calkit-python 0.41.22__tar.gz → 0.41.23__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 (356) hide show
  1. {calkit_python-0.41.22 → calkit_python-0.41.23}/PKG-INFO +1 -1
  2. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/cli/overleaf.py +24 -50
  3. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/overleaf.py +63 -0
  4. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/cli/test_overleaf.py +32 -0
  5. {calkit_python-0.41.22 → calkit_python-0.41.23}/.claude-plugin/marketplace.json +0 -0
  6. {calkit_python-0.41.22 → calkit_python-0.41.23}/.gitattributes +0 -0
  7. {calkit_python-0.41.22 → calkit_python-0.41.23}/.gitignore +0 -0
  8. {calkit_python-0.41.22 → calkit_python-0.41.23}/.gitmodules +0 -0
  9. {calkit_python-0.41.22 → calkit_python-0.41.23}/.pre-commit-config.yaml +0 -0
  10. {calkit_python-0.41.22 → calkit_python-0.41.23}/.prettierignore +0 -0
  11. {calkit_python-0.41.22 → calkit_python-0.41.23}/.prettierrc.json +0 -0
  12. {calkit_python-0.41.22 → calkit_python-0.41.23}/.python-version +0 -0
  13. {calkit_python-0.41.22 → calkit_python-0.41.23}/.vscode/launch.json +0 -0
  14. {calkit_python-0.41.22 → calkit_python-0.41.23}/.vscode/tasks.json +0 -0
  15. {calkit_python-0.41.22 → calkit_python-0.41.23}/AGENTS.md +0 -0
  16. {calkit_python-0.41.22 → calkit_python-0.41.23}/CITATION.cff +0 -0
  17. {calkit_python-0.41.22 → calkit_python-0.41.23}/CODE_OF_CONDUCT.md +0 -0
  18. {calkit_python-0.41.22 → calkit_python-0.41.23}/CONTRIBUTING.md +0 -0
  19. {calkit_python-0.41.22 → calkit_python-0.41.23}/LICENSE +0 -0
  20. {calkit_python-0.41.22 → calkit_python-0.41.23}/Makefile +0 -0
  21. {calkit_python-0.41.22 → calkit_python-0.41.23}/README.md +0 -0
  22. {calkit_python-0.41.22 → calkit_python-0.41.23}/agent-plugin/.claude-plugin/plugin.json +0 -0
  23. {calkit_python-0.41.22 → calkit_python-0.41.23}/agent-plugin/skills/add-pipeline-stage/SKILL.md +0 -0
  24. {calkit_python-0.41.22 → calkit_python-0.41.23}/agent-plugin/skills/conventions/SKILL.md +0 -0
  25. {calkit_python-0.41.22 → calkit_python-0.41.23}/agent-plugin/skills/create-pipeline/SKILL.md +0 -0
  26. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/__init__.py +0 -0
  27. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/__main__.py +0 -0
  28. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/calc.py +0 -0
  29. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/check.py +0 -0
  30. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/cli/__init__.py +0 -0
  31. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/cli/check.py +0 -0
  32. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/cli/cloud.py +0 -0
  33. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/cli/config.py +0 -0
  34. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/cli/core.py +0 -0
  35. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/cli/delete.py +0 -0
  36. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/cli/describe.py +0 -0
  37. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/cli/dev.py +0 -0
  38. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/cli/import_.py +0 -0
  39. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/cli/latex.py +0 -0
  40. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/cli/list.py +0 -0
  41. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/cli/main/__init__.py +0 -0
  42. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/cli/main/core.py +0 -0
  43. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/cli/main/xr.py +0 -0
  44. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/cli/new.py +0 -0
  45. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/cli/notebooks.py +0 -0
  46. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/cli/office.py +0 -0
  47. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/cli/scheduler.py +0 -0
  48. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/cli/update.py +0 -0
  49. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/cloud.py +0 -0
  50. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/conda.py +0 -0
  51. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/config.py +0 -0
  52. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/core.py +0 -0
  53. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/datasets.py +0 -0
  54. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/dependencies.py +0 -0
  55. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/detect.py +0 -0
  56. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/docker.py +0 -0
  57. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/dvc/__init__.py +0 -0
  58. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/dvc/core.py +0 -0
  59. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/dvc/zip.py +0 -0
  60. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/environments.py +0 -0
  61. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/fs.py +0 -0
  62. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/git.py +0 -0
  63. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/github.py +0 -0
  64. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/gui.py +0 -0
  65. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/install.py +0 -0
  66. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/invenio.py +0 -0
