sequenzo 0.1.24__cp311-cp311-macosx_10_9_x86_64.whl

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  1. _sequenzo_fastcluster.cpython-311-darwin.so +0 -0
  2. sequenzo/__init__.py +240 -0
  3. sequenzo/big_data/__init__.py +12 -0
  4. sequenzo/big_data/clara/__init__.py +26 -0
  5. sequenzo/big_data/clara/clara.py +474 -0
  6. sequenzo/big_data/clara/utils/__init__.py +27 -0
  7. sequenzo/big_data/clara/utils/aggregatecases.py +92 -0
  8. sequenzo/big_data/clara/utils/davies_bouldin.py +91 -0
  9. sequenzo/big_data/clara/utils/get_weighted_diss.cpython-311-darwin.so +0 -0
  10. sequenzo/big_data/clara/utils/wfcmdd.py +205 -0
  11. sequenzo/big_data/clara/visualization.py +88 -0
  12. sequenzo/clustering/KMedoids.py +178 -0
  13. sequenzo/clustering/__init__.py +30 -0
  14. sequenzo/clustering/clustering_c_code.cpython-311-darwin.so +0 -0
  15. sequenzo/clustering/hierarchical_clustering.py +1256 -0
  16. sequenzo/clustering/sequenzo_fastcluster/fastcluster.py +495 -0
  17. sequenzo/clustering/sequenzo_fastcluster/src/fastcluster.cpp +1877 -0
  18. sequenzo/clustering/sequenzo_fastcluster/src/fastcluster_python.cpp +1264 -0
  19. sequenzo/clustering/src/KMedoid.cpp +263 -0
  20. sequenzo/clustering/src/PAM.cpp +237 -0
  21. sequenzo/clustering/src/PAMonce.cpp +265 -0
  22. sequenzo/clustering/src/cluster_quality.cpp +496 -0
  23. sequenzo/clustering/src/cluster_quality.h +128 -0
  24. sequenzo/clustering/src/cluster_quality_backup.cpp +570 -0
  25. sequenzo/clustering/src/module.cpp +228 -0
  26. sequenzo/clustering/src/weightedinertia.cpp +111 -0
  27. sequenzo/clustering/utils/__init__.py +27 -0
  28. sequenzo/clustering/utils/disscenter.py +122 -0
  29. sequenzo/data_preprocessing/__init__.py +20 -0
  30. sequenzo/data_preprocessing/helpers.py +256 -0
  31. sequenzo/datasets/__init__.py +41 -0
  32. sequenzo/datasets/biofam.csv +2001 -0
  33. sequenzo/datasets/biofam_child_domain.csv +2001 -0
  34. sequenzo/datasets/biofam_left_domain.csv +2001 -0
  35. sequenzo/datasets/biofam_married_domain.csv +2001 -0
  36. sequenzo/datasets/chinese_colonial_territories.csv +12 -0
  37. sequenzo/datasets/country_co2_emissions.csv +194 -0
  38. sequenzo/datasets/country_co2_emissions_global_deciles.csv +195 -0
  39. sequenzo/datasets/country_co2_emissions_global_quintiles.csv +195 -0
  40. sequenzo/datasets/country_co2_emissions_local_deciles.csv +195 -0
  41. sequenzo/datasets/country_co2_emissions_local_quintiles.csv +195 -0
  42. sequenzo/datasets/country_gdp_per_capita.csv +194 -0
  43. sequenzo/datasets/mvad.csv +713 -0
  44. sequenzo/datasets/pairfam_family.csv +1867 -0
  45. sequenzo/datasets/polyadic_samplec1.csv +61 -0
  46. sequenzo/datasets/polyadic_samplep1.csv +61 -0
  47. sequenzo/datasets/polyadic_seqc1.csv +61 -0
  48. sequenzo/datasets/polyadic_seqp1.csv +61 -0
  49. sequenzo/define_sequence_data.py +609 -0
  50. sequenzo/dissimilarity_measures/__init__.py +31 -0
  51. sequenzo/dissimilarity_measures/c_code.cpython-311-darwin.so +0 -0
  52. sequenzo/dissimilarity_measures/get_distance_matrix.py +702 -0
  53. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +241 -0
  54. sequenzo/dissimilarity_measures/src/DHDdistance.cpp +148 -0
  55. sequenzo/dissimilarity_measures/src/LCPdistance.cpp +114 -0
  56. sequenzo/dissimilarity_measures/src/OMdistance.cpp +247 -0
  57. sequenzo/dissimilarity_measures/src/OMspellDistance.cpp +281 -0
  58. sequenzo/dissimilarity_measures/src/__init__.py +0 -0
  59. sequenzo/dissimilarity_measures/src/dist2matrix.cpp +63 -0
  60. sequenzo/dissimilarity_measures/src/dp_utils.h +160 -0
  61. sequenzo/dissimilarity_measures/src/module.cpp +34 -0
  62. sequenzo/dissimilarity_measures/src/setup.py +30 -0
  63. sequenzo/dissimilarity_measures/src/utils.h +25 -0
  64. sequenzo/dissimilarity_measures/src/xsimd/.github/cmake-test/main.cpp +6 -0
  65. sequenzo/dissimilarity_measures/src/xsimd/benchmark/main.cpp +159 -0
  66. sequenzo/dissimilarity_measures/src/xsimd/benchmark/xsimd_benchmark.hpp +565 -0
  67. sequenzo/dissimilarity_measures/src/xsimd/docs/source/conf.py +37 -0
  68. sequenzo/dissimilarity_measures/src/xsimd/examples/mandelbrot.cpp +330 -0
  69. sequenzo/dissimilarity_measures/src/xsimd/examples/pico_bench.hpp +246 -0
  70. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_arithmetic.hpp +266 -0
  71. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_complex.hpp +112 -0
  72. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_details.hpp +323 -0
  73. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_logical.hpp +218 -0
  74. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_math.hpp +2583 -0
  75. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_memory.hpp +880 -0
  76. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_rounding.hpp +72 -0
  77. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_swizzle.hpp +174 -0
  78. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_trigo.hpp +978 -0
  79. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx.hpp +1924 -0
  80. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx2.hpp +1144 -0
  81. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512bw.hpp +656 -0
  82. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512cd.hpp +28 -0
