sequenzo 0.1.17__cp39-cp39-win_amd64.whl → 0.1.18__cp39-cp39-win_amd64.whl

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Files changed (101) 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 +156 -156
  4. sequenzo/big_data/clara/utils/get_weighted_diss.cp39-win_amd64.pyd +0 -0
  5. sequenzo/clustering/clustering_c_code.cp39-win_amd64.pyd +0 -0
  6. sequenzo/clustering/hierarchical_clustering.py +202 -8
  7. sequenzo/define_sequence_data.py +34 -2
  8. sequenzo/dissimilarity_measures/c_code.cp39-win_amd64.pyd +0 -0
  9. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  10. sequenzo/dissimilarity_measures/src/DHDdistance.cpp +13 -37
  11. sequenzo/dissimilarity_measures/src/LCPdistance.cpp +13 -37
  12. sequenzo/dissimilarity_measures/src/OMdistance.cpp +12 -47
  13. sequenzo/dissimilarity_measures/src/OMspellDistance.cpp +103 -67
  14. sequenzo/dissimilarity_measures/src/dp_utils.h +160 -0
  15. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_arithmetic.hpp +41 -16
  16. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_complex.hpp +4 -0
  17. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_details.hpp +7 -0
  18. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_logical.hpp +10 -0
  19. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_math.hpp +127 -43
  20. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_memory.hpp +30 -2
  21. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_swizzle.hpp +174 -0
  22. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_trigo.hpp +14 -5
  23. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx.hpp +111 -54
  24. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx2.hpp +131 -9
  25. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512bw.hpp +11 -113
  26. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512dq.hpp +39 -7
  27. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512f.hpp +336 -30
  28. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi.hpp +9 -37
  29. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi2.hpp +58 -0
  30. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common.hpp +1 -0
  31. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common_fwd.hpp +35 -2
  32. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_constants.hpp +3 -1
  33. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_emulated.hpp +17 -0
  34. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx.hpp +13 -0
  35. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_sse.hpp +18 -0
  36. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma4.hpp +13 -0
  37. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_isa.hpp +8 -0
  38. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon.hpp +363 -34
  39. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon64.hpp +7 -0
  40. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_rvv.hpp +13 -0
  41. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_scalar.hpp +41 -4
  42. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse2.hpp +252 -16
  43. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse3.hpp +9 -0
  44. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_ssse3.hpp +12 -1
  45. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sve.hpp +7 -0
  46. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_vsx.hpp +892 -0
  47. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_wasm.hpp +78 -1
  48. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_arch.hpp +3 -1
  49. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_config.hpp +13 -2
  50. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_cpuid.hpp +5 -0
  51. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_inline.hpp +5 -1
  52. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_all_registers.hpp +2 -0
  53. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_api.hpp +64 -1
  54. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch.hpp +36 -0
  55. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_rvv_register.hpp +40 -31
  56. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_traits.hpp +8 -0
  57. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_vsx_register.hpp +77 -0
  58. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/xsimd.hpp +6 -0
  59. sequenzo/dissimilarity_measures/src/xsimd/test/test_basic_math.cpp +6 -0
  60. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch.cpp +54 -2
  61. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_bool.cpp +8 -0
  62. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_cast.cpp +11 -4
  63. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_complex.cpp +18 -0
  64. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_int.cpp +8 -14
  65. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_manip.cpp +216 -173
  66. sequenzo/dissimilarity_measures/src/xsimd/test/test_load_store.cpp +6 -0
  67. sequenzo/dissimilarity_measures/src/xsimd/test/test_memory.cpp +1 -1
  68. sequenzo/dissimilarity_measures/src/xsimd/test/test_power.cpp +7 -4
  69. sequenzo/dissimilarity_measures/src/xsimd/test/test_select.cpp +6 -2
  70. sequenzo/dissimilarity_measures/src/xsimd/test/test_shuffle.cpp +32 -18
  71. sequenzo/dissimilarity_measures/src/xsimd/test/test_utils.hpp +21 -24
  72. sequenzo/dissimilarity_measures/src/xsimd/test/test_xsimd_api.cpp +69 -9
  73. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +156 -156
  74. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cp39-win_amd64.pyd +0 -0
  75. sequenzo/dissimilarity_measures/utils/seqconc.c +156 -156
  76. sequenzo/dissimilarity_measures/utils/seqconc.cp39-win_amd64.pyd +0 -0
  77. sequenzo/dissimilarity_measures/utils/seqdss.c +156 -156
  78. sequenzo/dissimilarity_measures/utils/seqdss.cp39-win_amd64.pyd +0 -0
  79. sequenzo/dissimilarity_measures/utils/seqdur.c +156 -156
  80. sequenzo/dissimilarity_measures/utils/seqdur.cp39-win_amd64.pyd +0 -0
  81. sequenzo/dissimilarity_measures/utils/seqlength.c +156 -156
  82. sequenzo/dissimilarity_measures/utils/seqlength.cp39-win_amd64.pyd +0 -0
  83. sequenzo/sequence_characteristics/__init__.py +4 -0
