calkit-python 0.41.10__tar.gz → 0.41.11__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 (345) hide show
  1. {calkit_python-0.41.10 → calkit_python-0.41.11}/PKG-INFO +1 -1
  2. calkit_python-0.41.11/calkit/cli/describe.py +63 -0
  3. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/cli/list.py +18 -2
  4. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/cli/main/core.py +6 -1
  5. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/cli/update.py +558 -4
  6. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/core.py +12 -0
  7. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/pipeline.py +25 -10
  8. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/cli/main/test_core.py +16 -1
  9. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/cli/test_list.py +19 -2
  10. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/cli/test_update.py +136 -0
  11. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/test_pipeline.py +2 -0
  12. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/calkit-yaml.md +2 -1
  13. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/cli-reference.md +261 -6
  14. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/existing-project.md +7 -6
  15. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/index.md +1 -0
  16. {calkit_python-0.41.10 → calkit_python-0.41.11}/mkdocs.yml +1 -0
  17. calkit_python-0.41.11/vscode-ext/images/calkit-icon.svg +22 -0
  18. calkit_python-0.41.11/vscode-ext/package.json +571 -0
  19. {calkit_python-0.41.10 → calkit_python-0.41.11}/vscode-ext/src/environments.ts +104 -0
  20. calkit_python-0.41.11/vscode-ext/src/extension.ts +7547 -0
  21. {calkit_python-0.41.10 → calkit_python-0.41.11}/vscode-ext/src/notebooks.ts +25 -16
  22. calkit_python-0.41.11/vscode-ext/src/sidebar.ts +862 -0
  23. {calkit_python-0.41.10 → calkit_python-0.41.11}/vscode-ext/src/test/environments.test.ts +94 -0
  24. calkit_python-0.41.11/vscode-ext/src/test/notebooks.test.ts +126 -0
  25. calkit_python-0.41.11/vscode-ext/src/types.ts +72 -0
  26. calkit_python-0.41.10/calkit/cli/describe.py +0 -18
  27. calkit_python-0.41.10/vscode-ext/package.json +0 -141
  28. calkit_python-0.41.10/vscode-ext/src/extension.ts +0 -3660
  29. calkit_python-0.41.10/vscode-ext/src/test/notebooks.test.ts +0 -70
  30. calkit_python-0.41.10/vscode-ext/src/types.ts +0 -29
  31. {calkit_python-0.41.10 → calkit_python-0.41.11}/.claude-plugin/marketplace.json +0 -0
  32. {calkit_python-0.41.10 → calkit_python-0.41.11}/.gitattributes +0 -0
  33. {calkit_python-0.41.10 → calkit_python-0.41.11}/.gitignore +0 -0
  34. {calkit_python-0.41.10 → calkit_python-0.41.11}/.pre-commit-config.yaml +0 -0
  35. {calkit_python-0.41.10 → calkit_python-0.41.11}/.prettierignore +0 -0
  36. {calkit_python-0.41.10 → calkit_python-0.41.11}/.python-version +0 -0
  37. {calkit_python-0.41.10 → calkit_python-0.41.11}/.vscode/launch.json +0 -0
  38. {calkit_python-0.41.10 → calkit_python-0.41.11}/.vscode/tasks.json +0 -0
  39. {calkit_python-0.41.10 → calkit_python-0.41.11}/.yarnrc.yml +0 -0
  40. {calkit_python-0.41.10 → calkit_python-0.41.11}/AGENTS.md +0 -0
  41. {calkit_python-0.41.10 → calkit_python-0.41.11}/CITATION.cff +0 -0
  42. {calkit_python-0.41.10 → calkit_python-0.41.11}/CODE_OF_CONDUCT.md +0 -0
  43. {calkit_python-0.41.10 → calkit_python-0.41.11}/CONTRIBUTING.md +0 -0
  44. {calkit_python-0.41.10 → calkit_python-0.41.11}/LICENSE +0 -0
  45. {calkit_python-0.41.10 → calkit_python-0.41.11}/Makefile +0 -0
  46. {calkit_python-0.41.10 → calkit_python-0.41.11}/README.md +0 -0
  47. {calkit_python-0.41.10 → calkit_python-0.41.11}/agent-plugin/.claude-plugin/plugin.json +0 -0
  48. {calkit_python-0.41.10 → calkit_python-0.41.11}/agent-plugin/skills/add-pipeline-stage/SKILL.md +0 -0
  49. {calkit_python-0.41.10 → calkit_python-0.41.11}/agent-plugin/skills/conventions/SKILL.md +0 -0
  50. {calkit_python-0.41.10 → calkit_python-0.41.11}/agent-plugin/skills/create-pipeline/SKILL.md +0 -0
  51. {calkit_python-0.41.10 → calkit_python-0.41.11}/babel.config.js +0 -0
  52. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/__init__.py +0 -0
  53. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/__main__.py +0 -0
  54. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/calc.py +0 -0
  55. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/check.py +0 -0
  56. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/cli/__init__.py +0 -0
  57. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/cli/check.py +0 -0
  58. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/cli/cloud.py +0 -0
  59. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/cli/config.py +0 -0
  60. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/cli/core.py +0 -0
  61. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/cli/dev.py +0 -0
  62. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/cli/import_.py +0 -0
  63. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/cli/latex.py +0 -0
  64. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/cli/main/__init__.py +0 -0
