sequenzo 0.1.17__cp311-cp311-macosx_10_9_universal2.whl → 0.1.19__cp311-cp311-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 +155 -155
  4. sequenzo/big_data/clara/utils/get_weighted_diss.cpython-311-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-311-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 +155 -155
  61. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cpython-311-darwin.so +0 -0
  62. sequenzo/dissimilarity_measures/utils/seqconc.c +155 -155
  63. sequenzo/dissimilarity_measures/utils/seqconc.cpython-311-darwin.so +0 -0
  64. sequenzo/dissimilarity_measures/utils/seqdss.c +155 -155
  65. sequenzo/dissimilarity_measures/utils/seqdss.cpython-311-darwin.so +0 -0
  66. sequenzo/dissimilarity_measures/utils/seqdur.c +155 -155
  67. sequenzo/dissimilarity_measures/utils/seqdur.cpython-311-darwin.so +0 -0
  68. sequenzo/dissimilarity_measures/utils/seqlength.c +155 -155
  69. sequenzo/dissimilarity_measures/utils/seqlength.cpython-311-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
@@ -1,286 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2016 Gael Guennebaud <gael.guennebaud@inria.fr>
5
- //
6
- // This Source Code Form is subject to the terms of the Mozilla
7
- // Public License v. 2.0. If a copy of the MPL was not distributed
8
- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
9
-
10
-
11
- #ifndef EIGEN_BESSELFUNCTIONS_ARRAYAPI_H
12
- #define EIGEN_BESSELFUNCTIONS_ARRAYAPI_H
13
-
14
- namespace Eigen {
15
-
16
- /** \returns an expression of the coefficient-wise i0(\a x) to the given
17
- * arrays.
18
- *
19
- * It returns the modified Bessel function of the first kind of order zero.
20
- *
21
- * \param x is the argument
22
- *
23
- * \note This function supports only float and double scalar types. To support
24
- * other scalar types, the user has to provide implementations of i0(T) for
25
- * any scalar type T to be supported.
26
- *
27
- * \sa ArrayBase::bessel_i0()
28
- */
29
- template <typename Derived>
30
- EIGEN_STRONG_INLINE const Eigen::CwiseUnaryOp<
31
- Eigen::internal::scalar_bessel_i0_op<typename Derived::Scalar>, const Derived>
32
- bessel_i0(const Eigen::ArrayBase<Derived>& x) {
33
- return Eigen::CwiseUnaryOp<
34
- Eigen::internal::scalar_bessel_i0_op<typename Derived::Scalar>,
35
- const Derived>(x.derived());
36
- }
37
-
38
- /** \returns an expression of the coefficient-wise i0e(\a x) to the given
39
- * arrays.
40
- *
41
- * It returns the exponentially scaled modified Bessel
42
- * function of the first kind of order zero.
43
- *
44
- * \param x is the argument
45
- *
46
- * \note This function supports only float and double scalar types. To support
47
- * other scalar types, the user has to provide implementations of i0e(T) for
48
- * any scalar type T to be supported.
49
- *
50
- * \sa ArrayBase::bessel_i0e()
51
- */
52
- template <typename Derived>
53
- EIGEN_STRONG_INLINE const Eigen::CwiseUnaryOp<
54
- Eigen::internal::scalar_bessel_i0e_op<typename Derived::Scalar>, const Derived>
55
- bessel_i0e(const Eigen::ArrayBase<Derived>& x) {
56
- return Eigen::CwiseUnaryOp<
57
- Eigen::internal::scalar_bessel_i0e_op<typename Derived::Scalar>,
58
- const Derived>(x.derived());
59
- }
60
-
61
- /** \returns an expression of the coefficient-wise i1(\a x) to the given
62
- * arrays.
63
- *
64
- * It returns the modified Bessel function of the first kind of order one.
65
- *
66
- * \param x is the argument
67
- *
68
- * \note This function supports only float and double scalar types. To support
69
- * other scalar types, the user has to provide implementations of i1(T) for
70
- * any scalar type T to be supported.
71
- *
72
- * \sa ArrayBase::bessel_i1()
73
- */
74
- template <typename Derived>
75
- EIGEN_STRONG_INLINE const Eigen::CwiseUnaryOp<
76
- Eigen::internal::scalar_bessel_i1_op<typename Derived::Scalar>, const Derived>
77
- bessel_i1(const Eigen::ArrayBase<Derived>& x) {
78
- return Eigen::CwiseUnaryOp<
79
- Eigen::internal::scalar_bessel_i1_op<typename Derived::Scalar>,
80
- const Derived>(x.derived());
81
- }
82
-
83
- /** \returns an expression of the coefficient-wise i1e(\a x) to the given
84
- * arrays.
