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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-
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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) 2006-2008 Benoit Jacob <jacob.benoit.1@gmail.com>
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- // Copyright (C) 2008 Gael Guennebaud <gael.guennebaud@inria.fr>
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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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- #include <cstdlib>
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- #include <cerrno>
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- #include <ctime>
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- #include <iostream>
16
- #include <fstream>
17
- #include <string>
18
- #include <sstream>
19
- #include <vector>
20
- #include <typeinfo>
21
- #include <functional>
22
-
23
- // The following includes of STL headers have to be done _before_ the
24
- // definition of macros min() and max(). The reason is that many STL
25
- // implementations will not work properly as the min and max symbols collide
26
- // with the STL functions std:min() and std::max(). The STL headers may check
27
- // for the macro definition of min/max and issue a warning or undefine the
28
- // macros.
29
- //
30
- // Still, Windows defines min() and max() in windef.h as part of the regular
31
- // Windows system interfaces and many other Windows APIs depend on these
32
- // macros being available. To prevent the macro expansion of min/max and to
33
- // make Eigen compatible with the Windows environment all function calls of
34
- // std::min() and std::max() have to be written with parenthesis around the
35
- // function name.
36
- //
37
- // All STL headers used by Eigen should be included here. Because main.h is
38
- // included before any Eigen header and because the STL headers are guarded
39
- // against multiple inclusions, no STL header will see our own min/max macro
40
- // definitions.
41
- #include <limits>
42
- #include <algorithm>
43
- // Disable ICC's std::complex operator specializations so we can use our own.
44
- #define _OVERRIDE_COMPLEX_SPECIALIZATION_ 1
45
- #include <complex>
46
- #include <deque>
47
- #include <queue>
48
- #include <cassert>
49
- #include <list>
50
- #if __cplusplus >= 201103L || (defined(_MSVC_LANG) && _MSVC_LANG >= 201103L)
51
- #include <random>
52
- #include <chrono>
53
- #ifdef EIGEN_USE_THREADS
54
- #include <future>
55
- #endif
56
- #endif
57
-
58
- // Same for cuda_fp16.h
59
- #if defined(__CUDACC__) && !defined(EIGEN_NO_CUDA)
60
- // Means the compiler is either nvcc or clang with CUDA enabled
61
- #define EIGEN_CUDACC __CUDACC__
62
- #endif
63
- #if defined(EIGEN_CUDACC)
64
- #include <cuda.h>
65
- #define EIGEN_CUDA_SDK_VER (CUDA_VERSION * 10)
66
- #else
67
- #define EIGEN_CUDA_SDK_VER 0
68
- #endif
69
- #if EIGEN_CUDA_SDK_VER >= 70500
70
- #include <cuda_fp16.h>
71
- #endif
72
-
73
- // To test that all calls from Eigen code to std::min() and std::max() are
74
- // protected by parenthesis against macro expansion, the min()/max() macros
75
- // are defined here and any not-parenthesized min/max call will cause a
76
- // compiler error.
77
- #if !defined(__HIPCC__) && !defined(EIGEN_USE_SYCL)
78
- //
79
- // HIP header files include the following files
80
- // <thread>
81
- // <regex>
82
- // <unordered_map>
83
- // which seem to contain not-parenthesized calls to "max"/"min", triggering the following check and causing the compile to fail
84
- //
85
- // Including those header files before the following macro definition for "min" / "max", only partially resolves the issue
86
- // This is because other HIP header files also define "isnan" / "isinf" / "isfinite" functions, which are needed in other
87
- // headers.
88
- //
89
- // So instead choosing to simply disable this check for HIP
90
- //
91
- #define min(A,B) please_protect_your_min_with_parentheses
92
- #define max(A,B) please_protect_your_max_with_parentheses
93
- #define isnan(X) please_protect_your_isnan_with_parentheses
94
- #define isinf(X) please_protect_your_isinf_with_parentheses
95
- #define isfinite(X) please_protect_your_isfinite_with_parentheses
96
- #endif
97
-
98
-
99
- // test possible conflicts
100
- struct real {};
101
- struct imag {};
102
-
103
- #ifdef M_PI
104
- #undef M_PI
105
- #endif
106
- #define M_PI please_use_EIGEN_PI_instead_of_M_PI
107
-
108
- #define FORBIDDEN_IDENTIFIER (this_identifier_is_forbidden_to_avoid_clashes) this_identifier_is_forbidden_to_avoid_clashes
109
- // B0 is defined in POSIX header termios.h
110
- #define B0 FORBIDDEN_IDENTIFIER
111
- // `I` may be defined by complex.h:
112
- #define I FORBIDDEN_IDENTIFIER
113
-
114
- // Unit tests calling Eigen's blas library must preserve the default blocking size
115
- // to avoid troubles.
