phas 0.98.0__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 (300) hide show
  1. phas-0.98.0/.dockerignore +9 -0
  2. phas-0.98.0/.github/workflows/python-publish.yml +38 -0
  3. phas-0.98.0/.gitignore +16 -0
  4. phas-0.98.0/.readthedocs.yaml +28 -0
  5. phas-0.98.0/LICENSE.txt +674 -0
  6. phas-0.98.0/PKG-INFO +34 -0
  7. phas-0.98.0/README.md +2 -0
  8. phas-0.98.0/docker/histo_proc_base/Dockerfile +38 -0
  9. phas-0.98.0/docker/histo_proc_simple/Dockerfile +5 -0
  10. phas-0.98.0/docker/histo_proc_simple/README.md +12 -0
  11. phas-0.98.0/docker/histo_proc_simple/os_thumb.py +9 -0
  12. phas-0.98.0/docker/histo_proc_simple/prep_bucket.sh +209 -0
  13. phas-0.98.0/docker/phas/Dockerfile +52 -0
  14. phas-0.98.0/docker/phas/env.sh +8 -0
  15. phas-0.98.0/docker/phas/nginx.conf +66 -0
  16. phas-0.98.0/docker/phas/phas_nginx.conf +16 -0
  17. phas-0.98.0/docker/phas/phas_uwsgi.ini +48 -0
  18. phas-0.98.0/docker/phas/slide_server.sh +2 -0
  19. phas-0.98.0/docker/phas/supervisord.conf +22 -0
  20. phas-0.98.0/docs/Makefile +19 -0
  21. phas-0.98.0/docs/source/conf.py +182 -0
  22. phas-0.98.0/docs/source/index.rst +28 -0
  23. phas-0.98.0/docs/source/notes_tval.rst +30 -0
  24. phas-0.98.0/docs/source/org_data.rst +193 -0
  25. phas-0.98.0/docs/source/org_data_local.rst +195 -0
  26. phas-0.98.0/docs/source/production.rst +155 -0
  27. phas-0.98.0/docs/source/quick_start.rst +306 -0
  28. phas-0.98.0/docs/source/quick_start_docker.rst +187 -0
  29. phas-0.98.0/docs/source/requirements.txt +1 -0
  30. phas-0.98.0/docs/source/upgrading.rst +35 -0
  31. phas-0.98.0/libs/os_affine/src/CMakeLists.txt +28 -0
  32. phas-0.98.0/libs/os_affine/src/FastLinearInterpolator.h +900 -0
  33. phas-0.98.0/libs/os_affine/src/os_affine.cxx +202 -0
  34. phas-0.98.0/libs/os_affine/src/os_affine_api.h +207 -0
  35. phas-0.98.0/libs/os_affine/src/os_affine_impl.cxx +62 -0
  36. phas-0.98.0/libs/os_affine/src/setup.py +12 -0
  37. phas-0.98.0/phas/__init__.py +128 -0
  38. phas-0.98.0/phas/admin.py +278 -0
  39. phas-0.98.0/phas/auth.py +593 -0
  40. phas-0.98.0/phas/common.py +37 -0
  41. phas-0.98.0/phas/db.py +39 -0
  42. phas-0.98.0/phas/default_settings.py +7 -0
  43. phas-0.98.0/phas/delegate.py +141 -0
  44. phas-0.98.0/phas/dltrain.py +1625 -0
  45. phas-0.98.0/phas/dzi.py +706 -0
  46. phas-0.98.0/phas/gcs_handler.py +510 -0
  47. phas-0.98.0/phas/project_cli.py +1327 -0
  48. phas-0.98.0/phas/project_ref.py +395 -0
  49. phas-0.98.0/phas/requirements.txt +17 -0
  50. phas-0.98.0/phas/schema.sql +225 -0
  51. phas-0.98.0/phas/schema_dltrain.sql +102 -0
  52. phas-0.98.0/phas/schema_views.sql +34 -0
  53. phas-0.98.0/phas/slide.py +1792 -0
  54. phas-0.98.0/phas/slideref.py +170 -0
  55. phas-0.98.0/phas/sqlmod/add_access_level.sql +10 -0
  56. phas-0.98.0/phas/sqlmod/add_api_keys.sql +7 -0
  57. phas-0.98.0/phas/sqlmod/add_projects.sql +100 -0
  58. phas-0.98.0/phas/sqlmod/add_sample_and_sroi_views.sql +34 -0
  59. phas-0.98.0/phas/sqlmod/add_sampling_rois.sql +18 -0
  60. phas-0.98.0/phas/sqlmod/add_specimen_anon.sql +74 -0
  61. phas-0.98.0/phas/sqlmod/add_tags_and_task_slide_index.sql +21 -0
  62. phas-0.98.0/phas/sqlmod/add_user_task_slide_prefs.sql +11 -0
  63. phas-0.98.0/phas/static/DataTables/datatables.min.css +24 -0
  64. phas-0.98.0/phas/static/DataTables/datatables.min.js +42 -0
  65. phas-0.98.0/phas/static/colormaps.js +257 -0
  66. phas-0.98.0/phas/static/ellipsis_button.css +31 -0
  67. phas-0.98.0/phas/static/ellipsis_button.js +5 -0
  68. phas-0.98.0/phas/static/fabric/fabric.adapted.js +27108 -0
  69. phas-0.98.0/phas/static/favicon.ico +0 -0
  70. phas-0.98.0/phas/static/icons/dummy_patch.png +0 -0
  71. phas-0.98.0/phas/static/icons/microscope_icon.png +0 -0
  72. phas-0.98.0/phas/static/icons/microscope_icon_40.png +0 -0
  73. phas-0.98.0/phas/static/jquery-3.6.4.min.js +2 -0
  74. phas-0.98.0/phas/static/jquery-contextMenu/font/context-menu-icons.eot +0 -0
  75. phas-0.98.0/phas/static/jquery-contextMenu/font/context-menu-icons.ttf +0 -0
  76. phas-0.98.0/phas/static/jquery-contextMenu/font/context-menu-icons.woff +0 -0
