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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Examples
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<label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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Plugins
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1100
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1101
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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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<a href="../version-matrix/" class="md-nav__link">
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Version Matrix
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<a href="../docking/" class="md-nav__link">
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1199
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MD
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<li class="md-nav__item">
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<a href="../fep/" class="md-nav__link">
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1226
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1227
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<span class="md-ellipsis">
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1231
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FEP
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1232
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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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1238
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<input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
|
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<label class="md-nav__link md-nav__link--active" for="__toc">
|
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1291
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ML
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1300
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1301
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1303
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<span class="md-nav__icon md-icon"></span>
|
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</label>
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1306
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1307
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<a href="./" class="md-nav__link md-nav__link--active">
|
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1308
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ML
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1322
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</a>
|
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1323
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1324
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1325
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|
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1326
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<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
|
|
1327
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|
1328
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1329
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|
1330
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|
1331
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|
1332
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|
1333
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<label class="md-nav__title" for="__toc">
|
|
1334
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1335
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+
Table of contents
|
|
1336
|
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</label>
|
|
1337
|
+
<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
|
|
1338
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|
|
1339
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Example Library
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1742
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Example Data Provenance
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1744
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|
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1745
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|
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1746
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1748
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1753
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1754
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|
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1756
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Reproducibility
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Method References
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<a href="../../explanation/third-party-notices/" class="md-nav__link">
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Third-party Notices
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</nav>
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_10" >
|
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1952
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<div class="md-nav__link md-nav__container">
|
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1954
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<a href="../../development/" class="md-nav__link ">
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<span class="md-ellipsis">
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Development
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<label class="md-nav__link " for="__nav_10" id="__nav_10_label" tabindex="">
|
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1973
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<span class="md-nav__icon md-icon"></span>
|
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1974
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</label>
|
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1975
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1976
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</div>
|
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1977
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|
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1978
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<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_10_label" aria-expanded="false">
|
|
1979
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<label class="md-nav__title" for="__nav_10">
|
|
1980
|
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<span class="md-nav__icon md-icon"></span>
|
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1981
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1982
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|
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1983
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Development
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1984
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1985
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1986
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</label>
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<ul class="md-nav__list" data-md-scrollfix>
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Release Notes
|
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2004
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2005
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2006
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|
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2007
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</span>
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2010
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2011
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2012
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2020
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2022
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|
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<li class="md-nav__item">
|
|
2024
|
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<a href="../../development/tool-authoring/" class="md-nav__link">
|
|
2025
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|
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2026
|
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|
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|
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<span class="md-ellipsis">
|
|
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|
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|
|
2030
|
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|
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2031
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+
Tool Authoring
|
|
2032
|
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|
|
2033
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|
|
2034
|
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|
|
2035
|
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|
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2036
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|
|
2037
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2038
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|
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2039
|
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|
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2040
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<a href="../../development/documentation/" class="md-nav__link">
|
|
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2055
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2056
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<span class="md-ellipsis">
|
|
2057
|
+
|
|
2058
|
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|
|
2059
|
+
Documentation
|
|
2060
|
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|
|
2061
|
+
|
|
2062
|
+
|
|
2063
|
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|
|
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|
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|
|
2065
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|
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2066
|
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|
|
2067
|
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|
|
2068
|
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|
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2069
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2078
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|
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2079
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|
|
2080
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<a href="../../development/contributing/" class="md-nav__link">
|
|
2081
|
+
|
|
2082
|
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|
|
2083
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|
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2084
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+
<span class="md-ellipsis">
|
|
2085
|
+
|
|
2086
|
+
|
|
2087
|
+
Contributing
|
|
2088
|
+
|
|
2089
|
+
|
|
2090
|
+
|
|
2091
|
+
</span>
|
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2092
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|
|
2093
|
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2094
|
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|
|
2095
|
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</a>
|
|
2096
|
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|
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2097
|
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|
|
2098
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|
|
2099
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|
|
2100
|
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|
|
2101
|
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|
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2102
|
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2103
|
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|
|
2104
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|
|
2105
|
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|
|
2106
|
+
|
|
2107
|
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<li class="md-nav__item">
|
|
2108
|
+
<a href="../../development/security/" class="md-nav__link">
|
|
2109
|
+
|
|
2110
|
+
|
|
2111
|
+
|
|
2112
|
+
<span class="md-ellipsis">
|
|
2113
|
+
|
|
2114
|
+
|
|
2115
|
+
Security Reporting
|
|
2116
|
+
|
|
2117
|
+
|
|
2118
|
+
|
|
2119
|
+
</span>
|
|
2120
|
+
|
|
2121
|
+
|
|
2122
|
+
|
|
2123
|
+
</a>
|
|
2124
|
+
</li>
|
|
2125
|
+
|
|
2126
|
+
|
|
2127
|
+
|
|
2128
|
+
|
|
2129
|
+
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2130
|
+
|
|
2131
|
+
|
|
2132
|
+
|
|
2133
|
+
|
|
2134
|
+
|
|
2135
|
+
<li class="md-nav__item">
|
|
2136
|
+
<a href="../../development/release-readiness/" class="md-nav__link">
|
|
2137
|
+
|
|
2138
|
+
|
|
2139
|
+
|
|
2140
|
+
<span class="md-ellipsis">
|
|
2141
|
+
|
|
2142
|
+
|
|
2143
|
+
Release Readiness
|
|
2144
|
+
|
|
2145
|
+
|
|
2146
|
+
|
|
2147
|
+
</span>
|
|
2148
|
+
|
|
2149
|
+
|
|
2150
|
+
|
|
2151
|
+
</a>
|
|
2152
|
+
</li>
|
|
2153
|
+
|
|
2154
|
+
|
|
2155
|
+
|
|
2156
|
+
|
|
2157
|
+
|
|
2158
|
+
|
|
2159
|
+
|
|
2160
|
+
|
|
2161
|
+
|
|
2162
|
+
|
|
2163
|
+
<li class="md-nav__item">
|
|
2164
|
+
<a href="../../development/ci-publishing/" class="md-nav__link">
|
|
2165
|
+
|
|
2166
|
+
|
|
2167
|
+
|
|
2168
|
+
<span class="md-ellipsis">
|
|
2169
|
+
|
|
2170
|
+
|
|
2171
|
+
CI and Publishing
|
|
2172
|
+
|
|
2173
|
+
|
|
2174
|
+
|
|
2175
|
+
</span>
|
|
2176
|
+
|
|
2177
|
+
|
|
2178
|
+
|
|
2179
|
+
</a>
|
|
2180
|
+
</li>
|
|
2181
|
+
|
|
2182
|
+
|
|
2183
|
+
|
|
2184
|
+
|
|
2185
|
+
</ul>
|
|
2186
|
+
</nav>
|
|
2187
|
+
|
|
2188
|
+
</li>
|
|
2189
|
+
|
|
2190
|
+
|
|
2191
|
+
|
|
2192
|
+
</ul>
|
|
2193
|
+
</nav>
|
|
2194
|
+
</div>
|
|
2195
|
+
</div>
|
|
2196
|
+
</div>
|
|
2197
|
+
|
|
2198
|
+
|
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<h1 id="ml-plugin">ML Plugin<a class="headerlink" href="#ml-plugin" title="Permanent link">¶</a></h1>
|
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<p>Package: <code>caddforge-ml</code></p>
|
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<div class="admonition info">
|
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<p class="admonition-title">Public source tag</p>
|
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<p>This page describes <code>caddforge-ml</code> <code>0.4.0</code>, tagged as <code>v0.4.0</code>.
