caddforge-docs 0.3.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- caddforge_docs/__init__.py +1 -0
- caddforge_docs/cli.py +20 -0
- caddforge_docs/server.py +124 -0
- caddforge_docs/site/404.html +2118 -0
- caddforge_docs/site/assets/_mkdocstrings.css +237 -0
- caddforge_docs/site/assets/images/favicon.png +0 -0
- caddforge_docs/site/assets/javascripts/bundle.d7400e89.min.js +16 -0
- caddforge_docs/site/assets/javascripts/bundle.d7400e89.min.js.map +7 -0
- caddforge_docs/site/assets/javascripts/workers/search.2c215733.min.js +42 -0
- caddforge_docs/site/assets/javascripts/workers/search.2c215733.min.js.map +7 -0
- caddforge_docs/site/assets/licenses/W3C-Software-and-Document-2015.txt +15 -0
- caddforge_docs/site/assets/licenses/autogrid-COPYING-GPL-2.txt +339 -0
- caddforge_docs/site/assets/licenses/autogrid-GCC-RUNTIME-COPYING-GPL-3.txt +674 -0
- caddforge_docs/site/assets/licenses/autogrid-GCC-RUNTIME-EXCEPTION.txt +73 -0
- caddforge_docs/site/assets/licenses/autogrid-GCC-RUNTIME-NOTICE.txt +24 -0
- caddforge_docs/site/assets/licenses/caddforge-opencosmors-COPYING.txt +674 -0
- caddforge_docs/site/assets/licenses/caddforge-opencosmors-LICENSE.txt +165 -0
- caddforge_docs/site/assets/licenses/caddforge-unidock-tools-LICENSE.txt +202 -0
- caddforge_docs/site/assets/licenses/clipboard-LICENSE.txt +19 -0
- caddforge_docs/site/assets/licenses/escape-html-LICENSE.txt +2 -0
- caddforge_docs/site/assets/licenses/focus-visible-LICENSE.txt +4 -0
- caddforge_docs/site/assets/licenses/fontawesome-LICENSE.txt +165 -0
- caddforge_docs/site/assets/licenses/fuzzaldrin-plus-LICENSE.txt +21 -0
- caddforge_docs/site/assets/licenses/lunr-LICENSE.txt +17 -0
- caddforge_docs/site/assets/licenses/material-LICENSE.txt +20 -0
- caddforge_docs/site/assets/licenses/material-design-color-LICENSE.txt +31 -0
- caddforge_docs/site/assets/licenses/material-shadows-LICENSE.txt +31 -0
- caddforge_docs/site/assets/licenses/mkdocs-material-LICENSE.txt +19 -0
- caddforge_docs/site/assets/licenses/mkdocs-material-extensions-LICENSE.txt +21 -0
- caddforge_docs/site/assets/licenses/mkdocs-section-index-LICENSE.txt +21 -0
- caddforge_docs/site/assets/licenses/mkdocstrings-LICENSE.txt +15 -0
- caddforge_docs/site/assets/licenses/mkdocstrings-python-LICENSE.txt +15 -0
- caddforge_docs/site/assets/licenses/octicons-LICENSE.txt +21 -0
- caddforge_docs/site/assets/licenses/preact-LICENSE.txt +19 -0
- caddforge_docs/site/assets/licenses/properdocs-LICENSE.txt +26 -0
- caddforge_docs/site/assets/licenses/pymdown-extensions-LICENSE.txt +113 -0
- caddforge_docs/site/assets/licenses/rxjs-LICENSE.txt +180 -0
- caddforge_docs/site/assets/licenses/simple-LICENSE.txt +30 -0
- caddforge_docs/site/assets/licenses/tiny-emitter-LICENSE.txt +19 -0
- caddforge_docs/site/assets/licenses/tslib-LICENSE.txt +12 -0
- caddforge_docs/site/assets/licenses/zeno-rocha-components-LICENSE.txt +22 -0
- caddforge_docs/site/assets/stylesheets/main.ec1eaa64.min.css +1 -0
- caddforge_docs/site/assets/stylesheets/main.ec1eaa64.min.css.map +1 -0
- caddforge_docs/site/assets/stylesheets/palette.ab4e12ef.min.css +1 -0
- caddforge_docs/site/assets/stylesheets/palette.ab4e12ef.min.css.map +1 -0
- caddforge_docs/site/core/cli/index.html +2446 -0
- caddforge_docs/site/core/concepts/index.html +2340 -0
- caddforge_docs/site/core/configuration/index.html +2300 -0
- caddforge_docs/site/core/index.html +2170 -0
- caddforge_docs/site/core/jobs-results/index.html +2315 -0
- caddforge_docs/site/core/plugins/index.html +2200 -0
- caddforge_docs/site/core/slurm/index.html +2562 -0
- caddforge_docs/site/development/ci-publishing/index.html +2345 -0
- caddforge_docs/site/development/contributing/index.html +2311 -0
- caddforge_docs/site/development/documentation/index.html +2380 -0
- caddforge_docs/site/development/index.html +2201 -0
- caddforge_docs/site/development/release-notes/index.html +2504 -0
- caddforge_docs/site/development/release-readiness/index.html +2333 -0
- caddforge_docs/site/development/security/index.html +2181 -0
- caddforge_docs/site/development/tool-authoring/index.html +2435 -0
- caddforge_docs/site/examples/index.html +2465 -0
- caddforge_docs/site/examples/manifest.json +158 -0
- caddforge_docs/site/examples/minimize/component_overrides.yaml +14 -0
- caddforge_docs/site/examples/minimize/ligand_only.yaml +13 -0
- caddforge_docs/site/examples/minimize/pipeline_docking.yaml +84 -0
- caddforge_docs/site/examples/minimize/pipeline_scatter.yaml +49 -0
- caddforge_docs/site/examples/minimize/pocket_free_shell_restrained.yaml +13 -0
- caddforge_docs/site/examples/minimize/pocket_restrained.yaml +13 -0
- caddforge_docs/site/examples/minimize/prepared_metal.yaml +14 -0
- caddforge_docs/site/examples/minimize/sidechains_free_backbone_fixed.yaml +13 -0
- caddforge_docs/site/examples/minimize/sidechains_free_backbone_restrained.yaml +13 -0
- caddforge_docs/site/examples/pipelines/descriptor-model-and-candidate-filter.yaml +44 -0
- caddforge_docs/site/examples/pipelines/dock-extract-and-minimize-poses.yaml +85 -0
- caddforge_docs/site/examples/pipelines/docking-screen-and-rescore.yaml +55 -0
- caddforge_docs/site/examples/pipelines/flexible-gnina-to-openbpmd-to-md-to-abfe.yaml +189 -0
- caddforge_docs/site/examples/pipelines/gnina-flexible-complex-artifacts.yaml +52 -0
- caddforge_docs/site/examples/pipelines/minimize-a-multi-pose-sdf.yaml +46 -0
- caddforge_docs/site/examples/pipelines/pose-level-md-selection.yaml +95 -0
- caddforge_docs/site/examples/pipelines/result-collection-and-diagnostics.yaml +55 -0
- caddforge_docs/site/examples/quickstart/diagnostics.yaml +8 -0
- caddforge_docs/site/examples/quickstart/index.html +2172 -0
- caddforge_docs/site/examples/quickstart/pipeline.yaml +23 -0
- caddforge_docs/site/examples/quickstart/run.py +18 -0
- caddforge_docs/site/examples/quickstart/run_pipeline.py +6 -0
- caddforge_docs/site/examples/quickstart/scores.csv +7 -0
- caddforge_docs/site/examples/quickstart/values.csv +31 -0
- caddforge_docs/site/examples/run_tool.py +40 -0