85
- *
86
- * It returns the exponentially scaled modified Bessel
87
- * function of the first kind of order one.
88
- *
89
- * \param x is the argument
90
- *
91
- * \note This function supports only float and double scalar types. To support
92
- * other scalar types, the user has to provide implementations of i1e(T) for
93
- * any scalar type T to be supported.
94
- *
95
- * \sa ArrayBase::bessel_i1e()
96
- */
97
- template <typename Derived>
98
- EIGEN_STRONG_INLINE const Eigen::CwiseUnaryOp<
99
- Eigen::internal::scalar_bessel_i1e_op<typename Derived::Scalar>, const Derived>
100
- bessel_i1e(const Eigen::ArrayBase<Derived>& x) {
101
- return Eigen::CwiseUnaryOp<
102
- Eigen::internal::scalar_bessel_i1e_op<typename Derived::Scalar>,
103
- const Derived>(x.derived());
104
- }
105
-
106
- /** \returns an expression of the coefficient-wise k0(\a x) to the given
107
- * arrays.
108
- *
109
- * It returns the modified Bessel function of the second kind of order zero.
110
- *
111
- * \param x is the argument
112
- *
113
- * \note This function supports only float and double scalar types. To support
114
- * other scalar types, the user has to provide implementations of k0(T) for
115
- * any scalar type T to be supported.
116
- *
117
- * \sa ArrayBase::bessel_k0()
118
- */
119
- template <typename Derived>
120
- EIGEN_STRONG_INLINE const Eigen::CwiseUnaryOp<
121
- Eigen::internal::scalar_bessel_k0_op<typename Derived::Scalar>, const Derived>
122
- bessel_k0(const Eigen::ArrayBase<Derived>& x) {
123
- return Eigen::CwiseUnaryOp<
124
- Eigen::internal::scalar_bessel_k0_op<typename Derived::Scalar>,
125
- const Derived>(x.derived());
126
- }
127
-
128
- /** \returns an expression of the coefficient-wise k0e(\a x) to the given
129
- * arrays.
130
- *
131
- * It returns the exponentially scaled modified Bessel
132
- * function of the second kind of order zero.
133
- *
134
- * \param x is the argument
135
- *
136
- * \note This function supports only float and double scalar types. To support
137
- * other scalar types, the user has to provide implementations of k0e(T) for
138
- * any scalar type T to be supported.
139
- *
140
- * \sa ArrayBase::bessel_k0e()
141
- */
142
- template <typename Derived>
143
- EIGEN_STRONG_INLINE const Eigen::CwiseUnaryOp<
144
- Eigen::internal::scalar_bessel_k0e_op<typename Derived::Scalar>, const Derived>
145
- bessel_k0e(const Eigen::ArrayBase<Derived>& x) {
146
- return Eigen::CwiseUnaryOp<
147
- Eigen::internal::scalar_bessel_k0e_op<typename Derived::Scalar>,
148
- const Derived>(x.derived());
149
- }
150
-
151
- /** \returns an expression of the coefficient-wise k1(\a x) to the given
152
- * arrays.
153
- *
154
- * It returns the modified Bessel function of the second kind of order one.
155
- *
156
- * \param x is the argument
157
- *
158
- * \note This function supports only float and double scalar types. To support
159
- * other scalar types, the user has to provide implementations of k1(T) for
160
- * any scalar type T to be supported.
161
- *
162
- * \sa ArrayBase::bessel_k1()
163
- */
164
- template <typename Derived>
165
- EIGEN_STRONG_INLINE const Eigen::CwiseUnaryOp<
166
- Eigen::internal::scalar_bessel_k1_op<typename Derived::Scalar>, const Derived>
167
- bessel_k1(const Eigen::ArrayBase<Derived>& x) {
168
- return Eigen::CwiseUnaryOp<
169
- Eigen::internal::scalar_bessel_k1_op<typename Derived::Scalar>,
170
- const Derived>(x.derived());
171
- }
172
-
173
- /** \returns an expression of the coefficient-wise k1e(\a x) to the given
174
- * arrays.
175
- *
176
- * It returns the exponentially scaled modified Bessel
177
- * function of the second kind of order one.
178
- *
179
- * \param x is the argument
180
- *
181
- * \note This function supports only float and double scalar types. To support
182
- * other scalar types, the user has to provide implementations of k1e(T) for
183
- * any scalar type T to be supported.