|
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|
+
Published on PyPI; see the <a href="../version-matrix/">version matrix</a>.</p>
|
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|
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</div>
|
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<p>The ML plugin exposes model training, prediction, dimensionality reduction, model sweeps, and
|
|
2340
|
+
classifier threshold exploration workflows.</p>
|
|
2341
|
+
<h2 id="requirements-and-example-status">Requirements and example status<a class="headerlink" href="#requirements-and-example-status" title="Permanent link">¶</a></h2>
|
|
2342
|
+
<p>The <a href="../../examples/">example library</a> provides downloadable configuration
|
|
2343
|
+
templates for every workflow on this page, plus a shared Python runner. File paths
|
|
2344
|
+
refer to inputs you must prepare; these are not bundled research datasets. Schema
|
|
2345
|
+
validation does not establish scientific validity or engine availability. See the
|
|
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|
+
<a href="../version-matrix/">version matrix</a> for release tags and publication status.</p>
|
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2347
|
+
<h2 id="simple-gp"><code>simple-gp</code><a class="headerlink" href="#simple-gp" title="Permanent link">¶</a></h2>
|
|
2348
|
+
<p>Trains and predicts with a simple Gaussian process regression workflow.</p>
|
|
2349
|
+
<p>CLI:</p>
|
|
2350
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>caddforge<span class="w"> </span>run<span class="w"> </span>ml<span class="w"> </span>simple-gp<span class="w"> </span>--config<span class="w"> </span>simple_gp.yaml
|
|
2351
|
+
</code></pre></div>
|
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|
+
<p>YAML:</p>
|
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2353
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a><span class="nt">train_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/train.csv</span>
|
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2354
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+
<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a><span class="nt">target_column</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">y</span>
|
|
2355
|
+
<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a><span class="nt">feature_columns</span><span class="p">:</span><span class="w"> </span><span class="p p-Indicator">[</span><span class="nv">f1</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">f2</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">f3</span><span class="p p-Indicator">]</span>
|
|
2356
|
+
<a id="__codelineno-1-4" name="__codelineno-1-4" href="#__codelineno-1-4"></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>
|
|
2357
|
+
<a id="__codelineno-1-5" name="__codelineno-1-5" href="#__codelineno-1-5"></a><span class="nt">ignore_columns</span><span class="p">:</span><span class="w"> </span><span class="p p-Indicator">[</span><span class="nv">id</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">comment</span><span class="p p-Indicator">]</span>
|
|
2358
|
+
<a id="__codelineno-1-6" name="__codelineno-1-6" href="#__codelineno-1-6"></a><span class="nt">fingerprint_types</span><span class="p">:</span><span class="w"> </span><span class="p p-Indicator">[</span><span class="nv">morgan</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">atompair</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">featmorgan</span><span class="p p-Indicator">]</span>
|
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2359
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+
<a id="__codelineno-1-7" name="__codelineno-1-7" href="#__codelineno-1-7"></a><span class="nt">kernel</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">tanimoto</span>
|
|
2360
|
+
<a id="__codelineno-1-8" name="__codelineno-1-8" href="#__codelineno-1-8"></a><span class="nt">noise</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">0.05</span>
|
|
2361
|
+
<a id="__codelineno-1-9" name="__codelineno-1-9" href="#__codelineno-1-9"></a><span class="nt">test_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/test.csv</span>
|
|
2362
|
+
<a id="__codelineno-1-10" name="__codelineno-1-10" href="#__codelineno-1-10"></a><span class="nt">save_report</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">true</span>
|
|
2363
|
+
<a id="__codelineno-1-11" name="__codelineno-1-11" href="#__codelineno-1-11"></a><span class="nt">log_targets</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">false</span>
|
|
2364
|
+
<a id="__codelineno-1-12" name="__codelineno-1-12" href="#__codelineno-1-12"></a><span class="nt">generate_scatter_plot</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">true</span>
|
|
2365
|
+
<a id="__codelineno-1-13" name="__codelineno-1-13" href="#__codelineno-1-13"></a><span class="nt">scatter_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">gp_scatter.html</span>
|
|
2366
|
+
<a id="__codelineno-1-14" name="__codelineno-1-14" href="#__codelineno-1-14"></a><span class="nt">mode</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">train</span>
|
|
2367
|
+
<a id="__codelineno-1-15" name="__codelineno-1-15" href="#__codelineno-1-15"></a><span class="nt">model_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">simple_gp_model.joblib</span>
|
|
2368
|
+
<a id="__codelineno-1-16" name="__codelineno-1-16" href="#__codelineno-1-16"></a><span class="nt">id_column</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">id</span>
|
|
2369
|
+
</code></pre></div>
|
|
2370
|
+
<p>Python:</p>
|
|
2371
|
+
<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>
|
|
2372
|
+
<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>
|
|
2373
|
+
<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>
|
|
2374
|
+
<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">"ml"</span><span class="p">,</span> <span class="s2">"simple-gp"</span><span class="p">)</span>
|
|
2375
|
+
<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><span class="n">train_path</span><span class="o">=</span><span class="s2">"data/train.csv"</span><span class="p">,</span> <span class="n">target_column</span><span class="o">=</span><span class="s2">"y"</span><span class="p">,</span> <span class="n">test_path</span><span class="o">=</span><span class="s2">"data/test.csv"</span><span class="p">)</span>
|
|
2376
|
+
<a id="__codelineno-2-6" name="__codelineno-2-6" href="#__codelineno-2-6"></a><span class="n">workflow</span> <span class="o">=</span> <span class="n">spec</span><span class="o">.</span><span class="n">workflow_cls</span><span class="p">(</span><span class="n">cfg</span><span class="p">)</span>
|
|
2377
|
+
<a id="__codelineno-2-7" name="__codelineno-2-7" href="#__codelineno-2-7"></a><span class="n">job</span> <span class="o">=</span> <span class="n">submit_workflow</span><span class="p">(</span>
|
|
2378
|
+
<a id="__codelineno-2-8" name="__codelineno-2-8" href="#__codelineno-2-8"></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>
|
|
2379
|
+
<a id="__codelineno-2-9" name="__codelineno-2-9" href="#__codelineno-2-9"></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>
