sequenzo 0.1.18__cp312-cp312-win_amd64.whl → 0.1.20__cp312-cp312-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.cp312-win_amd64.pyd +0 -0
  4. sequenzo/clustering/KMedoids.py +39 -0
  5. sequenzo/clustering/clustering_c_code.cp312-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.cp312-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.cp312-win_amd64.pyd +0 -0
  13. sequenzo/dissimilarity_measures/utils/seqconc.c +154 -154
  14. sequenzo/dissimilarity_measures/utils/seqconc.cp312-win_amd64.pyd +0 -0
  15. sequenzo/dissimilarity_measures/utils/seqdss.c +154 -154
  16. sequenzo/dissimilarity_measures/utils/seqdss.cp312-win_amd64.pyd +0 -0
  17. sequenzo/dissimilarity_measures/utils/seqdur.c +154 -154
  18. sequenzo/dissimilarity_measures/utils/seqdur.cp312-win_amd64.pyd +0 -0
  19. sequenzo/dissimilarity_measures/utils/seqlength.c +154 -154
  20. sequenzo/dissimilarity_measures/utils/seqlength.cp312-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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@@ -1,388 +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_EXPR_H
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- #define EIGEN_CXX11_TENSOR_TENSOR_EXPR_H
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-
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- namespace Eigen {
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-
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- /** \class TensorExpr
16
- * \ingroup CXX11_Tensor_Module
17
- *
18
- * \brief Tensor expression classes.
19
- *
20
- * The TensorCwiseNullaryOp class applies a nullary operators to an expression.
21
- * This is typically used to generate constants.
22
- *
23
- * The TensorCwiseUnaryOp class represents an expression where a unary operator
24
- * (e.g. cwiseSqrt) is applied to an expression.
25
- *
26
- * The TensorCwiseBinaryOp class represents an expression where a binary
27
- * operator (e.g. addition) is applied to a lhs and a rhs expression.
28
- *
29
- */
30
- namespace internal {
31
- template<typename NullaryOp, typename XprType>
32
- struct traits<TensorCwiseNullaryOp<NullaryOp, XprType> >
33
- : traits<XprType>
34
- {
35
- typedef traits<XprType> XprTraits;
36
- typedef typename XprType::Scalar Scalar;
37
- typedef typename XprType::Nested XprTypeNested;
38
- typedef typename remove_reference<XprTypeNested>::type _XprTypeNested;
39
- static const int NumDimensions = XprTraits::NumDimensions;
40
- static const int Layout = XprTraits::Layout;
41
- typedef typename XprTraits::PointerType PointerType;
42
- enum {
43
- Flags = 0
44
- };
45
- };
46
-
47
- } // end namespace internal
48
-
49
-
50
-
51
- template<typename NullaryOp, typename XprType>
52
- class TensorCwiseNullaryOp : public TensorBase<TensorCwiseNullaryOp<NullaryOp, XprType>, ReadOnlyAccessors>
53
- {
54
- public:
55
- typedef typename Eigen::internal::traits<TensorCwiseNullaryOp>::Scalar Scalar;
56
- typedef typename Eigen::NumTraits<Scalar>::Real RealScalar;
57
- typedef typename XprType::CoeffReturnType CoeffReturnType;
58
- typedef TensorCwiseNullaryOp<NullaryOp, XprType> Nested;
59
- typedef typename Eigen::internal::traits<TensorCwiseNullaryOp>::StorageKind StorageKind;
60
- typedef typename Eigen::internal::traits<TensorCwiseNullaryOp>::Index Index;
61
-
62
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorCwiseNullaryOp(const XprType& xpr, const NullaryOp& func = NullaryOp())
63
- : m_xpr(xpr), m_functor(func) {}
64
-
65
- EIGEN_DEVICE_FUNC
66
- const typename internal::remove_all<typename XprType::Nested>::type&
67
- nestedExpression() const { return m_xpr; }
68
-
69
- EIGEN_DEVICE_FUNC
70
- const NullaryOp& functor() const { return m_functor; }
71
-
72
- protected:
73
- typename XprType::Nested m_xpr;
74
- const NullaryOp m_functor;
75
- };
76
-
77
-
78
-
79
- namespace internal {
80
- template<typename UnaryOp, typename XprType>
81
- struct traits<TensorCwiseUnaryOp<UnaryOp, XprType> >
82
- : traits<XprType>
83
- {
84
- // TODO(phli): Add InputScalar, InputPacket. Check references to
85
- // current Scalar/Packet to see if the intent is Input or Output.
