agox 3.9.0__tar.gz → 3.10.0rc1__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 (543) hide show
  1. {agox-3.9.0/agox.egg-info → agox-3.10.0rc1}/PKG-INFO +7 -4
  2. {agox-3.9.0 → agox-3.10.0rc1}/agox/__init__.py +1 -1
  3. {agox-3.9.0 → agox-3.10.0rc1}/agox/models/GPR/priors/repulsive.c +144 -162
  4. {agox-3.9.0 → agox-3.10.0rc1}/agox/models/descriptors/fingerprint_cython/angular_fingerprintFeature_cy.c +144 -162
  5. {agox-3.9.0 → agox-3.10.0rc1}/agox/module.py +29 -7
  6. {agox-3.9.0 → agox-3.10.0rc1}/agox/test/analysis_tests/test_descriptor_property.py +1 -1
  7. {agox-3.9.0 → agox-3.10.0rc1}/agox/test/analysis_tests/test_energy_property.py +2 -1
  8. {agox-3.9.0 → agox-3.10.0rc1}/agox/test/analysis_tests/test_restart_data.py +1 -1
  9. {agox-3.9.0 → agox-3.10.0rc1}/agox/test/conftest.py +47 -3
  10. agox-3.10.0rc1/agox/test/database_tests/conftest.py +65 -0
  11. {agox-3.9.0 → agox-3.10.0rc1}/agox/test/database_tests/database_test.py +1 -0
  12. agox-3.10.0rc1/agox/test/database_tests/database_test_memory.py +56 -0
  13. agox-3.10.0rc1/agox/test/database_tests/database_test_written.py +54 -0
  14. agox-3.10.0rc1/agox/test/datasets/databases/bh_test_databases/experiment.pckl +0 -0
  15. agox-3.10.0rc1/agox/test/evaluator_tests/check_callback_test.py +52 -0
  16. {agox-3.9.0 → agox-3.10.0rc1}/agox/test/generator_tests/generator_test.py +6 -2
  17. {agox-3.9.0 → agox-3.10.0rc1}/agox/test/generator_tests/test_sampling.py +1 -0
  18. agox-3.10.0rc1/agox/test/model_tests/test_calculator_model.py +69 -0
  19. agox-3.10.0rc1/agox/test/model_tests/test_composition_model.py +45 -0
  20. {agox-3.9.0 → agox-3.10.0rc1}/agox/test/model_tests/test_global_gpr_jax.py +2 -1
  21. {agox-3.9.0 → agox-3.10.0rc1}/agox/test/postprocessor_tests/postprocessor_test.py +4 -0
  22. agox-3.10.0rc1/agox/test/postprocessor_tests/ray_relax.py +72 -0
  23. agox-3.10.0rc1/agox/test/replica_exchange/conftest.py +66 -0
  24. agox-3.10.0rc1/agox/test/replica_exchange/test_sample.py +76 -0
  25. agox-3.10.0rc1/agox/test/replica_exchange/test_sampler.py +33 -0
  26. {agox-3.9.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/script_bh_bulk_vasp.py +9 -1
  27. {agox-3.9.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/script_bh_cluster_vasp.py +9 -1
  28. {agox-3.9.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_bh/script_bh_surface_vasp.py +9 -1
  29. {agox-3.9.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/script_gofee_bulk_vasp.py +8 -1
  30. {agox-3.9.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/script_gofee_cluster_vasp.py +8 -1
  31. {agox-3.9.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_gofee/script_gofee_surface_vasp.py +8 -0
  32. {agox-3.9.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_graph_filt/test_graph_filtering_gofee.py +1 -0
  33. {agox-3.9.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_md/test_md_bh.py +2 -1
  34. agox-3.10.0rc1/agox/test/run_tests/tests_pt/expected_outputs/rex_test/db0.db +0 -0
  35. agox-3.9.0/agox/test/run_tests/tests_pt/script_pt.py → agox-3.10.0rc1/agox/test/run_tests/tests_pt/script_rex.py +4 -6
  36. agox-3.10.0rc1/agox/test/run_tests/tests_pt/test_rex.py +10 -0
  37. agox-3.10.0rc1/agox/test/run_tests/tests_rex/expected_outputs/rex_emt_test/confinement_plot_RandomGenerator.png +0 -0