  83. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512dq.hpp +244 -0
  84. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512er.hpp +20 -0
  85. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512f.hpp +2650 -0
  86. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512ifma.hpp +20 -0
  87. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512pf.hpp +20 -0
  88. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi.hpp +77 -0
  89. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi2.hpp +131 -0
  90. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vnni_avx512bw.hpp +20 -0
  91. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vnni_avx512vbmi2.hpp +20 -0
  92. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avxvnni.hpp +20 -0
  93. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common.hpp +24 -0
  94. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common_fwd.hpp +77 -0
  95. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_constants.hpp +393 -0
  96. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_emulated.hpp +788 -0
  97. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx.hpp +93 -0
  98. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx2.hpp +46 -0
  99. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_sse.hpp +97 -0
  100. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma4.hpp +92 -0
  101. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_i8mm_neon64.hpp +17 -0
  102. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_isa.hpp +142 -0
  103. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon.hpp +3142 -0
  104. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon64.hpp +1543 -0
  105. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_rvv.hpp +1513 -0
  106. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_scalar.hpp +1260 -0
  107. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse2.hpp +2024 -0
  108. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse3.hpp +67 -0
  109. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse4_1.hpp +339 -0
  110. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse4_2.hpp +44 -0
  111. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_ssse3.hpp +186 -0
  112. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sve.hpp +1155 -0
  113. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_vsx.hpp +892 -0
  114. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_wasm.hpp +1780 -0
  115. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_arch.hpp +240 -0
  116. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_config.hpp +484 -0
  117. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_cpuid.hpp +269 -0
  118. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_inline.hpp +27 -0
  119. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/math/xsimd_rem_pio2.hpp +719 -0
  120. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/memory/xsimd_aligned_allocator.hpp +349 -0
  121. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/memory/xsimd_alignment.hpp +91 -0
  122. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_all_registers.hpp +55 -0
  123. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_api.hpp +2765 -0
  124. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx2_register.hpp +44 -0
  125. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512bw_register.hpp +51 -0
  126. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512cd_register.hpp +51 -0
  127. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512dq_register.hpp +51 -0
  128. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512er_register.hpp +51 -0
  129. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512f_register.hpp +77 -0
  130. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512ifma_register.hpp +51 -0
  131. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512pf_register.hpp +51 -0
  132. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512vbmi2_register.hpp +51 -0
  133. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512vbmi_register.hpp +51 -0
  134. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512vnni_avx512bw_register.hpp +54 -0
  135. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512vnni_avx512vbmi2_register.hpp +53 -0
  136. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx_register.hpp +64 -0
  137. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avxvnni_register.hpp +44 -0
  138. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch.hpp +1524 -0
  139. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch_constant.hpp +300 -0
  140. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_common_arch.hpp +47 -0
  141. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_emulated_register.hpp +80 -0
  142. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_fma3_avx2_register.hpp +50 -0
  143. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_fma3_avx_register.hpp +50 -0
  144. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_fma3_sse_register.hpp +50 -0
  145. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_fma4_register.hpp +50 -0
  146. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_i8mm_neon64_register.hpp +55 -0
  147. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_neon64_register.hpp +55 -0
