sequenzo 0.1.21__cp39-cp39-macosx_10_9_x86_64.whl

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  1. sequenzo/__init__.py +240 -0
  2. sequenzo/big_data/__init__.py +12 -0
  3. sequenzo/big_data/clara/__init__.py +26 -0
  4. sequenzo/big_data/clara/clara.py +467 -0
  5. sequenzo/big_data/clara/utils/__init__.py +27 -0
  6. sequenzo/big_data/clara/utils/aggregatecases.py +92 -0
  7. sequenzo/big_data/clara/utils/davies_bouldin.py +91 -0
  8. sequenzo/big_data/clara/utils/get_weighted_diss.cpython-39-darwin.so +0 -0
  9. sequenzo/big_data/clara/utils/wfcmdd.py +205 -0
  10. sequenzo/big_data/clara/visualization.py +88 -0
  11. sequenzo/clustering/KMedoids.py +196 -0
  12. sequenzo/clustering/__init__.py +30 -0
  13. sequenzo/clustering/clustering_c_code.cpython-39-darwin.so +0 -0
  14. sequenzo/clustering/hierarchical_clustering.py +1380 -0
  15. sequenzo/clustering/src/KMedoid.cpp +262 -0
  16. sequenzo/clustering/src/PAM.cpp +236 -0
  17. sequenzo/clustering/src/PAMonce.cpp +234 -0
  18. sequenzo/clustering/src/cluster_quality.cpp +496 -0
  19. sequenzo/clustering/src/cluster_quality.h +128 -0
  20. sequenzo/clustering/src/cluster_quality_backup.cpp +570 -0
  21. sequenzo/clustering/src/module.cpp +228 -0
  22. sequenzo/clustering/src/weightedinertia.cpp +111 -0
  23. sequenzo/clustering/utils/__init__.py +27 -0
  24. sequenzo/clustering/utils/disscenter.py +122 -0
  25. sequenzo/data_preprocessing/__init__.py +20 -0
  26. sequenzo/data_preprocessing/helpers.py +256 -0
  27. sequenzo/datasets/__init__.py +41 -0
  28. sequenzo/datasets/biofam.csv +2001 -0
  29. sequenzo/datasets/biofam_child_domain.csv +2001 -0
  30. sequenzo/datasets/biofam_left_domain.csv +2001 -0
  31. sequenzo/datasets/biofam_married_domain.csv +2001 -0
  32. sequenzo/datasets/chinese_colonial_territories.csv +12 -0
  33. sequenzo/datasets/country_co2_emissions.csv +194 -0
  34. sequenzo/datasets/country_co2_emissions_global_deciles.csv +195 -0
  35. sequenzo/datasets/country_co2_emissions_global_quintiles.csv +195 -0
  36. sequenzo/datasets/country_co2_emissions_local_deciles.csv +195 -0
  37. sequenzo/datasets/country_co2_emissions_local_quintiles.csv +195 -0
  38. sequenzo/datasets/country_gdp_per_capita.csv +194 -0
  39. sequenzo/datasets/mvad.csv +713 -0
  40. sequenzo/datasets/pairfam_family.csv +1867 -0
  41. sequenzo/datasets/polyadic_samplec1.csv +61 -0
  42. sequenzo/datasets/polyadic_samplep1.csv +61 -0
  43. sequenzo/datasets/polyadic_seqc1.csv +61 -0
  44. sequenzo/datasets/polyadic_seqp1.csv +61 -0
  45. sequenzo/define_sequence_data.py +609 -0
  46. sequenzo/dissimilarity_measures/__init__.py +31 -0
  47. sequenzo/dissimilarity_measures/c_code.cpython-39-darwin.so +0 -0
  48. sequenzo/dissimilarity_measures/get_distance_matrix.py +702 -0
  49. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +241 -0
  50. sequenzo/dissimilarity_measures/src/DHDdistance.cpp +148 -0
  51. sequenzo/dissimilarity_measures/src/LCPdistance.cpp +114 -0
  52. sequenzo/dissimilarity_measures/src/OMdistance.cpp +247 -0
  53. sequenzo/dissimilarity_measures/src/OMspellDistance.cpp +281 -0
  54. sequenzo/dissimilarity_measures/src/__init__.py +0 -0
  55. sequenzo/dissimilarity_measures/src/dist2matrix.cpp +63 -0
  56. sequenzo/dissimilarity_measures/src/dp_utils.h +160 -0
  57. sequenzo/dissimilarity_measures/src/module.cpp +34 -0
  58. sequenzo/dissimilarity_measures/src/setup.py +30 -0
  59. sequenzo/dissimilarity_measures/src/utils.h +25 -0
  60. sequenzo/dissimilarity_measures/src/xsimd/.github/cmake-test/main.cpp +6 -0
  61. sequenzo/dissimilarity_measures/src/xsimd/benchmark/main.cpp +159 -0
  62. sequenzo/dissimilarity_measures/src/xsimd/benchmark/xsimd_benchmark.hpp +565 -0
  63. sequenzo/dissimilarity_measures/src/xsimd/docs/source/conf.py +37 -0
  64. sequenzo/dissimilarity_measures/src/xsimd/examples/mandelbrot.cpp +330 -0
  65. sequenzo/dissimilarity_measures/src/xsimd/examples/pico_bench.hpp +246 -0
  66. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_arithmetic.hpp +266 -0
  67. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_complex.hpp +112 -0