  38. agox-3.10.0rc1/agox/test/run_tests/tests_rex/expected_outputs/rex_emt_test/confinement_plot_RattleGenerator.png +0 -0
  39. agox-3.10.0rc1/agox/test/run_tests/tests_rex/expected_outputs/rex_emt_test/db0.db +0 -0
  40. agox-3.10.0rc1/agox/test/run_tests/tests_rex/script_rex_dft.py +149 -0
  41. agox-3.10.0rc1/agox/test/run_tests/tests_rex/script_rex_emt.py +143 -0
  42. agox-3.9.0/agox/test/run_tests/tests_pt/test_pt.py → agox-3.10.0rc1/agox/test/run_tests/tests_rex/test_replica.py +2 -2
  43. {agox-3.9.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/script_rss_bulk_vasp.py +9 -0
  44. {agox-3.9.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/script_rss_cluster_vasp.py +8 -0
  45. {agox-3.9.0 → agox-3.10.0rc1}/agox/test/run_tests/tests_rss/script_rss_surface_vasp.py +9 -0
  46. agox-3.10.0rc1/agox/test/test_fixtures.py +15 -0
  47. {agox-3.9.0 → agox-3.10.0rc1}/agox/test/test_utils.py +4 -0
  48. {agox-3.9.0 → agox-3.10.0rc1/agox.egg-info}/PKG-INFO +7 -4
  49. {agox-3.9.0 → agox-3.10.0rc1}/agox.egg-info/SOURCES.txt +23 -202
  50. {agox-3.9.0 → agox-3.10.0rc1}/agox.egg-info/requires.txt +5 -2
  51. {agox-3.9.0 → agox-3.10.0rc1}/pyproject.toml +7 -2
  52. agox-3.9.0/agox/acquisitors/ABC_acquisitor.py +0 -207
  53. agox-3.9.0/agox/acquisitors/EI.py +0 -51
  54. agox-3.9.0/agox/acquisitors/LCB.py +0 -101
  55. agox-3.9.0/agox/acquisitors/LCB_penalty.py +0 -129
  56. agox-3.9.0/agox/acquisitors/LCB_power.py +0 -16
  57. agox-3.9.0/agox/acquisitors/__init__.py +0 -36
  58. agox-3.9.0/agox/acquisitors/meta_acquisitor.py +0 -23
  59. agox-3.9.0/agox/analysis/__init__.py +0 -26
  60. agox-3.9.0/agox/analysis/criterion/__init__.py +0 -5
  61. agox-3.9.0/agox/analysis/criterion/base_criterion/__init__.py +0 -1
  62. agox-3.9.0/agox/analysis/criterion/base_criterion/base_criterion.py +0 -20
  63. agox-3.9.0/agox/analysis/criterion/base_criterion/discrete_distribution.py +0 -51
  64. agox-3.9.0/agox/analysis/criterion/distance.py +0 -58
  65. agox-3.9.0/agox/analysis/criterion/threshold.py +0 -44
  66. agox-3.9.0/agox/analysis/plot/__init__.py +0 -8
  67. agox-3.9.0/agox/analysis/plot/property_plot.py +0 -44
  68. agox-3.9.0/agox/analysis/plot/success_plot.py +0 -36
  69. agox-3.9.0/agox/analysis/property/__init__.py +0 -4
  70. agox-3.9.0/agox/analysis/property/descriptor_property.py +0 -36
  71. agox-3.9.0/agox/analysis/property/energy.py +0 -38
  72. agox-3.9.0/agox/analysis/property/free_energy.py +0 -48
  73. agox-3.9.0/agox/analysis/property/property.py +0 -67
  74. agox-3.9.0/agox/analysis/search_analysis.py +0 -210
  75. agox-3.9.0/agox/analysis/search_data.py +0 -234
  76. agox-3.9.0/agox/candidates/ABC_candidate.py +0 -353
  77. agox-3.9.0/agox/candidates/__init__.py +0 -16
  78. agox-3.9.0/agox/candidates/standard.py +0 -27
  79. agox-3.9.0/agox/cli/cli_analysis.py +0 -178
  80. agox-3.9.0/agox/cli/cli_convert.py +0 -89
  81. agox-3.9.0/agox/cli/cli_graph_sorting.py +0 -238
  82. agox-3.9.0/agox/cli/cli_notebook.py +0 -108
  83. agox-3.9.0/agox/cli/cli_plot.py +0 -92
  84. agox-3.9.0/agox/cli/main.py +0 -22
  85. agox-3.9.0/agox/collectors/ABC_collector.py +0 -153
  86. agox-3.9.0/agox/collectors/__init__.py +0 -21
