sequenzo 0.1.31__cp310-cp310-macosx_10_9_x86_64.whl

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Files changed (299) hide show
  1. _sequenzo_fastcluster.cpython-310-darwin.so +0 -0
  2. sequenzo/__init__.py +349 -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 +476 -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-310-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-310-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 +22 -0
  30. sequenzo/data_preprocessing/helpers.py +303 -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/dyadic_children.csv +61 -0
  44. sequenzo/datasets/dyadic_parents.csv +61 -0
  45. sequenzo/datasets/mvad.csv +713 -0
  46. sequenzo/datasets/pairfam_activity_by_month.csv +1028 -0
  47. sequenzo/datasets/pairfam_activity_by_year.csv +1028 -0
  48. sequenzo/datasets/pairfam_family_by_month.csv +1028 -0
  49. sequenzo/datasets/pairfam_family_by_year.csv +1028 -0
  50. sequenzo/datasets/political_science_aid_shock.csv +166 -0
  51. sequenzo/datasets/political_science_donor_fragmentation.csv +157 -0
  52. sequenzo/define_sequence_data.py +1400 -0
  53. sequenzo/dissimilarity_measures/__init__.py +31 -0
  54. sequenzo/dissimilarity_measures/c_code.cpython-310-darwin.so +0 -0
  55. sequenzo/dissimilarity_measures/get_distance_matrix.py +762 -0
  56. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +246 -0
  57. sequenzo/dissimilarity_measures/src/DHDdistance.cpp +148 -0
  58. sequenzo/dissimilarity_measures/src/LCPdistance.cpp +114 -0
  59. sequenzo/dissimilarity_measures/src/LCPspellDistance.cpp +215 -0
  60. sequenzo/dissimilarity_measures/src/OMdistance.cpp +247 -0
  61. sequenzo/dissimilarity_measures/src/OMspellDistance.cpp +281 -0
  62. sequenzo/dissimilarity_measures/src/__init__.py +0 -0
  63. sequenzo/dissimilarity_measures/src/dist2matrix.cpp +63 -0
  64. sequenzo/dissimilarity_measures/src/dp_utils.h +160 -0
  65. sequenzo/dissimilarity_measures/src/module.cpp +40 -0
  66. sequenzo/dissimilarity_measures/src/setup.py +30 -0
  67. sequenzo/dissimilarity_measures/src/utils.h +25 -0
  68. sequenzo/dissimilarity_measures/src/xsimd/.github/cmake-test/main.cpp +6 -0
  69. sequenzo/dissimilarity_measures/src/xsimd/benchmark/main.cpp +159 -0
  70. sequenzo/dissimilarity_measures/src/xsimd/benchmark/xsimd_benchmark.hpp +565 -0
  71. sequenzo/dissimilarity_measures/src/xsimd/docs/source/conf.py +37 -0
  72. sequenzo/dissimilarity_measures/src/xsimd/examples/mandelbrot.cpp +330 -0
  73. sequenzo/dissimilarity_measures/src/xsimd/examples/pico_bench.hpp +246 -0
  74. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_arithmetic.hpp +266 -0
  75. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_complex.hpp +112 -0
  76. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_details.hpp +323 -0
  77. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_logical.hpp +218 -0
  78. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_math.hpp +2583 -0
  79. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_memory.hpp +880 -0
  80. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_rounding.hpp +72 -0
  81. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_swizzle.hpp +174 -0
  82. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_trigo.hpp +978 -0
  83. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx.hpp +1924 -0
  84. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx2.hpp +1144 -0
  85. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512bw.hpp +656 -0
  86. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512cd.hpp +28 -0
  87. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512dq.hpp +244 -0
  88. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512er.hpp +20 -0
  89. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512f.hpp +2650 -0
  90. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512ifma.hpp +20 -0
  91. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512pf.hpp +20 -0
  92. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi.hpp +77 -0
  93. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi2.hpp +131 -0
  94. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vnni_avx512bw.hpp +20 -0
  95. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vnni_avx512vbmi2.hpp +20 -0
  96. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avxvnni.hpp +20 -0
  97. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common.hpp +24 -0
