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

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Potentially problematic release.


This version of sequenzo might be problematic. Click here for more details.

Files changed (423) hide show
  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
  209. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_relax_snode.h +0 -83
  210. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseQR/SparseQR.h +0 -758
  211. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdDeque.h +0 -116
  212. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdList.h +0 -106
  213. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdVector.h +0 -131
  214. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/details.h +0 -84
  215. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SuperLUSupport/SuperLUSupport.h +0 -1025
  216. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/UmfPackSupport/UmfPackSupport.h +0 -642
  217. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Image.h +0 -82
  218. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Kernel.h +0 -79
  219. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/RealSvd2x2.h +0 -55
  220. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/blas.h +0 -440
  221. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapack.h +0 -152
  222. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke.h +0 -16292
  223. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke_mangling.h +0 -17
  224. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseBinaryOps.h +0 -358
  225. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseUnaryOps.h +0 -696
  226. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/BlockMethods.h +0 -1442
  227. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseBinaryOps.h +0 -115
  228. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseUnaryOps.h +0 -177
  229. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/IndexedViewMethods.h +0 -262
  230. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h +0 -152
  231. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h +0 -95
  232. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ReshapedMethods.h +0 -149
  233. sequenzo/dissimilarity_measures/src/eigen/blas/BandTriangularSolver.h +0 -97
  234. sequenzo/dissimilarity_measures/src/eigen/blas/GeneralRank1Update.h +0 -44
  235. sequenzo/dissimilarity_measures/src/eigen/blas/PackedSelfadjointProduct.h +0 -53
  236. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularMatrixVector.h +0 -79
  237. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularSolverVector.h +0 -88
  238. sequenzo/dissimilarity_measures/src/eigen/blas/Rank2Update.h +0 -57
  239. sequenzo/dissimilarity_measures/src/eigen/blas/common.h +0 -175
  240. sequenzo/dissimilarity_measures/src/eigen/blas/f2c/datatypes.h +0 -24
  241. sequenzo/dissimilarity_measures/src/eigen/blas/level1_cplx_impl.h +0 -155
  242. sequenzo/dissimilarity_measures/src/eigen/blas/level1_impl.h +0 -144
  243. sequenzo/dissimilarity_measures/src/eigen/blas/level1_real_impl.h +0 -122
  244. sequenzo/dissimilarity_measures/src/eigen/blas/level2_cplx_impl.h +0 -360
  245. sequenzo/dissimilarity_measures/src/eigen/blas/level2_impl.h +0 -553
  246. sequenzo/dissimilarity_measures/src/eigen/blas/level2_real_impl.h +0 -306
  247. sequenzo/dissimilarity_measures/src/eigen/blas/level3_impl.h +0 -702
  248. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/__init__.py +0 -1
  249. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/printers.py +0 -314
  250. sequenzo/dissimilarity_measures/src/eigen/lapack/lapack_common.h +0 -29
  251. sequenzo/dissimilarity_measures/src/eigen/scripts/relicense.py +0 -69
  252. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/Tensor.h +0 -554
  253. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorArgMax.h +0 -329
  254. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorAssign.h +0 -247
  255. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBase.h +0 -1176
  256. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBlock.h +0 -1559
  257. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBroadcasting.h +0 -1093
  258. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorChipping.h +0 -518
  259. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConcatenation.h +0 -377
  260. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContraction.h +0 -1023
  261. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionBlocking.h +0 -73
  262. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionCuda.h +0 -6
  263. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionGpu.h +0 -1413
  264. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionMapper.h +0 -575
  265. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionSycl.h +0 -1650
  266. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionThreadPool.h +0 -1679
  267. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConversion.h +0 -456
  268. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConvolution.h +0 -1132
  269. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConvolutionSycl.h +0 -544
  270. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorCostModel.h +0 -214
  271. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorCustomOp.h +0 -347
  272. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDevice.h +0 -137
  273. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceCuda.h +0 -6
  274. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceDefault.h +0 -104
  275. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceGpu.h +0 -389
  276. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceSycl.h +0 -1048
  277. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceThreadPool.h +0 -409
  278. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDimensionList.h +0 -236
  279. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDimensions.h +0 -490
  280. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorEvalTo.h +0 -236
  281. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorEvaluator.h +0 -983
  282. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorExecutor.h +0 -703
  283. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorExpr.h +0 -388
  284. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorFFT.h +0 -669
  285. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorFixedSize.h +0 -379
  286. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorForcedEval.h +0 -237
  287. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorForwardDeclarations.h +0 -191
  288. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorFunctors.h +0 -488
  289. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorGenerator.h +0 -302
  290. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorGlobalFunctions.h +0 -33
  291. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorGpuHipCudaDefines.h +0 -99
  292. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorGpuHipCudaUndefines.h +0 -44
  293. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorIO.h +0 -79
  294. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorImagePatch.h +0 -603
  295. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorIndexList.h +0 -738
  296. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorInflation.h +0 -247
  297. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorInitializer.h +0 -82
  298. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorIntDiv.h +0 -263
  299. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorLayoutSwap.h +0 -216
  300. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorMacros.h +0 -98
  301. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorMap.h +0 -327
  302. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorMeta.h +0 -311
  303. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorMorphing.h +0 -1102
  304. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorPadding.h +0 -708
  305. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorPatch.h +0 -291
  306. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorRandom.h +0 -322
  307. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReduction.h +0 -998
  308. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReductionCuda.h +0 -6