|
|
2380
|
+
<a id="__codelineno-2-10" name="__codelineno-2-10" href="#__codelineno-2-10"></a><span class="p">)</span>
|
|
2381
|
+
<a id="__codelineno-2-11" name="__codelineno-2-11" href="#__codelineno-2-11"></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>
|
|
2382
|
+
<a id="__codelineno-2-12" name="__codelineno-2-12" href="#__codelineno-2-12"></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>
|
|
2383
|
+
<a id="__codelineno-2-13" name="__codelineno-2-13" href="#__codelineno-2-13"></a> <span class="nb">print</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">metrics</span><span class="p">)</span>
|
|
2384
|
+
</code></pre></div>
|
|
2385
|
+
<p>Outputs to inspect: <code>results/predictions.csv</code>, <code>results/results.json</code>,
|
|
2386
|
+
<code>results/result_record.json</code>.</p>
|
|
2387
|
+
<h2 id="pca"><code>pca</code><a class="headerlink" href="#pca" title="Permanent link">¶</a></h2>
|
|
2388
|
+
<p>Runs principal component analysis over configured feature columns.</p>
|
|
2389
|
+
<p>CLI:</p>
|
|
2390
|
+
<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>run<span class="w"> </span>ml<span class="w"> </span>pca<span class="w"> </span>--config<span class="w"> </span>pca.yaml
|
|
2391
|
+
</code></pre></div>
|
|
2392
|
+
<p>YAML:</p>
|
|
2393
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a><span class="nt">data_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/features.csv</span>
|
|
2394
|
+
<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a><span class="nt">feature_columns</span><span class="p">:</span><span class="w"> </span><span class="p p-Indicator">[</span><span class="nv">f1</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">f2</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">f3</span><span class="p p-Indicator">]</span>
|
|
2395
|
+
<a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a><span class="nt">ignore_columns</span><span class="p">:</span><span class="w"> </span><span class="p p-Indicator">[</span><span class="nv">id</span><span class="p p-Indicator">]</span>
|
|
2396
|
+
<a id="__codelineno-4-4" name="__codelineno-4-4" href="#__codelineno-4-4"></a><span class="nt">n_components</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">5</span>
|
|
2397
|
+
<a id="__codelineno-4-5" name="__codelineno-4-5" href="#__codelineno-4-5"></a><span class="nt">standardize</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">true</span>
|
|
2398
|
+
<a id="__codelineno-4-6" name="__codelineno-4-6" href="#__codelineno-4-6"></a><span class="nt">drop_missing_rows</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">true</span>
|
|
2399
|
+
<a id="__codelineno-4-7" name="__codelineno-4-7" href="#__codelineno-4-7"></a><span class="nt">scores_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">pca_scores.csv</span>
|
|
2400
|
+
<a id="__codelineno-4-8" name="__codelineno-4-8" href="#__codelineno-4-8"></a><span class="nt">components_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">pca_components.csv</span>
|
|
2401
|
+
<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">results.json</span>
|
|
2402
|
+
</code></pre></div>
|
|
2403
|
+
<p>Python:</p>
|
|
2404
|
+
<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>
|
|
2405
|
+
<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>
|
|
2406
|
+
<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a>
|
|
2407
|
+
<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">"ml"</span><span class="p">,</span> <span class="s2">"pca"</span><span class="p">)</span>
|
|
2408
|
+
<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><span class="n">data_path</span><span class="o">=</span><span class="s2">"data/features.csv"</span><span class="p">,</span> <span class="n">n_components</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">backend</span><span class="o">=</span><span class="s2">"local"</span><span class="p">)</span>
|
|
2409
|
+
<a id="__codelineno-5-6" name="__codelineno-5-6" href="#__codelineno-5-6"></a><span class="n">workflow</span> <span class="o">=</span> <span class="n">spec</span><span class="o">.</span><span class="n">workflow_cls</span><span class="p">(</span><span class="n">cfg</span><span class="p">)</span>
|
|
2410
|
+
<a id="__codelineno-5-7" name="__codelineno-5-7" href="#__codelineno-5-7"></a><span class="n">job</span> <span class="o">=</span> <span class="n">submit_workflow</span><span class="p">(</span>
|
|
2411
|
+
<a id="__codelineno-5-8" name="__codelineno-5-8" href="#__codelineno-5-8"></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>
|
|
2412
|
+
<a id="__codelineno-5-9" name="__codelineno-5-9" href="#__codelineno-5-9"></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>
|
|
2413
|
+
<a id="__codelineno-5-10" name="__codelineno-5-10" href="#__codelineno-5-10"></a><span class="p">)</span>
|
|
2414
|
+
<a id="__codelineno-5-11" name="__codelineno-5-11" href="#__codelineno-5-11"></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>
|
|
2415
|
+
<a id="__codelineno-5-12" name="__codelineno-5-12" href="#__codelineno-5-12"></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>
|
|
2416
|
+
<a id="__codelineno-5-13" name="__codelineno-5-13" href="#__codelineno-5-13"></a> <span class="nb">print</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">metrics</span><span class="p">)</span>
|
|
2417
|
+
</code></pre></div>
|
|
2418
|
+
<p>Outputs to inspect: <code>results/pca_scores.csv</code>, <code>results/pca_components.csv</code>,
|
|
2419
|
+
<code>results/results.json</code>.</p>
|
|
2420
|
+
<h2 id="model-zoo"><code>model-zoo</code><a class="headerlink" href="#model-zoo" title="Permanent link">¶</a></h2>
|
|
2421
|
+
<p>Runs a scikit-learn model from the model registry for regression or classification.</p>
|
|
2422
|
+
<p>CLI:</p>
|
|
2423
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>caddforge<span class="w"> </span>run<span class="w"> </span>ml<span class="w"> </span>model-zoo<span class="w"> </span>--config<span class="w"> </span>model_zoo.yaml
|
|
2424
|
+
</code></pre></div>
|
|
2425
|
+
<p>YAML:</p>
|
|
2426
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a><span class="nt">train_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/train.csv</span>
|
|
2427
|
+
<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a><span class="nt">target_column</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">y</span>
|
|
2428
|
+
<a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a><span class="nt">feature_columns</span><span class="p">:</span><span class="w"> </span><span class="p p-Indicator">[</span><span class="nv">f1</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">f2</span><span class="p p-Indicator">]</span>
|
|
2429
|
+
<a id="__codelineno-7-4" name="__codelineno-7-4" href="#__codelineno-7-4"></a><span class="nt">model_name</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">random_forest</span>
|
|
2430
|
+
<a id="__codelineno-7-5" name="__codelineno-7-5" href="#__codelineno-7-5"></a><span class="nt">task</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">regression</span>
