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 +1,72 @@
1
+ /***************************************************************************
2
+ * Copyright (c) Johan Mabille, Sylvain Corlay, Wolf Vollprecht and *
3
+ * Martin Renou *
4
+ * Copyright (c) QuantStack *
5
+ * Copyright (c) Serge Guelton *
6
+ * *
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+ * Distributed under the terms of the BSD 3-Clause License. *
8
+ * *
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+ * The full license is in the file LICENSE, distributed with this software. *
10
+ ****************************************************************************/
11
+
12
+ #ifndef XSIMD_COMMON_ROUNDING_HPP
13
+ #define XSIMD_COMMON_ROUNDING_HPP
14
+
15
+ #include "./xsimd_common_details.hpp"
16
+
17
+ namespace xsimd
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+ {
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+
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+ namespace kernel
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+ {
22
+
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+ using namespace types;
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+
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+ // ceil
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+ template <class A, class T>
27
+ XSIMD_INLINE batch<T, A> ceil(batch<T, A> const& self, requires_arch<common>) noexcept
28
+ {
29
+ batch<T, A> truncated_self = trunc(self);
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+ return select(truncated_self < self, truncated_self + 1, truncated_self);
31
+ }
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+
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+ // floor
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+ template <class A, class T>
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+ XSIMD_INLINE batch<T, A> floor(batch<T, A> const& self, requires_arch<common>) noexcept
36
+ {
37
+ batch<T, A> truncated_self = trunc(self);
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+ return select(truncated_self > self, truncated_self - 1, truncated_self);
39
+ }
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+
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+ // round
42
+ template <class A, class T>
43
+ XSIMD_INLINE batch<T, A> round(batch<T, A> const& self, requires_arch<common>) noexcept
44
+ {
45
+ auto v = abs(self);
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+ auto c = ceil(v);
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+ auto cp = select(c - 0.5 > v, c - 1, c);
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+ return select(v > constants::maxflint<batch<T, A>>(), self, copysign(cp, self));
49
+ }
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+
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+ // trunc
52
+ template <class A, class T, class = typename std::enable_if<std::is_integral<T>::value, void>::type>
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+ XSIMD_INLINE batch<T, A> trunc(batch<T, A> const& self, requires_arch<common>) noexcept
54
+ {
55
+ return self;
56
+ }
57
+ template <class A>
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+ XSIMD_INLINE batch<float, A> trunc(batch<float, A> const& self, requires_arch<common>) noexcept
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+ {
60
+ return select(abs(self) < constants::maxflint<batch<float, A>>(), to_float(to_int(self)), self);
61
+ }
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+ template <class A>
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+ XSIMD_INLINE batch<double, A> trunc(batch<double, A> const& self, requires_arch<common>) noexcept
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+ {
65
+ return select(abs(self) < constants::maxflint<batch<double, A>>(), to_float(to_int(self)), self);
66
+ }
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+
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+ }
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+
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+ }
