sequenzo 0.1.17__cp310-cp310-macosx_10_9_universal2.whl → 0.1.19__cp310-cp310-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-310-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-310-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-310-darwin.so +0 -0
  62. sequenzo/dissimilarity_measures/utils/seqconc.c +155 -155
  63. sequenzo/dissimilarity_measures/utils/seqconc.cpython-310-darwin.so +0 -0
  64. sequenzo/dissimilarity_measures/utils/seqdss.c +155 -155
  65. sequenzo/dissimilarity_measures/utils/seqdss.cpython-310-darwin.so +0 -0
  66. sequenzo/dissimilarity_measures/utils/seqdur.c +155 -155
  67. sequenzo/dissimilarity_measures/utils/seqdur.cpython-310-darwin.so +0 -0
  68. sequenzo/dissimilarity_measures/utils/seqlength.c +155 -155
  69. sequenzo/dissimilarity_measures/utils/seqlength.cpython-310-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
@@ -1,379 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2014 Benoit Steiner <benoit.steiner.goog@gmail.com>
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
- #ifndef EIGEN_CXX11_TENSOR_TENSOR_FIXED_SIZE_H
11
- #define EIGEN_CXX11_TENSOR_TENSOR_FIXED_SIZE_H
12
-
13
- namespace Eigen {
14
-
15
- /** \class TensorFixedSize
16
- * \ingroup CXX11_Tensor_Module
17
- *
18
- * \brief The fixed sized version of the tensor class.
19
- *
20
- * The fixed sized equivalent of
21
- * Eigen::Tensor<float, 3> t(3, 5, 7);
22
- * is
23
- * Eigen::TensorFixedSize<float, Sizes<3,5,7>> t;
24
- */
25
-
26
- template<typename Scalar_, typename Dimensions_, int Options_, typename IndexType>
27
- class TensorFixedSize : public TensorBase<TensorFixedSize<Scalar_, Dimensions_, Options_, IndexType> >
28
- {
29
- public:
30
- typedef TensorFixedSize<Scalar_, Dimensions_, Options_, IndexType> Self;
31
- typedef TensorBase<TensorFixedSize<Scalar_, Dimensions_, Options_, IndexType> > Base;
32
- typedef typename Eigen::internal::nested<Self>::type Nested;
33
- typedef typename internal::traits<Self>::StorageKind StorageKind;
34
- typedef typename internal::traits<Self>::Index Index;
35
- typedef Scalar_ Scalar;
36
- typedef typename NumTraits<Scalar>::Real RealScalar;
37
- typedef typename Base::CoeffReturnType CoeffReturnType;
38
-
39
- static const int Options = Options_;
40
-
41
- enum {
42
- IsAligned = bool(EIGEN_MAX_ALIGN_BYTES>0),
43
- PacketAccess = (internal::packet_traits<Scalar>::size > 1),
44
- BlockAccess = false,
45
- PreferBlockAccess = false,
46
- Layout = Options_ & RowMajor ? RowMajor : ColMajor,
47
- CoordAccess = true,
48
- RawAccess = true
49
- };
50
-
51
- //===- Tensor block evaluation strategy (see TensorBlock.h) -------------===//
52
- typedef internal::TensorBlockNotImplemented TensorBlock;
53
- //===--------------------------------------------------------------------===//
54
-
55
- typedef Dimensions_ Dimensions;
56
- static const std::size_t NumIndices = Dimensions::count;
57
-
58
- protected:
59
- TensorStorage<Scalar, Dimensions, Options> m_storage;
60
-
61
- public:
62
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index rank() const { return NumIndices; }
63
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index dimension(std::size_t n) const { return m_storage.dimensions()[n]; }
64
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Dimensions& dimensions() const { return m_storage.dimensions(); }
65
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index size() const { return m_storage.size(); }
66
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Scalar *data() { return m_storage.data(); }
67
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Scalar *data() const { return m_storage.data(); }
68
-
69
- // This makes EIGEN_INITIALIZE_COEFFS_IF_THAT_OPTION_IS_ENABLED
70
- // work, because that uses base().coeffRef() - and we don't yet
71
- // implement a similar class hierarchy
72
- inline Self& base() { return *this; }
73
- inline const Self& base() const { return *this; }
74
-
75
- #if EIGEN_HAS_VARIADIC_TEMPLATES
76
- template<typename... IndexTypes>
77
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Scalar& coeff(Index firstIndex, IndexTypes... otherIndices) const
78
- {
79
- // The number of indices used to access a tensor coefficient must be equal to the rank of the tensor.