|
|
2431
|
+
<a id="__codelineno-7-6" name="__codelineno-7-6" href="#__codelineno-7-6"></a><span class="nt">test_size</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">0.2</span>
|
|
2432
|
+
<a id="__codelineno-7-7" name="__codelineno-7-7" href="#__codelineno-7-7"></a><span class="nt">random_state</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">123</span>
|
|
2433
|
+
<a id="__codelineno-7-8" name="__codelineno-7-8" href="#__codelineno-7-8"></a><span class="nt">standardize_targets</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">false</span>
|
|
2434
|
+
<a id="__codelineno-7-9" name="__codelineno-7-9" href="#__codelineno-7-9"></a><span class="nt">target_transform</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">none</span>
|
|
2435
|
+
<a id="__codelineno-7-10" name="__codelineno-7-10" href="#__codelineno-7-10"></a><span class="nt">positive_class</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">1</span>
|
|
2436
|
+
<a id="__codelineno-7-11" name="__codelineno-7-11" href="#__codelineno-7-11"></a><span class="nt">predictions_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">predictions.csv</span>
|
|
2437
|
+
<a id="__codelineno-7-12" name="__codelineno-7-12" href="#__codelineno-7-12"></a><span class="nt">results_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">results.json</span>
|
|
2438
|
+
<a id="__codelineno-7-13" name="__codelineno-7-13" href="#__codelineno-7-13"></a><span class="nt">metrics_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">metrics.json</span>
|
|
2439
|
+
<a id="__codelineno-7-14" name="__codelineno-7-14" href="#__codelineno-7-14"></a><span class="nt">mode</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">train</span>
|
|
2440
|
+
<a id="__codelineno-7-15" name="__codelineno-7-15" href="#__codelineno-7-15"></a><span class="nt">model_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">artifacts/model.joblib</span>
|
|
2441
|
+
</code></pre></div>
|
|
2442
|
+
<p>Python:</p>
|
|
2443
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></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>
|
|
2444
|
+
<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></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>
|
|
2445
|
+
<a id="__codelineno-8-3" name="__codelineno-8-3" href="#__codelineno-8-3"></a>
|
|
2446
|
+
<a id="__codelineno-8-4" name="__codelineno-8-4" href="#__codelineno-8-4"></a><span class="n">spec</span> <span class="o">=</span> <span class="n">get_tool</span><span class="p">(</span><span class="s2">"ml"</span><span class="p">,</span> <span class="s2">"model-zoo"</span><span class="p">)</span>
|
|
2447
|
+
<a id="__codelineno-8-5" name="__codelineno-8-5" href="#__codelineno-8-5"></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>
|
|
2448
|
+
<a id="__codelineno-8-6" name="__codelineno-8-6" href="#__codelineno-8-6"></a> <span class="n">train_path</span><span class="o">=</span><span class="s2">"data/train.csv"</span><span class="p">,</span>
|
|
2449
|
+
<a id="__codelineno-8-7" name="__codelineno-8-7" href="#__codelineno-8-7"></a> <span class="n">target_column</span><span class="o">=</span><span class="s2">"y"</span><span class="p">,</span>
|
|
2450
|
+
<a id="__codelineno-8-8" name="__codelineno-8-8" href="#__codelineno-8-8"></a> <span class="n">model_name</span><span class="o">=</span><span class="s2">"random_forest"</span><span class="p">,</span>
|
|
2451
|
+
<a id="__codelineno-8-9" name="__codelineno-8-9" href="#__codelineno-8-9"></a> <span class="n">task</span><span class="o">=</span><span class="s2">"regression"</span><span class="p">,</span>
|
|
2452
|
+
<a id="__codelineno-8-10" name="__codelineno-8-10" href="#__codelineno-8-10"></a> <span class="n">backend</span><span class="o">=</span><span class="s2">"local"</span><span class="p">,</span>
|
|
2453
|
+
<a id="__codelineno-8-11" name="__codelineno-8-11" href="#__codelineno-8-11"></a><span class="p">)</span>
|
|
2454
|
+
<a id="__codelineno-8-12" name="__codelineno-8-12" href="#__codelineno-8-12"></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>
|
|
2455
|
+
<a id="__codelineno-8-13" name="__codelineno-8-13" href="#__codelineno-8-13"></a><span class="n">job</span> <span class="o">=</span> <span class="n">submit_workflow</span><span class="p">(</span>
|
|
2456
|
+
<a id="__codelineno-8-14" name="__codelineno-8-14" href="#__codelineno-8-14"></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>
|
|
2457
|
+
<a id="__codelineno-8-15" name="__codelineno-8-15" href="#__codelineno-8-15"></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>
|
|
2458
|
+
<a id="__codelineno-8-16" name="__codelineno-8-16" href="#__codelineno-8-16"></a><span class="p">)</span>
|
|
2459
|
+
<a id="__codelineno-8-17" name="__codelineno-8-17" href="#__codelineno-8-17"></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>
|
|
2460
|
+
<a id="__codelineno-8-18" name="__codelineno-8-18" href="#__codelineno-8-18"></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>
|
|
2461
|
+
<a id="__codelineno-8-19" name="__codelineno-8-19" href="#__codelineno-8-19"></a> <span class="nb">print</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">metrics</span><span class="p">)</span>
|
|
2462
|
+
</code></pre></div>
|
|
2463
|
+
<p>Outputs to inspect: <code>results/predictions.csv</code>, <code>results/metrics.json</code>,
|
|
2464
|
+
<code>results/results.json</code>, <code>artifacts/model.joblib</code>.</p>
|
|
2465
|
+
<h2 id="model-factory"><code>model-factory</code><a class="headerlink" href="#model-factory" title="Permanent link">¶</a></h2>
|
|
2466
|
+
<p>Runs multiple model-zoo training jobs against the same data and aggregates metrics, uncertainty
|
|
2467
|
+
diagnostics, confusion summaries, and model artifacts. Predict-only execution is provided by
|
|
2468
|
+
<code>model-zoo</code>, not by the factory.</p>
|
|
2469
|
+
<p>CLI:</p>
|
|
2470
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>caddforge<span class="w"> </span>run<span class="w"> </span>ml<span class="w"> </span>model-factory<span class="w"> </span>--config<span class="w"> </span>model_factory.yaml
|
|
2471
|
+
</code></pre></div>
|
|
2472
|
+
<p>YAML:</p>
|
|
2473
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a><span class="nt">train_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">data/train.csv</span>
|
|
2474
|
+
<a id="__codelineno-10-2" name="__codelineno-10-2" href="#__codelineno-10-2"></a><span class="nt">target_column</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">y</span>
|
|
2475
|
+
<a id="__codelineno-10-3" name="__codelineno-10-3" href="#__codelineno-10-3"></a><span class="nt">task</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">regression</span>
|
|
2476
|
+
<a id="__codelineno-10-4" name="__codelineno-10-4" href="#__codelineno-10-4"></a><span class="nt">feature_columns</span><span class="p">:</span><span class="w"> </span><span class="p p-Indicator">[</span><span class="nv">f1</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">f2</span><span class="p p-Indicator">]</span>
|
|
2477
|
+
