sequenzo 0.1.18__cp310-cp310-macosx_10_9_universal2.whl → 0.1.20__cp310-cp310-macosx_10_9_universal2.whl

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  1. sequenzo/__init__.py +39 -7
  2. sequenzo/big_data/clara/utils/get_weighted_diss.c +155 -155
  3. sequenzo/big_data/clara/utils/get_weighted_diss.cpython-310-darwin.so +0 -0
  4. sequenzo/clustering/KMedoids.py +39 -0
  5. sequenzo/clustering/hierarchical_clustering.py +108 -6
  6. sequenzo/define_sequence_data.py +10 -1
  7. sequenzo/dissimilarity_measures/get_distance_matrix.py +2 -3
  8. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  9. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +155 -155
  10. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cpython-310-darwin.so +0 -0
  11. sequenzo/dissimilarity_measures/utils/seqconc.c +155 -155
  12. sequenzo/dissimilarity_measures/utils/seqconc.cpython-310-darwin.so +0 -0
  13. sequenzo/dissimilarity_measures/utils/seqdss.c +155 -155
  14. sequenzo/dissimilarity_measures/utils/seqdss.cpython-310-darwin.so +0 -0
  15. sequenzo/dissimilarity_measures/utils/seqdur.c +155 -155
  16. sequenzo/dissimilarity_measures/utils/seqdur.cpython-310-darwin.so +0 -0
  17. sequenzo/dissimilarity_measures/utils/seqlength.c +155 -155
  18. sequenzo/dissimilarity_measures/utils/seqlength.cpython-310-darwin.so +0 -0
  19. sequenzo/multidomain/cat.py +0 -53
  20. sequenzo/multidomain/dat.py +11 -3
  21. sequenzo/multidomain/idcd.py +0 -3
  22. sequenzo/multidomain/linked_polyad.py +0 -1
  23. sequenzo/openmp_setup.py +233 -0
  24. sequenzo/visualization/plot_transition_matrix.py +21 -22
  25. {sequenzo-0.1.18.dist-info → sequenzo-0.1.20.dist-info}/METADATA +71 -10
  26. sequenzo-0.1.20.dist-info/RECORD +215 -0
  27. sequenzo/dissimilarity_measures/setup.py +0 -35
  28. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  29. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  30. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  31. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  32. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  33. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  34. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  35. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  36. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  37. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  38. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  39. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  40. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  41. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  42. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  43. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  44. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  45. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  46. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  47. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  48. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  49. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  50. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  51. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  52. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  53. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  54. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  55. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  56. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  57. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  58. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  59. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  60. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  61. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  62. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  63. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  64. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  65. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  66. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  67. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  68. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  69. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  70. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  71. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  72. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  73. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  74. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  75. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  76. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  77. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  78. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  79. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  80. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  81. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  82. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  83. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  84. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  85. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  86. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  87. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  88. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  89. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  90. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  91. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  92. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  93. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  94. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  95. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  96. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  97. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  98. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  99. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  100. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  101. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  102. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  103. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  104. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  105. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_relax_snode.h +0 -83
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseQR/SparseQR.h +0 -758
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdDeque.h +0 -116
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdList.h +0 -106
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdVector.h +0 -131
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/details.h +0 -84
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SuperLUSupport/SuperLUSupport.h +0 -1025
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/UmfPackSupport/UmfPackSupport.h +0 -642
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Image.h +0 -82
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Kernel.h +0 -79
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/RealSvd2x2.h +0 -55
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/blas.h +0 -440
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapack.h +0 -152
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke.h +0 -16292
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke_mangling.h +0 -17
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseBinaryOps.h +0 -358
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseUnaryOps.h +0 -696