  68. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_details.hpp +323 -0
  69. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_logical.hpp +218 -0
  70. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_math.hpp +2583 -0
  71. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_memory.hpp +880 -0
  72. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_rounding.hpp +72 -0
  73. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_swizzle.hpp +174 -0
  74. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_trigo.hpp +978 -0
  75. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx.hpp +1924 -0
  76. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx2.hpp +1144 -0
  77. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512bw.hpp +656 -0
  78. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512cd.hpp +28 -0
  79. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512dq.hpp +244 -0
  80. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512er.hpp +20 -0
  81. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512f.hpp +2650 -0
  82. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512ifma.hpp +20 -0
  83. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512pf.hpp +20 -0
  84. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi.hpp +77 -0
  85. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi2.hpp +131 -0
  86. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vnni_avx512bw.hpp +20 -0
  87. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vnni_avx512vbmi2.hpp +20 -0
  88. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avxvnni.hpp +20 -0
  89. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common.hpp +24 -0
  90. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common_fwd.hpp +77 -0
  91. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_constants.hpp +393 -0
  92. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_emulated.hpp +788 -0
  93. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx.hpp +93 -0
  94. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx2.hpp +46 -0
  95. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_sse.hpp +97 -0
  96. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma4.hpp +92 -0
  97. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_i8mm_neon64.hpp +17 -0
  98. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_isa.hpp +142 -0
  99. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon.hpp +3142 -0
  100. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon64.hpp +1543 -0
  101. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_rvv.hpp +1513 -0
  102. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_scalar.hpp +1260 -0
  103. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse2.hpp +2024 -0
  104. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse3.hpp +67 -0
  105. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse4_1.hpp +339 -0
  106. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse4_2.hpp +44 -0
  107. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_ssse3.hpp +186 -0
  108. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sve.hpp +1155 -0
  109. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_vsx.hpp +892 -0
  110. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_wasm.hpp +1780 -0
  111. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_arch.hpp +240 -0
  112. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_config.hpp +484 -0
  113. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_cpuid.hpp +269 -0
  114. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_inline.hpp +27 -0
  115. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/math/xsimd_rem_pio2.hpp +719 -0
  116. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/memory/xsimd_aligned_allocator.hpp +349 -0
  117. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/memory/xsimd_alignment.hpp +91 -0
  118. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_all_registers.hpp +55 -0
  119. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_api.hpp +2765 -0