- caddforge_docs/site/examples/tools/datascience-csv-scatter.yaml +17 -0
- caddforge_docs/site/examples/tools/datascience-distribution-diagnostics.yaml +10 -0
- caddforge_docs/site/examples/tools/descriptors-ani-conformers.yaml +9 -0
- caddforge_docs/site/examples/tools/descriptors-ani-psa.yaml +9 -0
- caddforge_docs/site/examples/tools/descriptors-cluster-molecules.yaml +11 -0
- caddforge_docs/site/examples/tools/descriptors-phesa.yaml +7 -0
- caddforge_docs/site/examples/tools/docking-gnina.yaml +12 -0
- caddforge_docs/site/examples/tools/docking-idockya.yaml +8 -0
- caddforge_docs/site/examples/tools/docking-unidock.yaml +12 -0
- caddforge_docs/site/examples/tools/fep-openfe-abfe.yaml +53 -0
- caddforge_docs/site/examples/tools/fep-openfe-rbfe-septop.yaml +23 -0
- caddforge_docs/site/examples/tools/md-center-and-align.yaml +16 -0
- caddforge_docs/site/examples/tools/md-cluster-representative.yaml +16 -0
- caddforge_docs/site/examples/tools/md-extract-frames.yaml +17 -0
- caddforge_docs/site/examples/tools/md-fix-structure.yaml +20 -0
- caddforge_docs/site/examples/tools/md-grand.yaml +28 -0
- caddforge_docs/site/examples/tools/md-inducia.yaml +29 -0
- caddforge_docs/site/examples/tools/md-minimize.yaml +13 -0
- caddforge_docs/site/examples/tools/md-openbpmd.yaml +11 -0
- caddforge_docs/site/examples/tools/md-plain-md.yaml +28 -0
- caddforge_docs/site/examples/tools/ml-explore-classifier.yaml +5 -0
- caddforge_docs/site/examples/tools/ml-model-factory.yaml +32 -0
- caddforge_docs/site/examples/tools/ml-model-zoo.yaml +16 -0
- caddforge_docs/site/examples/tools/ml-pca.yaml +10 -0
- caddforge_docs/site/examples/tools/ml-simple-gp.yaml +17 -0
- caddforge_docs/site/examples/tools/qm-transfer-free-energy.yaml +11 -0
- caddforge_docs/site/explanation/references/index.html +2218 -0
- caddforge_docs/site/explanation/reproducibility/index.html +2306 -0
- caddforge_docs/site/explanation/third-party-notices/index.html +2599 -0
- caddforge_docs/site/getting-started/first-pipeline/index.html +2195 -0
- caddforge_docs/site/getting-started/first-workflow/index.html +2329 -0
- caddforge_docs/site/getting-started/index.html +2200 -0
- caddforge_docs/site/getting-started/installation/index.html +2541 -0
- caddforge_docs/site/gui/index.html +2267 -0
- caddforge_docs/site/gui/plugin-authoring/index.html +2280 -0
- caddforge_docs/site/gui/walkthrough/index.html +2181 -0
- caddforge_docs/site/how-to/jobs/index.html +2195 -0
- caddforge_docs/site/how-to/scatter/index.html +2193 -0
- caddforge_docs/site/how-to/troubleshooting/index.html +2429 -0
- caddforge_docs/site/index.html +2359 -0
- caddforge_docs/site/objects.inv +0 -0
- caddforge_docs/site/pipelines/artifacts/index.html +2314 -0
- caddforge_docs/site/pipelines/built-ins/index.html +2670 -0
- caddforge_docs/site/pipelines/examples/index.html +3186 -0
- caddforge_docs/site/pipelines/index.html +2164 -0
- caddforge_docs/site/pipelines/specification/index.html +2278 -0
- caddforge_docs/site/plugins/datascience/index.html +2405 -0
- caddforge_docs/site/plugins/descriptors/index.html +2609 -0
- caddforge_docs/site/plugins/docking/index.html +2480 -0
- caddforge_docs/site/plugins/fep/index.html +2508 -0
- caddforge_docs/site/plugins/index.html +2216 -0
- caddforge_docs/site/plugins/md/index.html +3795 -0
- caddforge_docs/site/plugins/ml/index.html +2815 -0
- caddforge_docs/site/plugins/qm/index.html +2309 -0
- caddforge_docs/site/plugins/version-matrix/index.html +2449 -0
- caddforge_docs/site/reference/api/index.html +4414 -0
- caddforge_docs/site/reference/index.html +2166 -0
- caddforge_docs/site/search/search_index.json +1 -0
- caddforge_docs/site/sitemap.xml +191 -0
- caddforge_docs/site/sitemap.xml.gz +0 -0
- caddforge_docs-0.3.0.dist-info/METADATA +158 -0
- caddforge_docs-0.3.0.dist-info/RECORD +152 -0
- caddforge_docs-0.3.0.dist-info/WHEEL +4 -0
- caddforge_docs-0.3.0.dist-info/entry_points.txt +2 -0
- caddforge_docs-0.3.0.dist-info/licenses/LICENSE +21 -0
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<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
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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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Specification
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Built-in Stages
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<a href="../../pipelines/examples/" class="md-nav__link">
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Examples
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1016
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</nav>
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<li class="md-nav__item md-nav__item--active md-nav__item--section md-nav__item--nested">
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
|
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<div class="md-nav__link md-nav__container">
|
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<a href="../" class="md-nav__link ">
|
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|
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1073
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Plugins
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1078
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1080
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1087
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1088
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<label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
|
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1089
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<span class="md-nav__icon md-icon"></span>
|
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1090
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</label>
|
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1091
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1092
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</div>
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1093