  87. agox-3.9.0/agox/collectors/parallel_tempering.py +0 -174
  88. agox-3.9.0/agox/collectors/ray_collector.py +0 -93
  89. agox-3.9.0/agox/collectors/standard.py +0 -74
  90. agox-3.9.0/agox/databases/ABC_database.py +0 -89
  91. agox-3.9.0/agox/databases/__init__.py +0 -14
  92. agox-3.9.0/agox/databases/concurrent_ordered.py +0 -41
  93. agox-3.9.0/agox/databases/database.py +0 -466
  94. agox-3.9.0/agox/databases/database_concurrent.py +0 -213
  95. agox-3.9.0/agox/databases/database_utilities.py +0 -143
  96. agox-3.9.0/agox/environments/ABC_environment.py +0 -163
  97. agox-3.9.0/agox/environments/__init__.py +0 -16
  98. agox-3.9.0/agox/environments/environment.py +0 -145
  99. agox-3.9.0/agox/evaluators/ABC_evaluator.py +0 -121
  100. agox-3.9.0/agox/evaluators/__init__.py +0 -24
  101. agox-3.9.0/agox/evaluators/local_optimization.py +0 -134
  102. agox-3.9.0/agox/evaluators/rattle.py +0 -24
  103. agox-3.9.0/agox/evaluators/single_point.py +0 -19
  104. agox-3.9.0/agox/generators/ABC_generator.py +0 -290
  105. agox-3.9.0/agox/generators/MD.py +0 -147
  106. agox-3.9.0/agox/generators/__init__.py +0 -55
  107. agox-3.9.0/agox/generators/block_generators/ABC_block.py +0 -171
  108. agox-3.9.0/agox/generators/block_generators/__init__.py +0 -2
  109. agox-3.9.0/agox/generators/block_generators/random.py +0 -57
  110. agox-3.9.0/agox/generators/block_generators/rattle.py +0 -82
  111. agox-3.9.0/agox/generators/ce_generator.py +0 -138
  112. agox-3.9.0/agox/generators/cog.py +0 -58
  113. agox-3.9.0/agox/generators/complementary_energy/attractor_methods/ABC_attractors.py +0 -31
  114. agox-3.9.0/agox/generators/complementary_energy/attractor_methods/__init__.py +0 -0
  115. agox-3.9.0/agox/generators/complementary_energy/attractor_methods/ce_attractors_another_structure.py +0 -67
  116. agox-3.9.0/agox/generators/complementary_energy/attractor_methods/ce_attractors_current_structure.py +0 -63
  117. agox-3.9.0/agox/generators/complementary_energy/attractor_methods/ce_attractors_interpolation.py +0 -71
  118. agox-3.9.0/agox/generators/complementary_energy/attractor_methods/ce_attractors_kmeans.py +0 -83
  119. agox-3.9.0/agox/generators/complementary_energy/ce_calculators.py +0 -235
  120. agox-3.9.0/agox/generators/permutation.py +0 -145
  121. agox-3.9.0/agox/generators/random.py +0 -74
  122. agox-3.9.0/agox/generators/rattle.py +0 -70
  123. agox-3.9.0/agox/generators/replace.py +0 -71
  124. agox-3.9.0/agox/generators/reuse.py +0 -62
  125. agox-3.9.0/agox/generators/sampling.py +0 -26
  126. agox-3.9.0/agox/generators/steepest_descent.py +0 -46
  127. agox-3.9.0/agox/generators/symmetry.py +0 -302
  128. agox-3.9.0/agox/generators/symmetry_permutation.py +0 -197
  129. agox-3.9.0/agox/generators/symmetry_rattle.py +0 -386
  130. agox-3.9.0/agox/generators/symmetry_utils/__init__.py +0 -0
  131. agox-3.9.0/agox/generators/symmetry_utils/symmetry_enforcer.py +0 -1611
  132. agox-3.9.0/agox/generators/symmetry_utils/symmetry_groups.py +0 -933
  133. agox-3.9.0/agox/helpers/__init__.py +0 -5
  134. agox-3.9.0/agox/helpers/confinement.py +0 -92
  135. agox-3.9.0/agox/helpers/gpaw_io.py +0 -179
  136. agox-3.9.0/agox/helpers/gpaw_subprocess.py +0 -59
  137. agox-3.9.0/agox/main/__init__.py +0 -5
  138. agox-3.9.0/agox/main/agox.py +0 -222