  120. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx2_register.hpp +44 -0
  121. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512bw_register.hpp +51 -0
  122. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512cd_register.hpp +51 -0
  123. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512dq_register.hpp +51 -0
  124. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512er_register.hpp +51 -0
  125. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512f_register.hpp +77 -0
  126. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512ifma_register.hpp +51 -0
  127. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512pf_register.hpp +51 -0
  128. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512vbmi2_register.hpp +51 -0
  129. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512vbmi_register.hpp +51 -0
  130. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512vnni_avx512bw_register.hpp +54 -0
  131. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512vnni_avx512vbmi2_register.hpp +53 -0
  132. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx_register.hpp +64 -0
  133. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avxvnni_register.hpp +44 -0
  134. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch.hpp +1524 -0
  135. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch_constant.hpp +300 -0
  136. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_common_arch.hpp +47 -0
  137. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_emulated_register.hpp +80 -0
  138. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_fma3_avx2_register.hpp +50 -0
  139. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_fma3_avx_register.hpp +50 -0
  140. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_fma3_sse_register.hpp +50 -0
  141. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_fma4_register.hpp +50 -0
  142. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_i8mm_neon64_register.hpp +55 -0
  143. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_neon64_register.hpp +55 -0
  144. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_neon_register.hpp +154 -0
  145. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_register.hpp +94 -0
  146. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_rvv_register.hpp +506 -0
  147. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_sse2_register.hpp +59 -0
  148. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_sse3_register.hpp +49 -0
  149. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_sse4_1_register.hpp +48 -0
  150. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_sse4_2_register.hpp +48 -0
  151. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_ssse3_register.hpp +48 -0
  152. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_sve_register.hpp +156 -0
  153. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_traits.hpp +337 -0
  154. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_utils.hpp +536 -0
  155. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_vsx_register.hpp +77 -0
  156. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_wasm_register.hpp +59 -0
  157. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/xsimd.hpp +75 -0
  158. sequenzo/dissimilarity_measures/src/xsimd/test/architectures/dummy.cpp +7 -0
  159. sequenzo/dissimilarity_measures/src/xsimd/test/doc/explicit_use_of_an_instruction_set.cpp +13 -0
  160. sequenzo/dissimilarity_measures/src/xsimd/test/doc/explicit_use_of_an_instruction_set_mean.cpp +24 -0
  161. sequenzo/dissimilarity_measures/src/xsimd/test/doc/explicit_use_of_an_instruction_set_mean_aligned.cpp +25 -0
  162. sequenzo/dissimilarity_measures/src/xsimd/test/doc/explicit_use_of_an_instruction_set_mean_arch_independent.cpp +28 -0
  163. sequenzo/dissimilarity_measures/src/xsimd/test/doc/explicit_use_of_an_instruction_set_mean_tag_dispatch.cpp +25 -0
  164. sequenzo/dissimilarity_measures/src/xsimd/test/doc/manipulating_abstract_batches.cpp +7 -0
  165. sequenzo/dissimilarity_measures/src/xsimd/test/doc/manipulating_parametric_batches.cpp +8 -0
