sequenzo 0.1.17__cp39-cp39-macosx_10_9_universal2.whl → 0.1.19__cp39-cp39-macosx_10_9_universal2.whl

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  1. sequenzo/__init__.py +64 -8
  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/KMedoids.py +39 -0
  6. sequenzo/clustering/hierarchical_clustering.py +304 -8
  7. sequenzo/define_sequence_data.py +44 -3
  8. sequenzo/dissimilarity_measures/c_code.cpython-39-darwin.so +0 -0
  9. sequenzo/dissimilarity_measures/get_distance_matrix.py +1 -2
  10. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  11. sequenzo/dissimilarity_measures/src/DHDdistance.cpp +13 -37
  12. sequenzo/dissimilarity_measures/src/LCPdistance.cpp +13 -37
  13. sequenzo/dissimilarity_measures/src/OMdistance.cpp +12 -47
  14. sequenzo/dissimilarity_measures/src/OMspellDistance.cpp +103 -67
  15. sequenzo/dissimilarity_measures/src/dp_utils.h +160 -0
  16. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_arithmetic.hpp +41 -16
  17. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_complex.hpp +4 -0
  18. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_details.hpp +7 -0
  19. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_logical.hpp +10 -0
  20. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_math.hpp +127 -43
  21. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_memory.hpp +30 -2
  22. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_swizzle.hpp +174 -0
  23. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_trigo.hpp +14 -5
  24. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx.hpp +111 -54
  25. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx2.hpp +131 -9
  26. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512bw.hpp +11 -113
  27. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512dq.hpp +39 -7
  28. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512f.hpp +336 -30
  29. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi.hpp +9 -37
  30. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi2.hpp +58 -0
  31. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common.hpp +1 -0
  32. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common_fwd.hpp +35 -2
  33. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_constants.hpp +3 -1
  34. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_emulated.hpp +17 -0
  35. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx.hpp +13 -0
  36. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_sse.hpp +18 -0
  37. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma4.hpp +13 -0
  38. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_isa.hpp +8 -0
  39. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon.hpp +363 -34
  40. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon64.hpp +7 -0
  41. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_rvv.hpp +13 -0
  42. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_scalar.hpp +41 -4
  43. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse2.hpp +252 -16
  44. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse3.hpp +9 -0
  45. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_ssse3.hpp +12 -1
  46. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sve.hpp +7 -0
  47. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_vsx.hpp +892 -0
  48. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_wasm.hpp +78 -1
  49. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_arch.hpp +3 -1
  50. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_config.hpp +13 -2
  51. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_cpuid.hpp +5 -0
  52. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_inline.hpp +5 -1
  53. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_all_registers.hpp +2 -0
  54. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_api.hpp +64 -1
  55. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch.hpp +36 -0
  56. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_rvv_register.hpp +40 -31
  57. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_traits.hpp +8 -0
  58. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_vsx_register.hpp +77 -0
  59. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/xsimd.hpp +6 -0
  60. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +157 -157
  61. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cpython-39-darwin.so +0 -0
  62. sequenzo/dissimilarity_measures/utils/seqconc.c +157 -157
  63. sequenzo/dissimilarity_measures/utils/seqconc.cpython-39-darwin.so +0 -0
  64. sequenzo/dissimilarity_measures/utils/seqdss.c +157 -157
  65. sequenzo/dissimilarity_measures/utils/seqdss.cpython-39-darwin.so +0 -0
  66. sequenzo/dissimilarity_measures/utils/seqdur.c +157 -157
  67. sequenzo/dissimilarity_measures/utils/seqdur.cpython-39-darwin.so +0 -0
  68. sequenzo/dissimilarity_measures/utils/seqlength.c +157 -157
  69. sequenzo/dissimilarity_measures/utils/seqlength.cpython-39-darwin.so +0 -0
  70. sequenzo/multidomain/cat.py +0 -53
  71. sequenzo/multidomain/idcd.py +0 -1
  72. sequenzo/openmp_setup.py +233 -0
  73. sequenzo/sequence_characteristics/__init__.py +4 -0
  74. sequenzo/sequence_characteristics/complexity_index.py +17 -57
  75. sequenzo/sequence_characteristics/overall_cross_sectional_entropy.py +177 -111
  76. sequenzo/sequence_characteristics/plot_characteristics.py +30 -11
  77. sequenzo/sequence_characteristics/simple_characteristics.py +1 -0
  78. sequenzo/sequence_characteristics/state_frequencies_and_entropy_per_sequence.py +9 -3
  79. sequenzo/sequence_characteristics/turbulence.py +47 -67
  80. sequenzo/sequence_characteristics/variance_of_spell_durations.py +19 -9
  81. sequenzo/sequence_characteristics/within_sequence_entropy.py +5 -58
  82. sequenzo/visualization/plot_sequence_index.py +58 -35
  83. sequenzo/visualization/plot_state_distribution.py +57 -36
  84. sequenzo/visualization/plot_transition_matrix.py +21 -22
  85. sequenzo/with_event_history_analysis/__init__.py +35 -0
  86. sequenzo/with_event_history_analysis/sequence_analysis_multi_state_model.py +850 -0
  87. sequenzo/with_event_history_analysis/sequence_history_analysis.py +283 -0
  88. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/METADATA +48 -14
  89. sequenzo-0.1.19.dist-info/RECORD +215 -0
  90. sequenzo/dissimilarity_measures/setup.py +0 -35