  148. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_neon_register.hpp +154 -0
  149. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_register.hpp +94 -0
  150. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_rvv_register.hpp +506 -0
  151. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_sse2_register.hpp +59 -0
  152. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_sse3_register.hpp +49 -0
  153. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_sse4_1_register.hpp +48 -0
  154. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_sse4_2_register.hpp +48 -0
  155. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_ssse3_register.hpp +48 -0
  156. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_sve_register.hpp +156 -0
  157. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_traits.hpp +337 -0
  158. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_utils.hpp +536 -0
  159. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_vsx_register.hpp +77 -0
  160. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_wasm_register.hpp +59 -0
  161. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/xsimd.hpp +75 -0
  162. sequenzo/dissimilarity_measures/src/xsimd/test/architectures/dummy.cpp +7 -0
  163. sequenzo/dissimilarity_measures/src/xsimd/test/doc/explicit_use_of_an_instruction_set.cpp +13 -0
  164. sequenzo/dissimilarity_measures/src/xsimd/test/doc/explicit_use_of_an_instruction_set_mean.cpp +24 -0
  165. sequenzo/dissimilarity_measures/src/xsimd/test/doc/explicit_use_of_an_instruction_set_mean_aligned.cpp +25 -0
  166. sequenzo/dissimilarity_measures/src/xsimd/test/doc/explicit_use_of_an_instruction_set_mean_arch_independent.cpp +28 -0
  167. sequenzo/dissimilarity_measures/src/xsimd/test/doc/explicit_use_of_an_instruction_set_mean_tag_dispatch.cpp +25 -0
  168. sequenzo/dissimilarity_measures/src/xsimd/test/doc/manipulating_abstract_batches.cpp +7 -0
  169. sequenzo/dissimilarity_measures/src/xsimd/test/doc/manipulating_parametric_batches.cpp +8 -0
  170. sequenzo/dissimilarity_measures/src/xsimd/test/doc/sum.hpp +31 -0
  171. sequenzo/dissimilarity_measures/src/xsimd/test/doc/sum_avx2.cpp +3 -0
  172. sequenzo/dissimilarity_measures/src/xsimd/test/doc/sum_sse2.cpp +3 -0
  173. sequenzo/dissimilarity_measures/src/xsimd/test/doc/writing_vectorized_code.cpp +11 -0
  174. sequenzo/dissimilarity_measures/src/xsimd/test/main.cpp +31 -0
  175. sequenzo/dissimilarity_measures/src/xsimd/test/test_api.cpp +230 -0
  176. sequenzo/dissimilarity_measures/src/xsimd/test/test_arch.cpp +217 -0
  177. sequenzo/dissimilarity_measures/src/xsimd/test/test_basic_math.cpp +183 -0
  178. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch.cpp +1049 -0
  179. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_bool.cpp +508 -0
  180. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_cast.cpp +409 -0
  181. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_complex.cpp +712 -0
  182. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_constant.cpp +286 -0
  183. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_float.cpp +141 -0
  184. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_int.cpp +365 -0
  185. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_manip.cpp +308 -0
  186. sequenzo/dissimilarity_measures/src/xsimd/test/test_bitwise_cast.cpp +222 -0
  187. sequenzo/dissimilarity_measures/src/xsimd/test/test_complex_exponential.cpp +226 -0
  188. sequenzo/dissimilarity_measures/src/xsimd/test/test_complex_hyperbolic.cpp +183 -0
  189. sequenzo/dissimilarity_measures/src/xsimd/test/test_complex_power.cpp +265 -0
  190. sequenzo/dissimilarity_measures/src/xsimd/test/test_complex_trigonometric.cpp +236 -0
  191. sequenzo/dissimilarity_measures/src/xsimd/test/test_conversion.cpp +248 -0
  192. sequenzo/dissimilarity_measures/src/xsimd/test/test_custom_default_arch.cpp +28 -0
  193. sequenzo/dissimilarity_measures/src/xsimd/test/test_error_gamma.cpp +170 -0
  194. sequenzo/dissimilarity_measures/src/xsimd/test/test_explicit_batch_instantiation.cpp +32 -0
  195. sequenzo/dissimilarity_measures/src/xsimd/test/test_exponential.cpp +202 -0
  196. sequenzo/dissimilarity_measures/src/xsimd/test/test_extract_pair.cpp +92 -0
  197. sequenzo/dissimilarity_measures/src/xsimd/test/test_fp_manipulation.cpp +77 -0
  198. sequenzo/dissimilarity_measures/src/xsimd/test/test_gnu_source.cpp +30 -0
  199. sequenzo/dissimilarity_measures/src/xsimd/test/test_hyperbolic.cpp +167 -0
  200. sequenzo/dissimilarity_measures/src/xsimd/test/test_load_store.cpp +304 -0
  201. sequenzo/dissimilarity_measures/src/xsimd/test/test_memory.cpp +61 -0
  202. sequenzo/dissimilarity_measures/src/xsimd/test/test_poly_evaluation.cpp +64 -0
  203. sequenzo/dissimilarity_measures/src/xsimd/test/test_power.cpp +184 -0
  204. sequenzo/dissimilarity_measures/src/xsimd/test/test_rounding.cpp +199 -0
  205. sequenzo/dissimilarity_measures/src/xsimd/test/test_select.cpp +101 -0
  206. sequenzo/dissimilarity_measures/src/xsimd/test/test_shuffle.cpp +760 -0
  207. sequenzo/dissimilarity_measures/src/xsimd/test/test_sum.cpp +4 -0
  208. sequenzo/dissimilarity_measures/src/xsimd/test/test_sum.hpp +34 -0
  209. sequenzo/dissimilarity_measures/src/xsimd/test/test_traits.cpp +172 -0