  166. sequenzo/dissimilarity_measures/src/xsimd/test/doc/sum.hpp +31 -0
  167. sequenzo/dissimilarity_measures/src/xsimd/test/doc/sum_avx2.cpp +3 -0
  168. sequenzo/dissimilarity_measures/src/xsimd/test/doc/sum_sse2.cpp +3 -0
  169. sequenzo/dissimilarity_measures/src/xsimd/test/doc/writing_vectorized_code.cpp +11 -0
  170. sequenzo/dissimilarity_measures/src/xsimd/test/main.cpp +31 -0
  171. sequenzo/dissimilarity_measures/src/xsimd/test/test_api.cpp +230 -0
  172. sequenzo/dissimilarity_measures/src/xsimd/test/test_arch.cpp +217 -0
  173. sequenzo/dissimilarity_measures/src/xsimd/test/test_basic_math.cpp +183 -0
  174. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch.cpp +1049 -0
  175. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_bool.cpp +508 -0
  176. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_cast.cpp +409 -0
  177. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_complex.cpp +712 -0
  178. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_constant.cpp +286 -0
  179. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_float.cpp +141 -0
  180. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_int.cpp +365 -0
  181. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_manip.cpp +308 -0
  182. sequenzo/dissimilarity_measures/src/xsimd/test/test_bitwise_cast.cpp +222 -0
  183. sequenzo/dissimilarity_measures/src/xsimd/test/test_complex_exponential.cpp +226 -0
  184. sequenzo/dissimilarity_measures/src/xsimd/test/test_complex_hyperbolic.cpp +183 -0
  185. sequenzo/dissimilarity_measures/src/xsimd/test/test_complex_power.cpp +265 -0
  186. sequenzo/dissimilarity_measures/src/xsimd/test/test_complex_trigonometric.cpp +236 -0
  187. sequenzo/dissimilarity_measures/src/xsimd/test/test_conversion.cpp +248 -0
  188. sequenzo/dissimilarity_measures/src/xsimd/test/test_custom_default_arch.cpp +28 -0
  189. sequenzo/dissimilarity_measures/src/xsimd/test/test_error_gamma.cpp +170 -0
  190. sequenzo/dissimilarity_measures/src/xsimd/test/test_explicit_batch_instantiation.cpp +32 -0
  191. sequenzo/dissimilarity_measures/src/xsimd/test/test_exponential.cpp +202 -0
  192. sequenzo/dissimilarity_measures/src/xsimd/test/test_extract_pair.cpp +92 -0
  193. sequenzo/dissimilarity_measures/src/xsimd/test/test_fp_manipulation.cpp +77 -0
  194. sequenzo/dissimilarity_measures/src/xsimd/test/test_gnu_source.cpp +30 -0
  195. sequenzo/dissimilarity_measures/src/xsimd/test/test_hyperbolic.cpp +167 -0
  196. sequenzo/dissimilarity_measures/src/xsimd/test/test_load_store.cpp +304 -0
  197. sequenzo/dissimilarity_measures/src/xsimd/test/test_memory.cpp +61 -0
  198. sequenzo/dissimilarity_measures/src/xsimd/test/test_poly_evaluation.cpp +64 -0
  199. sequenzo/dissimilarity_measures/src/xsimd/test/test_power.cpp +184 -0
  200. sequenzo/dissimilarity_measures/src/xsimd/test/test_rounding.cpp +199 -0
  201. sequenzo/dissimilarity_measures/src/xsimd/test/test_select.cpp +101 -0
  202. sequenzo/dissimilarity_measures/src/xsimd/test/test_shuffle.cpp +760 -0
  203. sequenzo/dissimilarity_measures/src/xsimd/test/test_sum.cpp +4 -0
  204. sequenzo/dissimilarity_measures/src/xsimd/test/test_sum.hpp +34 -0
  205. sequenzo/dissimilarity_measures/src/xsimd/test/test_traits.cpp +172 -0
  206. sequenzo/dissimilarity_measures/src/xsimd/test/test_trigonometric.cpp +208 -0
  207. sequenzo/dissimilarity_measures/src/xsimd/test/test_utils.hpp +611 -0
  208. sequenzo/dissimilarity_measures/src/xsimd/test/test_wasm/test_wasm_playwright.py +123 -0
  209. sequenzo/dissimilarity_measures/src/xsimd/test/test_xsimd_api.cpp +1460 -0
  210. sequenzo/dissimilarity_measures/utils/__init__.py +16 -0
  211. sequenzo/dissimilarity_measures/utils/get_LCP_length_for_2_seq.py +44 -0
  212. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cpython-39-darwin.so +0 -0
  213. sequenzo/dissimilarity_measures/utils/seqconc.cpython-39-darwin.so +0 -0
  214. sequenzo/dissimilarity_measures/utils/seqdss.cpython-39-darwin.so +0 -0
  215. sequenzo/dissimilarity_measures/utils/seqdur.cpython-39-darwin.so +0 -0