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1094
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<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
|
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1095
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+
<label class="md-nav__title" for="__nav_6">
|
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1096
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<span class="md-nav__icon md-icon"></span>
|
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1097
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1098
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1099
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Plugins
|
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1100
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|
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1101
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|
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1102
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</label>
|
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1103
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<ul class="md-nav__list" data-md-scrollfix>
|
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1110
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1111
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<li class="md-nav__item">
|
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<a href="../version-matrix/" class="md-nav__link">
|
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1114
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1115
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<span class="md-ellipsis">
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1118
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1119
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Version Matrix
|
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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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1125
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1126
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<a href="../docking/" class="md-nav__link">
|
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1142
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1143
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<a href="../descriptors/" class="md-nav__link">
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Descriptors
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1176
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1177
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1178
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1179
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<li class="md-nav__item">
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<a href="../md/" class="md-nav__link">
|
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1197
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1198
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1199
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1200
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<span class="md-ellipsis">
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MD
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<li class="md-nav__item">
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1224
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<a href="../fep/" class="md-nav__link">
|
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1225
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|
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1226
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|
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1227
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|
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1228
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<span class="md-ellipsis">
|
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1229
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1230
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1231
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FEP
|
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1232
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|
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1233
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|
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1234
|
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|
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1235
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</span>
|
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1236
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1237
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1238
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|
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1239
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1250
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<li class="md-nav__item">
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<a href="../qm/" class="md-nav__link">
|
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1254
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1255
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1257
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1258
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1259
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QM
|
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1260
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1261
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1262
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|
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1263
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<a href="../ml/" class="md-nav__link">
|
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1281
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1282
