easydiffraction 0.17.0__tar.gz โ†’ 0.18.0__tar.gz

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Files changed (1119) hide show
  1. easydiffraction-0.18.0/.codecov.yml +31 -0
  2. easydiffraction-0.18.0/.codefactorignore +15 -0
  3. easydiffraction-0.18.0/.copier-answers.yml +26 -0
  4. easydiffraction-0.18.0/.github/workflows/coverage.yml +70 -0
  5. easydiffraction-0.18.0/.github/workflows/docs.yml +194 -0
  6. easydiffraction-0.18.0/.github/workflows/tutorial-tests.yml +64 -0
  7. easydiffraction-0.18.0/.gitignore +61 -0
  8. easydiffraction-0.18.0/.prettierignore +41 -0
  9. easydiffraction-0.18.0/PKG-INFO +134 -0
  10. easydiffraction-0.18.0/THIRD_PARTY_LICENSES.md +25 -0
  11. easydiffraction-0.18.0/docs/dev/adrs/accepted/analysis-cif-fit-state.md +286 -0
  12. easydiffraction-0.18.0/docs/dev/adrs/accepted/category-owner-sections.md +208 -0
  13. easydiffraction-0.18.0/docs/dev/adrs/accepted/crysview-structure-visualization/crysview-threejs-demo.html +855 -0
  14. easydiffraction-0.18.0/docs/dev/adrs/accepted/crysview-structure-visualization.md +742 -0
  15. easydiffraction-0.18.0/docs/dev/adrs/accepted/display-ux.md +186 -0
  16. easydiffraction-0.18.0/docs/dev/adrs/accepted/fit-mode-categories.md +803 -0
  17. easydiffraction-0.18.0/docs/dev/adrs/accepted/fit-results-display-naming.md +336 -0
  18. easydiffraction-0.18.0/docs/dev/adrs/accepted/help-discoverability.md +65 -0
  19. easydiffraction-0.18.0/docs/dev/adrs/accepted/iucr-cif-tag-alignment.md +1164 -0
  20. easydiffraction-0.18.0/docs/dev/adrs/accepted/minimizer-category-consolidation.md +496 -0
  21. easydiffraction-0.18.0/docs/dev/adrs/accepted/minimizer-input-output-split.md +433 -0
  22. easydiffraction-0.18.0/docs/dev/adrs/accepted/pattern-display-unification.md +92 -0
  23. easydiffraction-0.18.0/docs/dev/adrs/accepted/plotting-docs-performance.md +466 -0
  24. easydiffraction-0.18.0/docs/dev/adrs/accepted/project-facade-and-persistence.md +104 -0
  25. easydiffraction-0.18.0/docs/dev/adrs/accepted/project-summary-rendering.md +2162 -0
  26. easydiffraction-0.18.0/docs/dev/adrs/accepted/python-cif-category-correspondence.md +382 -0
  27. easydiffraction-0.18.0/docs/dev/adrs/accepted/runtime-fit-results.md +43 -0
  28. easydiffraction-0.18.0/docs/dev/adrs/accepted/selector-families.md +57 -0
  29. easydiffraction-0.18.0/docs/dev/adrs/accepted/space-group-database/space_groups_overrides.yaml +11 -0
  30. easydiffraction-0.18.0/docs/dev/adrs/accepted/space-group-database.md +576 -0
  31. easydiffraction-0.18.0/docs/dev/adrs/accepted/switchable-category-api.md +65 -0
  32. easydiffraction-0.18.0/docs/dev/adrs/accepted/switchable-category-owned-selectors.md +1055 -0
  33. easydiffraction-0.18.0/docs/dev/adrs/accepted/undo-fit.md +320 -0
  34. easydiffraction-0.18.0/docs/dev/adrs/accepted/value-selector-discovery.md +223 -0
  35. easydiffraction-0.18.0/docs/dev/adrs/accepted/wyckoff-letter-detection.md +742 -0
  36. easydiffraction-0.18.0/docs/dev/adrs/index.md +60 -0
  37. easydiffraction-0.18.0/docs/dev/adrs/suggestions/background-auto-estimate.md +532 -0
  38. easydiffraction-0.18.0/docs/dev/adrs/suggestions/cif-numeric-precision.md +129 -0
  39. easydiffraction-0.18.0/docs/dev/adrs/suggestions/documentation-ci-build.md +189 -0
  40. easydiffraction-0.18.0/docs/dev/adrs/suggestions/parameter-posterior-summary.md +345 -0
  41. easydiffraction-0.18.0/docs/dev/benchmarking/20260519-103251_darwin-arm64_py314_tutorial-benchmarks.csv +24 -0
  42. easydiffraction-0.18.0/docs/dev/benchmarking/20260519-103500_darwin-arm64_py314_tutorial-benchmarks.csv +24 -0
  43. easydiffraction-0.18.0/docs/dev/benchmarking/20260519-121524_darwin-arm64_py314_tutorial-benchmarks.csv +24 -0
  44. easydiffraction-0.18.0/docs/dev/benchmarking/20260525-231754_darwin-arm64_py314_tutorial-benchmarks.csv +26 -0
  45. easydiffraction-0.18.0/docs/dev/benchmarking/20260526-000646_darwin-arm64_py314_tutorial-benchmarks.csv +26 -0
  46. easydiffraction-0.18.0/docs/dev/benchmarking/20260531-230149_darwin-arm64_py314_tutorial-benchmarks.csv +26 -0
  47. easydiffraction-0.18.0/docs/dev/issues/closed.md +217 -0
  48. easydiffraction-0.18.0/docs/dev/issues/open.md +1982 -0
  49. easydiffraction-0.18.0/docs/dev/package-structure/full.md +710 -0
  50. easydiffraction-0.18.0/docs/dev/package-structure/short.md +357 -0
  51. easydiffraction-0.18.0/docs/dev/plans/background-auto-estimate.md +276 -0
  52. easydiffraction-0.18.0/docs/dev/plans/pattern-display-unification.md +151 -0
  53. easydiffraction-0.18.0/docs/dev/plans/plotting-docs-performance.md +370 -0
  54. easydiffraction-0.18.0/docs/dev/plans/python-cif-category-correspondence.md +104 -0
  55. easydiffraction-0.18.0/docs/dev/plans/space-group-database.md +524 -0
  56. easydiffraction-0.18.0/docs/dev/plans/wyckoff-letter-detection.md +556 -0
  57. easydiffraction-0.18.0/docs/docs/api-reference/index.md +26 -0
  58. easydiffraction-0.18.0/docs/docs/api-reference/report.md +1 -0
  59. easydiffraction-0.18.0/docs/docs/assets/javascripts/ed-figures.js +401 -0
  60. easydiffraction-0.18.0/docs/docs/assets/javascripts/extra.js +240 -0
  61. easydiffraction-0.18.0/docs/docs/assets/javascripts/vendor/plotly/LICENSES.md +13 -0
  62. easydiffraction-0.18.0/docs/docs/assets/javascripts/vendor/plotly/plotly-cartesian.min.js +146 -0
  63. easydiffraction-0.18.0/docs/docs/assets/stylesheets/extra.css +511 -0
  64. easydiffraction-0.18.0/docs/docs/cli/index.md +184 -0
  65. easydiffraction-0.18.0/docs/docs/index.md +27 -0
  66. easydiffraction-0.18.0/docs/docs/quick-reference/index.md +440 -0
  67. easydiffraction-0.18.0/docs/docs/tutorials/ed-1.ipynb +320 -0
  68. easydiffraction-0.18.0/docs/docs/tutorials/ed-1.py +123 -0
  69. easydiffraction-0.18.0/docs/docs/tutorials/ed-10.ipynb +293 -0
  70. easydiffraction-0.18.0/docs/docs/tutorials/ed-10.py +109 -0
  71. easydiffraction-0.18.0/docs/docs/tutorials/ed-11.ipynb +323 -0
  72. easydiffraction-0.18.0/docs/docs/tutorials/ed-11.py +120 -0
  73. easydiffraction-0.18.0/docs/docs/tutorials/ed-12.ipynb +363 -0
  74. easydiffraction-0.18.0/docs/docs/tutorials/ed-12.py +139 -0
  75. easydiffraction-0.18.0/docs/docs/tutorials/ed-13.ipynb +2698 -0
  76. easydiffraction-0.18.0/docs/docs/tutorials/ed-13.py +1522 -0
  77. easydiffraction-0.18.0/docs/docs/tutorials/ed-14.ipynb +550 -0
  78. easydiffraction-0.18.0/docs/docs/tutorials/ed-14.py +203 -0
  79. easydiffraction-0.18.0/docs/docs/tutorials/ed-15.ipynb +457 -0
  80. easydiffraction-0.18.0/docs/docs/tutorials/ed-15.py +148 -0
  81. easydiffraction-0.18.0/docs/docs/tutorials/ed-16.ipynb +650 -0
  82. easydiffraction-0.18.0/docs/docs/tutorials/ed-16.py +262 -0
  83. easydiffraction-0.18.0/docs/docs/tutorials/ed-17.ipynb +883 -0
  84. easydiffraction-0.18.0/docs/docs/tutorials/ed-17.py +405 -0
  85. easydiffraction-0.18.0/docs/docs/tutorials/ed-18.ipynb +213 -0
  86. easydiffraction-0.18.0/docs/docs/tutorials/ed-18.py +67 -0
  87. easydiffraction-0.18.0/docs/docs/tutorials/ed-2.ipynb +565 -0