  65. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/cli/main/xr.py +0 -0
  66. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/cli/new.py +0 -0
  67. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/cli/notebooks.py +0 -0
  68. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/cli/office.py +0 -0
  69. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/cli/overleaf.py +0 -0
  70. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/cli/scheduler.py +0 -0
  71. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/cloud.py +0 -0
  72. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/conda.py +0 -0
  73. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/config.py +0 -0
  74. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/datasets.py +0 -0
  75. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/dependencies.py +0 -0
  76. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/detect.py +0 -0
  77. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/docker.py +0 -0
  78. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/dvc/__init__.py +0 -0
  79. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/dvc/core.py +0 -0
  80. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/dvc/zip.py +0 -0
  81. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/environments.py +0 -0
  82. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/fs.py +0 -0
  83. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/git.py +0 -0
  84. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/github.py +0 -0
  85. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/gui.py +0 -0
  86. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/install.py +0 -0
  87. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/invenio.py +0 -0
  88. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/julia.py +0 -0
  89. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/jupyter.py +0 -0
  90. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/jupyterlab/__init__.py +0 -0
  91. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/jupyterlab/routes.py +0 -0
  92. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/labextension/package.json +0 -0
  93. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/labextension/schemas/calkit/package.json.orig +0 -0
  94. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/labextension/schemas/calkit/plugin.json +0 -0
  95. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/labextension/static/502.9a2c5772a15466e923ef.js +0 -0
  96. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/labextension/static/695.2c41003a452d43d2b358.js +0 -0
  97. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/labextension/static/867.a42a046aa5108f54f8fb.js +0 -0
  98. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/labextension/static/909.e3f9cc3408834a7fdcc3.js +0 -0
  99. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/labextension/static/946.050af2abf7845cfbdbd2.js +0 -0
  100. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/labextension/static/946.050af2abf7845cfbdbd2.js.LICENSE.txt +0 -0
  101. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/labextension/static/b2f1c3efe70cb539d121.png +0 -0
  102. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/labextension/static/remoteEntry.65469af996e7a96aa983.js +0 -0
  103. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/labextension/static/style.js +0 -0
  104. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/labextension/static/third-party-licenses.json +0 -0
  105. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/licenses.py +0 -0
  106. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/magics.py +0 -0
  107. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/matlab.py +0 -0
  108. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/models/__init__.py +0 -0
  109. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/models/core.py +0 -0
  110. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/models/io.py +0 -0
  111. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/models/iteration.py +0 -0
  112. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/models/pipeline.py +0 -0
  113. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/notebooks.py +0 -0
  114. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/office.py +0 -0
  115. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/ops.py +0 -0
  116. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/overleaf.py +0 -0
  117. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/releases.py +0 -0
  118. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/server.py +0 -0
  119. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/templates/__init__.py +0 -0
  120. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/templates/core.py +0 -0
  121. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/templates/latex/__init__.py +0 -0
  122. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/templates/latex/article/paper.tex +0 -0
  123. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/templates/latex/core.py +0 -0
