
|
2169
|
+
</li>
|
|
2170
|
+
|
|
2171
|
+
|
|
2172
|
+
|
|
2173
|
+
|
|
2174
|
+
</ul>
|
|
2175
|
+
</nav>
|
|
2176
|
+
|
|
2177
|
+
</li>
|
|
2178
|
+
|
|
2179
|
+
|
|
2180
|
+
|
|
2181
|
+
</ul>
|
|
2182
|
+
</nav>
|
|
2183
|
+
</div>
|
|
2184
|
+
</div>
|
|
2185
|
+
</div>
|
|
2186
|
+
|
|
2187
|
+
|
|
2188
|
+
|
|
2189
|
+
<div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
|
|
2190
|
+
<div class="md-sidebar__scrollwrap">
|
|
2191
|
+
<div class="md-sidebar__inner">
|
|
2192
|
+
|
|
2193
|
+
|
|
2194
|
+
<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
|
|
2195
|
+
|
|
2196
|
+
|
|
2197
|
+
|
|
2198
|
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Runtime input and compression contracts
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Backends
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<h1 id="tool-authoring">Tool Authoring<a class="headerlink" href="#tool-authoring" title="Permanent link">¶</a></h1>
|
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<p>A tool plugin should provide a narrow integration layer around scientific workflow logic.</p>
|
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+
<h2 id="distribution-dependencies">Distribution dependencies<a class="headerlink" href="#distribution-dependencies" title="Permanent link">¶</a></h2>
|
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+
<p>Declare <code>caddforge-core>=0.21.0</code> in plugin <code>project.dependencies</code>; do not depend on
|
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2314
|
+
<code>caddforge</code>, which is the complete toolbox bundle. Keep Python imports and entry-point
|
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2315
|
+
groups under <code>caddforge</code>. Adding a public plugin to the bundle requires an explicit,
|
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2316
|
+
exact dependency pin and a newly tested bundle release. Only reviewed public components belong in the public bundle.</p>
|
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2317
|
+
<h2 id="optional-cli-commands">Optional CLI commands<a class="headerlink" href="#optional-cli-commands" title="Permanent link">¶</a></h2>
|
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2318
|
+
<p>An installed package can add a top-level CLI command through the <code>caddforge.cli_commands</code>
|
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2319
|
+
entry-point group. Core 0.21.0 introduces this interface. The entry-point name becomes the command
|
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|
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name; its target is a callable with a Typer-compatible signature and help docstring:</p>
|
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<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a><span class="k">[project.entry-points.</span><span class="s2">"caddforge.cli_commands"</span><span class="k">]</span>
|
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<a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a><span class="n">docs</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">"caddforge_docs.cli:docs"</span>
|
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|
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</code></pre></div>
|
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<p>Core registers these commands after its built-in commands and groups. Conflicts, duplicate command
|
|
2325
|
+
names, and extensions that fail to load or have unsupported signatures are logged and skipped,
|
|
2326
|
+
leaving built-in commands available. Keep extension imports lightweight and load expensive runtime
|
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|
+
dependencies only when the command executes. Removing the providing package removes its command
|
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|
+
from subsequent CLI invocations. Plugins that only expose scientific tools should continue to use
|
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2329
|
+
the <code>caddforge.tools</code> group.</p>
|
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2330
|
+
<h2 id="required-pieces">Required pieces<a class="headerlink" href="#required-pieces" title="Permanent link">¶</a></h2>
|
|
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|
+
<ul>
|
|
2332
|
+
<li>Config model with validation and YAML/JSON loading support.</li>
|
|
2333
|
+
<li>Workflow class that prepares and runs jobs.</li>
|
|
2334
|
+
<li>Tool metadata class registered through <code>caddforge.tools</code> entry points.</li>
|
|
2335
|
+
<li>Canonical <code>Result</code> output with metrics and paths.</li>
|
|
2336
|
+
<li>Tests for config validation, workflow setup, and result generation.</li>
|
|
2337
|
+
</ul>
|
|
2338
|
+
<h2 id="pipeline-contracts">Pipeline contracts<a class="headerlink" href="#pipeline-contracts" title="Permanent link">¶</a></h2>
|
|
2339
|
+
<p>Expose pipeline ports when a tool should participate in pipelines:</p>
|
|
2340
