sequenzo 0.1.18__cp310-cp310-win_amd64.whl → 0.1.20__cp310-cp310-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.cp310-win_amd64.pyd +0 -0
  4. sequenzo/clustering/KMedoids.py +39 -0
  5. sequenzo/clustering/clustering_c_code.cp310-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.cp310-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.cp310-win_amd64.pyd +0 -0
  13. sequenzo/dissimilarity_measures/utils/seqconc.c +154 -154
  14. sequenzo/dissimilarity_measures/utils/seqconc.cp310-win_amd64.pyd +0 -0
  15. sequenzo/dissimilarity_measures/utils/seqdss.c +154 -154
  16. sequenzo/dissimilarity_measures/utils/seqdss.cp310-win_amd64.pyd +0 -0
  17. sequenzo/dissimilarity_measures/utils/seqdur.c +154 -154
  18. sequenzo/dissimilarity_measures/utils/seqdur.cp310-win_amd64.pyd +0 -0
  19. sequenzo/dissimilarity_measures/utils/seqlength.c +154 -154
  20. sequenzo/dissimilarity_measures/utils/seqlength.cp310-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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@@ -1,338 +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) 2013 Christian Seiler <christian@iwakd.de>
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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_TENSORSYMMETRY_SYMMETRY_H
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- #define EIGEN_CXX11_TENSORSYMMETRY_SYMMETRY_H
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-
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- namespace Eigen {
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-
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- enum {
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- NegationFlag = 0x01,
17
- ConjugationFlag = 0x02
18
- };
19
-
20
- enum {
21
- GlobalRealFlag = 0x01,
22
- GlobalImagFlag = 0x02,
23
- GlobalZeroFlag = 0x03
24
- };
25
-
26
- namespace internal {
27
-
28
- template<std::size_t NumIndices, typename... Sym> struct tensor_symmetry_pre_analysis;
29
- template<std::size_t NumIndices, typename... Sym> struct tensor_static_symgroup;
30
- template<bool instantiate, std::size_t NumIndices, typename... Sym> struct tensor_static_symgroup_if;
31
- template<typename Tensor_> struct tensor_symmetry_calculate_flags;
32
- template<typename Tensor_> struct tensor_symmetry_assign_value;
33
- template<typename... Sym> struct tensor_symmetry_num_indices;
34
-
35
- } // end namespace internal
36
-
37
- template<int One_, int Two_>
38
- struct Symmetry
39
- {
40
- static_assert(One_ != Two_, "Symmetries must cover distinct indices.");
41
- constexpr static int One = One_;
42
- constexpr static int Two = Two_;
43
- constexpr static int Flags = 0;
44
- };
45
-
46
- template<int One_, int Two_>
47
- struct AntiSymmetry
48
- {
49
- static_assert(One_ != Two_, "Symmetries must cover distinct indices.");
50
- constexpr static int One = One_;
51
- constexpr static int Two = Two_;
52
- constexpr static int Flags = NegationFlag;
53
- };
54
-
55
- template<int One_, int Two_>
56
- struct Hermiticity
57
- {
58
- static_assert(One_ != Two_, "Symmetries must cover distinct indices.");
59
- constexpr static int One = One_;
60
- constexpr static int Two = Two_;
61
- constexpr static int Flags = ConjugationFlag;
62
- };
63
-
64
- template<int One_, int Two_>
65
- struct AntiHermiticity
66
- {
67
- static_assert(One_ != Two_, "Symmetries must cover distinct indices.");
68
- constexpr static int One = One_;
69
- constexpr static int Two = Two_;
70
- constexpr static int Flags = ConjugationFlag | NegationFlag;
71
- };
72
-
73
- /** \class DynamicSGroup
74
- * \ingroup TensorSymmetry_Module
75
- *
76
- * \brief Dynamic symmetry group
77
- *
78
- * The %DynamicSGroup class represents a symmetry group that need not be known at
79
- * compile time. It is useful if one wants to support arbitrary run-time defineable
80
- * symmetries for tensors, but it is also instantiated if a symmetry group is defined
81
- * at compile time that would be either too large for the compiler to reasonably
82
- * generate (using templates to calculate this at compile time is very inefficient)
83
- * or that the compiler could generate the group but that it wouldn't make sense to
84
- * unroll the loop for setting coefficients anymore.