  124. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/templates/latex/jfm/jfm.bst +0 -0
  125. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/templates/latex/jfm/jfm.cls +0 -0
  126. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/templates/latex/jfm/lineno-FLM.sty +0 -0
  127. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/templates/latex/jfm/paper.tex +0 -0
  128. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/templates/latex/jfm/upmath.sty +0 -0
  129. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/__init__.py +0 -0
  130. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/cli/__init__.py +0 -0
  131. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/cli/main/__init__.py +0 -0
  132. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/cli/main/test_subprojects.py +0 -0
  133. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/cli/main/test_xr.py +0 -0
  134. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/cli/test_check.py +0 -0
  135. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/cli/test_cloud.py +0 -0
  136. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/cli/test_config.py +0 -0
  137. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/cli/test_import.py +0 -0
  138. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/cli/test_latex.py +0 -0
  139. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/cli/test_new.py +0 -0
  140. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/cli/test_notebooks.py +0 -0
  141. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/cli/test_overleaf.py +0 -0
  142. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/cli/test_scheduler.py +0 -0
  143. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/dvc/__init__.py +0 -0
  144. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/dvc/test_core.py +0 -0
  145. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/dvc/test_zip.py +0 -0
  146. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/jupyterlab/__init__.py +0 -0
  147. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/jupyterlab/test_routes.py +0 -0
  148. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/models/__init__.py +0 -0
  149. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/models/test_iteration.py +0 -0
  150. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/models/test_pipeline.py +0 -0
  151. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/test_calc.py +0 -0
  152. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/test_check.py +0 -0
  153. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/test_cloud.py +0 -0
  154. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/test_conda.py +0 -0
  155. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/test_core.py +0 -0
  156. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/test_dependencies.py +0 -0
  157. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/test_detect.py +0 -0
  158. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/test_docker.py +0 -0
  159. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/test_environments.py +0 -0
  160. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/test_fs.py +0 -0
  161. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/test_git.py +0 -0
  162. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/test_install.py +0 -0
  163. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/test_invenio.py +0 -0
  164. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/test_julia.py +0 -0
  165. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/test_jupyter.py +0 -0
  166. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/test_licenses.py +0 -0
  167. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/test_magics.py +0 -0
  168. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/test_matlab.py +0 -0
  169. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/test_notebooks.py +0 -0
  170. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/test_releases.py +0 -0
  171. {calkit_python-0.41.10 → calkit_python-0.41.11}/calkit/tests/test_templates.py +0 -0
  172. {calkit_python-0.41.10 → calkit_python-0.41.11}/conftest.py +0 -0
  173. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/CNAME +0 -0
  174. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/ai-tools.md +0 -0
  175. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/apps.md +0 -0
  176. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/calculations.md +0 -0
  177. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/cloud-integration.md +0 -0
  178. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/datasets.md +0 -0
  179. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/dependencies.md +0 -0
  180. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/environments.md +0 -0
  181. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/examples.md +0 -0
  182. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/governance.md +0 -0
  183. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/help.md +0 -0