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1283
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1287
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ML
|
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1288
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1289
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1290
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1291
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1295
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1301
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1309
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<li class="md-nav__item md-nav__item--active">
|
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1310
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1311
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<input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
|
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1312
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1313
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1314
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1315
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1316
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1317
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<label class="md-nav__link md-nav__link--active" for="__toc">
|
|
1318
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|
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1319
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1320
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1321
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<span class="md-ellipsis">
|
|
1322
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|
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1323
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|
|
1324
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Data Science
|
|
1325
|
+
|
|
1326
|
+
|
|
1327
|
+
|
|
1328
|
+
</span>
|
|
1329
|
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|
|
1330
|
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|
|
1331
|
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|
|
1332
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<span class="md-nav__icon md-icon"></span>
|
|
1333
|
+
</label>
|
|
1334
|
+
|
|
1335
|
+
<a href="./" class="md-nav__link md-nav__link--active">
|
|
1336
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|
|
1337
|
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|
|
1338
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|
1339
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<span class="md-ellipsis">
|
|
1340
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|
|
1341
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|
|
1342
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+
Data Science
|
|
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Public Python API
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Explanation
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<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_9_label" aria-expanded="false">
|
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Security Reporting
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2066
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2067
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2068
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2069
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Release Readiness
|
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2095
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2096
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2097
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2100
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2101
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2112
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|
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2115
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2116
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2117
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<span class="md-ellipsis">
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2119
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2120
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2121
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CI and Publishing
|
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2122
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2123
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2124
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2125
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2128
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2129
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|
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2130
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2133
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2134
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2135
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</ul>
|
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2136
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</nav>
|
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2137
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2138
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2139
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2140
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2141
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+
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2142
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+
</ul>
|
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2143
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</nav>
|
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2144
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|
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2145
