sequenzo 0.1.17__cp39-cp39-macosx_10_9_universal2.whl → 0.1.18__cp39-cp39-macosx_10_9_universal2.whl

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Files changed (86) hide show
  1. sequenzo/__init__.py +25 -1
  2. sequenzo/big_data/clara/clara.py +1 -1
  3. sequenzo/big_data/clara/utils/get_weighted_diss.c +157 -157
  4. sequenzo/big_data/clara/utils/get_weighted_diss.cpython-39-darwin.so +0 -0
  5. sequenzo/clustering/hierarchical_clustering.py +202 -8
  6. sequenzo/define_sequence_data.py +34 -2
  7. sequenzo/dissimilarity_measures/c_code.cpython-39-darwin.so +0 -0
  8. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  9. sequenzo/dissimilarity_measures/src/DHDdistance.cpp +13 -37
  10. sequenzo/dissimilarity_measures/src/LCPdistance.cpp +13 -37
  11. sequenzo/dissimilarity_measures/src/OMdistance.cpp +12 -47
  12. sequenzo/dissimilarity_measures/src/OMspellDistance.cpp +103 -67
  13. sequenzo/dissimilarity_measures/src/dp_utils.h +160 -0
  14. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_arithmetic.hpp +41 -16
  15. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_complex.hpp +4 -0
  16. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_details.hpp +7 -0
  17. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_logical.hpp +10 -0
  18. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_math.hpp +127 -43
  19. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_memory.hpp +30 -2
  20. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_swizzle.hpp +174 -0
  21. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_trigo.hpp +14 -5
  22. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx.hpp +111 -54
  23. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx2.hpp +131 -9
  24. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512bw.hpp +11 -113
  25. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512dq.hpp +39 -7
  26. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512f.hpp +336 -30
  27. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi.hpp +9 -37
  28. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi2.hpp +58 -0
  29. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common.hpp +1 -0
  30. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common_fwd.hpp +35 -2
  31. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_constants.hpp +3 -1
  32. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_emulated.hpp +17 -0
  33. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx.hpp +13 -0
  34. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_sse.hpp +18 -0
  35. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma4.hpp +13 -0
  36. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_isa.hpp +8 -0
  37. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon.hpp +363 -34
  38. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon64.hpp +7 -0
  39. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_rvv.hpp +13 -0
  40. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_scalar.hpp +41 -4
  41. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse2.hpp +252 -16
  42. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse3.hpp +9 -0
  43. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_ssse3.hpp +12 -1
  44. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sve.hpp +7 -0
  45. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_vsx.hpp +892 -0
  46. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_wasm.hpp +78 -1
  47. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_arch.hpp +3 -1
  48. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_config.hpp +13 -2
  49. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_cpuid.hpp +5 -0
  50. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_inline.hpp +5 -1
  51. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_all_registers.hpp +2 -0
  52. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_api.hpp +64 -1
  53. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch.hpp +36 -0
  54. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_rvv_register.hpp +40 -31
  55. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_traits.hpp +8 -0
  56. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_vsx_register.hpp +77 -0
  57. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/xsimd.hpp +6 -0
  58. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +157 -157
  59. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cpython-39-darwin.so +0 -0
  60. sequenzo/dissimilarity_measures/utils/seqconc.c +157 -157
  61. sequenzo/dissimilarity_measures/utils/seqconc.cpython-39-darwin.so +0 -0
  62. sequenzo/dissimilarity_measures/utils/seqdss.c +157 -157
  63. sequenzo/dissimilarity_measures/utils/seqdss.cpython-39-darwin.so +0 -0
  64. sequenzo/dissimilarity_measures/utils/seqdur.c +157 -157
  65. sequenzo/dissimilarity_measures/utils/seqdur.cpython-39-darwin.so +0 -0
  66. sequenzo/dissimilarity_measures/utils/seqlength.c +157 -157
  67. sequenzo/dissimilarity_measures/utils/seqlength.cpython-39-darwin.so +0 -0
  68. sequenzo/sequence_characteristics/__init__.py +4 -0
  69. sequenzo/sequence_characteristics/complexity_index.py +17 -57
  70. sequenzo/sequence_characteristics/overall_cross_sectional_entropy.py +177 -111
  71. sequenzo/sequence_characteristics/plot_characteristics.py +30 -11
  72. sequenzo/sequence_characteristics/simple_characteristics.py +1 -0
  73. sequenzo/sequence_characteristics/state_frequencies_and_entropy_per_sequence.py +9 -3
  74. sequenzo/sequence_characteristics/turbulence.py +47 -67
  75. sequenzo/sequence_characteristics/variance_of_spell_durations.py +19 -9
  76. sequenzo/sequence_characteristics/within_sequence_entropy.py +5 -58
  77. sequenzo/visualization/plot_sequence_index.py +58 -35
  78. sequenzo/visualization/plot_state_distribution.py +57 -36
  79. sequenzo/with_event_history_analysis/__init__.py +35 -0
  80. sequenzo/with_event_history_analysis/sequence_analysis_multi_state_model.py +850 -0
  81. sequenzo/with_event_history_analysis/sequence_history_analysis.py +283 -0
  82. {sequenzo-0.1.17.dist-info → sequenzo-0.1.18.dist-info}/METADATA +7 -6
  83. {sequenzo-0.1.17.dist-info → sequenzo-0.1.18.dist-info}/RECORD +86 -79
  84. {sequenzo-0.1.17.dist-info → sequenzo-0.1.18.dist-info}/WHEEL +0 -0
  85. {sequenzo-0.1.17.dist-info → sequenzo-0.1.18.dist-info}/licenses/LICENSE +0 -0
  86. {sequenzo-0.1.17.dist-info → sequenzo-0.1.18.dist-info}/top_level.txt +0 -0