calkit-python 0.42.1__tar.gz → 0.44.0__tar.gz

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.
Files changed (861) hide show
  1. {calkit_python-0.42.1 → calkit_python-0.44.0}/.gitmodules +3 -0
  2. {calkit_python-0.42.1 → calkit_python-0.44.0}/AGENTS.md +4 -0
  3. {calkit_python-0.42.1 → calkit_python-0.44.0}/Makefile +25 -2
  4. {calkit_python-0.42.1 → calkit_python-0.44.0}/PKG-INFO +3 -3
  5. {calkit_python-0.42.1 → calkit_python-0.44.0}/README.md +2 -2
  6. calkit_python-0.44.0/actions/run/README.md +115 -0
  7. calkit_python-0.44.0/actions/run/action.yml +349 -0
  8. calkit_python-0.44.0/actions/run/example.yml +36 -0
  9. {calkit_python-0.42.1 → calkit_python-0.44.0}/agent-plugin/skills/conventions/SKILL.md +4 -0
  10. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/__init__.py +4 -0
  11. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/calc.py +19 -10
  12. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/check.py +1 -1
  13. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/cli/check.py +161 -24
  14. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/cli/describe.py +27 -0
  15. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/cli/import_.py +1 -3
  16. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/cli/list.py +2 -2
  17. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/cli/main/core.py +321 -195
  18. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/cli/new.py +80 -17
  19. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/cli/notebooks.py +351 -0
  20. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/cli/overleaf.py +445 -25
  21. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/cli/scheduler.py +29 -14
  22. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/cli/update.py +42 -40
  23. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/config.py +7 -0
  24. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/core.py +488 -86
  25. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/datasets.py +1 -1
  26. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/dependencies.py +58 -0
  27. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/detect.py +1 -1
  28. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/environments.py +330 -12
  29. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/git.py +90 -0
  30. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/install.py +1 -1
  31. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/jupyterlab/routes.py +1 -1
  32. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/latex.py +10 -2
  33. calkit_python-0.44.0/calkit/models/core.py +1209 -0
  34. calkit_python-0.44.0/calkit/models/io.py +77 -0
  35. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/models/iteration.py +17 -28
  36. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/models/pipeline.py +588 -96
  37. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/notebooks.py +24 -2
  38. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/overleaf.py +253 -45
  39. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/pipeline.py +5 -2
  40. calkit_python-0.44.0/calkit/resources/README.md +26 -0
  41. calkit_python-0.44.0/calkit/resources/__init__.py +144 -0
  42. calkit_python-0.44.0/calkit/resources/devcontainer/Dockerfile +72 -0
  43. calkit_python-0.44.0/calkit/resources/devcontainer/README.md +49 -0
  44. calkit_python-0.44.0/calkit/resources/devcontainer/base.json +25 -0
  45. calkit_python-0.44.0/calkit/resources/devcontainer/devcontainer.json +58 -0
  46. calkit_python-0.44.0/calkit/resources/devcontainer/scripts/check-envs.sh +58 -0
  47. calkit_python-0.44.0/calkit/resources/devcontainer/scripts/post-create.sh +50 -0
  48. calkit_python-0.44.0/calkit/resources/devcontainer/scripts/post-start.sh +46 -0
  49. calkit_python-0.44.0/calkit/resources/devcontainer/scripts/update-content.sh +12 -0
  50. calkit_python-0.44.0/calkit/resources/github-actions/example.yml +36 -0
  51. calkit_python-0.44.0/calkit/resources/vscode/README.md +23 -0
  52. calkit_python-0.44.0/calkit/resources/vscode/extensions.json +22 -0
  53. calkit_python-0.44.0/calkit/resources/vscode/settings.json +15 -0
  54. calkit_python-0.44.0/calkit/schema.py +71 -0
  55. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/tests/cli/main/test_core.py +227 -3
  56. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/tests/cli/test_check.py +104 -0
  57. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/tests/cli/test_new.py +38 -1
  58. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/tests/cli/test_overleaf.py +574 -17
  59. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/tests/cli/test_update.py +98 -0
  60. calkit_python-0.44.0/calkit/tests/models/test_core.py +203 -0
  61. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/tests/models/test_pipeline.py +298 -0
  62. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/tests/test_core.py +118 -10
  63. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/tests/test_dependencies.py +38 -0
  64. calkit_python-0.44.0/calkit/tests/test_docs_references.py +134 -0
  65. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/tests/test_environments.py +368 -0
  66. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/tests/test_git.py +54 -0
  67. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/tests/test_magics.py +14 -0
  68. {calkit_python-0.42.1 → calkit_python-0.44.0}/calkit/tests/test_notebooks.py +33 -0
  69. calkit_python-0.44.0/calkit/tests/test_resources.py +159 -0
  70. calkit_python-0.44.0/calkit/tests/test_schema.py +179 -0
  71. calkit_python-0.44.0/calkit/tests/test_workspace.py +1476 -0
  72. calkit_python-0.44.0/calkit/workspace.py +1890 -0
  73. calkit_python-0.44.0/docs/apps.md +140 -0
  74. calkit_python-0.44.0/docs/calkit-yaml.md +538 -0