80
- EIGEN_STATIC_ASSERT(sizeof...(otherIndices) + 1 == NumIndices, YOU_MADE_A_PROGRAMMING_MISTAKE)
81
- return coeff(array<Index, NumIndices>{{firstIndex, otherIndices...}});
82
- }
83
- #endif
84
-
85
- EIGEN_DEVICE_FUNC
86
- EIGEN_STRONG_INLINE const Scalar& coeff(const array<Index, NumIndices>& indices) const
87
- {
88
- eigen_internal_assert(checkIndexRange(indices));
89
- return m_storage.data()[linearizedIndex(indices)];
90
- }
91
-
92
- EIGEN_DEVICE_FUNC
93
- EIGEN_STRONG_INLINE const Scalar& coeff(Index index) const
94
- {
95
- eigen_internal_assert(index >= 0 && index < size());
96
- return m_storage.data()[index];
97
- }
98
-
99
- EIGEN_DEVICE_FUNC
100
- EIGEN_STRONG_INLINE const Scalar& coeff() const
101
- {
102
- EIGEN_STATIC_ASSERT(NumIndices == 0, YOU_MADE_A_PROGRAMMING_MISTAKE);
103
- return m_storage.data()[0];
104
- }
105
-
106
-
107
- #if EIGEN_HAS_VARIADIC_TEMPLATES
108
- template<typename... IndexTypes>
109
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Scalar& coeffRef(Index firstIndex, IndexTypes... otherIndices)
110
- {
111
- // The number of indices used to access a tensor coefficient must be equal to the rank of the tensor.
112
- EIGEN_STATIC_ASSERT(sizeof...(otherIndices) + 1 == NumIndices, YOU_MADE_A_PROGRAMMING_MISTAKE)
113
- return coeffRef(array<Index, NumIndices>{{firstIndex, otherIndices...}});
114
- }
115
- #endif
116
-
117
- EIGEN_DEVICE_FUNC
118
- EIGEN_STRONG_INLINE Scalar& coeffRef(const array<Index, NumIndices>& indices)
119
- {
120
- eigen_internal_assert(checkIndexRange(indices));
121
- return m_storage.data()[linearizedIndex(indices)];
122
- }
123
-
124
- EIGEN_DEVICE_FUNC
125
- EIGEN_STRONG_INLINE Scalar& coeffRef(Index index)
126
- {
127
- eigen_internal_assert(index >= 0 && index < size());
128
- return m_storage.data()[index];
129
- }
130
-
131
- EIGEN_DEVICE_FUNC
132
- EIGEN_STRONG_INLINE Scalar& coeffRef()
133
- {
134
- EIGEN_STATIC_ASSERT(NumIndices == 0, YOU_MADE_A_PROGRAMMING_MISTAKE);
135
- return m_storage.data()[0];
136
- }
137
-
138
- #if EIGEN_HAS_VARIADIC_TEMPLATES
139
- template<typename... IndexTypes>
140
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Scalar& operator()(Index firstIndex, IndexTypes... otherIndices) const
141
- {
142
- // The number of indices used to access a tensor coefficient must be equal to the rank of the tensor.