184
- *
185
- * \sa ArrayBase::bessel_k1e()
186
- */
187
- template <typename Derived>
188
- EIGEN_STRONG_INLINE const Eigen::CwiseUnaryOp<
189
- Eigen::internal::scalar_bessel_k1e_op<typename Derived::Scalar>, const Derived>
190
- bessel_k1e(const Eigen::ArrayBase<Derived>& x) {
191
- return Eigen::CwiseUnaryOp<
192
- Eigen::internal::scalar_bessel_k1e_op<typename Derived::Scalar>,
193
- const Derived>(x.derived());
194
- }
195
-
196
- /** \returns an expression of the coefficient-wise j0(\a x) to the given
197
- * arrays.
198
- *
199
- * It returns the Bessel function of the first kind of order zero.
200
- *
201
- * \param x is the argument
202
- *
203
- * \note This function supports only float and double scalar types. To support
204
- * other scalar types, the user has to provide implementations of j0(T) for
205
- * any scalar type T to be supported.
206
- *
207
- * \sa ArrayBase::bessel_j0()
208
- */
209
- template <typename Derived>
210
- EIGEN_STRONG_INLINE const Eigen::CwiseUnaryOp<
211
- Eigen::internal::scalar_bessel_j0_op<typename Derived::Scalar>, const Derived>
212
- bessel_j0(const Eigen::ArrayBase<Derived>& x) {
213
- return Eigen::CwiseUnaryOp<
214
- Eigen::internal::scalar_bessel_j0_op<typename Derived::Scalar>,
215
- const Derived>(x.derived());
216
- }
217
-
218
- /** \returns an expression of the coefficient-wise y0(\a x) to the given
219
- * arrays.
220
- *
221
- * It returns the Bessel function of the second kind of order zero.
222
- *
223
- * \param x is the argument
224
- *
225
- * \note This function supports only float and double scalar types. To support
226
- * other scalar types, the user has to provide implementations of y0(T) for
227
- * any scalar type T to be supported.
228
- *
229
- * \sa ArrayBase::bessel_y0()
230
- */
231
- template <typename Derived>
232
- EIGEN_STRONG_INLINE const Eigen::CwiseUnaryOp<
233
- Eigen::internal::scalar_bessel_y0_op<typename Derived::Scalar>, const Derived>
234
- bessel_y0(const Eigen::ArrayBase<Derived>& x) {
235
- return Eigen::CwiseUnaryOp<
236
- Eigen::internal::scalar_bessel_y0_op<typename Derived::Scalar>,
237
- const Derived>(x.derived());
238
- }
239
-
240
- /** \returns an expression of the coefficient-wise j1(\a x) to the given
241
- * arrays.
242
- *
243
- * It returns the modified Bessel function of the first kind of order one.
244
- *
245
- * \param x is the argument
246
- *
247
- * \note This function supports only float and double scalar types. To support
248
- * other scalar types, the user has to provide implementations of j1(T) for
249
- * any scalar type T to be supported.
250
- *
251
- * \sa ArrayBase::bessel_j1()
252
- */
253
- template <typename Derived>
254
- EIGEN_STRONG_INLINE const Eigen::CwiseUnaryOp<
255
- Eigen::internal::scalar_bessel_j1_op<typename Derived::Scalar>, const Derived>
256
- bessel_j1(const Eigen::ArrayBase<Derived>& x) {
257
- return Eigen::CwiseUnaryOp<
258
- Eigen::internal::scalar_bessel_j1_op<typename Derived::Scalar>,
259
- const Derived>(x.derived());
260
- }
261
-
262
- /** \returns an expression of the coefficient-wise y1(\a x) to the given
263
- * arrays.
264
- *
265
- * It returns the Bessel function of the second kind of order one.
266
- *
267
- * \param x is the argument
268
- *
269
- * \note This function supports only float and double scalar types. To support
270
- * other scalar types, the user has to provide implementations of y1(T) for
271
- * any scalar type T to be supported.
