phasesmith 0.1.0__tar.gz

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Files changed (190) hide show
  1. phasesmith-0.1.0/Cargo.lock +1262 -0
  2. phasesmith-0.1.0/Cargo.toml +21 -0
  3. phasesmith-0.1.0/LICENSE +21 -0
  4. phasesmith-0.1.0/PKG-INFO +538 -0
  5. phasesmith-0.1.0/README.md +503 -0
  6. phasesmith-0.1.0/THIRD_PARTY_NOTICES.md +93 -0
  7. phasesmith-0.1.0/crates/phasesmith-core/Cargo.toml +27 -0
  8. phasesmith-0.1.0/crates/phasesmith-core/README.md +503 -0
  9. phasesmith-0.1.0/crates/phasesmith-core/benches/profile.rs +407 -0
  10. phasesmith-0.1.0/crates/phasesmith-core/src/background.rs +150 -0
  11. phasesmith-0.1.0/crates/phasesmith-core/src/cw.rs +563 -0
  12. phasesmith-0.1.0/crates/phasesmith-core/src/cw_components.rs +625 -0
  13. phasesmith-0.1.0/crates/phasesmith-core/src/cw_contributions.rs +1330 -0
  14. phasesmith-0.1.0/crates/phasesmith-core/src/cw_fcj.rs +86 -0
  15. phasesmith-0.1.0/crates/phasesmith-core/src/fcj.rs +648 -0
  16. phasesmith-0.1.0/crates/phasesmith-core/src/lib.rs +48 -0
  17. phasesmith-0.1.0/crates/phasesmith-core/src/profile.rs +855 -0
  18. phasesmith-0.1.0/crates/phasesmith-core/src/radiation.rs +138 -0
  19. phasesmith-0.1.0/crates/phasesmith-core/src/tch.rs +493 -0
  20. phasesmith-0.1.0/crates/phasesmith-core/src/tof.rs +985 -0
  21. phasesmith-0.1.0/crates/phasesmith-crystallography/Cargo.toml +35 -0
  22. phasesmith-0.1.0/crates/phasesmith-crystallography/README.md +503 -0
  23. phasesmith-0.1.0/crates/phasesmith-crystallography/benches/reflection_generation.rs +64 -0
  24. phasesmith-0.1.0/crates/phasesmith-crystallography/benches/scattering.rs +46 -0
  25. phasesmith-0.1.0/crates/phasesmith-crystallography/benches/structure_factor.rs +100 -0
  26. phasesmith-0.1.0/crates/phasesmith-crystallography/src/cell.rs +458 -0
  27. phasesmith-0.1.0/crates/phasesmith-crystallography/src/intensity_correction.rs +352 -0
  28. phasesmith-0.1.0/crates/phasesmith-crystallography/src/lib.rs +46 -0
  29. phasesmith-0.1.0/crates/phasesmith-crystallography/src/p1.rs +856 -0
  30. phasesmith-0.1.0/crates/phasesmith-crystallography/src/reflection.rs +671 -0
  31. phasesmith-0.1.0/crates/phasesmith-crystallography/src/scattering.rs +526 -0
  32. phasesmith-0.1.0/crates/phasesmith-crystallography/src/scattering_data.rs +4800 -0
  33. phasesmith-0.1.0/crates/phasesmith-crystallography/src/structure_factor.rs +1994 -0
  34. phasesmith-0.1.0/crates/phasesmith-crystallography/src/symmetry.rs +1237 -0
  35. phasesmith-0.1.0/crates/phasesmith-engine/Cargo.toml +26 -0
  36. phasesmith-0.1.0/crates/phasesmith-engine/README.md +503 -0
  37. phasesmith-0.1.0/crates/phasesmith-engine/benches/structural_pattern.rs +309 -0
  38. phasesmith-0.1.0/crates/phasesmith-engine/src/lib.rs +36 -0
  39. phasesmith-0.1.0/crates/phasesmith-engine/src/prepared_structural_phase.rs +414 -0
  40. phasesmith-0.1.0/crates/phasesmith-engine/src/structural_multiphase.rs +549 -0
  41. phasesmith-0.1.0/crates/phasesmith-engine/src/structural_pattern.rs +1370 -0
  42. phasesmith-0.1.0/crates/phasesmith-engine/src/structural_spectrum.rs +793 -0
  43. phasesmith-0.1.0/crates/phasesmith-execution/Cargo.toml +17 -0
  44. phasesmith-0.1.0/crates/phasesmith-execution/README.md +503 -0
  45. phasesmith-0.1.0/crates/phasesmith-execution/src/lib.rs +291 -0
  46. phasesmith-0.1.0/crates/phasesmith-io/Cargo.toml +19 -0
  47. phasesmith-0.1.0/crates/phasesmith-io/README.md +503 -0