  139. agox-3.9.0/agox/main/state.py +0 -153
  140. agox-3.9.0/agox/models/ABC_model.py +0 -585
  141. agox-3.9.0/agox/models/GPR/GPR.py +0 -844
  142. agox-3.9.0/agox/models/GPR/__init__.py +0 -5
  143. agox-3.9.0/agox/models/GPR/kernels/__init__.py +0 -1
  144. agox-3.9.0/agox/models/GPR/kernels/kernels.py +0 -141
  145. agox-3.9.0/agox/models/GPR/local_mean.py +0 -50
  146. agox-3.9.0/agox/models/GPR/priors/__init__.py +0 -1
  147. agox-3.9.0/agox/models/GPR/priors/setup.py +0 -6
  148. agox-3.9.0/agox/models/GPR/sGPR.py +0 -785
  149. agox-3.9.0/agox/models/GPR/sGPR_ensemble.py +0 -106
  150. agox-3.9.0/agox/models/__init__.py +0 -15
  151. agox-3.9.0/agox/models/datasets/__init__.py +0 -1
  152. agox-3.9.0/agox/models/datasets/loader.py +0 -11
  153. agox-3.9.0/agox/models/descriptors/ABC_descriptor.py +0 -156
  154. agox-3.9.0/agox/models/descriptors/__init__.py +0 -8
  155. agox-3.9.0/agox/models/descriptors/acsf.py +0 -198
  156. agox-3.9.0/agox/models/descriptors/exponential_density.py +0 -131
  157. agox-3.9.0/agox/models/descriptors/fingerprint.py +0 -126
  158. agox-3.9.0/agox/models/descriptors/fingerprint_cython/__init__.py +0 -0
  159. agox-3.9.0/agox/models/descriptors/fingerprint_cython/setup.py +0 -6
  160. agox-3.9.0/agox/models/descriptors/fingerprint_jax/__init__.py +0 -0
  161. agox-3.9.0/agox/models/descriptors/fingerprint_jax/fingerprint_jax.py +0 -346
  162. agox-3.9.0/agox/models/descriptors/fingerprint_jax/utils.py +0 -337
  163. agox-3.9.0/agox/models/descriptors/scale_select_descriptor.py +0 -78
  164. agox-3.9.0/agox/models/descriptors/simple_fingerprint.py +0 -67
  165. agox-3.9.0/agox/models/descriptors/soap.py +0 -166
  166. agox-3.9.0/agox/models/descriptors/spectral_graph_descriptor.py +0 -84
  167. agox-3.9.0/agox/models/descriptors/type_descriptor.py +0 -49
  168. agox-3.9.0/agox/models/descriptors/voronoi.py +0 -270
  169. agox-3.9.0/agox/models/descriptors/voronoi_site.py +0 -118
  170. agox-3.9.0/agox/models/priors/constant.py +0 -12
  171. agox-3.9.0/agox/models/schnetpack/__init__.py +0 -0
  172. agox-3.9.0/agox/models/schnetpack/schnetpack.py +0 -381
  173. agox-3.9.0/agox/observer/__init__.py +0 -6
  174. agox-3.9.0/agox/observer/finalization_handler.py +0 -52
  175. agox-3.9.0/agox/observer/observer.py +0 -217
  176. agox-3.9.0/agox/observer/observer_handler.py +0 -187
  177. agox-3.9.0/agox/observer/observer_method.py +0 -123
  178. agox-3.9.0/agox/postprocessors/ABC_postprocess.py +0 -104
  179. agox-3.9.0/agox/postprocessors/__init__.py +0 -35
  180. agox-3.9.0/agox/postprocessors/centering.py +0 -37
  181. agox-3.9.0/agox/postprocessors/disjoint_filtering.py +0 -82
  182. agox-3.9.0/agox/postprocessors/minimum_dist.py +0 -88
  183. agox-3.9.0/agox/postprocessors/ray_relax.py +0 -165
  184. agox-3.9.0/agox/postprocessors/relax.py +0 -100
  185. agox-3.9.0/agox/postprocessors/surface_centering.py +0 -92
  186. agox-3.9.0/agox/postprocessors/wrap.py +0 -17
  187. agox-3.9.0/agox/samplers/ABC_sampler.py +0 -223
  188. agox-3.9.0/agox/samplers/__init__.py +0 -36
  189. agox-3.9.0/agox/samplers/concurrent_tempering.py +0 -179
  190. agox-3.9.0/agox/samplers/fixed_sampler.py +0 -39
  191. agox-3.9.0/agox/samplers/genetic.py +0 -215