<a id="__codelineno-10-5" name="__codelineno-10-5" href="#__codelineno-10-5"></a><span class="nt">ignore_columns</span><span class="p">:</span><span class="w"> </span><span class="p p-Indicator">[</span><span class="nv">compound_id</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">measured_at</span><span class="p p-Indicator">]</span>
|
|
2478
|
+
<a id="__codelineno-10-6" name="__codelineno-10-6" href="#__codelineno-10-6"></a><span class="nt">test_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">null</span>
|
|
2479
|
+
<a id="__codelineno-10-7" name="__codelineno-10-7" href="#__codelineno-10-7"></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>
|
|
2480
|
+
<a id="__codelineno-10-8" name="__codelineno-10-8" href="#__codelineno-10-8"></a><span class="nt">fingerprint_types</span><span class="p">:</span><span class="w"> </span><span class="p p-Indicator">[</span><span class="nv">morgan</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">atompair</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">featmorgan</span><span class="p p-Indicator">]</span>
|
|
2481
|
+
<a id="__codelineno-10-9" name="__codelineno-10-9" href="#__codelineno-10-9"></a><span class="nt">fp_bits</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">2048</span>
|
|
2482
|
+
<a id="__codelineno-10-10" name="__codelineno-10-10" href="#__codelineno-10-10"></a><span class="nt">fp_radius</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">2</span>
|
|
2483
|
+
<a id="__codelineno-10-11" name="__codelineno-10-11" href="#__codelineno-10-11"></a><span class="nt">fp_use_chirality</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">true</span>
|
|
2484
|
+
<a id="__codelineno-10-12" name="__codelineno-10-12" href="#__codelineno-10-12"></a><span class="nt">model_names</span><span class="p">:</span><span class="w"> </span><span class="p p-Indicator">[</span><span class="nv">ridge</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">random_forest</span><span class="p p-Indicator">,</span><span class="w"> </span><span class="nv">xgboost</span><span class="p p-Indicator">]</span>
|
|
2485
|
+
<a id="__codelineno-10-13" name="__codelineno-10-13" href="#__codelineno-10-13"></a><span class="nt">model_params</span><span class="p">:</span>
|
|
2486
|
+
<a id="__codelineno-10-14" name="__codelineno-10-14" href="#__codelineno-10-14"></a><span class="w"> </span><span class="nt">random_forest</span><span class="p">:</span>
|
|
2487
|
+
<a id="__codelineno-10-15" name="__codelineno-10-15" href="#__codelineno-10-15"></a><span class="w"> </span><span class="nt">n_estimators</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">500</span>
|
|
2488
|
+
<a id="__codelineno-10-16" name="__codelineno-10-16" href="#__codelineno-10-16"></a><span class="w"> </span><span class="nt">random_state</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">123</span>
|
|
2489
|
+
<a id="__codelineno-10-17" name="__codelineno-10-17" href="#__codelineno-10-17"></a><span class="nt">calibrate</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">false</span>
|
|
2490
|
+
<a id="__codelineno-10-18" name="__codelineno-10-18" href="#__codelineno-10-18"></a><span class="nt">calibrate_method</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">sigmoid</span>
|
|
2491
|
+
<a id="__codelineno-10-19" name="__codelineno-10-19" href="#__codelineno-10-19"></a><span class="nt">test_size</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">0.2</span>
|
|
2492
|
+
<a id="__codelineno-10-20" name="__codelineno-10-20" href="#__codelineno-10-20"></a><span class="nt">random_state</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">123</span>
|
|
2493
|
+
<a id="__codelineno-10-21" name="__codelineno-10-21" href="#__codelineno-10-21"></a><span class="nt">predictions_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">predictions.csv</span>
|
|
2494
|
+
<a id="__codelineno-10-22" name="__codelineno-10-22" href="#__codelineno-10-22"></a><span class="nt">results_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">results.json</span>
|
|
2495
|
+
<a id="__codelineno-10-23" name="__codelineno-10-23" href="#__codelineno-10-23"></a><span class="nt">metrics_filename</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">metrics.json</span>
|
|
2496
|
+
<a id="__codelineno-10-24" name="__codelineno-10-24" href="#__codelineno-10-24"></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>
|
|
2497
|
+
<a id="__codelineno-10-25" name="__codelineno-10-25" href="#__codelineno-10-25"></a><span class="nt">classification_thresholds</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">null</span>
|
|
2498
|
+
<a id="__codelineno-10-26" name="__codelineno-10-26" href="#__codelineno-10-26"></a><span class="nt">time_column</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">measured_at</span>
|
|
2499
|
+
<a id="__codelineno-10-27" name="__codelineno-10-27" href="#__codelineno-10-27"></a><span class="nt">standardize_targets</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">false</span>
|
|
2500
|
+
<a id="__codelineno-10-28" name="__codelineno-10-28" href="#__codelineno-10-28"></a><span class="nt">positive_class</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">null</span>
|
|
2501
|
+
<a id="__codelineno-10-29" name="__codelineno-10-29" href="#__codelineno-10-29"></a><span class="nt">target_transform</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">none</span>
|
|
2502
|
+
<a id="__codelineno-10-30" name="__codelineno-10-30" href="#__codelineno-10-30"></a><span class="nt">drop_non_positive_targets</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">true</span>
|
|
2503
|
+
<a id="__codelineno-10-31" name="__codelineno-10-31" href="#__codelineno-10-31"></a><span class="c1"># log_targets: false # deprecated alias for target_transform: log</span>
|
|
2504
|
+
</code></pre></div>
|
|
2505
|
+
<p>Set <code>task</code> explicitly when possible. With an explicit task and no <code>model_names</code>, the factory runs
|
|
2506
|
+
all compatible registry models. If both values are omitted, the factory attempts every registered
|
|
2507
|
+
model and each subrun infers its own task, so incompatible model/task combinations can be included.</p>
|
|
2508
|
+
<h3 id="model-factory-configuration">Model-factory configuration<a class="headerlink" href="#model-factory-configuration" title="Permanent link">¶</a></h3>
|
|
2509
|
+
<p>These are all options defined by <code>ModelFactoryConfig</code>. Shared options inherited from the core,
|
|
2510
|
+
including <code>backend</code>, <code>run_directory</code>, <code>registry_path</code>, <code>job_name</code>, result export, and Slurm
|
|
2511
|
+
settings, are described in <a href="../../core/configuration/">Configuration</a>.</p>
|
|
2512
|
+
<table>
|
|
2513
|
+
<thead>
|
|
2514
|
+
<tr>
|
|
2515
|
+
<th>Option</th>
|
|
2516
|
+
<th>Type and default</th>
|
|
2517
|
+
<th>Description</th>
|
|
2518
|
+
</tr>
|
|
2519
|
+
</thead>
|
|
2520
|
+
<tbody>
|
|
2521
|
+
<tr>
|
|
2522
|
+
<td><code>train_path</code></td>
|
|
2523
|
+
<td>path, required</td>
|
|
2524
|
+
<td>Training CSV containing the target and every configured training column.</td>
|
|
2525
|
+
</tr>
|
|
2526
|
+
<tr>
|
|
2527
|
+
<td><code>target_column</code></td>