  48. phasesmith-0.1.0/crates/phasesmith-io/src/cif/import.rs +1395 -0
  49. phasesmith-0.1.0/crates/phasesmith-io/src/cif/mod.rs +305 -0
  50. phasesmith-0.1.0/crates/phasesmith-io/src/cif/syntax.rs +373 -0
  51. phasesmith-0.1.0/crates/phasesmith-io/src/lib.rs +20 -0
  52. phasesmith-0.1.0/crates/phasesmith-io/src/powder.rs +551 -0
  53. phasesmith-0.1.0/crates/phasesmith-io/src/space_groups.rs +262 -0
  54. phasesmith-0.1.0/crates/phasesmith-io/tests/cif.rs +274 -0
  55. phasesmith-0.1.0/crates/phasesmith-io/tests/powder.rs +194 -0
  56. phasesmith-0.1.0/crates/phasesmith-io/tests/space_groups.rs +114 -0
  57. phasesmith-0.1.0/crates/phasesmith-model/Cargo.toml +18 -0
  58. phasesmith-0.1.0/crates/phasesmith-model/README.md +503 -0
  59. phasesmith-0.1.0/crates/phasesmith-model/src/lib.rs +743 -0
  60. phasesmith-0.1.0/crates/phasesmith-model/tests/domain.rs +196 -0
  61. phasesmith-0.1.0/crates/phasesmith-persistence/Cargo.toml +26 -0
  62. phasesmith-0.1.0/crates/phasesmith-persistence/README.md +503 -0
  63. phasesmith-0.1.0/crates/phasesmith-persistence/src/arrays.rs +513 -0
  64. phasesmith-0.1.0/crates/phasesmith-persistence/src/lib.rs +537 -0
  65. phasesmith-0.1.0/crates/phasesmith-persistence/src/report.rs +216 -0
  66. phasesmith-0.1.0/crates/phasesmith-persistence/src/rietveld_wire.rs +993 -0
  67. phasesmith-0.1.0/crates/phasesmith-persistence/src/wire.rs +851 -0
  68. phasesmith-0.1.0/crates/phasesmith-persistence/tests/project.rs +482 -0
  69. phasesmith-0.1.0/crates/phasesmith-persistence/tests/rietveld.rs +425 -0
  70. phasesmith-0.1.0/crates/phasesmith-py/Cargo.toml +31 -0
  71. phasesmith-0.1.0/crates/phasesmith-py/README.md +503 -0
  72. phasesmith-0.1.0/crates/phasesmith-py/src/lib.rs +4028 -0
  73. phasesmith-0.1.0/crates/phasesmith-py/src/rietveld.rs +961 -0
  74. phasesmith-0.1.0/crates/phasesmith-validation/Cargo.toml +32 -0
  75. phasesmith-0.1.0/crates/phasesmith-validation/README.md +503 -0
  76. phasesmith-0.1.0/crates/phasesmith-validation/src/bin/phasesmith-validation.rs +42 -0
  77. phasesmith-0.1.0/crates/phasesmith-validation/src/dataset.rs +455 -0
  78. phasesmith-0.1.0/crates/phasesmith-validation/src/lib.rs +18 -0
  79. phasesmith-0.1.0/crates/phasesmith-validation/src/pbso4.rs +1224 -0
  80. phasesmith-0.1.0/crates/phasesmith-validation/src/qarr.rs +705 -0
  81. phasesmith-0.1.0/crates/phasesmith-validation/src/report.rs +284 -0
  82. phasesmith-0.1.0/crates/phasesmith-validation/src/sucrose.rs +420 -0
  83. phasesmith-0.1.0/crates/phasesmith-validation/tests/cli.rs +20 -0
  84. phasesmith-0.1.0/crates/phasesmith-validation/tests/contracts.rs +165 -0
  85. phasesmith-0.1.0/crates/phasesmith-validation/tests/pbso4.rs +139 -0
  86. phasesmith-0.1.0/crates/phasesmith-validation/tests/qarr.rs +103 -0
  87. phasesmith-0.1.0/crates/phasesmith-validation/tests/sucrose.rs +74 -0
  88. phasesmith-0.1.0/crates/phasesmith-workflows/Cargo.toml +38 -0
  89. phasesmith-0.1.0/crates/phasesmith-workflows/README.md +503 -0
  90. phasesmith-0.1.0/crates/phasesmith-workflows/benches/backgrounds.rs +65 -0
  91. phasesmith-0.1.0/crates/phasesmith-workflows/benches/lebail.rs +210 -0
  92. phasesmith-0.1.0/crates/phasesmith-workflows/benches/rietveld.rs +207 -0
  93. phasesmith-0.1.0/crates/phasesmith-workflows/examples/joint_pbso4.rs +467 -0
  94. phasesmith-0.1.0/crates/phasesmith-workflows/src/backgrounds.rs +955 -0
  95. phasesmith-0.1.0/crates/phasesmith-workflows/src/constraints.rs +674 -0