  184. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/hpc.md +0 -0
  185. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/img/c-to-the-k-white.svg +0 -0
  186. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/img/calkit-fragmentation-compendium.png +0 -0
  187. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/img/calkit-no-bg.png +0 -0
  188. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/img/connect-zenodo.png +0 -0
  189. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/img/jupyterlab/all-green.png +0 -0
  190. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/img/jupyterlab/collect-data-stale.png +0 -0
  191. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/img/jupyterlab/new-env.png +0 -0
  192. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/img/jupyterlab/new-notebook.png +0 -0
  193. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/img/jupyterlab/pipeline-badge.png +0 -0
  194. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/img/jupyterlab-params.png +0 -0
  195. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/img/plos-osi-code-2024-03.png +0 -0
  196. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/img/vscode-nb-params.png +0 -0
  197. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/index.md +0 -0
  198. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/installation.md +0 -0
  199. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/jupyterlab.md +0 -0
  200. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/local-server.md +0 -0
  201. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/notebooks.md +0 -0
  202. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/overleaf.md +0 -0
  203. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/pipeline/index.md +0 -0
  204. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/pipeline/manual-steps.md +0 -0
  205. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/pipeline/running-and-logging.md +0 -0
  206. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/quickstart.md +0 -0
  207. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/references.md +0 -0
  208. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/releases.md +0 -0
  209. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/reproducibility.md +0 -0
  210. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/subprojects.md +0 -0
  211. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/adding-latex-pub-docker.md +0 -0
  212. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/ai-agents.md +0 -0
  213. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/conda-envs.md +0 -0
  214. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/first-project.md +0 -0
  215. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/github-actions.md +0 -0
  216. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/actions-repo-secrets.png +0 -0
  217. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/latex-codespaces/building-codespace.png +0 -0
  218. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/latex-codespaces/codespaces-secrets-2.png +0 -0
  219. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/latex-codespaces/editor-split.png +0 -0
  220. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/latex-codespaces/go-to-linked-code.png +0 -0
  221. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/latex-codespaces/issue-from-selection.png +0 -0
  222. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/latex-codespaces/new-project.png +0 -0
  223. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/latex-codespaces/new-pub-2.png +0 -0
  224. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/latex-codespaces/new-token.png +0 -0
  225. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/latex-codespaces/paper.tex.png +0 -0
  226. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/latex-codespaces/project-home-3.png +0 -0
  227. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/latex-codespaces/push.png +0 -0
  228. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/latex-codespaces/stage.png +0 -0
  229. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/office/anakin-excel.jpg +0 -0
  230. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/office/chart-more-rows.png +0 -0
  231. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/office/create-project.png +0 -0
  232. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/office/elsevier-research-data-guidelines.png +0 -0
  233. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/office/excel-chart.png +0 -0
  234. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/office/excel-data.png +0 -0
  235. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/office/insert-link-to-file.png +0 -0
  236. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/office/needs-clone.png +0 -0
  237. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/office/new-stage.png +0 -0
  238. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/office/phd-comics-version-control.webp +0 -0