  91. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  92. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  93. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  94. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  95. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  96. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  97. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  98. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  99. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  100. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  101. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  102. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  103. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  104. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  105. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  170. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  171. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  172. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  173. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  174. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  175. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  176. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  177. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  178. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  179. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  180. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  181. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  182. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  183. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  184. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  185. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  186. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  187. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  188. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  189. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  190. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  191. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  192. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  193. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  194. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  195. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  196. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  197. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  198. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  199. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  200. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  201. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  202. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  203. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  204. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  205. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  206. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  207. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  208. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
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  403. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/HipVectorCompatibility.h +0 -67
  404. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsArrayAPI.h +0 -167
  405. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsBFloat16.h +0 -58
  406. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsFunctors.h +0 -330
  407. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsHalf.h +0 -58
  408. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsImpl.h +0 -2045
  409. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsPacketMath.h +0 -79
  410. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/BesselFunctions.h +0 -46
  411. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/SpecialFunctions.h +0 -16
  412. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/BesselFunctions.h +0 -46
  413. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/SpecialFunctions.h +0 -16
  414. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/GPU/SpecialFunctions.h +0 -369
  415. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/BesselFunctions.h +0 -54
  416. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/SpecialFunctions.h +0 -34
  417. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/Spline.h +0 -507
  418. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFitting.h +0 -431
  419. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFwd.h +0 -93
  420. sequenzo-0.1.17.dist-info/RECORD +0 -537
  421. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/WHEEL +0 -0
  422. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/licenses/LICENSE +0 -0
  423. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/top_level.txt +0 -0
@@ -67,6 +67,64 @@ namespace xsimd
67
67
  {
68
68
  return _mm512_maskz_expand_epi8(mask.mask(), self);
69
69
  }
70
+
71
+ // rotl
72
+ template <class A, class T, class = typename std::enable_if<std::is_integral<T>::value, void>::type>
73
+ XSIMD_INLINE batch<T, A> rotl(batch<T, A> const& self, int32_t other, requires_arch<avx512vbmi2>) noexcept
74
+ {
75
+ XSIMD_IF_CONSTEXPR(sizeof(T) == 2)
76
+ {
77
+ return _mm512_shldv_epi16(self, self, _mm512_set1_epi16(static_cast<uint16_t>(other)));
78
+ }
79
+ else
80
+ {
81
+ return rotl(self, other, avx512bw {});
82
+ }
83
+ }
84
+
85
+ template <size_t count, class A, class T, class = typename std::enable_if<std::is_integral<T>::value, void>::type>
86
+ XSIMD_INLINE batch<T, A> rotl(batch<T, A> const& self, requires_arch<avx512vbmi2>) noexcept
87
+ {
88
+ constexpr auto bits = std::numeric_limits<T>::digits + std::numeric_limits<T>::is_signed;
89
+ static_assert(count < bits, "Count must be less than the number of bits in T");
90
+ XSIMD_IF_CONSTEXPR(sizeof(T) == 2)
91
+ {
92
+ return _mm512_shldi_epi16(self, self, count);
93
+ }
94
+ else
95
+ {
96
+ return rotl<count>(self, avx512bw {});
97
+ }
98
+ }
99
+
100
+ // rotr
101
+ template <class A, class T, class = typename std::enable_if<std::is_integral<T>::value, void>::type>
102
+ XSIMD_INLINE batch<T, A> rotr(batch<T, A> const& self, int32_t other, requires_arch<avx512vbmi2>) noexcept
103
+ {
104
+ XSIMD_IF_CONSTEXPR(sizeof(T) == 2)
105
+ {
106
+ return _mm512_shrdv_epi16(self, self, _mm512_set1_epi16(static_cast<uint16_t>(other)));
107
+ }
108
+ else
109
+ {
110
+ return rotr(self, other, avx512bw {});
111
+ }
112
+ }
113
+
114
+ template <size_t count, class A, class T, class = typename std::enable_if<std::is_integral<T>::value, void>::type>
115
+ XSIMD_INLINE batch<T, A> rotr(batch<T, A> const& self, requires_arch<avx512vbmi2>) noexcept
116
+ {
117
+ constexpr auto bits = std::numeric_limits<T>::digits + std::numeric_limits<T>::is_signed;
118
+ static_assert(count < bits, "count must be less than the number of bits in T");
119
+ XSIMD_IF_CONSTEXPR(sizeof(T) == 2)
120
+ {
121
+ return _mm512_shrdi_epi16(self, self, count);
122
+ }
123
+ else
124
+ {
125
+ return rotr<count>(self, avx512bw {});
126
+ }
127
+ }
70
128
  }
71
129
  }
72
130
 
