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 +1,409 @@
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
+ #if !XSIMD_WITH_NEON || XSIMD_WITH_NEON64
18
+ namespace detail
19
+ {
20
+ template <class T_out, class T_in>
21
+ inline typename std::enable_if<std::is_unsigned<T_in>::value && std::is_integral<T_out>::value, bool>::type
22
+ is_convertible(T_in value)
23
+ {
24
+ return static_cast<uint64_t>(value) <= static_cast<uint64_t>(std::numeric_limits<T_out>::max());
25
+ }
26
+
27
+ template <class T_out, class T_in>
28
+ inline typename std::enable_if<std::is_integral<T_in>::value && std::is_signed<T_in>::value && std::is_integral<T_out>::value && std::is_signed<T_out>::value, bool>::type
29
+ is_convertible(T_in value)
30
+ {
31
+ int64_t signed_value = static_cast<int64_t>(value);
32
+ return signed_value < static_cast<int64_t>(std::numeric_limits<T_out>::max()) && signed_value >= static_cast<int64_t>(std::numeric_limits<T_out>::lowest());
33
+ }
34
+
35
+ template <class T_out, class T_in>
36
+ inline typename std::enable_if<std::is_integral<T_in>::value && std::is_signed<T_in>::value && std::is_unsigned<T_out>::value, bool>::type
37
+ is_convertible(T_in value)
38
+ {
39
+ return value >= 0 && is_convertible<T_out>(static_cast<uint64_t>(value));
40
+ }
41
+
42
+ template <class T_out, class T_in>
43
+ inline typename std::enable_if<std::is_floating_point<T_in>::value && std::is_integral<T_out>::value, bool>::type
44
+ is_convertible(T_in value)
45
+ {
46
+ return value < static_cast<T_in>(std::numeric_limits<T_out>::max()) && value >= static_cast<T_in>(std::numeric_limits<T_out>::lowest());
47
+ }
48
+
49
+ template <class T_out, class T_in>
50
+ inline typename std::enable_if<std::is_floating_point<T_out>::value, bool>::type
51
+ is_convertible(T_in)
52
+ {
53
+ return true;
54
+ }
55
+
56
+ template <typename Arch, typename From, typename To>
57
+ using uses_fast_cast = std::is_same<xsimd::kernel::detail::conversion_type<Arch, From, To>,
58
+ xsimd::kernel::detail::with_fast_conversion>;
59
+ }
60
+
61
+ template <class CP>
62
+ struct batch_cast_test
63
+ {
64
+ static constexpr size_t N = CP::size;
65
+ static constexpr size_t A = CP::alignment;
66
+
67
+ using int8_batch = xsimd::batch<int8_t>;
68
+ using uint8_batch = xsimd::batch<uint8_t>;
69
+ using int16_batch = xsimd::batch<int16_t>;
70
+ using uint16_batch = xsimd::batch<uint16_t>;
71
+ using int32_batch = xsimd::batch<int32_t>;
72
+ using uint32_batch = xsimd::batch<uint32_t>;
73
+ using int64_batch = xsimd::batch<int64_t>;
74
+ using uint64_batch = xsimd::batch<uint64_t>;
75
+ using float_batch = xsimd::batch<float>;
76
+ using double_batch = xsimd::batch<double>;
77
+
78
+ std::vector<uint64_t> int_test_values;
79
+ std::vector<float> float_test_values;
80
+ std::vector<double> double_test_values;
81
+
82
+ batch_cast_test()
83
+ {
84
+ int_test_values = {
85
+ 0,
86
+ 0x01,
87
+ 0x7f,
88
+ 0x80,
89
+ 0xff,
90
+ 0x0100,
91
+ 0x7fff,
92
+ 0x8000,
93
+ 0xffff,
94
+ 0x00010000,
95
+ 0x7fffffff,
96
+ 0x80000000,
97
+ 0xffffffff,
98
+ 0x0000000100000000,
99
+ 0x7fffffffffffffff,
100
+ 0x8000000000000000,
101
+ 0xffffffffffffffff
102
+ };
103
+
104
+ float_test_values = {
105
+ 0.0f,
106
+ 1.0f,
107
+ -1.0f,
108
+ 127.0f,
109
+ 128.0f,
110
+ -128.0f,
111
+ 255.0f,
112
+ 256.0f,
113
+ -256.0f,
