sequenzo 0.1.18__cp311-cp311-win_amd64.whl → 0.1.20__cp311-cp311-win_amd64.whl

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  1. sequenzo/__init__.py +39 -7
  2. sequenzo/big_data/clara/utils/get_weighted_diss.c +154 -154
  3. sequenzo/big_data/clara/utils/get_weighted_diss.cp311-win_amd64.pyd +0 -0
  4. sequenzo/clustering/KMedoids.py +39 -0
  5. sequenzo/clustering/clustering_c_code.cp311-win_amd64.pyd +0 -0
  6. sequenzo/clustering/hierarchical_clustering.py +108 -6
  7. sequenzo/define_sequence_data.py +10 -1
  8. sequenzo/dissimilarity_measures/c_code.cp311-win_amd64.pyd +0 -0
  9. sequenzo/dissimilarity_measures/get_distance_matrix.py +2 -3
  10. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  11. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +154 -154
  12. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cp311-win_amd64.pyd +0 -0
  13. sequenzo/dissimilarity_measures/utils/seqconc.c +154 -154
  14. sequenzo/dissimilarity_measures/utils/seqconc.cp311-win_amd64.pyd +0 -0
  15. sequenzo/dissimilarity_measures/utils/seqdss.c +154 -154
  16. sequenzo/dissimilarity_measures/utils/seqdss.cp311-win_amd64.pyd +0 -0
  17. sequenzo/dissimilarity_measures/utils/seqdur.c +154 -154
  18. sequenzo/dissimilarity_measures/utils/seqdur.cp311-win_amd64.pyd +0 -0
  19. sequenzo/dissimilarity_measures/utils/seqlength.c +154 -154
  20. sequenzo/dissimilarity_measures/utils/seqlength.cp311-win_amd64.pyd +0 -0
  21. sequenzo/multidomain/cat.py +0 -53
  22. sequenzo/multidomain/dat.py +11 -3
  23. sequenzo/multidomain/idcd.py +0 -3
  24. sequenzo/multidomain/linked_polyad.py +0 -1
  25. sequenzo/openmp_setup.py +233 -0
  26. sequenzo/visualization/plot_transition_matrix.py +21 -22
  27. {sequenzo-0.1.18.dist-info → sequenzo-0.1.20.dist-info}/METADATA +71 -10
  28. sequenzo-0.1.20.dist-info/RECORD +272 -0
  29. sequenzo/dissimilarity_measures/setup.py +0 -35
  30. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  31. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  32. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  33. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  34. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  35. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  36. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  37. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  38. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  39. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  40. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  41. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  42. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  43. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  44. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  45. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  46. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  47. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  48. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  49. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  50. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  51. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  52. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  53. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  54. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  55. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  56. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  57. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  58. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  59. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  60. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  61. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  62. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  63. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  64. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  65. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  66. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  67. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  68. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  69. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  70. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  71. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  72. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  73. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  74. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  75. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  76. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  77. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  78. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  79. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  80. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  81. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  82. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  83. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  84. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  85. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  86. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  87. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  88. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  89. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  90. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  91. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  92. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  93. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  94. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  95. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  96. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  97. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  98. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  99. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  100. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  101. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  102. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  103. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  104. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  105. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_relax_snode.h +0 -83