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/BlockMethods.h +0 -1442
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseBinaryOps.h +0 -115
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseUnaryOps.h +0 -177
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/IndexedViewMethods.h +0 -262
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h +0 -152
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h +0 -95
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ReshapedMethods.h +0 -149
  170. sequenzo/dissimilarity_measures/src/eigen/blas/BandTriangularSolver.h +0 -97
  171. sequenzo/dissimilarity_measures/src/eigen/blas/GeneralRank1Update.h +0 -44
  172. sequenzo/dissimilarity_measures/src/eigen/blas/PackedSelfadjointProduct.h +0 -53
  173. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularMatrixVector.h +0 -79
  174. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularSolverVector.h +0 -88
  175. sequenzo/dissimilarity_measures/src/eigen/blas/Rank2Update.h +0 -57
  176. sequenzo/dissimilarity_measures/src/eigen/blas/common.h +0 -175
  177. sequenzo/dissimilarity_measures/src/eigen/blas/f2c/datatypes.h +0 -24
  178. sequenzo/dissimilarity_measures/src/eigen/blas/level1_cplx_impl.h +0 -155
  179. sequenzo/dissimilarity_measures/src/eigen/blas/level1_impl.h +0 -144
  180. sequenzo/dissimilarity_measures/src/eigen/blas/level1_real_impl.h +0 -122
  181. sequenzo/dissimilarity_measures/src/eigen/blas/level2_cplx_impl.h +0 -360
  182. sequenzo/dissimilarity_measures/src/eigen/blas/level2_impl.h +0 -553
  183. sequenzo/dissimilarity_measures/src/eigen/blas/level2_real_impl.h +0 -306
  184. sequenzo/dissimilarity_measures/src/eigen/blas/level3_impl.h +0 -702
  185. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/__init__.py +0 -1
  186. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/printers.py +0 -314
  187. sequenzo/dissimilarity_measures/src/eigen/lapack/lapack_common.h +0 -29
  188. sequenzo/dissimilarity_measures/src/eigen/scripts/relicense.py +0 -69
  189. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/Tensor.h +0 -554
  190. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorArgMax.h +0 -329
  191. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorAssign.h +0 -247
  192. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBase.h +0 -1176
  193. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBlock.h +0 -1559
  194. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBroadcasting.h +0 -1093
  195. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorChipping.h +0 -518
  196. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConcatenation.h +0 -377
  197. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContraction.h +0 -1023
  198. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionBlocking.h +0 -73
  199. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionCuda.h +0 -6
  200. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionGpu.h +0 -1413
  201. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionMapper.h +0 -575
  202. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionSycl.h +0 -1650
  203. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionThreadPool.h +0 -1679
  204. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConversion.h +0 -456
  205. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConvolution.h +0 -1132
  206. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConvolutionSycl.h +0 -544
  207. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorCostModel.h +0 -214
  208. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorCustomOp.h +0 -347
  209. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDevice.h +0 -137
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  359. {sequenzo-0.1.18.dist-info → sequenzo-0.1.20.dist-info}/licenses/LICENSE +0 -0
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@@ -1,236 +0,0 @@
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- // This file is part of Eigen, a lightweight C++ template library
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- // for linear algebra.
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- //
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- // Copyright (C) 2014 Benoit Steiner <benoit.steiner.goog@gmail.com>
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- //
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- // This Source Code Form is subject to the terms of the Mozilla
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- // Public License v. 2.0. If a copy of the MPL was not distributed
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- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
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-
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- #ifndef EIGEN_CXX11_TENSOR_TENSOR_EVAL_TO_H
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- #define EIGEN_CXX11_TENSOR_TENSOR_EVAL_TO_H
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-
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- namespace Eigen {
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-
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- /** \class TensorForcedEval
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- * \ingroup CXX11_Tensor_Module
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- *
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- * \brief Tensor reshaping class.
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- *
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- *
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- */
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- namespace internal {
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- template<typename XprType, template <class> class MakePointer_>
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- struct traits<TensorEvalToOp<XprType, MakePointer_> >
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- {
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- // Type promotion to handle the case where the types of the lhs and the rhs are different.
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- typedef typename XprType::Scalar Scalar;
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- typedef traits<XprType> XprTraits;
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- typedef typename XprTraits::StorageKind StorageKind;
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- typedef typename XprTraits::Index Index;
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- typedef typename XprType::Nested Nested;
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- typedef typename remove_reference<Nested>::type _Nested;
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- static const int NumDimensions = XprTraits::NumDimensions;
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- static const int Layout = XprTraits::Layout;
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- typedef typename MakePointer_<Scalar>::Type PointerType;
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-
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- enum {
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- Flags = 0
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- };
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- template <class T>
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- struct MakePointer {
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- // Intermediate typedef to workaround MSVC issue.