|
|
2528
|
+
<td>string, required</td>
|
|
2529
|
+
<td>Column to predict. Numeric values are required for regression and threshold-binned classification.</td>
|
|
2530
|
+
</tr>
|
|
2531
|
+
<tr>
|
|
2532
|
+
<td><code>task</code></td>
|
|
2533
|
+
<td><code>regression</code>, <code>classification</code>, or <code>null</code>; default <code>null</code></td>
|
|
2534
|
+
<td>Task passed to every model-zoo subrun. If omitted, a subrun infers classification for thresholded or non-numeric targets and regression otherwise. An explicit value also filters automatic model selection.</td>
|
|
2535
|
+
</tr>
|
|
2536
|
+
<tr>
|
|
2537
|
+
<td><code>feature_columns</code></td>
|
|
2538
|
+
<td>list of strings or <code>null</code>; default <code>null</code></td>
|
|
2539
|
+
<td>Numeric features. When omitted, all columns except the target, SMILES column, and ignored columns are selected. They are concatenated with fingerprints when SMILES are also configured.</td>
|
|
2540
|
+
</tr>
|
|
2541
|
+
<tr>
|
|
2542
|
+
<td><code>ignore_columns</code></td>
|
|
2543
|
+
<td>list of strings; default <code>[]</code></td>
|
|
2544
|
+
<td>Excludes columns from automatic feature selection only. It does not alter explicit <code>feature_columns</code>.</td>
|
|
2545
|
+
</tr>
|
|
2546
|
+
<tr>
|
|
2547
|
+
<td><code>test_path</code></td>
|
|
2548
|
+
<td>path or <code>null</code>; default <code>null</code></td>
|
|
2549
|
+
<td>External evaluation CSV. When present, all training rows are fitted; otherwise the training CSV is split into fit and holdout sets.</td>
|
|
2550
|
+
</tr>
|
|
2551
|
+
<tr>
|
|
2552
|
+
<td><code>smiles_column</code></td>
|
|
2553
|
+
<td>string or <code>null</code>; default <code>null</code></td>
|
|
2554
|
+
<td>SMILES column from which RDKit fingerprints are generated. Fingerprints can supplement or replace tabular features.</td>
|
|
2555
|
+
</tr>
|
|
2556
|
+
<tr>
|
|
2557
|
+
<td><code>fingerprint_types</code></td>
|
|
2558
|
+
<td>list of strings; default <code>[morgan, atompair, featmorgan]</code></td>
|
|
2559
|
+
<td>Fingerprints concatenated per molecule. Supported values: <code>morgan</code>, <code>atompair</code>, and <code>featmorgan</code>. Used only when <code>smiles_column</code> is set.</td>
|
|
2560
|
+
</tr>
|
|
2561
|
+
<tr>
|
|
2562
|
+
<td><code>fp_bits</code></td>
|
|
2563
|
+
<td>integer; default <code>2048</code></td>
|
|
2564
|
+
<td>Number of bits per fingerprint type. Total fingerprint width is <code>fp_bits</code> multiplied by the number of types.</td>
|
|
2565
|
+
</tr>
|
|
2566
|
+
<tr>
|
|
2567
|
+
<td><code>fp_radius</code></td>
|
|
2568
|
+
<td>integer; default <code>2</code></td>
|
|
2569
|
+
<td>Radius for Morgan and feature-Morgan fingerprints.</td>
|
|
2570
|
+
</tr>
|
|
2571
|
+
<tr>
|
|
2572
|
+
<td><code>fp_use_chirality</code></td>
|
|
2573
|
+
<td>boolean; default <code>true</code></td>
|
|
2574
|
+
<td>Include chirality in fingerprint generation.</td>
|
|
2575
|
+
</tr>
|
|
2576
|
+
<tr>
|
|
2577
|
+
<td><code>model_names</code></td>
|
|
2578
|
+
<td>list of strings or <code>null</code>; default <code>null</code></td>
|
|
2579
|
+
<td>Registry models to run. Valid values are <code>ridge</code>, <code>lasso</code>, <code>elasticnet</code>, <code>bayesian_ridge</code>, <code>logistic_regression</code>, <code>random_forest</code>, <code>extra_trees</code>, <code>svm</code>, <code>knn</code>, <code>gaussian_process</code>, and <code>xgboost</code>. With an explicit task, <code>null</code> selects every compatible model.</td>
|
|
2580
|
+
</tr>
|
|
2581
|
+
<tr>
|
|
2582
|
+
<td><code>model_params</code></td>
|
|
2583
|
+
<td>mapping; default <code>{}</code></td>
|
|
2584
|
+
<td>Estimator keyword arguments keyed by model name. Each nested mapping is passed directly to the corresponding scikit-learn or XGBoost constructor.</td>
|
|
2585
|
+
</tr>
|
|
2586
|
+
<tr>
|
|
2587
|
+
<td><code>calibrate</code></td>
|
|
2588
|
+
<td>boolean; default <code>false</code></td>
|
|
2589
|
+
<td>For classification, calibrate probabilities with three-fold <code>CalibratedClassifierCV</code>. Ignored for regression.</td>
|
|
2590
|
+
</tr>
|
|
2591
|
+
<tr>
|
|
2592
|
+
<td><code>calibrate_method</code></td>
|
|
2593
|
+
<td><code>sigmoid</code> or <code>isotonic</code>; default <code>sigmoid</code></td>
|
|
2594
|
+
<td>Probability calibration method used when calibration is enabled.</td>
|
|
2595
|
+
</tr>
|
|
2596
|
+
<tr>
|
|
2597
|
+
<td><code>test_size</code></td>
|
|
2598
|
+
<td>float from <code>0.0</code> to <code>0.9</code>; default <code>0.2</code></td>
|
|
2599
|
+
<td>Holdout fraction when <code>test_path</code> is absent; use a positive value when a holdout is required. Splitting is chronological with <code>time_column</code>; otherwise it is random and classification is stratified when possible.</td>
|
|
2600
|
+
</tr>
|
|
2601
|
+
<tr>
|
|
2602
|
+
<td><code>random_state</code></td>
|
|
2603
|
+
<td>integer; default <code>123</code></td>
|
|
2604
|
+
<td>Seed for the random holdout split. Estimator seeds must be set separately in <code>model_params</code>.</td>
|
|
2605
|
+
</tr>
|
|
2606
|
+
<tr>
|
|
2607
|
+
<td><code>predictions_filename</code></td>
|
|
2608
|
+
<td>string; default <code>predictions.csv</code></td>
|
|
2609
|
+
<td>Predictions filename in each model subrun's <code>results/</code> directory.</td>
|
|
2610
|
+
</tr>
|
|
2611
|
+
<tr>
|
|
2612
|
+
<td><code>results_filename</code></td>
|
|
2613
|
+
<td>string; default <code>results.json</code></td>
|
|
2614
|
+
<td>Model-zoo summary filename in each model subrun's <code>results/</code> directory.</td>
|
|
2615
|
+
</tr>
|
|
2616
|
+
<tr>
|
|
2617
|
+
<td><code>metrics_filename</code></td>
|
|
2618
|
+
<td>string; default <code>metrics.json</code></td>
|
|
2619
|
+
<td>Metrics filename in each model subrun's <code>results/</code> directory.</td>
|
|
2620
|
+
</tr>
|
|
2621
|
+
<tr>
|
|
2622
|
+
<td><code>id_column</code></td>
|
|
2623
|
+
<td>string or <code>null</code>; default <code>null</code></td>
|
|
2624
|
+
<td>Column copied to per-model predictions as <code>id</code>; row indices are used when omitted.</td>
|
|
2625
|
+
</tr>
|
|
2626
|
+
<tr>
|
|
2627
|
+
<td><code>classification_thresholds</code></td>
|
|
2628
|
+
<td>list of floats or <code>null</code>; default <code>null</code></td>
|
|
2629
|
+
<td>Sorted boundaries used with classification to bin a continuous target using <code>numpy.digitize</code>. N thresholds produce N+1 integer classes. Factory confusion summaries require a binary outcome.</td>
|
|
2630
|
+
</tr>
|
|
2631
|
+
<tr>
|
|
2632
|
+
<td><code>time_column</code></td>
|
|
2633
|
+
<td>string or <code>null</code>; default <code>null</code></td>
|
|
2634
|
+
<td>Datetime-like column for chronological splitting when no external test CSV is supplied. The newest holdout fraction is evaluated.</td>
|
|
2635
|
+
</tr>
|
|
2636
|
+
<tr>
|
|
2637
|
+
<td><code>standardize_targets</code></td>
|
|
2638
|
+
<td>boolean; default <code>false</code></td>
|
|
2639
|
+
<td>Regression only. Standardizes the target after any transform, then reverses standardization and transformation for predictions and metrics.</td>
|