@@ -18,6 +18,7 @@
18
18
  #include "./common/xsimd_common_math.hpp"
19
19
  #include "./common/xsimd_common_memory.hpp"
20
20
  #include "./common/xsimd_common_rounding.hpp"
21
+ #include "./common/xsimd_common_swizzle.hpp"
21
22
  #include "./common/xsimd_common_trigo.hpp"
22
23
 
23
24
  #endif
@@ -3,6 +3,7 @@
3
3
  * Martin Renou *
4
4
  * Copyright (c) QuantStack *
5
5
  * Copyright (c) Serge Guelton *
6
+ * Copyright (c) Marco Barbone *
6
7
  * *
7
8
  * Distributed under the terms of the BSD 3-Clause License. *
8
9
  * *
@@ -25,8 +26,12 @@ namespace xsimd
25
26
  XSIMD_INLINE batch<T, A> abs(batch<T, A> const& self, requires_arch<common>) noexcept;
26
27
  template <class A, class T, class = typename std::enable_if<std::is_integral<T>::value, void>::type>
27
28
  XSIMD_INLINE batch<T, A> bitwise_lshift(batch<T, A> const& self, batch<T, A> const& other, requires_arch<common>) noexcept;
29
+ template <size_t shift, class A, class T, class = typename std::enable_if<std::is_integral<T>::value, void>::type>
30
+ XSIMD_INLINE batch<T, A> bitwise_lshift(batch<T, A> const& self, requires_arch<common>) noexcept;
28
31
  template <class A, class T, class = typename std::enable_if<std::is_integral<T>::value, void>::type>
29
32
  XSIMD_INLINE batch<T, A> bitwise_rshift(batch<T, A> const& self, batch<T, A> const& other, requires_arch<common>) noexcept;
33
+ template <size_t shift, class A, class T, class = typename std::enable_if<std::is_integral<T>::value, void>::type>
34
+ XSIMD_INLINE batch<T, A> bitwise_rshift(batch<T, A> const& self, requires_arch<common>) noexcept;
30
35
  template <class A, class T>
31
36
  XSIMD_INLINE batch_bool<T, A> gt(batch<T, A> const& self, batch<T, A> const& other, requires_arch<common>) noexcept;
32
37
  template <class A, class T, class = typename std::enable_if<std::is_integral<T>::value, void>::type>
@@ -35,9 +40,37 @@ namespace xsimd
35
40
  XSIMD_INLINE batch<T, A> sadd(batch<T, A> const& self, batch<T, A> const& other, requires_arch<common>) noexcept;
36
41
  template <class A, class T, class = typename std::enable_if<std::is_integral<T>::value, void>::type>
37
42
  XSIMD_INLINE batch<T, A> ssub(batch<T, A> const& self, batch<T, A> const& other, requires_arch<common>) noexcept;
38
- template <class A, class T, class = typename std::enable_if<std::is_integral<T>::value, void>::type>
39
- XSIMD_INLINE T hadd(batch<T, A> const& self, requires_arch<common>) noexcept;
43
+ template <class A, class T, class = typename std::enable_if<std::is_scalar<T>::value, void>::type>
44
+ XSIMD_INLINE T reduce_add(batch<T, A> const& self, requires_arch<common>) noexcept;
45
+ template <class A, class T, class = typename std::enable_if<std::is_scalar<T>::value, void>::type>
46
+ XSIMD_INLINE T reduce_mul(batch<T, A> const& self, requires_arch<common>) noexcept;
47
+ template <class A, class T, class STy>
48
+ XSIMD_INLINE batch<T, A> rotl(batch<T, A> const& self, STy other, requires_arch<common>) noexcept;
49
+ template <size_t count, class A, class T>
50
+ XSIMD_INLINE batch<T, A> rotl(batch<T, A> const& self, requires_arch<common>) noexcept;
51
+ template <class A, class T, class STy>
52
+ XSIMD_INLINE batch<T, A> rotr(batch<T, A> const& self, STy other, requires_arch<common>) noexcept;
53
+ template <size_t count, class A, class T>
54
+ XSIMD_INLINE batch<T, A> rotr(batch<T, A> const& self, requires_arch<common>) noexcept;
55
+ // Forward declarations for pack-level helpers
56
+ namespace detail
57
+ {
58
+ template <typename T, T... Vs>
59
+ XSIMD_INLINE constexpr bool is_identity() noexcept;
60
+ template <typename T, class A, T... Vs>
61
+ XSIMD_INLINE constexpr bool is_identity(batch_constant<T, A, Vs...>) noexcept;
62
+ template <typename T, class A, T... Vs>
63
+ XSIMD_INLINE constexpr bool is_all_different(batch_constant<T, A, Vs...>) noexcept;
64
+ template <typename T, class A, T... Vs>
65
+ XSIMD_INLINE constexpr bool is_dup_lo(batch_constant<T, A, Vs...>) noexcept;
66
+ template <typename T, class A, T... Vs>
67
+ XSIMD_INLINE constexpr bool is_dup_hi(batch_constant<T, A, Vs...>) noexcept;
68
+ template <typename T, class A, T... Vs>
69
+ XSIMD_INLINE constexpr bool is_cross_lane(batch_constant<T, A, Vs...>) noexcept;
70
+ template <typename T, class A, T... Vs>
71
+ XSIMD_INLINE constexpr bool no_duplicates(batch_constant<T, A, Vs...>) noexcept;
40
72
 