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</div>
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2146
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|
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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
|
+
<div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
|
|
2151
|
+
<div class="md-sidebar__scrollwrap">
|
|
2152
|
+
<div class="md-sidebar__inner">
|
|
2153
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+
|
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2154
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+
|
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2155
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+
<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
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2156
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+
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2157
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2158
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|
2159
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2160
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2161
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2162
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<label class="md-nav__title" for="__toc">
|
|
2163
|
+
<span class="md-nav__icon md-icon"></span>
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2164
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Table of contents
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2165
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+
</label>
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2166
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+
<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
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2167
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2168
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<li class="md-nav__item">
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2169
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<a href="#requirements-and-example-status" class="md-nav__link">
|
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2170
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+
<span class="md-ellipsis">
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|
2171
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+
|
|
2172
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+
Requirements and example status
|
|
2173
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+
|
|
2174
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+
</span>
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|
2175
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+
</a>
|
|
2176
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2177
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</li>
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2178
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2179
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<li class="md-nav__item">
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2180
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<a href="#csv-scatter" class="md-nav__link">
|
|
2181
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<span class="md-ellipsis">
|
|
2182
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+
|
|
2183
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+
csv-scatter
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|
2184
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+
|
|
2185
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+
</span>
|
|
2186
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</a>
|
|
2187
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2188
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</li>
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2189
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|
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2190
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<li class="md-nav__item">
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2191
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<a href="#distribution-diagnostics" class="md-nav__link">
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2192
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<span class="md-ellipsis">
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|
2193
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|
|
2194
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distribution-diagnostics
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|
2195
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+
|
|
2196
|
+
</span>
|
|
2197
|
+
</a>
|
|
2198
|
+
|
|
2199
|
+
</li>
|
|
2200
|
+
|
|
2201
|
+
<li class="md-nav__item">
|
|
2202
|
+
<a href="#compressed-inputs" class="md-nav__link">
|
|
2203
|
+
<span class="md-ellipsis">
|
|
2204
|
+
|
|
2205
|
+
Compressed inputs
|
|
2206
|
+
|
|
2207
|
+
</span>
|
|
2208
|
+
</a>
|
|
2209
|
+
|
|
2210
|
+
</li>
|
|
2211
|
+
|
|
2212
|
+
</ul>
|
|
2213
|
+
|
|
2214
|
+
</nav>
|
|
2215
|
+
</div>
|
|
2216
|
+
</div>
|
|
2217
|
+
</div>
|
|
2218
|
+
|
|
2219
|
+
|
|
2220
|
+
|
|
2221
|
+
<div class="md-content" data-md-component="content">
|
|
2222
|
+
|
|
2223
|
+
<article class="md-content__inner md-typeset">
|
|
2224
|
+
|
|
2225
|
+
|
|
2226
|
+
|
|
2227
|
+
|
|
2228
|
+
|
|
2229
|
+
|
|
2230
|
+
|
|
2231
|
+
|
|
2232
|
+
<h1 id="data-science-plugin">Data Science Plugin<a class="headerlink" href="#data-science-plugin" title="Permanent link">¶</a></h1>
|
|
2233
|
+
<p>Package: <code>caddforge-datascience</code></p>
|
|
2234
|
+
<div class="admonition info">
|
|
2235
|
+
<p class="admonition-title">Public source tag</p>
|
|
2236
|
+
<p>This page describes <code>caddforge-datascience</code> <code>0.5.0</code>, tagged as <code>v0.5.0</code>.
|
|
2237
|
+
Published on PyPI; see the <a href="../version-matrix/">version matrix</a>.</p>
|
|
2238