  239. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/office/pipeline-out-of-date.png +0 -0
  240. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/office/status-more-rows.png +0 -0
  241. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/office/uncommitted-changes.png +0 -0
  242. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/office/untracked-data.png +0 -0
  243. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/office/updated-publication.png +0 -0
  244. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/office/word-to-pdf-stage-2.png +0 -0
  245. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/office/workflow-page.png +0 -0
  246. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/openfoam/clone.png +0 -0
  247. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/openfoam/create-project.png +0 -0
  248. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/openfoam/datasets-page.png +0 -0
  249. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/openfoam/figure-on-website-updated.png +0 -0
  250. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/openfoam/figure-on-website.png +0 -0
  251. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/openfoam/new-token.png +0 -0
  252. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/openfoam/reclone.png +0 -0
  253. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/openfoam/status-after-import-dataset.png +0 -0
  254. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/quick-actions.png +0 -0
  255. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/run-proc.png +0 -0
  256. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/vscode-slurm-notebook/create-calkit-env.png +0 -0
  257. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/vscode-slurm-notebook/create-inner-env.png +0 -0
  258. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/vscode-slurm-notebook/create-new-calkit-env.png +0 -0
  259. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/vscode-slurm-notebook/select-calkit-env.png +0 -0
  260. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/vscode-slurm-notebook/slurm-job-running.png +0 -0
  261. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/vscode-slurm-notebook/slurm-launch-options.png +0 -0
  262. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/img/vscode-slurm-notebook/starting-slurm-job.png +0 -0
  263. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/jupyterlab.md +0 -0
  264. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/latex-codespaces.md +0 -0
  265. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/matlab.md +0 -0
  266. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/notebook-pipeline.md +0 -0
  267. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/office.md +0 -0
  268. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/openfoam.md +0 -0
  269. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/procedures.md +0 -0
  270. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/tutorials/vscode-slurm-notebook.md +0 -0
  271. {calkit_python-0.41.10 → calkit_python-0.41.11}/docs/version-control.md +0 -0
  272. {calkit_python-0.41.10 → calkit_python-0.41.11}/flake.lock +0 -0
  273. {calkit_python-0.41.10 → calkit_python-0.41.11}/flake.nix +0 -0
  274. {calkit_python-0.41.10 → calkit_python-0.41.11}/install.json +0 -0
  275. {calkit_python-0.41.10 → calkit_python-0.41.11}/jest.config.js +0 -0
  276. {calkit_python-0.41.10 → calkit_python-0.41.11}/jupyter-config/server-config/calkit.json +0 -0
  277. {calkit_python-0.41.10 → calkit_python-0.41.11}/package.json +0 -0
  278. {calkit_python-0.41.10 → calkit_python-0.41.11}/pyproject.toml +0 -0
  279. {calkit_python-0.41.10 → calkit_python-0.41.11}/schema/plugin.json +0 -0
  280. {calkit_python-0.41.10 → calkit_python-0.41.11}/scripts/generate-docs-references.py +0 -0
  281. {calkit_python-0.41.10 → calkit_python-0.41.11}/scripts/install.ps1 +0 -0
  282. {calkit_python-0.41.10 → calkit_python-0.41.11}/scripts/install.sh +0 -0
  283. {calkit_python-0.41.10 → calkit_python-0.41.11}/scripts/make-calk9.sh +0 -0
  284. {calkit_python-0.41.10 → calkit_python-0.41.11}/scripts/sync-docs.py +0 -0
  285. {calkit_python-0.41.10 → calkit_python-0.41.11}/src/__tests__/useQueries.spec.ts +0 -0
  286. {calkit_python-0.41.10 → calkit_python-0.41.11}/src/calkit-config.ts +0 -0
  287. {calkit_python-0.41.10 → calkit_python-0.41.11}/src/cell-output-marker.ts +0 -0
  288. {calkit_python-0.41.10 → calkit_python-0.41.11}/src/components/commit-dialog.tsx +0 -0
  289. {calkit_python-0.41.10 → calkit_python-0.41.11}/src/components/environment-editor.tsx +0 -0
  290. {calkit_python-0.41.10 → calkit_python-0.41.11}/src/components/notebook-registration.tsx +0 -0
  291. {calkit_python-0.41.10 → calkit_python-0.41.11}/src/components/notebook-toolbar.tsx +0 -0
  292. {calkit_python-0.41.10 → calkit_python-0.41.11}/src/components/pipeline-status-bar.tsx +0 -0
  293. {calkit_python-0.41.10 → calkit_python-0.41.11}/src/components/project-info-editor.tsx +0 -0
  294. {calkit_python-0.41.10 → calkit_python-0.41.11}/src/components/sidebar-settings.tsx +0 -0
