caddforge-docs 0.3.0__py3-none-any.whl

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Files changed (152) hide show
  1. caddforge_docs/__init__.py +1 -0
  2. caddforge_docs/cli.py +20 -0
  3. caddforge_docs/server.py +124 -0
  4. caddforge_docs/site/404.html +2118 -0
  5. caddforge_docs/site/assets/_mkdocstrings.css +237 -0
  6. caddforge_docs/site/assets/images/favicon.png +0 -0
  7. caddforge_docs/site/assets/javascripts/bundle.d7400e89.min.js +16 -0
  8. caddforge_docs/site/assets/javascripts/bundle.d7400e89.min.js.map +7 -0
  9. caddforge_docs/site/assets/javascripts/workers/search.2c215733.min.js +42 -0
  10. caddforge_docs/site/assets/javascripts/workers/search.2c215733.min.js.map +7 -0
  11. caddforge_docs/site/assets/licenses/W3C-Software-and-Document-2015.txt +15 -0
  12. caddforge_docs/site/assets/licenses/autogrid-COPYING-GPL-2.txt +339 -0
  13. caddforge_docs/site/assets/licenses/autogrid-GCC-RUNTIME-COPYING-GPL-3.txt +674 -0
  14. caddforge_docs/site/assets/licenses/autogrid-GCC-RUNTIME-EXCEPTION.txt +73 -0
  15. caddforge_docs/site/assets/licenses/autogrid-GCC-RUNTIME-NOTICE.txt +24 -0
  16. caddforge_docs/site/assets/licenses/caddforge-opencosmors-COPYING.txt +674 -0
  17. caddforge_docs/site/assets/licenses/caddforge-opencosmors-LICENSE.txt +165 -0
  18. caddforge_docs/site/assets/licenses/caddforge-unidock-tools-LICENSE.txt +202 -0
  19. caddforge_docs/site/assets/licenses/clipboard-LICENSE.txt +19 -0
  20. caddforge_docs/site/assets/licenses/escape-html-LICENSE.txt +2 -0
  21. caddforge_docs/site/assets/licenses/focus-visible-LICENSE.txt +4 -0
  22. caddforge_docs/site/assets/licenses/fontawesome-LICENSE.txt +165 -0
  23. caddforge_docs/site/assets/licenses/fuzzaldrin-plus-LICENSE.txt +21 -0
  24. caddforge_docs/site/assets/licenses/lunr-LICENSE.txt +17 -0
  25. caddforge_docs/site/assets/licenses/material-LICENSE.txt +20 -0
  26. caddforge_docs/site/assets/licenses/material-design-color-LICENSE.txt +31 -0
  27. caddforge_docs/site/assets/licenses/material-shadows-LICENSE.txt +31 -0
  28. caddforge_docs/site/assets/licenses/mkdocs-material-LICENSE.txt +19 -0
  29. caddforge_docs/site/assets/licenses/mkdocs-material-extensions-LICENSE.txt +21 -0
  30. caddforge_docs/site/assets/licenses/mkdocs-section-index-LICENSE.txt +21 -0
  31. caddforge_docs/site/assets/licenses/mkdocstrings-LICENSE.txt +15 -0
  32. caddforge_docs/site/assets/licenses/mkdocstrings-python-LICENSE.txt +15 -0
  33. caddforge_docs/site/assets/licenses/octicons-LICENSE.txt +21 -0
  34. caddforge_docs/site/assets/licenses/preact-LICENSE.txt +19 -0
  35. caddforge_docs/site/assets/licenses/properdocs-LICENSE.txt +26 -0
  36. caddforge_docs/site/assets/licenses/pymdown-extensions-LICENSE.txt +113 -0
  37. caddforge_docs/site/assets/licenses/rxjs-LICENSE.txt +180 -0
  38. caddforge_docs/site/assets/licenses/simple-LICENSE.txt +30 -0
  39. caddforge_docs/site/assets/licenses/tiny-emitter-LICENSE.txt +19 -0
  40. caddforge_docs/site/assets/licenses/tslib-LICENSE.txt +12 -0
  41. caddforge_docs/site/assets/licenses/zeno-rocha-components-LICENSE.txt +22 -0
  42. caddforge_docs/site/assets/stylesheets/main.ec1eaa64.min.css +1 -0
  43. caddforge_docs/site/assets/stylesheets/main.ec1eaa64.min.css.map +1 -0
  44. caddforge_docs/site/assets/stylesheets/palette.ab4e12ef.min.css +1 -0
  45. caddforge_docs/site/assets/stylesheets/palette.ab4e12ef.min.css.map +1 -0
  46. caddforge_docs/site/core/cli/index.html +2446 -0
  47. caddforge_docs/site/core/concepts/index.html +2340 -0
  48. caddforge_docs/site/core/configuration/index.html +2300 -0
  49. caddforge_docs/site/core/index.html +2170 -0
  50. caddforge_docs/site/core/jobs-results/index.html +2315 -0