  75. {calkit_python-0.42.1 → calkit_python-0.44.0}/docs/cli-reference.md +181 -50
  76. calkit_python-0.44.0/docs/environments.md +1130 -0
  77. {calkit_python-0.42.1 → calkit_python-0.44.0}/docs/index.md +1 -1
  78. {calkit_python-0.42.1 → calkit_python-0.44.0}/docs/installation.md +1 -1
  79. {calkit_python-0.42.1 → calkit_python-0.44.0}/docs/latex.md +2 -2
  80. {calkit_python-0.42.1 → calkit_python-0.44.0}/docs/overleaf.md +163 -5
  81. calkit_python-0.44.0/docs/pipeline/index.md +708 -0
  82. calkit_python-0.42.1/docs/dependencies.md → calkit_python-0.44.0/docs/requirements.md +98 -36
  83. calkit_python-0.44.0/docs/schemas/calkit.json +7653 -0
  84. {calkit_python-0.42.1 → calkit_python-0.44.0}/docs/tutorials/adding-latex-pub-docker.md +2 -5
  85. {calkit_python-0.42.1 → calkit_python-0.44.0}/docs/tutorials/github-actions.md +7 -2
  86. {calkit_python-0.42.1 → calkit_python-0.44.0}/docs/tutorials/procedures.md +17 -27
  87. {calkit_python-0.42.1 → calkit_python-0.44.0}/hub/backend/app/api/routes/projects/core.py +422 -102
  88. {calkit_python-0.42.1 → calkit_python-0.44.0}/hub/backend/app/core.py +19 -0
  89. {calkit_python-0.42.1 → calkit_python-0.44.0}/hub/backend/app/dvc.py +2 -2
  90. {calkit_python-0.42.1 → calkit_python-0.44.0}/hub/backend/app/git.py +2 -6
  91. {calkit_python-0.42.1 → calkit_python-0.44.0}/hub/backend/app/models/core.py +12 -3
  92. {calkit_python-0.42.1 → calkit_python-0.44.0}/hub/backend/app/models/projects.py +5 -0
  93. {calkit_python-0.42.1 → calkit_python-0.44.0}/hub/backend/app/projects.py +305 -34
  94. {calkit_python-0.42.1 → calkit_python-0.44.0}/hub/backend/app/tests/api/routes/projects/test_core.py +490 -5
  95. {calkit_python-0.42.1 → calkit_python-0.44.0}/hub/backend/app/tests/test_projects.py +340 -0
  96. {calkit_python-0.42.1 → calkit_python-0.44.0}/hub/frontend/Makefile +11 -4
  97. {calkit_python-0.42.1 → calkit_python-0.44.0}/hub/frontend/src/client/index.ts +9 -0
  98. {calkit_python-0.42.1 → calkit_python-0.44.0}/hub/frontend/src/client/schemas.gen.ts +46 -3
  99. {calkit_python-0.42.1 → calkit_python-0.44.0}/hub/frontend/src/client/sdk.gen.ts +103 -0
  100. {calkit_python-0.42.1 → calkit_python-0.44.0}/hub/frontend/src/client/types.gen.ts +116 -3
  101. {calkit_python-0.42.1 → calkit_python-0.44.0}/hub/frontend/src/components/Common/PdfDocumentViewer.tsx +2 -2
  102. {calkit_python-0.42.1 → calkit_python-0.44.0}/hub/frontend/src/components/Common/SidebarItems.tsx +1 -1
  103. {calkit_python-0.42.1 → calkit_python-0.44.0}/hub/frontend/src/components/Files/FileEditorModal.tsx +2 -1
  104. {calkit_python-0.42.1 → calkit_python-0.44.0}/hub/frontend/src/components/Notebooks/NotebookView.tsx +24 -0
  105. {calkit_python-0.42.1 → calkit_python-0.44.0}/hub/frontend/src/components/Pipeline/StageEditorModal.tsx +2 -1
  106. {calkit_python-0.42.1 → calkit_python-0.44.0}/hub/frontend/src/components/Publications/LatexEditor.tsx +2 -1
  107. {calkit_python-0.42.1 → calkit_python-0.44.0}/hub/frontend/src/lib/api.ts +13 -3
  108. {calkit_python-0.42.1 → calkit_python-0.44.0}/hub/frontend/src/routeTree.gen.ts +79 -0
  109. calkit_python-0.44.0/hub/frontend/src/routes/_layout/$accountName/$projectName/_layout/app.tsx +15 -0
  110. calkit_python-0.44.0/hub/frontend/src/routes/_layout/$accountName/$projectName/_layout/apps/$appName.tsx +90 -0
  111. calkit_python-0.44.0/hub/frontend/src/routes/_layout/$accountName/$projectName/_layout/apps/index.tsx +49 -0
  112. calkit_python-0.44.0/hub/frontend/src/routes/_layout/$accountName/$projectName/_layout/apps.tsx +124 -0
  113. {calkit_python-0.42.1 → calkit_python-0.44.0}/hub/frontend/src/routes/_layout/$accountName/$projectName/_layout/notebooks.tsx +63 -5
  114. {calkit_python-0.42.1 → calkit_python-0.44.0}/mkdocs.yml +1 -1
  115. {calkit_python-0.42.1 → calkit_python-0.44.0}/pyproject.toml +24 -1
  116. {calkit_python-0.42.1 → calkit_python-0.44.0}/scripts/generate-docs-references.py +327 -49
  117. calkit_python-0.44.0/scripts/list-changes.py +115 -0
  118. calkit_python-0.44.0/scripts/sync-resources.py +65 -0
  119. {calkit_python-0.42.1 → calkit_python-0.44.0}/uv.lock +22 -39
  120. calkit_python-0.44.0/vscode-ext/.gitignore +5 -0
  121. calkit_python-0.44.0/vscode-ext/changelog-notes.md +21 -0
  122. {calkit_python-0.42.1 → calkit_python-0.44.0}/vscode-ext/package.json +11 -1
  123. calkit_python-0.44.0/vscode-ext/schemas/calkit.json +7653 -0
  124. calkit_python-0.44.0/vscode-ext/scripts/gen-changelog.js +150 -0
  125. {calkit_python-0.42.1 → calkit_python-0.44.0}/vscode-ext/src/environments.ts +1 -1
  126. {calkit_python-0.42.1 → calkit_python-0.44.0}/vscode-ext/src/sidebar.ts +27 -0
  127. {calkit_python-0.42.1 → calkit_python-0.44.0}/vscode-ext/src/test/environments.test.ts +3 -3
  128. {calkit_python-0.42.1 → calkit_python-0.44.0}/vscode-ext/src/test/kernel-selection.test.ts +1 -1
  129. {calkit_python-0.42.1 → calkit_python-0.44.0}/vscode-ext/src/types.ts +11 -0
  130. calkit_python-0.42.1/calkit/models/core.py +0 -484
  131. calkit_python-0.42.1/calkit/models/io.py +0 -53
  132. calkit_python-0.42.1/calkit/tests/models/test_core.py +0 -56
  133. calkit_python-0.42.1/docs/apps.md +0 -9
  134. calkit_python-0.42.1/docs/calkit-yaml.md +0 -42
  135. calkit_python-0.42.1/docs/environments.md +0 -784
  136. calkit_python-0.42.1/docs/pipeline/index.md +0 -480
  137. calkit_python-0.42.1/hub/frontend/src/routes/_layout/$accountName/$projectName/_layout/app.tsx +0 -64
  138. calkit_python-0.42.1/vscode-ext/.gitignore +0 -3
  139. calkit_python-0.42.1/vscode-ext/CHANGELOG.md +0 -6
  140. {calkit_python-0.42.1 → calkit_python-0.44.0}/.claude-plugin/marketplace.json +0 -0
  141. {calkit_python-0.42.1 → calkit_python-0.44.0}/.dockerignore +0 -0