  309. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReductionGpu.h +0 -966
  310. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReductionSycl.h +0 -582
  311. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorRef.h +0 -454
  312. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReverse.h +0 -465
  313. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorScan.h +0 -528
  314. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorScanSycl.h +0 -513
  315. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorShuffling.h +0 -471
  316. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorStorage.h +0 -161
  317. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorStriding.h +0 -346
  318. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorTrace.h +0 -303
  319. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorTraits.h +0 -264
  320. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorUInt128.h +0 -249
  321. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorVolumePatch.h +0 -629
  322. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/TensorSymmetry/DynamicSymmetry.h +0 -293
  323. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/TensorSymmetry/StaticSymmetry.h +0 -236
  324. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/TensorSymmetry/Symmetry.h +0 -338
  325. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/TensorSymmetry/util/TemplateGroupTheory.h +0 -669
  326. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/Barrier.h +0 -67
  327. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/EventCount.h +0 -249
  328. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/NonBlockingThreadPool.h +0 -486
  329. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/RunQueue.h +0 -236
  330. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadCancel.h +0 -23
  331. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadEnvironment.h +0 -40
  332. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadLocal.h +0 -301
  333. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadPoolInterface.h +0 -48
  334. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadYield.h +0 -20
  335. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/util/CXX11Meta.h +0 -537
  336. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/util/CXX11Workarounds.h +0 -88
  337. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/util/EmulateArray.h +0 -261
  338. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/util/MaxSizeVector.h +0 -158
  339. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/AutoDiff/AutoDiffJacobian.h +0 -108
  340. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/AutoDiff/AutoDiffScalar.h +0 -730
  341. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/AutoDiff/AutoDiffVector.h +0 -220
  342. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/BVH/BVAlgorithms.h +0 -293
  343. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/BVH/KdBVH.h +0 -223
  344. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Eigenvalues/ArpackSelfAdjointEigenSolver.h +0 -790
  345. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/EulerAngles/EulerAngles.h +0 -355
  346. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/EulerAngles/EulerSystem.h +0 -305
  347. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/FFT/ei_fftw_impl.h +0 -261
  348. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/FFT/ei_kissfft_impl.h +0 -449
  349. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h +0 -187
  350. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/DGMRES.h +0 -511
  351. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/GMRES.h +0 -335
  352. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/IDRS.h +0 -436
  353. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/IncompleteLU.h +0 -90
  354. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/IterationController.h +0 -154
  355. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/MINRES.h +0 -267
  356. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/Scaling.h +0 -193
  357. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/KroneckerProduct/KroneckerTensorProduct.h +0 -305
  358. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LMcovar.h +0 -84
  359. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LMonestep.h +0 -202
  360. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LMpar.h +0 -160
  361. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LMqrsolv.h +0 -188
  362. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LevenbergMarquardt.h +0 -396
  363. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixExponential.h +0 -441
  364. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixFunction.h +0 -569
  365. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixLogarithm.h +0 -373
  366. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixPower.h +0 -705
  367. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixSquareRoot.h +0 -368
  368. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/StemFunction.h +0 -117
  369. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MoreVectorization/MathFunctions.h +0 -95
  370. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/HybridNonLinearSolver.h +0 -601
  371. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/LevenbergMarquardt.h +0 -657
  372. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/chkder.h +0 -66
  373. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/covar.h +0 -70
  374. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/dogleg.h +0 -107
  375. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/fdjac1.h +0 -79
  376. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/lmpar.h +0 -298
  377. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/qrsolv.h +0 -91
  378. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/r1mpyq.h +0 -30
  379. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/r1updt.h +0 -99
  380. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/rwupdt.h +0 -49
  381. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NumericalDiff/NumericalDiff.h +0 -130
  382. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/Companion.h +0 -280
  383. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/PolynomialSolver.h +0 -428
  384. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/PolynomialUtils.h +0 -143
  385. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineInplaceLU.h +0 -352
  386. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineMatrix.h +0 -862
  387. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineMatrixBase.h +0 -212
  388. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineProduct.h +0 -295
  389. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineStorage.h +0 -259
  390. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineUtil.h +0 -89
  391. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/BlockOfDynamicSparseMatrix.h +0 -122
  392. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/BlockSparseMatrix.h +0 -1079
  393. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/DynamicSparseMatrix.h +0 -404
  394. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/MarketIO.h +0 -282
  395. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h +0 -247
  396. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/RandomSetter.h +0 -349
  397. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsArrayAPI.h +0 -286
  398. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsBFloat16.h +0 -68
  399. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsFunctors.h +0 -357
  400. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsHalf.h +0 -66
  401. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsImpl.h +0 -1959
  402. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsPacketMath.h +0 -118
  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
@@ -1,575 +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_CONTRACTION_MAPPER_H
11
- #define EIGEN_CXX11_TENSOR_TENSOR_CONTRACTION_MAPPER_H
12
-
13
- namespace Eigen {
14
-
15
- namespace internal {
16
-
17
- enum {
18
- Rhs = 0,
19
- Lhs = 1
20
- };
21
-
22
- /*
23
- * Implementation of the Eigen blas_data_mapper class for tensors.
