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 +1,217 @@
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 <numeric>
16
+ #include <type_traits>
17
+
18
+ #include "test_sum.hpp"
19
+ #include "test_utils.hpp"
20
+
21
+ #ifndef XSIMD_DEFAULT_ARCH
22
+ static_assert(xsimd::default_arch::supported(), "default arch must be supported");
23
+ static_assert(std::is_same<xsimd::default_arch, xsimd::best_arch>::value, "default arch is the best available");
24
+ static_assert(xsimd::supported_architectures::contains<xsimd::default_arch>(), "default arch is supported");
25
+ static_assert(xsimd::all_architectures::contains<xsimd::default_arch>(), "default arch is a valid arch");
26
+ #endif
27
+
28
+ #if !XSIMD_WITH_SVE
29
+ static_assert((std::is_same<xsimd::default_arch, xsimd::neon64>::value || !xsimd::neon64::supported()), "on arm, without sve, the best we can do is neon64");
30
+ #endif
31
+
32
+ struct check_supported
33
+ {
34
+ template <class Arch>
35
+ void operator()(Arch) const
36
+ {
37
+ static_assert(Arch::supported(), "not supported?");
38
+ }
39
+ };
40
+
41
+ struct check_cpu_has_intruction_set
42
+ {
43
+ template <class Arch>
44
+ void operator()(Arch arch) const
45
+ {
46
+ static_assert(std::is_same<decltype(xsimd::available_architectures().has(arch)), bool>::value,
47
+ "cannot test instruction set availability on CPU");
48
+ }
49
+ };
50
+
51
+ struct check_available
52
+ {
53
+ template <class Arch>
54
+ void operator()(Arch) const
55
+ {
56
+ CHECK_UNARY(Arch::available());
57
+ }
58
+ };
59
+
60
+ template <class T>
61
+ static bool try_load()
62
+ {
63
+ static_assert(std::is_same<xsimd::batch<T>, decltype(xsimd::load_aligned(std::declval<T*>()))>::value,
64
+ "loading the expected type");
65
+ static_assert(std::is_same<xsimd::batch<T>, decltype(xsimd::load_unaligned(std::declval<T*>()))>::value,
66
+ "loading the expected type");
67
+ return true;
68
+ }
69
+
70
+ template <class... Tys>
71
+ void try_loads()
72
+ {
73
+ (void)std::initializer_list<bool> { try_load<Tys>()... };
74
+ }
75
+
76
+ TEST_CASE("[multi arch support]")
77
+ {
78
+
79
+ SUBCASE("xsimd::supported_architectures")
80
+ {
81
+ xsimd::supported_architectures::for_each(check_supported {});
82
+ }
83
+
84
+ SUBCASE("xsimd::available_architectures::has")
85
+ {
86
+ xsimd::all_architectures::for_each(check_cpu_has_intruction_set {});
87
+ }
88
+
89
+ SUBCASE("xsimd::default_arch::name")
90
+ {
91
+ constexpr char const* name = xsimd::default_arch::name();
92
+ (void)name;
93
+ }
94
+
95
+ SUBCASE("xsimd::default_arch::available")
96
+ {
97
+ CHECK_UNARY(xsimd::default_arch::available());
98
+ }
99
+
100
+ SUBCASE("xsimd::arch_list<...>::alignment()")
101
+ {
102
+ static_assert(xsimd::arch_list<xsimd::common>::alignment() == 0,
103
+ "common");
104
+ static_assert(xsimd::arch_list<xsimd::sse2>::alignment()
105
+ == xsimd::sse2::alignment(),
106
+ "one architecture");
107
+ static_assert(xsimd::arch_list<xsimd::avx512f, xsimd::sse2>::alignment()
108
+ == xsimd::avx512f::alignment(),
109
+ "two architectures");
110
+ }
111
+
112
+ SUBCASE("xsimd::dispatch(...)")