  77. phas-0.98.0/phas/static/jquery-contextMenu/font/context-menu-icons.woff2 +0 -0
  78. phas-0.98.0/phas/static/jquery-contextMenu/jquery.contextMenu.min.css +16 -0
  79. phas-0.98.0/phas/static/jquery-contextMenu/jquery.contextMenu.min.css.map +1 -0
  80. phas-0.98.0/phas/static/jquery-contextMenu/jquery.contextMenu.min.js +2 -0
  81. phas-0.98.0/phas/static/jquery-contextMenu/jquery.contextMenu.min.js.map +1 -0
  82. phas-0.98.0/phas/static/jquery-contextMenu/jquery.ui.position.min.js +6 -0
  83. phas-0.98.0/phas/static/jquery-ui/images/ui-icons_444444_256x240.png +0 -0
  84. phas-0.98.0/phas/static/jquery-ui/images/ui-icons_555555_256x240.png +0 -0
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  88. phas-0.98.0/phas/static/jquery-ui/images/ui-icons_ffffff_256x240.png +0 -0
  89. phas-0.98.0/phas/static/jquery-ui/jquery-hex-colorpicker-min.js +1 -0
  90. phas-0.98.0/phas/static/jquery-ui/jquery-hex-colorpicker.css +38 -0
  91. phas-0.98.0/phas/static/jquery-ui/jquery-ui-style.css +1312 -0
  92. phas-0.98.0/phas/static/jquery-ui/jquery-ui.css +1312 -0
  93. phas-0.98.0/phas/static/jquery-ui/jquery-ui.js +18706 -0
  94. phas-0.98.0/phas/static/js.cookie.js +163 -0
  95. phas-0.98.0/phas/static/mousetrap.min.js +11 -0
  96. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/LICENSE.txt +28 -0
  97. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/changelog.txt +501 -0
  98. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/button_grouphover.png +0 -0
  99. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/button_hover.png +0 -0
  100. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/button_pressed.png +0 -0
  101. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/button_rest.png +0 -0
  102. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/flip_grouphover.png +0 -0
  103. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/flip_hover.png +0 -0
  104. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/flip_pressed.png +0 -0
  105. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/flip_rest.png +0 -0
  106. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/fullpage_grouphover.png +0 -0
  107. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/fullpage_hover.png +0 -0
  108. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/fullpage_pressed.png +0 -0
  109. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/fullpage_rest.png +0 -0
  110. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/home_grouphover.png +0 -0
  111. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/home_hover.png +0 -0
  112. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/home_pressed.png +0 -0
  113. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/home_rest.png +0 -0
  114. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/next_grouphover.png +0 -0
  115. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/next_hover.png +0 -0
  116. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/next_pressed.png +0 -0
  117. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/next_rest.png +0 -0
  118. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/previous_grouphover.png +0 -0
  119. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/previous_hover.png +0 -0
  120. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/previous_pressed.png +0 -0
  121. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/previous_rest.png +0 -0
  122. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/rotateleft_grouphover.png +0 -0
  123. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/rotateleft_hover.png +0 -0
  124. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/rotateleft_pressed.png +0 -0
  125. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/rotateleft_rest.png +0 -0
  126. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/rotateright_grouphover.png +0 -0
  127. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/rotateright_hover.png +0 -0
  128. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/rotateright_pressed.png +0 -0
  129. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/rotateright_rest.png +0 -0