  51. caddforge_docs/site/core/plugins/index.html +2200 -0
  52. caddforge_docs/site/core/slurm/index.html +2562 -0
  53. caddforge_docs/site/development/ci-publishing/index.html +2345 -0
  54. caddforge_docs/site/development/contributing/index.html +2311 -0
  55. caddforge_docs/site/development/documentation/index.html +2380 -0
  56. caddforge_docs/site/development/index.html +2201 -0
  57. caddforge_docs/site/development/release-notes/index.html +2504 -0
  58. caddforge_docs/site/development/release-readiness/index.html +2333 -0
  59. caddforge_docs/site/development/security/index.html +2181 -0
  60. caddforge_docs/site/development/tool-authoring/index.html +2435 -0
  61. caddforge_docs/site/examples/index.html +2465 -0
  62. caddforge_docs/site/examples/manifest.json +158 -0
  63. caddforge_docs/site/examples/minimize/component_overrides.yaml +14 -0
  64. caddforge_docs/site/examples/minimize/ligand_only.yaml +13 -0
  65. caddforge_docs/site/examples/minimize/pipeline_docking.yaml +84 -0
  66. caddforge_docs/site/examples/minimize/pipeline_scatter.yaml +49 -0
  67. caddforge_docs/site/examples/minimize/pocket_free_shell_restrained.yaml +13 -0
  68. caddforge_docs/site/examples/minimize/pocket_restrained.yaml +13 -0
  69. caddforge_docs/site/examples/minimize/prepared_metal.yaml +14 -0
  70. caddforge_docs/site/examples/minimize/sidechains_free_backbone_fixed.yaml +13 -0
  71. caddforge_docs/site/examples/minimize/sidechains_free_backbone_restrained.yaml +13 -0
  72. caddforge_docs/site/examples/pipelines/descriptor-model-and-candidate-filter.yaml +44 -0
  73. caddforge_docs/site/examples/pipelines/dock-extract-and-minimize-poses.yaml +85 -0
  74. caddforge_docs/site/examples/pipelines/docking-screen-and-rescore.yaml +55 -0
  75. caddforge_docs/site/examples/pipelines/flexible-gnina-to-openbpmd-to-md-to-abfe.yaml +189 -0
  76. caddforge_docs/site/examples/pipelines/gnina-flexible-complex-artifacts.yaml +52 -0
  77. caddforge_docs/site/examples/pipelines/minimize-a-multi-pose-sdf.yaml +46 -0
  78. caddforge_docs/site/examples/pipelines/pose-level-md-selection.yaml +95 -0
  79. caddforge_docs/site/examples/pipelines/result-collection-and-diagnostics.yaml +55 -0
  80. caddforge_docs/site/examples/quickstart/diagnostics.yaml +8 -0
  81. caddforge_docs/site/examples/quickstart/index.html +2172 -0
  82. caddforge_docs/site/examples/quickstart/pipeline.yaml +23 -0
  83. caddforge_docs/site/examples/quickstart/run.py +18 -0
  84. caddforge_docs/site/examples/quickstart/run_pipeline.py +6 -0
  85. caddforge_docs/site/examples/quickstart/scores.csv +7 -0
  86. caddforge_docs/site/examples/quickstart/values.csv +31 -0
  87. caddforge_docs/site/examples/run_tool.py +40 -0
  88. caddforge_docs/site/examples/tools/datascience-csv-scatter.yaml +17 -0
  89. caddforge_docs/site/examples/tools/datascience-distribution-diagnostics.yaml +10 -0
  90. caddforge_docs/site/examples/tools/descriptors-ani-conformers.yaml +9 -0
  91. caddforge_docs/site/examples/tools/descriptors-ani-psa.yaml +9 -0
  92. caddforge_docs/site/examples/tools/descriptors-cluster-molecules.yaml +11 -0
  93. caddforge_docs/site/examples/tools/descriptors-phesa.yaml +7 -0
  94. caddforge_docs/site/examples/tools/docking-gnina.yaml +12 -0
  95. caddforge_docs/site/examples/tools/docking-idockya.yaml +8 -0
  96. caddforge_docs/site/examples/tools/docking-unidock.yaml +12 -0
  97. caddforge_docs/site/examples/tools/fep-openfe-abfe.yaml +53 -0
  98. caddforge_docs/site/examples/tools/fep-openfe-rbfe-septop.yaml +23 -0
  99. caddforge_docs/site/examples/tools/md-center-and-align.yaml +16 -0
  100. caddforge_docs/site/examples/tools/md-cluster-representative.yaml +16 -0