113
+ {
114
+ float data[17] = { 1.f, 2.f, 3.f, 4.f, 5.f, 6.f, 7.f, 8.f, 9.f, 10.f, 11.f, 12.f, 13.f, 14.f, 15.f, 16.f, 17.f };
115
+ float ref = std::accumulate(std::begin(data), std::end(data), 0.f);
116
+
117
+ // platform specific
118
+ {
119
+ auto dispatched = xsimd::dispatch(sum {});
120
+ float res = dispatched(data, 17);
121
+ CHECK_EQ(ref, res);
122
+ }
123
+
124
+ // only highest available
125
+ {
126
+ auto dispatched = xsimd::dispatch<xsimd::arch_list<xsimd::best_arch>>(sum {});
127
+ float res = dispatched(data, 17);
128
+ CHECK_EQ(ref, res);
129
+ }
130
+
131
+ #if XSIMD_WITH_AVX && XSIMD_WITH_SSE2
132
+ static_assert(xsimd::supported_architectures::contains<xsimd::avx>() && xsimd::supported_architectures::contains<xsimd::sse2>(), "consistent supported architectures");
133
+ {
134
+ auto dispatched = xsimd::dispatch<xsimd::arch_list<xsimd::avx, xsimd::sse2>>(sum {});
135
+ float res = dispatched(data, 17);
136
+ CHECK_EQ(ref, res);
137
+ }
138
+ #endif
139
+ }
140
+
141
+ SUBCASE("xsimd::make_sized_batch_t")
142
+ {
143
+ using batch4f = xsimd::make_sized_batch_t<float, 4>;
144
+ using batch2d = xsimd::make_sized_batch_t<double, 2>;
145
+ using batch4c = xsimd::make_sized_batch_t<std::complex<float>, 4>;
146
+ using batch2z = xsimd::make_sized_batch_t<std::complex<double>, 2>;
147
+ using batch4i32 = xsimd::make_sized_batch_t<int32_t, 4>;
148
+ using batch4u32 = xsimd::make_sized_batch_t<uint32_t, 4>;
149
+
150
+ using batch8f = xsimd::make_sized_batch_t<float, 8>;
151
+ using batch4d = xsimd::make_sized_batch_t<double, 4>;
152
+ using batch8c = xsimd::make_sized_batch_t<std::complex<float>, 8>;
153
+ using batch4z = xsimd::make_sized_batch_t<std::complex<double>, 4>;
154
+ using batch8i32 = xsimd::make_sized_batch_t<int32_t, 8>;
155
+ using batch8u32 = xsimd::make_sized_batch_t<uint32_t, 8>;
156
+
157
+ #if XSIMD_WITH_SSE2 || XSIMD_WITH_NEON || XSIMD_WITH_NEON64 || XSIMD_WITH_SVE || (XSIMD_WITH_RVV && XSIMD_RVV_BITS == 128)
158
+ CHECK_EQ(4, size_t(batch4f::size));
159
+ CHECK_EQ(4, size_t(batch4c::size));
160
+ CHECK_EQ(4, size_t(batch4i32::size));
161
+ CHECK_EQ(4, size_t(batch4u32::size));
162
+
163
+ CHECK_UNARY(bool(std::is_same<float, batch4f::value_type>::value));
164
+ CHECK_UNARY(bool(std::is_same<std::complex<float>, batch4c::value_type>::value));
165
+ CHECK_UNARY(bool(std::is_same<int32_t, batch4i32::value_type>::value));
166
+ CHECK_UNARY(bool(std::is_same<uint32_t, batch4u32::value_type>::value));
167
+
168
+ #if XSIMD_WITH_SSE2 || XSIMD_WITH_NEON64 || XSIMD_WITH_SVE || XSIMD_WITH_RVV
169
+ CHECK_EQ(2, size_t(batch2d::size));
170
+ CHECK_EQ(2, size_t(batch2z::size));
171
+ CHECK_UNARY(bool(std::is_same<double, batch2d::value_type>::value));
172
+ CHECK_UNARY(bool(std::is_same<std::complex<double>, batch2z::value_type>::value));
173
+ #else
174
+ CHECK_UNARY(bool(std::is_same<void, batch2d>::value));
175
+ #endif
176
+
177
+ #endif
178
+ #if !XSIMD_WITH_AVX && !XSIMD_WITH_FMA3 && !(XSIMD_WITH_SVE && XSIMD_SVE_BITS == 256) && !(XSIMD_WITH_RVV && XSIMD_RVV_BITS == 256)
179
+ CHECK_UNARY(bool(std::is_same<void, batch8f>::value));
180
+ CHECK_UNARY(bool(std::is_same<void, batch4d>::value));