  130. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/zoomin_grouphover.png +0 -0
  131. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/zoomin_hover.png +0 -0
  132. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/zoomin_pressed.png +0 -0
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  134. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/zoomout_grouphover.png +0 -0
  135. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/zoomout_hover.png +0 -0
  136. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/zoomout_pressed.png +0 -0
  137. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/images/zoomout_rest.png +0 -0
  138. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/openseadragon.js +22494 -0
  139. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/openseadragon.js.map +1 -0
  140. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/openseadragon.min.js +9 -0
  141. phas-0.98.0/phas/static/openseadragon-bin-2.4.0/openseadragon.min.js.map +1 -0
  142. phas-0.98.0/phas/static/openseadragon-fabricjs-overlay.js +137 -0
  143. phas-0.98.0/phas/static/openseadragon-filtering.js +541 -0
  144. phas-0.98.0/phas/static/openseadragon-paperjs-overlay.js +110 -0
  145. phas-0.98.0/phas/static/openseadragon-scalebar.js +474 -0
  146. phas-0.98.0/phas/static/paper-full.js +17472 -0
  147. phas-0.98.0/phas/static/paper-full.min.js +32 -0
  148. phas-0.98.0/phas/static/pure/HISTORY.md +469 -0
  149. phas-0.98.0/phas/static/pure/LICENSE.md +52 -0
  150. phas-0.98.0/phas/static/pure/README.md +185 -0
  151. phas-0.98.0/phas/static/pure/base-context-min.css +11 -0
  152. phas-0.98.0/phas/static/pure/base-context.css +480 -0
  153. phas-0.98.0/phas/static/pure/base-min.css +11 -0
  154. phas-0.98.0/phas/static/pure/base.css +463 -0
  155. phas-0.98.0/phas/static/pure/bower.json +9 -0
  156. phas-0.98.0/phas/static/pure/buttons-core-min.css +7 -0
  157. phas-0.98.0/phas/static/pure/buttons-core.css +48 -0
  158. phas-0.98.0/phas/static/pure/buttons-min.css +7 -0
  159. phas-0.98.0/phas/static/pure/buttons.css +128 -0
  160. phas-0.98.0/phas/static/pure/forms-min.css +7 -0
  161. phas-0.98.0/phas/static/pure/forms-nr-min.css +7 -0
  162. phas-0.98.0/phas/static/pure/forms-nr.css +318 -0
  163. phas-0.98.0/phas/static/pure/forms.css +383 -0
  164. phas-0.98.0/phas/static/pure/grids-core-min.css +7 -0
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  166. phas-0.98.0/phas/static/pure/grids-min.css +7 -0
  167. phas-0.98.0/phas/static/pure/grids-responsive-min.css +7 -0
  168. phas-0.98.0/phas/static/pure/grids-responsive-old-ie-min.css +7 -0
  169. phas-0.98.0/phas/static/pure/grids-responsive-old-ie.css +7 -0
  170. phas-0.98.0/phas/static/pure/grids-responsive.css +861 -0
  171. phas-0.98.0/phas/static/pure/grids-units-min.css +7 -0
  172. phas-0.98.0/phas/static/pure/grids-units.css +217 -0
  173. phas-0.98.0/phas/static/pure/grids.css +292 -0
  174. phas-0.98.0/phas/static/pure/js/ui.js +46 -0
  175. phas-0.98.0/phas/static/pure/layouts/marketing-old-ie.css +297 -0
  176. phas-0.98.0/phas/static/pure/layouts/marketing.css +287 -0
  177. phas-0.98.0/phas/static/pure/layouts/side-menu-old-ie.css +255 -0
  178. phas-0.98.0/phas/static/pure/layouts/side-menu.css +248 -0
  179. phas-0.98.0/phas/static/pure/menus-core-min.css +7 -0
  180. phas-0.98.0/phas/static/pure/menus-core.css +41 -0
  181. phas-0.98.0/phas/static/pure/menus-dropdown-min.css +7 -0
  182. phas-0.98.0/phas/static/pure/menus-dropdown.css +44 -0
  183. phas-0.98.0/phas/static/pure/menus-horizontal-min.css +7 -0
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  186. phas-0.98.0/phas/static/pure/menus-scrollable-min.css +7 -0
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  188. phas-0.98.0/phas/static/pure/menus-skin-min.css +7 -0
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  196. phas-0.98.0/phas/static/pure/tables.css +81 -0
  197. phas-0.98.0/phas/templates/admin/user_management.html +764 -0
  198. phas-0.98.0/phas/templates/auth/edit_profile.html +38 -0