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseQR/SparseQR.h +0 -758
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdDeque.h +0 -116
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdList.h +0 -106
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdVector.h +0 -131
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/details.h +0 -84
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SuperLUSupport/SuperLUSupport.h +0 -1025
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/UmfPackSupport/UmfPackSupport.h +0 -642
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Image.h +0 -82
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Kernel.h +0 -79
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/RealSvd2x2.h +0 -55
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/blas.h +0 -440
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapack.h +0 -152
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke.h +0 -16292
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke_mangling.h +0 -17
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseBinaryOps.h +0 -358
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseUnaryOps.h +0 -696
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/BlockMethods.h +0 -1442
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseBinaryOps.h +0 -115
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseUnaryOps.h +0 -177
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/IndexedViewMethods.h +0 -262
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h +0 -152
  170. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h +0 -95
  171. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ReshapedMethods.h +0 -149
  172. sequenzo/dissimilarity_measures/src/eigen/bench/BenchSparseUtil.h +0 -149
  173. sequenzo/dissimilarity_measures/src/eigen/bench/BenchTimer.h +0 -199
  174. sequenzo/dissimilarity_measures/src/eigen/bench/BenchUtil.h +0 -92
  175. sequenzo/dissimilarity_measures/src/eigen/bench/basicbenchmark.h +0 -63
  176. sequenzo/dissimilarity_measures/src/eigen/bench/btl/generic_bench/utils/utilities.h +0 -90
  177. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/blas.h +0 -675
  178. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/c_interface_base.h +0 -73
  179. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemm_common.h +0 -67
  180. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemv_common.h +0 -69
  181. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchsolver.h +0 -573
  182. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchstyle.h +0 -95
  183. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/benchmark.h +0 -49
  184. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/tensor_benchmarks.h +0 -597
  185. sequenzo/dissimilarity_measures/src/eigen/blas/BandTriangularSolver.h +0 -97
  186. sequenzo/dissimilarity_measures/src/eigen/blas/GeneralRank1Update.h +0 -44
  187. sequenzo/dissimilarity_measures/src/eigen/blas/PackedSelfadjointProduct.h +0 -53
  188. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularMatrixVector.h +0 -79
  189. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularSolverVector.h +0 -88
  190. sequenzo/dissimilarity_measures/src/eigen/blas/Rank2Update.h +0 -57
  191. sequenzo/dissimilarity_measures/src/eigen/blas/common.h +0 -175
  192. sequenzo/dissimilarity_measures/src/eigen/blas/f2c/datatypes.h +0 -24
  193. sequenzo/dissimilarity_measures/src/eigen/blas/level1_cplx_impl.h +0 -155
  194. sequenzo/dissimilarity_measures/src/eigen/blas/level1_impl.h +0 -144
  195. sequenzo/dissimilarity_measures/src/eigen/blas/level1_real_impl.h +0 -122
  196. sequenzo/dissimilarity_measures/src/eigen/blas/level2_cplx_impl.h +0 -360
  197. sequenzo/dissimilarity_measures/src/eigen/blas/level2_impl.h +0 -553
  198. sequenzo/dissimilarity_measures/src/eigen/blas/level2_real_impl.h +0 -306
  199. sequenzo/dissimilarity_measures/src/eigen/blas/level3_impl.h +0 -702
  200. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/__init__.py +0 -1
  201. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/printers.py +0 -314
  202. sequenzo/dissimilarity_measures/src/eigen/demos/mandelbrot/mandelbrot.h +0 -71
  203. sequenzo/dissimilarity_measures/src/eigen/demos/mix_eigen_and_c/binary_library.h +0 -71
  204. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/camera.h +0 -118
  205. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/gpuhelper.h +0 -207
  206. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/icosphere.h +0 -30
  207. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/quaternion_demo.h +0 -114
  208. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/trackball.h +0 -42
  209. sequenzo/dissimilarity_measures/src/eigen/lapack/lapack_common.h +0 -29
  210. sequenzo/dissimilarity_measures/src/eigen/scripts/relicense.py +0 -69
  211. sequenzo/dissimilarity_measures/src/eigen/test/AnnoyingScalar.h +0 -165
  212. sequenzo/dissimilarity_measures/src/eigen/test/MovableScalar.h +0 -35
  213. sequenzo/dissimilarity_measures/src/eigen/test/SafeScalar.h +0 -30
  214. sequenzo/dissimilarity_measures/src/eigen/test/bug1213.h +0 -8
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  398. {sequenzo-0.1.18.dist-info → sequenzo-0.1.20.dist-info}/licenses/LICENSE +0 -0
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@@ -1,311 +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) 2015 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_META_H
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- #define EIGEN_CXX11_TENSOR_TENSOR_META_H
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-