143
- EIGEN_STATIC_ASSERT(sizeof...(otherIndices) + 1 == NumIndices, YOU_MADE_A_PROGRAMMING_MISTAKE)
144
- return this->operator()(array<Index, NumIndices>{{firstIndex, otherIndices...}});
145
- }
146
- #else
147
- EIGEN_DEVICE_FUNC
148
- EIGEN_STRONG_INLINE const Scalar& operator()(Index i0, Index i1) const
149
- {
150
- if (Options&RowMajor) {
151
- const Index index = i1 + i0 * m_storage.dimensions()[1];
152
- return m_storage.data()[index];
153
- } else {
154
- const Index index = i0 + i1 * m_storage.dimensions()[0];
155
- return m_storage.data()[index];
156
- }
157
- }
158
- EIGEN_DEVICE_FUNC
159
- EIGEN_STRONG_INLINE const Scalar& operator()(Index i0, Index i1, Index i2) const
160
- {
161
- if (Options&RowMajor) {
162
- const Index index = i2 + m_storage.dimensions()[2] * (i1 + m_storage.dimensions()[1] * i0);
163
- return m_storage.data()[index];
164
- } else {
165
- const Index index = i0 + m_storage.dimensions()[0] * (i1 + m_storage.dimensions()[1] * i2);
166
- return m_storage.data()[index];
167
- }
168
- }
169
- EIGEN_DEVICE_FUNC
170
- EIGEN_STRONG_INLINE const Scalar& operator()(Index i0, Index i1, Index i2, Index i3) const
171
- {
172
- if (Options&RowMajor) {
173
- const Index index = i3 + m_storage.dimensions()[3] * (i2 + m_storage.dimensions()[2] * (i1 + m_storage.dimensions()[1] * i0));
174
- return m_storage.data()[index];
175
- } else {
176
- const Index index = i0 + m_storage.dimensions()[0] * (i1 + m_storage.dimensions()[1] * (i2 + m_storage.dimensions()[2] * i3));
177
- return m_storage.data()[index];
178
- }
179
- }
180
- EIGEN_DEVICE_FUNC
181
- EIGEN_STRONG_INLINE const Scalar& operator()(Index i0, Index i1, Index i2, Index i3, Index i4) const
182
- {
183
- if (Options&RowMajor) {
184
- const Index index = i4 + m_storage.dimensions()[4] * (i3 + m_storage.dimensions()[3] * (i2 + m_storage.dimensions()[2] * (i1 + m_storage.dimensions()[1] * i0)));
185
- return m_storage.data()[index];
186
- } else {
187
- const Index index = i0 + m_storage.dimensions()[0] * (i1 + m_storage.dimensions()[1] * (i2 + m_storage.dimensions()[2] * (i3 + m_storage.dimensions()[3] * i4)));
188
- return m_storage.data()[index];
189
- }
190
- }
191
- #endif
192
-
193
-
194
- EIGEN_DEVICE_FUNC
195
- EIGEN_STRONG_INLINE const Scalar& operator()(const array<Index, NumIndices>& indices) const
196
- {
197
- eigen_assert(checkIndexRange(indices));
198
- return coeff(indices);
199
- }
200
-
201
- EIGEN_DEVICE_FUNC
202
- EIGEN_STRONG_INLINE const Scalar& operator()(Index index) const
203
- {
204
- eigen_internal_assert(index >= 0 && index < size());
205
- return coeff(index);
206
- }
207
-
208
- EIGEN_DEVICE_FUNC
209
- EIGEN_STRONG_INLINE const Scalar& operator()() const
210
- {
211
- EIGEN_STATIC_ASSERT(NumIndices == 0, YOU_MADE_A_PROGRAMMING_MISTAKE);
212
- return coeff();
213
- }
214
-
215
- EIGEN_DEVICE_FUNC
216
- EIGEN_STRONG_INLINE const Scalar& operator[](Index index) const
217
- {
218
- // The bracket operator is only for vectors, use the parenthesis operator instead.
219
- EIGEN_STATIC_ASSERT(NumIndices == 1, YOU_MADE_A_PROGRAMMING_MISTAKE);
220
- return coeff(index);
221
- }
222
-
223
- #if EIGEN_HAS_VARIADIC_TEMPLATES
224
- template<typename... IndexTypes>
225
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Scalar& operator()(Index firstIndex, IndexTypes... otherIndices)
226
- {
227
- // The number of indices used to access a tensor coefficient must be equal to the rank of the tensor.