  210. sequenzo/dissimilarity_measures/src/xsimd/test/test_trigonometric.cpp +208 -0
  211. sequenzo/dissimilarity_measures/src/xsimd/test/test_utils.hpp +611 -0
  212. sequenzo/dissimilarity_measures/src/xsimd/test/test_wasm/test_wasm_playwright.py +123 -0
  213. sequenzo/dissimilarity_measures/src/xsimd/test/test_xsimd_api.cpp +1460 -0
  214. sequenzo/dissimilarity_measures/utils/__init__.py +16 -0
  215. sequenzo/dissimilarity_measures/utils/get_LCP_length_for_2_seq.py +44 -0
  216. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cpython-311-darwin.so +0 -0
  217. sequenzo/dissimilarity_measures/utils/seqconc.cpython-311-darwin.so +0 -0
  218. sequenzo/dissimilarity_measures/utils/seqdss.cpython-311-darwin.so +0 -0
  219. sequenzo/dissimilarity_measures/utils/seqdur.cpython-311-darwin.so +0 -0
  220. sequenzo/dissimilarity_measures/utils/seqlength.cpython-311-darwin.so +0 -0
  221. sequenzo/multidomain/__init__.py +23 -0
  222. sequenzo/multidomain/association_between_domains.py +311 -0
  223. sequenzo/multidomain/cat.py +431 -0
  224. sequenzo/multidomain/combt.py +519 -0
  225. sequenzo/multidomain/dat.py +89 -0
  226. sequenzo/multidomain/idcd.py +139 -0
  227. sequenzo/multidomain/linked_polyad.py +292 -0
  228. sequenzo/openmp_setup.py +233 -0
  229. sequenzo/prefix_tree/__init__.py +43 -0
  230. sequenzo/prefix_tree/individual_level_indicators.py +1274 -0
  231. sequenzo/prefix_tree/system_level_indicators.py +465 -0
  232. sequenzo/prefix_tree/utils.py +54 -0
  233. sequenzo/sequence_characteristics/__init__.py +40 -0
  234. sequenzo/sequence_characteristics/complexity_index.py +49 -0
  235. sequenzo/sequence_characteristics/overall_cross_sectional_entropy.py +220 -0
  236. sequenzo/sequence_characteristics/plot_characteristics.py +593 -0
  237. sequenzo/sequence_characteristics/simple_characteristics.py +311 -0
  238. sequenzo/sequence_characteristics/state_frequencies_and_entropy_per_sequence.py +39 -0
  239. sequenzo/sequence_characteristics/turbulence.py +155 -0
  240. sequenzo/sequence_characteristics/variance_of_spell_durations.py +86 -0
  241. sequenzo/sequence_characteristics/within_sequence_entropy.py +43 -0
  242. sequenzo/suffix_tree/__init__.py +48 -0
  243. sequenzo/suffix_tree/individual_level_indicators.py +1638 -0
  244. sequenzo/suffix_tree/system_level_indicators.py +456 -0
  245. sequenzo/suffix_tree/utils.py +56 -0
  246. sequenzo/visualization/__init__.py +29 -0
  247. sequenzo/visualization/plot_mean_time.py +194 -0
  248. sequenzo/visualization/plot_modal_state.py +276 -0
  249. sequenzo/visualization/plot_most_frequent_sequences.py +147 -0
  250. sequenzo/visualization/plot_relative_frequency.py +404 -0
  251. sequenzo/visualization/plot_sequence_index.py +951 -0
  252. sequenzo/visualization/plot_single_medoid.py +153 -0
  253. sequenzo/visualization/plot_state_distribution.py +627 -0
  254. sequenzo/visualization/plot_transition_matrix.py +190 -0
  255. sequenzo/visualization/utils/__init__.py +23 -0
  256. sequenzo/visualization/utils/utils.py +310 -0
  257. sequenzo/with_event_history_analysis/__init__.py +35 -0
  258. sequenzo/with_event_history_analysis/sequence_analysis_multi_state_model.py +850 -0
  259. sequenzo/with_event_history_analysis/sequence_history_analysis.py +283 -0
  260. sequenzo-0.1.24.dist-info/METADATA +255 -0
  261. sequenzo-0.1.24.dist-info/RECORD +264 -0
  262. sequenzo-0.1.24.dist-info/WHEEL +5 -0
  263. sequenzo-0.1.24.dist-info/licenses/LICENSE +28 -0
  264. sequenzo-0.1.24.dist-info/top_level.txt +2 -0
@@ -0,0 +1,760 @@
1
+ /***************************************************************************
2
+ * Copyright (c) Johan Mabille, Sylvain Corlay, Wolf Vollprecht and *
3
+ * Martin Renou *
4
+ * Copyright (c) QuantStack *
5
+ * Copyright (c) Serge Guelton *
6
+ * *
7
+ * Distributed under the terms of the BSD 3-Clause License. *
8
+ * *
9
+ * The full license is in the file LICENSE, distributed with this software. *
10
+ ****************************************************************************/
11
+
12
+ #include "xsimd/xsimd.hpp"
13
+ #ifndef XSIMD_NO_SUPPORTED_ARCHITECTURE
14
+
15
+ #include "test_utils.hpp"
16
+
17
+ #ifdef __linux__
18
+ #include "endian.h"
19
+ #if BYTE_ORDER == BIG_ENDIAN
20
+ #define XSIMD_NO_SLIDE
21
+ #endif
22
+ #endif
23
+
24
+ #include <numeric>
25
+
26
+ namespace
27
+ {
28
+ template <typename T, std::size_t N>
29
+ struct zip_base
30
+ {
31
+ using shuffle_vector_type = std::array<T, N>;
32
+ shuffle_vector_type lhs_in, rhs_in, exp_lo, exp_hi;
33
+
34
+ std::vector<shuffle_vector_type> create_vectors()
35
+ {
36
+ std::vector<shuffle_vector_type> vects;
37
+ vects.reserve(4);
38
+
39
+ /* Generate input data: lhs, rhs */
40
+ for (size_t i = 0; i < N; ++i)
41
+ {
42
+ lhs_in[i] = static_cast<T>('A' + 2 * i + 1);
43
+ rhs_in[i] = static_cast<T>('A' + 2 * i);
44
+ }
45
+ vects.push_back(std::move(lhs_in));
46
+ vects.push_back(std::move(rhs_in));
47
+
48
+ /* Expected zipped data */
49
+ for (size_t i = 0; i < N / 2; ++i)
50
+ {
51
+ exp_lo[2 * i] = lhs_in[i];
52
+ exp_lo[2 * i + 1] = rhs_in[i];
53
+ exp_hi[2 * i] = lhs_in[i + N / 2];
54
+ exp_hi[2 * i + 1] = rhs_in[i + N / 2];
55
+ }
56
+ vects.push_back(std::move(exp_lo));
57
+ vects.push_back(std::move(exp_hi));
58