24
- */
25
- /// The make pointer class is used by sycl in order to build the mapper class on the device. For other platform the default make pointer is used which
26
- /// is scalar * for CoeffLoader.
27
- template <typename Tensor, bool HasRawAccess, template <class> class MakePointer_ = MakePointer>
28
- struct CoeffLoader;
29
-
30
- template <typename Scalar, typename Index, int side, typename Tensor,
31
- typename nocontract_t, typename contract_t, int packet_size,
32
- bool inner_dim_contiguous, bool inner_dim_reordered, int Alignment,
33
- template <class> class MakePointer_ = MakePointer>
34
- class BaseTensorContractionMapper;
35
-
36
- template <typename Tensor, bool HasRawAccess, template <class> class MakePointer_>
37
- struct CoeffLoader {
38
- enum {
39
- DirectOffsets = false
40
- };
41
-
42
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE CoeffLoader(const Tensor& tensor) : m_tensor(tensor) { }
43
-
44
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE void offsetBuffer(typename Tensor::Index) {
45
- eigen_assert(false && "unsupported");
46
- }
47
-
48
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE const typename MakePointer_<const typename Tensor::Scalar>::Type
49
- data() const {
50
- eigen_assert(false && "unsupported");
51
- return NULL;
52
- }
53
-
54
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE typename Tensor::Scalar coeff(typename Tensor::Index index) const { return m_tensor.coeff(index); }
55
-
56
- template<int LoadMode> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
57
- typename Tensor::PacketReturnType packet(typename Tensor::Index index) const
58
- {
59
- return m_tensor.template packet<LoadMode>(index);
60
- }
61
-
62
- #ifdef EIGEN_USE_SYCL
63
- // The placeholder accessors require to be bound to a command group handler for SYCL
64
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void bind(cl::sycl::handler &cgh) const {
65
- m_tensor.bind(cgh);
66
- }
67
- #endif
68
-
69
- private:
70
- const Tensor m_tensor;
71
- };
72
-
73
- template <typename Tensor, template <class> class MakePointer_>
74
- struct CoeffLoader<Tensor, true, MakePointer_> {
75
- enum {
76
- DirectOffsets = true
77
- };
78
-
79
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE CoeffLoader(const Tensor& tensor) : m_data(tensor.data()) {}
80
-
81
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE void offsetBuffer(typename Tensor::Index offset) {
82
- m_data += offset;
83
- }
84
-
85
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE const typename MakePointer_<const typename Tensor::Scalar>::Type
86
- data() const {
87
- return m_data;
88
- }
89
-
90
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE typename Tensor::Scalar coeff(typename Tensor::Index index) const { return loadConstant(m_data+index); }
91
-
92
- template<int LoadMode> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
93
- typename Tensor::PacketReturnType packet(typename Tensor::Index index) const
94
- {
95
- return internal::ploadt_ro<typename Tensor::PacketReturnType, LoadMode>(m_data + index);
96
- }
97
-
98
- #ifdef EIGEN_USE_SYCL
99
- // The placeholder accessors require to be bound to a command group handler for SYCL
100
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void bind(cl::sycl::handler &cgh) const {
101
- m_data.bind(cgh);
102
- }
103
- #endif
104
- private:
105
- typedef typename Tensor::Scalar Scalar;
106
-
107
- typename MakePointer_<const Scalar>::Type m_data;
108
- };
109
-
110
- template<typename Scalar, typename Index, int side,
111
- typename Tensor,
112
- typename nocontract_t, typename contract_t,
113
- int packet_size, bool inner_dim_contiguous, int Alignment, template <class> class MakePointer_ = MakePointer>
114
- class SimpleTensorContractionMapper {
115
- public:
116
- EIGEN_DEVICE_FUNC
117
- SimpleTensorContractionMapper(const Tensor& tensor,
118
- const nocontract_t& nocontract_strides,
119
- const nocontract_t& ij_strides,
120
- const contract_t& contract_strides,
121
- const contract_t& k_strides) :
122
- m_tensor(tensor),
123
- m_nocontract_strides(nocontract_strides),
124
- m_ij_strides(ij_strides),
125
- m_contract_strides(contract_strides),