  101. caddforge_docs/site/examples/tools/md-extract-frames.yaml +17 -0
  102. caddforge_docs/site/examples/tools/md-fix-structure.yaml +20 -0
  103. caddforge_docs/site/examples/tools/md-grand.yaml +28 -0
  104. caddforge_docs/site/examples/tools/md-inducia.yaml +29 -0
  105. caddforge_docs/site/examples/tools/md-minimize.yaml +13 -0
  106. caddforge_docs/site/examples/tools/md-openbpmd.yaml +11 -0
  107. caddforge_docs/site/examples/tools/md-plain-md.yaml +28 -0
  108. caddforge_docs/site/examples/tools/ml-explore-classifier.yaml +5 -0
  109. caddforge_docs/site/examples/tools/ml-model-factory.yaml +32 -0
  110. caddforge_docs/site/examples/tools/ml-model-zoo.yaml +16 -0
  111. caddforge_docs/site/examples/tools/ml-pca.yaml +10 -0
  112. caddforge_docs/site/examples/tools/ml-simple-gp.yaml +17 -0
  113. caddforge_docs/site/examples/tools/qm-transfer-free-energy.yaml +11 -0
  114. caddforge_docs/site/explanation/references/index.html +2218 -0
  115. caddforge_docs/site/explanation/reproducibility/index.html +2306 -0
  116. caddforge_docs/site/explanation/third-party-notices/index.html +2599 -0
  117. caddforge_docs/site/getting-started/first-pipeline/index.html +2195 -0
  118. caddforge_docs/site/getting-started/first-workflow/index.html +2329 -0
  119. caddforge_docs/site/getting-started/index.html +2200 -0
  120. caddforge_docs/site/getting-started/installation/index.html +2541 -0
  121. caddforge_docs/site/gui/index.html +2267 -0
  122. caddforge_docs/site/gui/plugin-authoring/index.html +2280 -0
  123. caddforge_docs/site/gui/walkthrough/index.html +2181 -0
  124. caddforge_docs/site/how-to/jobs/index.html +2195 -0
  125. caddforge_docs/site/how-to/scatter/index.html +2193 -0
  126. caddforge_docs/site/how-to/troubleshooting/index.html +2429 -0
  127. caddforge_docs/site/index.html +2359 -0
  128. caddforge_docs/site/objects.inv +0 -0
  129. caddforge_docs/site/pipelines/artifacts/index.html +2314 -0
  130. caddforge_docs/site/pipelines/built-ins/index.html +2670 -0
  131. caddforge_docs/site/pipelines/examples/index.html +3186 -0
  132. caddforge_docs/site/pipelines/index.html +2164 -0
  133. caddforge_docs/site/pipelines/specification/index.html +2278 -0
  134. caddforge_docs/site/plugins/datascience/index.html +2405 -0
  135. caddforge_docs/site/plugins/descriptors/index.html +2609 -0
  136. caddforge_docs/site/plugins/docking/index.html +2480 -0
  137. caddforge_docs/site/plugins/fep/index.html +2508 -0
  138. caddforge_docs/site/plugins/index.html +2216 -0
  139. caddforge_docs/site/plugins/md/index.html +3795 -0
  140. caddforge_docs/site/plugins/ml/index.html +2815 -0
  141. caddforge_docs/site/plugins/qm/index.html +2309 -0
  142. caddforge_docs/site/plugins/version-matrix/index.html +2449 -0
  143. caddforge_docs/site/reference/api/index.html +4414 -0
  144. caddforge_docs/site/reference/index.html +2166 -0
  145. caddforge_docs/site/search/search_index.json +1 -0
  146. caddforge_docs/site/sitemap.xml +191 -0
  147. caddforge_docs/site/sitemap.xml.gz +0 -0
  148. caddforge_docs-0.3.0.dist-info/METADATA +158 -0
  149. caddforge_docs-0.3.0.dist-info/RECORD +152 -0
  150. caddforge_docs-0.3.0.dist-info/WHEEL +4 -0
  151. caddforge_docs-0.3.0.dist-info/entry_points.txt +2 -0
  152. caddforge_docs-0.3.0.dist-info/licenses/LICENSE +21 -0
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+ Metadata-Version: 2.5
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+ Name: caddforge-docs
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+ Version: 0.3.0
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+ Summary: Central documentation site for the CADDForge toolbox.