+
59
+ return vects;
60
+ }
61
+ };
62
+ }
63
+
64
+ template <class B>
65
+ struct zip_test : zip_base<typename B::value_type, B::size>
66
+ {
67
+ using batch_type = B;
68
+ using value_type = typename B::value_type;
69
+ static constexpr size_t size = B::size;
70
+ using zip_base<value_type, size>::create_vectors;
71
+
72
+ void zip_low()
73
+ {
74
+ auto zipped_vecs = create_vectors();
75
+ auto v_lhs = zipped_vecs[0];
76
+ auto v_rhs = zipped_vecs[1];
77
+ auto v_exp_lo = zipped_vecs[2];
78
+
79
+ B b_lhs = B::load_unaligned(v_lhs.data());
80
+ B b_rhs = B::load_unaligned(v_rhs.data());
81
+ B b_exp_lo = B::load_unaligned(v_exp_lo.data());
82
+
83
+ B b_res_lo = xsimd::zip_lo(b_lhs, b_rhs);
84
+ CHECK_BATCH_EQ(b_res_lo, b_exp_lo);
85
+ }
86
+ void zip_hi()
87
+ {
88
+ auto zipped_vecs = create_vectors();
89
+ auto v_lhs = zipped_vecs[0];
90
+ auto v_rhs = zipped_vecs[1];
91
+ auto v_exp_hi = zipped_vecs[3];
92
+
93
+ B b_lhs = B::load_unaligned(v_lhs.data());
94
+ B b_rhs = B::load_unaligned(v_rhs.data());
95
+ B b_exp_hi = B::load_unaligned(v_exp_hi.data());
96
+
97
+ B b_res_hi = xsimd::zip_hi(b_lhs, b_rhs);
98
+ CHECK_BATCH_EQ(b_res_hi, b_exp_hi);
99
+ }
100
+ };
101
+
102
+ #if !XSIMD_WITH_AVX512F || XSIMD_WITH_AVX512BW
103
+ #define ZIP_BATCH_TYPES BATCH_TYPES
104
+ #else
105
+ #define ZIP_BATCH_TYPES xsimd::batch<float>, xsimd::batch<double>, xsimd::batch<int32_t>, xsimd::batch<int64_t>
106
+ #endif
107
+
108
+ TEST_CASE_TEMPLATE("[zip]", B, ZIP_BATCH_TYPES)
109
+
110
+ {
111
+ zip_test<B> Test;
112
+ SUBCASE("zip low") { Test.zip_low(); }
113
+ SUBCASE("zip high") { Test.zip_hi(); }
114
+ }
115
+
116
+ namespace
117
+ {
118
+ template <typename T, std::size_t N>
119
+ struct init_slide_base
120
+ {
121
+ using slide_vector_type = std::array<T, N>;
122
+ slide_vector_type v_in,
123
+ v_left0, v_left_full, v_left_half, v_left_above_half, v_left_below_half, v_left_one,
124
+ v_right0, v_right_full, v_right_half, v_right_above_half, v_right_below_half, v_right_one;
125
+ static constexpr unsigned full_slide = N * sizeof(T);
126
+ static constexpr unsigned half_slide = full_slide / 2;
127
+ static constexpr unsigned above_half_slide = half_slide + half_slide / 2;
128
+ static constexpr unsigned below_half_slide = half_slide / 2;
129
+ static constexpr bool activate_above_below_checks = above_half_slide / sizeof(T) * sizeof(T) == above_half_slide;
130
+
131
+ init_slide_base()
132
+ {
133
+ std::iota(v_in.begin(), v_in.end(), 1);
134
+
135
+ v_left0 = v_in;
136
+
137
+ std::fill(v_left_full.begin(), v_left_full.end(), 0);
138
+
139
+ std::fill(v_left_half.begin(), v_left_half.end(), 0);
140
+ std::iota(v_left_half.begin() + half_slide / sizeof(T), v_left_half.end(), 1);
141
+
142
+ std::fill(v_left_one.begin(), v_left_one.end(), 0);
143
+ std::iota(v_left_one.begin() + 1, v_left_one.end(), 1);
144
+
145
+ if (activate_above_below_checks)
146
+ {
147
+ std::fill(v_left_above_half.begin(), v_left_above_half.end(), 0);
148
+ std::iota(v_left_above_half.begin() + above_half_slide / sizeof(T), v_left_above_half.end(), 1);
149
+
150
+ std::fill(v_left_below_half.begin(), v_left_below_half.end(), 0);
151
+ std::iota(v_left_below_half.begin() + below_half_slide / sizeof(T), v_left_below_half.end(), 1);
152
+ }
153
+
154
+ v_right0 = v_in;
155
+
156
+ std::fill(v_right_full.begin(), v_right_full.end(), 0);
157
+
158
+ std::fill(v_right_half.begin(), v_right_half.end(), 0);
159
+ std::iota(v_right_half.begin(), v_right_half.begin() + half_slide / sizeof(T), v_in[half_slide / sizeof(T)]);
160
+
161
+ std::fill(v_right_one.begin(), v_right_one.end(), 0);
162
+ std::iota(v_right_one.begin(), v_right_one.begin() + full_slide / sizeof(T) - 1, v_in[1]);
163
+
164
+ if (activate_above_below_checks)
165
+ {
166
+ std::fill(v_right_above_half.begin(), v_right_above_half.end(), 0);
167
+ std::iota(v_right_above_half.begin(), v_right_above_half.begin() + (full_slide - above_half_slide) / sizeof(T), v_in[above_half_slide / sizeof(T)]);
168
+
169
+ std::fill(v_right_below_half.begin(), v_right_below_half.end(), 0);
170
+ std::iota(v_right_below_half.begin(), v_right_below_half.begin() + (full_slide - below_half_slide) / sizeof(T), v_in[below_half_slide / sizeof(T)]);
171
+ }
172
+ }
173
+ };
174
+ }
175
+
176
+ template <class B>
177
+ struct slide_test : public init_slide_base<typename B::value_type, B::size>
178
+ {
179
+ using batch_type = B;
180
+ using value_type = typename B::value_type;
181
+ static constexpr size_t size = B::size;
182
+ using base = init_slide_base<typename B::value_type, B::size>;
183
+ using base::above_half_slide;
184
+ using base::activate_above_below_checks;
185
+ using base::below_half_slide;
186
+ using base::full_slide;
187
+ using base::half_slide;
188
+
189
+ void slide_left()
190
+ {
191
+ B b_in = B::load_unaligned(this->v_in.data());
192
+ B b_left0 = B::load_unaligned(this->v_left0.data());
193
+ B b_left_full = B::load_unaligned(this->v_left_full.data());
194
+ B b_left_half = B::load_unaligned(this->v_left_half.data());
195
+ B b_left_one = B::load_unaligned(this->v_left_one.data());
196
+ B b_left_above_half = B::load_unaligned(this->v_left_above_half.data());
197
+ B b_left_below_half = B::load_unaligned(this->v_left_below_half.data());
198
+
199