  192. agox-3.9.0/agox/samplers/kernel_similarity.py +0 -150
  193. agox-3.9.0/agox/samplers/kmeans.py +0 -203
  194. agox-3.9.0/agox/samplers/metropolis.py +0 -95
  195. agox-3.9.0/agox/samplers/parallel_tempering.py +0 -282
  196. agox-3.9.0/agox/samplers/spectral_graph.py +0 -158
  197. agox-3.9.0/agox/test/__init__.py +0 -0
  198. agox-3.9.0/agox/test/datasets/databases/bh_test_databases/experiment.pckl +0 -0
  199. agox-3.9.0/agox/test/model_tests/__init__.py +0 -0
  200. agox-3.9.0/agox/test/run_tests/tests_pt/expected_outputs/pt_test/db0.db +0 -0
  201. agox-3.9.0/agox/test/run_tests/tests_pt/expected_outputs/pt_test/db0_tracker.npz +0 -0
  202. agox-3.9.0/agox/utils/__init__.py +0 -1
  203. agox-3.9.0/agox/utils/cache.py +0 -70
  204. agox-3.9.0/agox/utils/constraints/__init__.py +0 -1
  205. agox-3.9.0/agox/utils/constraints/box_constraint.py +0 -165
  206. agox-3.9.0/agox/utils/convert_database.py +0 -101
  207. agox-3.9.0/agox/utils/decorators.py +0 -22
  208. agox-3.9.0/agox/utils/filters/ABC_filter.py +0 -102
  209. agox-3.9.0/agox/utils/filters/__init__.py +0 -25
  210. agox-3.9.0/agox/utils/filters/all.py +0 -25
  211. agox-3.9.0/agox/utils/filters/energy.py +0 -34
  212. agox-3.9.0/agox/utils/filters/feature_distance.py +0 -95
  213. agox-3.9.0/agox/utils/filters/filter.py +0 -57
  214. agox-3.9.0/agox/utils/filters/kmeans_energy.py +0 -57
  215. agox-3.9.0/agox/utils/filters/none.py +0 -25
  216. agox-3.9.0/agox/utils/filters/random.py +0 -29
  217. agox-3.9.0/agox/utils/filters/sparse_filter.py +0 -72
  218. agox-3.9.0/agox/utils/filters/voronoi.py +0 -118
  219. agox-3.9.0/agox/utils/graph_sorting.py +0 -145
  220. agox-3.9.0/agox/utils/jupyter_interactive.py +0 -383
  221. agox-3.9.0/agox/utils/matplotlib_utils.py +0 -18
  222. agox-3.9.0/agox/utils/metrics/__init__.py +0 -17
  223. agox-3.9.0/agox/utils/metrics/calibration.py +0 -270
  224. agox-3.9.0/agox/utils/metrics/metrics.py +0 -21
  225. agox-3.9.0/agox/utils/numerical_derivative.py +0 -22
  226. agox-3.9.0/agox/utils/plot/__init__.py +0 -4
  227. agox-3.9.0/agox/utils/plot/colors.py +0 -255
  228. agox-3.9.0/agox/utils/plot/plot_atoms.py +0 -159
  229. agox-3.9.0/agox/utils/plot/plot_cell.py +0 -82
  230. agox-3.9.0/agox/utils/plot/plot_parity.py +0 -186
  231. agox-3.9.0/agox/utils/plot/utils.py +0 -60
  232. agox-3.9.0/agox/utils/ray/__init__.py +0 -4
  233. agox-3.9.0/agox/utils/ray/actor.py +0 -71
  234. agox-3.9.0/agox/utils/ray/pool.py +0 -509
  235. agox-3.9.0/agox/utils/ray/pool_startup.py +0 -87
  236. agox-3.9.0/agox/utils/ray/pool_user.py +0 -184
  237. agox-3.9.0/agox/utils/ray/startup.py +0 -159
  238. agox-3.9.0/agox/utils/sparsifiers/ABC_sparsifier.py +0 -124
  239. agox-3.9.0/agox/utils/sparsifiers/CUR.py +0 -24
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  249. agox-3.9.0/agox/writer/writer.py +0 -38
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  540. {agox-3.9.0 → agox-3.10.0rc1}/agox.egg-info/entry_points.txt +0 -0
  541. {agox-3.9.0 → agox-3.10.0rc1}/agox.egg-info/top_level.txt +0 -0
  542. {agox-3.9.0 → agox-3.10.0rc1}/setup.cfg +0 -0
  543. {agox-3.9.0 → agox-3.10.0rc1}/setup.py +0 -0
{agox-3.9.0/agox.egg-info → agox-3.10.0rc1}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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- Metadata-Version: 2.1