228
- EIGEN_STATIC_ASSERT(sizeof...(otherIndices) + 1 == NumIndices, YOU_MADE_A_PROGRAMMING_MISTAKE)
229
- return operator()(array<Index, NumIndices>{{firstIndex, otherIndices...}});
230
- }
231
- #else
232
- EIGEN_DEVICE_FUNC
233
- EIGEN_STRONG_INLINE Scalar& operator()(Index i0, Index i1)
234
- {
235
- if (Options&RowMajor) {
236
- const Index index = i1 + i0 * m_storage.dimensions()[1];
237
- return m_storage.data()[index];
238
- } else {
239
- const Index index = i0 + i1 * m_storage.dimensions()[0];
240
- return m_storage.data()[index];
241
- }
242
- }
243
- EIGEN_DEVICE_FUNC
244
- EIGEN_STRONG_INLINE Scalar& operator()(Index i0, Index i1, Index i2)
245
- {
246
- if (Options&RowMajor) {
247
- const Index index = i2 + m_storage.dimensions()[2] * (i1 + m_storage.dimensions()[1] * i0);
248
- return m_storage.data()[index];
249
- } else {
250
- const Index index = i0 + m_storage.dimensions()[0] * (i1 + m_storage.dimensions()[1] * i2);
251
- return m_storage.data()[index];
252
- }
253
- }
254
- EIGEN_DEVICE_FUNC
255
- EIGEN_STRONG_INLINE Scalar& operator()(Index i0, Index i1, Index i2, Index i3)
256
- {
257
- if (Options&RowMajor) {
258
- const Index index = i3 + m_storage.dimensions()[3] * (i2 + m_storage.dimensions()[2] * (i1 + m_storage.dimensions()[1] * i0));
259
- return m_storage.data()[index];
260
- } else {
261
- const Index index = i0 + m_storage.dimensions()[0] * (i1 + m_storage.dimensions()[1] * (i2 + m_storage.dimensions()[2] * i3));
262
- return m_storage.data()[index];
263
- }
264
- }
265
- EIGEN_DEVICE_FUNC
266
- EIGEN_STRONG_INLINE Scalar& operator()(Index i0, Index i1, Index i2, Index i3, Index i4)
267
- {
268
- if (Options&RowMajor) {
269
- const Index index = i4 + m_storage.dimensions()[4] * (i3 + m_storage.dimensions()[3] * (i2 + m_storage.dimensions()[2] * (i1 + m_storage.dimensions()[1] * i0)));
270
- return m_storage.data()[index];
271
- } else {
272
- const Index index = i0 + m_storage.dimensions()[0] * (i1 + m_storage.dimensions()[1] * (i2 + m_storage.dimensions()[2] * (i3 + m_storage.dimensions()[3] * i4)));
273
- return m_storage.data()[index];
274
- }
275
- }
276
- #endif
277
-
278
- EIGEN_DEVICE_FUNC
279
- EIGEN_STRONG_INLINE Scalar& operator()(const array<Index, NumIndices>& indices)
280
- {
281
- eigen_assert(checkIndexRange(indices));
282
- return coeffRef(indices);
283
- }
284
-
285
- EIGEN_DEVICE_FUNC
286
- EIGEN_STRONG_INLINE Scalar& operator()(Index index)
287
- {
288
- eigen_assert(index >= 0 && index < size());
289
- return coeffRef(index);
290
- }
291
-
292
- EIGEN_DEVICE_FUNC
293
- EIGEN_STRONG_INLINE Scalar& operator()()
294
- {
295
- EIGEN_STATIC_ASSERT(NumIndices == 0, YOU_MADE_A_PROGRAMMING_MISTAKE);
296
- return coeffRef();
297
- }
298
-
299
- EIGEN_DEVICE_FUNC
300
- EIGEN_STRONG_INLINE Scalar& operator[](Index index)
301
- {
302
- // The bracket operator is only for vectors, use the parenthesis operator instead
303
- EIGEN_STATIC_ASSERT(NumIndices == 1, YOU_MADE_A_PROGRAMMING_MISTAKE)
304
- return coeffRef(index);
305
- }
306
-
307
- EIGEN_DEVICE_FUNC
308
- EIGEN_STRONG_INLINE TensorFixedSize()
309
- : m_storage()
310
- {
311
- }
312
-
313
- EIGEN_DEVICE_FUNC
314
- EIGEN_STRONG_INLINE TensorFixedSize(const Self& other)
315
- : m_storage(other.m_storage)
316
- {
317
- }
318
-
319
- #if EIGEN_HAS_RVALUE_REFERENCES
320
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorFixedSize(Self&& other)
321
- : m_storage(other.m_storage)
322
- {
323
- }
324
- #endif
325
-
326
- template<typename OtherDerived>
327
- EIGEN_DEVICE_FUNC
328
- EIGEN_STRONG_INLINE TensorFixedSize(const TensorBase<OtherDerived, ReadOnlyAccessors>& other)
329
- {
330
- typedef TensorAssignOp<TensorFixedSize, const OtherDerived> Assign;
331
- Assign assign(*this, other.derived());
332
- internal::TensorExecutor<const Assign, DefaultDevice>::run(assign, DefaultDevice());
333
- }
334
- template<typename OtherDerived>
335
- EIGEN_DEVICE_FUNC
336
- EIGEN_STRONG_INLINE TensorFixedSize(const TensorBase<OtherDerived, WriteAccessors>& other)
337
- {
338
- typedef TensorAssignOp<TensorFixedSize, const OtherDerived> Assign;
339
- Assign assign(*this, other.derived());
340
- internal::TensorExecutor<const Assign, DefaultDevice>::run(assign, DefaultDevice());
341
- }
342
-
343
- // FIXME: check that the dimensions of other match the dimensions of *this.