+ B b_res_left0 = xsimd::slide_left<0>(b_in);
200
+ INFO("slide_left 0");
201
+ CHECK_BATCH_EQ(b_res_left0, b_left0);
202
+
203
+ B b_res_left_full = xsimd::slide_left<full_slide>(b_in);
204
+ INFO("slide_left full");
205
+ CHECK_BATCH_EQ(b_res_left_full, b_left_full);
206
+
207
+ #ifndef XSIMD_NO_SLIDE
208
+ B b_res_left_half = xsimd::slide_left<half_slide>(b_in);
209
+ INFO("slide_left half_slide");
210
+ CHECK_BATCH_EQ(b_res_left_half, b_left_half);
211
+
212
+ B b_res_left_one = xsimd::slide_left<sizeof(value_type)>(b_in);
213
+ INFO("slide_left one_slide");
214
+ CHECK_BATCH_EQ(b_res_left_one, b_left_one);
215
+
216
+ if (activate_above_below_checks)
217
+ {
218
+ B b_res_left_above_half = xsimd::slide_left<above_half_slide>(b_in);
219
+ INFO("slide_left above_half_slide");
220
+ CHECK_BATCH_EQ(b_res_left_above_half, b_left_above_half);
221
+
222
+ B b_res_left_below_half = xsimd::slide_left<below_half_slide>(b_in);
223
+ INFO("slide_left below_half_slide");
224
+ CHECK_BATCH_EQ(b_res_left_below_half, b_left_below_half);
225
+ }
226
+ #endif
227
+ }
228
+
229
+ void slide_right()
230
+ {
231
+ B b_in = B::load_unaligned(this->v_in.data());
232
+ B b_right0 = B::load_unaligned(this->v_right0.data());
233
+ B b_right_full = B::load_unaligned(this->v_right_full.data());
234
+ B b_right_half = B::load_unaligned(this->v_right_half.data());
235
+ B b_right_one = B::load_unaligned(this->v_right_one.data());
236
+ B b_right_above_half = B::load_unaligned(this->v_right_above_half.data());
237
+ B b_right_below_half = B::load_unaligned(this->v_right_below_half.data());
238
+
239
+ B b_res_right0 = xsimd::slide_right<0>(b_in);
240
+ INFO("slide_right 0");
241
+ CHECK_BATCH_EQ(b_res_right0, b_right0);
242
+
243
+ B b_res_right_full = xsimd::slide_right<full_slide>(b_in);
244
+ INFO("slide_right full");
245
+ CHECK_BATCH_EQ(b_res_right_full, b_right_full);
246
+
247
+ #ifndef XSIMD_NO_SLIDE
248
+ B b_res_right_half = xsimd::slide_right<half_slide>(b_in);
249
+ INFO("slide_right half_slide");
250
+ CHECK_BATCH_EQ(b_res_right_half, b_right_half);
251
+
252
+ B b_res_right_one = xsimd::slide_right<sizeof(value_type)>(b_in);
253
+ INFO("slide_right one_slide");
254
+ CHECK_BATCH_EQ(b_res_right_one, b_right_one);
255
+
256
+ if (activate_above_below_checks)
257
+ {
258
+ B b_res_right_above_half = xsimd::slide_right<above_half_slide>(b_in);
259
+ INFO("slide_right above_half_slide");
260
+ CHECK_BATCH_EQ(b_res_right_above_half, b_right_above_half);
261
+
262
+ B b_res_right_below_half = xsimd::slide_right<below_half_slide>(b_in);
263
+ INFO("slide_right below_half_slide");
264
+ CHECK_BATCH_EQ(b_res_right_below_half, b_right_below_half);
265
+ }
266
+ #endif
267
+ }
268
+ };
269
+
270
+ TEST_CASE_TEMPLATE("[slide]", B, BATCH_INT_TYPES)
271
+ {
272
+ slide_test<B> Test;
273
+ SUBCASE("slide_left")
274
+ {
275
+ Test.slide_left();
276
+ }
277
+ SUBCASE("slide_right")
278
+ {
279
+ Test.slide_right();
280
+ }
281
+ }
282
+
283
+ template <class B>
284
+ struct compress_test
285
+ {
286
+ using batch_type = B;
287
+ using value_type = typename B::value_type;
288
+ using mask_batch_type = typename B::batch_bool_type;
289
+
290
+ static constexpr size_t size = B::size;
291
+ std::array<value_type, size> input;
292
+ std::array<bool, size> mask;
293
+ std::array<value_type, size> expected;
294
+
295
+ compress_test()
296
+ {
297
+ for (size_t i = 0; i < size; ++i)
298
+ {
299
+ input[i] = static_cast<value_type>(i);
300
+ }
301
+ }
302
+
303
+ void full()
304
+ {
305
+ std::fill(mask.begin(), mask.end(), true);
306
+
307
+ for (size_t i = 0; i < size; ++i)
308
+ expected[i] = input[i];
309
+
310
+ auto b = xsimd::compress(
311
+ batch_type::load_unaligned(input.data()),
312
+ mask_batch_type::load_unaligned(mask.data()));
313
+ CHECK_BATCH_EQ(b, expected);
314
+ }
315
+
316
+ void empty()
317
+ {
318
+ std::fill(mask.begin(), mask.end(), false);
319
+
320
+ for (size_t i = 0; i < size; ++i)
321
+ expected[i] = 0;
322
+
323
+ auto b = xsimd::compress(
324
+ batch_type::load_unaligned(input.data()),
325
+ mask_batch_type::load_unaligned(mask.data()));
326
+ CHECK_BATCH_EQ(b, expected);
327
+ }
328
+
329
+ void interleave()
330
+ {
331
+ for (size_t i = 0; i < size; ++i)
332
+ mask[i] = i % 2 == 0;
333
+
334
+ for (size_t i = 0; i < size; ++i)
335
+ expected[i] = i < size / 2 ? input[2 * i] : 0;
336
+
337
+ auto b = xsimd::compress(
338
+ batch_type::load_unaligned(input.data()),
339
+ mask_batch_type::load_unaligned(mask.data()));
340
+ CHECK_BATCH_EQ(b, expected);
341
+ }
342
+
343
+ void common()
344
+ {
345
+ for (size_t i = 0; i < size; ++i)
346
+ mask[i] = i % 3 == 0;
347
+
348
+ for (size_t i = 0; i < size; ++i)
349
+ expected[i] = i < size / 3 ? input[3 * i] : 0;
350
+
351
+ auto b = xsimd::compress(
352
+ batch_type::load_unaligned(input.data()),
353
+ mask_batch_type::load_unaligned(mask.data()));
354
+ CHECK_BATCH_EQ(b, expected);
355
+ }
356
+ };
357
+
358
+ #define XSIMD_COMPRESS_TYPES BATCH_FLOAT_TYPES, xsimd::batch<uint8_t>, xsimd::batch<int8_t>, xsimd::batch<uint16_t>, xsimd::batch<int16_t>, xsimd::batch<uint32_t>, xsimd::batch<int32_t>, xsimd::batch<uint64_t>, xsimd::batch<int64_t>
359
+
360
+ TEST_CASE_TEMPLATE("[compress]", B, XSIMD_COMPRESS_TYPES)
361
+ {
362
+ compress_test<B> Test;