  216. sequenzo/dissimilarity_measures/utils/seqlength.cpython-39-darwin.so +0 -0
  217. sequenzo/multidomain/__init__.py +23 -0
  218. sequenzo/multidomain/association_between_domains.py +311 -0
  219. sequenzo/multidomain/cat.py +431 -0
  220. sequenzo/multidomain/combt.py +519 -0
  221. sequenzo/multidomain/dat.py +89 -0
  222. sequenzo/multidomain/idcd.py +139 -0
  223. sequenzo/multidomain/linked_polyad.py +292 -0
  224. sequenzo/openmp_setup.py +233 -0
  225. sequenzo/prefix_tree/__init__.py +43 -0
  226. sequenzo/prefix_tree/individual_level_indicators.py +1274 -0
  227. sequenzo/prefix_tree/system_level_indicators.py +465 -0
  228. sequenzo/prefix_tree/utils.py +54 -0
  229. sequenzo/sequence_characteristics/__init__.py +40 -0
  230. sequenzo/sequence_characteristics/complexity_index.py +49 -0
  231. sequenzo/sequence_characteristics/overall_cross_sectional_entropy.py +220 -0
  232. sequenzo/sequence_characteristics/plot_characteristics.py +593 -0
  233. sequenzo/sequence_characteristics/simple_characteristics.py +311 -0
  234. sequenzo/sequence_characteristics/state_frequencies_and_entropy_per_sequence.py +39 -0
  235. sequenzo/sequence_characteristics/turbulence.py +155 -0
  236. sequenzo/sequence_characteristics/variance_of_spell_durations.py +86 -0
  237. sequenzo/sequence_characteristics/within_sequence_entropy.py +43 -0
  238. sequenzo/suffix_tree/__init__.py +48 -0
  239. sequenzo/suffix_tree/individual_level_indicators.py +1638 -0
  240. sequenzo/suffix_tree/system_level_indicators.py +456 -0
  241. sequenzo/suffix_tree/utils.py +56 -0
  242. sequenzo/visualization/__init__.py +29 -0
  243. sequenzo/visualization/plot_mean_time.py +194 -0
  244. sequenzo/visualization/plot_modal_state.py +276 -0
  245. sequenzo/visualization/plot_most_frequent_sequences.py +147 -0
  246. sequenzo/visualization/plot_relative_frequency.py +404 -0
  247. sequenzo/visualization/plot_sequence_index.py +937 -0
  248. sequenzo/visualization/plot_single_medoid.py +153 -0
  249. sequenzo/visualization/plot_state_distribution.py +613 -0
  250. sequenzo/visualization/plot_transition_matrix.py +190 -0
  251. sequenzo/visualization/utils/__init__.py +23 -0
  252. sequenzo/visualization/utils/utils.py +310 -0
  253. sequenzo/with_event_history_analysis/__init__.py +35 -0
  254. sequenzo/with_event_history_analysis/sequence_analysis_multi_state_model.py +850 -0
  255. sequenzo/with_event_history_analysis/sequence_history_analysis.py +283 -0
  256. sequenzo-0.1.21.dist-info/METADATA +308 -0
  257. sequenzo-0.1.21.dist-info/RECORD +254 -0
  258. sequenzo-0.1.21.dist-info/WHEEL +5 -0
  259. sequenzo-0.1.21.dist-info/licenses/LICENSE +28 -0
  260. sequenzo-0.1.21.dist-info/top_level.txt +1 -0
@@ -0,0 +1,265 @@
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
+ template <class B>
18
+ struct complex_power_test
19
+ {
20
+ using batch_type = B;
21
+ using real_batch_type = typename B::real_batch;
22
+ using value_type = typename B::value_type;
23
+ using real_value_type = typename value_type::value_type;
24
+ static constexpr size_t size = B::size;
25
+ using vector_type = std::vector<value_type>;
26
+ using real_vector_type = std::vector<real_value_type>;
27
+
28
+ size_t nb_input;
29
+ real_vector_type lhs_p;
30
+ vector_type lhs_nn;
31
+ vector_type lhs_pn;
32
+ vector_type lhs_np;
33
+ vector_type lhs_pp;
34
+ vector_type rhs;
35
+ vector_type expected;
36
+ vector_type res;
37
+
38
+ complex_power_test()
39
+ {
40
+ nb_input = 10000 * size;
41
+ lhs_p.resize(nb_input);
42
+ lhs_nn.resize(nb_input);
43
+ lhs_pn.resize(nb_input);
44
+ lhs_np.resize(nb_input);
45
+ lhs_pp.resize(nb_input);
46
+ rhs.resize(nb_input);
47
+ for (size_t i = 0; i < nb_input; ++i)
48
+ {
49
+ real_value_type real = (real_value_type(i) / 4 + real_value_type(1.2) * std::sqrt(real_value_type(i + 0.25))) / 100;
50
+ real_value_type imag = (real_value_type(i) / 7 + real_value_type(1.7) * std::sqrt(real_value_type(i + 0.37))) / 100;
51
+ lhs_p[i] = real;
52
+ lhs_nn[i] = value_type(-real, -imag);
53
+ lhs_pn[i] = value_type(real, -imag);
54
+ lhs_np[i] = value_type(-real, imag);