86
- typedef typename result_of<UnaryOp(typename XprType::Scalar)>::type Scalar;
87
- typedef traits<XprType> XprTraits;
88
- typedef typename XprType::Nested XprTypeNested;
89
- typedef typename remove_reference<XprTypeNested>::type _XprTypeNested;
90
- static const int NumDimensions = XprTraits::NumDimensions;
91
- static const int Layout = XprTraits::Layout;
92
- typedef typename TypeConversion<Scalar,
93
- typename XprTraits::PointerType
94
- >::type
95
- PointerType;
96
- };
97
-
98
- template<typename UnaryOp, typename XprType>
99
- struct eval<TensorCwiseUnaryOp<UnaryOp, XprType>, Eigen::Dense>
100
- {
101
- typedef const TensorCwiseUnaryOp<UnaryOp, XprType>& type;
102
- };
103
-
104
- template<typename UnaryOp, typename XprType>
105
- struct nested<TensorCwiseUnaryOp<UnaryOp, XprType>, 1, typename eval<TensorCwiseUnaryOp<UnaryOp, XprType> >::type>
106
- {
107
- typedef TensorCwiseUnaryOp<UnaryOp, XprType> type;
108
- };
109
-
110
- } // end namespace internal
111
-
112
-
113
-
114
- template<typename UnaryOp, typename XprType>
115
- class TensorCwiseUnaryOp : public TensorBase<TensorCwiseUnaryOp<UnaryOp, XprType>, ReadOnlyAccessors>
116
- {
117
- public:
118
- // TODO(phli): Add InputScalar, InputPacket. Check references to
119
- // current Scalar/Packet to see if the intent is Input or Output.
120
- typedef typename Eigen::internal::traits<TensorCwiseUnaryOp>::Scalar Scalar;
121
- typedef typename Eigen::NumTraits<Scalar>::Real RealScalar;
122
- typedef Scalar CoeffReturnType;
123
- typedef typename Eigen::internal::nested<TensorCwiseUnaryOp>::type Nested;
124
- typedef typename Eigen::internal::traits<TensorCwiseUnaryOp>::StorageKind StorageKind;
125
- typedef typename Eigen::internal::traits<TensorCwiseUnaryOp>::Index Index;
126
-
127
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorCwiseUnaryOp(const XprType& xpr, const UnaryOp& func = UnaryOp())
128
- : m_xpr(xpr), m_functor(func) {}
129
-
130
- EIGEN_DEVICE_FUNC
131
- const UnaryOp& functor() const { return m_functor; }
132
-
133
- /** \returns the nested expression */
134
- EIGEN_DEVICE_FUNC
135
- const typename internal::remove_all<typename XprType::Nested>::type&
136
- nestedExpression() const { return m_xpr; }
137
-
138
- protected:
139
- typename XprType::Nested m_xpr;
140
- const UnaryOp m_functor;
141
- };
142
-
143
-
144
- namespace internal {
145
- template<typename BinaryOp, typename LhsXprType, typename RhsXprType>
146
- struct traits<TensorCwiseBinaryOp<BinaryOp, LhsXprType, RhsXprType> >
147
- {
148
- // Type promotion to handle the case where the types of the lhs and the rhs
149
- // are different.
150
- // TODO(phli): Add Lhs/RhsScalar, Lhs/RhsPacket. Check references to
151
- // current Scalar/Packet to see if the intent is Inputs or Output.