  142. {calkit_python-0.42.1 → calkit_python-0.44.0}/.gitattributes +0 -0
  143. {calkit_python-0.42.1 → calkit_python-0.44.0}/.gitignore +0 -0
  144. {calkit_python-0.42.1 → calkit_python-0.44.0}/.pre-commit-config.yaml +0 -0
  145. {calkit_python-0.42.1 → calkit_python-0.44.0}/.prettierignore +0 -0
  146. {calkit_python-0.42.1 → calkit_python-0.44.0}/.prettierrc.json +0 -0
  147. {calkit_python-0.42.1 → calkit_python-0.44.0}/.python-version +0 -0
  148. {calkit_python-0.42.1 → calkit_python-0.44.0}/.vscode/launch.json +0 -0
  149. {calkit_python-0.42.1 → calkit_python-0.44.0}/.vscode/tasks.json +0 -0
  150. {calkit_python-0.42.1 → calkit_python-0.44.0}/CITATION.cff +0 -0
  151. {calkit_python-0.42.1 → calkit_python-0.44.0}/CODE_OF_CONDUCT.md +0 -0
  152. {calkit_python-0.42.1 → calkit_python-0.44.0}/CONTRIBUTING.md +0 -0
  153. {calkit_python-0.42.1 → calkit_python-0.44.0}/LICENSE +0 -0
  154. {calkit_python-0.42.1 → calkit_python-0.44.0}/agent-plugin/.claude-plugin/plugin.json +0 -0
  155. {calkit_python-0.42.1 → calkit_python-0.44.0}/agent-plugin/skills/add-pipeline-stage/SKILL.md +0 -0
  156. {calkit_python-0.42.1 → calkit_python-0.44.0}/agent-plugin/skills/create-pipeline/SKILL.md +0 -0
  157. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/.gitignore +0 -0
  158. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/README.md +0 -0
  159. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/options.html +0 -0
  160. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/package-lock.json +0 -0
  161. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/package.json +0 -0
  162. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/popup.html +0 -0
  163. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/public/icons/calkit-128.png +0 -0
  164. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/public/icons/calkit-16.png +0 -0
  165. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/public/icons/calkit-32.png +0 -0
  166. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/public/icons/calkit-48.png +0 -0
  167. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/public/icons/calkit.svg +0 -0
  168. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/public/manifest.json +0 -0
  169. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/scripts/build-content.mjs +0 -0
  170. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/scripts/package-manifest.mjs +0 -0
  171. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/scripts/store-screenshots.py +0 -0
  172. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/scripts/watch.mjs +0 -0
  173. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/src/background/index.ts +0 -0
  174. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/src/content/github.ts +0 -0
  175. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/src/content/overleaf.ts +0 -0
  176. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/src/content/references.ts +0 -0
  177. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/src/core/api.ts +0 -0
  178. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/src/core/auth.ts +0 -0
  179. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/src/core/calkit-yaml.test.ts +0 -0
  180. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/src/core/calkit-yaml.ts +0 -0
  181. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/src/core/detect.test.ts +0 -0
  182. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/src/core/detect.ts +0 -0
  183. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/src/core/hub-url.ts +0 -0
  184. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/src/core/hubs.test.ts +0 -0
  185. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/src/core/hubs.ts +0 -0
  186. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/src/core/latex.test.ts +0 -0
  187. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/src/core/latex.ts +0 -0
  188. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/src/core/lifecycle.ts +0 -0
  189. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/src/core/messages.test.ts +0 -0
  190. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/src/core/messages.ts +0 -0
  191. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/src/core/pickers.ts +0 -0
  192. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/src/core/storage.ts +0 -0
  193. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/src/core/types.ts +0 -0
  194. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/src/core/ui.test.ts +0 -0
  195. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/src/core/ui.ts +0 -0
  196. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/src/options/options.ts +0 -0
  197. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/src/popup/popup.css +0 -0
  198. {calkit_python-0.42.1 → calkit_python-0.44.0}/browser-ext/src/popup/popup.ts +0 -0
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@@ -1,3 +1,6 @@
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  [submodule "examples/basic"]
2
2
  path = examples/basic
3
3
  url = https://github.com/calkit/example-basic.git
4
+ [submodule "examples/ssh"]
5
+ path = examples/ssh
6
+ url = git@github.com:calkit/example-ssh.git
@@ -6,6 +6,10 @@
6
6
  - The JupyterLab extension lives in `src`
7
7
  - The VS Code extension lives in `vscode-ext`
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8
  - The Chrome extension lives in `browser-ext`
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+ - GitHub Actions live in `actions`, e.g., `calkit/calkit/actions/run`
10
+ - Config Calkit installs into projects, e.g., the dev container, VS Code, and
11
+ GitHub Actions configs, lives in `calkit/resources`; see the README there
12
+ before editing, since some of those files are generated
9
13
 