  84. sequenzo/sequence_characteristics/complexity_index.py +17 -57
  85. sequenzo/sequence_characteristics/overall_cross_sectional_entropy.py +177 -111
  86. sequenzo/sequence_characteristics/plot_characteristics.py +30 -11
  87. sequenzo/sequence_characteristics/simple_characteristics.py +1 -0
  88. sequenzo/sequence_characteristics/state_frequencies_and_entropy_per_sequence.py +9 -3
  89. sequenzo/sequence_characteristics/turbulence.py +47 -67
  90. sequenzo/sequence_characteristics/variance_of_spell_durations.py +19 -9
  91. sequenzo/sequence_characteristics/within_sequence_entropy.py +5 -58
  92. sequenzo/visualization/plot_sequence_index.py +58 -35
  93. sequenzo/visualization/plot_state_distribution.py +57 -36
  94. sequenzo/with_event_history_analysis/__init__.py +35 -0
  95. sequenzo/with_event_history_analysis/sequence_analysis_multi_state_model.py +850 -0
  96. sequenzo/with_event_history_analysis/sequence_history_analysis.py +283 -0
  97. {sequenzo-0.1.17.dist-info → sequenzo-0.1.18.dist-info}/METADATA +7 -6
  98. {sequenzo-0.1.17.dist-info → sequenzo-0.1.18.dist-info}/RECORD +101 -94
  99. {sequenzo-0.1.17.dist-info → sequenzo-0.1.18.dist-info}/WHEEL +0 -0
  100. {sequenzo-0.1.17.dist-info → sequenzo-0.1.18.dist-info}/licenses/LICENSE +0 -0
  101. {sequenzo-0.1.17.dist-info → sequenzo-0.1.18.dist-info}/top_level.txt +0 -0
sequenzo/__init__.py CHANGED
@@ -85,6 +85,7 @@ from .sequence_characteristics import (
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  get_number_of_transitions,
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  get_turbulence,
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+ get_complexity_index,
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  get_within_sequence_entropy,
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  get_spell_duration_variance,
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  get_state_freq_and_entropy_per_seq,
@@ -95,6 +96,18 @@ from .sequence_characteristics import (
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  )
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+ # Event History Analysis (SAMM)
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+ from .with_event_history_analysis import (
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+ SAMM,
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+ sequence_analysis_multi_state_model,
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+ plot_samm,
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+ seqsammseq,
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+ set_typology,
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+ seqsammeha,
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+ # Keep old names for backward compatibility
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+ seqsamm
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+ )
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+
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  # Define `__all__` to specify the public API when using `from sequenzo import *`
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  __all__ = [
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  # Datasets
@@ -175,10 +188,21 @@ __all__ = [
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  "get_subsequences_all_sequences",
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  "get_number_of_transitions",
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  "get_turbulence",
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+ "get_complexity_index",
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  "get_within_sequence_entropy",
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  "get_spell_duration_variance",
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  "get_state_freq_and_entropy_per_seq",
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  "get_cross_sectional_entropy",
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  "plot_longitudinal_characteristics",
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- "plot_cross_sectional_characteristics"
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+ "plot_cross_sectional_characteristics",
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+
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+ # Event History Analysis (SAMM)
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+ "SAMM",
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+ "sequence_analysis_multi_state_model",
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+ "plot_samm",
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+ "seqsammseq",
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+ "set_typology",
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+ "seqsammeha",
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+ # Keep old names for backward compatibility
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+ "seqsamm"
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  ]
sequenzo/big_data/clara/clara.py CHANGED
@@ -439,7 +439,7 @@ if __name__ == '__main__':
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  # ===============================
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  # detailed
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  # ===============================
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- df = pd.read_csv("D:/college/research/QiQi/sequenzo/data_and_output/sampled_data_sets/detailed_data/sampled_1000_data.csv")
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+ df = pd.read_csv("/Users/xinyi/Projects/sequenzo/sequenzo/data_and_output/sampled_data_sets/detailed_data/sampled_1000_data.csv")
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  time = list(df.columns)[4:]
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  states = ['data', 'data & intensive math', 'hardware', 'research', 'software', 'software & hardware', 'support & test']
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  sequence_data = SequenceData(df[['worker_id', 'C1', 'C2', 'C3', 'C4', 'C5', 'C6', 'C7', 'C8', 'C9', 'C10']],