152
- typedef typename result_of<
153
- BinaryOp(typename LhsXprType::Scalar,
154
- typename RhsXprType::Scalar)>::type Scalar;
155
- typedef traits<LhsXprType> XprTraits;
156
- typedef typename promote_storage_type<
157
- typename traits<LhsXprType>::StorageKind,
158
- typename traits<RhsXprType>::StorageKind>::ret StorageKind;
159
- typedef typename promote_index_type<
160
- typename traits<LhsXprType>::Index,
161
- typename traits<RhsXprType>::Index>::type Index;
162
- typedef typename LhsXprType::Nested LhsNested;
163
- typedef typename RhsXprType::Nested RhsNested;
164
- typedef typename remove_reference<LhsNested>::type _LhsNested;
165
- typedef typename remove_reference<RhsNested>::type _RhsNested;
166
- static const int NumDimensions = XprTraits::NumDimensions;
167
- static const int Layout = XprTraits::Layout;
168
- typedef typename TypeConversion<Scalar,
169
- typename conditional<Pointer_type_promotion<typename LhsXprType::Scalar, Scalar>::val,
170
- typename traits<LhsXprType>::PointerType,
171
- typename traits<RhsXprType>::PointerType>::type
172
- >::type
173
- PointerType;
174
- enum {
175
- Flags = 0
176
- };
177
- };
178
-
179
- template<typename BinaryOp, typename LhsXprType, typename RhsXprType>
180
- struct eval<TensorCwiseBinaryOp<BinaryOp, LhsXprType, RhsXprType>, Eigen::Dense>
181
- {
182
- typedef const TensorCwiseBinaryOp<BinaryOp, LhsXprType, RhsXprType>& type;
183
- };
184
-
185
- template<typename BinaryOp, typename LhsXprType, typename RhsXprType>
186
- struct nested<TensorCwiseBinaryOp<BinaryOp, LhsXprType, RhsXprType>, 1, typename eval<TensorCwiseBinaryOp<BinaryOp, LhsXprType, RhsXprType> >::type>
187
- {
188
- typedef TensorCwiseBinaryOp<BinaryOp, LhsXprType, RhsXprType> type;
189
- };
190
-
191
- } // end namespace internal
192
-
193
-
194
-
195
- template<typename BinaryOp, typename LhsXprType, typename RhsXprType>
196
- class TensorCwiseBinaryOp : public TensorBase<TensorCwiseBinaryOp<BinaryOp, LhsXprType, RhsXprType>, ReadOnlyAccessors>
197
- {
198
- public:
199
- // TODO(phli): Add Lhs/RhsScalar, Lhs/RhsPacket. Check references to
200
- // current Scalar/Packet to see if the intent is Inputs or Output.
201
- typedef typename Eigen::internal::traits<TensorCwiseBinaryOp>::Scalar Scalar;
202
- typedef typename Eigen::NumTraits<Scalar>::Real RealScalar;
203
- typedef Scalar CoeffReturnType;
204
- typedef typename Eigen::internal::nested<TensorCwiseBinaryOp>::type Nested;
205
- typedef typename Eigen::internal::traits<TensorCwiseBinaryOp>::StorageKind StorageKind;
206
- typedef typename Eigen::internal::traits<TensorCwiseBinaryOp>::Index Index;
207
-
208
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorCwiseBinaryOp(const LhsXprType& lhs, const RhsXprType& rhs, const BinaryOp& func = BinaryOp())
209
- : m_lhs_xpr(lhs), m_rhs_xpr(rhs), m_functor(func) {}
210
-
211
- EIGEN_DEVICE_FUNC
212
- const BinaryOp& functor() const { return m_functor; }
213
-
214
- /** \returns the nested expressions */
215
- EIGEN_DEVICE_FUNC
216
- const typename internal::remove_all<typename LhsXprType::Nested>::type&
217
- lhsExpression() const { return m_lhs_xpr; }
218
-
219
- EIGEN_DEVICE_FUNC
220
- const typename internal::remove_all<typename RhsXprType::Nested>::type&
221
- rhsExpression() const { return m_rhs_xpr; }
222
-
223
- protected:
224
- typename LhsXprType::Nested m_lhs_xpr;
225
- typename RhsXprType::Nested m_rhs_xpr;
226
- const BinaryOp m_functor;
227
- };
228
-
229
-
230
- namespace internal {
231
- template<typename TernaryOp, typename Arg1XprType, typename Arg2XprType, typename Arg3XprType>
232
- struct traits<TensorCwiseTernaryOp<TernaryOp, Arg1XprType, Arg2XprType, Arg3XprType> >
233
- {
234
- // Type promotion to handle the case where the types of the args are different.