|
+
</div>
|
|
2239
|
+
<p>The data-science plugin provides generic data utilities as CADDForge tools.</p>
|
|
2240
|
+
<h2 id="requirements-and-example-status">Requirements and example status<a class="headerlink" href="#requirements-and-example-status" title="Permanent link">¶</a></h2>
|
|
2241
|
+
<p>The <a href="../../examples/">example library</a> provides downloadable configuration
|
|
2242
|
+
templates for every workflow on this page, plus a shared Python runner. File paths
|
|
2243
|
+
refer to inputs you must prepare; these are not bundled research datasets. Schema
|
|
2244
|
+
validation does not establish scientific validity or engine availability. See the
|
|
2245
|
+
<a href="../version-matrix/">version matrix</a> for release tags and publication status.</p>
|
|
2246
|
+
<h2 id="csv-scatter"><code>csv-scatter</code><a class="headerlink" href="#csv-scatter" title="Permanent link">¶</a></h2>
|
|
2247
|
+
<p>Generates an interactive Bokeh scatter plot from a CSV/TSV file with optional color mapping,
|
|
2248
|
+
molecule hover images, and threshold sliders.</p>
|
|
2249
|
+
<p>CLI:</p>
|
|
2250
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>caddforge<span class="w"> </span>show-config<span class="w"> </span>datascience<span class="w"> </span>csv-scatter
|
|
2251
|
+
<a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a>caddforge<span class="w"> </span>run<span class="w"> </span>datascience<span class="w"> </span>csv-scatter<span class="w"> </span>--config<span class="w"> </span>csv_scatter.yaml
|
|
2252
|
+
</code></pre></div>
|
|
2253
|
+
<p>YAML:</p>
|
|
2254
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a><span class="nt">csv_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/metrics.csv</span>
|
|
2255
|
+
<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a><span class="nt">x_column</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">feature_x</span>
|
|
2256
|
+
<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a><span class="nt">y_column</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">feature_y</span>
|
|
2257
|
+
<a id="__codelineno-1-4" name="__codelineno-1-4" href="#__codelineno-1-4"></a><span class="nt">color_column</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">feature_group</span>
|
|
2258
|
+
<a id="__codelineno-1-5" name="__codelineno-1-5" href="#__codelineno-1-5"></a><span class="nt">smiles_column</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">smiles</span>
|
|
2259
|
+
<a id="__codelineno-1-6" name="__codelineno-1-6" href="#__codelineno-1-6"></a><span class="nt">id_column</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">compound_id</span>
|
|
2260
|
+
<a id="__codelineno-1-7" name="__codelineno-1-7" href="#__codelineno-1-7"></a><span class="nt">hover_columns</span><span class="p">:</span><span class="w"> </span><span class="p p-Indicator">[</span><span class="nv">compute_time</span><span class="p p-Indicator">]</span>
|
|
2261
|
+
<a id="__codelineno-1-8" name="__codelineno-1-8" href="#__codelineno-1-8"></a><span class="nt">x_scale</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">linear</span>
|
|
2262
|
+
<a id="__codelineno-1-9" name="__codelineno-1-9" href="#__codelineno-1-9"></a><span class="nt">y_scale</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">log</span>
|
|
2263
|
+
<a id="__codelineno-1-10" name="__codelineno-1-10" href="#__codelineno-1-10"></a><span class="nt">palette</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">viridis</span>
|
|
2264
|
+
<a id="__codelineno-1-11" name="__codelineno-1-11" href="#__codelineno-1-11"></a><span class="nt">thresholds_enabled</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">true</span>
|
|
2265
|
+
<a id="__codelineno-1-12" name="__codelineno-1-12" href="#__codelineno-1-12"></a><span class="nt">x_positive_direction</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">low</span>
|
|
2266
|
+
<a id="__codelineno-1-13" name="__codelineno-1-13" href="#__codelineno-1-13"></a><span class="nt">y_positive_direction</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">high</span>
|
|
2267
|
+
<a id="__codelineno-1-14" name="__codelineno-1-14" href="#__codelineno-1-14"></a><span class="nt">point_size</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">10</span>
|
|
2268
|
+
<a id="__codelineno-1-15" name="__codelineno-1-15" href="#__codelineno-1-15"></a><span class="nt">alpha</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">0.8</span>
|
|
2269
|
+
<a id="__codelineno-1-16" name="__codelineno-1-16" href="#__codelineno-1-16"></a><span class="nt">title</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">Synthetic metrics</span>
|
|
2270
|
+
</code></pre></div>
|
|
2271
|
+
<p>Python:</p>
|
|
2272
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a><span class="kn">from</span><span class="w"> </span><span class="nn">caddforge.core.execution</span><span class="w"> </span><span class="kn">import</span> <span class="n">load_result_for_job</span><span class="p">,</span> <span class="n">submit_workflow</span>
|
|
2273
|
+
<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a><span class="kn">from</span><span class="w"> </span><span class="nn">caddforge.plugins</span><span class="w"> </span><span class="kn">import</span> <span class="n">get_tool</span>
|
|
2274
|
+
<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>
|
|
2275
|
+
<a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a><span class="n">spec</span> <span class="o">=</span> <span class="n">get_tool</span><span class="p">(</span><span class="s2">"datascience"</span><span class="p">,</span> <span class="s2">"csv-scatter"</span><span class="p">)</span>
|
|
2276
|
+
<a id="__codelineno-2-5" name="__codelineno-2-5" href="#__codelineno-2-5"></a><span class="n">cfg</span> <span class="o">=</span> <span class="n">spec</span><span class="o">.</span><span class="n">config_cls</span><span class="p">(</span>
|
|
2277
|
+