55
+ lhs_pp[i] = value_type(real, imag);
56
+ rhs[i] = value_type(real_value_type(10.2) / (i + 2) + real_value_type(0.25),
57
+ real_value_type(9.1) / (i + 3) + real_value_type(0.45));
58
+ }
59
+ expected.resize(nb_input);
60
+ res.resize(nb_input);
61
+ }
62
+
63
+ void test_abs()
64
+ {
65
+ real_vector_type real_expected(nb_input), real_res(nb_input);
66
+ std::transform(lhs_np.cbegin(), lhs_np.cend(), real_expected.begin(),
67
+ [](const value_type& v)
68
+ { using std::abs; return abs(v); });
69
+ batch_type in;
70
+ real_batch_type out;
71
+ for (size_t i = 0; i < nb_input; i += size)
72
+ {
73
+ detail::load_batch(in, lhs_np, i);
74
+ out = abs(in);
75
+ detail::store_batch(out, real_res, i);
76
+ }
77
+ size_t diff = detail::get_nb_diff(real_res, real_expected);
78
+ CHECK_EQ(diff, 0);
79
+ }
80
+
81
+ void test_arg()
82
+ {
83
+ real_vector_type real_expected(nb_input), real_res(nb_input);
84
+ std::transform(lhs_np.cbegin(), lhs_np.cend(), real_expected.begin(),
85
+ [](const value_type& v)
86
+ { using std::arg; return arg(v); });
87
+ batch_type in;
88
+ real_batch_type out;
89
+ for (size_t i = 0; i < nb_input; i += size)
90
+ {
91
+ detail::load_batch(in, lhs_np, i);
92
+ out = arg(in);
93
+ detail::store_batch(out, real_res, i);
94
+ }
95
+ size_t diff = detail::get_nb_diff(real_res, real_expected);
96
+ CHECK_EQ(diff, 0);
97
+ }
98
+
99
+ void test_pow()
100
+ {
101
+ std::transform(lhs_np.cbegin(), lhs_np.cend(), rhs.cbegin(), expected.begin(),
102
+ [](const value_type& l, const value_type& r)
103
+ { using std::pow; return pow(l, r); });
104
+ batch_type lhs_in, rhs_in, out;
105
+ for (size_t i = 0; i < nb_input; i += size)
106
+ {
107
+ detail::load_batch(lhs_in, lhs_np, i);
108
+ detail::load_batch(rhs_in, rhs, i);
109
+ out = pow(lhs_in, rhs_in);
110
+ detail::store_batch(out, res, i);
111
+ }
112
+ size_t diff = detail::get_nb_diff_near(res, expected, std::numeric_limits<real_value_type>::epsilon());
113
+ CHECK_EQ(diff, 0);
114
+ }
115
+
116
+ void test_pow_real_complex()
117
+ {
118
+ std::transform(lhs_p.cbegin(), lhs_p.cend(), lhs_pp.cbegin(), expected.begin(),
119
+ [](const real_value_type& l, const value_type& r)
120
+ { using std::pow; return pow(l, r); });
121
+ batch_type rhs_in, out;
122
+ real_batch_type lhs_in;
123
+ for (size_t i = 0; i < nb_input; i += size)
124
+ {
125
+ detail::load_batch(lhs_in, lhs_p, i);
126
+ detail::load_batch(rhs_in, lhs_pp, i);
127
+ out = pow(lhs_in, rhs_in);
128
+ detail::store_batch(out, res, i);
129
+ }
130
+ size_t diff = detail::get_nb_diff_near(res, expected, std::numeric_limits<real_value_type>::epsilon());
131
+ CHECK_EQ(diff, 0);
132
+ }
133
+
134
+ void test_pow_complex_real()
135
+ {
136
+ std::transform(lhs_pp.cbegin(), lhs_pp.cend(), lhs_p.cbegin(), expected.begin(),
137
+ [](const value_type& l, const real_value_type& r)
138
+ { using std::pow; return pow(l, r); });
139
+ batch_type rhs_in, out;
140
+ real_batch_type lhs_in;
141
+ for (size_t i = 0; i < nb_input; i += size)
142
+ {
143
+ detail::load_batch(lhs_in, lhs_p, i);
144
+ detail::load_batch(rhs_in, lhs_pp, i);
145
+ out = pow(lhs_in, rhs_in);
146
+ detail::store_batch(out, res, i);
147
+ }
148
+ size_t diff = detail::get_nb_diff_near(res, expected, std::numeric_limits<real_value_type>::epsilon());
149
+ CHECK_EQ(diff, 0);
150
+ }
151
+
152
+ void test_sqrt_nn()
153
+ {
154
+ std::transform(lhs_nn.cbegin(), lhs_nn.cend(), expected.begin(),
155
+ [](const value_type& v)
156
+ { using std::sqrt; return sqrt(v); });
157
+ batch_type in, out;
158
+ for (size_t i = 0; i < nb_input; i += size)
159
+ {
160
+ detail::load_batch(in, lhs_nn, i);
161
+ out = sqrt(in);
162
+ detail::store_batch(out, res, i);
163
+ }
164
+ size_t diff = detail::get_nb_diff(res, expected);
165
+ CHECK_EQ(diff, 0);
166
+ }
167
+
168
+ void test_sqrt_pn()
169
+ {
170
+ std::transform(lhs_pn.cbegin(), lhs_pn.cend(), expected.begin(),
171
+ [](const value_type& v)
172
+ { using std::sqrt; return sqrt(v); });
173
+ batch_type in, out;
174
+ for (size_t i = 0; i < nb_input; i += size)
175
+ {
176