126
- m_k_strides(k_strides) { }
127
-
128
- enum {
129
- DirectOffsets = CoeffLoader<Tensor, Tensor::RawAccess, MakePointer_>::DirectOffsets
130
- };
131
-
132
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE void offsetBuffer(typename Tensor::Index offset) {
133
- m_tensor.offsetBuffer(offset);
134
- }
135
-
136
- EIGEN_DEVICE_FUNC
137
- EIGEN_STRONG_INLINE void prefetch(Index /*i*/) { }
138
-
139
- EIGEN_DEVICE_FUNC
140
- EIGEN_STRONG_INLINE Scalar operator()(Index row) const {
141
- // column major assumption
142
- return operator()(row, 0);
143
- }
144
-
145
- EIGEN_DEVICE_FUNC
146
- EIGEN_STRONG_INLINE Scalar operator()(Index row, Index col) const {
147
- return m_tensor.coeff(computeIndex(row, col));
148
- }
149
-
150
- EIGEN_DEVICE_FUNC
151
- EIGEN_STRONG_INLINE Index computeIndex(Index row, Index col) const {
152
- const bool left = (side == Lhs);
153
- EIGEN_UNUSED_VARIABLE(left); // annoying bug in g++8.1: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=85963
154
- Index nocontract_val = left ? row : col;
155
- Index linidx = 0;
156
- EIGEN_UNROLL_LOOP
157
- for (int i = static_cast<int>(array_size<nocontract_t>::value) - 1; i > 0; i--) {
158
- const Index idx = nocontract_val / m_ij_strides[i];
159
- linidx += idx * m_nocontract_strides[i];
160
- nocontract_val -= idx * m_ij_strides[i];
161
- }
162
- if (array_size<typename Tensor::Dimensions>::value > array_size<contract_t>::value) {
163
- if (side == Lhs && inner_dim_contiguous) {
164
- eigen_assert(m_nocontract_strides[0] == 1);
165
- linidx += nocontract_val;
166
- } else {
167
- linidx += nocontract_val * m_nocontract_strides[0];
168
- }
169
- }
170
-
171
- Index contract_val = left ? col : row;
172
- if(array_size<contract_t>::value > 0) {
173
- EIGEN_UNROLL_LOOP
174
- for (int i = static_cast<int>(array_size<contract_t>::value) - 1; i > 0; i--) {
175
- const Index idx = contract_val / m_k_strides[i];
176
- linidx += idx * m_contract_strides[i];
177
- contract_val -= idx * m_k_strides[i];
178
- }
179
-
180
- if (side == Rhs && inner_dim_contiguous) {
181
- eigen_assert(m_contract_strides[0] == 1);
182
- linidx += contract_val;
183
- } else {
184
- linidx += contract_val * m_contract_strides[0];
185
- }
186
- }
187
-
188
- return linidx;
189
- }
190
-
191
- EIGEN_DEVICE_FUNC
192
- EIGEN_STRONG_INLINE IndexPair<Index> computeIndexPair(Index row, Index col, const Index distance) const {
193
- const bool left = (side == Lhs);
194
- EIGEN_UNUSED_VARIABLE(left); // annoying bug in g++8.1: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=85963
195
- Index nocontract_val[2] = {left ? row : col, left ? row + distance : col};
196
- Index linidx[2] = {0, 0};
197
- if (array_size<typename Tensor::Dimensions>::value > array_size<contract_t>::value) {
198
- EIGEN_UNROLL_LOOP
199
- for (int i = static_cast<int>(array_size<nocontract_t>::value) - 1; i > 0; i--) {
200
- const Index idx0 = nocontract_val[0] / m_ij_strides[i];
201
- const Index idx1 = nocontract_val[1] / m_ij_strides[i];
202
- linidx[0] += idx0 * m_nocontract_strides[i];
203
- linidx[1] += idx1 * m_nocontract_strides[i];
204
- nocontract_val[0] -= idx0 * m_ij_strides[i];
205
- nocontract_val[1] -= idx1 * m_ij_strides[i];
206
- }
207
- if (side == Lhs && inner_dim_contiguous) {
208
- eigen_assert(m_nocontract_strides[0] == 1);
209
- linidx[0] += nocontract_val[0];
210
- linidx[1] += nocontract_val[1];
211
- } else {
212
- linidx[0] += nocontract_val[0] * m_nocontract_strides[0];
213
- linidx[1] += nocontract_val[1] * m_nocontract_strides[0];
214
- }
215
- }
216
-
217
- Index contract_val[2] = {left ? col : row, left ? col : row + distance};
218
- if (array_size<contract_t>::value> 0) {
219
- EIGEN_UNROLL_LOOP
220
- for (int i = static_cast<int>(array_size<contract_t>::value) - 1; i > 0; i--) {
221
- const Index idx0 = contract_val[0] / m_k_strides[i];
222
- const Index idx1 = contract_val[1] / m_k_strides[i];
223
- linidx[0] += idx0 * m_contract_strides[i];
224
- linidx[1] += idx1 * m_contract_strides[i];
225
- contract_val[0] -= idx0 * m_k_strides[i];
226
- contract_val[1] -= idx1 * m_k_strides[i];
227
- }
228
-
229
- if (side == Rhs && inner_dim_contiguous) {