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- namespace Eigen {
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-
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- template<bool cond> struct Cond {};
16
-
17
- template<typename T1, typename T2> EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE
18
- const T1& choose(Cond<true>, const T1& first, const T2&) {
19
- return first;
20
- }
21
-
22
- template<typename T1, typename T2> EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE
23
- const T2& choose(Cond<false>, const T1&, const T2& second) {
24
- return second;
25
- }
26
-
27
-
28
- template <typename T, typename X, typename Y>
29
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE
30
- T divup(const X x, const Y y) {
31
- return static_cast<T>((x + y - 1) / y);
32
- }
33
-
34
- template <typename T>
35
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE
36
- T divup(const T x, const T y) {
37
- return static_cast<T>((x + y - 1) / y);
38
- }
39
-
40
- template <size_t n> struct max_n_1 {
41
- static const size_t size = n;
42
- };
43
- template <> struct max_n_1<0> {
44
- static const size_t size = 1;
45
- };
46
-
47
-
48
- // Default packet types
49
- template <typename Scalar, typename Device>
50
- struct PacketType : internal::packet_traits<Scalar> {
51
- typedef typename internal::packet_traits<Scalar>::type type;
52
- };
53
-
54
- // For CUDA packet types when using a GpuDevice
55
- #if defined(EIGEN_USE_GPU) && defined(EIGEN_HAS_GPU_FP16)
56
-
57
- typedef ulonglong2 Packet4h2;
58
- template<>
59
- struct PacketType<half, GpuDevice> {
60
- typedef Packet4h2 type;
61
- static const int size = 8;
62
- enum {
63
- HasAdd = 1,
64
- HasSub = 1,
65
- HasMul = 1,
66
- HasNegate = 1,
67
- HasAbs = 1,
68
- HasArg = 0,
69
- HasAbs2 = 0,
70
- HasMin = 1,
71
- HasMax = 1,
72
- HasConj = 0,
73
- HasSetLinear = 0,
74
- HasBlend = 0,
75
-
76
- HasDiv = 1,
77
- HasSqrt = 1,
78
- HasRsqrt = 1,
79
- HasExp = 1,
80
- HasExpm1 = 0,
81
- HasLog = 1,
82
- HasLog1p = 0,
83
- HasLog10 = 0,
84
- HasPow = 1,
85
- };
86
- };
87
- #endif
88
-
89
- #if defined(EIGEN_USE_SYCL)
90
-
91
- namespace TensorSycl {
92
- namespace internal {
93
-
94
- template <typename Index, Index A, Index B> struct PlusOp {
95
- static constexpr Index Value = A + B;
96
- };
97
-
98
- template <typename Index, Index A, Index B> struct DivOp {
99
- static constexpr Index Value = A / B;
100
- };
101
-
102
- template <typename Index, Index start, Index end, Index step,
103
- template <class Indx, Indx...> class StepOp>
104
- struct static_for {
105
- template <typename UnaryOperator>
106
- static EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void loop(UnaryOperator op) {
107
- op(start);
108
- static_for<Index, StepOp<Index, start, step>::Value, end, step,
109
- StepOp>::loop(op);
110
- }
111
- };
112
- template <typename Index, Index end, Index step,
113
- template <class Indx, Indx...> class StepOp>
114
- struct static_for<Index, end, end, step, StepOp> {
115
- template <typename UnaryOperator>
116
- static EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void loop(UnaryOperator) {}
117
- };
118
-
119
- template <typename OutScalar, typename Device, bool Vectorizable>
120
- struct Vectorise {
121
- static const int PacketSize = 1;
122
- typedef OutScalar PacketReturnType;
123
- };
124
-
125
- template <typename OutScalar, typename Device>
126
- struct Vectorise<OutScalar, Device, true> {
127
- static const int PacketSize = Eigen::PacketType<OutScalar, Device>::size;
128
- typedef typename Eigen::PacketType<OutScalar, Device>::type PacketReturnType;
129
- };
130
-
131
- static EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE Index roundUp(Index x, Index y) {
132
- return ((((x) + (y)-1) / (y)) * (y));
133
- }
134
-
135
- } // namespace internal
136
- } // namespace TensorSycl
137
-
138
- template <>
139
- struct PacketType<half, SyclDevice> {
140
- typedef half type;
141
- static const int size = 1;
142
- enum {
143
- HasAdd = 0,
144
- HasSub = 0,
145
- HasMul = 0,
146
- HasNegate = 0,
147
- HasAbs = 0,
148
- HasArg = 0,
149
- HasAbs2 = 0,
150
- HasMin = 0,
151
- HasMax = 0,
152
- HasConj = 0,
153
- HasSetLinear = 0,
154
- HasBlend = 0
155
- };
156
- };
157
- template <typename Scalar>
158
- struct PacketType<Scalar, SyclDevice> : internal::default_packet_traits {
159
- typedef Scalar type;
160
- typedef Scalar half;
161
- enum {
162
- Vectorizable = 0,
163
- size = 1,
164
- AlignedOnScalar = 0,
165
- HasHalfPacket = 0
166
- };
167
- enum {
168
- HasAdd = 0,
169
- HasSub = 0,
170
- HasMul = 0,
171
- HasNegate = 0,
172
- HasAbs = 0,
173
- HasAbs2 = 0,
174
- HasMin = 0,
175
- HasMax = 0,
176
- HasConj = 0,
177
- HasSetLinear = 0
178
- };
179
-
180
- };
181
-
182
- template <typename Scalar>
183
- struct PacketType<Scalar, const SyclDevice> : PacketType<Scalar, SyclDevice>{};
184
-
185
- #ifndef EIGEN_DONT_VECTORIZE_SYCL
186
- #define PACKET_TYPE(CVQual, Type, val, lengths, DEV)\
187
- template<> struct PacketType<CVQual Type, DEV> : internal::sycl_packet_traits<val, lengths> \
188
- {\
189
- typedef typename internal::packet_traits<Type>::type type;\
190
- typedef typename internal::packet_traits<Type>::half half;\
191
- };
192
-
193
-
194
- PACKET_TYPE(const, float, 1, 4, SyclDevice)
195
- PACKET_TYPE(, float, 1, 4, SyclDevice)
196
- PACKET_TYPE(const, float, 1, 4, const SyclDevice)
197
- PACKET_TYPE(, float, 1, 4, const SyclDevice)
198
-
199
- PACKET_TYPE(const, double, 0, 2, SyclDevice)
200
- PACKET_TYPE(, double, 0, 2, SyclDevice)
201
- PACKET_TYPE(const, double, 0, 2, const SyclDevice)
202
- PACKET_TYPE(, double, 0, 2, const SyclDevice)
203
- #undef PACKET_TYPE
204
-
205
- template<> struct PacketType<half, const SyclDevice>: PacketType<half, SyclDevice>{};
206
- template<> struct PacketType<const half, const SyclDevice>: PacketType<half, SyclDevice>{};
207
- #endif
208
- #endif
209
-
210
- // Tuple mimics std::pair but works on e.g. nvcc.