114
+ 32767.0f,
115
+ 32768.0f,
116
+ -32768.0f,
117
+ 65535.0f,
118
+ 65536.0f,
119
+ -65536.0f,
120
+ 2147483647.0f,
121
+ 2147483648.0f,
122
+ -2147483648.0f,
123
+ 4294967167.0f
124
+ };
125
+
126
+ double_test_values = {
127
+ 0.0,
128
+ 1.0,
129
+ -1.0,
130
+ 127.0,
131
+ 128.0,
132
+ -128.0,
133
+ 255.0,
134
+ 256.0,
135
+ -256.0,
136
+ 32767.0,
137
+ 32768.0,
138
+ -32768.0,
139
+ 65535.0,
140
+ 65536.0,
141
+ -65536.0,
142
+ 2147483647.0,
143
+ 2147483648.0,
144
+ -2147483648.0,
145
+ 4294967295.0,
146
+ 4294967296.0,
147
+ -4294967296.0,
148
+ 9223372036854775807.0,
149
+ 9223372036854775808.0,
150
+ -9223372036854775808.0,
151
+ 18446744073709550591.0
152
+ };
153
+ }
154
+
155
+ void test_bool_cast() const
156
+ {
157
+ test_bool_cast_impl<float_batch, int32_batch>("batch bool cast float -> int32");
158
+ test_bool_cast_impl<float_batch, uint32_batch>("batch bool cast float -> uint32");
159
+ test_bool_cast_impl<int32_batch, float_batch>("batch bool cast int32 -> float");
160
+ test_bool_cast_impl<uint32_batch, float_batch>("batch bool cast uint32 -> float");
161
+ test_bool_cast_impl<float_batch, float_batch>("batch bool cast float -> float");
162
+ }
163
+
164
+ void test_cast() const
165
+ {
166
+ for (const auto& test_value : int_test_values)
167
+ {
168
+ test_cast_impl<int8_batch, int8_batch>(test_value, "batch cast int8 -> int8");
169
+ test_cast_impl<int8_batch, uint8_batch>(test_value, "batch cast int8 -> uint8");
170
+ test_cast_impl<uint8_batch, int8_batch>(test_value, "batch cast uint8 -> int8");
171
+ test_cast_impl<uint8_batch, uint8_batch>(test_value, "batch cast uint8 -> uint8");
172
+
173
+ test_cast_impl<int16_batch, int16_batch>(test_value, "batch cast int16 -> int16");
174
+ test_cast_impl<int16_batch, uint16_batch>(test_value, "batch cast int16 -> uint16");
175
+ test_cast_impl<uint16_batch, int16_batch>(test_value, "batch cast uint16 -> int16");
176
+ test_cast_impl<uint16_batch, uint16_batch>(test_value, "batch cast uint16 -> uint16");
177
+
178
+ test_cast_impl<int32_batch, int32_batch>(test_value, "batch cast int32 -> int32");
179
+ test_cast_impl<int32_batch, uint32_batch>(test_value, "batch cast int32 -> uint32");
180
+ test_cast_impl<int32_batch, float_batch>(test_value, "batch cast int32 -> float");
181
+ test_cast_impl<uint32_batch, int32_batch>(test_value, "batch cast uint32 -> int32");
182
+ test_cast_impl<uint32_batch, uint32_batch>(test_value, "batch cast uint32 -> uint32");
183
+ test_cast_impl<uint32_batch, float_batch>(test_value, "batch cast uint32 -> float");
184
+
185
+ test_cast_impl<int64_batch, int64_batch>(test_value, "batch cast int64 -> int64");
186
+ test_cast_impl<int64_batch, uint64_batch>(test_value, "batch cast int64 -> uint64");
187
+ test_cast_impl<int64_batch, double_batch>(test_value, "batch cast int64 -> double");
188
+ test_cast_impl<uint64_batch, int64_batch>(test_value, "batch cast uint64 -> int64");
189
+ test_cast_impl<uint64_batch, uint64_batch>(test_value, "batch cast uint64 -> uint64");
190
+ test_cast_impl<uint64_batch, double_batch>(test_value, "batch cast uint64 -> double");
191
+ }
192
+
193
+ for (const auto& test_value : float_test_values)
194
+ {
195
+ test_cast_impl<float_batch, int32_batch>(test_value, "batch cast float -> int32");
196
+ test_cast_impl<float_batch, uint32_batch>(test_value, "batch cast float -> uint32");