235
- typedef typename result_of<
236
- TernaryOp(typename Arg1XprType::Scalar,
237
- typename Arg2XprType::Scalar,
238
- typename Arg3XprType::Scalar)>::type Scalar;
239
- typedef traits<Arg1XprType> XprTraits;
240
- typedef typename traits<Arg1XprType>::StorageKind StorageKind;
241
- typedef typename traits<Arg1XprType>::Index Index;
242
- typedef typename Arg1XprType::Nested Arg1Nested;
243
- typedef typename Arg2XprType::Nested Arg2Nested;
244
- typedef typename Arg3XprType::Nested Arg3Nested;
245
- typedef typename remove_reference<Arg1Nested>::type _Arg1Nested;
246
- typedef typename remove_reference<Arg2Nested>::type _Arg2Nested;
247
- typedef typename remove_reference<Arg3Nested>::type _Arg3Nested;
248
- static const int NumDimensions = XprTraits::NumDimensions;
249
- static const int Layout = XprTraits::Layout;
250
- typedef typename TypeConversion<Scalar,
251
- typename conditional<Pointer_type_promotion<typename Arg2XprType::Scalar, Scalar>::val,
252
- typename traits<Arg2XprType>::PointerType,
253
- typename traits<Arg3XprType>::PointerType>::type
254
- >::type
255
- PointerType;
256
- enum {
257
- Flags = 0
258
- };
259
- };
260
-
261
- template<typename TernaryOp, typename Arg1XprType, typename Arg2XprType, typename Arg3XprType>
262
- struct eval<TensorCwiseTernaryOp<TernaryOp, Arg1XprType, Arg2XprType, Arg3XprType>, Eigen::Dense>
263
- {
264
- typedef const TensorCwiseTernaryOp<TernaryOp, Arg1XprType, Arg2XprType, Arg3XprType>& type;
265
- };
266
-
267
- template<typename TernaryOp, typename Arg1XprType, typename Arg2XprType, typename Arg3XprType>
268
- struct nested<TensorCwiseTernaryOp<TernaryOp, Arg1XprType, Arg2XprType, Arg3XprType>, 1, typename eval<TensorCwiseTernaryOp<TernaryOp, Arg1XprType, Arg2XprType, Arg3XprType> >::type>
269
- {
270
- typedef TensorCwiseTernaryOp<TernaryOp, Arg1XprType, Arg2XprType, Arg3XprType> type;
271
- };
272
-
273
- } // end namespace internal
274
-
275
-
276
-
277
- template<typename TernaryOp, typename Arg1XprType, typename Arg2XprType, typename Arg3XprType>
278
- class TensorCwiseTernaryOp : public TensorBase<TensorCwiseTernaryOp<TernaryOp, Arg1XprType, Arg2XprType, Arg3XprType>, ReadOnlyAccessors>
279
- {
280
- public:
281
- typedef typename Eigen::internal::traits<TensorCwiseTernaryOp>::Scalar Scalar;
282
- typedef typename Eigen::NumTraits<Scalar>::Real RealScalar;
283
- typedef Scalar CoeffReturnType;
284
- typedef typename Eigen::internal::nested<TensorCwiseTernaryOp>::type Nested;
285
- typedef typename Eigen::internal::traits<TensorCwiseTernaryOp>::StorageKind StorageKind;
286
- typedef typename Eigen::internal::traits<TensorCwiseTernaryOp>::Index Index;
287
-
288
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorCwiseTernaryOp(const Arg1XprType& arg1, const Arg2XprType& arg2, const Arg3XprType& arg3, const TernaryOp& func = TernaryOp())
289
- : m_arg1_xpr(arg1), m_arg2_xpr(arg2), m_arg3_xpr(arg3), m_functor(func) {}
290
-
291
- EIGEN_DEVICE_FUNC
292
- const TernaryOp& functor() const { return m_functor; }
293
-
294
- /** \returns the nested expressions */
295
- EIGEN_DEVICE_FUNC
296
- const typename internal::remove_all<typename Arg1XprType::Nested>::type&
297
- arg1Expression() const { return m_arg1_xpr; }
298
-
299
- EIGEN_DEVICE_FUNC
300
- const typename internal::remove_all<typename Arg2XprType::Nested>::type&
301
- arg2Expression() const { return m_arg2_xpr; }
302
-
303
- EIGEN_DEVICE_FUNC
304
- const typename internal::remove_all<typename Arg3XprType::Nested>::type&
305
- arg3Expression() const { return m_arg3_xpr; }