10
14
  ## Working
11
15
 
@@ -17,7 +17,7 @@ frontend-client: ## Regenerate the hub frontend's API client.
17
17
  @$(MAKE) -C hub/frontend client
18
18
 
19
19
  .PHONY: format
20
- format: sync-docs ## Automatically format files.
20
+ format: sync-docs sync-resources ## Automatically format files.
21
21
  @echo "🚀 Linting code with pre-commit"
22
22
  @uv run pre-commit run -a
23
23
 
@@ -44,13 +44,36 @@ test-cov: ## Test the code coverage with pytest.
44
44
  test-docs: sync-docs ## Test if documentation can be built without warnings or errors.
45
45
  @uv run mkdocs build -s
46
46
 
47
+ .PHONY: schema
48
+ schema: ## Generate the published JSON schema for calkit.yaml.
49
+ @echo "🚀 Generating calkit.yaml JSON schema"
50
+ @uv run calkit describe schema -o docs/schemas/calkit.json
51
+ @cp docs/schemas/calkit.json vscode-ext/schemas/calkit.json
52
+
47
53
  .PHONY: sync-docs
48
- sync-docs: ## Sync documentation content from docs/*.md into README.md.
54
+ sync-docs: schema ## Sync documentation content from docs/*.md into README.md.
49
55
  @echo "🚀 Generating docs references"
50
56
  @uv run python scripts/generate-docs-references.py
51
57
  @echo "🚀 Syncing documentation"
52
58
  @uv run python scripts/sync-docs.py
53
59
 
60
+ .PHONY: changes
61
+ changes: ## List each product's commits since its last release.
62
+ @uv run python scripts/list-changes.py
63
+
64
+ .PHONY: sync-resources
65
+ sync-resources: ## Regenerate the dev container spec from the VS Code config.
66
+ @echo "🚀 Syncing project resources"
67
+ @uv run python scripts/sync-resources.py
68
+
69
+ .PHONY: devcontainer-image
70
+ devcontainer-image: ## Build the dev container image and smoke test it.
71
+ @echo "🚀 Building the dev container image"
72
+ @docker build -t calkit/devcontainer:dev calkit/resources/devcontainer
73
+ @echo "🚀 Smoke testing the dev container image"
74
+ @docker run --rm calkit/devcontainer:dev bash -c \
75
+ "calkit --version && uv --version && pixi --version && conda --version"
76
+
54
77
  .PHONY: docs
55
78
  docs: sync-docs ## Build and serve the documentation.
56
79
  @uv run mkdocs serve --livereload
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.5
2
2
  Name: calkit-python
3
- Version: 0.42.1
3
+ Version: 0.44.0
4
4
  Summary: Reproducibility simplified.
5
5
  Project-URL: Homepage, https://calkit.org
6
6
  Project-URL: Issues, https://github.com/calkit/calkit/issues
@@ -96,7 +96,7 @@ without the cognitive overhead.
96
96
 
97
97
  <!-- https://docs.google.com/drawings/d/1XMGnbgYYNFAVUBDyUaCyLfRB7efvJdrnrKmFlNmT19o/edit -->
98
98
 
99
- ![pipeline](docs/img/pipeline.png)
99
+ ![pipeline](https://docs.calkit.org/img/pipeline.png)
100
100
 
101
101
  ## Features
102
102
 
@@ -261,7 +261,7 @@ This re-execs the CLI via `uvx --from calkit-python@<version> calkit`,
261
261
  so it requires [uv](https://docs.astral.sh/uv/) on `PATH`.
262
262
  You can also declare a minimum version in `calkit.yaml`;
263
263
  see
264
- [Pinning the Calkit CLI version](https://docs.calkit.org/dependencies.md#pinning-the-calkit-cli-version).
264
+ [Pinning the Calkit CLI version](https://docs.calkit.org/requirements.md#pinning-the-calkit-cli-version).
265
265
 
266
266
  ### Calkit Assistant
267
267
 
@@ -37,7 +37,7 @@ without the cognitive overhead.
37
37
 
38
38
  <!-- https://docs.google.com/drawings/d/1XMGnbgYYNFAVUBDyUaCyLfRB7efvJdrnrKmFlNmT19o/edit -->
39
39
 
40
- ![pipeline](docs/img/pipeline.png)
40
+ ![pipeline](https://docs.calkit.org/img/pipeline.png)
41
41
 
42
42
  ## Features
43
43
 
@@ -202,7 +202,7 @@ This re-execs the CLI via `uvx --from calkit-python@<version> calkit`,
202
202
  so it requires [uv](https://docs.astral.sh/uv/) on `PATH`.
203
203
  You can also declare a minimum version in `calkit.yaml`;
204
204
  see
205
- [Pinning the Calkit CLI version](https://docs.calkit.org/dependencies.md#pinning-the-calkit-cli-version).
205
+ [Pinning the Calkit CLI version](https://docs.calkit.org/requirements.md#pinning-the-calkit-cli-version).
206
206
 