  98. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common_fwd.hpp +77 -0
  99. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_constants.hpp +393 -0
  100. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_emulated.hpp +788 -0
  101. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx.hpp +93 -0
  102. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx2.hpp +46 -0
  103. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_sse.hpp +97 -0
  104. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma4.hpp +92 -0
  105. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_i8mm_neon64.hpp +17 -0
  106. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_isa.hpp +142 -0
  107. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon.hpp +3142 -0
  108. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon64.hpp +1543 -0
  109. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_rvv.hpp +1513 -0
  110. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_scalar.hpp +1260 -0
  111. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse2.hpp +2024 -0
  112. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse3.hpp +67 -0
  113. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse4_1.hpp +339 -0
  114. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse4_2.hpp +44 -0
  115. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_ssse3.hpp +186 -0
  116. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sve.hpp +1155 -0
  117. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_vsx.hpp +892 -0
  118. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_wasm.hpp +1780 -0
  119. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_arch.hpp +240 -0
  120. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_config.hpp +484 -0
  121. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_cpuid.hpp +269 -0
  122. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_inline.hpp +27 -0
  123. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/math/xsimd_rem_pio2.hpp +719 -0
  124. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/memory/xsimd_aligned_allocator.hpp +349 -0
  125. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/memory/xsimd_alignment.hpp +91 -0
  126. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_all_registers.hpp +55 -0
  127. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_api.hpp +2765 -0
  128. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx2_register.hpp +44 -0
  129. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512bw_register.hpp +51 -0
  130. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512cd_register.hpp +51 -0
  131. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512dq_register.hpp +51 -0
  132. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512er_register.hpp +51 -0
  133. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512f_register.hpp +77 -0
  134. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512ifma_register.hpp +51 -0
  135. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512pf_register.hpp +51 -0
  136. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512vbmi2_register.hpp +51 -0
  137. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512vbmi_register.hpp +51 -0
  138. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512vnni_avx512bw_register.hpp +54 -0
  139. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512vnni_avx512vbmi2_register.hpp +53 -0
  140. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx_register.hpp +64 -0
  141. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avxvnni_register.hpp +44 -0
  142. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch.hpp +1524 -0
  143. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch_constant.hpp +300 -0
  144. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_common_arch.hpp +47 -0
  145. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_emulated_register.hpp +80 -0
  146. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_fma3_avx2_register.hpp +50 -0
  147. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_fma3_avx_register.hpp +50 -0
  148. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_fma3_sse_register.hpp +50 -0
  149. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_fma4_register.hpp +50 -0
  150. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_i8mm_neon64_register.hpp +55 -0
  151. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_neon64_register.hpp +55 -0