116
- #ifndef EIGEN_NO_DEBUG_SMALL_PRODUCT_BLOCKS
117
- #define EIGEN_DEBUG_SMALL_PRODUCT_BLOCKS
118
- #endif
119
-
120
- // shuts down ICC's remark #593: variable "XXX" was set but never used
121
- #define TEST_SET_BUT_UNUSED_VARIABLE(X) EIGEN_UNUSED_VARIABLE(X)
122
-
123
- #ifdef TEST_ENABLE_TEMPORARY_TRACKING
124
-
125
- static long int nb_temporaries;
126
- static long int nb_temporaries_on_assert = -1;
127
-
128
- inline void on_temporary_creation(long int size) {
129
- // here's a great place to set a breakpoint when debugging failures in this test!
130
- if(size!=0) nb_temporaries++;
131
- if(nb_temporaries_on_assert>0) assert(nb_temporaries<nb_temporaries_on_assert);
132
- }
133
-
134
- #define EIGEN_DENSE_STORAGE_CTOR_PLUGIN { on_temporary_creation(size); }
135
-
136
- #define VERIFY_EVALUATION_COUNT(XPR,N) {\
137
- nb_temporaries = 0; \
138
- XPR; \
139
- if(nb_temporaries!=(N)) { std::cerr << "nb_temporaries == " << nb_temporaries << "\n"; }\
140
- VERIFY( (#XPR) && nb_temporaries==(N) ); \
141
- }
142
-
143
- #endif
144
-
145
- #include "split_test_helper.h"
146
-
147
- #ifdef NDEBUG
148
- #undef NDEBUG
149
- #endif
150
-
151
- // On windows CE, NDEBUG is automatically defined <assert.h> if NDEBUG is not defined.
152
- #ifndef DEBUG
153
- #define DEBUG
154
- #endif
155
-
156
- // bounds integer values for AltiVec
157
- #if defined(__ALTIVEC__) || defined(__VSX__)
158
- #define EIGEN_MAKING_DOCS
159
- #endif
160
-
161
- #define DEFAULT_REPEAT 10
162
-
163
- namespace Eigen
164
- {
165
- static std::vector<std::string> g_test_stack;
166
- // level == 0 <=> abort if test fail
167
- // level >= 1 <=> warning message to std::cerr if test fail
168
- static int g_test_level = 0;
169
- static int g_repeat = 1;
170
- static unsigned int g_seed = 0;
171
- static bool g_has_set_repeat = false, g_has_set_seed = false;
172
-
173
- class EigenTest
174
- {
175
- public:
176
- EigenTest() : m_func(0) {}
177
- EigenTest(const char* a_name, void (*func)(void))
178
- : m_name(a_name), m_func(func)
179
- {
180
- get_registered_tests().push_back(this);
181
- }
182
- const std::string& name() const { return m_name; }
183
- void operator()() const { m_func(); }
184
-
185
- static const std::vector<EigenTest*>& all() { return get_registered_tests(); }
186
- protected:
187
- static std::vector<EigenTest*>& get_registered_tests()
188
- {
189
- static std::vector<EigenTest*>* ms_registered_tests = new std::vector<EigenTest*>();
190
- return *ms_registered_tests;
191
- }
192
- std::string m_name;
193
- void (*m_func)(void);
194
- };
195
-
196
- // Declare and register a test, e.g.:
197
- // EIGEN_DECLARE_TEST(mytest) { ... }
198
- // will create a function:
199
- // void test_mytest() { ... }
200
- // that will be automatically called.