344
- // Unfortunately this isn't possible yet when the rhs is an expression.
345
- EIGEN_TENSOR_INHERIT_ASSIGNMENT_EQUAL_OPERATOR(TensorFixedSize)
346
-
347
-
348
- protected:
349
- EIGEN_DEVICE_FUNC
350
- EIGEN_STRONG_INLINE bool checkIndexRange(const array<Index, NumIndices>& /*indices*/) const
351
- {
352
- using internal::array_apply_and_reduce;
353
- using internal::array_zip_and_reduce;
354
- using internal::greater_equal_zero_op;
355
- using internal::logical_and_op;
356
- using internal::lesser_op;
357
-
358
- return true;
359
- // check whether the indices are all >= 0
360
- /* array_apply_and_reduce<logical_and_op, greater_equal_zero_op>(indices) &&
361
- // check whether the indices fit in the dimensions
362
- array_zip_and_reduce<logical_and_op, lesser_op>(indices, m_storage.dimensions());*/
363
- }
364
-
365
- EIGEN_DEVICE_FUNC
366
- EIGEN_STRONG_INLINE Index linearizedIndex(const array<Index, NumIndices>& indices) const
367
- {
368
- if (Options&RowMajor) {
369
- return m_storage.dimensions().IndexOfRowMajor(indices);
370
- } else {
371
- return m_storage.dimensions().IndexOfColMajor(indices);
372
- }
373
- }
374
- };
375
-
376
-
377
- } // end namespace Eigen
378
-
379
- #endif // EIGEN_CXX11_TENSOR_TENSOR_FIXED_SIZE_H
@@ -1,237 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2014 Benoit Steiner <benoit.steiner.goog@gmail.com>
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
- #ifndef EIGEN_CXX11_TENSOR_TENSOR_FORCED_EVAL_H
11
- #define EIGEN_CXX11_TENSOR_TENSOR_FORCED_EVAL_H
12
-
13
- namespace Eigen {
14
-
15
- /** \class TensorForcedEval
16
- * \ingroup CXX11_Tensor_Module
17
- *
18
- * \brief Tensor reshaping class.
19
- *
20
- *
21
- */
22
- namespace internal {
23
- template<typename XprType>
24
- struct traits<TensorForcedEvalOp<XprType> >
25
- {
26
- // Type promotion to handle the case where the types of the lhs and the rhs are different.