207
207
  ### Calkit Assistant
208
208
 
@@ -0,0 +1,115 @@
1
+ # Calkit run GitHub Action
2
+
3
+ A GitHub Action to run a Calkit project's pipeline and optionally save results
4
+ (commit and push) to Git and DVC.
5
+
6
+ The action lives in the Calkit repo because it's a thin wrapper around a
7
+ sequence of CLI commands, and it reads `calkit list environments` output to
8
+ decide what tooling to install.
9
+ Keeping it here means a change to either is tested against the other before
10
+ release.
11
+
12
+ ## Usage
13
+
14
+ Reference the action by a Calkit release tag:
15
+
16
+ ```yaml
17
+ - uses: calkit/calkit/actions/run@v0.43.0
18
+ ```
19
+
20
+ The easiest way to add it to a project is:
21
+
22
+ ```sh
23
+ calkit update github-actions
24
+ ```
25
+
26
+ which writes the workflow below to `.github/workflows/run-calkit.yml`,
27
+ pinned to the version of Calkit that wrote it.
28
+ Rerun it after upgrading Calkit to move the pin.
29
+
30
+ <!-- Do not edit the snippet below since it is automatically populated -->
31
+ <!-- snippet:example.yml:start -->
32
+
33
+ ```yaml
34
+ name: Run pipeline
35
+
36
+ on:
37
+ push:
38
+ branches:
39
+ - main
40
+ pull_request:
41
+ workflow_dispatch:
42
+
43
+ permissions:
44
+ contents: write
45
+ id-token: write
46
+
47
+ # Make sure we only ever run one per branch so we don't have issues pushing
48
+ # after running the pipeline
49
+ concurrency:
50
+ group: calkit-run-${{ github.ref }}
51
+ cancel-in-progress: false
52
+
53
+ jobs:
54
+ main:
55
+ name: Run
56
+ runs-on: ubuntu-latest
57
+ steps:
58
+ - uses: actions/checkout@v4
59
+ with:
60
+ # For PRs, checkout the head ref to avoid detached HEAD
61
+ ref: ${{ github.head_ref || github.ref_name }}
62
+ token: ${{ secrets.GITHUB_TOKEN }}
63
+ - name: Configure Git credentials
64
+ run: |
65
+ git config user.name github-actions[bot]
66
+ git config user.email 41898282+github-actions[bot]@users.noreply.github.com
67
+ # This action automatically runs necessary setup steps based on environments
68
+ - name: Run Calkit
69
+ uses: calkit/calkit/actions/run@main
70
+ ```
71
+
72
+ <!-- snippet:example.yml:end -->
73
+
74
+ Note the permissions, concurrency, and checkout options.
75
+ The action detects required environment kinds from `calkit.yaml` and sets up
76
+ needed tooling (for example Calkit via `uv`, Julia, Pixi, Conda, R, MATLAB,
77
+ and Docker Buildx) before running.
78
+
79
+ ## Configuration
80
+
81
+ If simply running the pipeline is desired, the `save` option can be set to
82
+ `false`.
83
+ Additionally, caching DVC data can be disabled with `cache_dvc: false`.
84
+ When caching is enabled, the action saves DVC cache entries using the current
85
+ branch name plus the current commit SHA.
86
+ The restore step first looks for the
87
+ most recent cache for the current branch and then falls back to the default
88
+ branch cache if the current branch cache doesn't exist yet.
89
+
90
+ ## System dependencies
91
+
92
+ System dependencies like `uv`, `pixi`, `conda`, `juliaup` will be installed
93
+ automatically if missing, and if the project has an environment with the
94
+ corresponding kind.
95
+ If you'd like control over which versions are used, you can add setup steps
96
+ before the Calkit Action, and Calkit will detect and skip installation.
97
+
98
+ ## Development
99
+
100
+ `example.yml` is the source for both the snippet above and the copy bundled
101
+ into the Python package at `calkit/resources/github-actions`.
102
+ After editing it, run `make sync-resources`.
103
+
104
+ CI runs the action against real example projects on every pull request that
105
+ touches this directory, with Calkit installed from the working tree first, so
106
+ the action exercises the CLI being changed rather than the last release.
107
+
108
+ ## Previous home
109
+
110
+ This action was previously published from
111
+ [`calkit/run-action`](https://github.com/calkit/run-action), which is no
112
+ longer maintained.
113
+ Workflows referencing `calkit/run-action@v2` still work, but should be
114
+ updated to `calkit/calkit/actions/run@<version>`, which
115
+ `calkit update github-actions` will do in place.
@@ -0,0 +1,349 @@
1
+ name: Run Calkit
2
+ description: >
3
+ Run a Calkit project pipeline and optionally commit and push results to Git
4
+ and DVC remotes.
5
+ branding:
6
+ icon: arrow-right
7
+ color: green
8
+ inputs:
9
+ save:
10
+ description: Whether or not to save (commit and push) results to Git and DVC remotes.
11
+ default: "true"
12
+ dvc_token:
13
+ description:
14