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a><span class="n">InputPort</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s2">"ligands"</span><span class="p">,</span> <span class="n">kind</span><span class="o">=</span><span class="n">ArtifactKind</span><span class="o">.</span><span class="n">MOLECULE_COLLECTION</span><span class="p">,</span> <span class="n">config_field</span><span class="o">=</span><span class="s2">"ligand_paths"</span><span class="p">)</span>
|
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2341
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+
<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a><span class="n">OutputPort</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s2">"scores"</span><span class="p">,</span> <span class="n">kind</span><span class="o">=</span><span class="n">ArtifactKind</span><span class="o">.</span><span class="n">TABULAR_SCORES</span><span class="p">,</span> <span class="n">result_path_key</span><span class="o">=</span><span class="s2">"best_scores_csv"</span><span class="p">)</span>
|
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2342
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+
<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a><span class="n">OutputPort</span><span class="p">(</span>
|
|
2343
|
+
<a id="__codelineno-1-4" name="__codelineno-1-4" href="#__codelineno-1-4"></a> <span class="n">name</span><span class="o">=</span><span class="s2">"pose_files"</span><span class="p">,</span>
|
|
2344
|
+
<a id="__codelineno-1-5" name="__codelineno-1-5" href="#__codelineno-1-5"></a> <span class="n">kind</span><span class="o">=</span><span class="n">ArtifactKind</span><span class="o">.</span><span class="n">POSE_COLLECTION</span><span class="p">,</span>
|
|
2345
|
+
<a id="__codelineno-1-6" name="__codelineno-1-6" href="#__codelineno-1-6"></a> <span class="n">result_path_key</span><span class="o">=</span><span class="s2">"pose_manifest_csv"</span><span class="p">,</span>
|
|
2346
|
+
<a id="__codelineno-1-7" name="__codelineno-1-7" href="#__codelineno-1-7"></a> <span class="n">required</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
|
|
2347
|
+
<a id="__codelineno-1-8" name="__codelineno-1-8" href="#__codelineno-1-8"></a> <span class="n">path_collection_column</span><span class="o">=</span><span class="s2">"pose_file"</span><span class="p">,</span>
|
|
2348
|
+
<a id="__codelineno-1-9" name="__codelineno-1-9" href="#__codelineno-1-9"></a><span class="p">)</span>
|
|
2349
|
+
</code></pre></div>
|
|
2350
|
+
<p>Use declared ports or explicit <code>outputs</code> mappings. Do not force downstream stages to infer paths
|
|
2351
|
+
from tool-specific output directories.</p>
|
|
2352
|
+
<h3 id="runtime-input-and-compression-contracts">Runtime input and compression contracts<a class="headerlink" href="#runtime-input-and-compression-contracts" title="Permanent link">¶</a></h3>
|
|
2353
|
+
<p>Set <code>InputPort.config_field</code> to the configuration path that receives a pipeline artifact. Core also
|
|
2354
|
+
uses declared inputs to materialize transparent gzip wrappers immediately before execution. For a
|
|
2355
|
+
nested collection, set <code>runtime_selector</code>, for example <code>input_files[].path</code>. Mark a selector with
|
|
2356
|
+
<code>InputCompressionPolicy.NATIVE</code> when the scientific tool consumes the compressed stream itself.</p>
|
|
2357
|
+
<p>Outputs requested with a <code>.gz</code> suffix require an <code>OutputPort.config_field</code> so core can distinguish
|
|
2358
|
+
the requested destination from an existing compressed input and finalize it atomically.</p>
|
|
2359
|
+
<p>Structured collection fields can declare a <code>SplitContract</code> that identifies the path member to
|
|
2360
|
+
split, preserves sibling metadata in every shard, and selects a deterministic reducer for shard
|
|
2361
|
+
outputs.</p>
|
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2362
|
+
<h2 id="scratch-publication-helpers">Scratch publication helpers<a class="headerlink" href="#scratch-publication-helpers" title="Permanent link">¶</a></h2>
|
|
2363
|
+
<p>Use <code>LogSync</code> for mutable stdout, stderr, or progress snapshots written in scratch. Set
|
|
2364
|
+
<code>atomic=True</code> for structured snapshots and inspect its <code>LogSyncReport</code> when the final publication
|
|
2365
|
+
state belongs in the result. Synchronization failures are retried and must not change scientific
|
|
2366
|
+
job status.</p>
|
|
2367
|
+
<p>Use <code>ArtifactSyncQueue</code> for completed immutable artifacts. It publishes by atomic replacement,
|
|
2368
|
+
retries transient failures, and reports unresolved files after the final pass. Do not place
|
|
2369
|
+
tool-specific behavior in these core helpers.</p>
|
|
2370
|
+
<h2 id="backends">Backends<a class="headerlink" href="#backends" title="Permanent link">¶</a></h2>
|
|
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|
+
<p>Workflow code should not contain Slurm-specific or local-process orchestration. Submit and track jobs
|
|
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|
+
through the core backend interfaces.</p>
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