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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PyOCL runtime dependency
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|
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|
|
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<span class="md-ellipsis">
|
|
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|
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|
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1740
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Explanation
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|
1741
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|
|
1742
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1743
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|
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1744
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|
|
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|
|
1750
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|
|
1751
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<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_9_label" aria-expanded="false">
|
|
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<label class="md-nav__title" for="__nav_9">
|
|
1753
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<span class="md-nav__icon md-icon"></span>
|
|
1754
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|
|
1755
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|
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1756
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Explanation
|
|
1757
|
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|
|
1758
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|
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1759
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</label>
|
|
1760
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|
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1761
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|
1762
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1763
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2141
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2142
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</label>
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2156
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2157
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2158
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<a href="#pyocl-runtime-dependency" class="md-nav__link">
|
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2159
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<span class="md-ellipsis">
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2160
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|
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2161
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PyOCL runtime dependency
|
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2162
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|
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2163
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</span>
|
|
2164
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</a>
|
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2165
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<a href="#maintained-third-party-distributions" class="md-nav__link">
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2170
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|
2171
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2172
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Maintained third-party distributions
|
|
2173
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2174
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</span>
|
|
2175
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</a>
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2176
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2178
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<a href="#maintenance-rule" class="md-nav__link">
|
|
2181
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<span class="md-ellipsis">
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2182
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+
|
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2183