+ DVC token for pushing results. If not provided, will be obtained
15
+ via GitHub OIDC.
16
+ required: false
17
+ pull_dvc:
18
+ description: Whether or not to pull DVC data before running.
19
+ required: false
20
+ default: "true"
21
+ cache_dvc:
22
+ description: Whether or not to cache DVC data.
23
+ required: false
24
+ default: "true"
25
+ run_args:
26
+ description: Arguments passed to calkit run command.
27
+ required: false
28
+ default: ""
29
+ outputs: {}
30
+ runs:
31
+ using: composite
32
+ steps:
33
+ - name: Check for uv and Calkit
34
+ id: tools
35
+ shell: bash
36
+ run: |
37
+ set -euo pipefail
38
+ if command -v uv >/dev/null 2>&1; then
39
+ echo "uv_missing=false" >> "$GITHUB_OUTPUT"
40
+ else
41
+ echo "uv_missing=true" >> "$GITHUB_OUTPUT"
42
+ fi
43
+ if command -v calkit >/dev/null 2>&1; then
44
+ echo "calkit_missing=false" >> "$GITHUB_OUTPUT"
45
+ else
46
+ echo "calkit_missing=true" >> "$GITHUB_OUTPUT"
47
+ fi
48
+
49
+ # uv is only needed up front to install Calkit; uv-venv projects that
50
+ # need uv but already have Calkit are handled by the uv step after
51
+ # detection.
52
+ - name: Setup uv
53
+ if: ${{ steps.tools.outputs.uv_missing == 'true' && steps.tools.outputs.calkit_missing == 'true' }}
54
+ uses: astral-sh/setup-uv@v5
55
+
56
+ - name: Install Calkit
57
+ if: ${{ steps.tools.outputs.calkit_missing == 'true' }}
58
+ shell: bash
59
+ run: |
60
+ uv tool install calkit-python
61
+ echo "$HOME/.local/bin" >> "$GITHUB_PATH"
62
+
63
+ - name: Detect setup requirements
64
+ id: detect
65
+ shell: bash
66
+ run: |
67
+ set -euo pipefail
68
+
69
+ # Let Calkit parse its own config so we only look at the
70
+ # `environments` section (a real YAML parse that also resolves
71
+ # includes), rather than grepping every `kind:` in the file --
72
+ # pipeline stages, dependencies, datasets, etc. all use `kind:` too.
73
+ kinds=$(calkit list environments 2>/dev/null \
74
+ | grep -E '^[[:space:]]+kind:' \
75
+ | sed -E 's/^[[:space:]]+kind:[[:space:]]*//; s/[[:space:]]+#.*$//' \
76
+ | tr -d "\"'" | sort -u || true)
77
+ echo "Detected environment kinds: $(echo "$kinds" | paste -sd, -)"
78
+
79
+ has_kind() {
80
+ printf '%s\n' "$kinds" | grep -qx "$1"
81
+ }
82
+
83
+ if command -v python >/dev/null 2>&1 || command -v python3 >/dev/null 2>&1; then
84
+ python_missing=false
85
+ else
86
+ python_missing=true
87
+ fi
88
+
89
+ if command -v uv >/dev/null 2>&1; then
90
+ uv_missing=false
91
+ else
92
+ uv_missing=true
93
+ fi
94
+
95
+ if command -v conda >/dev/null 2>&1; then
96
+ conda_missing=false
97
+ else
98
+ conda_missing=true
99
+ fi
100
+
101
+ if command -v pixi >/dev/null 2>&1; then
102
+ pixi_missing=false
103
+ else
104
+ pixi_missing=true
105
+ fi
106
+
107
+ # Calkit manages Julia versions via juliaup (e.g. `juliaup add
108
+ # 1.11.7` for a `julia: "1.11.7"` environment), so juliaup -- not a
109
+ # fixed Julia -- is what must be present. We deliberately gate only on
110
+ # juliaup and ignore any plain `julia` on the runner: hosted runner
111
+ # images ship a pinned Julia that usually won't match the project's
112
+ # required version, and without juliaup Calkit can't install the right
113
+ # one. Users who manage Julia themselves should install juliaup, which
114
+ # this then detects and leaves alone.
115
+ if command -v juliaup >/dev/null 2>&1; then
116
+ juliaup_missing=false
117
+ else
118
+ juliaup_missing=true
119
+ fi
120
+
121
+ if command -v Rscript >/dev/null 2>&1 || command -v R >/dev/null 2>&1; then
122
+ r_missing=false
123
+ else
124
+ r_missing=true
125
+ fi
126
+
127
+ if command -v matlab >/dev/null 2>&1; then
128
+ matlab_missing=false
129
+ else
130
+ matlab_missing=true
131
+ fi
132
+
133
+ if command -v docker >/dev/null 2>&1 && docker buildx version >/dev/null 2>&1; then
134
+ docker_buildx_missing=false
135
+ else
136
+ docker_buildx_missing=true
137
+ fi
138
+
139
+ needs_python=false
140
+ needs_uv=false
141
+ needs_conda=false
142
+ needs_pixi=false
143
+ needs_julia=false
144
+ needs_r=false
145
+ needs_matlab=false
146
+ needs_docker=false
147
+ docker_cli_missing=false
148
+ unsupported_kinds=""
149
+
150
+ if has_kind "uv-venv" || has_kind "venv" || has_kind "uv"; then
151
+ if [ "$python_missing" = true ]; then
152
+ needs_python=true
153
+ fi
154
+ fi
155
+ # uv is installed up front to install Calkit, so it is normally
156
+ # already present here; this covers the case where Calkit was
157
+ # pre-installed (so we skipped the initial uv setup) but uv is not.
158
+ if has_kind "uv-venv" || has_kind "uv"; then
159