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+
72
+ #endif
@@ -0,0 +1,174 @@
1
+ /***************************************************************************
2
+ * Copyright (c) Johan Mabille, Sylvain Corlay, Wolf Vollprecht and *
3
+ * Martin Renou *
4
+ * Copyright (c) QuantStack *
5
+ * Copyright (c) Serge Guelton *
6
+ * Copyright (c) Marco Barbone *
7
+ * *
8
+ * Distributed under the terms of the BSD 3-Clause License. *
9
+ * *
10
+ * The full license is in the file LICENSE, distributed with this software.*
11
+ ****************************************************************************/
12
+ #ifndef XSIMD_COMMON_SWIZZLE_HPP
13
+ #define XSIMD_COMMON_SWIZZLE_HPP
14
+
15
+ #include <cstddef>
16
+ #include <cstdint>
17
+ #include <type_traits>
18
+
19
+ namespace xsimd
20
+ {
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+ template <typename T, class A, T... Values>
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+ struct batch_constant;
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+
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+ namespace kernel
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+ {
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+ namespace detail
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+ {
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+ // ────────────────────────────────────────────────────────────────────────
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+ // get_at<I,Values...> → the I-th element of the pack
30
+ template <typename T, std::size_t I, T V0, T... Vs>
31
+ struct get_at
32
+ {
33
+ static constexpr T value = get_at<T, I - 1, Vs...>::value;
34
+ };
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+ template <typename T, T V0, T... Vs>
36
+ struct get_at<T, 0, V0, Vs...>
37
+ {
38
+ static constexpr T value = V0;
39
+ };
40
+
41
+ // ────────────────────────────────────────────────────────────────────────
42
+ // 1) identity_impl
43
+ template <std::size_t /*I*/, typename T>
44
+ XSIMD_INLINE constexpr bool identity_impl() noexcept { return true; }
45
+ template <std::size_t I, typename T, T V0, T... Vs>
46
+ XSIMD_INLINE constexpr bool identity_impl() noexcept
47
+ {
48
+ return V0 == static_cast<T>(I)
49
+ && identity_impl<I + 1, T, Vs...>();
50
+ }
51
+
52
+ // ────────────────────────────────────────────────────────────────────────
53
+ // 2) bitmask_impl
54
+ template <std::size_t /*I*/, std::size_t /*N*/, typename T>
55
+ XSIMD_INLINE constexpr std::uint32_t bitmask_impl() noexcept { return 0u; }
56
+ template <std::size_t I, std::size_t N, typename T, T V0, T... Vs>
57
+ XSIMD_INLINE constexpr std::uint32_t bitmask_impl() noexcept
58
+ {
59
+ return (1u << (static_cast<std::uint32_t>(V0) & (N - 1)))
60
+ | bitmask_impl<I + 1, N, T, Vs...>();
61
+ }
62
+
63
+ // ────────────────────────────────────────────────────────────────────────
64
+ // 3) dup_lo_impl
65
+ template <std::size_t I, std::size_t N, typename T,
66
+ T... Vs, typename std::enable_if<I == N / 2, int>::type = 0>
67
+ XSIMD_INLINE constexpr bool dup_lo_impl() noexcept { return true; }
68
+
69
+ template <std::size_t I, std::size_t N, typename T,
70
+ T... Vs, typename std::enable_if<(I < N / 2), int>::type = 0>
71
+ XSIMD_INLINE constexpr bool dup_lo_impl() noexcept
72
+ {
73
+ return get_at<T, I, Vs...>::value < static_cast<T>(N / 2)
74
+ && get_at<T, I + N / 2, Vs...>::value == get_at<T, I, Vs...>::value
75
+ && dup_lo_impl<I + 1, N, T, Vs...>();
76
+ }
77
+
78
+ // ────────────────────────────────────────────────────────────────────────
79
+ // 4) dup_hi_impl
80
+ template <std::size_t I, std::size_t N, typename T,
81
+ T... Vs, typename std::enable_if<I == N / 2, int>::type = 0>
82
+ XSIMD_INLINE constexpr bool dup_hi_impl() noexcept { return true; }
83
+
84
+ template <std::size_t I, std::size_t N, typename T,
85
+ T... Vs, typename std::enable_if<(I < N / 2), int>::type = 0>
86
+ XSIMD_INLINE constexpr bool dup_hi_impl() noexcept
87
+ {
88
+ return get_at<T, I, Vs...>::value >= static_cast<T>(N / 2)