211
- template <typename U, typename V> struct Tuple {
212
- public:
213
- U first;
214
- V second;
215
-
216
- typedef U first_type;
217
- typedef V second_type;
218
-
219
- EIGEN_CONSTEXPR EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
220
- Tuple() : first(), second() {}
221
-
222
- EIGEN_CONSTEXPR EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
223
- Tuple(const U& f, const V& s) : first(f), second(s) {}
224
-
225
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
226
- void swap(Tuple& rhs) {
227
- using numext::swap;
228
- swap(first, rhs.first);
229
- swap(second, rhs.second);
230
- }
231
- };
232
-
233
- template <typename U, typename V>
234
- EIGEN_CONSTEXPR EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
235
- bool operator==(const Tuple<U, V>& x, const Tuple<U, V>& y) {
236
- return (x.first == y.first && x.second == y.second);
237
- }
238
-
239
- template <typename U, typename V>
240
- EIGEN_CONSTEXPR EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
241
- bool operator!=(const Tuple<U, V>& x, const Tuple<U, V>& y) {
242
- return !(x == y);
243
- }
244
-
245
-
246
- // Can't use std::pairs on cuda devices
247
- template <typename Idx> struct IndexPair {
248
- EIGEN_CONSTEXPR EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE IndexPair() : first(0), second(0) {}
249
- EIGEN_CONSTEXPR EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE IndexPair(Idx f, Idx s) : first(f), second(s) {}
250
-
251
- EIGEN_DEVICE_FUNC void set(IndexPair<Idx> val) {
252
- first = val.first;
253
- second = val.second;
254
- }
255
-
256
- Idx first;
257
- Idx second;
258
- };
259
-
260
-
261
- #ifdef EIGEN_HAS_SFINAE
262
- namespace internal {
263
-
264
- template<typename IndexType, typename Index, Index... Is>
265
- EIGEN_CONSTEXPR EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
266
- array<Index, sizeof...(Is)> customIndices2Array(IndexType& idx, numeric_list<Index, Is...>) {
267
- return { idx[Is]... };
268
- }
269
- template<typename IndexType, typename Index>
270
- EIGEN_CONSTEXPR EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
271
- array<Index, 0> customIndices2Array(IndexType&, numeric_list<Index>) {
272
- return array<Index, 0>();
273
- }
274
-
275
- /** Make an array (for index/dimensions) out of a custom index */
276
- template<typename Index, std::size_t NumIndices, typename IndexType>
277
- EIGEN_CONSTEXPR EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
278
- array<Index, NumIndices> customIndices2Array(IndexType& idx) {
279
- return customIndices2Array(idx, typename gen_numeric_list<Index, NumIndices>::type{});
280
- }
281
-
282
-
283
- template <typename B, typename D>
284
- struct is_base_of
285
- {
286
-
287
- typedef char (&yes)[1];
288
- typedef char (&no)[2];
289
-
290
- template <typename BB, typename DD>
291
- struct Host
292
- {
293
- operator BB*() const;
294
- operator DD*();
295
- };
296
-
297
- template<typename T>
298
- static yes check(D*, T);
299
- static no check(B*, int);
300
-
301
- static const bool value = sizeof(check(Host<B,D>(), int())) == sizeof(yes);
302
- };
303
-
304
- }
305
- #endif
306
-
307
-
308
-
309
- } // namespace Eigen
310
-
311
- #endif // EIGEN_CXX11_TENSOR_TENSOR_META_H