  295. {calkit_python-0.41.10 → calkit_python-0.41.11}/src/components/sidebar.tsx +0 -0
  296. {calkit_python-0.41.10 → calkit_python-0.41.11}/src/components/stage-editor.tsx +0 -0
  297. {calkit_python-0.41.10 → calkit_python-0.41.11}/src/feature-flags.ts +0 -0
  298. {calkit_python-0.41.10 → calkit_python-0.41.11}/src/file-browser-menu.ts +0 -0
  299. {calkit_python-0.41.10 → calkit_python-0.41.11}/src/hooks/__tests__/useQueries.test.tsx +0 -0
  300. {calkit_python-0.41.10 → calkit_python-0.41.11}/src/hooks/useQueries.ts +0 -0
  301. {calkit_python-0.41.10 → calkit_python-0.41.11}/src/icons.ts +0 -0
  302. {calkit_python-0.41.10 → calkit_python-0.41.11}/src/index.ts +0 -0
  303. {calkit_python-0.41.10 → calkit_python-0.41.11}/src/io-tracker.ts +0 -0
  304. {calkit_python-0.41.10 → calkit_python-0.41.11}/src/pipeline-state.ts +0 -0
  305. {calkit_python-0.41.10 → calkit_python-0.41.11}/src/queryClient.ts +0 -0
  306. {calkit_python-0.41.10 → calkit_python-0.41.11}/src/request.ts +0 -0
  307. {calkit_python-0.41.10 → calkit_python-0.41.11}/src/shims-mainmenu.d.ts +0 -0
  308. {calkit_python-0.41.10 → calkit_python-0.41.11}/style/base.css +0 -0
  309. {calkit_python-0.41.10 → calkit_python-0.41.11}/style/cell-output-marker.css +0 -0
  310. {calkit_python-0.41.10 → calkit_python-0.41.11}/style/environment-editor.css +0 -0
  311. {calkit_python-0.41.10 → calkit_python-0.41.11}/style/environment-selector.css +0 -0
  312. {calkit_python-0.41.10 → calkit_python-0.41.11}/style/img/calkit-no-bg.png +0 -0
  313. {calkit_python-0.41.10 → calkit_python-0.41.11}/style/index.css +0 -0
  314. {calkit_python-0.41.10 → calkit_python-0.41.11}/style/index.js +0 -0
  315. {calkit_python-0.41.10 → calkit_python-0.41.11}/style/notebook-toolbar.css +0 -0
  316. {calkit_python-0.41.10 → calkit_python-0.41.11}/style/pipeline-status-bar.css +0 -0
  317. {calkit_python-0.41.10 → calkit_python-0.41.11}/style/sidebar.css +0 -0
  318. {calkit_python-0.41.10 → calkit_python-0.41.11}/test/dvc-md5-dir/osx-arm64.txt +0 -0
  319. {calkit_python-0.41.10 → calkit_python-0.41.11}/test/nb-julia.ipynb +0 -0
  320. {calkit_python-0.41.10 → calkit_python-0.41.11}/test/nb-params.ipynb +0 -0
  321. {calkit_python-0.41.10 → calkit_python-0.41.11}/test/nb-subdir.ipynb +0 -0
  322. {calkit_python-0.41.10 → calkit_python-0.41.11}/test/pipeline.ipynb +0 -0
  323. {calkit_python-0.41.10 → calkit_python-0.41.11}/test/script.py +0 -0
  324. {calkit_python-0.41.10 → calkit_python-0.41.11}/test/test-log.log +0 -0
  325. {calkit_python-0.41.10 → calkit_python-0.41.11}/tsconfig.json +0 -0
  326. {calkit_python-0.41.10 → calkit_python-0.41.11}/tsconfig.test.json +0 -0
  327. {calkit_python-0.41.10 → calkit_python-0.41.11}/ui-tests/.gitignore +0 -0
  328. {calkit_python-0.41.10 → calkit_python-0.41.11}/ui-tests/README.md +0 -0
  329. {calkit_python-0.41.10 → calkit_python-0.41.11}/ui-tests/jupyter_server_test_config.py +0 -0
  330. {calkit_python-0.41.10 → calkit_python-0.41.11}/ui-tests/package.json +0 -0
  331. {calkit_python-0.41.10 → calkit_python-0.41.11}/ui-tests/playwright.config.js +0 -0
  332. {calkit_python-0.41.10 → calkit_python-0.41.11}/ui-tests/tests/calkit.spec.ts +0 -0
  333. {calkit_python-0.41.10 → calkit_python-0.41.11}/ui-tests/yarn.lock +0 -0
  334. {calkit_python-0.41.10 → calkit_python-0.41.11}/uv.lock +0 -0
  335. {calkit_python-0.41.10 → calkit_python-0.41.11}/vscode-ext/.gitignore +0 -0
  336. {calkit_python-0.41.10 → calkit_python-0.41.11}/vscode-ext/.vscodeignore +0 -0
  337. {calkit_python-0.41.10 → calkit_python-0.41.11}/vscode-ext/CHANGELOG.md +0 -0
  338. {calkit_python-0.41.10 → calkit_python-0.41.11}/vscode-ext/LICENSE +0 -0
  339. {calkit_python-0.41.10 → calkit_python-0.41.11}/vscode-ext/README.md +0 -0
  340. {calkit_python-0.41.10 → calkit_python-0.41.11}/vscode-ext/images/calkit-no-bg.png +0 -0
  341. {calkit_python-0.41.10 → calkit_python-0.41.11}/vscode-ext/package-lock.json +0 -0
  342. {calkit_python-0.41.10 → calkit_python-0.41.11}/vscode-ext/scripts/set-proposed-api.js +0 -0
  343. {calkit_python-0.41.10 → calkit_python-0.41.11}/vscode-ext/src/test/kernel-selection.test.ts +0 -0
  344. {calkit_python-0.41.10 → calkit_python-0.41.11}/vscode-ext/tsconfig.json +0 -0
  345. {calkit_python-0.41.10 → calkit_python-0.41.11}/yarn.lock +0 -0
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: calkit-python
3
- Version: 0.41.10
3
+ Version: 0.41.11
4
4
  Summary: Reproducibility simplified.
5
5
  Project-URL: Homepage, https://calkit.org
6
6
  Project-URL: Issues, https://github.com/calkit/calkit/issues
@@ -0,0 +1,63 @@
1
+ """CLI for describing things."""
2
+
3
+ from __future__ import annotations
4
+
5
+ import json
6
+ from typing import Annotated
7
+
8
+ import typer
9
+
10
+ import calkit
11
+ from calkit.cli import raise_error
12
+ from calkit.environments import get_env_lock_fpath
13
+
14
+ describe_app = typer.Typer(no_args_is_help=True)
15
+
16
+
17
+ @describe_app.command(name="system")
18
+ def describe_system():
19
+ """Describe the system."""