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- typedef MakePointer_<T> MakePointerT;
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- typedef typename MakePointerT::Type Type;
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-
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-
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- };
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- };
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-
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- template<typename XprType, template <class> class MakePointer_>
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- struct eval<TensorEvalToOp<XprType, MakePointer_>, Eigen::Dense>
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- {
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- typedef const TensorEvalToOp<XprType, MakePointer_>& type;
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- };
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-
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- template<typename XprType, template <class> class MakePointer_>
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- struct nested<TensorEvalToOp<XprType, MakePointer_>, 1, typename eval<TensorEvalToOp<XprType, MakePointer_> >::type>
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- {
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- typedef TensorEvalToOp<XprType, MakePointer_> type;
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- };
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-
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- } // end namespace internal
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-
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-
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-
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-
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- template<typename XprType, template <class> class MakePointer_>
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- class TensorEvalToOp : public TensorBase<TensorEvalToOp<XprType, MakePointer_>, ReadOnlyAccessors>
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- {
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- public:
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- typedef typename Eigen::internal::traits<TensorEvalToOp>::Scalar Scalar;
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- typedef typename Eigen::NumTraits<Scalar>::Real RealScalar;
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- typedef typename internal::remove_const<typename XprType::CoeffReturnType>::type CoeffReturnType;
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- typedef typename MakePointer_<CoeffReturnType>::Type PointerType;
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- typedef typename Eigen::internal::nested<TensorEvalToOp>::type Nested;
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- typedef typename Eigen::internal::traits<TensorEvalToOp>::StorageKind StorageKind;
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- typedef typename Eigen::internal::traits<TensorEvalToOp>::Index Index;
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-
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- static const int NumDims = Eigen::internal::traits<TensorEvalToOp>::NumDimensions;
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-
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- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorEvalToOp(PointerType buffer, const XprType& expr)
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- : m_xpr(expr), m_buffer(buffer) {}
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-
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- EIGEN_DEVICE_FUNC
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- const typename internal::remove_all<typename XprType::Nested>::type&
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- expression() const { return m_xpr; }
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-
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- EIGEN_DEVICE_FUNC PointerType buffer() const { return m_buffer; }
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-
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- protected:
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- typename XprType::Nested m_xpr;
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- PointerType m_buffer;
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- };
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-
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-
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-
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- template<typename ArgType, typename Device, template <class> class MakePointer_>
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- struct TensorEvaluator<const TensorEvalToOp<ArgType, MakePointer_>, Device>
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- {
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- typedef TensorEvalToOp<ArgType, MakePointer_> XprType;
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- typedef typename ArgType::Scalar Scalar;
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- typedef typename TensorEvaluator<ArgType, Device>::Dimensions Dimensions;
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- typedef typename XprType::Index Index;