  152. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_neon_register.hpp +154 -0
  153. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_register.hpp +94 -0
  154. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_rvv_register.hpp +506 -0
  155. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_sse2_register.hpp +59 -0
  156. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_sse3_register.hpp +49 -0
  157. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_sse4_1_register.hpp +48 -0
  158. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_sse4_2_register.hpp +48 -0
  159. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_ssse3_register.hpp +48 -0
  160. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_sve_register.hpp +156 -0
  161. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_traits.hpp +337 -0
  162. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_utils.hpp +536 -0
  163. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_vsx_register.hpp +77 -0
  164. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_wasm_register.hpp +59 -0
  165. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/xsimd.hpp +75 -0
  166. sequenzo/dissimilarity_measures/src/xsimd/test/architectures/dummy.cpp +7 -0
  167. sequenzo/dissimilarity_measures/src/xsimd/test/doc/explicit_use_of_an_instruction_set.cpp +13 -0
  168. sequenzo/dissimilarity_measures/src/xsimd/test/doc/explicit_use_of_an_instruction_set_mean.cpp +24 -0
  169. sequenzo/dissimilarity_measures/src/xsimd/test/doc/explicit_use_of_an_instruction_set_mean_aligned.cpp +25 -0
  170. sequenzo/dissimilarity_measures/src/xsimd/test/doc/explicit_use_of_an_instruction_set_mean_arch_independent.cpp +28 -0
  171. sequenzo/dissimilarity_measures/src/xsimd/test/doc/explicit_use_of_an_instruction_set_mean_tag_dispatch.cpp +25 -0
  172. sequenzo/dissimilarity_measures/src/xsimd/test/doc/manipulating_abstract_batches.cpp +7 -0
  173. sequenzo/dissimilarity_measures/src/xsimd/test/doc/manipulating_parametric_batches.cpp +8 -0
  174. sequenzo/dissimilarity_measures/src/xsimd/test/doc/sum.hpp +31 -0
  175. sequenzo/dissimilarity_measures/src/xsimd/test/doc/sum_avx2.cpp +3 -0
  176. sequenzo/dissimilarity_measures/src/xsimd/test/doc/sum_sse2.cpp +3 -0
  177. sequenzo/dissimilarity_measures/src/xsimd/test/doc/writing_vectorized_code.cpp +11 -0
  178. sequenzo/dissimilarity_measures/src/xsimd/test/main.cpp +31 -0
  179. sequenzo/dissimilarity_measures/src/xsimd/test/test_api.cpp +230 -0
  180. sequenzo/dissimilarity_measures/src/xsimd/test/test_arch.cpp +217 -0
  181. sequenzo/dissimilarity_measures/src/xsimd/test/test_basic_math.cpp +183 -0
  182. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch.cpp +1049 -0
  183. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_bool.cpp +508 -0
  184. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_cast.cpp +409 -0
  185. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_complex.cpp +712 -0
  186. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_constant.cpp +286 -0
  187. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_float.cpp +141 -0
  188. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_int.cpp +365 -0
  189. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_manip.cpp +308 -0
  190. sequenzo/dissimilarity_measures/src/xsimd/test/test_bitwise_cast.cpp +222 -0
  191. sequenzo/dissimilarity_measures/src/xsimd/test/test_complex_exponential.cpp +226 -0
  192. sequenzo/dissimilarity_measures/src/xsimd/test/test_complex_hyperbolic.cpp +183 -0
  193. sequenzo/dissimilarity_measures/src/xsimd/test/test_complex_power.cpp +265 -0
  194. sequenzo/dissimilarity_measures/src/xsimd/test/test_complex_trigonometric.cpp +236 -0
  195. sequenzo/dissimilarity_measures/src/xsimd/test/test_conversion.cpp +248 -0
  196. sequenzo/dissimilarity_measures/src/xsimd/test/test_custom_default_arch.cpp +28 -0
  197. sequenzo/dissimilarity_measures/src/xsimd/test/test_error_gamma.cpp +170 -0
  198. sequenzo/dissimilarity_measures/src/xsimd/test/test_explicit_batch_instantiation.cpp +32 -0
  199. sequenzo/dissimilarity_measures/src/xsimd/test/test_exponential.cpp +202 -0
  200. sequenzo/dissimilarity_measures/src/xsimd/test/test_extract_pair.cpp +92 -0
  201. sequenzo/dissimilarity_measures/src/xsimd/test/test_fp_manipulation.cpp +77 -0
  202. sequenzo/dissimilarity_measures/src/xsimd/test/test_gnu_source.cpp +30 -0