  88. easydiffraction-0.18.0/docs/docs/tutorials/ed-2.py +237 -0
  89. easydiffraction-0.18.0/docs/docs/tutorials/ed-20.ipynb +833 -0
  90. easydiffraction-0.18.0/docs/docs/tutorials/ed-20.py +386 -0
  91. easydiffraction-0.18.0/docs/docs/tutorials/ed-21.ipynb +783 -0
  92. easydiffraction-0.18.0/docs/docs/tutorials/ed-21.py +364 -0
  93. easydiffraction-0.18.0/docs/docs/tutorials/ed-22.ipynb +635 -0
  94. easydiffraction-0.18.0/docs/docs/tutorials/ed-22.py +278 -0
  95. easydiffraction-0.18.0/docs/docs/tutorials/ed-23.ipynb +290 -0
  96. easydiffraction-0.18.0/docs/docs/tutorials/ed-23.py +110 -0
  97. easydiffraction-0.18.0/docs/docs/tutorials/ed-24.ipynb +277 -0
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  99. easydiffraction-0.18.0/docs/docs/tutorials/ed-25.ipynb +769 -0
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  101. easydiffraction-0.18.0/docs/docs/tutorials/ed-26.ipynb +376 -0
  102. easydiffraction-0.18.0/docs/docs/tutorials/ed-26.py +151 -0
  103. easydiffraction-0.18.0/docs/docs/tutorials/ed-3.ipynb +1730 -0
  104. easydiffraction-0.18.0/docs/docs/tutorials/ed-3.py +696 -0
  105. easydiffraction-0.18.0/docs/docs/tutorials/ed-4.ipynb +744 -0
  106. easydiffraction-0.18.0/docs/docs/tutorials/ed-4.py +328 -0
  107. easydiffraction-0.18.0/docs/docs/tutorials/ed-5.ipynb +669 -0
  108. easydiffraction-0.18.0/docs/docs/tutorials/ed-5.py +298 -0
  109. easydiffraction-0.18.0/docs/docs/tutorials/ed-6.ipynb +862 -0
  110. easydiffraction-0.18.0/docs/docs/tutorials/ed-6.py +352 -0
  111. easydiffraction-0.18.0/docs/docs/tutorials/ed-7.ipynb +958 -0
  112. easydiffraction-0.18.0/docs/docs/tutorials/ed-7.py +364 -0
  113. easydiffraction-0.18.0/docs/docs/tutorials/ed-8.ipynb +745 -0
  114. easydiffraction-0.18.0/docs/docs/tutorials/ed-8.py +368 -0
  115. easydiffraction-0.18.0/docs/docs/tutorials/ed-9.ipynb +727 -0
  116. easydiffraction-0.18.0/docs/docs/tutorials/ed-9.py +312 -0
  117. easydiffraction-0.18.0/docs/docs/tutorials/index.json +177 -0
  118. easydiffraction-0.18.0/docs/docs/tutorials/index.md +150 -0
  119. easydiffraction-0.18.0/docs/docs/user-guide/analysis-workflow/analysis.md +435 -0
  120. easydiffraction-0.18.0/docs/docs/user-guide/analysis-workflow/experiment.md +599 -0
  121. easydiffraction-0.18.0/docs/docs/user-guide/analysis-workflow/index.md +36 -0
  122. easydiffraction-0.18.0/docs/docs/user-guide/analysis-workflow/model.md +299 -0
  123. easydiffraction-0.18.0/docs/docs/user-guide/analysis-workflow/project.md +293 -0
  124. easydiffraction-0.18.0/docs/docs/user-guide/analysis-workflow/report.md +116 -0
  125. easydiffraction-0.18.0/docs/docs/user-guide/concept.md +119 -0
  126. easydiffraction-0.18.0/docs/docs/user-guide/data-format.md +237 -0
  127. easydiffraction-0.18.0/docs/docs/user-guide/first-steps.md +189 -0
  128. easydiffraction-0.18.0/docs/docs/user-guide/index.md +24 -0
  129. easydiffraction-0.18.0/docs/docs/user-guide/parameters/expt_type.md +33 -0
  130. easydiffraction-0.18.0/docs/docs/user-guide/parameters/instrument.md +57 -0
  131. easydiffraction-0.18.0/docs/docs/user-guide/parameters/peak.md +69 -0
  132. easydiffraction-0.18.0/docs/docs/user-guide/parameters.md +292 -0
  133. easydiffraction-0.18.0/docs/mkdocs.yml +262 -0
  134. easydiffraction-0.18.0/docs/overrides/main.html +61 -0
  135. easydiffraction-0.18.0/pixi.lock +12863 -0
  136. easydiffraction-0.18.0/pixi.toml +337 -0
  137. easydiffraction-0.18.0/pyproject.toml +434 -0
  138. easydiffraction-0.18.0/src/easydiffraction/__init__.py +22 -0
  139. easydiffraction-0.18.0/src/easydiffraction/__main__.py +288 -0
  140. easydiffraction-0.18.0/src/easydiffraction/analysis/__init__.py +41 -0
  141. easydiffraction-0.18.0/src/easydiffraction/analysis/analysis.py +2995 -0
  142. easydiffraction-0.18.0/src/easydiffraction/analysis/calculators/crysfml.py +376 -0
  143. easydiffraction-0.18.0/src/easydiffraction/analysis/calculators/cryspy.py +1239 -0
  144. easydiffraction-0.18.0/src/easydiffraction/analysis/calculators/pdffit.py +177 -0
  145. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/__init__.py +35 -0
  146. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/aliases/default.py +149 -0
  147. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/constraints/default.py +194 -0
  148. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/fit_parameter_correlations/default.py +179 -0
  149. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/fit_parameters/default.py +428 -0
  150. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/fit_result/__init__.py +7 -0
  151. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/fit_result/base.py +162 -0
  152. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/fit_result/bayesian.py +277 -0
  153. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/fit_result/default.py +9 -0
  154. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/fit_result/lsq.py +592 -0
  155. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/fitting_mode/__init__.py +8 -0
  156. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/fitting_mode/default.py +57 -0
  157. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/fitting_mode/factory.py +17 -0
  158. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/joint_fit/default.py +100 -0
  159. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/minimizer/__init__.py +19 -0
  160. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/minimizer/base.py +101 -0
  161. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/minimizer/bayesian_base.py +229 -0
  162. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/minimizer/bumps.py +28 -0
  163. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/minimizer/bumps_amoeba.py +28 -0
  164. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/minimizer/bumps_de.py +28 -0
  165. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/minimizer/bumps_dream.py +44 -0
  166. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/minimizer/bumps_lm.py +28 -0
  167. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/minimizer/dfols.py +28 -0
  168. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/minimizer/emcee.py +128 -0
  169. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/minimizer/factory.py +18 -0
  170. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/minimizer/lmfit.py +28 -0
  171. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/minimizer/lmfit_least_squares.py +28 -0
  172. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/minimizer/lmfit_leastsq.py +28 -0
  173. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/minimizer/lsq_base.py +58 -0
  174. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/sequential_fit/default.py +139 -0
  175. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/sequential_fit_extract/default.py +174 -0
  176. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/software/__init__.py +9 -0