  199. phas-0.98.0/phas/templates/auth/login.html +25 -0
  200. phas-0.98.0/phas/templates/auth/register.html +67 -0
  201. phas-0.98.0/phas/templates/auth/request_reset.html +20 -0
  202. phas-0.98.0/phas/templates/auth/reset.html +74 -0
  203. phas-0.98.0/phas/templates/base.html +71 -0
  204. phas-0.98.0/phas/templates/dbtrain/label_picker.html +85 -0
  205. phas-0.98.0/phas/templates/dbtrain/label_table.html +5 -0
  206. phas-0.98.0/phas/templates/dbtrain/label_table_bare.html +166 -0
  207. phas-0.98.0/phas/templates/dbtrain/labelset_editor.html +315 -0
  208. phas-0.98.0/phas/templates/dbtrain/sample_table.html +7 -0
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  210. phas-0.98.0/phas/templates/dbtrain/task_sample_listing.html +319 -0
  211. phas-0.98.0/phas/templates/slide/block_detail.html +50 -0
  212. phas-0.98.0/phas/templates/slide/index.html +34 -0
  213. phas-0.98.0/phas/templates/slide/projects_tasks.html +401 -0
  214. phas-0.98.0/phas/templates/slide/slide_view.html +3134 -0
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  217. phas-0.98.0/pyproject.toml +42 -0
  218. phas-0.98.0/samples/config/histoannot_prod_nginx.conf +41 -0
  219. phas-0.98.0/samples/dltrain/bftrain_samples.csv +1689 -0
  220. phas-0.98.0/samples/dltrain/hnl-11-15_train.csv +3197 -0
  221. phas-0.98.0/samples/dltrain/tanglethon2019_results.csv +11523 -0
  222. phas-0.98.0/samples/dltrain/tanglethon2019_slides.txt +733 -0
  223. phas-0.98.0/samples/dltrain/tcount2019_results.csv +2524 -0
  224. phas-0.98.0/samples/dltrain/tcount2019_results_rated.csv +2522 -0
  225. phas-0.98.0/samples/fixmat.py +36 -0
  226. phas-0.98.0/samples/labelsets/bf_bkg_wildcat.json +6 -0
  227. phas-0.98.0/samples/labelsets/bf_labelset.json +5 -0
  228. phas-0.98.0/samples/labelsets/cndr-sampling.json +77 -0
  229. phas-0.98.0/samples/labelsets/cndr-tau.json +102 -0
  230. phas-0.98.0/samples/labelsets/dots-sampling.json +1 -0
  231. phas-0.98.0/samples/labelsets/dots_he_gray_white.json +11 -0
  232. phas-0.98.0/samples/labelsets/empty_labelset.json +3 -0
  233. phas-0.98.0/samples/labelsets/ftld-tau.json +87 -0
  234. phas-0.98.0/samples/labelsets/ftld-tdp.json +76 -0
  235. phas-0.98.0/samples/labelsets/generate_labelset.ipynb +102 -0
  236. phas-0.98.0/samples/labelsets/generic_boxeval.json +12 -0
  237. phas-0.98.0/samples/labelsets/mtl-diag-sampling.json +77 -0
  238. phas-0.98.0/samples/labelsets/mtl_diag.json +18 -0
  239. phas-0.98.0/samples/labelsets/mtl_neuronal_val.json +10 -0
  240. phas-0.98.0/samples/labelsets/mtl_sadhana_hotspots.json +3 -0
  241. phas-0.98.0/samples/labelsets/mtl_stereology.json +8 -0
  242. phas-0.98.0/samples/labelsets/mtl_threads_validation.json +9 -0
  243. phas-0.98.0/samples/labelsets/tanglethon.json +18 -0
  244. phas-0.98.0/samples/labelsets/tangleval.json +15 -0
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  257. phas-0.98.0/samples/tasks/annot_neuronal_val.json +9 -0
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  273. phas-0.98.0/samples/tasks/ftld-tau-valprep.json +9 -0
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  275. phas-0.98.0/samples/tasks/ftld-tdp-train.json +14 -0
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  277. phas-0.98.0/samples/tasks/hsg/annot_allen.json +6 -0
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  281. phas-0.98.0/samples/tasks/irwin-R13-valid.json +16 -0
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  285. phas-0.98.0/samples/tasks/local_annot.json +9 -0
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  287. phas-0.98.0/samples/tasks/mtl_browse.json +6 -0
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  289. phas-0.98.0/samples/tasks/mtl_diag_sampling.json +10 -0
  290. phas-0.98.0/samples/tasks/mtl_neuronal_val.json +14 -0
  291. phas-0.98.0/samples/tasks/mtl_nissl_stereology.json +15 -0
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  293. phas-0.98.0/samples/tasks/mtl_sadhana_hotspots.json +11 -0
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+ # This workflow will upload a Python Package using Twine when a release is created