  203. sequenzo/dissimilarity_measures/src/xsimd/test/test_hyperbolic.cpp +167 -0
  204. sequenzo/dissimilarity_measures/src/xsimd/test/test_load_store.cpp +304 -0
  205. sequenzo/dissimilarity_measures/src/xsimd/test/test_memory.cpp +61 -0
  206. sequenzo/dissimilarity_measures/src/xsimd/test/test_poly_evaluation.cpp +64 -0
  207. sequenzo/dissimilarity_measures/src/xsimd/test/test_power.cpp +184 -0
  208. sequenzo/dissimilarity_measures/src/xsimd/test/test_rounding.cpp +199 -0
  209. sequenzo/dissimilarity_measures/src/xsimd/test/test_select.cpp +101 -0
  210. sequenzo/dissimilarity_measures/src/xsimd/test/test_shuffle.cpp +760 -0
  211. sequenzo/dissimilarity_measures/src/xsimd/test/test_sum.cpp +4 -0
  212. sequenzo/dissimilarity_measures/src/xsimd/test/test_sum.hpp +34 -0
  213. sequenzo/dissimilarity_measures/src/xsimd/test/test_traits.cpp +172 -0
  214. sequenzo/dissimilarity_measures/src/xsimd/test/test_trigonometric.cpp +208 -0
  215. sequenzo/dissimilarity_measures/src/xsimd/test/test_utils.hpp +611 -0
  216. sequenzo/dissimilarity_measures/src/xsimd/test/test_wasm/test_wasm_playwright.py +123 -0
  217. sequenzo/dissimilarity_measures/src/xsimd/test/test_xsimd_api.cpp +1460 -0
  218. sequenzo/dissimilarity_measures/utils/__init__.py +16 -0
  219. sequenzo/dissimilarity_measures/utils/get_LCP_length_for_2_seq.py +44 -0
  220. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cpython-310-darwin.so +0 -0
  221. sequenzo/dissimilarity_measures/utils/seqconc.cpython-310-darwin.so +0 -0
  222. sequenzo/dissimilarity_measures/utils/seqdss.cpython-310-darwin.so +0 -0
  223. sequenzo/dissimilarity_measures/utils/seqdur.cpython-310-darwin.so +0 -0
  224. sequenzo/dissimilarity_measures/utils/seqlength.cpython-310-darwin.so +0 -0
  225. sequenzo/multidomain/__init__.py +23 -0
  226. sequenzo/multidomain/association_between_domains.py +311 -0
  227. sequenzo/multidomain/cat.py +597 -0
  228. sequenzo/multidomain/combt.py +519 -0
  229. sequenzo/multidomain/dat.py +81 -0
  230. sequenzo/multidomain/idcd.py +139 -0
  231. sequenzo/multidomain/linked_polyad.py +292 -0
  232. sequenzo/openmp_setup.py +233 -0
  233. sequenzo/prefix_tree/__init__.py +62 -0
  234. sequenzo/prefix_tree/hub.py +114 -0
  235. sequenzo/prefix_tree/individual_level_indicators.py +1321 -0
  236. sequenzo/prefix_tree/spell_individual_level_indicators.py +580 -0
  237. sequenzo/prefix_tree/spell_level_indicators.py +297 -0
  238. sequenzo/prefix_tree/system_level_indicators.py +544 -0
  239. sequenzo/prefix_tree/utils.py +54 -0
  240. sequenzo/seqhmm/__init__.py +95 -0
  241. sequenzo/seqhmm/advanced_optimization.py +305 -0
  242. sequenzo/seqhmm/bootstrap.py +411 -0
  243. sequenzo/seqhmm/build_hmm.py +142 -0
  244. sequenzo/seqhmm/build_mhmm.py +136 -0
  245. sequenzo/seqhmm/build_nhmm.py +121 -0
  246. sequenzo/seqhmm/fit_mhmm.py +62 -0
  247. sequenzo/seqhmm/fit_model.py +61 -0
  248. sequenzo/seqhmm/fit_nhmm.py +76 -0
  249. sequenzo/seqhmm/formulas.py +289 -0
  250. sequenzo/seqhmm/forward_backward_nhmm.py +276 -0
  251. sequenzo/seqhmm/gradients_nhmm.py +306 -0
  252. sequenzo/seqhmm/hmm.py +291 -0
  253. sequenzo/seqhmm/mhmm.py +314 -0
  254. sequenzo/seqhmm/model_comparison.py +238 -0
  255. sequenzo/seqhmm/multichannel_em.py +282 -0
  256. sequenzo/seqhmm/multichannel_utils.py +138 -0
  257. sequenzo/seqhmm/nhmm.py +270 -0
  258. sequenzo/seqhmm/nhmm_utils.py +191 -0
  259. sequenzo/seqhmm/predict.py +137 -0
  260. sequenzo/seqhmm/predict_mhmm.py +142 -0
  261. sequenzo/seqhmm/simulate.py +878 -0
  262. sequenzo/seqhmm/utils.py +218 -0
  263. sequenzo/seqhmm/visualization.py +910 -0
  264. sequenzo/sequence_characteristics/__init__.py +40 -0
  265. sequenzo/sequence_characteristics/complexity_index.py +49 -0
  266. sequenzo/sequence_characteristics/overall_cross_sectional_entropy.py +220 -0
  267. sequenzo/sequence_characteristics/plot_characteristics.py +593 -0
  268. sequenzo/sequence_characteristics/simple_characteristics.py +311 -0
  269. sequenzo/sequence_characteristics/state_frequencies_and_entropy_per_sequence.py +39 -0
  270. sequenzo/sequence_characteristics/turbulence.py +155 -0
  271. sequenzo/sequence_characteristics/variance_of_spell_durations.py +86 -0
  272. sequenzo/sequence_characteristics/within_sequence_entropy.py +43 -0
  273. sequenzo/suffix_tree/__init__.py +66 -0
  274. sequenzo/suffix_tree/hub.py +114 -0
  275. sequenzo/suffix_tree/individual_level_indicators.py +1679 -0