  67. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/julia.py +0 -0
  68. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/jupyter.py +0 -0
  69. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/jupyterlab/__init__.py +0 -0
  70. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/jupyterlab/routes.py +0 -0
  71. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/labextension/package.json +0 -0
  72. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/labextension/schemas/calkit/package.json.orig +0 -0
  73. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/labextension/schemas/calkit/plugin.json +0 -0
  74. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/labextension/static/502.9a2c5772a15466e923ef.js +0 -0
  75. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/labextension/static/695.2c41003a452d43d2b358.js +0 -0
  76. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/labextension/static/867.a42a046aa5108f54f8fb.js +0 -0
  77. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/labextension/static/909.e3f9cc3408834a7fdcc3.js +0 -0
  78. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/labextension/static/946.050af2abf7845cfbdbd2.js +0 -0
  79. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/labextension/static/946.050af2abf7845cfbdbd2.js.LICENSE.txt +0 -0
  80. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/labextension/static/b2f1c3efe70cb539d121.png +0 -0
  81. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/labextension/static/remoteEntry.ac9035764d5b2adbb542.js +0 -0
  82. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/labextension/static/style.js +0 -0
  83. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/labextension/static/third-party-licenses.json +0 -0
  84. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/licenses.py +0 -0
  85. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/magics.py +0 -0
  86. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/matlab.py +0 -0
  87. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/models/__init__.py +0 -0
  88. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/models/core.py +0 -0
  89. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/models/io.py +0 -0
  90. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/models/iteration.py +0 -0
  91. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/models/pipeline.py +0 -0
  92. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/notebooks.py +0 -0
  93. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/office.py +0 -0
  94. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/ops.py +0 -0
  95. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/pipeline.py +0 -0
  96. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/releases.py +0 -0
  97. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/server.py +0 -0
  98. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/templates/__init__.py +0 -0
  99. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/templates/core.py +0 -0
  100. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/templates/latex/__init__.py +0 -0
  101. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/templates/latex/article/paper.tex +0 -0
  102. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/templates/latex/core.py +0 -0
  103. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/templates/latex/jfm/jfm.bst +0 -0
  104. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/templates/latex/jfm/jfm.cls +0 -0
  105. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/templates/latex/jfm/lineno-FLM.sty +0 -0
  106. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/templates/latex/jfm/paper.tex +0 -0
  107. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/templates/latex/jfm/upmath.sty +0 -0
  108. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/__init__.py +0 -0
  109. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/cli/__init__.py +0 -0
  110. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/cli/main/__init__.py +0 -0
  111. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/cli/main/test_core.py +0 -0
  112. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/cli/main/test_lock.py +0 -0
  113. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/cli/main/test_subprojects.py +0 -0
  114. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/cli/main/test_xr.py +0 -0
  115. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/cli/test_check.py +0 -0
  116. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/cli/test_cloud.py +0 -0
  117. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/cli/test_config.py +0 -0
  118. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/cli/test_delete.py +0 -0
  119. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/cli/test_import.py +0 -0
  120. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/cli/test_latex.py +0 -0
  121. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/cli/test_list.py +0 -0
  122. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/cli/test_new.py +0 -0
  123. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/cli/test_notebooks.py +0 -0
  124. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/cli/test_scheduler.py +0 -0