230
- eigen_assert(m_contract_strides[0] == 1);
231
- linidx[0] += contract_val[0];
232
- linidx[1] += contract_val[1];
233
- } else {
234
- linidx[0] += contract_val[0] * m_contract_strides[0];
235
- linidx[1] += contract_val[1] * m_contract_strides[0];
236
- }
237
- }
238
- return IndexPair<Index>(linidx[0], linidx[1]);
239
- }
240
-
241
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE Index firstAligned(Index size) const {
242
- // Only claim alignment when we can compute the actual stride (ie when we're
243
- // dealing with the lhs with inner_dim_contiguous. This is because the
244
- // matrix-vector product relies on the stride when dealing with aligned inputs.
245
- return (Alignment == Aligned) && (side == Lhs) && inner_dim_contiguous ? 0 : size;
246
- }
247
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE Index stride() const {
248
- return ((side == Lhs) && inner_dim_contiguous && array_size<contract_t>::value > 0) ? m_contract_strides[0] : 1;
249
- }
250
-
251
- #ifdef EIGEN_USE_SYCL
252
- // The placeholder accessors require to be bound to a command group handler for SYCL
253
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void bind(cl::sycl::handler &cgh) const {
254
- m_tensor.bind(cgh);
255
- }
256
- #endif
257
-
258
- const CoeffLoader<Tensor, Tensor::RawAccess, MakePointer_>& tensor() const {
259
- return m_tensor;
260
- }
261
-
262
- const nocontract_t& nocontract_strides() const {
263
- return m_nocontract_strides;
264
- }
265
- const nocontract_t& ij_strides() const { return m_ij_strides; }
266
- const contract_t& contract_strides() const { return m_contract_strides; }
267
- const contract_t& k_strides() const { return m_k_strides; }
268
-
269
- protected:
270
- CoeffLoader<Tensor, Tensor::RawAccess, MakePointer_> m_tensor;
271
- const nocontract_t m_nocontract_strides;
272
- const nocontract_t m_ij_strides;
273
- const contract_t m_contract_strides;
274
- const contract_t m_k_strides;
275
- };
276
-
277
- template<typename Scalar, typename Index, int side,
278
- typename Tensor,
279
- typename nocontract_t, typename contract_t,
280
- int packet_size, bool inner_dim_contiguous,
281
- bool inner_dim_reordered, int Alignment, template <class> class MakePointer_>
282
- class BaseTensorContractionMapper : public SimpleTensorContractionMapper<Scalar, Index, side, Tensor, nocontract_t, contract_t, packet_size, inner_dim_contiguous, Alignment, MakePointer_>
283
- {
284
- public:
285
- typedef SimpleTensorContractionMapper<Scalar, Index, side, Tensor, nocontract_t, contract_t, packet_size, inner_dim_contiguous, Alignment, MakePointer_> ParentMapper;
286
-
287
- EIGEN_DEVICE_FUNC
288
- BaseTensorContractionMapper(const Tensor& tensor,
289
- const nocontract_t& nocontract_strides,
290
- const nocontract_t& ij_strides,
291
- const contract_t& contract_strides,
292
- const contract_t& k_strides) :
293
- ParentMapper(tensor, nocontract_strides, ij_strides, contract_strides, k_strides) { }
294
-
295
- template <typename PacketT,int AlignmentType>
296
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
297
- typename internal::enable_if<internal::unpacket_traits<PacketT>::size==packet_size,PacketT>::type
298
- load(Index i, Index j) const
299
- {
300
- // whole method makes column major assumption
301
-
302
- // don't need to add offsets for now (because operator handles that)
303
- // current code assumes packet size must be a multiple of 2
304
- EIGEN_STATIC_ASSERT(packet_size % 2 == 0, YOU_MADE_A_PROGRAMMING_MISTAKE);
305
-
306
- if (Tensor::PacketAccess && inner_dim_contiguous && !inner_dim_reordered) {
307
- const Index index = this->computeIndex(i, j);
308
- eigen_assert(this->computeIndex(i+packet_size-1, j) == index + packet_size-1);
309
- return this->m_tensor.template packet<AlignmentType>(index);
310
- }
311
-
312
- const IndexPair<Index> indexPair = this->computeIndexPair(i, j, packet_size - 1);
313
- const Index first = indexPair.first;
314
- const Index lastIdx = indexPair.second;
315
-
316
- // We can always do optimized packet reads from left hand side right now, because
317
- // the vertical matrix dimension on the left hand side is never contracting.