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Maintenance rule
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|
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2185
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2197
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+
|
|
2198
|
+
|
|
2199
|
+
<div class="md-content" data-md-component="content">
|
|
2200
|
+
|
|
2201
|
+
<article class="md-content__inner md-typeset">
|
|
2202
|
+
|
|
2203
|
+
|
|
2204
|
+
|
|
2205
|
+
|
|
2206
|
+
|
|
2207
|
+
|
|
2208
|
+
|
|
2209
|
+
|
|
2210
|
+
<h1 id="caddforge-version-matrix">CADDForge Version Matrix<a class="headerlink" href="#caddforge-version-matrix" title="Permanent link">¶</a></h1>
|
|
2211
|
+
<p>These docs describe the public sources in the new repositories. Assigned versions
|
|
2212
|
+
and Git tags below identify reviewed source revisions; package-index publication
|
|
2213
|
+
is recorded separately. Inherited baselines are the copied versions and current
|
|
2214
|
+
bundle pins. Pending entries still await new public release versions and tags.</p>
|
|
2215
|
+
<table>
|
|
2216
|
+
<thead>
|
|
2217
|
+
<tr>
|
|
2218
|
+
<th>Distribution</th>
|
|
2219
|
+
<th>Inherited baseline</th>
|
|
2220
|
+
<th>New public version</th>
|
|
2221
|
+
<th>Public commit / tag</th>
|
|
2222
|
+
<th>Package-index publication</th>
|
|
2223
|
+
</tr>
|
|
2224
|
+
</thead>
|
|
2225
|
+
<tbody>
|
|
2226
|
+
<tr>
|
|
2227
|
+
<td><code>caddforge-core</code></td>
|
|
2228
|
+
<td><code>0.21.0</code></td>
|
|
2229
|
+
<td><code>0.22.0</code></td>
|
|
2230
|
+
<td><code>d7c5f210fea8</code> / <code>v0.22.0</code></td>
|
|
2231
|
+
<td><a href="https://pypi.org/project/caddforge-core/0.22.0/">Published on PyPI</a></td>
|
|
2232
|
+
</tr>
|
|
2233
|
+
<tr>
|
|
2234
|
+
<td><code>caddforge-datascience</code></td>
|
|
2235
|
+
<td><code>0.4.0</code></td>
|
|
2236
|
+
<td><code>0.5.0</code></td>
|
|
2237
|
+
<td><code>403c1af1e466</code> / <code>v0.5.0</code></td>
|
|
2238
|
+
<td><a href="https://pypi.org/project/caddforge-datascience/0.5.0/">Published on PyPI</a></td>
|
|
2239
|
+
</tr>
|
|
2240
|
+
<tr>
|
|
2241
|
+
<td><code>caddforge-descriptors</code></td>
|
|
2242
|
+
<td><code>0.10.1</code></td>
|
|
2243
|
+
<td><code>0.11.0</code></td>
|
|
2244
|
+
<td><code>728f9e9fddd0</code> / <code>v0.11.0</code></td>
|
|
2245
|
+
<td><a href="https://pypi.org/project/caddforge-descriptors/0.11.0/">Published on PyPI</a></td>
|
|
2246
|
+
</tr>
|
|
2247
|
+
<tr>
|
|
2248
|
+
<td><code>caddforge-docking</code></td>
|
|
2249
|
+
<td><code>0.6.1</code></td>
|
|
2250
|
+
<td><code>0.7.0</code></td>
|
|
2251
|
+
<td><code>2410dbc387f5</code> / <code>v0.7.0</code></td>
|
|
2252
|
+
<td><a href="https://pypi.org/project/caddforge-docking/0.7.0/">Published on PyPI</a></td>
|
|
2253
|
+
</tr>
|
|
2254
|
+
<tr>
|
|
2255
|
+
<td><code>caddforge-fep</code></td>
|
|
2256
|
+
<td><code>0.6.0</code></td>
|
|
2257
|
+
<td><code>0.7.0</code></td>
|
|
2258
|
+
<td><code>d44dcf342b6f</code> / <code>v0.7.0</code></td>
|
|
2259
|
+
<td><a href="https://pypi.org/project/caddforge-fep/0.7.0/">Published on PyPI</a></td>
|
|
2260
|
+
</tr>
|
|
2261
|
+
<tr>
|
|
2262
|
+
<td><code>caddforge-gui</code></td>
|
|
2263
|
+
<td><code>0.5.0</code></td>
|
|
2264
|
+
<td><code>0.6.0</code></td>
|
|
2265
|
+
<td><code>c73c1155ef4a</code> / <code>v0.6.0</code></td>
|
|
2266
|
+
<td><a href="https://pypi.org/project/caddforge-gui/0.6.0/">Published on PyPI</a></td>
|
|
2267
|
+
</tr>
|
|
2268
|
+
<tr>
|
|
2269
|
+
<td><code>caddforge-md</code></td>
|
|
2270
|
+
<td><code>0.12.1</code></td>
|
|
2271
|
+
<td><code>0.13.0</code></td>
|
|
2272
|
+
<td><code>8668328affe3</code> / <code>v0.13.0</code></td>
|
|
2273
|
+
<td>Not yet on PyPI</td>
|
|
2274
|
+
</tr>
|
|
2275
|
+
<tr>
|
|
2276
|
+
<td><code>caddforge-ml</code></td>
|
|
2277
|
+
<td><code>0.3.0</code></td>
|
|
2278
|
+
<td><code>0.4.0</code></td>
|
|
2279
|
+
<td><code>132459f04fdf</code> / <code>v0.4.0</code></td>
|
|
2280
|
+
<td><a href="https://pypi.org/project/caddforge-ml/0.4.0/">Published on PyPI</a></td>
|
|
2281
|
+
</tr>
|
|
2282
|
+
<tr>
|
|
2283
|
+
<td><code>caddforge-qm</code></td>
|
|
2284
|
+
<td><code>0.2.1</code></td>
|
|
2285
|
+
<td><code>0.3.0</code></td>
|
|
2286
|
+
<td><code>fb24d32fc966</code> / <code>v0.3.0</code></td>
|
|
2287
|
+
<td><a href="https://pypi.org/project/caddforge-qm/0.3.0/">Published on PyPI</a></td>