  276. sequenzo/suffix_tree/spell_individual_level_indicators.py +493 -0
  277. sequenzo/suffix_tree/spell_level_indicators.py +248 -0
  278. sequenzo/suffix_tree/system_level_indicators.py +535 -0
  279. sequenzo/suffix_tree/utils.py +56 -0
  280. sequenzo/version_check.py +283 -0
  281. sequenzo/visualization/__init__.py +29 -0
  282. sequenzo/visualization/plot_mean_time.py +222 -0
  283. sequenzo/visualization/plot_modal_state.py +276 -0
  284. sequenzo/visualization/plot_most_frequent_sequences.py +147 -0
  285. sequenzo/visualization/plot_relative_frequency.py +405 -0
  286. sequenzo/visualization/plot_sequence_index.py +1175 -0
  287. sequenzo/visualization/plot_single_medoid.py +153 -0
  288. sequenzo/visualization/plot_state_distribution.py +651 -0
  289. sequenzo/visualization/plot_transition_matrix.py +190 -0
  290. sequenzo/visualization/utils/__init__.py +23 -0
  291. sequenzo/visualization/utils/utils.py +310 -0
  292. sequenzo/with_event_history_analysis/__init__.py +35 -0
  293. sequenzo/with_event_history_analysis/sequence_analysis_multi_state_model.py +850 -0
  294. sequenzo/with_event_history_analysis/sequence_history_analysis.py +283 -0
  295. sequenzo-0.1.31.dist-info/METADATA +286 -0
  296. sequenzo-0.1.31.dist-info/RECORD +299 -0
  297. sequenzo-0.1.31.dist-info/WHEEL +5 -0
  298. sequenzo-0.1.31.dist-info/licenses/LICENSE +28 -0
  299. sequenzo-0.1.31.dist-info/top_level.txt +2 -0
@@ -0,0 +1,393 @@
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
+ #ifndef XSIMD_NUMERICAL_CONSTANT_HPP
13
+ #define XSIMD_NUMERICAL_CONSTANT_HPP
14
+
15
+ #include <limits>
16
+
17
+ #include "../types/xsimd_utils.hpp"
18
+
19
+ namespace xsimd
20
+ {
21
+
22
+ namespace constants
23
+ {
24
+
25
+ #define XSIMD_DEFINE_CONSTANT(NAME, SINGLE, DOUBLE) \
26
+ template <class T> \
27
+ XSIMD_INLINE T NAME() noexcept \
28
+ { \
29
+ return T(NAME<typename T::value_type>()); \
30
+ } \
31
+ template <> \
32
+ XSIMD_INLINE float NAME<float>() noexcept \
33
+ { \
34
+ return SINGLE; \
35
+ } \
36
+ template <> \
37
+ XSIMD_INLINE double NAME<double>() noexcept \
38
+ { \
39
+ return DOUBLE; \
40
+ }
41
+
42
+ #define XSIMD_DEFINE_CONSTANT_HEX(NAME, SINGLE, DOUBLE) \
43
+ template <class T> \
44
+ XSIMD_INLINE T NAME() noexcept \
45
+ { \
46
+ return T(NAME<typename T::value_type>()); \
47
+ } \
48
+ template <> \
49
+ XSIMD_INLINE float NAME<float>() noexcept \
50
+ { \
51
+ return bit_cast<float>((uint32_t)SINGLE); \
52
+ } \
53
+ template <> \
54
+ XSIMD_INLINE double NAME<double>() noexcept \
55
+ { \
56
+ return bit_cast<double>((uint64_t)DOUBLE); \
57
+ }
58
+
59
+ // Under fast-math, GCC might replace signmask (minus zero) by zero
60
+ #if defined(__FAST_MATH__) && defined(__GNUC__) && !defined(__clang__)
61
+ #pragma GCC push_options
62
+ #pragma GCC optimize("signed-zeros")
63
+ #endif
64
+ #ifndef __FAST_MATH__
65
+ XSIMD_DEFINE_CONSTANT(infinity, (std::numeric_limits<float>::infinity()), (std::numeric_limits<double>::infinity()))
66
+ XSIMD_DEFINE_CONSTANT(minusinfinity, (-infinity<float>()), (-infinity<double>()))
67
+ #endif
68
+ XSIMD_DEFINE_CONSTANT(invlog_2, 1.442695040888963407359924681001892137426645954152986f, 1.442695040888963407359924681001892137426645954152986)
69
+ XSIMD_DEFINE_CONSTANT_HEX(invlog_2hi, 0x3fb8b000, 0x3ff7154765200000)
70
+ XSIMD_DEFINE_CONSTANT_HEX(invlog_2lo, 0xb9389ad4, 0x3de705fc2eefa200)
71
+ XSIMD_DEFINE_CONSTANT(invlog10_2, 3.32192809488736234787031942949f, 3.32192809488736234787031942949)
72
+ XSIMD_DEFINE_CONSTANT_HEX(invpi, 0x3ea2f983, 0x3fd45f306dc9c883)
73
+ XSIMD_DEFINE_CONSTANT(log_2, 0.6931471805599453094172321214581765680755001343602553f, 0.6931471805599453094172321214581765680755001343602553)
74
+ XSIMD_DEFINE_CONSTANT_HEX(log_2hi, 0x3f318000, 0x3fe62e42fee00000)
75
+ XSIMD_DEFINE_CONSTANT_HEX(log_2lo, 0xb95e8083, 0x3dea39ef35793c76)
76
+ XSIMD_DEFINE_CONSTANT_HEX(log10_2hi, 0x3e9a0000, 0x3fd3440000000000)
77
+ XSIMD_DEFINE_CONSTANT_HEX(log10_2lo, 0x39826a14, 0x3ed3509f79fef312)
78
+ XSIMD_DEFINE_CONSTANT_HEX(logeps, 0xc17f1402, 0xc04205966f2b4f12)
79
+ XSIMD_DEFINE_CONSTANT_HEX(logpi, 0x3f928682, 0x3ff250d048e7a1bd)
80
+ XSIMD_DEFINE_CONSTANT_HEX(logsqrt2pi, 0x3f6b3f8e, 0x3fed67f1c864beb5)
81
+ XSIMD_DEFINE_CONSTANT(maxflint, 16777216.0f, 9007199254740992.0)
82
+ XSIMD_DEFINE_CONSTANT(maxlog, 88.3762626647949f, 709.78271289338400)
83
+ XSIMD_DEFINE_CONSTANT(maxlog2, 127.0f, 1023.)