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+ Author-email: Manuel Sellner <manuel.sellner@idorsia.com>, Christoph Sager <christoph.sager@idorsia.com>
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+ License: MIT
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+ License-File: LICENSE
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+ Requires-Python: >=3.10
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+ Requires-Dist: caddforge-core>=0.21.0
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+ Provides-Extra: docs
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+ Requires-Dist: hatchling>=1.26; extra == 'test'
19
+ Requires-Dist: jsonschema>=4.18; extra == 'test'
20
+ Requires-Dist: pytest>=7.0; extra == 'test'
21
+ Requires-Dist: rich>=13.8; extra == 'test'
22
+ Requires-Dist: tomli>=2; (python_version < '3.11') and extra == 'test'
23
+ Description-Content-Type: text/markdown
24
+
25
+ # CADDForge Documentation
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+
27
+ Central documentation site for the CADDForge toolbox.
28
+
29
+ These sources describe the reviewed public snapshots in the
30
+ [version matrix](docs/plugins/version-matrix.md). Documentation release `0.3.0`
31
+ is identified by source tag `v0.3.0`; package-index publication remains pending.
32
+ Release tags identify source revisions; package-index publication is separate.
33
+ See the [release notes](docs/development/release-notes.md) for the packaged changes.
34
+
35
+ ## View installed documentation
36
+
37
+ The planned public bundle includes `caddforge-docs` automatically; its pins
38
+ and release remain pending. For core-only or selective installations, install
39
+ the documentation package into the same environment once its new public release
40
+ is available. Until then, use the source installation under [Local preview](#local-preview):
41
+
42
+ ```bash
43
+ python -m pip install caddforge-docs
44
+ caddforge docs
45
+ ```
46
+
47
+ `caddforge docs` is available only when `caddforge-docs` is installed. The package installs
48
+ `caddforge-core>=0.21.0` automatically; core 0.21.0 includes CLI extension
49
+ discovery. The built site ships with the docs package, so viewing it requires no checkout,
50
+ documentation build tools, or network connection. Its content matches the installed docs release.
51
+
52
+ The command opens the default browser and keeps serving until you press Ctrl+C. By default it binds
53
+ to `127.0.0.1` on an automatically assigned port. Override the listening address or port as needed:
54
+
55
+ ```bash
56
+ caddforge docs --host 0.0.0.0 --port 8001
57
+ caddforge docs --host localhost --no-browser
58
+ caddforge docs --host ::1
59
+ ```
60
+
61
+ Hostnames, IPv4, and IPv6 addresses are supported. With wildcard bindings (`0.0.0.0` or `::`), the
62
+ automatic browser opens the matching loopback URL. The terminal prints the listening address and
63
+ browser URL; remote clients can use the server's reachable hostname or address and the printed port.
64
+ `--no-browser` keeps the server running without launching a browser. If automatic opening fails,
65
+ use the printed URL manually.
66
+
67
+ ## Local preview
68
+
69
+ ```bash
70
+ python -m pip install -r requirements.txt
71
+ properdocs serve
72
+ ```
73
+
74
+ Then open <http://127.0.0.1:8000>.