|
|
2288
|
+
</tr>
|
|
2289
|
+
<tr>
|
|
2290
|
+
<td><code>caddforge</code></td>
|
|
2291
|
+
<td><code>0.22.1</code></td>
|
|
2292
|
+
<td>Pending</td>
|
|
2293
|
+
<td>Pending</td>
|
|
2294
|
+
<td>Pending</td>
|
|
2295
|
+
</tr>
|
|
2296
|
+
<tr>
|
|
2297
|
+
<td><code>caddforge-docs</code></td>
|
|
2298
|
+
<td><code>0.2.1</code></td>
|
|
2299
|
+
<td><code>0.3.0</code></td>
|
|
2300
|
+
<td><code>v0.3.0</code></td>
|
|
2301
|
+
<td>Publication pending</td>
|
|
2302
|
+
</tr>
|
|
2303
|
+
</tbody>
|
|
2304
|
+
</table>
|
|
2305
|
+
<p>Publication status was checked on <strong>2026-10-15</strong>. All nine public component
|
|
2306
|
+
source tags exist. Eight corresponding versions are published on PyPI; MD
|
|
2307
|
+
<code>0.13.0</code> is tagged and awaiting publication. Documentation <code>0.3.0</code> is tagged
|
|
2308
|
+
<code>v0.3.0</code> and awaits publication. The updated bundle still needs its new release
|
|
2309
|
+
version and tag. A later release may change this package-index status.</p>
|
|
2310
|
+
<p>The public snapshot removes ESOL from descriptors and Glide / Glide WS from
|
|
2311
|
+
docking, including their Python exports and GUI integrations. Those interfaces
|
|
2312
|
+
are not available in this source tree. The copied MD fixes and encoded PheSA
|
|
2313
|
+
reference support remain present. All migrated plugins require
|
|
2314
|
+
<code>caddforge-core>=0.21.0</code>.</p>
|
|
2315
|
+
<p>The bundle's current dependency pins are the baselines above. Its default
|
|
2316
|
+
installation includes the built documentation viewer without documentation
|
|
2317
|
+
authoring or test extras. The bundle must be updated to the new public component versions and
|
|
2318
|
+
validated with <code>caddforge-docs==0.3.0</code> before release. Installing the inherited
|
|
2319
|
+
versions does not install these source changes.</p>
|
|
2320
|
+
<p>Continue each package's existing version sequence and choose unused versions
|
|
2321
|
+
after checking existing artifacts. The bundle's <code>0.x</code> series remains initial
|
|
2322
|
+
development; <code>1.0.0</code> is reserved for a future stable public API commitment.
|
|
2323
|
+
Bundle and component versions evolve independently.</p>
|
|
2324
|
+
<h2 id="pyocl-runtime-dependency">PyOCL runtime dependency<a class="headerlink" href="#pyocl-runtime-dependency" title="Permanent link">¶</a></h2>
|
|
2325
|
+
<p>The edited QM, descriptors, and docking sources require the public
|
|
2326
|
+
<a href="https://pypi.org/project/pyocl-idor/"><code>pyocl-idor</code></a> distribution, version <code>0.8.3</code>
|
|
2327
|
+
or newer. The Python import package remains <code>pyocl</code>. Java 21 or newer is required.
|
|
2328
|
+
This dependency change is not present in the inherited CADDForge releases above;
|
|
2329
|
+
include it in the new component releases and then update the bundle pins.</p>
|
|
2330
|
+
<h2 id="maintained-third-party-distributions">Maintained third-party distributions<a class="headerlink" href="#maintained-third-party-distributions" title="Permanent link">¶</a></h2>
|
|
2331
|
+
<p>The <code>third-party/</code> source workspace maintains these independent redistributions
|
|
2332
|
+
of the exact upstream revisions currently required by QM and docking. Both
|
|
2333
|
+
initial releases are tagged and published on PyPI. Their repositories include
|
|
2334
|
+
GitHub release workflows.</p>
|
|
2335
|
+
<table>
|
|
2336
|
+
<thead>
|
|
2337
|
+
<tr>
|
|
2338
|
+
<th>Distribution</th>
|
|
2339
|
+
<th>Released version</th>
|
|
2340
|
+
<th>Upstream source</th>
|
|
2341
|
+
<th>Maintained release / commit</th>
|
|
2342
|
+
</tr>
|
|
2343
|
+
</thead>
|
|
2344
|
+
<tbody>
|
|
2345
|
+
<tr>
|
|
2346
|
+
<td><a href="https://pypi.org/project/caddforge-opencosmors/0.0.1/"><code>caddforge-opencosmors</code></a></td>
|
|
2347
|
+
<td><code>0.0.1</code></td>
|
|
2348
|
+
<td>openCOSMO-RS_py commit <code>64e42bbfa1d9eda93714d7a346d5cbfdeb8dc5d1</code> (upstream metadata <code>0.0.1</code>)</td>
|
|
2349
|
+
<td><a href="https://github.com/idorsia/caddforge-opencosmors/tree/v0.0.1">v0.0.1</a>, <code>d582e7b0a1cf</code></td>
|
|
2350
|
+
</tr>
|
|
2351
|
+
<tr>
|
|
2352
|
+
<td><a href="https://pypi.org/project/caddforge-unidock-tools/1.1.3/"><code>caddforge-unidock-tools</code></a></td>
|
|
2353
|
+
<td><code>1.1.3</code></td>