272
- *
273
- * \sa ArrayBase::bessel_y1()
274
- */
275
- template <typename Derived>
276
- EIGEN_STRONG_INLINE const Eigen::CwiseUnaryOp<
277
- Eigen::internal::scalar_bessel_y1_op<typename Derived::Scalar>, const Derived>
278
- bessel_y1(const Eigen::ArrayBase<Derived>& x) {
279
- return Eigen::CwiseUnaryOp<
280
- Eigen::internal::scalar_bessel_y1_op<typename Derived::Scalar>,
281
- const Derived>(x.derived());
282
- }
283
-
284
- } // end namespace Eigen
285
-
286
- #endif // EIGEN_BESSELFUNCTIONS_ARRAYAPI_H
@@ -1,68 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // This Source Code Form is subject to the terms of the Mozilla
5
- // Public License v. 2.0. If a copy of the MPL was not distributed
6
- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
7
-
8
- #ifndef EIGEN_BESSELFUNCTIONS_BFLOAT16_H
9
- #define EIGEN_BESSELFUNCTIONS_BFLOAT16_H
10
-
11
- namespace Eigen {
12
- namespace numext {
13
-
14
- #if EIGEN_HAS_C99_MATH
15
- template <>
16
- EIGEN_STRONG_INLINE EIGEN_DEVICE_FUNC Eigen::bfloat16 bessel_i0(const Eigen::bfloat16& x) {
17
- return Eigen::bfloat16(Eigen::numext::bessel_i0(static_cast<float>(x)));
18
- }
19
- template <>
20
- EIGEN_STRONG_INLINE EIGEN_DEVICE_FUNC Eigen::bfloat16 bessel_i0e(const Eigen::bfloat16& x) {
21
- return Eigen::bfloat16(Eigen::numext::bessel_i0e(static_cast<float>(x)));
22
- }
23
- template <>
24
- EIGEN_STRONG_INLINE EIGEN_DEVICE_FUNC Eigen::bfloat16 bessel_i1(const Eigen::bfloat16& x) {
25
- return Eigen::bfloat16(Eigen::numext::bessel_i1(static_cast<float>(x)));
26
- }
27
- template <>
28
- EIGEN_STRONG_INLINE EIGEN_DEVICE_FUNC Eigen::bfloat16 bessel_i1e(const Eigen::bfloat16& x) {
29
- return Eigen::bfloat16(Eigen::numext::bessel_i1e(static_cast<float>(x)));
30
- }
31
- template <>
32
- EIGEN_STRONG_INLINE EIGEN_DEVICE_FUNC Eigen::bfloat16 bessel_j0(const Eigen::bfloat16& x) {
33
- return Eigen::bfloat16(Eigen::numext::bessel_j0(static_cast<float>(x)));
34
- }
35
- template <>
36
- EIGEN_STRONG_INLINE EIGEN_DEVICE_FUNC Eigen::bfloat16 bessel_j1(const Eigen::bfloat16& x) {
37
- return Eigen::bfloat16(Eigen::numext::bessel_j1(static_cast<float>(x)));
38
- }
39
- template <>
40
- EIGEN_STRONG_INLINE EIGEN_DEVICE_FUNC Eigen::bfloat16 bessel_y0(const Eigen::bfloat16& x) {
41
- return Eigen::bfloat16(Eigen::numext::bessel_y0(static_cast<float>(x)));
42
- }
43
- template <>
44
- EIGEN_STRONG_INLINE EIGEN_DEVICE_FUNC Eigen::bfloat16 bessel_y1(const Eigen::bfloat16& x) {
45
- return Eigen::bfloat16(Eigen::numext::bessel_y1(static_cast<float>(x)));
46
- }
47
- template <>
48
- EIGEN_STRONG_INLINE EIGEN_DEVICE_FUNC Eigen::bfloat16 bessel_k0(const Eigen::bfloat16& x) {
49
- return Eigen::bfloat16(Eigen::numext::bessel_k0(static_cast<float>(x)));
50
- }
51
- template <>
52
- EIGEN_STRONG_INLINE EIGEN_DEVICE_FUNC Eigen::bfloat16 bessel_k0e(const Eigen::bfloat16& x) {
53
- return Eigen::bfloat16(Eigen::numext::bessel_k0e(static_cast<float>(x)));
54
- }
55
- template <>
56
- EIGEN_STRONG_INLINE EIGEN_DEVICE_FUNC Eigen::bfloat16 bessel_k1(const Eigen::bfloat16& x) {
57
- return Eigen::bfloat16(Eigen::numext::bessel_k1(static_cast<float>(x)));
58
- }
59
- template <>
60
- EIGEN_STRONG_INLINE EIGEN_DEVICE_FUNC Eigen::bfloat16 bessel_k1e(const Eigen::bfloat16& x) {
61
- return Eigen::bfloat16(Eigen::numext::bessel_k1e(static_cast<float>(x)));
62
- }
63
- #endif
64
-
65
- } // end namespace numext
66
- } // end namespace Eigen
67
-
68
- #endif // EIGEN_BESSELFUNCTIONS_BFLOAT16_H