75
+
76
+ Alternatively, install the optional docs dependencies from `pyproject.toml`:
77
+
78
+ ```bash
79
+ python -m pip install ".[docs]"
80
+ ```
81
+
82
+ For an editable install, `python -m pip install -e ".[docs]"` also builds the packaged site.
83
+ Reinstall after editing sources to refresh `caddforge docs`, or use `properdocs serve --open` for
84
+ live authoring. The packaged site is generated under `src/caddforge_docs/site/` and ignored by Git.
85
+ For source installations, install a compatible core revision first:
86
+ `python -m pip install -e ../caddforge-core`. See the documented version matrix.
87
+
88
+ ## Build
89
+
90
+ ```bash
91
+ properdocs build --strict
92
+ ```
93
+
94
+ The generated static site is written to `site/`.
95
+
96
+ To build distributable documentation packages:
97
+
98
+ ```bash
99
+ python -m pip install build
100
+ python -m build
101
+ ```
102
+
103
+ Wheel builds run ProperDocs in strict mode and include all rendered pages and assets. The source
104
+ distribution includes the Markdown, configuration, and build hook needed to rebuild the wheel.
105
+ Build dependencies are installed in the isolated build environment and are not runtime requirements.
106
+
107
+ To run tests, install the authoring and test extras, then run `python -m pytest -q`:
108
+
109
+ ```bash
110
+ python -m pip install -e ".[docs,test]"
111
+ python -m pytest -q
112
+ ```
113
+
114
+ ## Publishing
115
+
116
+ This repository has separate package and site workflows:
117
+
118
+ - `.github/workflows/release.yml` builds and tests the installed wheel on
119
+ Python 3.10 and 3.12, then publishes to PyPI only for pushed `v*` tags.
120
+ - `.github/workflows/pages.yml` validates and optionally deploys GitHub Pages.
121
+
122
+ Update the explicit version in `pyproject.toml` before creating a matching
123
+ annotated release tag. Configure a PyPI Trusted Publisher for this repository,
124
+ `release.yml`, and the `pypi` environment. Release core and data-science first;
125
+ the installed-wheel tests execute the documented tutorials with those public packages.
126
+
127
+ The MkDocs source is platform-neutral.
128
+
129
+ ## Public documentation and validation
130
+
131
+ Start with `docs/getting-started/first-workflow.md` and `first-pipeline.md` for runnable
132
+ examples with invented input data. The example library supplies configurations for
133
+ 26 public scientific workflows. Heavyweight templates require prepared inputs and
134
+ external engines; they are not bundled experimental datasets.
135
+
136
+ ```bash
137
+ python -m pip install -r requirements.txt -r requirements-test.txt
138
+ python scripts/validate_examples.py
139
+ properdocs build --strict
140
+ python scripts/check_links.py site
141
+ python -m pytest -q
142
+ ```
143
+
144
+ Install compatible public core/data-science packages before requiring tutorial tests
145
+ with `python -m pytest tests/test_examples.py -q --require-examples`.
146
+ Public API reference generation uses an explicit AST allowlist; builds do not discover
147
+ installed scientific plugins. Wheel builds render the site in strict mode and
148
+ check local links in rendered pages.
149
+
150
+ See [contributing](CONTRIBUTING.md), [security reporting](SECURITY.md), and the
151
+ [release checklist](docs/development/release-readiness.md). The project uses MIT;
152
+ bundled third-party assets retain the licences listed in the
153
+ [third-party notices](docs/explanation/third-party-notices.md). Public-index
154
+ availability remains a release prerequisite.
155
+ Pages deployment requires `DOCS_PUBLISH_ENABLED=true` and is separate from
156
+ package publication. Branch pushes, pull requests, and manual runs never
157
+ publish packages; pushing a matching `v*` release tag publishes the tested
158
+ wheel and source archive through the configured PyPI Trusted Publisher.
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+ The MIT License (MIT)
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+
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+ Copyright (c) 2026 The CADDForge Authors
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+
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+ Permission is hereby granted, free of charge, to any person obtaining a copy
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+ of this software and associated documentation files (the "Software"), to deal
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+ in the Software without restriction, including without limitation the rights
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+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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+ copies of the Software, and to permit persons to whom the Software is
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+ furnished to do so, subject to the following conditions:
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+
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+ The above copyright notice and this permission notice shall be included in
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+ all copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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+ THE SOFTWARE.