|
|
2354
|
+
<td>Uni-Dock tag <code>1.1.3</code>, commit <code>caf3161b28f7ceb5aa3b13bc98a505cb76a39db3</code>, subdirectory <code>unidock_tools</code> (upstream Python metadata <code>0.0.1</code>)</td>
|
|
2355
|
+
<td><a href="https://github.com/idorsia/caddforge-unidock-tools/tree/v1.1.3">v1.1.3</a>, <code>449555ac267d</code></td>
|
|
2356
|
+
</tr>
|
|
2357
|
+
</tbody>
|
|
2358
|
+
</table>
|
|
2359
|
+
<p>These distributions retain the upstream Python code, parameter data, import
|
|
2360
|
+
names, and <code>unidocktools</code> CLI. Uni-Dock Tools includes a rebuilt
|
|
2361
|
+
<code>4.2.9+caddforge.1</code> AutoGrid executable with complete GPL-licensed source, a
|
|
2362
|
+
legacy compatibility patch, and an offline build helper in both artifacts. Its
|
|
2363
|
+
wheel targets <code>manylinux_2_28_x86_64</code> (Linux x86-64, glibc 2.28 or newer).
|
|
2364
|
+
The matching GCC OpenMP runtime is linked statically with its Runtime Library
|
|
2365
|
+
Exception and complete notices, so no separate <code>libgomp</code> installation is needed.
|
|
2366
|
+
The original executable with unverified corresponding source is excluded. See <a href="../../explanation/third-party-notices/#scientific-runtime-dependencies">Third-party Notices</a>
|
|
2367
|
+
for the licence split and source-distribution requirements.</p>
|
|
2368
|
+
<p>Both distributions were installed together from public PyPI in a fresh Python
|
|
2369
|
+
3.12 Linux x86-64 environment. Dependency consistency, imports, command help,
|
|
2370
|
+
the bundled AutoGrid executable and source hashes, and a water/ethanol COSMO-RS
|
|
2371
|
+
numerical regression passed. This validates these dependency releases, not a
|
|
2372
|
+
complete public CADDForge bundle installation.</p>
|
|
2373
|
+
<p>The edited QM and docking sources now require <code>caddforge-opencosmors==0.0.1</code>
|
|
2374
|
+
and <code>caddforge-unidock-tools==1.1.3</code>, respectively. These named requirements
|
|
2375
|
+
replace the previous pinned Git dependencies. Release the affected
|
|
2376
|
+
components, then update and test the bundle pins; the inherited component
|
|
2377
|
+
versions above do not contain this dependency change.</p>
|
|
2378
|
+
<h2 id="maintenance-rule">Maintenance rule<a class="headerlink" href="#maintenance-rule" title="Permanent link">¶</a></h2>
|
|
2379
|
+
<p>When the reviewed sources are committed and tagged, replace the pending entries
|
|
2380
|
+
with the actual public versions, commits, and tags, and record publication status
|
|
2381
|
+
separately. Update bundle pins, installation examples, plugin callouts, and release
|
|
2382
|
+
notes in the same release work. Do not recreate historical tags on new initial
|
|
2383
|
+
commits or label inherited baselines as releases of this snapshot.</p>
|
|
2384
|
+
<p>Local validation may use temporary VCS version overrides at the inherited
|
|
2385
|
+
baselines. Such overrides do not assign release versions; never publish those
|
|
2386
|
+
validation artifacts.</p>
|
|
2387
|
+
|
|
2388
|
+
|
|
2389
|
+
|
|
2390
|
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2391
|
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2392
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2393
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2395
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2396
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2397
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2398
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2399
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|
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2400
|
+
</article>
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2401
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</div>
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2406
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+
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2407
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<button type="button" class="md-top md-icon" data-md-component="top" hidden>
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2409
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2420
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2421
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2422
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