  177. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/software/base.py +82 -0
  178. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/software/default.py +85 -0
  179. easydiffraction-0.18.0/src/easydiffraction/analysis/categories/software/factory.py +17 -0
  180. easydiffraction-0.18.0/src/easydiffraction/analysis/enums.py +74 -0
  181. easydiffraction-0.18.0/src/easydiffraction/analysis/fit_helpers/__init__.py +8 -0
  182. easydiffraction-0.18.0/src/easydiffraction/analysis/fit_helpers/_diagnostics.py +174 -0
  183. easydiffraction-0.18.0/src/easydiffraction/analysis/fit_helpers/bayesian.py +786 -0
  184. easydiffraction-0.18.0/src/easydiffraction/analysis/fit_helpers/reporting.py +298 -0
  185. easydiffraction-0.18.0/src/easydiffraction/analysis/fitting.py +426 -0
  186. easydiffraction-0.18.0/src/easydiffraction/analysis/minimizers/__init__.py +14 -0
  187. easydiffraction-0.18.0/src/easydiffraction/analysis/minimizers/base.py +456 -0
  188. easydiffraction-0.18.0/src/easydiffraction/analysis/minimizers/bumps_dream.py +1028 -0
  189. easydiffraction-0.18.0/src/easydiffraction/analysis/minimizers/emcee.py +1271 -0
  190. easydiffraction-0.18.0/src/easydiffraction/analysis/minimizers/emcee_defaults.py +26 -0
  191. easydiffraction-0.18.0/src/easydiffraction/analysis/minimizers/enums.py +73 -0
  192. easydiffraction-0.18.0/src/easydiffraction/analysis/sequential.py +1335 -0
  193. easydiffraction-0.18.0/src/easydiffraction/core/__init__.py +8 -0
  194. easydiffraction-0.18.0/src/easydiffraction/core/category.py +271 -0
  195. easydiffraction-0.18.0/src/easydiffraction/core/collection.py +183 -0
  196. easydiffraction-0.18.0/src/easydiffraction/core/datablock.py +136 -0
  197. easydiffraction-0.18.0/src/easydiffraction/core/display_handler.py +30 -0
  198. easydiffraction-0.18.0/src/easydiffraction/core/errors.py +13 -0
  199. easydiffraction-0.18.0/src/easydiffraction/core/guard.py +269 -0
  200. easydiffraction-0.18.0/src/easydiffraction/core/posterior.py +45 -0
  201. easydiffraction-0.18.0/src/easydiffraction/core/singleton.py +138 -0
  202. easydiffraction-0.18.0/src/easydiffraction/core/switchable.py +104 -0
  203. easydiffraction-0.18.0/src/easydiffraction/core/units_vocabulary.py +69 -0
  204. easydiffraction-0.18.0/src/easydiffraction/core/validation.py +383 -0
  205. easydiffraction-0.18.0/src/easydiffraction/core/variable.py +837 -0
  206. easydiffraction-0.18.0/src/easydiffraction/crystallography/__init__.py +6 -0
  207. easydiffraction-0.18.0/src/easydiffraction/crystallography/crystallography.py +1122 -0
  208. easydiffraction-0.18.0/src/easydiffraction/crystallography/space_groups.json.gz +0 -0
  209. easydiffraction-0.18.0/src/easydiffraction/crystallography/space_groups.py +36 -0
  210. easydiffraction-0.18.0/src/easydiffraction/datablocks/experiment/categories/background/base.py +74 -0
  211. easydiffraction-0.18.0/src/easydiffraction/datablocks/experiment/categories/background/line_segment.py +204 -0
  212. easydiffraction-0.18.0/src/easydiffraction/datablocks/experiment/categories/calculator/__init__.py +10 -0
  213. easydiffraction-0.18.0/src/easydiffraction/datablocks/experiment/categories/calculator/default.py +101 -0
  214. easydiffraction-0.18.0/src/easydiffraction/datablocks/experiment/categories/calculator/factory.py +17 -0
  215. easydiffraction-0.18.0/src/easydiffraction/datablocks/experiment/categories/data/bragg_pd.py +777 -0
  216. easydiffraction-0.18.0/src/easydiffraction/datablocks/experiment/categories/data/total_pd.py +404 -0
  217. easydiffraction-0.18.0/src/easydiffraction/datablocks/experiment/categories/diffrn/default.py +167 -0
  218. easydiffraction-0.18.0/src/easydiffraction/datablocks/experiment/categories/excluded_regions/default.py +188 -0
  219. easydiffraction-0.18.0/src/easydiffraction/datablocks/experiment/categories/experiment_type/default.py +153 -0
  220. easydiffraction-0.18.0/src/easydiffraction/datablocks/experiment/categories/extinction/base.py +57 -0
  221. easydiffraction-0.18.0/src/easydiffraction/datablocks/experiment/categories/extinction/becker_coppens.py +142 -0
  222. easydiffraction-0.18.0/src/easydiffraction/datablocks/experiment/categories/instrument/cwl.py +140 -0
  223. easydiffraction-0.18.0/src/easydiffraction/datablocks/experiment/categories/instrument/tof.py +210 -0
  224. easydiffraction-0.18.0/src/easydiffraction/datablocks/experiment/categories/linked_crystal/default.py +104 -0
  225. easydiffraction-0.18.0/src/easydiffraction/datablocks/experiment/categories/linked_phases/default.py +108 -0
  226. easydiffraction-0.18.0/src/easydiffraction/datablocks/experiment/categories/peak/base.py +90 -0
  227. easydiffraction-0.18.0/src/easydiffraction/datablocks/experiment/categories/peak/cwl_mixins.py +378 -0
  228. easydiffraction-0.18.0/src/easydiffraction/datablocks/experiment/categories/peak/tof_mixins.py +622 -0
  229. easydiffraction-0.18.0/src/easydiffraction/datablocks/experiment/categories/peak/total_mixins.py +213 -0
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  1033. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/analysis/minimizers/test_bumps_de.py +0 -0
  1034. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/analysis/minimizers/test_bumps_dream.py +0 -0
  1035. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/analysis/minimizers/test_bumps_lm.py +0 -0
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  1038. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/analysis/minimizers/test_factory.py +0 -0
  1039. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/analysis/minimizers/test_lmfit.py +0 -0
  1040. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/analysis/minimizers/test_lmfit_least_squares.py +0 -0
  1041. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/analysis/minimizers/test_lmfit_leastsq.py +0 -0
  1042. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/analysis/test_analysis_show_empty.py +0 -0
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  1044. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/core/test_category_owner.py +0 -0
  1045. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/core/test_collection.py +0 -0
  1046. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/core/test_diagnostic.py +0 -0
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  1048. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/core/test_identity.py +0 -0
  1049. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/core/test_metadata.py +0 -0
  1050. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/core/test_singletons.py +0 -0
  1051. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/core/test_validation.py +0 -0
  1052. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/crystallography/test_crystallography_coverage.py +0 -0
  1053. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/datablocks/experiment/categories/background/test_base.py +0 -0