85
- */
86
- class DynamicSGroup;
87
-
88
- /** \internal
89
- *
90
- * \class DynamicSGroupFromTemplateArgs
91
- * \ingroup TensorSymmetry_Module
92
- *
93
- * \brief Dynamic symmetry group, initialized from template arguments
94
- *
95
- * This class is a child class of DynamicSGroup. It uses the template arguments
96
- * specified to initialize itself.
97
- */
98
- template<typename... Gen>
99
- class DynamicSGroupFromTemplateArgs;
100
-
101
- /** \class StaticSGroup
102
- * \ingroup TensorSymmetry_Module
103
- *
104
- * \brief Static symmetry group
105
- *
106
- * This class represents a symmetry group that is known and resolved completely
107
- * at compile time. Ideally, no run-time penalty is incurred compared to the
108
- * manual unrolling of the symmetry.
109
- *
110
- * <b><i>CAUTION:</i></b>
111
- *
112
- * Do not use this class directly for large symmetry groups. The compiler
113
- * may run into a limit, or segfault or in the very least will take a very,
114
- * very, very long time to compile the code. Use the SGroup class instead
115
- * if you want a static group. That class contains logic that will
116
- * automatically select the DynamicSGroup class instead if the symmetry
117
- * group becomes too large. (In that case, unrolling may not even be
118
- * beneficial.)
119
- */
120
- template<typename... Gen>
121
- class StaticSGroup;
122
-
123
- /** \class SGroup
124
- * \ingroup TensorSymmetry_Module
125
- *
126
- * \brief Symmetry group, initialized from template arguments
127
- *
128
- * This class represents a symmetry group whose generators are already
129
- * known at compile time. It may or may not be resolved at compile time,
130
- * depending on the estimated size of the group.
131
- *
132
- * \sa StaticSGroup
133
- * \sa DynamicSGroup
134
- */
135
- template<typename... Gen>
136
- class SGroup : public internal::tensor_symmetry_pre_analysis<internal::tensor_symmetry_num_indices<Gen...>::value, Gen...>::root_type
137
- {
138
- public:
139
- constexpr static std::size_t NumIndices = internal::tensor_symmetry_num_indices<Gen...>::value;
140
- typedef typename internal::tensor_symmetry_pre_analysis<NumIndices, Gen...>::root_type Base;
141
-
142
- // make standard constructors + assignment operators public
143
- inline SGroup() : Base() { }
144
- inline SGroup(const SGroup<Gen...>& other) : Base(other) { }
145
- inline SGroup(SGroup<Gen...>&& other) : Base(other) { }
146
- inline SGroup<Gen...>& operator=(const SGroup<Gen...>& other) { Base::operator=(other); return *this; }
147
- inline SGroup<Gen...>& operator=(SGroup<Gen...>&& other) { Base::operator=(other); return *this; }
148
-
149
- // all else is defined in the base class
150
- };
151
-
152
- namespace internal {
153
-
154
- template<typename... Sym> struct tensor_symmetry_num_indices
155
- {
156
- constexpr static std::size_t value = 1;
157
- };
158
-
159
- template<int One_, int Two_, typename... Sym> struct tensor_symmetry_num_indices<Symmetry<One_, Two_>, Sym...>
160
- {
161
- private:
162
- constexpr static std::size_t One = static_cast<std::size_t>(One_);
163
- constexpr static std::size_t Two = static_cast<std::size_t>(Two_);
164
- constexpr static std::size_t Three = tensor_symmetry_num_indices<Sym...>::value;
165
-
166
- // don't use std::max, since it's not constexpr until C++14...