  125. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/cli/test_update.py +0 -0
  126. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/dvc/__init__.py +0 -0
  127. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/dvc/test_core.py +0 -0
  128. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/dvc/test_zip.py +0 -0
  129. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/jupyterlab/__init__.py +0 -0
  130. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/jupyterlab/conftest.py +0 -0
  131. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/jupyterlab/test_routes.py +0 -0
  132. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/models/__init__.py +0 -0
  133. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/models/test_core.py +0 -0
  134. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/models/test_iteration.py +0 -0
  135. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/models/test_pipeline.py +0 -0
  136. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/test_calc.py +0 -0
  137. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/test_check.py +0 -0
  138. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/test_cloud.py +0 -0
  139. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/test_conda.py +0 -0
  140. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/test_core.py +0 -0
  141. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/test_dependencies.py +0 -0
  142. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/test_detect.py +0 -0
  143. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/test_docker.py +0 -0
  144. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/test_environments.py +0 -0
  145. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/test_fs.py +0 -0
  146. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/test_git.py +0 -0
  147. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/test_install.py +0 -0
  148. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/test_invenio.py +0 -0
  149. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/test_julia.py +0 -0
  150. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/test_jupyter.py +0 -0
  151. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/test_licenses.py +0 -0
  152. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/test_magics.py +0 -0
  153. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/test_matlab.py +0 -0
  154. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/test_notebooks.py +0 -0
  155. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/test_pipeline.py +0 -0
  156. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/test_releases.py +0 -0
  157. {calkit_python-0.41.22 → calkit_python-0.41.23}/calkit/tests/test_templates.py +0 -0
  158. {calkit_python-0.41.22 → calkit_python-0.41.23}/docs/CNAME +0 -0
  159. {calkit_python-0.41.22 → calkit_python-0.41.23}/docs/acknowledgements.md +0 -0
  160. {calkit_python-0.41.22 → calkit_python-0.41.23}/docs/ai-tools.md +0 -0
  161. {calkit_python-0.41.22 → calkit_python-0.41.23}/docs/apps.md +0 -0
  162. {calkit_python-0.41.22 → calkit_python-0.41.23}/docs/calculations.md +0 -0
  163. {calkit_python-0.41.22 → calkit_python-0.41.23}/docs/calkit-yaml.md +0 -0
  164. {calkit_python-0.41.22 → calkit_python-0.41.23}/docs/cli-reference.md +0 -0
  165. {calkit_python-0.41.22 → calkit_python-0.41.23}/docs/cloud-integration.md +0 -0
  166. {calkit_python-0.41.22 → calkit_python-0.41.23}/docs/datasets.md +0 -0
  167. {calkit_python-0.41.22 → calkit_python-0.41.23}/docs/dependencies.md +0 -0
  168. {calkit_python-0.41.22 → calkit_python-0.41.23}/docs/environments.md +0 -0
  169. {calkit_python-0.41.22 → calkit_python-0.41.23}/docs/examples.md +0 -0
  170. {calkit_python-0.41.22 → calkit_python-0.41.23}/docs/governance.md +0 -0
  171. {calkit_python-0.41.22 → calkit_python-0.41.23}/docs/help.md +0 -0
  172. {calkit_python-0.41.22 → calkit_python-0.41.23}/docs/hpc.md +0 -0
  173. {calkit_python-0.41.22 → calkit_python-0.41.23}/docs/img/c-to-the-k-white.svg +0 -0
  174. {calkit_python-0.41.22 → calkit_python-0.41.23}/docs/img/calkit-fragmentation-compendium.png +0 -0
  175. {calkit_python-0.41.22 → calkit_python-0.41.23}/docs/img/calkit-no-bg.png +0 -0
  176. {calkit_python-0.41.22 → calkit_python-0.41.23}/docs/img/caltech.png +0 -0
  177. {calkit_python-0.41.22 → calkit_python-0.41.23}/docs/img/connect-zenodo.png +0 -0
  178. {calkit_python-0.41.22 → calkit_python-0.41.23}/docs/img/jupyterlab/all-green.png +0 -0
  179. {calkit_python-0.41.22 → calkit_python-0.41.23}/docs/img/jupyterlab/collect-data-stale.png +0 -0
  180. {calkit_python-0.41.22 → calkit_python-0.41.23}/docs/img/jupyterlab/new-env.png +0 -0
  181. {calkit_python-0.41.22 → calkit_python-0.41.23}/docs/img/jupyterlab/new-notebook.png +0 -0
  182. {calkit_python-0.41.22 → calkit_python-0.41.23}/docs/img/jupyterlab/pipeline-badge.png +0 -0
  183. {calkit_python-0.41.22 → calkit_python-0.41.23}/docs/img/jupyterlab-params.png +0 -0
  184. {calkit_python-0.41.22 → calkit_python-0.41.23}/docs/img/pipeline.png +0 -0
  185. {calkit_python-0.41.22 → calkit_python-0.41.23}/docs/img/plos-osi-code-2024-03.png +0 -0
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4
4
  Summary: Reproducibility simplified.