  1054. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/datablocks/experiment/categories/background/test_chebyshev.py +0 -0
  1055. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/datablocks/experiment/categories/background/test_enums.py +0 -0
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  1058. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/datablocks/experiment/categories/data/test_bragg_pd.py +0 -0
  1059. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/datablocks/experiment/categories/data/test_factory.py +0 -0
  1060. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/datablocks/experiment/categories/data/test_total_pd.py +0 -0
  1061. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/datablocks/experiment/categories/instrument/test_base.py +0 -0
  1062. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/datablocks/experiment/categories/instrument/test_cwl.py +0 -0
  1063. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/datablocks/experiment/categories/instrument/test_factory.py +0 -0
  1064. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/datablocks/experiment/categories/instrument/test_tof.py +0 -0
  1065. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/datablocks/experiment/categories/peak/test_cwl.py +0 -0
  1066. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/datablocks/experiment/categories/peak/test_factory.py +0 -0
  1067. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/datablocks/experiment/categories/peak/test_tof.py +0 -0
  1068. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/datablocks/experiment/categories/peak/test_tof_mixins.py +0 -0
  1069. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/datablocks/experiment/categories/peak/test_total.py +0 -0
  1070. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/datablocks/experiment/categories/peak/test_total_mixins.py +0 -0
  1071. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/datablocks/experiment/categories/refln/test_bragg_pd.py +0 -0
  1072. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/datablocks/experiment/categories/test_diffrn.py +0 -0
  1073. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/datablocks/experiment/categories/test_excluded_regions.py +0 -0
  1074. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/datablocks/experiment/categories/test_experiment_type.py +0 -0
  1075. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/datablocks/experiment/categories/test_extinction.py +0 -0
  1076. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/datablocks/experiment/categories/test_linked_crystal.py +0 -0
  1077. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/datablocks/experiment/categories/test_linked_phases.py +0 -0
  1078. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/datablocks/experiment/item/test_bragg_sc.py +0 -0
  1079. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/datablocks/experiment/item/test_enums.py +0 -0
  1080. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/datablocks/experiment/item/test_enums_coverage.py +0 -0
  1081. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/datablocks/experiment/item/test_factory_coverage.py +0 -0
  1082. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/datablocks/experiment/item/test_total_pd.py +0 -0
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  1084. {easydiffraction-0.17.0/src/easydiffraction/project โ†’ easydiffraction-0.18.0/tests/unit/easydiffraction/datablocks/structure}/categories/__init__.py +0 -0
  1085. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/datablocks/structure/categories/test_atom_site_aniso.py +0 -0
  1086. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/datablocks/structure/categories/test_cell.py +0 -0
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  1090. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/datablocks/structure/test_collection_coverage.py +0 -0
  1091. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/display/plotters/test_base.py +0 -0
  1092. {easydiffraction-0.17.0/src/easydiffraction/summary โ†’ easydiffraction-0.18.0/tests/unit/easydiffraction/display/tablers}/__init__.py +0 -0
  1093. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/display/tablers/test_rich.py +0 -0
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  1098. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/display/test_utils.py +0 -0
  1099. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/io/cif/test_parse.py +0 -0
  1100. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/io/test_ascii.py +0 -0
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  1108. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/utils/test_environment_coverage.py +0 -0
  1109. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/utils/test_logging.py +0 -0
  1110. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tests/unit/easydiffraction/utils/test_logging_coverage.py +0 -0
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  1113. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tools/generate_package_docs.py +0 -0
  1114. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tools/license_headers.py +0 -0
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  1116. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tools/param_consistency.py +0 -0
  1117. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tools/test_scripts.py +0 -0
  1118. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tools/update_docs_assets.py +0 -0
  1119. {easydiffraction-0.17.0 โ†’ easydiffraction-0.18.0}/tools/update_github_labels.py +0 -0
@@ -0,0 +1,31 @@
1
+ # Codecov configuration
2
+ # https://docs.codecov.com/docs/codecov-yaml
3
+
4
+ github_checks:
5
+ annotations: true
6
+
7
+ ignore:
8
+ - 'src/easydiffraction/report/templates/html/vendor/**'
9
+ - 'src/easydiffraction/report/templates/tex/styles/**'
10
+ - 'src/easydiffraction/utils/_vendored/jupyter_dark_detect/**'
11
+
12
+ comment:
13
+ layout: 'reach, diff, flags, files'
14
+ behavior: default
15
+ require_changes: false
16
+ require_base: false
17
+ require_head: true
18
+
19
+ coverage:
20
+ status:
21
+ project:
22
+ default:
23
+ target: auto
24
+ threshold: 1%
25
+ # Make project coverage informational (won't block PR)
26
+ informational: true
27
+ patch:
28
+ default:
29
+ target: auto
30
+ # Require patch coverage but with threshold
31
+ threshold: 1%
@@ -0,0 +1,15 @@
1
+ # CodeFactor exclude patterns configuration must be done online:
2
+ # https://www.codefactor.io/repository/github/easyscience/diffraction-lib/ignore
3
+ #
4
+ # Last updated: 2026-05-29
5
+ #
6
+ # Exclude patterns:
7
+ # deps/**
8
+ # docs/**
9
+ # src/easydiffraction/report/templates/html/vendor/**
10
+ # src/easydiffraction/report/templates/tex/styles/**
11
+ # src/easydiffraction/utils/_vendored/jupyter_dark_detect/**
12
+ # tests/**
13
+ # tmp/**
14
+ # tools/**
15
+ # tutorials/**
@@ -0,0 +1,26 @@
1
+ # WARNING: Do not edit this file manually.