167
- constexpr static std::size_t maxOneTwoPlusOne = ((One > Two) ? One : Two) + 1;
168
- public:
169
- constexpr static std::size_t value = (maxOneTwoPlusOne > Three) ? maxOneTwoPlusOne : Three;
170
- };
171
-
172
- template<int One_, int Two_, typename... Sym> struct tensor_symmetry_num_indices<AntiSymmetry<One_, Two_>, Sym...>
173
- : public tensor_symmetry_num_indices<Symmetry<One_, Two_>, Sym...> {};
174
- template<int One_, int Two_, typename... Sym> struct tensor_symmetry_num_indices<Hermiticity<One_, Two_>, Sym...>
175
- : public tensor_symmetry_num_indices<Symmetry<One_, Two_>, Sym...> {};
176
- template<int One_, int Two_, typename... Sym> struct tensor_symmetry_num_indices<AntiHermiticity<One_, Two_>, Sym...>
177
- : public tensor_symmetry_num_indices<Symmetry<One_, Two_>, Sym...> {};
178
-
179
- /** \internal
180
- *
181
- * \class tensor_symmetry_pre_analysis
182
- * \ingroup TensorSymmetry_Module
183
- *
184
- * \brief Pre-select whether to use a static or dynamic symmetry group
185
- *
186
- * When a symmetry group could in principle be determined at compile time,
187
- * this template implements the logic whether to actually do that or whether
188
- * to rather defer that to runtime.
189
- *
190
- * The logic is as follows:
191
- * <dl>
192
- * <dt><b>No generators (trivial symmetry):</b></dt>
193
- * <dd>Use a trivial static group. Ideally, this has no performance impact
194
- * compared to not using symmetry at all. In practice, this might not
195
- * be the case.</dd>
196
- * <dt><b>More than 4 generators:</b></dt>
197
- * <dd>Calculate the group at run time, it is likely far too large for the
198
- * compiler to be able to properly generate it in a realistic time.</dd>
199
- * <dt><b>Up to and including 4 generators:</b></dt>
200
- * <dd>Actually enumerate all group elements, but then check how many there
201
- * are. If there are more than 16, it is unlikely that unrolling the
202
- * loop (as is done in the static compile-time case) is sensible, so
203
- * use a dynamic group instead. If there are at most 16 elements, actually
204
- * use that static group. Note that the largest group with 4 generators
205
- * still compiles with reasonable resources.</dd>
206
- * </dl>
207
- *
208
- * Note: Example compile time performance with g++-4.6 on an Intenl Core i5-3470
209
- * with 16 GiB RAM (all generators non-redundant and the subgroups don't
210
- * factorize):
211
- *
212
- * # Generators -O0 -ggdb -O2
213
- * -------------------------------------------------------------------
214
- * 1 0.5 s / 250 MiB 0.45s / 230 MiB
215
- * 2 0.5 s / 260 MiB 0.5 s / 250 MiB
216
- * 3 0.65s / 310 MiB 0.62s / 310 MiB
217
- * 4 2.2 s / 860 MiB 1.7 s / 770 MiB
218
- * 5 130 s / 13000 MiB 120 s / 11000 MiB
219
- *
220
- * It is clear that everything is still very efficient up to 4 generators, then
221
- * the memory and CPU requirements become unreasonable. Thus we only instantiate
222
- * the template group theory logic if the number of generators supplied is 4 or
223
- * lower, otherwise this will be forced to be done during runtime, where the
224
- * algorithm is reasonably fast.