5
5
  Project-URL: Homepage, https://calkit.org
6
6
  Project-URL: Issues, https://github.com/calkit/calkit/issues
@@ -16,6 +16,20 @@ from calkit.cli import AliasGroup, raise_error, warn
16
16
 
17
17
  overleaf_app = typer.Typer(cls=AliasGroup, no_args_is_help=True)
18
18
 
19
+ # Shown when a pull from Overleaf fails, most commonly due to an invalid or
20
+ # expired token. Calkit authenticates only with the token in its config, but a
21
+ # stale token cached by the OS credential manager from an earlier version can
22
+ # still interfere, so we point users there as a fallback.
23
+ PULL_FAILED_MESSAGE = (
24
+ "Failed to pull from Overleaf; "
25
+ "check that your Overleaf token is valid\n"
26
+ "Run 'calkit config get overleaf_token' and ensure that it matches one in "
27
+ "your Overleaf account settings (https://overleaf.com/user/settings).\n"
28
+ "If it looks correct but pulling still fails, delete any saved "
29
+ "'git.overleaf.com' credential from your OS credential manager (Windows "
30
+ "Credential Manager, macOS Keychain, or your Linux keyring) and try again."
31
+ )
32
+
19
33
 
20
34
  def _extract_title_from_tex(tex_file_path: str) -> str | None:
21
35
  """Extract the title from a LaTeX file."""
@@ -169,8 +183,6 @@ def import_publication(
169
183
  ] = False,
170
184
  ):
171
185
  """Import a publication from an Overleaf project."""
172
- import git
173
-
174
186
  from calkit.cli.main import ignore as git_ignore
175
187
  from calkit.cli.new import new_latex_stage
176
188
 
@@ -202,16 +214,13 @@ def import_publication(
202
214
  overleaf_dir = os.path.join(".calkit", "overleaf")
203
215
  os.makedirs(overleaf_dir, exist_ok=True)
204
216
  git_ignore(overleaf_dir, no_commit=no_commit)
205
- overleaf_project_dir = os.path.join(overleaf_dir, overleaf_project_id)
206
- git_clone_url = calkit.overleaf.get_git_remote_url(
207
- project_id=overleaf_project_id, token=overleaf_token
208
- )
217
+ overleaf_project_dir = calkit.overleaf.get_project_dir(overleaf_project_id)
209
218
  if os.path.isdir(overleaf_project_dir):
210
219
  warn("This Overleaf project has already been cloned; removing")
211
220
  shutil.rmtree(overleaf_project_dir)
212
221
  # Clone the Overleaf project
213
222
  typer.echo("Cloning Overleaf project")
214
- git.Repo.clone_from(git_clone_url, overleaf_project_dir)
223
+ calkit.overleaf.clone(overleaf_project_id, overleaf_token)
215
224
  # Detect target path if not specified
216
225
  if target_path is None:
217
226
  ol_contents = os.listdir(
@@ -428,8 +437,6 @@ def sync(
428
437
  ] = False,
429
438
  ):
430
439
  """Sync folders with Overleaf."""
431
- import git
432
-
433
440
  # TODO: We should probably ensure the pipeline isn't stale
434
441
  # Read all synced folders, fixing legacy schema if applicable
435
442
  overleaf_info = calkit.overleaf.get_sync_info(fix_legacy=True)
@@ -504,32 +511,15 @@ def sync(
504
511
  "or use --auto-commit/-a to automatically commit them."