2
+ # Any changes will be overwritten by Copier.
3
+ _commit: v0.12.0
4
+ _src_path: gh:easyscience/templates
5
+ app_docs_url: https://easyscience.github.io/diffraction-app
6
+ app_doi: 10.5281/zenodo.18163581
7
+ app_package_name: easydiffraction_app
8
+ app_python: '3.14'
9
+ app_repo_name: diffraction-app
10
+ home_page_url: https://easyscience.github.io/diffraction
11
+ home_repo_name: diffraction
12
+ lib_docs_url: https://easyscience.github.io/diffraction-lib
13
+ lib_doi: 10.5281/zenodo.18163581
14
+ lib_package_name: easydiffraction
15
+ lib_python_max: '3.14'
16
+ lib_python_min: '3.12'
17
+ lib_repo_name: diffraction-lib
18
+ project_contact_email: support@easydiffraction.org
19
+ project_copyright_years: 2021-2026
20
+ project_extended_description: A software for calculating diffraction patterns based
21
+ on a structural model and refining its parameters against experimental data
22
+ project_name: EasyDiffraction
23
+ project_short_description: Diffraction data analysis
24
+ project_shortcut: ED
25
+ project_type: both
26
+ template_type: lib
@@ -0,0 +1,70 @@
1
+ name: Coverage checks
2
+
3
+ on:
4
+ # Trigger the workflow on push to develop
5
+ push:
6
+ branches:
7
+ - develop
8
+ # Trigger the workflow on pull request
9
+ pull_request:
10
+ # Allows you to run this workflow manually from the Actions tab
11
+ workflow_dispatch:
12
+
13
+ # Need permissions to trigger the dashboard build workflow
14
+ permissions:
15
+ actions: write
16
+ contents: read
17
+
18
+ # Allow only one concurrent workflow per PR or branch ref.
19
+ # Cancel in-progress runs only for pull requests, but let branch push runs finish.
20
+ concurrency:
21
+ group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
22
+ cancel-in-progress: ${{ github.event_name == 'pull_request' }}
23
+
24
+ # Set the environment variables to be used in all jobs defined in this workflow
25
+ env:
26
+ CI_BRANCH: ${{ github.head_ref || github.ref_name }}
27
+
28
+ jobs:
29
+ # Job 1: Run docstring coverage
30
+ docstring-coverage:
31
+ runs-on: ubuntu-latest
32
+
33
+ steps:
34
+ - name: Check-out repository
35
+ uses: actions/checkout@v6
36
+
37
+ - name: Set up pixi
38
+ uses: ./.github/actions/setup-pixi
39
+
40
+ - name: Run docstring coverage
41
+ run: pixi run docstring-coverage
42
+
43
+ # Job 2: Run unit tests with coverage and upload to Codecov
44
+ unit-tests-coverage:
45
+ runs-on: ubuntu-latest
46
+
47
+ steps:
48
+ - name: Check-out repository
49
+ uses: actions/checkout@v6
50
+
51
+ - name: Set up pixi
52
+ uses: ./.github/actions/setup-pixi
53
+
54
+ - name: Run unit tests with coverage
55
+ run: pixi run unit-tests-coverage --cov-report=xml:coverage-unit.xml
56
+
57
+ - name: Upload unit tests coverage to Codecov
58
+ if: ${{ !cancelled() }}
59
+ uses: ./.github/actions/upload-codecov
60
+ with:
61
+ name: unit-tests-job
62
+ flags: unittests
63
+ files: ./coverage-unit.xml
64
+ token: ${{ secrets.CODECOV_TOKEN }}
65
+
66
+ # Job 4: Build and publish dashboard (reusable workflow)
67
+ run-reusable-workflows:
68
+ needs: [docstring-coverage, unit-tests-coverage] # depend on the previous jobs
69
+ uses: ./.github/workflows/dashboard.yml
70
+ secrets: inherit
@@ -0,0 +1,194 @@
1
+ # This workflow builds and deploys documentation for the project.
2
+ #
3
+ # Overview:
4
+ # - Converts tutorial Python scripts to Jupyter notebooks and executes them.
5
+ # - Builds the documentation site using MkDocs with the Material theme.
6
+ # - Uploads the built site as an artifact for local inspection.
7
+ # - Deploys versioned documentation to the gh-pages branch using Mike:
8
+ # - For release tags (v*): deploys to a versioned folder (e.g., /0.9.1/) and updates /latest/.
9
+ # - For branches: deploys to /dev/.
10
+ #
11
+ # The action summary page will contain a link to the built artifact for downloading
12
+ # and inspecting, as well as a link to the deployed documentation site.
13
+
14
+ name: Docs build and deployment
15
+
16
+ on:
17
+ # Trigger the workflow on push
18
+ push:
19
+ # Selected branches
20
+ branches: [develop] # master and main are already verified in PR
21
+ # Runs on creating a new tag starting with 'v', e.g. 'v1.0.3'
22
+ tags: ['v*']
23
+ # Trigger the workflow on pull request
24
+ pull_request:
25
+ # Selected branches
26
+ branches: [master, main, develop]
27
+ # Allows you to run this workflow manually from the Actions tab
28
+ workflow_dispatch:
29
+
30
+ # - Non-tagged pushes and pull requests all use `docs-dev` group, so
31
+ # they cancel each other.
32
+ # - Tagged pushes use their own group like docs-v1.2.3, so they do not
33
+ # cancel non-tagged runs, and non-tagged runs do not cancel them.
34
+ concurrency:
35
+ group: >-
36
+ ${{ startsWith(github.ref, 'refs/tags/v')
37
+ && format('docs-{0}', github.ref_name)
38
+ || 'docs-dev' }}
39
+ cancel-in-progress: true
40
+
41
+ # Set the environment variables to be used in all jobs defined in this workflow
42
+ env:
43
+ # CI_BRANCH - the branch name (used in mkdocs.yml)
44
+ # For PRs: github.head_ref is the source branch
45
+ # For pushes: github.ref_name is the branch
46
+ # For tags: github.ref_name is the tag name
47
+ # GITHUB_REPOSITORY - the repository name (used in mkdocs.yml)
48
+ # NOTEBOOKS_DIR - the directory containing the Jupyter notebooks (used in mkdocs.yml)
49
+ DEFAULT_BRANCH: ${{ github.event.repository.default_branch }}
50
+ DEVELOP_BRANCH: develop
51
+ CI_BRANCH: ${{ github.head_ref || github.ref_name }}
52
+ IS_RELEASE_TAG: ${{ startsWith(github.ref, 'refs/tags/v') }}
53
+ GITHUB_REPOSITORY: ${{ github.repository }}
54
+ NOTEBOOKS_DIR: tutorials
55
+
56
+ jobs:
57
+ # Single job that builds and deploys documentation.