20
+ system_info = calkit.get_system_info()
21
+ typer.echo(json.dumps(system_info, indent=2))
22
+
23
+
24
+ @describe_app.command(name="env")
25
+ def describe_env(
26
+ name: Annotated[
27
+ str,
28
+ typer.Option("--name", "-n", help="Environment name."),
29
+ ],
30
+ ):
31
+ """Describe a single environment, including spec and lock file paths."""
32
+ ck_info = calkit.load_calkit_info()
33
+ envs: dict = ck_info.get("environments", {})
34
+ if name not in envs:
35
+ raise_error(f"Environment '{name}' not found.")
36
+ env = envs[name]
37
+ lock_path = get_env_lock_fpath(env=env, env_name=name)
38
+ result = {
39
+ "kind": env.get("kind"),
40
+ "spec_path": env.get("path"),
41
+ "lock_path": lock_path,
42
+ "prefix": env.get("prefix"),
43
+ "python": env.get("python"),
44
+ }
45
+ typer.echo(json.dumps(result, indent=2))
46
+
47
+
48
+ @describe_app.command(name="envs")
49
+ def describe_envs():
50
+ """Describe all environments, including spec and lock file paths."""
51
+ ck_info = calkit.load_calkit_info()
52
+ envs: dict = ck_info.get("environments", {})
53
+ result = {}
54
+ for env_name, env in envs.items():
55
+ lock_path = get_env_lock_fpath(env=env, env_name=env_name)
56
+ result[env_name] = {
57
+ "kind": env.get("kind"),
58
+ "spec_path": env.get("path"),
59
+ "lock_path": lock_path,
60
+ "prefix": env.get("prefix"),
61
+ "python": env.get("python"),
62
+ }
63
+ typer.echo(json.dumps(result, indent=2))
@@ -7,7 +7,7 @@ from typing import Annotated, Literal
7
7
  import typer
8
8
 
9
9
  import calkit
10
- from calkit.cli import AliasGroup, warn
10
+ from calkit.cli import AliasGroup, raise_error, warn
11
11
 
12
12
  list_app = typer.Typer(cls=AliasGroup, no_args_is_help=True)
13
13
 
@@ -167,12 +167,28 @@ def list_stages(
167
167
  list[str] | None,
168
168
  typer.Option("--kind", "-k", help="Filter stages by kind."),
169
169
  ] = None,
170
+ stale_only: Annotated[
171
+ bool, typer.Option("--stale", help="Show only stale stages.")
172
+ ] = False,
170
173
  ):
171
174
  """List pipeline stages."""
172
- stages = calkit.load_calkit_info().get("pipeline", {}).get("stages", {})
175
+ ck_info = calkit.load_calkit_info()
176
+ stages = ck_info.get("pipeline", {}).get("stages", {})
177
+ # If we only want stale stages, we need to get the status first.
178
+ # This compiles the pipeline, cleans notebooks, and checks environments,
179
+ # all of which can affect whether a stage is stale, so we don't skip them.
180
+ if stale_only:
181
+ status = calkit.pipeline.get_status(ck_info=ck_info)
182
+ if status.errors:
183
+ raise_error(
184
+ "Failed to determine stale stages: " + "; ".join(status.errors)
185
+ )
186
+ stale_stage_names = status.stale_stage_names
173
187
  for name, stage in stages.items():
174
188
  if kinds is not None and stage.get("kind") not in kinds:
175
189
  continue
190
+ if stale_only and name not in stale_stage_names:
191
+ continue
176
192
  typer.echo(name)
177
193
 
178
194
 
@@ -196,7 +196,12 @@ def init(
196
196
  repo = calkit.git.get_repo()
197
197
  repo.git.add(".dvc")
198
198
  repo.git.commit("-m", "Initialize DVC")
199
- # TODO: Initialize `calkit.yaml`
199
+ # Create an empty calkit.yaml if one doesn't already exist
200
+ if not os.path.isfile("calkit.yaml"):
201
+ with open("calkit.yaml", "w"):
202
+ pass
203
+ repo.git.add("calkit.yaml")
204
+ repo.git.commit("-m", "Initialize Calkit")
200
205
  # TODO: Initialize `dvc.yaml`
201
206
  # TODO: Add a sane .gitignore file
202
207
  # TODO: Add a sane LICENSE file?