505
512
  )
506
513
  # Ensure we've cloned the Overleaf project
507
- overleaf_project_dir = os.path.join(
508
- ".calkit", "overleaf", overleaf_project_id
514
+ overleaf_repo = calkit.overleaf.get_repo(
515
+ overleaf_project_id, str(overleaf_token)
509
516
  )
510
- overleaf_remote_url = calkit.overleaf.get_git_remote_url(
511
- project_id=overleaf_project_id, token=str(overleaf_token)
512
- )
513
- if not os.path.isdir(overleaf_project_dir):
514
- overleaf_repo = git.Repo.clone_from(
515
- overleaf_remote_url, to_path=overleaf_project_dir
516
- )
517
- else:
518
- overleaf_repo = calkit.git.get_repo(overleaf_project_dir)
519
517
  # Pull the latest version in the Overleaf project
520
518
  typer.echo("Pulling the latest version from Overleaf")
521
- # Ensure that our current Overleaf remote URL is correct
522
- overleaf_repo.git.remote("set-url", "origin", overleaf_remote_url)
523
519
  try:
524
520
  overleaf_repo.git.pull()
525
521
  except Exception:
526
- raise_error(
527
- "Failed to pull from Overleaf; "
528
- "check that your Overleaf token is valid\n"
529
- "Run 'calkit config get overleaf_token' and ensure that "
530
- "it matches one in your Overleaf account settings "
531
- "(https://overleaf.com/user/settings)"
532
- )
522
+ raise_error(PULL_FAILED_MESSAGE)
533
523
  if resolve:
534
524
  last_sync_commit = resolving_info["last_overleaf_commit"]
535
525
  else:
@@ -608,8 +598,6 @@ def get_status(
608
598
  ] = None,
609
599
  ):
610
600
  """Check the status of folders synced with Overleaf in a project."""
611
- import git
612
-
613
601
  # Read all synced folders, fixing legacy schema if applicable
614
602
  overleaf_info = calkit.overleaf.get_sync_info(fix_legacy=False)
615
603
  if not overleaf_info:
@@ -642,32 +630,18 @@ def get_status(
642
630
  )
643
631
  wdir = path_in_project
644
632
  # Ensure we've cloned the Overleaf project
645
- overleaf_project_dir = os.path.join(
646
- ".calkit", "overleaf", overleaf_project_id
633
+ overleaf_project_dir = calkit.overleaf.get_project_dir(
634
+ overleaf_project_id
647
635
  )
648
- overleaf_remote_url = calkit.overleaf.get_git_remote_url(
649
- project_id=overleaf_project_id, token=str(overleaf_token)
636
+ overleaf_repo = calkit.overleaf.get_repo(
637
+ overleaf_project_id, str(overleaf_token)
650
638
  )
651
- if not os.path.isdir(overleaf_project_dir):
652
- overleaf_repo = git.Repo.clone_from(
653
- overleaf_remote_url, to_path=overleaf_project_dir
654
- )
655
- else:
656
- overleaf_repo = calkit.git.get_repo(overleaf_project_dir)
657
639
  # Pull the latest version in the Overleaf project
658
640
  typer.echo("Pulling the latest version from Overleaf")
659
- # Ensure that our current Overleaf remote URL is correct
660
- overleaf_repo.git.remote("set-url", "origin", overleaf_remote_url)
661
641
  try:
662
642
  overleaf_repo.git.pull()
663
643
  except Exception:
664
- raise_error(
665
- "Failed to pull from Overleaf; "
666
- "check that your Overleaf token is valid\n"
667
- "Run 'calkit config get overleaf_token' and ensure that "
668
- "it matches one in your Overleaf account settings "
669
- "(https://overleaf.com/user/settings)"
670
- )
644
+ raise_error(PULL_FAILED_MESSAGE)
671
645
  last_sync_commit = sync_data.get("last_sync_commit")
672
646
  if last_sync_commit:
673
647
  commits_since = calkit.overleaf.get_commits_since_last_sync(
@@ -30,6 +30,69 @@ def get_git_remote_url(project_id: str, token: str) -> str:
30
30
  return f"https://git:{token}@git.overleaf.com/{project_id}"
31
31
 
32
32
 
33
+ # Git config options that force authentication to use only the token embedded
34
+ # in the Overleaf remote URL, never a credential saved in the operating
35
+ # system's credential store (macOS Keychain, Windows Credential Manager, etc.).
36
+ # An expired token can linger in that store and shadow a freshly set one, which
37
+ # otherwise makes it impossible to recover a project after a token expires.
38
+ _CREDENTIAL_CLONE_OPTIONS = [
39
+ "-c credential.helper=",
40
+ "-c credential.interactive=false",
41
+ ]
42
+
43
+
44
+ def _disable_credential_store(repo: git.Repo) -> None:
45
+ """Configure a cloned Overleaf repo so git authenticates only with the
46
+ token embedded in its remote URL, ignoring the OS credential store.