58
+ # Uses macOS runner for consistent Plotly chart rendering.
59
+ build-deploy-docs:
60
+ runs-on: ubuntu-latest # macos-latest
61
+
62
+ permissions:
63
+ contents: write # Required for pushing to the gh-pages branch
64
+
65
+ steps:
66
+ # Setting DOCS_VERSION to be used in mkdocs.yml, and then in the
67
+ # main.html template. It defines the versioned docs subfolder name
68
+ # in the gh-pages branch. If it's a release tag, use the version
69
+ # number without the 'v' prefix, otherwise use 'dev'.
70
+ # Setting RELEASE_VERSION to be used in mkdocs.yml to show
71
+ # the latest release version in the index.md file. If it's a
72
+ # release tag, use the tag name, otherwise use the branch name
73
+ # for development builds.
74
+ - name: Set extra env variables
75
+ shell: bash
76
+ run: |
77
+ if [[ "${IS_RELEASE_TAG}" == "true" ]]; then
78
+ RELEASE_VERSION="${GITHUB_REF_NAME}"
79
+ DOCS_VERSION="${RELEASE_VERSION#v}"
80
+ else
81
+ RELEASE_VERSION="${CI_BRANCH}"
82
+ DOCS_VERSION="dev"
83
+ fi
84
+ echo "RELEASE_VERSION=${RELEASE_VERSION}" >> "$GITHUB_ENV"
85
+ echo "DOCS_VERSION=${DOCS_VERSION}" >> "$GITHUB_ENV"
86
+
87
+ # Check out the repository source code.
88
+ # Note: The gh-pages branch is fetched separately later for mike deployment.
89
+ - name: Checkout repository
90
+ uses: actions/checkout@v6
91
+
92
+ # Activate dark mode to create documentation with Plotly charts in dark mode
93
+ # Need a better solution to automatically switch the chart colour theme based on the mkdocs material switcher
94
+ # Something similar to mkdocs_plotly_plugin https://haoda-li.github.io/mkdocs-plotly-plugin/,
95
+ # but for generating documentation from notepads
96
+ #- name: Activate dark mode
97
+ # run: |
98
+ # brew install dark-mode
99
+ # dark-mode status
100
+ # dark-mode on
101
+ # dark-mode status
102
+
103
+ # Set up the pixi package manager and install dependencies from pixi.toml.
104
+ # Uses frozen lockfile to ensure reproducible builds.
105
+ - name: Set up pixi
106
+ uses: ./.github/actions/setup-pixi
107
+ # Pre-import the main package to exclude info messages from the docs
108
+ # E.g., Matplotlib may print messages to stdout/stderr when first
109
+ # imported. This step allows to avoid "Matplotlib is building the font
110
+ # cache" messages during notebook execution.
111
+ - name: Pre-build site step
112
+ run: pixi run python -c "import easydiffraction"
113
+
114
+ # Prepare the Jupyter notebooks for documentation (strip output, etc.).
115
+ - name: Prepare notebooks
116
+ run: pixi run notebook-prepare
117
+
118
+ # Execute all Jupyter notebooks to generate output cells (plots, tables, etc.).
119
+ # Uses multiple cores for parallel execution to speed up the process.
120
+ - name: Run notebooks
121
+ # if: false # Temporarily disabled to speed up the docs build
122
+ run: pixi run notebook-exec-ci
123
+
124
+ # Sync the canonical Three.js snapshot into the docs assets so
125
+ # MkDocs can serve it (belt-and-braces; docs-build also depends on
126
+ # this task).
127
+ - name: Sync vendored JS into docs assets
128
+ run: pixi run docs-sync-vendored-js
129
+
130
+ # Build the static files for the documentation site for local inspection
131
+ # Input: docs/ directory containing the Markdown files
132
+ # Output: site/ directory containing the generated HTML files
133
+ - name: Build site for local check
134
+ run: pixi run docs-build-local
135
+
136
+ # Upload the static files from the site/ directory to be used for
137
+ # local check
138
+ - name: Upload built site as artifact
139
+ uses: ./.github/actions/upload-artifact
140
+ with:
141
+ name: site-local_easydiffraction-lib-${{ env.RELEASE_VERSION }}
142
+ path: docs/site/
143
+
144
+ # Create GitHub App token for pushing to gh-pages as easyscience[bot].
145
+ - name: Setup easyscience[bot]
146
+ id: bot
147
+ uses: ./.github/actions/setup-easyscience-bot
148
+ with:
149
+ app-id: ${{ vars.EASYSCIENCE_APP_ID }}
150
+ private-key: ${{ secrets.EASYSCIENCE_APP_KEY }}
151
+
152
+ # Configure git identity and remote URL so mike pushes as easyscience[bot].
153
+ - name: Configure git for pushing
154
+ run: |
155
+ set -euo pipefail
156
+ git config user.name "easyscience[bot]"
157
+ git config user.email "${{ vars.EASYSCIENCE_APP_ID }}+easyscience[bot]@users.noreply.github.com"
158
+ git remote set-url origin "https://x-access-token:${{ steps.bot.outputs.token }}@github.com/${{ github.repository }}.git"
159
+
160
+ # Fetch the gh-pages branch to ensure mike has the latest remote state.
161
+ # This is required because the checkout step only fetches the source branch,
162
+ # not the gh-pages branch that mike needs to update.
163
+ - name: Fetch gh-pages branch
164
+ run: |
165
+ git fetch origin gh-pages:gh-pages 2>/dev/null || true
166
+
167
+ # Deploy versioned documentation using mike (MkDocs plugin for versioning).
168
+ # - For release tags (v*): deploys to versioned folder (e.g., /0.9.1/) and aliases to /latest/.
169
+ # - For branches: deploys to /dev/.
170
+ # The "${RELEASE_VERSION#v}" syntax strips the 'v' prefix (v0.9.1 -> 0.9.1).
171
+ # Also sets 'latest' as the default version for the version selector.