<a id="__codelineno-2-6" name="__codelineno-2-6" href="#__codelineno-2-6"></a> <span class="n">csv_path</span><span class="o">=</span><span class="s2">"data/metrics.csv"</span><span class="p">,</span>
|
|
2278
|
+
<a id="__codelineno-2-7" name="__codelineno-2-7" href="#__codelineno-2-7"></a> <span class="n">x_column</span><span class="o">=</span><span class="s2">"feature_x"</span><span class="p">,</span>
|
|
2279
|
+
<a id="__codelineno-2-8" name="__codelineno-2-8" href="#__codelineno-2-8"></a> <span class="n">y_column</span><span class="o">=</span><span class="s2">"feature_y"</span><span class="p">,</span>
|
|
2280
|
+
<a id="__codelineno-2-9" name="__codelineno-2-9" href="#__codelineno-2-9"></a> <span class="n">color_column</span><span class="o">=</span><span class="s2">"feature_group"</span><span class="p">,</span>
|
|
2281
|
+
<a id="__codelineno-2-10" name="__codelineno-2-10" href="#__codelineno-2-10"></a> <span class="n">backend</span><span class="o">=</span><span class="s2">"local"</span><span class="p">,</span>
|
|
2282
|
+
<a id="__codelineno-2-11" name="__codelineno-2-11" href="#__codelineno-2-11"></a><span class="p">)</span>
|
|
2283
|
+
<a id="__codelineno-2-12" name="__codelineno-2-12" href="#__codelineno-2-12"></a><span class="n">workflow</span> <span class="o">=</span> <span class="n">spec</span><span class="o">.</span><span class="n">workflow_cls</span><span class="p">(</span><span class="n">cfg</span><span class="p">)</span>
|
|
2284
|
+
<a id="__codelineno-2-13" name="__codelineno-2-13" href="#__codelineno-2-13"></a><span class="n">job</span> <span class="o">=</span> <span class="n">submit_workflow</span><span class="p">(</span>
|
|
2285
|
+
<a id="__codelineno-2-14" name="__codelineno-2-14" href="#__codelineno-2-14"></a> <span class="n">workflow</span><span class="p">,</span> <span class="n">cfg</span><span class="p">,</span> <span class="n">backend_name</span><span class="o">=</span><span class="n">cfg</span><span class="o">.</span><span class="n">backend</span><span class="p">,</span>
|
|
2286
|
+
<a id="__codelineno-2-15" name="__codelineno-2-15" href="#__codelineno-2-15"></a> <span class="n">input_ports</span><span class="o">=</span><span class="nb">tuple</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="n">spec</span><span class="o">.</span><span class="n">plugin</span><span class="p">,</span> <span class="s2">"input_ports"</span><span class="p">,</span> <span class="p">())),</span>
|
|
2287
|
+
<a id="__codelineno-2-16" name="__codelineno-2-16" href="#__codelineno-2-16"></a><span class="p">)</span>
|
|
2288
|
+
<a id="__codelineno-2-17" name="__codelineno-2-17" href="#__codelineno-2-17"></a><span class="n">result</span> <span class="o">=</span> <span class="n">load_result_for_job</span><span class="p">(</span><span class="n">job</span><span class="p">)</span>
|
|
2289
|
+
<a id="__codelineno-2-18" name="__codelineno-2-18" href="#__codelineno-2-18"></a><span class="k">if</span> <span class="n">result</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
|
|
2290
|
+
<a id="__codelineno-2-19" name="__codelineno-2-19" href="#__codelineno-2-19"></a> <span class="nb">print</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">paths</span><span class="p">)</span>
|
|
2291
|
+
</code></pre></div>
|
|
2292
|
+
<p>Outputs to inspect:</p>
|
|
2293
|
+
<ul>
|
|
2294
|
+
<li><code>results/<plot html></code>: interactive plot</li>
|
|
2295
|
+
<li><code>results/result_record.json</code>: canonical result</li>
|
|
2296
|
+
</ul>
|
|
2297
|
+
<h2 id="distribution-diagnostics"><code>distribution-diagnostics</code><a class="headerlink" href="#distribution-diagnostics" title="Permanent link">¶</a></h2>
|
|
2298
|
+
<p>Diagnoses whether a numeric column looks approximately normal or log-normal using summary
|
|
2299
|
+
statistics, normality tests, histograms, and Q-Q plots.</p>
|
|
2300
|
+
<p>CLI:</p>
|
|
2301
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>caddforge<span class="w"> </span>show-config<span class="w"> </span>datascience<span class="w"> </span>distribution-diagnostics
|
|
2302
|
+
<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>caddforge<span class="w"> </span>run<span class="w"> </span>datascience<span class="w"> </span>distribution-diagnostics<span class="w"> </span>--config<span class="w"> </span>distribution_diagnostics.yaml
|
|
2303
|
+
</code></pre></div>
|
|
2304
|
+
<p>YAML:</p>
|
|
2305
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a><span class="nt">csv_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/assay_values.csv</span>
|
|
2306
|
+
<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a><span class="nt">column</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">pIC50</span>
|
|
2307
|
+
<a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a><span class="nt">bins</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">50</span>
|
|
2308
|
+
<a id="__codelineno-4-4" name="__codelineno-4-4" href="#__codelineno-4-4"></a><span class="nt">clip_std</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">null</span>
|
|
2309
|
+
<a id="__codelineno-4-5" name="__codelineno-4-5" href="#__codelineno-4-5"></a><span class="nt">sample_size</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">5000</span>
|
|
2310
|
+
<a id="__codelineno-4-6" name="__codelineno-4-6" href="#__codelineno-4-6"></a><span class="nt">random_seed</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">0</span>
|
|
2311
|
+
<a id="__codelineno-4-7" name="__codelineno-4-7" href="#__codelineno-4-7"></a><span class="nt">include_log</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">true</span>
|
|
2312
|
+
<a id="__codelineno-4-8" name="__codelineno-4-8" href="#__codelineno-4-8"></a><span class="nt">plot_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">distribution_diagnostics.png</span>
|
|
2313
|
+
<a id="__codelineno-4-9" name="__codelineno-4-9" href="#__codelineno-4-9"></a><span class="nt">results_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">distribution_report.json</span>
|
|
2314
|
+
</code></pre></div>
|
|
2315
|
+
<p>Python:</p>
|