197
+ test_cast_impl<float_batch, float_batch>(test_value, "batch cast float -> float");
198
+ }
199
+
200
+ for (const auto& test_value : double_test_values)
201
+ {
202
+ test_cast_impl<double_batch, int64_batch>(test_value, "batch cast double -> int64");
203
+ test_cast_impl<double_batch, uint64_batch>(test_value, "batch cast double -> uint64");
204
+ test_cast_impl<double_batch, double_batch>(test_value, "batch cast double -> double");
205
+ }
206
+ }
207
+
208
+ #if 0 && XSIMD_X86_INSTR_SET >= XSIMD_X86_AVX_VERSION
209
+ template <size_t Align = A>
210
+ typename std::enable_if<Align >= 32, void>::type test_cast_sizeshift1() const
211
+ {
212
+ for (const auto& test_value : int_test_values)
213
+ {
214
+ test_cast_impl<int8_batch, int16_batch>(test_value, "batch cast int8 -> int16");
215
+ test_cast_impl<int8_batch, uint16_batch>(test_value, "batch cast int8 -> uint16");
216
+ test_cast_impl<uint8_batch, int16_batch>(test_value, "batch cast uint8 -> int16");
217
+ test_cast_impl<uint8_batch, uint16_batch>(test_value, "batch cast uint8 -> uint16");
218
+
219
+ test_cast_impl<int16_batch, int8_batch>(test_value, "batch cast int16 -> int8");
220
+ test_cast_impl<int16_batch, uint8_batch>(test_value, "batch cast int16 -> uint8");
221
+ test_cast_impl<int16_batch, int32_batch>(test_value, "batch cast int16 -> int32");
222
+ test_cast_impl<int16_batch, uint32_batch>(test_value, "batch cast int16 -> uint32");
223
+ test_cast_impl<int16_batch, float_batch>(test_value, "batch cast int16 -> float");
224
+ test_cast_impl<uint16_batch, int8_batch>(test_value, "batch cast uint16 -> int8");
225
+ test_cast_impl<uint16_batch, uint8_batch>(test_value, "batch cast uint16 -> uint8");
226
+ test_cast_impl<uint16_batch, int32_batch>(test_value, "batch cast uint16 -> int32");
227
+ test_cast_impl<uint16_batch, uint32_batch>(test_value, "batch cast uint16 -> uint32");
228
+ test_cast_impl<uint16_batch, float_batch>(test_value, "batch cast uint16 -> float");
229
+
230
+ test_cast_impl<int32_batch, int16_batch>(test_value, "batch cast int32 -> int16");
231
+ test_cast_impl<int32_batch, uint16_batch>(test_value, "batch cast int32 -> uint16");
232
+ test_cast_impl<int32_batch, int64_batch>(test_value, "batch cast int32 -> int64");
233
+ test_cast_impl<int32_batch, uint64_batch>(test_value, "batch cast int32 -> uint64");
234
+ test_cast_impl<int32_batch, double_batch>(test_value, "batch cast int32 -> double");
235
+ test_cast_impl<uint32_batch, int16_batch>(test_value, "batch cast uint32 -> int16");
236
+ test_cast_impl<uint32_batch, uint16_batch>(test_value, "batch cast uint32 -> uint16");
237
+ test_cast_impl<uint32_batch, int64_batch>(test_value, "batch cast uint32 -> int64");
238
+ test_cast_impl<uint32_batch, uint64_batch>(test_value, "batch cast uint32 -> uint64");
239
+ test_cast_impl<uint32_batch, double_batch>(test_value, "batch cast uint32 -> double");
240
+
241
+ test_cast_impl<int64_batch, int32_batch>(test_value, "batch cast int64 -> int32");
242
+ test_cast_impl<int64_batch, uint32_batch>(test_value, "batch cast int64 -> uint32");
243
+ test_cast_impl<int64_batch, float_batch>(test_value, "batch cast int64 -> float");
244
+ test_cast_impl<uint64_batch, int32_batch>(test_value, "batch cast uint64 -> int32");
245