172
+ - name: Rebuild and deploy docs with mike
173
+ run: |
174
+ # Exit on error (-e), undefined vars (-u), and pipeline failures (pipefail)
175
+ set -euo pipefail
176
+
177
+ REPO_NAME="${{ github.event.repository.name }}"
178
+ BASE_URL="https://easyscience.github.io/${REPO_NAME}"
179
+
180
+ # Deploy the release version and update the "latest" alias
181
+ if [[ "${IS_RELEASE_TAG}" == "true" ]]; then
182
+ pixi run docs-deploy-pre "${RELEASE_VERSION#v}" latest
183
+ pixi run docs-set-default-pre latest
184
+ DEPLOYMENT_URL="${BASE_URL}/latest"
185
+
186
+ # Deploy/update the "dev" alias (or whatever your convention is)
187
+ else
188
+ pixi run docs-deploy-pre dev
189
+ DEPLOYMENT_URL="${BASE_URL}/dev"
190
+
191
+ fi
192
+
193
+ # Add links to the action summary page for easy access
194
+ echo "๐Ÿ”— deployment url [${DEPLOYMENT_URL}](${DEPLOYMENT_URL})" >> "${GITHUB_STEP_SUMMARY}"
@@ -0,0 +1,64 @@
1
+ name: Tutorial tests
2
+
3
+ on:
4
+ # Trigger the workflow on push
5
+ push:
6
+ # Selected branches
7
+ branches: [develop] # master and main are already verified in PR
8
+ # Trigger the workflow on pull request
9
+ pull_request:
10
+ branches: ['**']
11
+ # Trigger the workflow on workflow_call (to be called from other workflows)
12
+ # Needed, as standard schedule triggers the master branch only, but we want
13
+ # to run this workflow on develop branch.
14
+ workflow_call:
15
+ # Allows you to run this workflow manually from the Actions tab
16
+ workflow_dispatch:
17
+
18
+ permissions:
19
+ contents: read
20
+
21
+ # Allow only one concurrent workflow, skipping runs queued between the run
22
+ # in-progress and latest queued. And cancel in-progress runs.
23
+ concurrency:
24
+ group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
25
+ cancel-in-progress: true
26
+
27
+ # Set the environment variables to be used in all jobs defined in this workflow
28
+ env:
29
+ CI_BRANCH: ${{ github.head_ref || github.ref_name }}
30
+
31
+ jobs:
32
+ # Job 1: Test tutorials as scripts and notebooks on multiple OS
33
+ tutorial-tests:
34
+ strategy:
35
+ fail-fast: false
36
+ matrix:
37
+ os: [ubuntu-latest, macos-latest, windows-latest]
38
+
39
+ runs-on: ${{ matrix.os }}
40
+
41
+ steps:
42
+ - name: Checkout repository
43
+ uses: actions/checkout@v6
44
+
45
+ - name: Set up pixi
46
+ uses: ./.github/actions/setup-pixi
47
+
48
+ - name: Test tutorials as python scripts
49
+ shell: bash
50
+ run: pixi run script-tests-checked
51
+
52
+ - name: Prepare notebooks
53
+ shell: bash
54
+ run: pixi run notebook-prepare
55
+
56
+ - name: Test tutorials as notebooks
57
+ shell: bash
58
+ run: pixi run notebook-tests-checked
59
+
60
+ # Job 2: Build and publish dashboard (reusable workflow)
61
+ run-reusable-workflows:
62
+ needs: tutorial-tests # depend on previous job
63
+ uses: ./.github/workflows/dashboard.yml
64
+ secrets: inherit
@@ -0,0 +1,61 @@
1
+ # Python
2
+ __pycache__/
3
+ .venv/
4
+ .coverage
5
+ .pyc
6
+
7
+ # Pixi
8
+ .pixi/
9
+
10
+ # PyInstaller
11
+ dist/
12
+ build/
13
+ *.spec
14
+
15
+ # MkDocs
16
+ docs/site/
17
+
18
+ # Generated docs-serving copy of the canonical Three.js (synced from
19
+ # src/ by `pixi run docs-sync-vendored-js`; the source of truth is src/)
20
+ docs/docs/assets/javascripts/vendor/threejs/
21
+
22
+ # Jupyter Notebooks
23
+ .ipynb_checkpoints
24
+
25
+ # Node
26
+ node_modules/
27
+
28
+ # QtCreator
29
+ *.autosave
30
+ *.qmlproject.user
31
+ *.qmlproject.user.*
32
+ *.pyproject.user
33
+ *.pyproject.user.*
34
+ CMakeLists.txt.user*
35
+
36
+ # PyCharm
37
+ .idea/
38
+
39
+ # VS Code
40
+ .vscode/
41
+
42
+ # macOS
43
+ .DS_Store
44
+ *.app
45
+ *.dmg
46
+
47
+ # Misc
48
+ .cache/
49
+ *.log
50
+ *.zip
51
+
52
+ # Agents
53
+ AGENTS.md
54
+ CLAUDE.md
55
+
56
+ # ED
57
+ # Used to fetch tutorials data during their runtime. Need to have '/' at
58
+ # the beginning to avoid ignoring 'data' module in the src/.
59
+ /data/
60
+ /projects/
61
+ /tmp/
@@ -0,0 +1,41 @@
1
+ # Git
2
+ .git/
3
+
4
+ # Copier
5
+ .copier-answers*.yml
6
+
7
+ # Pixi
8
+ .pixi
9
+ pixi.lock
10
+
11
+ # MkDocs
12
+ docs/overrides/
13
+ docs/site/
14
+ docs/docs/assets/
15
+
16
+ # Python
17
+ .pytest_cache/
18
+
19
+ # MyPy
20
+ .mypy_cache/
21
+
22
+ # Ruff
23
+ .ruff_cache/
24
+
25
+ # Node
26
+ node_modules
27
+
28
+ # Vendored snapshots
29
+ src/easydiffraction/display/structure/renderers/vendor/
30
+ src/easydiffraction/report/templates/html/vendor/
31
+ src/easydiffraction/report/templates/tex/styles/
32
+ src/easydiffraction/utils/_vendored/jupyter_dark_detect/
33
+
34
+ # Tox
35
+ .tox
36
+
37
+ # Misc
38
+ .benchmarks
39
+ .cache
40
+ deps/
41
+ tmp/
@@ -0,0 +1,134 @@
1
+ Metadata-Version: 2.4
2
+ Name: easydiffraction
3
+ Version: 0.18.0
4
+ Summary: Diffraction data analysis
5
+ Project-URL: Homepage, https://easydiffraction.org
6
+ Project-URL: Documentation, https://easyscience.github.io/diffraction-lib
7
+ Project-URL: Release Notes, https://github.com/easyscience/diffraction-lib/releases
8
+ Project-URL: Source Code, https://github.com/easyscience/diffraction-lib
9
+ Project-URL: Issue Tracker, https://github.com/easyscience/diffraction-lib/issues
10
+ Author: EasyScience contributors
11
+ License-Expression: BSD-3-Clause
12
+ License-File: LICENSE
13
+ Classifier: Intended Audience :: Science/Research
14
+ Classifier: License :: OSI Approved :: BSD License
15
+ Classifier: Operating System :: OS Independent
16
+ Classifier: Programming Language :: Python :: 3
17
+ Classifier: Programming Language :: Python :: 3 :: Only
18
+ Classifier: Programming Language :: Python :: 3.12
19
+ Classifier: Programming Language :: Python :: 3.13
20