181
+ CHECK_UNARY(bool(std::is_same<void, batch8c>::value));
182
+ CHECK_UNARY(bool(std::is_same<void, batch4z>::value));
183
+ CHECK_UNARY(bool(std::is_same<void, batch8i32>::value));
184
+ CHECK_UNARY(bool(std::is_same<void, batch8u32>::value));
185
+ #else
186
+ CHECK_EQ(8, size_t(batch8f::size));
187
+ CHECK_EQ(8, size_t(batch8i32::size));
188
+ CHECK_EQ(8, size_t(batch8u32::size));
189
+ CHECK_EQ(4, size_t(batch4d::size));
190
+
191
+ CHECK_EQ(8, size_t(batch8c::size));
192
+ CHECK_EQ(4, size_t(batch4z::size));
193
+
194
+ CHECK_UNARY(bool(std::is_same<float, batch8f::value_type>::value));
195
+ CHECK_UNARY(bool(std::is_same<double, batch4d::value_type>::value));
196
+ CHECK_UNARY(bool(std::is_same<int32_t, batch8i32::value_type>::value));
197
+ CHECK_UNARY(bool(std::is_same<uint32_t, batch8u32::value_type>::value));
198
+ CHECK_UNARY(bool(std::is_same<std::complex<float>, batch8c::value_type>::value));
199
+ CHECK_UNARY(bool(std::is_same<std::complex<double>, batch4z::value_type>::value));
200
+ #endif
201
+ }
202
+
203
+ SUBCASE("xsimd::load_(un)aligned(...) return type")
204
+ {
205
+ // make sure load_aligned / load_unaligned work for the default arch and
206
+ // return the appropriate type.
207
+ using type_list = xsimd::mpl::type_list<short, int, long, float, std::complex<float>
208
+ #if XSIMD_WITH_NEON64 || !XSIMD_WITH_NEON
209
+ ,
210
+ double, std::complex<double>
211
+ #endif
212
+ >;
213
+ try_loads<type_list>();
214
+ }
215
+ }
216
+
217
+ #endif
@@ -0,0 +1,183 @@
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
+ #ifndef __FAST_MATH__
18
+ namespace detail
19
+ {
20
+ template <class T, bool is_int = std::is_integral<typename T::value_type>::value>
21
+ struct infinity_tester
22
+ {
23
+ static void test_isfinite()
24
+ {
25
+ T input(1);
26
+ INFO("input: ", input);
27
+ CHECK_UNARY(xsimd::all(xsimd::isfinite(input)));
28
+ }
29
+
30
+ static void test_isinf()
31
+ {
32
+ T input(1);
33
+ INFO("input: ", input);
34
+ CHECK_FALSE(xsimd::any(xsimd::isinf(input)));
35
+ }
36
+ };
37
+
38
+ template <class T>
39
+ struct infinity_tester<T, false>
40
+ {
41
+ static void test_isfinite()
42
+ {
43
+ T input = xsimd::infinity<T>();
44
+ CHECK_FALSE(xsimd::any(xsimd::isfinite(input)));
45
+ }
46
+ static void test_isinf()
47
+ {
48
+ T input = xsimd::infinity<T>();
49
+ CHECK_UNARY(xsimd::all(xsimd::isinf(input)));
50
+ }
51
+ };
52
+ }
53
+ #endif
54
+
55
+ template <class B>
56
+ struct basic_math_test
57
+ {
58
+ using batch_type = B;
59
+ using value_type = typename B::value_type;
60
+ static constexpr size_t size = B::size;
61
+ using array_type = std::array<value_type, size>;
62
+
63
+ array_type lhs;
64
+ array_type rhs;
65
+ array_type clip_input;
66
+ array_type from_input;
67
+
68
+ basic_math_test()
69
+ {
70
+ for (size_t i = 0; i < size; ++i)
71
+ {
72
+ lhs[i] = value_type(i) / 4 + value_type(1.2) * std::sqrt(value_type(i + 0.25)) + value_type(1.);
73
+ rhs[i] = value_type(10.2) / (i + 2) + value_type(0.25) + value_type(1.);
74
+ clip_input[i] = static_cast<value_type>(i) * value_type(0.25);
75
+ from_input[i] = rhs[i] - value_type(1);
76
+ }
77
+ }
78
+
79
+ void test_fmod() const