306
-
307
- protected:
308
- typename Arg1XprType::Nested m_arg1_xpr;
309
- typename Arg2XprType::Nested m_arg2_xpr;
310
- typename Arg3XprType::Nested m_arg3_xpr;
311
- const TernaryOp m_functor;
312
- };
313
-
314
-
315
- namespace internal {
316
- template<typename IfXprType, typename ThenXprType, typename ElseXprType>
317
- struct traits<TensorSelectOp<IfXprType, ThenXprType, ElseXprType> >
318
- : traits<ThenXprType>
319
- {
320
- typedef typename traits<ThenXprType>::Scalar Scalar;
321
- typedef traits<ThenXprType> XprTraits;
322
- typedef typename promote_storage_type<typename traits<ThenXprType>::StorageKind,
323
- typename traits<ElseXprType>::StorageKind>::ret StorageKind;
324
- typedef typename promote_index_type<typename traits<ElseXprType>::Index,
325
- typename traits<ThenXprType>::Index>::type Index;
326
- typedef typename IfXprType::Nested IfNested;
327
- typedef typename ThenXprType::Nested ThenNested;
328
- typedef typename ElseXprType::Nested ElseNested;
329
- static const int NumDimensions = XprTraits::NumDimensions;
330
- static const int Layout = XprTraits::Layout;
331
- typedef typename conditional<Pointer_type_promotion<typename ThenXprType::Scalar, Scalar>::val,
332
- typename traits<ThenXprType>::PointerType,
333
- typename traits<ElseXprType>::PointerType>::type PointerType;
334
- };
335
-
336
- template<typename IfXprType, typename ThenXprType, typename ElseXprType>
337
- struct eval<TensorSelectOp<IfXprType, ThenXprType, ElseXprType>, Eigen::Dense>
338
- {
339
- typedef const TensorSelectOp<IfXprType, ThenXprType, ElseXprType>& type;
340
- };
341
-
342
- template<typename IfXprType, typename ThenXprType, typename ElseXprType>
343
- struct nested<TensorSelectOp<IfXprType, ThenXprType, ElseXprType>, 1, typename eval<TensorSelectOp<IfXprType, ThenXprType, ElseXprType> >::type>
344
- {
345
- typedef TensorSelectOp<IfXprType, ThenXprType, ElseXprType> type;
346
- };
347
-
348
- } // end namespace internal
349
-
350
-
351
- template<typename IfXprType, typename ThenXprType, typename ElseXprType>
352
- class TensorSelectOp : public TensorBase<TensorSelectOp<IfXprType, ThenXprType, ElseXprType>, ReadOnlyAccessors>
353
- {
354
- public:
355
- typedef typename Eigen::internal::traits<TensorSelectOp>::Scalar Scalar;
356
- typedef typename Eigen::NumTraits<Scalar>::Real RealScalar;
357
- typedef typename internal::promote_storage_type<typename ThenXprType::CoeffReturnType,
358
- typename ElseXprType::CoeffReturnType>::ret CoeffReturnType;
359
- typedef typename Eigen::internal::nested<TensorSelectOp>::type Nested;
360
- typedef typename Eigen::internal::traits<TensorSelectOp>::StorageKind StorageKind;
361
- typedef typename Eigen::internal::traits<TensorSelectOp>::Index Index;
362
-
363
- EIGEN_DEVICE_FUNC
364
- TensorSelectOp(const IfXprType& a_condition,
365
- const ThenXprType& a_then,
366
- const ElseXprType& a_else)
367
- : m_condition(a_condition), m_then(a_then), m_else(a_else)
368
- { }
369
-
370
- EIGEN_DEVICE_FUNC
371
- const IfXprType& ifExpression() const { return m_condition; }
372
-
373
- EIGEN_DEVICE_FUNC
374
- const ThenXprType& thenExpression() const { return m_then; }
375
-
376
- EIGEN_DEVICE_FUNC
377
- const ElseXprType& elseExpression() const { return m_else; }
378
-
379
- protected:
380
- typename IfXprType::Nested m_condition;
381
- typename ThenXprType::Nested m_then;
382
- typename ElseXprType::Nested m_else;
383
- };
384
-
385
-
386
- } // end namespace Eigen
387
-
388
- #endif // EIGEN_CXX11_TENSOR_TENSOR_EXPR_H