+ Classifier: Programming Language :: Python :: 3.14
21
+ Classifier: Topic :: Scientific/Engineering
22
+ Requires-Python: >=3.12
23
+ Requires-Dist: asciichartpy
24
+ Requires-Dist: asteval
25
+ Requires-Dist: bumps
26
+ Requires-Dist: crysfml
27
+ Requires-Dist: cryspy
28
+ Requires-Dist: darkdetect
29
+ Requires-Dist: dfo-ls
30
+ Requires-Dist: diffpy-pdffit2
31
+ Requires-Dist: diffpy-utils
32
+ Requires-Dist: emcee
33
+ Requires-Dist: gemmi
34
+ Requires-Dist: h5py
35
+ Requires-Dist: lmfit
36
+ Requires-Dist: numpy
37
+ Requires-Dist: pandas
38
+ Requires-Dist: pillow
39
+ Requires-Dist: plotly
40
+ Requires-Dist: pooch
41
+ Requires-Dist: rich
42
+ Requires-Dist: scipy
43
+ Requires-Dist: sympy
44
+ Requires-Dist: typeguard
45
+ Requires-Dist: typer
46
+ Requires-Dist: uncertainties
47
+ Requires-Dist: varname
48
+ Provides-Extra: dev
49
+ Requires-Dist: build; extra == 'dev'
50
+ Requires-Dist: copier; extra == 'dev'
51
+ Requires-Dist: docstripy; extra == 'dev'
52
+ Requires-Dist: format-docstring; extra == 'dev'
53
+ Requires-Dist: gitpython; extra == 'dev'
54
+ Requires-Dist: interrogate; extra == 'dev'
55
+ Requires-Dist: jinja2; extra == 'dev'
56
+ Requires-Dist: jupyterquiz; extra == 'dev'
57
+ Requires-Dist: jupytext; extra == 'dev'
58
+ Requires-Dist: mike; extra == 'dev'
59
+ Requires-Dist: mkdocs; extra == 'dev'
60
+ Requires-Dist: mkdocs-autorefs; extra == 'dev'
61
+ Requires-Dist: mkdocs-jupyter; extra == 'dev'
62
+ Requires-Dist: mkdocs-markdownextradata-plugin; extra == 'dev'
63
+ Requires-Dist: mkdocs-material; extra == 'dev'
64
+ Requires-Dist: mkdocs-plugin-inline-svg; extra == 'dev'
65
+ Requires-Dist: mkdocstrings-python; extra == 'dev'
66
+ Requires-Dist: nbmake; extra == 'dev'
67
+ Requires-Dist: nbqa; extra == 'dev'
68
+ Requires-Dist: nbstripout; extra == 'dev'
69
+ Requires-Dist: pre-commit; extra == 'dev'
70
+ Requires-Dist: pydoclint; extra == 'dev'
71
+ Requires-Dist: pytest; extra == 'dev'
72
+ Requires-Dist: pytest-cov; extra == 'dev'
73
+ Requires-Dist: pytest-xdist; extra == 'dev'
74
+ Requires-Dist: pyyaml; extra == 'dev'
75
+ Requires-Dist: radon; extra == 'dev'
76
+ Requires-Dist: ruff; extra == 'dev'
77
+ Requires-Dist: spdx-headers; extra == 'dev'
78
+ Requires-Dist: validate-pyproject[all]; extra == 'dev'
79
+ Requires-Dist: versioningit; extra == 'dev'
80
+ Description-Content-Type: text/markdown
81
+
82
+ <p>
83
+ <picture>
84
+ <!-- light mode logo -->
85
+ <source media='(prefers-color-scheme: light)' srcset='https://raw.githubusercontent.com/easyscience/assets-branding/refs/heads/master/easydiffraction/logos/light.svg'>
86
+ <!-- dark mode logo -->
87
+ <source media='(prefers-color-scheme: dark)' srcset='https://raw.githubusercontent.com/easyscience/assets-branding/refs/heads/master/easydiffraction/logos/dark.svg'>
88
+ <!-- default logo == light mode logo -->
89
+ <img src='https://raw.githubusercontent.com/easyscience/assets-branding/refs/heads/master/easydiffraction/logos/light.svg' alt='EasyDiffraction'>
90
+ </picture>
91
+ </p>
92
+
93
+ **EasyDiffraction** is a software for calculating diffraction patterns
94
+ based on a structural model and refining its parameters against
95
+ experimental data.
96
+
97
+ <!-- HOME REPOSITORY SECTION -->
98
+
99
+ **EasyDiffraction** is developed both as a Python library and as a
100
+ cross-platform desktop application.
101
+
102
+ Here, we focus on the Python library. For the graphical user interface
103
+ (GUI), please see the corresponding
104
+ [GUI resources](https://github.com/easyscience/diffraction-app).
105
+
106
+ License:
107
+ [BSD 3-Clause](https://github.com/easyscience/diffraction-lib/blob/master/LICENSE)
108
+
109
+ ## Useful Links
110
+
111
+ ### For Users
112
+
113
+ - ๐Ÿ“–
114
+ [Documentation](https://easyscience.github.io/diffraction-lib/latest)
115
+ - ๐Ÿš€
116
+ [Getting Started](https://easyscience.github.io/diffraction-lib/latest/introduction)
117
+ - ๐Ÿงช
118
+ [Tutorials](https://easyscience.github.io/diffraction-lib/latest/tutorials)
119
+ - ๐Ÿ’ฌ
120
+ [Get in Touch](https://easyscience.github.io/diffraction-lib/latest/introduction/#get-in-touch)
121
+ - ๐Ÿงพ
122
+ [Citation](https://easyscience.github.io/diffraction-lib/latest/introduction/#citation)
123
+
124
+ ### For Contributors
125
+
126
+ - ๐Ÿง‘โ€๐Ÿ’ป [Source Code](https://github.com/easyscience/diffraction-lib)
127
+ - ๐Ÿž
128
+ [Issue Tracker](https://github.com/easyscience/diffraction-lib/issues)
129
+ - ๐Ÿ’ก
130
+ [Discussions](https://github.com/easyscience/diffraction-lib/discussions)
131
+ - ๐Ÿค
132
+ [Contributing Guide](https://github.com/easyscience/diffraction-lib/blob/master/CONTRIBUTING.md)
133
+ - ๐Ÿ›ก
134
+ [Code of Conduct](https://github.com/easyscience/.github/blob/master/CODE_OF_CONDUCT.md)
@@ -0,0 +1,25 @@
1
+ # Third-Party Licenses
2
+
3
+ This file indexes third-party assets vendored in this repository.
4
+
5
+ ## Report LaTeX Styles
6
+
7
+ The vendored report LaTeX style files are documented in
8
+ `src/easydiffraction/report/templates/tex/styles/LICENSES.md`.
9
+
10
+ ## Report HTML Assets
11
+
12
+ The vendored report HTML assets are documented in
13
+ `src/easydiffraction/report/templates/html/vendor/LICENSES.md`.
14
+
15
+ ## Structure-View Three.js
16
+
17
+ The vendored Three.js assets for the crysview structure view (MIT) are
18
+ documented in
19
+ `src/easydiffraction/display/structure/renderers/vendor/threejs/LICENSES.md`.
20
+
21
+ ## Structure-View Element Data
22
+
23
+ The bundled per-element radii and colour palettes (with per-source
24
+ provenance) are documented in
25
+ `src/easydiffraction/display/structure/assets/LICENSES.md`.