80
+ {
81
+ array_type expected;
82
+ std::transform(
83
+ lhs.cbegin(), lhs.cend(), rhs.cbegin(), expected.begin(),
84
+ [](const value_type& l, const value_type& r)
85
+ { return std::fmod(l, r); });
86
+ batch_type res = xsimd::fmod(batch_lhs(), batch_rhs());
87
+ CHECK_BATCH_EQ(res, expected);
88
+ }
89
+
90
+ void test_remainder() const
91
+ {
92
+ array_type expected;
93
+ std::transform(lhs.cbegin(), lhs.cend(), rhs.cbegin(), expected.begin(),
94
+ [](const value_type& l, const value_type& r)
95
+ { return std::remainder(l, r); });
96
+ batch_type res = xsimd::remainder(batch_lhs(), batch_rhs());
97
+ CHECK_BATCH_EQ(res, expected);
98
+ }
99
+
100
+ void test_fdim() const
101
+ {
102
+ array_type expected;
103
+ std::transform(lhs.cbegin(), lhs.cend(), rhs.cbegin(), expected.begin(),
104
+ [](const value_type& l, const value_type& r)
105
+ { return std::fdim(l, r); });
106
+ batch_type res = xsimd::fdim(batch_lhs(), batch_rhs());
107
+ CHECK_BATCH_EQ(res, expected);
108
+ }
109
+
110
+ void test_clip()
111
+ {
112
+ value_type clip_lo = static_cast<value_type>(0.5);
113
+ value_type clip_hi = static_cast<value_type>(1.);
114
+ array_type expected;
115
+ std::transform(clip_input.cbegin(), clip_input.cend(), expected.begin(),
116
+ [clip_lo, clip_hi](const value_type& l)
117
+ {
118
+ return l < clip_lo ? clip_lo : clip_hi < l ? clip_hi
119
+ : l;
120
+ });
121
+ batch_type res = xsimd::clip(batch_clip_input(), batch_type(clip_lo), batch_type(clip_hi));
122
+ CHECK_BATCH_EQ(res, expected);
123
+ }
124
+
125
+ #ifndef __FAST_MATH__
126
+ void test_isfinite()
127
+ {
128
+ detail::infinity_tester<batch_type>::test_isfinite();
129
+ }
130
+
131
+ void test_isinf()
132
+ {
133
+ detail::infinity_tester<batch_type>::test_isinf();
134
+ }
135
+ #endif
136
+
137
+ void test_nextafter()
138
+ {
139
+ array_type expected;
140
+ std::transform(from_input.cbegin(), from_input.cend(), rhs.cbegin(), expected.begin(),
141
+ [](const value_type& l, const value_type& r)
142
+ { return std::nextafter(l, r); });
143
+ batch_type res = xsimd::nextafter(batch_from_input(), batch_rhs());
144
+ CHECK_BATCH_EQ(res, expected);
145
+ }
146
+
147
+ private:
148
+ batch_type batch_lhs() const
149
+ {
150
+ return batch_type::load_unaligned(lhs.data());
151
+ }
152
+
153
+ batch_type batch_rhs() const
154
+ {
155
+ return batch_type::load_unaligned(rhs.data());
156
+ }
157
+
158
+ batch_type batch_clip_input() const
159
+ {
160
+ return batch_type::load_unaligned(clip_input.data());
161
+ }
162
+
163
+ batch_type batch_from_input() const
164
+ {
165
+ return batch_type::load_unaligned(from_input.data());
166
+ }
167
+ };
168
+
169
+ TEST_CASE_TEMPLATE("[basic math tests]", B, BATCH_MATH_TYPES)
170
+ {
171
+ basic_math_test<B> Test;
172
+
173
+ SUBCASE("fmod") { Test.test_fmod(); }
174
+ SUBCASE("remainder") { Test.test_remainder(); }
175
+ SUBCASE("fdim") { Test.test_fdim(); }
176
+ SUBCASE("clip") { Test.test_clip(); }
177
+ #ifndef __FAST_MATH__
178
+ SUBCASE("isfinite") { Test.test_isfinite(); }
179
+ SUBCASE("isinf") { Test.test_isinf(); }
180
+ #endif
181
+ SUBCASE("nextafter") { Test.test_nextafter(); }
182
+ }
183
+ #endif