  96. phasesmith-0.1.0/crates/phasesmith-workflows/src/lattice.rs +921 -0
  97. phasesmith-0.1.0/crates/phasesmith-workflows/src/lebail.rs +2778 -0
  98. phasesmith-0.1.0/crates/phasesmith-workflows/src/lib.rs +106 -0
  99. phasesmith-0.1.0/crates/phasesmith-workflows/src/parameters.rs +403 -0
  100. phasesmith-0.1.0/crates/phasesmith-workflows/src/quantitative.rs +153 -0
  101. phasesmith-0.1.0/crates/phasesmith-workflows/src/residuals.rs +200 -0
  102. phasesmith-0.1.0/crates/phasesmith-workflows/src/rietveld.rs +1210 -0
  103. phasesmith-0.1.0/crates/phasesmith-workflows/src/rietveld_general_objective.rs +814 -0
  104. phasesmith-0.1.0/crates/phasesmith-workflows/src/rietveld_general_parameters.rs +666 -0
  105. phasesmith-0.1.0/crates/phasesmith-workflows/src/rietveld_general_solver.rs +1194 -0
  106. phasesmith-0.1.0/crates/phasesmith-workflows/src/rietveld_joint.rs +573 -0
  107. phasesmith-0.1.0/crates/phasesmith-workflows/src/rietveld_joint_solver.rs +973 -0
  108. phasesmith-0.1.0/crates/phasesmith-workflows/src/rietveld_objective.rs +327 -0
  109. phasesmith-0.1.0/crates/phasesmith-workflows/src/rietveld_parameters.rs +760 -0
  110. phasesmith-0.1.0/crates/phasesmith-workflows/src/rietveld_project.rs +320 -0
  111. phasesmith-0.1.0/crates/phasesmith-workflows/src/rietveld_recipe.rs +902 -0
  112. phasesmith-0.1.0/crates/phasesmith-workflows/src/rietveld_solver.rs +824 -0
  113. phasesmith-0.1.0/crates/phasesmith-workflows/src/runtime.rs +852 -0
  114. phasesmith-0.1.0/crates/phasesmith-workflows/src/sample_physics.rs +656 -0
  115. phasesmith-0.1.0/crates/phasesmith-workflows/tests/backgrounds.rs +236 -0
  116. phasesmith-0.1.0/crates/phasesmith-workflows/tests/constraints.rs +231 -0
  117. phasesmith-0.1.0/crates/phasesmith-workflows/tests/lattice.rs +406 -0
  118. phasesmith-0.1.0/crates/phasesmith-workflows/tests/lebail.rs +994 -0
  119. phasesmith-0.1.0/crates/phasesmith-workflows/tests/quantitative.rs +45 -0
  120. phasesmith-0.1.0/crates/phasesmith-workflows/tests/residuals.rs +152 -0
  121. phasesmith-0.1.0/crates/phasesmith-workflows/tests/rietveld.rs +588 -0
  122. phasesmith-0.1.0/crates/phasesmith-workflows/tests/rietveld_general.rs +750 -0
  123. phasesmith-0.1.0/crates/phasesmith-workflows/tests/rietveld_general_solver.rs +726 -0
  124. phasesmith-0.1.0/crates/phasesmith-workflows/tests/rietveld_joint.rs +649 -0
  125. phasesmith-0.1.0/crates/phasesmith-workflows/tests/rietveld_parameters.rs +547 -0
  126. phasesmith-0.1.0/crates/phasesmith-workflows/tests/rietveld_project.rs +279 -0
  127. phasesmith-0.1.0/crates/phasesmith-workflows/tests/rietveld_recipe.rs +509 -0
  128. phasesmith-0.1.0/crates/phasesmith-workflows/tests/rietveld_solver.rs +297 -0
  129. phasesmith-0.1.0/crates/phasesmith-workflows/tests/rietveld_topology.rs +336 -0
  130. phasesmith-0.1.0/crates/phasesmith-workflows/tests/runtime.rs +307 -0
  131. phasesmith-0.1.0/crates/phasesmith-workflows/tests/sample_physics.rs +438 -0
  132. phasesmith-0.1.0/pyproject.toml +55 -0
  133. phasesmith-0.1.0/python/phasesmith/__init__.py +400 -0
  134. phasesmith-0.1.0/python/phasesmith/_api.py +216 -0
  135. phasesmith-0.1.0/python/phasesmith/_native_persistence.py +543 -0
  136. phasesmith-0.1.0/python/phasesmith/background.py +172 -0
  137. phasesmith-0.1.0/python/phasesmith/background_reference.py +43 -0
  138. phasesmith-0.1.0/python/phasesmith/calculation.py +426 -0
  139. phasesmith-0.1.0/python/phasesmith/control.py +103 -0