+ detail::load_batch(in, lhs_pn, i);
177
+ out = sqrt(in);
178
+ detail::store_batch(out, res, i);
179
+ }
180
+ size_t diff = detail::get_nb_diff(res, expected);
181
+ CHECK_EQ(diff, 0);
182
+ }
183
+
184
+ void test_sqrt_np()
185
+ {
186
+ std::transform(lhs_np.cbegin(), lhs_np.cend(), expected.begin(),
187
+ [](const value_type& v)
188
+ { using std::sqrt; return sqrt(v); });
189
+ batch_type in, out;
190
+ for (size_t i = 0; i < nb_input; i += size)
191
+ {
192
+ detail::load_batch(in, lhs_np, i);
193
+ out = sqrt(in);
194
+ detail::store_batch(out, res, i);
195
+ }
196
+ size_t diff = detail::get_nb_diff(res, expected);
197
+ CHECK_EQ(diff, 0);
198
+ }
199
+
200
+ void test_sqrt_pp()
201
+ {
202
+ std::transform(lhs_pp.cbegin(), lhs_pp.cend(), expected.begin(),
203
+ [](const value_type& v)
204
+ { using std::sqrt; return sqrt(v); });
205
+ batch_type in, out;
206
+ for (size_t i = 0; i < nb_input; i += size)
207
+ {
208
+ detail::load_batch(in, lhs_pp, i);
209
+ out = sqrt(in);
210
+ detail::store_batch(out, res, i);
211
+ }
212
+ size_t diff = detail::get_nb_diff(res, expected);
213
+ CHECK_EQ(diff, 0);
214
+ }
215
+ };
216
+
217
+ TEST_CASE_TEMPLATE("[complex power]", B, BATCH_COMPLEX_TYPES)
218
+ {
219
+ complex_power_test<B> Test;
220
+ SUBCASE("abs")
221
+ {
222
+ Test.test_abs();
223
+ }
224
+
225
+ SUBCASE("arg")
226
+ {
227
+ Test.test_arg();
228
+ }
229
+
230
+ SUBCASE("pow")
231
+ {
232
+ Test.test_pow();
233
+ }
234
+
235
+ SUBCASE("pow real complex")
236
+ {
237
+ Test.test_pow_real_complex();
238
+ }
239
+
240
+ SUBCASE("pow complex real")
241
+ {
242
+ Test.test_pow_complex_real();
243
+ }
244
+
245
+ SUBCASE("sqrt_nn")
246
+ {
247
+ Test.test_sqrt_nn();
248
+ }
249
+
250
+ SUBCASE("sqrt_pn")
251
+ {
252
+ Test.test_sqrt_pn();
253
+ }
254
+
255
+ SUBCASE("sqrt_np")
256
+ {
257
+ Test.test_sqrt_np();
258
+ }
259
+
260
+ SUBCASE("sqrt_pp")
261
+ {
262
+ Test.test_sqrt_pp();
263
+ }
264
+ }
265
+ #endif
@@ -0,0 +1,236 @@
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
+
14
+ #ifndef XSIMD_NO_SUPPORTED_ARCHITECTURE
15
+
16
+ #include "test_utils.hpp"
17
+
18
+ template <class B>
19
+ struct complex_trigonometric_test
20
+ {
21
+ using batch_type = B;
22
+ using real_batch_type = typename B::real_batch;
23
+ using value_type = typename B::value_type;
24
+ using real_value_type = typename value_type::value_type;
25
+ static constexpr size_t size = B::size;
26
+ using vector_type = std::vector<value_type>;
27
+
28
+ size_t nb_input;
29
+ vector_type input;
30
+ vector_type ainput;
31
+ vector_type atan_input;
32
+ vector_type expected;
33
+ vector_type res;
34
+
35
+ complex_trigonometric_test()
36
+ {
37
+ nb_input = size * 10000;
38
+ input.resize(nb_input);
39
+ ainput.resize(nb_input);
40
+ atan_input.resize(nb_input);
41
+ for (size_t i = 0; i < nb_input; ++i)
42
+ {
43
+ input[i] = value_type(real_value_type(0.) + i * real_value_type(80.) / nb_input,
44
+ real_value_type(0.1) + i * real_value_type(56.) / nb_input);
45
+ ainput[i] = value_type(real_value_type(-1.) + real_value_type(2.) * i / nb_input,
46
+ real_value_type(-1.1) + real_value_type(2.1) * i / nb_input);
47
+ atan_input[i] = value_type(real_value_type(-10.) + i * real_value_type(20.) / nb_input,
48
+ real_value_type(-9.) + i * real_value_type(21.) / nb_input);
49
+ }
50
+ expected.resize(nb_input);
51
+ res.resize(nb_input);
52
+ }
53
+
54
+ void test_sin()
55
+ {
56
+ std::transform(input.cbegin(), input.cend(), expected.begin(),
57
+ [](const value_type& v)
58
+ { using std::sin; return sin(v); });
59
+ batch_type in, out;
60
+ for (size_t i = 0; i < nb_input; i += size)
61
+ {
62
+ detail::load_batch(in, input, i);
63
+ out = sin(in);
64
+ detail::store_batch(out, res, i);
65
+ }
66
+ size_t diff = detail::get_nb_diff(res, expected);
67
+ CHECK_EQ(diff, 0);
68
+ }
69
+
70
+ void test_cos()
71
+ {
72
+ std::transform(input.cbegin(), input.cend(), expected.begin(),
73
+ [](const value_type& v)
74
+ { using std::cos; return cos(v); });
75
+ batch_type in, out;
76
+ for (size_t i = 0; i < nb_input; i += size)
77
+ {
78