+ test_cast_impl<uint64_batch, uint32_batch>(test_value, "batch cast uint64 -> uint32");
246
+ test_cast_impl<uint64_batch, float_batch>(test_value, "batch cast uint64 -> float");
247
+ }
248
+
249
+ for (const auto& test_value : float_test_values)
250
+ {
251
+ test_cast_impl<float_batch, int16_batch>(test_value, "batch cast float -> int16");
252
+ test_cast_impl<float_batch, uint16_batch>(test_value, "batch cast float -> uint16");
253
+ test_cast_impl<float_batch, int64_batch>(test_value, "batch cast float -> int64");
254
+ test_cast_impl<float_batch, uint64_batch>(test_value, "batch cast float -> uint64");
255
+ test_cast_impl<float_batch, double_batch>(test_value, "batch cast float -> double");
256
+ }
257
+
258
+ for (const auto& test_value : double_test_values)
259
+ {
260
+ test_cast_impl<double_batch, int32_batch>(test_value, "batch cast double -> int32");
261
+ test_cast_impl<double_batch, uint32_batch>(test_value, "batch cast double -> uint32");
262
+ test_cast_impl<double_batch, float_batch>(test_value, "batch cast double -> float");
263
+ }
264
+ }
265
+
266
+ template <size_t Align = A>
267
+ typename std::enable_if<Align < 32, void>::type test_cast_sizeshift1() const
268
+ {
269
+ }
270
+ #endif
271
+
272
+ #if 0 && XSIMD_X86_INSTR_SET >= XSIMD_X86_AVX512_VERSION
273
+ template <size_t Align = A>
274
+ typename std::enable_if<Align >= 64, void>::type test_cast_sizeshift2() const
275
+ {
276
+ for (const auto& test_value : int_test_values)
277
+ {
278
+ test_cast_impl<int8_batch, int32_batch>(test_value, "batch cast int8 -> int32");
279
+ test_cast_impl<int8_batch, uint32_batch>(test_value, "batch cast int8 -> uint32");
280
+ test_cast_impl<int8_batch, float_batch>(test_value, "batch cast int8 -> float");
281
+ test_cast_impl<uint8_batch, int32_batch>(test_value, "batch cast uint8 -> int32");
282
+ test_cast_impl<uint8_batch, uint32_batch>(test_value, "batch cast uint8 -> uint32");
283
+ test_cast_impl<uint8_batch, float_batch>(test_value, "batch cast uint8 -> float");
284
+
285
+ test_cast_impl<int16_batch, int64_batch>(test_value, "batch cast int16 -> int64");
286
+ test_cast_impl<int16_batch, uint64_batch>(test_value, "batch cast int16 -> uint64");
287
+ test_cast_impl<int16_batch, double_batch>(test_value, "batch cast int16 -> double");
288
+ test_cast_impl<uint16_batch, int64_batch>(test_value, "batch cast uint16 -> int64");
289
+ test_cast_impl<uint16_batch, uint64_batch>(test_value, "batch cast uint16 -> uint64");
290
+ test_cast_impl<uint16_batch, double_batch>(test_value, "batch cast uint16 -> double");
291
+
292
+ test_cast_impl<int32_batch, int8_batch>(test_value, "batch cast int32 -> int8");
293
+ test_cast_impl<int32_batch, uint8_batch>(test_value, "batch cast int32 -> uint8");
294
+ test_cast_impl<uint32_batch, int8_batch>(test_value, "batch cast uint32 -> int8");
295
+ test_cast_impl<uint32_batch, uint8_batch>(test_value, "batch cast uint32 -> uint8");
296
+
297
+ test_cast_impl<int64_batch, int16_batch>(test_value, "batch cast int64 -> int16");
298
+ test_cast_impl<int64_batch, uint16_batch>(test_value, "batch cast int64 -> uint16");
299
+ test_cast_impl<uint64_batch, int16_batch>(test_value, "batch cast uint64 -> int16");
300
+ test_cast_impl<uint64_batch, uint16_batch>(test_value, "batch cast uint64 -> uint16");
301
+ }
302
+
303
+ for (const auto& test_value : float_test_values)