318
- // On the right hand side we need to check if the contracting dimensions may have
319
- // been shuffled first.
320
- if (Tensor::PacketAccess &&
321
- (side == Lhs || internal::array_size<contract_t>::value <= 1 || !inner_dim_reordered) &&
322
- (lastIdx - first) == (packet_size - 1)) {
323
-
324
- return this->m_tensor.template packet<AlignmentType>(first);
325
- }
326
-
327
- EIGEN_ALIGN_MAX Scalar data[packet_size];
328
-
329
- data[0] = this->m_tensor.coeff(first);
330
- EIGEN_UNROLL_LOOP
331
- for (Index k = 1; k < packet_size - 1; k += 2) {
332
- const IndexPair<Index> internal_pair = this->computeIndexPair(i + k, j, 1);
333
- data[k] = this->m_tensor.coeff(internal_pair.first);
334
- data[k + 1] = this->m_tensor.coeff(internal_pair.second);
335
- }
336
- data[packet_size - 1] = this->m_tensor.coeff(lastIdx);
337
-
338
- return pload<PacketT>(data);
339
- }
340
-
341
- template <typename PacketT,int AlignmentType>
342
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
343
- typename internal::enable_if<internal::unpacket_traits<PacketT>::size!=packet_size,PacketT>::type
344
- load(Index i, Index j) const
345
- {
346
- const Index requested_packet_size = internal::unpacket_traits<PacketT>::size;
347
- EIGEN_ALIGN_MAX Scalar data[requested_packet_size];
348
-
349
- const IndexPair<Index> indexPair = this->computeIndexPair(i, j, requested_packet_size - 1);
350
- const Index first = indexPair.first;
351
- const Index lastIdx = indexPair.second;
352
-
353
- data[0] = this->m_tensor.coeff(first);
354
- for (Index k = 1; k < requested_packet_size - 1; k += 2) {
355
- const IndexPair<Index> internal_pair = this->computeIndexPair(i + k, j, 1);
356
- data[k] = this->m_tensor.coeff(internal_pair.first);
357
- data[k + 1] = this->m_tensor.coeff(internal_pair.second);
358
- }
359
- data[requested_packet_size - 1] = this->m_tensor.coeff(lastIdx);
360
-
361
- return pload<PacketT>(data);
362
- }
363
-
364
- template <typename PacketT,int AlignmentType>
365
- EIGEN_DEVICE_FUNC
366
- EIGEN_STRONG_INLINE PacketT loadPacket(Index i, Index j) const {
367
- return this->load<PacketT,AlignmentType>(i,j);
368
- }
369
- };
370
-
371
-
372
- template<typename Scalar, typename Index, int side,
373
- typename Tensor,
374
- typename nocontract_t, typename contract_t,
375
- bool inner_dim_contiguous,
376
- bool inner_dim_reordered, int Alignment, template <class> class MakePointer_>
377
- class BaseTensorContractionMapper<Scalar, Index, side, Tensor, nocontract_t, contract_t, 1, inner_dim_contiguous, inner_dim_reordered, Alignment, MakePointer_>
378
- : public SimpleTensorContractionMapper<Scalar, Index, side, Tensor, nocontract_t, contract_t, 1, inner_dim_contiguous, Alignment, MakePointer_>
379
- {
380
- public:
381
- typedef SimpleTensorContractionMapper<Scalar, Index, side, Tensor, nocontract_t, contract_t, 1, inner_dim_contiguous, Alignment, MakePointer_> ParentMapper;
382
-
383
- EIGEN_DEVICE_FUNC
384
- BaseTensorContractionMapper(const Tensor& tensor,
385
- const nocontract_t& nocontract_strides,
386
- const nocontract_t& ij_strides,
387
- const contract_t& contract_strides,
388
- const contract_t& k_strides) :
389
- ParentMapper(tensor, nocontract_strides, ij_strides, contract_strides, k_strides) { }
390
-
391
- template <typename PacketT,int> EIGEN_DEVICE_FUNC
392
- EIGEN_STRONG_INLINE PacketT loadPacket(Index i, Index j) const {
393
- EIGEN_ALIGN_MAX Scalar data[1];
394
- data[0] = this->m_tensor.coeff(this->computeIndex(i, j));
395
- return pload<PacketT>(data);
396
- }
397
- template <typename PacketT,int> EIGEN_DEVICE_FUNC
398
- EIGEN_STRONG_INLINE PacketT load(Index i, Index j) const {
399
- EIGEN_ALIGN_MAX Scalar data[1];
400
- data[0] = this->m_tensor.coeff(this->computeIndex(i, j));
401
- return pload<PacketT>(data);
402
- }
403
- };
404
-
405
-
406
- template<typename Scalar, typename Index, int side,
407
- typename Tensor,
408