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- typedef typename internal::remove_const<typename XprType::CoeffReturnType>::type CoeffReturnType;
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- typedef typename PacketType<CoeffReturnType, Device>::type PacketReturnType;
106
- static const int PacketSize = PacketType<CoeffReturnType, Device>::size;
107
- typedef typename Eigen::internal::traits<XprType>::PointerType TensorPointerType;
108
- typedef StorageMemory<CoeffReturnType, Device> Storage;
109
- typedef typename Storage::Type EvaluatorPointerType;
110
- enum {
111
- IsAligned = TensorEvaluator<ArgType, Device>::IsAligned,
112
- PacketAccess = TensorEvaluator<ArgType, Device>::PacketAccess,
113
- BlockAccess = true,
114
- PreferBlockAccess = false,
115
- Layout = TensorEvaluator<ArgType, Device>::Layout,
116
- CoordAccess = false, // to be implemented
117
- RawAccess = true
118
- };
119
-
120
- static const int NumDims = internal::traits<ArgType>::NumDimensions;
121
-
122
- //===- Tensor block evaluation strategy (see TensorBlock.h) -------------===//
123
- typedef internal::TensorBlockDescriptor<NumDims, Index> TensorBlockDesc;
124
- typedef internal::TensorBlockScratchAllocator<Device> TensorBlockScratch;
125
-
126
- typedef typename TensorEvaluator<const ArgType, Device>::TensorBlock
127
- ArgTensorBlock;
128
-
129
- typedef internal::TensorBlockAssignment<
130
- CoeffReturnType, NumDims, typename ArgTensorBlock::XprType, Index>
131
- TensorBlockAssignment;
132
- //===--------------------------------------------------------------------===//
133
-
134
- EIGEN_STRONG_INLINE TensorEvaluator(const XprType& op, const Device& device)
135
- : m_impl(op.expression(), device), m_buffer(device.get(op.buffer())), m_expression(op.expression()){}
136
-
137
-
138
- EIGEN_STRONG_INLINE ~TensorEvaluator() {
139
- }
140
-
141
-
142
- EIGEN_DEVICE_FUNC const Dimensions& dimensions() const { return m_impl.dimensions(); }
143
-
144
- EIGEN_STRONG_INLINE bool evalSubExprsIfNeeded(EvaluatorPointerType scalar) {
145
- EIGEN_UNUSED_VARIABLE(scalar);
146
- eigen_assert(scalar == NULL);
147
- return m_impl.evalSubExprsIfNeeded(m_buffer);
148
- }
149
-
150
- #ifdef EIGEN_USE_THREADS
151
- template <typename EvalSubExprsCallback>
152
- EIGEN_STRONG_INLINE void evalSubExprsIfNeededAsync(
153
- EvaluatorPointerType scalar, EvalSubExprsCallback done) {
154
- EIGEN_UNUSED_VARIABLE(scalar);
155
- eigen_assert(scalar == NULL);
156
- m_impl.evalSubExprsIfNeededAsync(m_buffer, std::move(done));
157
- }
158
- #endif
159
-
160
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void evalScalar(Index i) {
161
- m_buffer[i] = m_impl.coeff(i);
162
- }
163
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void evalPacket(Index i) {
164
- internal::pstoret<CoeffReturnType, PacketReturnType, Aligned>(m_buffer + i, m_impl.template packet<TensorEvaluator<ArgType, Device>::IsAligned ? Aligned : Unaligned>(i));
165
- }
166
-
167
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
168
- internal::TensorBlockResourceRequirements getResourceRequirements() const {
169
- return m_impl.getResourceRequirements();
170
- }
171
-
172
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void evalBlock(
173
- TensorBlockDesc& desc, TensorBlockScratch& scratch) {
174
- // Add `m_buffer` as destination buffer to the block descriptor.
175
- desc.template AddDestinationBuffer<Layout>(
176
- /*dst_base=*/m_buffer + desc.offset(),
177
- /*dst_strides=*/internal::strides<Layout>(m_impl.dimensions()));
178
-
179
- ArgTensorBlock block =
180
- m_impl.block(desc, scratch, /*root_of_expr_ast=*/true);
181
-
182
- // If block was evaluated into a destination buffer, there is no need to do
183
- // an assignment.
184
- if (block.kind() != internal::TensorBlockKind::kMaterializedInOutput) {
185
- TensorBlockAssignment::Run(
186
- TensorBlockAssignment::target(
187
- desc.dimensions(), internal::strides<Layout>(m_impl.dimensions()),
188
- m_buffer, desc.offset()),
189
- block.expr());
190
- }
191
- block.cleanup();
192
- }
193
-
194
- EIGEN_STRONG_INLINE void cleanup() {
195
- m_impl.cleanup();
196
- }
197
-
198
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE CoeffReturnType coeff(Index index) const
199
- {
200
- return m_buffer[index];
201
- }
202
-
203
- template<int LoadMode>
204
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE PacketReturnType packet(Index index) const
205
- {
206
- return internal::ploadt<PacketReturnType, LoadMode>(m_buffer + index);
207
- }
208
-
209
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorOpCost costPerCoeff(bool vectorized) const {
210
- // We assume that evalPacket or evalScalar is called to perform the
211
- // assignment and account for the cost of the write here.
212
- return m_impl.costPerCoeff(vectorized) +
213
- TensorOpCost(0, sizeof(CoeffReturnType), 0, vectorized, PacketSize);
214
- }
215
-
216
- EIGEN_DEVICE_FUNC EvaluatorPointerType data() const { return m_buffer; }
217
- ArgType expression() const { return m_expression; }
218
- #ifdef EIGEN_USE_SYCL
219
- // binding placeholder accessors to a command group handler for SYCL
220
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void bind(cl::sycl::handler &cgh) const {
221
- m_impl.bind(cgh);
222
- m_buffer.bind(cgh);
223
- }
224
- #endif
225
-
226
-
227
- private:
228
- TensorEvaluator<ArgType, Device> m_impl;
229
- EvaluatorPointerType m_buffer;
230
- const ArgType m_expression;
231
- };
232
-
233
-
234
- } // end namespace Eigen
235
-
236
- #endif // EIGEN_CXX11_TENSOR_TENSOR_EVAL_TO_H