27
- typedef typename XprType::Scalar Scalar;
28
- typedef traits<XprType> XprTraits;
29
- typedef typename traits<XprType>::StorageKind StorageKind;
30
- typedef typename traits<XprType>::Index Index;
31
- typedef typename XprType::Nested Nested;
32
- typedef typename remove_reference<Nested>::type _Nested;
33
- static const int NumDimensions = XprTraits::NumDimensions;
34
- static const int Layout = XprTraits::Layout;
35
- typedef typename XprTraits::PointerType PointerType;
36
-
37
- enum {
38
- Flags = 0
39
- };
40
- };
41
-
42
- template<typename XprType>
43
- struct eval<TensorForcedEvalOp<XprType>, Eigen::Dense>
44
- {
45
- typedef const TensorForcedEvalOp<XprType>& type;
46
- };
47
-
48
- template<typename XprType>
49
- struct nested<TensorForcedEvalOp<XprType>, 1, typename eval<TensorForcedEvalOp<XprType> >::type>
50
- {
51
- typedef TensorForcedEvalOp<XprType> type;
52
- };
53
-
54
- } // end namespace internal
55
-
56
-
57
-
58
- template<typename XprType>
59
- class TensorForcedEvalOp : public TensorBase<TensorForcedEvalOp<XprType>, ReadOnlyAccessors>
60
- {
61
- public:
62
- typedef typename Eigen::internal::traits<TensorForcedEvalOp>::Scalar Scalar;
63
- typedef typename Eigen::NumTraits<Scalar>::Real RealScalar;
64
- typedef typename internal::remove_const<typename XprType::CoeffReturnType>::type CoeffReturnType;
65
- typedef typename Eigen::internal::nested<TensorForcedEvalOp>::type Nested;
66
- typedef typename Eigen::internal::traits<TensorForcedEvalOp>::StorageKind StorageKind;
67
- typedef typename Eigen::internal::traits<TensorForcedEvalOp>::Index Index;
68
-
69
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorForcedEvalOp(const XprType& expr)
70
- : m_xpr(expr) {}
71
-
72
- EIGEN_DEVICE_FUNC
73
- const typename internal::remove_all<typename XprType::Nested>::type&
74
- expression() const { return m_xpr; }
75
-
76
- protected:
77
- typename XprType::Nested m_xpr;
78
- };
79
-
80
- namespace internal {
81
- template <typename Device, typename CoeffReturnType>
82
- struct non_integral_type_placement_new{
83
- template <typename StorageType>
84
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void operator()(Index numValues, StorageType m_buffer) {
85
- // Initialize non-trivially constructible types.
86
- if (!internal::is_arithmetic<CoeffReturnType>::value) {
87
- for (Index i = 0; i < numValues; ++i) new (m_buffer + i) CoeffReturnType();
88
- }
89
- }
90
- };
91
-
92
- // SYCL does not support non-integral types
93
- // having new (m_buffer + i) CoeffReturnType() causes the following compiler error for SYCL Devices
94
- // no matching function for call to 'operator new'
95
- template <typename CoeffReturnType>
96
- struct non_integral_type_placement_new<Eigen::SyclDevice, CoeffReturnType> {
97
- template <typename StorageType>
98
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void operator()(Index, StorageType) {
99
- }
100
- };
101
- } // end namespace internal
102
-
103
- template<typename ArgType_, typename Device>
104
- struct TensorEvaluator<const TensorForcedEvalOp<ArgType_>, Device>
105
- {
106
- typedef const typename internal::remove_all<ArgType_>::type ArgType;
107
- typedef TensorForcedEvalOp<ArgType> XprType;
108
- typedef typename ArgType::Scalar Scalar;
109
- typedef typename TensorEvaluator<ArgType, Device>::Dimensions Dimensions;
110
- typedef typename XprType::Index Index;
111
- typedef typename XprType::CoeffReturnType CoeffReturnType;
112
- typedef typename PacketType<CoeffReturnType, Device>::type PacketReturnType;
113
- static const int PacketSize = PacketType<CoeffReturnType, Device>::size;
114
- typedef typename Eigen::internal::traits<XprType>::PointerType TensorPointerType;
115
- typedef StorageMemory<CoeffReturnType, Device> Storage;
116
- typedef typename Storage::Type EvaluatorPointerType;
117
-
118
- enum {
119
- IsAligned = true,
120
- PacketAccess = (PacketType<CoeffReturnType, Device>::size > 1),
121
- BlockAccess = internal::is_arithmetic<CoeffReturnType>::value,
122
- PreferBlockAccess = false,
123
- Layout = TensorEvaluator<ArgType, Device>::Layout,
124
- RawAccess = true
125
- };
126
-
127
- static const int NumDims = internal::traits<ArgType>::NumDimensions;
128
-
129
- //===- Tensor block evaluation strategy (see TensorBlock.h) -------------===//
130
- typedef internal::TensorBlockDescriptor<NumDims, Index> TensorBlockDesc;