+ detail::load_batch(in, input, i);
79
+ out = cos(in);
80
+ detail::store_batch(out, res, i);
81
+ }
82
+ size_t diff = detail::get_nb_diff(res, expected);
83
+ CHECK_EQ(diff, 0);
84
+ }
85
+
86
+ void test_sincos()
87
+ {
88
+ vector_type expected2(nb_input), res2(nb_input);
89
+ std::transform(input.cbegin(), input.cend(), expected.begin(),
90
+ [](const value_type& v)
91
+ { using std::sin; return sin(v); });
92
+ std::transform(input.cbegin(), input.cend(), expected2.begin(),
93
+ [](const value_type& v)
94
+ { using std::cos; return cos(v); });
95
+ batch_type in, out1, out2;
96
+ for (size_t i = 0; i < nb_input; i += size)
97
+ {
98
+ detail::load_batch(in, input, i);
99
+ std::tie(out1, out2) = sincos(in);
100
+ detail::store_batch(out1, res, i);
101
+ detail::store_batch(out2, res2, i);
102
+ }
103
+ size_t diff = detail::get_nb_diff(res, expected);
104
+ CHECK_EQ(diff, 0);
105
+ diff = detail::get_nb_diff(res2, expected2);
106
+ CHECK_EQ(diff, 0);
107
+ }
108
+
109
+ void test_tan()
110
+ {
111
+ test_conditional_tan<real_value_type>();
112
+ }
113
+
114
+ void test_asin()
115
+ {
116
+ std::transform(ainput.cbegin(), ainput.cend(), expected.begin(),
117
+ [](const value_type& v)
118
+ { using std::asin; return asin(v); });
119
+ batch_type in, out;
120
+ for (size_t i = 0; i < nb_input; i += size)
121
+ {
122
+ detail::load_batch(in, ainput, i);
123
+ out = asin(in);
124
+ detail::store_batch(out, res, i);
125
+ }
126
+ size_t diff = detail::get_nb_diff(res, expected);
127
+ CHECK_EQ(diff, 0);
128
+ }
129
+
130
+ void test_acos()
131
+ {
132
+ std::transform(ainput.cbegin(), ainput.cend(), expected.begin(),
133
+ [](const value_type& v)
134
+ { using std::acos; return acos(v); });
135
+ batch_type in, out;
136
+ for (size_t i = 0; i < nb_input; i += size)
137
+ {
138
+ detail::load_batch(in, ainput, i);
139
+ out = acos(in);
140
+ detail::store_batch(out, res, i);
141
+ }
142
+ size_t diff = detail::get_nb_diff(res, expected);
143
+ CHECK_EQ(diff, 0);
144
+ }
145
+
146
+ void test_atan()
147
+ {
148
+ std::transform(atan_input.cbegin(), atan_input.cend(), expected.begin(),
149
+ [](const value_type& v)
150
+ { using std::atan; return atan(v); });
151
+ batch_type in, out;
152
+ for (size_t i = 0; i < nb_input; i += size)
153
+ {
154
+ detail::load_batch(in, atan_input, i);
155
+ out = atan(in);
156
+ detail::store_batch(out, res, i);
157
+ }
158
+ size_t diff = detail::get_nb_diff(res, expected);
159
+ CHECK_EQ(diff, 0);
160
+ }
161
+
162
+ private:
163
+ void test_tan_impl()
164
+ {
165
+ std::transform(input.cbegin(), input.cend(), expected.begin(),
166
+ [](const value_type& v)
167
+ { using std::tan; return tan(v); });
168
+ batch_type in, out;
169
+ for (size_t i = 0; i < nb_input; i += size)
170
+ {
171
+ detail::load_batch(in, input, i);
172
+ out = tan(in);
173
+ detail::store_batch(out, res, i);
174
+ }
175
+ size_t diff = detail::get_nb_diff(res, expected);
176
+ CHECK_EQ(diff, 0);
177
+ }
178
+
179
+ template <class T, typename std::enable_if<!std::is_same<T, float>::value, int>::type = 0>
180
+ void test_conditional_tan()
181
+ {
182
+ test_tan_impl();
183
+ }
184
+
185
+ template <class T, typename std::enable_if<std::is_same<T, float>::value, int>::type = 0>
186
+ void test_conditional_tan()
187
+ {
188
+ #if (XSIMD_ARM_INSTR_SET >= XSIMD_ARM7_NEON_VERSION)
189
+ #if DEBUG_ACCURACY
190
+ test_tan_impl();
191
+ #endif
192
+ #else
193
+ test_tan_impl();
194
+ #endif
195
+ }
196
+ };
197
+
198
+ TEST_CASE_TEMPLATE("[complex trigonometric]", B, BATCH_COMPLEX_TYPES)
199
+ {
200
+ complex_trigonometric_test<B> Test;
201
+ SUBCASE("sin")
202
+ {
203
+ Test.test_sin();
204
+ }
205
+
206
+ SUBCASE("cos")
207
+ {
208
+ Test.test_cos();
209
+ }
210
+
211
+ SUBCASE("sincos")
212
+ {
213
+ Test.test_sincos();
214
+ }
215
+
216
+ SUBCASE("tan")
217
+ {
218
+ Test.test_tan();
219
+ }
220
+
221
+ SUBCASE("asin")
222
+ {
223
+ Test.test_asin();
224
+ }
225
+
226
+ SUBCASE("acos")
227
+ {
228
+ Test.test_acos();
229
+ }
230
+
231
+ SUBCASE("atan")
232
+ {
233
+ Test.test_atan();
234
+ }
235
+ }
236
+ #endif