- typename nocontract_t, typename contract_t,
409
- int packet_size,
410
- bool inner_dim_contiguous, bool inner_dim_reordered, int Alignment, template <class> class MakePointer_=MakePointer>
411
- class TensorContractionSubMapper {
412
- public:
413
-
414
- typedef BaseTensorContractionMapper<Scalar, Index, side, Tensor, nocontract_t, contract_t, packet_size, inner_dim_contiguous, inner_dim_reordered, Alignment, MakePointer_> ParentMapper;
415
- typedef TensorContractionSubMapper<Scalar, Index, side, Tensor, nocontract_t, contract_t, packet_size, inner_dim_contiguous, inner_dim_reordered, Alignment, MakePointer_> Self;
416
- typedef Self LinearMapper;
417
-
418
- enum {
419
- // We can use direct offsets iff the parent mapper supports then and we can compute the strides.
420
- // TODO: we should also enable direct offsets for the Rhs case.
421
- UseDirectOffsets = ParentMapper::DirectOffsets && (side == Lhs) && inner_dim_contiguous && (array_size<contract_t>::value > 0)
422
- };
423
-
424
- EIGEN_DEVICE_FUNC TensorContractionSubMapper(const ParentMapper& base_mapper, Index vert_offset, Index horiz_offset)
425
- : m_base_mapper(base_mapper), m_vert_offset(vert_offset), m_horiz_offset(horiz_offset) {
426
- // Bake the offsets into the buffer used by the base mapper whenever possible. This avoids the need to recompute
427
- // this offset every time we attempt to access a coefficient.
428
- if (UseDirectOffsets) {
429
- Index stride = m_base_mapper.stride();
430
- m_base_mapper.offsetBuffer(vert_offset + horiz_offset * stride);
431
- }
432
- }
433
-
434
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE Scalar operator()(Index i) const {
435
- if (UseDirectOffsets) {
436
- return m_base_mapper(i, 0);
437
- }
438
- return m_base_mapper(i + m_vert_offset, m_horiz_offset);
439
- }
440
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE Scalar operator()(Index i, Index j) const {
441
- if (UseDirectOffsets) {
442
- return m_base_mapper(i, j);
443
- }
444
- return m_base_mapper(i + m_vert_offset, j + m_horiz_offset);
445
- }
446
-
447
- template <typename PacketT>
448
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE PacketT loadPacket(Index i) const {
449
- if (UseDirectOffsets) {
450
- return m_base_mapper.template loadPacket<PacketT,Alignment>(i, 0);
451
- }
452
- return m_base_mapper.template loadPacket<PacketT,Alignment>(i + m_vert_offset, m_horiz_offset);
453
- }
454
-
455
- template <typename PacketT>
456
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE PacketT loadPacket(Index i, Index j) const {
457
- if (UseDirectOffsets) {
458
- return m_base_mapper.template loadPacket<PacketT,Alignment>(i, j);
459
- }
460
- return m_base_mapper.template loadPacket<PacketT,Alignment>(i + m_vert_offset, j + m_horiz_offset);
461
- }
462
-
463
- template <typename PacketT, int AlignmentType>
464
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE PacketT loadPacket(Index i, Index j) const {
465
- if (UseDirectOffsets) {
466
- return m_base_mapper.template load<PacketT,AlignmentType>(i, j);
467
- }
468
- return m_base_mapper.template loadPacket<PacketT,AlignmentType>(i + m_vert_offset, j + m_horiz_offset);
469
- }
470
-
471
- template <typename PacketT>
472
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE void storePacket(Index i, const PacketT& p) const {
473
- if (UseDirectOffsets) {
474
- m_base_mapper.storePacket(i, 0, p);
475
- }
476
- m_base_mapper.storePacket(i + m_vert_offset, m_horiz_offset, p);
477
- }
478
-
479
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE LinearMapper getLinearMapper(Index i, Index j) const {
480
- if (UseDirectOffsets) {
481
- return LinearMapper(m_base_mapper, i, j);
482
- }
483
- return LinearMapper(m_base_mapper, i + m_vert_offset, j + m_horiz_offset);
484
- }
485
-
486
- template <typename PacketT, int AlignmentType>
487
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE PacketT load(Index i) const {
488