84
+ XSIMD_DEFINE_CONSTANT(maxlog10, 38.23080825805664f, 308.2547155599167)
85
+ XSIMD_DEFINE_CONSTANT_HEX(mediumpi, 0x43490fdb, 0x412921fb54442d18)
86
+ XSIMD_DEFINE_CONSTANT(minlog, -88.3762626647949f, -708.3964185322641)
87
+ XSIMD_DEFINE_CONSTANT(minlog2, -127.0f, -1023.)
88
+ XSIMD_DEFINE_CONSTANT(minlog10, -37.89999771118164f, -308.2547155599167)
89
+ XSIMD_DEFINE_CONSTANT_HEX(nan, 0xffffffff, 0xffffffffffffffff)
90
+ XSIMD_DEFINE_CONSTANT_HEX(oneosqrteps, 0x453504f3, 0x4190000000000000)
91
+ XSIMD_DEFINE_CONSTANT_HEX(oneotwoeps, 0x4a800000, 0x4320000000000000)
92
+ XSIMD_DEFINE_CONSTANT_HEX(pi, 0x40490fdb, 0x400921fb54442d18)
93
+ XSIMD_DEFINE_CONSTANT_HEX(pio_2lo, 0xb33bbd2e, 0x3c91a62633145c07)
94
+ XSIMD_DEFINE_CONSTANT_HEX(pio_4lo, 0xb2bbbd2e, 0x3c81a62633145c07)
95
+ XSIMD_DEFINE_CONSTANT_HEX(pio2, 0x3fc90fdb, 0x3ff921fb54442d18)
96
+ XSIMD_DEFINE_CONSTANT_HEX(pio2_1, 0x3fc90f80, 0x3ff921fb54400000)
97
+ XSIMD_DEFINE_CONSTANT_HEX(pio2_1t, 0x37354443, 0x3dd0b4611a626331)
98
+ XSIMD_DEFINE_CONSTANT_HEX(pio2_2, 0x37354400, 0x3dd0b4611a600000)
99
+ XSIMD_DEFINE_CONSTANT_HEX(pio2_2t, 0x2e85a308, 0x3ba3198a2e037073)
100
+ XSIMD_DEFINE_CONSTANT_HEX(pio2_3, 0x2e85a300, 0x3ba3198a2e000000)
101
+ XSIMD_DEFINE_CONSTANT_HEX(pio2_3t, 0x248d3132, 0x397b839a252049c1)
102
+ XSIMD_DEFINE_CONSTANT_HEX(pio4, 0x3f490fdb, 0x3fe921fb54442d18)
103
+ XSIMD_DEFINE_CONSTANT_HEX(signmask, 0x80000000, 0x8000000000000000)
104
+ XSIMD_DEFINE_CONSTANT(smallestposval, std::numeric_limits<float>::min(), std::numeric_limits<double>::min())
105
+ XSIMD_DEFINE_CONSTANT_HEX(sqrt_2pi, 0x40206c99, 0x40040d931ff62704)
106
+ XSIMD_DEFINE_CONSTANT_HEX(sqrteps, 0x39b504f3, 0x3e50000000000000)
107
+ XSIMD_DEFINE_CONSTANT_HEX(tanpio8, 0x3ed413cd, 0x3fda827999fcef31)
108
+ XSIMD_DEFINE_CONSTANT_HEX(tan3pio8, 0x401a827a, 0x4003504f333f9de6)
109
+ XSIMD_DEFINE_CONSTANT_HEX(twentypi, 0x427b53d1, 0x404f6a7a2955385e)
110
+ XSIMD_DEFINE_CONSTANT_HEX(twoopi, 0x3f22f983, 0x3fe45f306dc9c883)
111
+ XSIMD_DEFINE_CONSTANT(twotonmb, 8388608.0f, 4503599627370496.0)
112
+ XSIMD_DEFINE_CONSTANT_HEX(twotonmbo3, 0x3ba14518, 0x3ed428a2f98d7286)
113
+ #if defined(__FAST_MATH__) && defined(__GNUC__) && !defined(__clang__)
114
+ #pragma GCC pop_options
115
+ #endif
116
+
117
+ #undef XSIMD_DEFINE_CONSTANT
118
+ #undef XSIMD_DEFINE_CONSTANT_HEX
119
+
120
+ template <class T>
121
+ constexpr T allbits() noexcept;
122
+
123
+ template <class T>
124
+ constexpr as_integer_t<T> mask1frexp() noexcept;
125
+
126
+ template <class T>
127
+ constexpr as_integer_t<T> mask2frexp() noexcept;
128
+
129
+ template <class T>
130
+ constexpr as_integer_t<T> maxexponent() noexcept;
131
+
132
+ template <class T>
133
+ constexpr as_integer_t<T> maxexponentm1() noexcept;
134
+
135
+ template <class T>
136
+ constexpr int32_t nmb() noexcept;
137
+
138
+ template <class T>
139
+ constexpr T zero() noexcept;
140
+
141
+ template <class T>
142
+ constexpr T minvalue() noexcept;