+ if [ "$uv_missing" = true ]; then
160
+ needs_uv=true
161
+ fi
162
+ fi
163
+ if has_kind "conda"; then
164
+ if [ "$conda_missing" = true ]; then
165
+ needs_conda=true
166
+ fi
167
+ if [ "$python_missing" = true ]; then
168
+ needs_python=true
169
+ fi
170
+ fi
171
+ if has_kind "pixi"; then
172
+ if [ "$pixi_missing" = true ]; then
173
+ needs_pixi=true
174
+ fi
175
+ fi
176
+ if has_kind "julia"; then
177
+ if [ "$juliaup_missing" = true ]; then
178
+ needs_julia=true
179
+ fi
180
+ fi
181
+ if has_kind "renv"; then
182
+ if [ "$r_missing" = true ]; then
183
+ needs_r=true
184
+ fi
185
+ fi
186
+ if has_kind "matlab"; then
187
+ if [ "$matlab_missing" = true ]; then
188
+ needs_matlab=true
189
+ fi
190
+ fi
191
+ if has_kind "docker"; then
192
+ if command -v docker >/dev/null 2>&1; then
193
+ if [ "$docker_buildx_missing" = true ]; then
194
+ needs_docker=true
195
+ fi
196
+ else
197
+ docker_cli_missing=true
198
+ fi
199
+ fi
200
+
201
+ # These kinds do not have a direct setup action in this composite action.
202
+ if has_kind "ssh"; then unsupported_kinds="${unsupported_kinds}ssh,"; fi
203
+ if has_kind "slurm"; then unsupported_kinds="${unsupported_kinds}slurm,"; fi
204
+ if has_kind "pbs"; then unsupported_kinds="${unsupported_kinds}pbs,"; fi
205
+ if has_kind "nix"; then unsupported_kinds="${unsupported_kinds}nix,"; fi
206
+ unsupported_kinds="${unsupported_kinds%,}"
207
+
208
+ echo "needs_python=${needs_python}" >> "$GITHUB_OUTPUT"
209
+ echo "needs_uv=${needs_uv}" >> "$GITHUB_OUTPUT"
210
+ echo "needs_conda=${needs_conda}" >> "$GITHUB_OUTPUT"
211
+ echo "needs_pixi=${needs_pixi}" >> "$GITHUB_OUTPUT"
212
+ echo "needs_julia=${needs_julia}" >> "$GITHUB_OUTPUT"
213
+ echo "needs_r=${needs_r}" >> "$GITHUB_OUTPUT"
214
+ echo "needs_matlab=${needs_matlab}" >> "$GITHUB_OUTPUT"
215
+ echo "needs_docker=${needs_docker}" >> "$GITHUB_OUTPUT"
216
+ echo "docker_cli_missing=${docker_cli_missing}" >> "$GITHUB_OUTPUT"
217
+ echo "unsupported_kinds=${unsupported_kinds}" >> "$GITHUB_OUTPUT"
218
+
219
+ - name: Setup uv for uv and uv-venv environments
220
+ if: ${{ steps.detect.outputs.needs_uv == 'true' }}
221
+ uses: astral-sh/setup-uv@v5
222
+
223
+ - name: Setup Python
224
+ if: ${{ steps.detect.outputs.needs_python == 'true' }}
225
+ uses: actions/setup-python@v5
226
+ with:
227
+ python-version: "3.x"
228
+
229
+ - name: Setup Miniconda
230
+ if: ${{ steps.detect.outputs.needs_conda == 'true' }}
231
+ uses: conda-incubator/setup-miniconda@v3
232
+ with:
233
+ auto-activate-base: true
234
+ conda-remove-defaults: true
235
+
236
+ - name: Setup Pixi
237
+ if: ${{ steps.detect.outputs.needs_pixi == 'true' }}
238
+ uses: prefix-dev/setup-pixi@v0.9.6
239
+ with:
240
+ run-install: false
241
+
242
+ # Install juliaup (not a fixed Julia) so Calkit can install and select
243
+ # the exact Julia version(s) declared in each environment via
244
+ # `juliaup add`. The channel here is just a default bootstrap install.
245
+ - name: Setup juliaup
246
+ if: ${{ steps.detect.outputs.needs_julia == 'true' }}
247
+ uses: julia-actions/install-juliaup@v2
248
+ with:
249
+ channel: "1"
250
+
251
+ - name: Setup R
252
+ if: ${{ steps.detect.outputs.needs_r == 'true' }}
253
+ uses: r-lib/actions/setup-r@v2
254
+
255
+ - name: Setup MATLAB
256
+ if: ${{ steps.detect.outputs.needs_matlab == 'true' }}
257
+ uses: matlab-actions/setup-matlab@v2
258
+
259
+ - name: Setup Docker Buildx
260
+ if: ${{ steps.detect.outputs.needs_docker == 'true' }}
261
+ uses: docker/setup-buildx-action@v3
262
+
263
+ - name: Report unsupported environment kinds
264
+ if: ${{ steps.detect.outputs.unsupported_kinds != '' }}
265
+ shell: bash
266
+ run: |
267
+ echo "::notice::Detected environment kinds without explicit setup action: ${{ steps.detect.outputs.unsupported_kinds }}"
268
+
269
+ - name: Report missing Docker CLI for docker environments
270
+ if: ${{ steps.detect.outputs.docker_cli_missing == 'true' }}
271
+ shell: bash
272
+ run: |
273
+ echo "::notice::Detected kind 'docker' in calkit.yaml, but Docker CLI is not available on this runner. Install Docker on the runner to use docker environments."
274
+
275
+ - name: Restore DVC cache for current branch
276
+ if: ${{ inputs.cache_dvc == 'true' }}
277
+ id: cache-dvc-restore
278
+ uses: actions/cache/restore@v5
279
+ with:
280
+ path: .dvc/cache
281
+ key: >-
282
+ ${{ runner.os }}-dvc-cache-${{ github.head_ref || github.ref_name }}-${{ github.sha }}
283
+ restore-keys: |
284
+ ${{ runner.os }}-dvc-cache-${{ github.head_ref || github.ref_name }}-
285