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+ # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
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+
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+ # This workflow uses actions that are not certified by GitHub.
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+ # They are provided by a third-party and are governed by
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+ # separate terms of service, privacy policy, and support
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+ # documentation.
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+ name: Upload Python Package
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+ types: [published]
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+ jobs:
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+ deploy:
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+ runs-on: ubuntu-latest
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+ steps:
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+ - uses: actions/checkout@v4
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+ - name: Set up Python
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+ uses: actions/setup-python@v3
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+ with:
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+ python-version: '3.x'
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+ - name: Install dependencies
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+ run: |
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+ python -m pip install --upgrade pip
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+ pip install build
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+ - name: Build package
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+ run: python -m build
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+ - name: Publish package
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+ uses: pypa/gh-action-pypi-publish@release/v1
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+ *~
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+ # Read the Docs configuration file for Sphinx projects
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+ # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
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+
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+ # Required
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+ version: 2
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+
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+ # Set the OS, Python version and other tools you might need
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+ build:
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+ os: ubuntu-22.04
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+ tools:
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+ python: "3.12"
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+ # Build documentation in the "docs/" directory with Sphinx
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+ sphinx:
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+ configuration: docs/source/conf.py
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+ # Optionally build your docs in additional formats such as PDF and ePub
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+ # formats:
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+ # - pdf
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+ # - epub
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+ # Optional but recommended, declare the Python requirements required
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+ # to build your documentation
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+ # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
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+ python:
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+ install:
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+ - requirements: docs/source/requirements.txt
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