143
+
144
+ template <class T>
145
+ constexpr T maxvalue() noexcept;
146
+
147
+ /**************************
148
+ * allbits implementation *
149
+ **************************/
150
+
151
+ namespace detail
152
+ {
153
+ template <class T, bool = std::is_integral<T>::value>
154
+ struct allbits_impl
155
+ {
156
+ static constexpr T get_value() noexcept
157
+ {
158
+ return T(~0);
159
+ }
160
+ };
161
+
162
+ template <class T>
163
+ struct allbits_impl<T, false>
164
+ {
165
+ static constexpr T get_value() noexcept
166
+ {
167
+ return nan<T>();
168
+ }
169
+ };
170
+ }
171
+
172
+ template <class T>
173
+ XSIMD_INLINE constexpr T allbits() noexcept
174
+ {
175
+ return T(detail::allbits_impl<typename T::value_type>::get_value());
176
+ }
177
+
178
+ /*****************************
179
+ * mask1frexp implementation *
180
+ *****************************/
181
+
182
+ template <class T>
183
+ XSIMD_INLINE constexpr as_integer_t<T> mask1frexp() noexcept
184
+ {
185
+ return as_integer_t<T>(mask1frexp<typename T::value_type>());
186
+ }
187
+
188
+ template <>
189
+ XSIMD_INLINE constexpr int32_t mask1frexp<float>() noexcept
190
+ {
191
+ return 0x7f800000;
192
+ }
193
+
194
+ template <>
195
+ XSIMD_INLINE constexpr int64_t mask1frexp<double>() noexcept
196
+ {
197
+ return 0x7ff0000000000000;
198
+ }
199
+
200
+ /*****************************
201
+ * mask2frexp implementation *
202
+ *****************************/
203
+
204
+ template <class T>
205
+ XSIMD_INLINE constexpr as_integer_t<T> mask2frexp() noexcept
206
+ {
207
+ return as_integer_t<T>(mask2frexp<typename T::value_type>());
208
+ }
209
+
210
+ template <>
211
+ XSIMD_INLINE constexpr int32_t mask2frexp<float>() noexcept
212
+ {
213
+ return 0x3f000000;
214
+ }
215
+
216
+ template <>
217
+ XSIMD_INLINE constexpr int64_t mask2frexp<double>() noexcept
218
+ {
219
+ return 0x3fe0000000000000;
220
+ }
221
+
222
+ /******************************
223
+ * maxexponent implementation *
224
+ ******************************/
225
+
226
+ template <class T>
227
+ XSIMD_INLINE constexpr as_integer_t<T> maxexponent() noexcept
228
+ {
229
+ return as_integer_t<T>(maxexponent<typename T::value_type>());
230
+ }
231
+
232
+ template <>
233
+ XSIMD_INLINE constexpr int32_t maxexponent<float>() noexcept
234
+ {
235
+ return 127;
236
+ }
237
+
238
+ template <>
239
+ XSIMD_INLINE constexpr int64_t maxexponent<double>() noexcept
240
+ {
241
+ return 1023;
242
+ }
243
+
244
+ /******************************
245
+ * maxexponent implementation *
246
+ ******************************/
247
+
248
+ template <class T>
249
+ XSIMD_INLINE constexpr as_integer_t<T> maxexponentm1() noexcept
250
+ {
251
+ return as_integer_t<T>(maxexponentm1<typename T::value_type>());
252
+ }
253
+
254
+ template <>
255
+ XSIMD_INLINE constexpr int32_t maxexponentm1<float>() noexcept
256
+ {
257
+ return 126;
258
+ }
259
+
260
+ template <>
261
+ XSIMD_INLINE constexpr int64_t maxexponentm1<double>() noexcept