89
+ && get_at<T, I, Vs...>::value < static_cast<T>(N)
90
+ && get_at<T, I + N / 2, Vs...>::value == get_at<T, I, Vs...>::value
91
+ && dup_hi_impl<I + 1, N, T, Vs...>();
92
+ }
93
+
94
+ // ────────────────────────────────────────────────────────────────────────
95
+ // 1) helper to get the I-th value from the Vs pack
96
+ template <std::size_t I, uint32_t Head, uint32_t... Tail>
97
+ struct get_nth_value
98
+ {
99
+ static constexpr uint32_t value = get_nth_value<I - 1, Tail...>::value;
100
+ };
101
+ template <uint32_t Head, uint32_t... Tail>
102
+ struct get_nth_value<0, Head, Tail...>
103
+ {
104
+ static constexpr uint32_t value = Head;
105
+ };
106
+
107
+ // ────────────────────────────────────────────────────────────────────────
108
+ // 2) recursive cross‐lane test: true if any output‐lane i pulls from the opposite half
109
+ template <std::size_t I,
110
+ std::size_t N,
111
+ std::size_t H,
112
+ uint32_t... Vs>
113
+ struct cross_impl
114
+ {
115
+ // does element I cross? (i.e. i<H but V>=H) or (i>=H but V<H)
116
+ static constexpr uint32_t Vi = get_nth_value<I, Vs...>::value;
117
+ static constexpr bool curr = (I < H ? (Vi >= H) : (Vi < H));
118
+ static constexpr bool next = cross_impl<I + 1, N, H, Vs...>::value;
119
+ static constexpr bool value = curr || next;
120
+ };
121
+ template <std::size_t N, std::size_t H, uint32_t... Vs>
122
+ struct cross_impl<N, N, H, Vs...>
123
+ {
124
+ static constexpr bool value = false;
125
+ };
126
+ template <std::size_t I, std::size_t N, typename T,
127
+ T... Vs>
128
+ XSIMD_INLINE constexpr bool no_duplicates_impl() noexcept
129
+ {
130
+ // build the bitmask of (Vs & (N-1)) across all lanes
131
+ return detail::bitmask_impl<0, N, T, Vs...>() == ((1u << N) - 1u);
132
+ }
133
+ template <uint32_t... Vs>
134
+ XSIMD_INLINE constexpr bool no_duplicates_v() noexcept
135
+ {
136
+ // forward to your existing no_duplicates_impl
137
+ return no_duplicates_impl<0, sizeof...(Vs), uint32_t, Vs...>();
138
+ }
139
+ template <uint32_t... Vs>
140
+ XSIMD_INLINE constexpr bool is_cross_lane() noexcept
141
+ {
142
+ static_assert(sizeof...(Vs) >= 1, "Need at least one lane");
143
+ return cross_impl<0, sizeof...(Vs), sizeof...(Vs) / 2, Vs...>::value;
144
+ }
145
+ template <typename T, T... Vs>
146
+ XSIMD_INLINE constexpr bool is_identity() noexcept { return detail::identity_impl<0, T, Vs...>(); }
147
+ template <typename T, T... Vs>
148
+ XSIMD_INLINE constexpr bool is_all_different() noexcept
149
+ {
150
+ return detail::bitmask_impl<0, sizeof...(Vs), T, Vs...>() == ((1u << sizeof...(Vs)) - 1);
151
+ }
152
+
153
+ template <typename T, T... Vs>
154
+ XSIMD_INLINE constexpr bool is_dup_lo() noexcept { return detail::dup_lo_impl<0, sizeof...(Vs), T, Vs...>(); }
155
+ template <typename T, T... Vs>
156
+ XSIMD_INLINE constexpr bool is_dup_hi() noexcept { return detail::dup_hi_impl<0, sizeof...(Vs), T, Vs...>(); }
157
+ template <typename T, class A, T... Vs>
158
+ XSIMD_INLINE constexpr bool is_identity(batch_constant<T, A, Vs...>) noexcept { return is_identity<T, Vs...>(); }
159
+ template <typename T, class A, T... Vs>
160
+ XSIMD_INLINE constexpr bool is_all_different(batch_constant<T, A, Vs...>) noexcept { return is_all_different<T, Vs...>(); }
161
+ template <typename T, class A, T... Vs>
162
+ XSIMD_INLINE constexpr bool is_dup_lo(batch_constant<T, A, Vs...>) noexcept { return is_dup_lo<T, Vs...>(); }
163
+ template <typename T, class A, T... Vs>
164
+ XSIMD_INLINE constexpr bool is_dup_hi(batch_constant<T, A, Vs...>) noexcept { return is_dup_hi<T, Vs...>(); }
165
+ template <typename T, class A, T... Vs>
166
+ XSIMD_INLINE constexpr bool is_cross_lane(batch_constant<T, A, Vs...>) noexcept { return detail::is_cross_lane<Vs...>(); }
167
+ template <typename T, class A, T... Vs>
168
+ XSIMD_INLINE constexpr bool no_duplicates(batch_constant<T, A, Vs...>) noexcept { return no_duplicates_impl<0, sizeof...(Vs), T, Vs...>(); }
169
+
170
+ } // namespace detail
171
+ } // namespace kernel
172
+ } // namespace xsimd
173
+
174
+ #endif // XSIMD_COMMON_SWIZZLE_HPP