131
- typedef internal::TensorBlockScratchAllocator<Device> TensorBlockScratch;
132
-
133
- typedef typename internal::TensorMaterializedBlock<CoeffReturnType, NumDims,
134
- Layout, Index>
135
- TensorBlock;
136
- //===--------------------------------------------------------------------===//
137
-
138
- TensorEvaluator(const XprType& op, const Device& device)
139
- : m_impl(op.expression(), device), m_op(op.expression()),
140
- m_device(device), m_buffer(NULL)
141
- { }
142
-
143
- EIGEN_DEVICE_FUNC const Dimensions& dimensions() const { return m_impl.dimensions(); }
144
-
145
- EIGEN_STRONG_INLINE bool evalSubExprsIfNeeded(EvaluatorPointerType) {
146
- const Index numValues = internal::array_prod(m_impl.dimensions());
147
- m_buffer = m_device.get((CoeffReturnType*)m_device.allocate_temp(numValues * sizeof(CoeffReturnType)));
148
-
149
- internal::non_integral_type_placement_new<Device, CoeffReturnType>()(numValues, m_buffer);
150
-
151
- typedef TensorEvalToOp< const typename internal::remove_const<ArgType>::type > EvalTo;
152
- EvalTo evalToTmp(m_device.get(m_buffer), m_op);
153
-
154
- internal::TensorExecutor<
155
- const EvalTo, typename internal::remove_const<Device>::type,
156
- /*Vectorizable=*/internal::IsVectorizable<Device, const ArgType>::value,
157
- /*Tiling=*/internal::IsTileable<Device, const ArgType>::value>::
158
- run(evalToTmp, m_device);
159
-
160
- return true;
161
- }
162
-
163
- #ifdef EIGEN_USE_THREADS
164
- template <typename EvalSubExprsCallback>
165
- EIGEN_STRONG_INLINE void evalSubExprsIfNeededAsync(
166
- EvaluatorPointerType, EvalSubExprsCallback done) {
167
- const Index numValues = internal::array_prod(m_impl.dimensions());
168
- m_buffer = m_device.get((CoeffReturnType*)m_device.allocate_temp(
169
- numValues * sizeof(CoeffReturnType)));
170
- typedef TensorEvalToOp<const typename internal::remove_const<ArgType>::type>
171
- EvalTo;
172
- EvalTo evalToTmp(m_device.get(m_buffer), m_op);
173
-
174
- auto on_done = std::bind([](EvalSubExprsCallback done_) { done_(true); },
175
- std::move(done));
176
- internal::TensorAsyncExecutor<
177
- const EvalTo, typename internal::remove_const<Device>::type,
178
- decltype(on_done),
179
- /*Vectorizable=*/internal::IsVectorizable<Device, const ArgType>::value,
180
- /*Tiling=*/internal::IsTileable<Device, const ArgType>::value>::
181
- runAsync(evalToTmp, m_device, std::move(on_done));
182
- }
183
- #endif
184
-
185
- EIGEN_STRONG_INLINE void cleanup() {
186
- m_device.deallocate_temp(m_buffer);
187
- m_buffer = NULL;
188
- }
189
-
190
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE CoeffReturnType coeff(Index index) const
191
- {
192
- return m_buffer[index];
193
- }
194
-
195
- template<int LoadMode>
196
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE PacketReturnType packet(Index index) const
197
- {
198
- return internal::ploadt<PacketReturnType, LoadMode>(m_buffer + index);
199
- }
200
-
201
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
202
- internal::TensorBlockResourceRequirements getResourceRequirements() const {
203
- return internal::TensorBlockResourceRequirements::any();
204
- }
205
-
206
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorBlock
207
- block(TensorBlockDesc& desc, TensorBlockScratch& scratch,
208
- bool /*root_of_expr_ast*/ = false) const {
209
- assert(m_buffer != NULL);
210
- return TensorBlock::materialize(m_buffer, m_impl.dimensions(), desc, scratch);
211
- }
212
-
213
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorOpCost costPerCoeff(bool vectorized) const {
214
- return TensorOpCost(sizeof(CoeffReturnType), 0, 0, vectorized, PacketSize);
215
- }
216
-
217
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
218
- EvaluatorPointerType data() const { return m_buffer; }
219
-
220
- #ifdef EIGEN_USE_SYCL
221
- // binding placeholder accessors to a command group handler for SYCL
222
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void bind(cl::sycl::handler &cgh) const {
223
- m_buffer.bind(cgh);
224
- m_impl.bind(cgh);
225
- }
226
- #endif
227
- private:
228
- TensorEvaluator<ArgType, Device> m_impl;
229
- const ArgType m_op;
230
- const Device EIGEN_DEVICE_REF m_device;
231
- EvaluatorPointerType m_buffer;
232
- };
233
-
234
-
235
- } // end namespace Eigen
236
-
237
- #endif // EIGEN_CXX11_TENSOR_TENSOR_FORCED_EVAL_H