363
+ SUBCASE("empty")
364
+ {
365
+ Test.empty();
366
+ }
367
+ SUBCASE("full")
368
+ {
369
+ Test.full();
370
+ }
371
+ // SUBCASE("interleave")
372
+ //{
373
+ // Test.interleave();
374
+ // }
375
+ // SUBCASE("common")
376
+ //{
377
+ // Test.common();
378
+ // }
379
+ }
380
+
381
+ template <class B>
382
+ struct expand_test
383
+ {
384
+ using batch_type = B;
385
+ using value_type = typename B::value_type;
386
+ using mask_batch_type = typename B::batch_bool_type;
387
+
388
+ static constexpr size_t size = B::size;
389
+ std::array<value_type, size> input;
390
+ std::array<bool, size> mask;
391
+ std::array<value_type, size> expected;
392
+
393
+ expand_test()
394
+ {
395
+ for (size_t i = 0; i < size; ++i)
396
+ {
397
+ input[i] = static_cast<value_type>(i);
398
+ }
399
+ }
400
+
401
+ void full()
402
+ {
403
+ std::fill(mask.begin(), mask.end(), true);
404
+
405
+ for (size_t i = 0; i < size; ++i)
406
+ expected[i] = input[i];
407
+
408
+ auto b = xsimd::expand(
409
+ batch_type::load_unaligned(input.data()),
410
+ mask_batch_type::load_unaligned(mask.data()));
411
+ CHECK_BATCH_EQ(b, expected);
412
+ }
413
+
414
+ void empty()
415
+ {
416
+ std::fill(mask.begin(), mask.end(), false);
417
+
418
+ for (size_t i = 0; i < size; ++i)
419
+ expected[i] = 0;
420
+
421
+ auto b = xsimd::expand(
422
+ batch_type::load_unaligned(input.data()),
423
+ mask_batch_type::load_unaligned(mask.data()));
424
+ CHECK_BATCH_EQ(b, expected);
425
+ }
426
+
427
+ void interleave()
428
+ {
429
+ for (size_t i = 0; i < size; ++i)
430
+ mask[i] = i % 2 == 0;
431
+
432
+ for (size_t i = 0, j = 0; i < size; ++i)
433
+ expected[i] = mask[i] ? input[j++] : 0;
434
+
435
+ auto b = xsimd::expand(
436
+ batch_type::load_unaligned(input.data()),
437
+ mask_batch_type::load_unaligned(mask.data()));
438
+ CHECK_BATCH_EQ(b, expected);
439
+ }
440
+
441
+ void common()
442
+ {
443
+ for (size_t i = 0; i < size; ++i)
444
+ mask[i] = i % 3 == 0;
445
+
446
+ for (size_t i = 0, j = 0; i < size; ++i)
447
+ expected[i] = mask[i] ? input[j++] : 0;
448
+
449
+ auto b = xsimd::expand(
450
+ batch_type::load_unaligned(input.data()),
451
+ mask_batch_type::load_unaligned(mask.data()));
452
+ CHECK_BATCH_EQ(b, expected);
453
+ }
454
+ };
455
+
456
+ #define XSIMD_EXPAND_TYPES XSIMD_COMPRESS_TYPES
457
+
458
+ TEST_CASE_TEMPLATE("[expand]", B, XSIMD_EXPAND_TYPES)
459
+ {
460
+ expand_test<B> Test;
461
+ SUBCASE("empty")
462
+ {
463
+ Test.empty();
464
+ }
465
+ SUBCASE("full")
466
+ {
467
+ Test.full();
468
+ }
469
+ SUBCASE("interleave")
470
+ {
471
+ Test.interleave();
472
+ }
473
+ SUBCASE("common")
474
+ {
475
+ Test.common();
476
+ }
477
+ }
478
+
479
+ template <class B>
480
+ struct shuffle_test
481
+ {
482
+ using batch_type = B;
483
+ using value_type = typename B::value_type;
484
+ using arch_type = typename B::arch_type;
485
+ using mask_type = xsimd::as_unsigned_integer_t<value_type>;
486
+ static constexpr size_t size = B::size;
487
+ std::array<value_type, size> lhs;
488
+ std::array<value_type, size> rhs;
489
+
490
+ shuffle_test()
491
+ {
492
+ for (size_t i = 0; i < size; ++i)
493
+ {
494
+ lhs[i] = static_cast<value_type>(i);
495
+ rhs[i] = static_cast<value_type>(i + size);
496
+ }
497
+ }
498
+
499
+ void no_op()
500
+ {
501
+ B b_lhs = B::load_unaligned(lhs.data());
502
+ B b_rhs = B::load_unaligned(rhs.data());
503
+
504
+ struct no_op_lhs_generator
505
+ {
506
+ static constexpr size_t get(size_t index, size_t /*size*/)
507
+ {
508
+ return index;
509
+ }
510
+ };
511
+
512
+ INFO("no op lhs");
513
+ B b_res_lhs = xsimd::shuffle(b_lhs, b_rhs, xsimd::make_batch_constant<mask_type, no_op_lhs_generator, arch_type>());
514
+ CHECK_BATCH_EQ(b_res_lhs, b_lhs);
515
+
516
+ struct no_op_rhs_generator
517
+ {
518
+ static constexpr size_t get(size_t index, size_t size)
519
+ {
520
+ return index + size;
521
+ }
522
+ };
523
+
524
+ INFO("no op rhs");
525
+ B b_res_rhs = xsimd::shuffle(b_lhs, b_rhs, xsimd::make_batch_constant<mask_type, no_op_rhs_generator, arch_type>());
526
+ CHECK_BATCH_EQ(b_res_rhs, b_rhs);
527
+ }
528
+
529
+ void common()
530
+ {
531
+ B b_lhs = B::load_unaligned(lhs.data());
532
+ B b_rhs = B::load_unaligned(rhs.data());
533
+
534
+ struct common_generator
535
+ {
536
+ static constexpr size_t get(size_t index, size_t size)
537
+ {
538
+ return (index & 1) ? (size - index - 1) : (size + (size - index - 1));
539
+ }
540
+ };
541
+
542
+ std::array<value_type, size> ref;
543
+ for (size_t i = 0; i < size; ++i)
544
+ {
545
+ size_t ri = size - i - 1;
546
+ ref[i] = (i & 1) ? lhs[ri] : rhs[ri];
547
+ }
548
+ B b_ref = B::load_unaligned(ref.data());
549
+
550
+ B b_res = xsimd::shuffle(b_lhs, b_rhs, xsimd::make_batch_constant<mask_type, common_generator, arch_type>());
551
+ CHECK_BATCH_EQ(b_res, b_ref);
552
+ }
553
+
554
+ void pick()
555
+ {
556
+ B b_lhs = B::load_unaligned(lhs.data());
557
+ B b_rhs = B::load_unaligned(rhs.data());
558
+
559
+ struct pick_generator
560
+ {
561
+ static constexpr size_t get(size_t index, size_t size)
562
+ {
563
+ return index > 2 ? 0 : size;
564
+ }
565
+ };
566
+
567
+ std::array<value_type, size> ref;
568
+ for (size_t i = 0; i < size; ++i)
569
+ ref[i] = (i > 2) ? lhs[0] : rhs[0];
570
+ B b_ref = B::load_unaligned(ref.data());
571
+