73
+ }
41
74
  }
42
75
  }
43
76
 
@@ -61,7 +61,10 @@ namespace xsimd
61
61
  #pragma GCC push_options
62
62
  #pragma GCC optimize("signed-zeros")
63
63
  #endif
64
+ #ifndef __FAST_MATH__
64
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
65
68
  XSIMD_DEFINE_CONSTANT(invlog_2, 1.442695040888963407359924681001892137426645954152986f, 1.442695040888963407359924681001892137426645954152986)
66
69
  XSIMD_DEFINE_CONSTANT_HEX(invlog_2hi, 0x3fb8b000, 0x3ff7154765200000)
67
70
  XSIMD_DEFINE_CONSTANT_HEX(invlog_2lo, 0xb9389ad4, 0x3de705fc2eefa200)
@@ -83,7 +86,6 @@ namespace xsimd
83
86
  XSIMD_DEFINE_CONSTANT(minlog, -88.3762626647949f, -708.3964185322641)
84
87
  XSIMD_DEFINE_CONSTANT(minlog2, -127.0f, -1023.)
85
88
  XSIMD_DEFINE_CONSTANT(minlog10, -37.89999771118164f, -308.2547155599167)
86
- XSIMD_DEFINE_CONSTANT(minusinfinity, (-infinity<float>()), (-infinity<double>()))
87
89
  XSIMD_DEFINE_CONSTANT_HEX(nan, 0xffffffff, 0xffffffffffffffff)
88
90
  XSIMD_DEFINE_CONSTANT_HEX(oneosqrteps, 0x453504f3, 0x4190000000000000)
89
91
  XSIMD_DEFINE_CONSTANT_HEX(oneotwoeps, 0x4a800000, 0x4320000000000000)
@@ -230,6 +230,13 @@ namespace xsimd
230
230
  return r;
231
231
  }
232
232
 
233
+ // first
234
+ template <class A, class T, size_t N = 8 * sizeof(T) * batch<T, A>::size>
235
+ T XSIMD_INLINE first(batch<T, A> const& self, requires_arch<emulated<N>>) noexcept
236
+ {
237
+ return self.data[0];
238
+ }
239
+
233
240
  #if 0
234
241
  // count
235
242
  template <class A, class T, size_t N = 8 * sizeof(T) * batch<T, A>::size>
@@ -594,6 +601,16 @@ namespace xsimd
594
601
  { return xsimd::min(x, y); });
595
602
  }
596
603
 