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+ Metadata-Version: 2.4
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  Name: agox
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- Version: 3.9.0
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+ Version: 3.10.0rc1
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  Summary: Atomistic Global Optimziation X is a framework for structure optimization in materials science.
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  Author: AGOX Developers
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  Author-email: "Mads-Peter V. Christiansen" <machri@phys.au.dk>, Nikolaj Rønne <nronne@phys.au.dk>, Bjørk Hammer <hammer@phys.au.dk>
@@ -30,8 +30,6 @@ Requires-Dist: importlib-resources>1.3; python_version < "3.9"
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  Requires-Dist: dscribe>=2.0.0
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  Requires-Dist: nbformat
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  Requires-Dist: typing_extensions
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- Requires-Dist: jax
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- Requires-Dist: jaxlib
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  Requires-Dist: ray
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  Requires-Dist: rich-click>=1.8.3
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  Provides-Extra: test
@@ -43,8 +41,13 @@ Requires-Dist: furo; extra == "docs"
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  Requires-Dist: sphinx-autoapi; extra == "docs"
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  Requires-Dist: sphinx-copybutton; extra == "docs"
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  Requires-Dist: sphinx-tabs; extra == "docs"
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+ Provides-Extra: torchjax
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+ Requires-Dist: torch; extra == "torchjax"
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+ Requires-Dist: jax; extra == "torchjax"
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+ Requires-Dist: jaxlib; extra == "torchjax"
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  Provides-Extra: all
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  Requires-Dist: agox[docs,test]; extra == "all"
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+ Dynamic: license-file
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  # Atomistic Global Optimization X (AGOX)
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{agox-3.9.0 → agox-3.10.0rc1}/agox/__init__.py RENAMED
@@ -1,7 +1,7 @@
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  import os
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2
 
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  # Versioning
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- __version_info__ = (3, 9, 0)
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+ __version_info__ = (3, 10, 0)
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  __version__ = "{}.{}.{}".format(*__version_info__)
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  # Extra versioning - Mainly for managing Pypi releases.