572
+ B b_res = xsimd::shuffle(b_lhs, b_rhs, xsimd::make_batch_constant<mask_type, pick_generator, arch_type>());
573
+ CHECK_BATCH_EQ(b_res, b_ref);
574
+ }
575
+
576
+ void shuffle()
577
+ {
578
+ B b_lhs = B::load_unaligned(lhs.data());
579
+ B b_rhs = B::load_unaligned(rhs.data());
580
+
581
+ {
582
+ struct shuffle_lo_generator
583
+ {
584
+ static constexpr size_t get(size_t index, size_t size)
585
+ {
586
+ return size - index - 1;
587
+ }
588
+ };
589
+
590
+ std::array<value_type, size> ref;
591
+ for (size_t i = 0; i < size; ++i)
592
+ ref[i] = lhs[size - i - 1];
593
+ B b_ref = B::load_unaligned(ref.data());
594
+
595
+ INFO("shuffle first batch");
596
+ B b_res = xsimd::shuffle(b_lhs, b_rhs, xsimd::make_batch_constant<mask_type, shuffle_lo_generator, arch_type>());
597
+ CHECK_BATCH_EQ(b_res, b_ref);
598
+ }
599
+
600
+ {
601
+ struct shuffle_hi_generator
602
+ {
603
+ static constexpr size_t get(size_t index, size_t size)
604
+ {
605
+ return size + size - index - 1;
606
+ }
607
+ };
608
+
609
+ std::array<value_type, size> ref;
610
+ for (size_t i = 0; i < size; ++i)
611
+ ref[i] = rhs[size - i - 1];
612
+ B b_ref = B::load_unaligned(ref.data());
613
+
614
+ INFO("shuffle second batch");
615
+ B b_res = xsimd::shuffle(b_lhs, b_rhs, xsimd::make_batch_constant<mask_type, shuffle_hi_generator, arch_type>());
616
+ CHECK_BATCH_EQ(b_res, b_ref);
617
+ }
618
+ }
619
+
620
+ void transpose()
621
+ {
622
+ B b_lhs = B::load_unaligned(lhs.data());
623
+ std::array<B, size> b_matrix;
624
+ for (size_t i = 0; i < size; ++i)
625
+ b_matrix[i] = b_lhs;
626
+ std::array<value_type, size * size> ref_matrix;
627
+ for (size_t i = 0; i < size; ++i)
628
+ for (size_t j = 0; j < size; ++j)
629
+ ref_matrix[i * size + j] = lhs[i];
630
+
631
+ INFO("transpose");
632
+ xsimd::transpose(b_matrix.data(), b_matrix.data() + b_matrix.size());
633
+ for (size_t i = 0; i < size; ++i)
634
+ {
635
+ CHECK_BATCH_EQ(b_matrix[i], B::load_unaligned(&ref_matrix[i * size]));
636
+ }
637
+ }
638
+
639
+ void select()
640
+ {
641
+ B b_lhs = B::load_unaligned(lhs.data());
642
+ B b_rhs = B::load_unaligned(rhs.data());
643
+
644
+ struct select_generator
645
+ {
646
+ static constexpr size_t get(size_t index, size_t size)
647
+ {
648
+ return (index % 3) ? (index + size) : index;
649
+ }
650
+ };
651
+
652
+ std::array<value_type, size> ref;
653
+ for (size_t i = 0; i < size; ++i)
654
+ ref[i] = (i % 3) ? rhs[i] : lhs[i];
655
+ B b_ref = B::load_unaligned(ref.data());
656
+
657
+ INFO("select");
658
+ B b_res = xsimd::shuffle(b_lhs, b_rhs, xsimd::make_batch_constant<mask_type, select_generator, arch_type>());
659
+ CHECK_BATCH_EQ(b_res, b_ref);
660
+ }
661
+
662
+ void zip()
663
+ {
664
+ B b_lhs = B::load_unaligned(lhs.data());
665
+ B b_rhs = B::load_unaligned(rhs.data());
666
+
667
+ struct zip_lo_generator
668
+ {
669
+ static constexpr size_t get(size_t index, size_t size)
670
+ {
671
+ return (index & 1) ? (index / 2 + size) : index / 2;
672
+ }
673
+ };
674
+
675
+ std::array<value_type, size> ref_lo;
676
+ for (size_t i = 0; i < size; ++i)
677
+ ref_lo[i] = (i & 1) ? rhs[i / 2] : lhs[i / 2];
678
+ B b_ref_lo = B::load_unaligned(ref_lo.data());
679
+
680
+ INFO("zip_lo");
681
+ B b_res_lo = xsimd::shuffle(b_lhs, b_rhs, xsimd::make_batch_constant<mask_type, zip_lo_generator, arch_type>());
682
+ CHECK_BATCH_EQ(b_res_lo, b_ref_lo);
683
+
684
+ struct zip_hi_generator
685
+ {
686
+ static constexpr size_t get(size_t index, size_t size)
687
+ {
688
+ return (index & 1) ? (size / 2 + index / 2 + size) : (size / 2 + index / 2);
689
+ }
690
+ };
691
+
692
+ std::array<value_type, size> ref_hi;
693
+ for (size_t i = 0; i < size; ++i)
694
+ {
695
+ ref_hi[i] = (i & 1) ? rhs[size / 2 + i / 2] : lhs[size / 2 + i / 2];
696
+ }
697
+ B b_ref_hi = B::load_unaligned(ref_hi.data());
698
+
699
+ INFO("zip_hi");
700
+ B b_res_hi = xsimd::shuffle(b_lhs, b_rhs, xsimd::make_batch_constant<mask_type, zip_hi_generator, arch_type>());
701
+ CHECK_BATCH_EQ(b_res_hi, b_ref_hi);
702
+ }
703
+ };
704
+
705
+ #define XSIMD_SHUFFLE_TYPES BATCH_FLOAT_TYPES, xsimd::batch<uint32_t>, xsimd::batch<int32_t>, xsimd::batch<uint64_t>, xsimd::batch<int64_t>
706
+
707
+ TEST_CASE_TEMPLATE("[shuffle]", B, XSIMD_SHUFFLE_TYPES)
708
+ {
709
+ shuffle_test<B> Test;
710
+ SUBCASE("no-op")
711
+ {
712
+ Test.no_op();
713
+ }
714
+ SUBCASE("common")
715
+ {
716
+ Test.common();
717
+ }
718
+ SUBCASE("pick")
719
+ {
720
+ Test.pick();
721
+ }
722
+ SUBCASE("select")
723
+ {
724
+ Test.select();
725
+ }
726
+ SUBCASE("shuffle")
727
+ {
728
+ Test.shuffle();
729
+ }
730
+ SUBCASE("transpose")
731
+ {
732
+ Test.transpose();
733
+ }
734
+ SUBCASE("zip")
735
+ {
736
+ Test.zip();
737
+ }
738
+ }
739
+
740
+ TEST_CASE_TEMPLATE("[small integer transpose]", B, xsimd::batch<uint16_t>, xsimd::batch<int16_t>, xsimd::batch<uint8_t>, xsimd::batch<int8_t>)
741
+ {
742
+ shuffle_test<B> Test;
743
+ SUBCASE("transpose")
744
+ {
745
+ Test.transpose();
746
+ }
747
+ }
748
+
749
+ #if (XSIMD_WITH_SSE2 && !XSIMD_WITH_AVX)
750
+ TEST_CASE_TEMPLATE("[small integer shuffle]", B, xsimd::batch<uint16_t>, xsimd::batch<int16_t>)
751
+ {
752
+ shuffle_test<B> Test;
753
+ SUBCASE("shuffle")
754
+ {
755
+ Test.shuffle();
756
+ }
757
+ }
758
+ #endif
759
+
760
+ #endif