604
+ // reduce_mul
605
+ template <class A, class T, size_t N = 8 * sizeof(T) * batch<T, A>::size>
606
+ XSIMD_INLINE T reduce_mul(batch<T, A> const& self, requires_arch<emulated<N>>) noexcept
607
+ {
608
+ constexpr size_t size = batch<T, A>::size;
609
+ std::array<T, size> buffer;
610
+ self.store_unaligned(buffer.data());
611
+ return std::accumulate(buffer.begin() + 1, buffer.end(), *buffer.begin(), std::multiplies<T>());
612
+ }
613
+
597
614
  // rsqrt
598
615
  template <class A, class T, size_t N = 8 * sizeof(T) * batch<T, A>::size>
599
616
  XSIMD_INLINE batch<T, A> rsqrt(batch<T, A> const& self, requires_arch<emulated<N>>) noexcept
@@ -73,6 +73,19 @@ namespace xsimd
73
73
  return _mm256_fmsub_pd(x, y, z);
74
74
  }
75
75
 
76
+ // fmas
77
+ template <class A>
78
+ XSIMD_INLINE batch<float, A> fmas(batch<float, A> const& x, batch<float, A> const& y, batch<float, A> const& z, requires_arch<fma3<avx>>) noexcept
79
+ {
80
+ return _mm256_fmaddsub_ps(x, y, z);
81
+ }
82
+
83
+ template <class A>
84
+ XSIMD_INLINE batch<double, A> fmas(batch<double, A> const& x, batch<double, A> const& y, batch<double, A> const& z, requires_arch<fma3<avx>>) noexcept
85
+ {
86
+ return _mm256_fmaddsub_pd(x, y, z);
87
+ }
88
+
76
89
  }
77
90
 
78
91
  }
@@ -71,6 +71,24 @@ namespace xsimd
71
71
  {
72
72
  return _mm_fmsub_pd(x, y, z);
73
73
  }
74
+ // fms
75
+ template <class A>
76
+ XSIMD_INLINE batch<float, A> fmas(batch<float, A> const& x,
77
+ batch<float, A> const& y,
78
+ batch<float, A> const& z,
79
+ requires_arch<fma3<sse4_2>>) noexcept
80
+ {
81
+ return _mm_fmaddsub_ps(x, y, z);
82
+ }
83
+
84
+ template <class A>
85
+ XSIMD_INLINE batch<double, A> fmas(batch<double, A> const& x,
86
+ batch<double, A> const& y,
87
+ batch<double, A> const& z,
88
+ requires_arch<fma3<sse4_2>>) noexcept
89
+ {
90
+ return _mm_fmaddsub_pd(x, y, z);
91
+ }
74
92
 
75
93
  }
76
94
 
@@ -72,6 +72,19 @@ namespace xsimd
72
72
  {
73
73
  return _mm_msub_pd(x, y, z);
74
74
  }
75
+
76
+ // fmas
77
+ template <class A>
78
+ XSIMD_INLINE batch<float, A> fmas(batch<float, A> const& x, batch<float, A> const& y, batch<float, A> const& z, requires_arch<fma4>) noexcept
79
+ {
80
+ return _mm_maddsub_ps(x, y, z);
81
+ }
82
+
83
+ template <class A>
84
+ XSIMD_INLINE batch<double, A> fmas(batch<double, A> const& x, batch<double, A> const& y, batch<double, A> const& z, requires_arch<fma4>) noexcept
85
+ {
86
+ return _mm_maddsub_pd(x, y, z);
87
+ }
75
88
  }
76
89
 
77
90
  }
@@ -72,6 +72,10 @@
72
72
  #include "./xsimd_avx512f.hpp"
73
73
  #endif
74
74
 
75
+ #if XSIMD_WITH_AVX512DQ
76
+ #include "./xsimd_avx512dq.hpp"
77
+ #endif
78
+
75
79
  #if XSIMD_WITH_AVX512BW
76
80
  #include "./xsimd_avx512bw.hpp"
77
81
  #endif
@@ -128,6 +132,10 @@
128
132
  #include "./xsimd_wasm.hpp"
129
133
  #endif
130
134
 
135
+ #if XSIMD_WITH_VSX
136
+ #include "./xsimd_vsx.hpp"
137
+ #endif
138
+
131
139
  // Must come last to have access to all conversion specializations.
132
140
  #include "./xsimd_common.hpp"
133
141