225
- */
226
- template<std::size_t NumIndices>
227
- struct tensor_symmetry_pre_analysis<NumIndices>
228
- {
229
- typedef StaticSGroup<> root_type;
230
- };
231
-
232
- template<std::size_t NumIndices, typename Gen_, typename... Gens_>
233
- struct tensor_symmetry_pre_analysis<NumIndices, Gen_, Gens_...>
234
- {
235
- constexpr static std::size_t max_static_generators = 4;
236
- constexpr static std::size_t max_static_elements = 16;
237
- typedef tensor_static_symgroup_if<(sizeof...(Gens_) + 1 <= max_static_generators), NumIndices, Gen_, Gens_...> helper;
238
- constexpr static std::size_t possible_size = helper::size;
239
-
240
- typedef typename conditional<
241
- possible_size == 0 || possible_size >= max_static_elements,
242
- DynamicSGroupFromTemplateArgs<Gen_, Gens_...>,
243
- typename helper::type
244
- >::type root_type;
245
- };
246
-
247
- template<bool instantiate, std::size_t NumIndices, typename... Gens>
248
- struct tensor_static_symgroup_if
249
- {
250
- constexpr static std::size_t size = 0;
251
- typedef void type;
252
- };
253
-
254
- template<std::size_t NumIndices, typename... Gens>
255
- struct tensor_static_symgroup_if<true, NumIndices, Gens...> : tensor_static_symgroup<NumIndices, Gens...> {};
256
-
257
- template<typename Tensor_>
258
- struct tensor_symmetry_assign_value
259
- {
260
- typedef typename Tensor_::Index Index;
261
- typedef typename Tensor_::Scalar Scalar;
262
- constexpr static std::size_t NumIndices = Tensor_::NumIndices;
263
-
264
- static inline int run(const std::array<Index, NumIndices>& transformed_indices, int transformation_flags, int dummy, Tensor_& tensor, const Scalar& value_)
265
- {
266
- Scalar value(value_);
267
- if (transformation_flags & ConjugationFlag)
268
- value = numext::conj(value);
269
- if (transformation_flags & NegationFlag)
270
- value = -value;
271
- tensor.coeffRef(transformed_indices) = value;
272
- return dummy;
273
- }
274
- };
275
-
276
- template<typename Tensor_>
277
- struct tensor_symmetry_calculate_flags
278
- {
279
- typedef typename Tensor_::Index Index;
280
- constexpr static std::size_t NumIndices = Tensor_::NumIndices;
281
-
282
- static inline int run(const std::array<Index, NumIndices>& transformed_indices, int transform_flags, int current_flags, const std::array<Index, NumIndices>& orig_indices)
283
- {
284
- if (transformed_indices == orig_indices) {
285
- if (transform_flags & (ConjugationFlag | NegationFlag))
286
- return current_flags | GlobalImagFlag; // anti-hermitian diagonal
287
- else if (transform_flags & ConjugationFlag)
288
- return current_flags | GlobalRealFlag; // hermitian diagonal
289
- else if (transform_flags & NegationFlag)
290
- return current_flags | GlobalZeroFlag; // anti-symmetric diagonal
291
- }
292
- return current_flags;
293
- }
294
- };
295
-
296
- template<typename Tensor_, typename Symmetry_, int Flags = 0>
297
- class tensor_symmetry_value_setter
298
- {
299
- public:
300
- typedef typename Tensor_::Index Index;
301
- typedef typename Tensor_::Scalar Scalar;
302
- constexpr static std::size_t NumIndices = Tensor_::NumIndices;
303
-
304
- inline tensor_symmetry_value_setter(Tensor_& tensor, Symmetry_ const& symmetry, std::array<Index, NumIndices> const& indices)
305
- : m_tensor(tensor), m_symmetry(symmetry), m_indices(indices) { }
306
-
307
- inline tensor_symmetry_value_setter<Tensor_, Symmetry_, Flags>& operator=(Scalar const& value)
308
- {
309
- doAssign(value);
310
- return *this;
311
- }
312
- private:
313
- Tensor_& m_tensor;
314
- Symmetry_ m_symmetry;
315
- std::array<Index, NumIndices> m_indices;
316
-
317
- inline void doAssign(Scalar const& value)
318
- {
319
- #ifdef EIGEN_TENSOR_SYMMETRY_CHECK_VALUES
320
- int value_flags = m_symmetry.template apply<internal::tensor_symmetry_calculate_flags<Tensor_>, int>(m_indices, m_symmetry.globalFlags(), m_indices);
321
- if (value_flags & GlobalRealFlag)
322
- eigen_assert(numext::imag(value) == 0);
323
- if (value_flags & GlobalImagFlag)
324
- eigen_assert(numext::real(value) == 0);
325
- #endif
326
- m_symmetry.template apply<internal::tensor_symmetry_assign_value<Tensor_>, int>(m_indices, 0, m_tensor, value);
327
- }
328
- };
329
-
330
- } // end namespace internal
331
-
332
- } // end namespace Eigen
333
-
334
- #endif // EIGEN_CXX11_TENSORSYMMETRY_SYMMETRY_H
335
-
336
- /*
337
- * kate: space-indent on; indent-width 2; mixedindent off; indent-mode cstyle;
338
- */