|
2640
|
+
</tr>
|
|
2641
|
+
<tr>
|
|
2642
|
+
<td><code>positive_class</code></td>
|
|
2643
|
+
<td>integer or <code>null</code>; default <code>null</code></td>
|
|
2644
|
+
<td>Positive label for binary probability and confusion diagnostics. Subruns prefer class <code>1</code>, then the highest class, when omitted; factory confusion summaries default to <code>1</code>.</td>
|
|
2645
|
+
</tr>
|
|
2646
|
+
<tr>
|
|
2647
|
+
<td><code>log_targets</code></td>
|
|
2648
|
+
<td>boolean; default <code>false</code></td>
|
|
2649
|
+
<td>Deprecated alias for <code>target_transform: log</code>. It cannot be combined with a non-<code>none</code> target transform.</td>
|
|
2650
|
+
</tr>
|
|
2651
|
+
<tr>
|
|
2652
|
+
<td><code>target_transform</code></td>
|
|
2653
|
+
<td><code>none</code>, <code>log</code>, or <code>log1p</code>; default <code>none</code></td>
|
|
2654
|
+
<td>Regression-only transform applied before optional standardization and inverted for outputs. <code>log</code> requires targets greater than zero; <code>log1p</code> requires targets greater than -1.</td>
|
|
2655
|
+
</tr>
|
|
2656
|
+
<tr>
|
|
2657
|
+
<td><code>drop_non_positive_targets</code></td>
|
|
2658
|
+
<td>boolean; default <code>true</code></td>
|
|
2659
|
+
<td>Drops targets invalid for the selected log transform. If false, invalid targets cause the run to fail.</td>
|
|
2660
|
+
</tr>
|
|
2661
|
+
</tbody>
|
|
2662
|
+
</table>
|
|
2663
|
+
<p>Model compatibility:</p>
|
|
2664
|
+
<table>
|
|
2665
|
+
<thead>
|
|
2666
|
+
<tr>
|
|
2667
|
+
<th>Task</th>
|
|
2668
|
+
<th>Models</th>
|
|
2669
|
+
</tr>
|
|
2670
|
+
</thead>
|
|
2671
|
+
<tbody>
|
|
2672
|
+
<tr>
|
|
2673
|
+
<td>Regression only</td>
|
|
2674
|
+
<td><code>ridge</code>, <code>lasso</code>, <code>elasticnet</code>, <code>bayesian_ridge</code>, <code>gaussian_process</code></td>
|
|
2675
|
+
</tr>
|
|
2676
|
+
<tr>
|
|
2677
|
+
<td>Classification only</td>
|
|
2678
|
+
<td><code>logistic_regression</code></td>
|
|
2679
|
+
</tr>
|
|
2680
|
+
<tr>
|
|
2681
|
+
<td>Regression and classification</td>
|
|
2682
|
+
<td><code>random_forest</code>, <code>extra_trees</code>, <code>svm</code>, <code>knn</code>, <code>xgboost</code></td>
|
|
2683
|
+
</tr>
|
|
2684
|
+
</tbody>
|
|
2685
|
+
</table>
|
|
2686
|
+
<p>Python:</p>
|
|
2687
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></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>
|
|
2688
|
+
<a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></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>
|
|
2689
|
+
<a id="__codelineno-11-3" name="__codelineno-11-3" href="#__codelineno-11-3"></a>
|
|
2690
|
+
<a id="__codelineno-11-4" name="__codelineno-11-4" href="#__codelineno-11-4"></a><span class="n">spec</span> <span class="o">=</span> <span class="n">get_tool</span><span class="p">(</span><span class="s2">"ml"</span><span class="p">,</span> <span class="s2">"model-factory"</span><span class="p">)</span>
|
|
2691
|
+
<a id="__codelineno-11-5" name="__codelineno-11-5" href="#__codelineno-11-5"></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>
|
|
2692
|
+
<a id="__codelineno-11-6" name="__codelineno-11-6" href="#__codelineno-11-6"></a> <span class="n">train_path</span><span class="o">=</span><span class="s2">"data/train.csv"</span><span class="p">,</span>
|
|
2693
|
+
<a id="__codelineno-11-7" name="__codelineno-11-7" href="#__codelineno-11-7"></a> <span class="n">target_column</span><span class="o">=</span><span class="s2">"y"</span><span class="p">,</span>
|
|
2694
|
+
<a id="__codelineno-11-8" name="__codelineno-11-8" href="#__codelineno-11-8"></a> <span class="n">task</span><span class="o">=</span><span class="s2">"regression"</span><span class="p">,</span>
|
|
2695
|
+
<a id="__codelineno-11-9" name="__codelineno-11-9" href="#__codelineno-11-9"></a> <span class="n">backend</span><span class="o">=</span><span class="s2">"local"</span><span class="p">,</span>
|
|
2696
|
+
<a id="__codelineno-11-10" name="__codelineno-11-10" href="#__codelineno-11-10"></a><span class="p">)</span>
|
|
2697
|
+
<a id="__codelineno-11-11" name="__codelineno-11-11" href="#__codelineno-11-11"></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>
|
|
2698
|
+
<a id="__codelineno-11-12" name="__codelineno-11-12" href="#__codelineno-11-12"></a><span class="n">job</span> <span class="o">=</span> <span class="n">submit_workflow</span><span class="p">(</span>
|
|
2699
|
+
<a id="__codelineno-11-13" name="__codelineno-11-13" href="#__codelineno-11-13"></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>
|
|
2700
|
+
<a id="__codelineno-11-14" name="__codelineno-11-14" href="#__codelineno-11-14"></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>
|
|
2701
|
+
<a id="__codelineno-11-15" name="__codelineno-11-15" href="#__codelineno-11-15"></a><span class="p">)</span>
|
|
2702
|
+
<a id="__codelineno-11-16" name="__codelineno-11-16" href="#__codelineno-11-16"></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>
|
|
2703
|
+
<a id="__codelineno-11-17" name="__codelineno-11-17" href="#__codelineno-11-17"></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>
|
|
2704
|
+
<a id="__codelineno-11-18" name="__codelineno-11-18" href="#__codelineno-11-18"></a> <span class="nb">print</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">metrics</span><span class="p">)</span>
|
|
2705
|
+
</code></pre></div>
|
|
2706
|
+
<p>Outputs to inspect:</p>
|
|
2707
|
+
<ul>
|
|
2708
|
+
<li><code>results/summary.csv</code> and <code>results/summary.json</code>: one row per model with prefixed metrics,
|
|
2709
|
+
optional uncertainty-to-error correlation, and binary confusion values. Regression summaries
|
|
2710
|
+
also include OLS slope, intercept, R2, and RMSE diagnostics.</li>
|
|
2711
|
+
<li><code><model-name>/</code>: complete model-zoo subruns with predictions, metrics, results, logs, and model
|
|
2712
|
+
bundles.</li>
|
|
2713
|
+
<li><code>artifacts/<model-name>_model.joblib</code>: pooled copies of generated model bundles.</li>
|
|
2714
|
+
<li><code>results/result_record.json</code>: canonical result exposing <code>summary_csv</code>, <code>summary_json</code>, and <code>log</code>
|
|
2715
|
+
paths.</li>
|
|
2716
|
+
</ul>
|
|
2717
|
+
<h2 id="explore-classifier"><code>explore-classifier</code><a class="headerlink" href="#explore-classifier" title="Permanent link">¶</a></h2>
|
|
2718
|
+
<p>Launches an interactive Streamlit UI for classifier threshold exploration.</p>
|
|
2719
|
+
<p>CLI:</p>
|
|
2720
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a>caddforge<span class="w"> </span>run<span class="w"> </span>ml<span class="w"> </span>explore-classifier<span class="w"> </span>--config<span class="w"> </span>explore_classifier.yaml
|
|
2721
|
+
</code></pre></div>
|
|
2722
|
+
<p>YAML:</p>
|
|
2723
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a><span class="nt">job_id</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">existing_model_job_id</span>
|
|
2724
|
+
<a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a><span class="nt">run_base</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">runs</span>
|
|
2725
|
+