262
+ {
263
+ return 1022;
264
+ }
265
+
266
+ /**********************
267
+ * nmb implementation *
268
+ **********************/
269
+
270
+ template <class T>
271
+ XSIMD_INLINE constexpr int32_t nmb() noexcept
272
+ {
273
+ return nmb<typename T::value_type>();
274
+ }
275
+
276
+ template <>
277
+ XSIMD_INLINE constexpr int32_t nmb<float>() noexcept
278
+ {
279
+ return 23;
280
+ }
281
+
282
+ template <>
283
+ XSIMD_INLINE constexpr int32_t nmb<double>() noexcept
284
+ {
285
+ return 52;
286
+ }
287
+
288
+ /***********************
289
+ * zero implementation *
290
+ ***********************/
291
+
292
+ template <class T>
293
+ XSIMD_INLINE constexpr T zero() noexcept
294
+ {
295
+ return T(typename T::value_type(0));
296
+ }
297
+
298
+ /***************************
299
+ * minvalue implementation *
300
+ ***************************/
301
+
302
+ namespace detail
303
+ {
304
+ template <class T>
305
+ struct minvalue_impl
306
+ {
307
+ static constexpr T get_value() noexcept
308
+ {
309
+ return std::numeric_limits<typename T::value_type>::min();
310
+ }
311
+ };
312
+
313
+ template <class T>
314
+ struct minvalue_common
315
+ {
316
+ static constexpr T get_value() noexcept
317
+ {
318
+ return std::numeric_limits<T>::min();
319
+ }
320
+ };
321
+
322
+ template <>
323
+ struct minvalue_impl<int8_t> : minvalue_common<int8_t>
324
+ {
325
+ };
326
+ template <>
327
+ struct minvalue_impl<uint8_t> : minvalue_common<uint8_t>
328
+ {
329
+ };
330
+ template <>
331
+ struct minvalue_impl<int16_t> : minvalue_common<int16_t>
332
+ {
333
+ };
334
+ template <>
335
+ struct minvalue_impl<uint16_t> : minvalue_common<uint16_t>
336
+ {
337
+ };
338
+ template <>
339
+ struct minvalue_impl<int32_t> : minvalue_common<int32_t>
340
+ {
341
+ };
342
+ template <>
343
+ struct minvalue_impl<uint32_t> : minvalue_common<uint32_t>
344
+ {
345
+ };
346
+ template <>
347
+ struct minvalue_impl<int64_t> : minvalue_common<int64_t>
348
+ {
349
+ };
350
+ template <>
351
+ struct minvalue_impl<uint64_t> : minvalue_common<uint64_t>
352
+ {
353
+ };
354
+
355
+ template <>
356
+ struct minvalue_impl<float>
357
+ {
358
+ XSIMD_INLINE static float get_value() noexcept
359
+ {
360
+ return bit_cast<float>((uint32_t)0xff7fffff);
361
+ }
362
+ };
363
+
364
+ template <>
365
+ struct minvalue_impl<double>
366
+ {
367
+ XSIMD_INLINE static double get_value() noexcept
368
+ {
369
+ return bit_cast<double>((uint64_t)0xffefffffffffffff);
370
+ }
371
+ };
372
+ }
373
+
374
+ template <class T>
375
+ constexpr T minvalue() noexcept
376
+ {
377
+ return T(detail::minvalue_impl<typename T::value_type>::get_value());
378
+ }
379
+
380
+ /***************************
381
+ * maxvalue implementation *
382
+ ***************************/
383
+
384
+ template <class T>
385
+ constexpr T maxvalue() noexcept
386
+ {
387
+ return T(std::numeric_limits<typename T::value_type>::max());
388
+ }
389
+ }
390
+
391
+ }
392
+
393
+ #endif