304
+ {
305
+ test_cast_impl<float_batch, int8_batch>(test_value, "batch cast float -> int8");
306
+ test_cast_impl<float_batch, uint8_batch>(test_value, "batch cast float -> uint8");
307
+ }
308
+
309
+ for (const auto& test_value : double_test_values)
310
+ {
311
+ test_cast_impl<double_batch, int16_batch>(test_value, "batch cast double -> int16");
312
+ test_cast_impl<double_batch, uint16_batch>(test_value, "batch cast double -> uint16");
313
+ }
314
+ }
315
+
316
+ template <size_t Align = A>
317
+ typename std::enable_if<Align < 64, void>::type test_cast_sizeshift2() const
318
+ {
319
+ }
320
+ #endif
321
+
322
+ private:
323
+ template <class B_in, class B_out, class T>
324
+ void test_cast_impl(T test_value, const std::string& name) const
325
+ {
326
+ using T_in = typename B_in::value_type;
327
+ using T_out = typename B_out::value_type;
328
+ using B_common_in = xsimd::batch<T_in>;
329
+ using B_common_out = xsimd::batch<T_out>;
330
+
331
+ auto clamp = [](T v)
332
+ {
333
+ return static_cast<T_in>(xsimd::min(v, static_cast<T>(std::numeric_limits<T_in>::max() - 1)));
334
+ };
335
+
336
+ T_in in_test_value = clamp(test_value);
337
+ if (detail::is_convertible<T_out>(in_test_value))
338
+ {
339
+ B_common_out res = xsimd::batch_cast<T_out>(B_common_in(in_test_value));
340
+ INFO(name);
341
+ T_out scalar_ref = static_cast<T_out>(in_test_value);
342
+ T_out scalar_res = res.get(0);
343
+ CHECK_SCALAR_EQ(scalar_ref, scalar_res);
344
+ }
345
+ }
346
+
347
+ template <class B_in, class B_out>
348
+ void test_bool_cast_impl(const std::string& name) const
349
+ {
350
+ using T_in = typename B_in::value_type;
351
+ using T_out = typename B_out::value_type;
352
+ using B_common_in = xsimd::batch_bool<T_in>;
353
+ using B_common_out = xsimd::batch_bool<T_out>;
354
+
355
+ B_common_in all_true_in(true);
356
+ B_common_out all_true_res = xsimd::batch_bool_cast<T_out>(all_true_in);
357
+ INFO(name);
358
+ CHECK_SCALAR_EQ(all_true_res.get(0), true);
359
+
360
+ B_common_in all_false_in(false);
361
+ B_common_out all_false_res = xsimd::batch_bool_cast<T_out>(all_false_in);
362
+ INFO(name);
363
+ CHECK_SCALAR_EQ(all_false_res.get(0), false);
364
+ }
365
+ };
366
+
367
+ TEST_CASE_TEMPLATE("[xsimd cast tests]", B, CONVERSION_TYPES)
368
+ {
369
+ batch_cast_test<B> Test;
370
+
371
+ SUBCASE("bool cast")
372
+ {
373
+ Test.test_bool_cast();
374
+ }
375
+
376
+ SUBCASE("cast")
377
+ {
378
+ Test.test_cast();
379
+ }
380
+ }
381
+ #endif
382
+ #if 0 && XSIMD_X86_INSTR_SET >= XSIMD_X86_AVX_VERSION
383
+ TYPED_TEST(batch_cast_test, cast_sizeshift1)
384
+ {
385
+ this->test_cast_sizeshift1();
386
+ }
387
+ #endif
388
+
389
+ #if 0 && XSIMD_X86_INSTR_SET >= XSIMD_X86_AVX512_VERSION
390
+ TYPED_TEST(batch_cast_test, cast_sizeshift2)
391
+ {
392
+ this->test_cast_sizeshift2();
393
+ }
394
+ #endif
395
+
396
+ #if XSIMD_WITH_SSE2
397
+ TEST_CASE_TEMPLATE("[xsimd cast tests]", B, CONVERSION_TYPES)
398
+ {
399
+ SUBCASE("use fastcast")
400
+ {
401
+ using A = xsimd::default_arch;
402
+ static_assert(detail::uses_fast_cast<A, int32_t, float>::value,
403
+ "expected int32 to float conversion to use fast_cast");
404
+ static_assert(detail::uses_fast_cast<A, float, int32_t>::value,
405
+ "expected float to int32 conversion to use fast_cast");
406
+ }
407
+ }
408
+ #endif
409
+ #endif