+ ${{ runner.os }}-dvc-cache-${{ github.event.repository.default_branch }}-
286
+
287
+ - name: Get GitHub OIDC token
288
+ if: ${{ !inputs.dvc_token && (inputs.save == 'true' || inputs.pull_dvc ==
289
+ 'true') }}
290
+ id: get-oidc-token
291
+ shell: bash
292
+ run: |
293
+ OIDC_TOKEN=$(curl -H "Authorization: Bearer $ACTIONS_ID_TOKEN_REQUEST_TOKEN" "$ACTIONS_ID_TOKEN_REQUEST_URL&audience=calkit.io" -s | jq -r '.value')
294
+ if [ -z "$OIDC_TOKEN" ] || [ "$OIDC_TOKEN" == "null" ]; then
295
+ echo "Failed to obtain OIDC token"
296
+ exit 1
297
+ fi
298
+ echo "::add-mask::$OIDC_TOKEN"
299
+ echo "oidc-token=$OIDC_TOKEN" >> $GITHUB_OUTPUT
300
+
301
+ - name: Exchange OIDC token for Calkit token
302
+ if: ${{ !inputs.dvc_token && (inputs.save == 'true' || inputs.pull_dvc ==
303
+ 'true') }}
304
+ id: get-calkit-token
305
+ shell: bash
306
+ run: |
307
+ CALKIT_TOKEN=$(curl -X POST https://api.calkit.io/login/github-oidc \
308
+ -H "Authorization: Bearer ${{ steps.get-oidc-token.outputs.oidc-token }}" \
309
+ -s | jq -r '.access_token')
310
+ if [ -z "$CALKIT_TOKEN" ] || [ "$CALKIT_TOKEN" == "null" ]; then
311
+ echo "Failed to obtain Calkit token"
312
+ exit 1
313
+ fi
314
+ echo "::add-mask::$CALKIT_TOKEN"
315
+ echo "calkit-token=$CALKIT_TOKEN" >> $GITHUB_OUTPUT
316
+
317
+ - run: calkit config remote-auth
318
+ if: ${{ inputs.save == 'true' || inputs.pull_dvc == 'true' }}
319
+ shell: bash
320
+ env:
321
+ CALKIT_TOKEN: ${{ inputs.dvc_token || steps.get-calkit-token.outputs.calkit-token }}
322
+ CALKIT_DVC_TOKEN: ${{ inputs.dvc_token || steps.get-calkit-token.outputs.calkit-token }}
323
+
324
+ - run: calkit dvc pull
325
+ if: ${{ inputs.pull_dvc == 'true' }}
326
+ shell: bash
327
+ continue-on-error: true
328
+ env:
329
+ CALKIT_TOKEN: ${{ inputs.dvc_token || steps.get-calkit-token.outputs.calkit-token }}
330
+ CALKIT_DVC_TOKEN: ${{ inputs.dvc_token || steps.get-calkit-token.outputs.calkit-token }}
331
+
332
+ - run: calkit run ${{ inputs.run_args }}
333
+ shell: bash
334
+
335
+ - run: calkit save -am "Run pipeline"
336
+ if: ${{ inputs.save == 'true' }}
337
+ shell: bash
338
+ env:
339
+ CALKIT_TOKEN: ${{ inputs.dvc_token || steps.get-calkit-token.outputs.calkit-token }}
340
+ CALKIT_DVC_TOKEN: ${{ inputs.dvc_token || steps.get-calkit-token.outputs.calkit-token }}
341
+
342
+ - name: Save DVC cache
343
+ if: ${{ inputs.cache_dvc == 'true' }}
344
+ id: cache-dvc-save
345
+ uses: actions/cache/save@v5
346
+ with:
347
+ path: .dvc/cache
348
+ key: >-
349
+ ${{ runner.os }}-dvc-cache-${{ github.head_ref || github.ref_name }}-${{ github.sha }}
@@ -0,0 +1,36 @@
1
+ name: Run pipeline
2
+
3
+ on:
4
+ push:
5
+ branches:
6
+ - main
7
+ pull_request:
8
+ workflow_dispatch:
9
+
10
+ permissions:
11
+ contents: write
12
+ id-token: write
13
+
14
+ # Make sure we only ever run one per branch so we don't have issues pushing
15
+ # after running the pipeline
16
+ concurrency:
17
+ group: calkit-run-${{ github.ref }}
18
+ cancel-in-progress: false
19
+
20
+ jobs:
21
+ main:
22
+ name: Run
23
+ runs-on: ubuntu-latest
24
+ steps:
25
+ - uses: actions/checkout@v4
26
+ with:
27
+ # For PRs, checkout the head ref to avoid detached HEAD
28
+ ref: ${{ github.head_ref || github.ref_name }}
29
+ token: ${{ secrets.GITHUB_TOKEN }}
30
+ - name: Configure Git credentials
31
+ run: |
32
+ git config user.name github-actions[bot]
33
+ git config user.email 41898282+github-actions[bot]@users.noreply.github.com
34
+ # This action automatically runs necessary setup steps based on environments
35
+ - name: Run Calkit
36
+ uses: calkit/calkit/actions/run@main
@@ -18,6 +18,10 @@ is `calkit.yaml`, the project's metadata database.
18
18
 
19
19
  `calkit.yaml` lives at the repo root and contains:
20
20
 
21
+ - `requirements`—what must be true of the machine before anything runs
22
+ (apps on `PATH`, environmental variables, setup steps, machine
23
+ properties like CPU count); formerly called `dependencies`, which
24
+ still works
21
25
  - `environments`—computational environments (Python venvs, Conda, Docker,
22
26
  R, Julia, MATLAB, etc.)
23
27
  - `pipeline.stages`—the reproducible pipeline
@@ -38,6 +38,8 @@ if TYPE_CHECKING:
38
38
  overleaf,
39
39
  pipeline,
40
40
  releases,
41
+ resources,
42
+ schema,
41
43
  server,
42
44
  templates,
43
45
  )
@@ -61,6 +63,7 @@ _SUBMODULES = {
61
63
  "github",
62
64
  "invenio",
63
65
  "releases",
66
+ "resources",
64
67
  "licenses",
65
68
  "overleaf",
66
69
  "julia",
@@ -76,6 +79,7 @@ _SUBMODULES = {
76
79
  "install",
77
80
  "magics",
78
81
  "ops",
82
+ "schema",
79
83
  "server",
80
84
  }
81
85