- EIGEN_STATIC_ASSERT((internal::is_same<PacketT, PacketT>::value), YOU_MADE_A_PROGRAMMING_MISTAKE);
489
- const int ActualAlignment = (AlignmentType == Aligned) && (Alignment == Aligned) ? Aligned : Unaligned;
490
- if (UseDirectOffsets) {
491
- return m_base_mapper.template loadPacket<PacketT,ActualAlignment>(i, 0);
492
- }
493
- return m_base_mapper.template loadPacket<PacketT,ActualAlignment>(i + m_vert_offset, m_horiz_offset);
494
- }
495
-
496
- template <typename PacketT>
497
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE bool aligned(Index) const {
498
- return false;
499
- }
500
-
501
- #ifdef EIGEN_USE_SYCL
502
- // The placeholder accessors require to be bound to a command group handler for SYCL
503
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void bind(cl::sycl::handler &cgh) const {
504
- m_base_mapper.bind(cgh);
505
- }
506
- #endif
507
-
508
- const ParentMapper& base_mapper() const { return m_base_mapper; }
509
- Index vert_offset() const { return m_vert_offset; }
510
- Index horiz_offset() const { return m_horiz_offset; }
511
-
512
- private:
513
- ParentMapper m_base_mapper;
514
- const Index m_vert_offset;
515
- const Index m_horiz_offset;
516
- };
517
-
518
-
519
- template<typename Scalar_, typename Index, int side,
520
- typename Tensor,
521
- typename nocontract_t, typename contract_t,
522
- int packet_size,
523
- bool inner_dim_contiguous, bool inner_dim_reordered, int Alignment, template <class> class MakePointer_=MakePointer>
524
- class TensorContractionInputMapper
525
- : public BaseTensorContractionMapper<Scalar_, Index, side, Tensor, nocontract_t, contract_t, packet_size, inner_dim_contiguous, inner_dim_reordered, Alignment, MakePointer_> {
526
-
527
- public:
528
- typedef Scalar_ Scalar;
529
- typedef BaseTensorContractionMapper<Scalar, Index, side, Tensor, nocontract_t, contract_t, packet_size, inner_dim_contiguous, inner_dim_reordered, Alignment, MakePointer_> Base;
530
- typedef TensorContractionSubMapper<Scalar, Index, side, Tensor, nocontract_t, contract_t, packet_size, inner_dim_contiguous, inner_dim_reordered, Alignment, MakePointer_> SubMapper;
531
- typedef SubMapper VectorMapper;
532
-
533
- EIGEN_DEVICE_FUNC TensorContractionInputMapper(const Tensor& tensor,
534
- const nocontract_t& nocontract_strides,
535
- const nocontract_t& ij_strides,
536
- const contract_t& contract_strides,
537
- const contract_t& k_strides)
538
- : Base(tensor, nocontract_strides, ij_strides, contract_strides, k_strides) { }
539
-
540
- EIGEN_DEVICE_FUNC
541
- EIGEN_STRONG_INLINE SubMapper getSubMapper(Index i, Index j) const {
542
- return SubMapper(*this, i, j);
543
- }
544
-
545
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE VectorMapper getVectorMapper(Index i, Index j) const {
546
- return VectorMapper(*this, i, j);
547
- }
548
-
549
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE const CoeffLoader<Tensor, Tensor::RawAccess, MakePointer_>& get_tensor() const {
550
- return Base::m_tensor;
551
- }
552
- };
553
-
554
-
555
- template <typename T> struct TensorContractionInputMapperTrait;
556
-
557
- template<typename Scalar_, typename Index_, int side_,
558
- typename Tensor_,
559
- typename nocontract_t_, typename contract_t_,
560
- int packet_size_,
561
- bool inner_dim_contiguous_, bool inner_dim_reordered_, int Alignment_, template <class> class MakePointer_>
562
- struct TensorContractionInputMapperTrait<TensorContractionInputMapper<Scalar_, Index_, side_, Tensor_,
563
- nocontract_t_, contract_t_, packet_size_, inner_dim_contiguous_,
564
- inner_dim_reordered_, Alignment_, MakePointer_> > {
565
-
566
- typedef Tensor_ XprType;
567
- static const bool inner_dim_contiguous = inner_dim_contiguous_;
568
- static const bool inner_dim_reordered = inner_dim_reordered_;
569
- };
570
-
571
-
572
- } // end namespace internal
573
- } // end namespace Eigen
574
-
575
- #endif // EIGEN_CXX11_TENSOR_TENSOR_CONTRACTION_MAPPER_H