47
+
48
+ Setting an empty ``credential.helper`` in the repo's local config resets
49
+ the list of helpers inherited from the system and global config, so no
50
+ stale token can be read from (or written to) the credential store.
51
+ """
52
+ repo.git.config("credential.helper", "")
53
+ repo.git.config("credential.interactive", "false")
54
+
55
+
56
+ def get_project_dir(project_id: str) -> str:
57
+ """Return the local directory into which an Overleaf project is cloned,
58
+ relative to the Calkit project working directory.
59
+ """
60
+ return os.path.join(".calkit", "overleaf", project_id)
61
+
62
+
63
+ def clone(project_id: str, token: str) -> git.Repo:
64
+ """Clone an Overleaf project, authenticating only with ``token``."""
65
+ repo = git.Repo.clone_from(
66
+ get_git_remote_url(project_id=project_id, token=token),
67
+ get_project_dir(project_id),
68
+ multi_options=_CREDENTIAL_CLONE_OPTIONS,
69
+ allow_unsafe_options=True,
70
+ )
71
+ _disable_credential_store(repo)
72
+ return repo
73
+
74
+
75
+ def get_repo(project_id: str, token: str) -> git.Repo:
76
+ """Return the Overleaf repo for ``project_id``, cloning it if it does not
77
+ yet exist.
78
+
79
+ When the repo already exists, its remote URL is refreshed so a freshly set
80
+ token takes effect, and credential handling is reset so a stale token from
81
+ the OS credential store is never used.
82
+ """
83
+ dest = get_project_dir(project_id)
84
+ if not os.path.isdir(dest):
85
+ return clone(project_id, token)
86
+ repo = calkit.git.get_repo(dest)
87
+ repo.git.remote(
88
+ "set-url",
89
+ "origin",
90
+ get_git_remote_url(project_id=project_id, token=token),
91
+ )
92
+ _disable_credential_store(repo)
93
+ return repo
94
+
95
+
33
96
  def project_id_to_url(project_id: str) -> str:
34
97
  return f"https://www.overleaf.com/project/{project_id}"
35
98
 
@@ -409,3 +409,35 @@ def test_overleaf_sync_trailing_slash_or_space(tmp_dir):
409
409
  text=True,
410
410
  )
411
411
  assert res2.returncode == 0, f"Trailing space sync failed: {res2.stderr}"
412
+
413
+
414
+ def test_get_repo_disables_credential_store(tmp_dir):
415
+ # Set up a repo to act as the Overleaf remote (in the test env the remote
416
+ # URL is a local directory)
417
+ pid = str(uuid.uuid4())
418
+ _make_temp_overleaf_project(pid)
419
+ dest = calkit.overleaf.get_project_dir(pid)
420
+ # A fresh clone should reset the credential helper for that repo so only
421
+ # the token in its remote URL is used, never a stale one from the OS
422
+ # credential store
423
+ repo = calkit.overleaf.clone(pid, "sometoken")
424
+ assert os.path.isdir(os.path.join(dest, ".git"))
425
+ assert repo.git.config(["--local", "--get", "credential.helper"]) == ""
426
+ assert (
427
+ repo.git.config(["--local", "--get", "credential.interactive"])
428
+ == "false"
429
+ )
430
+ # Opening an already-cloned project should refresh the remote URL so an
431
+ # updated token takes effect, and keep the credential store disabled
432
+ repo2 = calkit.overleaf.get_repo(pid, "newtoken")
433
+ assert repo2.git.remote(
434
+ ["get-url", "origin"]
435
+ ) == calkit.overleaf.get_git_remote_url(pid, "newtoken")
436
+ assert repo2.git.config(["--local", "--get", "credential.helper"]) == ""
437
+ # A project that has not yet been cloned should be cloned
438
+ pid2 = str(uuid.uuid4())
439
+ _make_temp_overleaf_project(pid2)
440
+ calkit.overleaf.get_repo(pid2, "sometoken")
441
+ assert os.path.isdir(
442
+ os.path.join(calkit.overleaf.get_project_dir(pid2), ".git")
443
+ )
File without changes