<a id="__codelineno-13-3" name="__codelineno-13-3" href="#__codelineno-13-3"></a><span class="nt">model_name</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">random_forest</span>
|
|
2726
|
+
<a id="__codelineno-13-4" name="__codelineno-13-4" href="#__codelineno-13-4"></a><span class="nt">positive_class</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">1</span>
|
|
2727
|
+
</code></pre></div>
|
|
2728
|
+
<p>Python:</p>
|
|
2729
|
+
<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></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>
|
|
2730
|
+
<a id="__codelineno-14-2" name="__codelineno-14-2" href="#__codelineno-14-2"></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>
|
|
2731
|
+
<a id="__codelineno-14-3" name="__codelineno-14-3" href="#__codelineno-14-3"></a>
|
|
2732
|
+
<a id="__codelineno-14-4" name="__codelineno-14-4" href="#__codelineno-14-4"></a><span class="n">spec</span> <span class="o">=</span> <span class="n">get_tool</span><span class="p">(</span><span class="s2">"ml"</span><span class="p">,</span> <span class="s2">"explore-classifier"</span><span class="p">)</span>
|
|
2733
|
+
<a id="__codelineno-14-5" name="__codelineno-14-5" href="#__codelineno-14-5"></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>
|
|
2734
|
+
<a id="__codelineno-14-6" name="__codelineno-14-6" href="#__codelineno-14-6"></a> <span class="n">job_id</span><span class="o">=</span><span class="s2">"existing_model_job_id"</span><span class="p">,</span>
|
|
2735
|
+
<a id="__codelineno-14-7" name="__codelineno-14-7" href="#__codelineno-14-7"></a> <span class="n">run_base</span><span class="o">=</span><span class="s2">"runs"</span><span class="p">,</span>
|
|
2736
|
+
<a id="__codelineno-14-8" name="__codelineno-14-8" href="#__codelineno-14-8"></a> <span class="n">model_name</span><span class="o">=</span><span class="s2">"random_forest"</span><span class="p">,</span>
|
|
2737
|
+
<a id="__codelineno-14-9" name="__codelineno-14-9" href="#__codelineno-14-9"></a> <span class="n">backend</span><span class="o">=</span><span class="s2">"local"</span><span class="p">,</span>
|
|
2738
|
+
<a id="__codelineno-14-10" name="__codelineno-14-10" href="#__codelineno-14-10"></a><span class="p">)</span>
|
|
2739
|
+
<a id="__codelineno-14-11" name="__codelineno-14-11" href="#__codelineno-14-11"></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>
|
|
2740
|
+
<a id="__codelineno-14-12" name="__codelineno-14-12" href="#__codelineno-14-12"></a><span class="n">job</span> <span class="o">=</span> <span class="n">submit_workflow</span><span class="p">(</span>
|
|
2741
|
+
<a id="__codelineno-14-13" name="__codelineno-14-13" href="#__codelineno-14-13"></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>
|
|
2742
|
+
<a id="__codelineno-14-14" name="__codelineno-14-14" href="#__codelineno-14-14"></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>
|
|
2743
|
+
<a id="__codelineno-14-15" name="__codelineno-14-15" href="#__codelineno-14-15"></a><span class="p">)</span>
|
|
2744
|
+
<a id="__codelineno-14-16" name="__codelineno-14-16" href="#__codelineno-14-16"></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>
|
|
2745
|
+
<a id="__codelineno-14-17" name="__codelineno-14-17" href="#__codelineno-14-17"></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>
|
|
2746
|
+
<a id="__codelineno-14-18" name="__codelineno-14-18" href="#__codelineno-14-18"></a> <span class="nb">print</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">status</span><span class="o">.</span><span class="n">value</span><span class="p">)</span>
|
|
2747
|
+
</code></pre></div>
|
|
2748
|
+
<p>Outputs to inspect: Streamlit UI session, saved threshold JSON under <code>artifacts/</code>, updated model
|
|
2749
|
+
artifact when possible.</p>
|
|
2750
|
+
<h2 id="compressed-inputs">Compressed inputs<a class="headerlink" href="#compressed-inputs" title="Permanent link">¶</a></h2>
|
|
2751
|
+
<p>Training, test, and PCA CSV inputs may be supplied as <code>.csv.gz</code>. They are expanded only at runtime,
|
|
2752
|
+
and saved configurations retain the compressed source paths.</p>
|
|
2753
|
+
|
|
2754
|
+
|
|
2755
|
+
|
|
2756
|
+
|
|
2757
|
+
|
|
2758
|
+
|
|
2759
|
+
|
|
2760
|
+
|
|
2761
|
+
|
|
2762
|
+
|
|
2763
|
+
|
|
2764
|
+
|
|
2765
|
+
|
|
2766
|
+
</article>
|
|
2767
|
+
</div>
|
|
2768
|
+
|
|
2769
|
+
|
|
2770
|
+
<script>var target=document.getElementById(location.hash.slice(1));target&&target.name&&(target.checked=target.name.startsWith("__tabbed_"))</script>
|
|
2771
|
+
</div>
|
|
2772
|
+
|
|
2773
|
+
<button type="button" class="md-top md-icon" data-md-component="top" hidden>
|
|
2774
|
+
|
|
2775
|
+
<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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2776
|
+
Back to top
|
|
2777
|
+
</button>
|
|
2778
|
+
|
|
2779
|
+
</main>
|
|
2780
|
+
|
|
2781
|
+
<footer class="md-footer">
|
|
2782
|
+
|
|
2783
|
+
<div class="md-footer-meta md-typeset">
|
|
2784
|
+
<div class="md-footer-meta__inner md-grid">
|
|
2785
|
+
<div class="md-copyright">
|
|
2786
|
+
|
|
2787
|
+
|
|
2788
|
+
Made with
|
|
2789
|
+
<a href="https://squidfunk.github.io/mkdocs-material/" target="_blank" rel="noopener">
|
|
2790
|
+
Material for MkDocs
|
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2791
|
+
</a>
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2792
|
+
|
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2793
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+
</div>
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2794
|
+
|
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2795
|
+
</div>
|
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2796
|
+
</div>
|
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2797
|
+
</footer>
|
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2798
|
+
|
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2799
|
+
</div>
|
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2800
|
+
<div class="md-dialog" data-md-component="dialog">
|
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2801
|
+
<div class="md-dialog__inner md-typeset"></div>
|
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2802
|
+
</div>
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2803
|
+
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2804
|
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2805
|
+
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2806
|
+
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2807
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2808
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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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|
+
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|
+
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2811
|
+
<script src="../../assets/javascripts/bundle.d7400e89.min.js"></script>
|
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2812
|
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</body>
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</html>
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