|
2316
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a><span class="kn">from</span><span class="w"> </span><span class="nn">caddforge.core.execution</span><span class="w"> </span><span class="kn">import</span> <span class="n">load_result_for_job</span><span class="p">,</span> <span class="n">submit_workflow</span>
|
|
2317
|
+
<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a><span class="kn">from</span><span class="w"> </span><span class="nn">caddforge.plugins</span><span class="w"> </span><span class="kn">import</span> <span class="n">get_tool</span>
|
|
2318
|
+
<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>
|
|
2319
|
+
<a id="__codelineno-5-4" name="__codelineno-5-4" href="#__codelineno-5-4"></a><span class="n">spec</span> <span class="o">=</span> <span class="n">get_tool</span><span class="p">(</span><span class="s2">"datascience"</span><span class="p">,</span> <span class="s2">"distribution-diagnostics"</span><span class="p">)</span>
|
|
2320
|
+
<a id="__codelineno-5-5" name="__codelineno-5-5" href="#__codelineno-5-5"></a><span class="n">cfg</span> <span class="o">=</span> <span class="n">spec</span><span class="o">.</span><span class="n">config_cls</span><span class="p">(</span>
|
|
2321
|
+
<a id="__codelineno-5-6" name="__codelineno-5-6" href="#__codelineno-5-6"></a> <span class="n">csv_path</span><span class="o">=</span><span class="s2">"data/assay_values.csv"</span><span class="p">,</span> <span class="n">column</span><span class="o">=</span><span class="s2">"pIC50"</span><span class="p">,</span>
|
|
2322
|
+
<a id="__codelineno-5-7" name="__codelineno-5-7" href="#__codelineno-5-7"></a> <span class="n">results_filename</span><span class="o">=</span><span class="s2">"distribution_report.json"</span><span class="p">,</span>
|
|
2323
|
+
<a id="__codelineno-5-8" name="__codelineno-5-8" href="#__codelineno-5-8"></a><span class="p">)</span>
|
|
2324
|
+
<a id="__codelineno-5-9" name="__codelineno-5-9" href="#__codelineno-5-9"></a><span class="n">workflow</span> <span class="o">=</span> <span class="n">spec</span><span class="o">.</span><span class="n">workflow_cls</span><span class="p">(</span><span class="n">cfg</span><span class="p">)</span>
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<a id="__codelineno-5-10" name="__codelineno-5-10" href="#__codelineno-5-10"></a><span class="n">job</span> <span class="o">=</span> <span class="n">submit_workflow</span><span class="p">(</span>
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<a id="__codelineno-5-11" name="__codelineno-5-11" href="#__codelineno-5-11"></a> <span class="n">workflow</span><span class="p">,</span> <span class="n">cfg</span><span class="p">,</span> <span class="n">backend_name</span><span class="o">=</span><span class="n">cfg</span><span class="o">.</span><span class="n">backend</span><span class="p">,</span>
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<a id="__codelineno-5-12" name="__codelineno-5-12" href="#__codelineno-5-12"></a> <span class="n">input_ports</span><span class="o">=</span><span class="nb">tuple</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="n">spec</span><span class="o">.</span><span class="n">plugin</span><span class="p">,</span> <span class="s2">"input_ports"</span><span class="p">,</span> <span class="p">())),</span>
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<a id="__codelineno-5-13" name="__codelineno-5-13" href="#__codelineno-5-13"></a><span class="p">)</span>
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<a id="__codelineno-5-14" name="__codelineno-5-14" href="#__codelineno-5-14"></a><span class="n">result</span> <span class="o">=</span> <span class="n">load_result_for_job</span><span class="p">(</span><span class="n">job</span><span class="p">)</span>
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<a id="__codelineno-5-15" name="__codelineno-5-15" href="#__codelineno-5-15"></a><span class="k">if</span> <span class="n">result</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
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<a id="__codelineno-5-16" name="__codelineno-5-16" href="#__codelineno-5-16"></a> <span class="nb">print</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">paths</span><span class="p">[</span><span class="s2">"report_json"</span><span class="p">])</span>
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</code></pre></div>
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<p>Outputs to inspect:</p>
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<ul>
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<li><code>results/distribution_report.json</code>: statistics and diagnostics</li>
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<li><code>results/distribution_diagnostics.png</code>: diagnostic plot</li>
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<li><code>results/result_record.json</code>: canonical result</li>
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<h2 id="compressed-inputs">Compressed inputs<a class="headerlink" href="#compressed-inputs" title="Permanent link">¶</a></h2>
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<p><code>csv-scatter</code> accepts <code>.csv.gz</code> and <code>.tsv.gz</code>; <code>distribution-diagnostics</code> accepts <code>.csv.gz</code>.
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CADDForge expands these inputs only at workflow runtime and preserves the configured compressed
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path in provenance.</p>
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</div>
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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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</main>
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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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<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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