  140. phasesmith-0.1.0/python/phasesmith/crystallography.py +620 -0
  141. phasesmith-0.1.0/python/phasesmith/crystallography_reference.py +205 -0
  142. phasesmith-0.1.0/python/phasesmith/cw.py +196 -0
  143. phasesmith-0.1.0/python/phasesmith/execution.py +90 -0
  144. phasesmith-0.1.0/python/phasesmith/extensions.py +291 -0
  145. phasesmith-0.1.0/python/phasesmith/fcj.py +147 -0
  146. phasesmith-0.1.0/python/phasesmith/instrument.py +107 -0
  147. phasesmith-0.1.0/python/phasesmith/integrations/__init__.py +5 -0
  148. phasesmith-0.1.0/python/phasesmith/integrations/dioptas.py +269 -0
  149. phasesmith-0.1.0/python/phasesmith/intensity_corrections.py +187 -0
  150. phasesmith-0.1.0/python/phasesmith/io/__init__.py +20 -0
  151. phasesmith-0.1.0/python/phasesmith/io/_gemmi.py +792 -0
  152. phasesmith-0.1.0/python/phasesmith/io/cif.py +172 -0
  153. phasesmith-0.1.0/python/phasesmith/io/powder.py +126 -0
  154. phasesmith-0.1.0/python/phasesmith/io/space_groups.py +56 -0
  155. phasesmith-0.1.0/python/phasesmith/oracle/__init__.py +16 -0
  156. phasesmith-0.1.0/python/phasesmith/oracle/_pinned_probe.py +91 -0
  157. phasesmith-0.1.0/python/phasesmith/oracle/conventions.py +26 -0
  158. phasesmith-0.1.0/python/phasesmith/oracle/fixtures.py +200 -0
  159. phasesmith-0.1.0/python/phasesmith/oracle/gsasii.py +96 -0
  160. phasesmith-0.1.0/python/phasesmith/pattern.py +345 -0
  161. phasesmith-0.1.0/python/phasesmith/persistence.py +1693 -0
  162. phasesmith-0.1.0/python/phasesmith/phase.py +311 -0
  163. phasesmith-0.1.0/python/phasesmith/project.py +270 -0
  164. phasesmith-0.1.0/python/phasesmith/py.typed +1 -0
  165. phasesmith-0.1.0/python/phasesmith/quantitative.py +136 -0
  166. phasesmith-0.1.0/python/phasesmith/radiation.py +337 -0
  167. phasesmith-0.1.0/python/phasesmith/reference.py +1074 -0
  168. phasesmith-0.1.0/python/phasesmith/refinement/__init__.py +175 -0
  169. phasesmith-0.1.0/python/phasesmith/refinement/background.py +410 -0
  170. phasesmith-0.1.0/python/phasesmith/refinement/core.py +495 -0
  171. phasesmith-0.1.0/python/phasesmith/refinement/lattice.py +685 -0
  172. phasesmith-0.1.0/python/phasesmith/refinement/lebail.py +1533 -0
  173. phasesmith-0.1.0/python/phasesmith/refinement/rietveld.py +2783 -0
  174. phasesmith-0.1.0/python/phasesmith/refinement/runtime.py +295 -0
  175. phasesmith-0.1.0/python/phasesmith/refinement/scipy.py +54 -0
  176. phasesmith-0.1.0/python/phasesmith/refinement/workflow.py +477 -0
  177. phasesmith-0.1.0/python/phasesmith/reporting.py +192 -0
  178. phasesmith-0.1.0/python/phasesmith/results.py +173 -0
  179. phasesmith-0.1.0/python/phasesmith/sample.py +302 -0
  180. phasesmith-0.1.0/python/phasesmith/scattering.py +487 -0
  181. phasesmith-0.1.0/python/phasesmith/scattering_reference.py +80 -0
  182. phasesmith-0.1.0/python/phasesmith/structural_calculation.py +1090 -0
  183. phasesmith-0.1.0/python/phasesmith/structure.py +341 -0
  184. phasesmith-0.1.0/python/phasesmith/symmetry.py +418 -0
  185. phasesmith-0.1.0/python/phasesmith/symmetry_reference.py +131 -0
  186. phasesmith-0.1.0/python/phasesmith/terminal.py +128 -0
  187. phasesmith-0.1.0/python/phasesmith/tof.py +121 -0
  188. phasesmith-0.1.0/python/phasesmith/validation/__init__.py +37 -0
  189. phasesmith-0.1.0/python/phasesmith/validation/datasets.py +282 -0
  190. phasesmith-0.1.0/python/phasesmith/validation/real_data.py +1095 -0
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