201
- #define EIGEN_DECLARE_TEST(X) \
202
- void EIGEN_CAT(test_,X) (); \
203
- static EigenTest EIGEN_CAT(test_handler_,X) (EIGEN_MAKESTRING(X), & EIGEN_CAT(test_,X)); \
204
- void EIGEN_CAT(test_,X) ()
205
- }
206
-
207
- #define TRACK std::cerr << __FILE__ << " " << __LINE__ << std::endl
208
- // #define TRACK while()
209
-
210
- #define EIGEN_DEFAULT_IO_FORMAT IOFormat(4, 0, " ", "\n", "", "", "", "")
211
-
212
- #if (defined(_CPPUNWIND) || defined(__EXCEPTIONS)) && !defined(__CUDA_ARCH__) && !defined(__HIP_DEVICE_COMPILE__) && !defined(__SYCL_DEVICE_ONLY__)
213
- #define EIGEN_EXCEPTIONS
214
- #endif
215
-
216
- #ifndef EIGEN_NO_ASSERTION_CHECKING
217
-
218
- namespace Eigen
219
- {
220
- static const bool should_raise_an_assert = false;
221
-
222
- // Used to avoid to raise two exceptions at a time in which
223
- // case the exception is not properly caught.
224
- // This may happen when a second exceptions is triggered in a destructor.
225
- static bool no_more_assert = false;
226
- static bool report_on_cerr_on_assert_failure = true;
227
-
228
- struct eigen_assert_exception
229
- {
230
- eigen_assert_exception(void) {}
231
- ~eigen_assert_exception() { Eigen::no_more_assert = false; }
232
- };
233
-
234
- struct eigen_static_assert_exception
235
- {
236
- eigen_static_assert_exception(void) {}
237
- ~eigen_static_assert_exception() { Eigen::no_more_assert = false; }
238
- };
239
- }
240
- // If EIGEN_DEBUG_ASSERTS is defined and if no assertion is triggered while
241
- // one should have been, then the list of executed assertions is printed out.
242
- //
243
- // EIGEN_DEBUG_ASSERTS is not enabled by default as it
244
- // significantly increases the compilation time
245
- // and might even introduce side effects that would hide
246
- // some memory errors.
247
- #ifdef EIGEN_DEBUG_ASSERTS
248
-
249
- namespace Eigen
250
- {
251
- namespace internal
252
- {
253
- static bool push_assert = false;
254
- }
255
- static std::vector<std::string> eigen_assert_list;
256
- }
257
- #define eigen_assert(a) \
258
- if( (!(a)) && (!no_more_assert) ) \
259
- { \
260
- if(report_on_cerr_on_assert_failure) \
261
- std::cerr << #a << " " __FILE__ << "(" << __LINE__ << ")\n"; \
262
- Eigen::no_more_assert = true; \
263
- EIGEN_THROW_X(Eigen::eigen_assert_exception()); \
264
- } \
265
- else if (Eigen::internal::push_assert) \
266
- { \
267
- eigen_assert_list.push_back(std::string(EIGEN_MAKESTRING(__FILE__) " (" EIGEN_MAKESTRING(__LINE__) ") : " #a) ); \
268
- }
269
-
270
- #ifdef EIGEN_EXCEPTIONS
271
- #define VERIFY_RAISES_ASSERT(a) \
272
- { \
273
- Eigen::no_more_assert = false; \
274
- Eigen::eigen_assert_list.clear(); \
275
- Eigen::internal::push_assert = true; \
276
- Eigen::report_on_cerr_on_assert_failure = false; \
277
- try { \
278
- a; \
279
- std::cerr << "One of the following asserts should have been triggered:\n"; \
280
- for (uint ai=0 ; ai<eigen_assert_list.size() ; ++ai) \
281
- std::cerr << " " << eigen_assert_list[ai] << "\n"; \
282
- VERIFY(Eigen::should_raise_an_assert && # a); \
283
- } catch (Eigen::eigen_assert_exception) { \
284
- Eigen::internal::push_assert = false; VERIFY(true); \
285
- } \
286
- Eigen::report_on_cerr_on_assert_failure = true; \
287
- Eigen::internal::push_assert = false; \
288
- }
289
- #endif //EIGEN_EXCEPTIONS
290
-
291
- #elif !defined(__CUDACC__) && !defined(__HIPCC__) && !defined(SYCL_DEVICE_ONLY) // EIGEN_DEBUG_ASSERTS
292
- // see bug 89. The copy_bool here is working around a bug in gcc <= 4.3
293
- #define eigen_assert(a) \
294
- if( (!Eigen::internal::copy_bool(a)) && (!no_more_assert) )\
295
- { \
296
- Eigen::no_more_assert = true; \
297
- if(report_on_cerr_on_assert_failure) \
298
- eigen_plain_assert(a); \
299
- else \
300
- EIGEN_THROW_X(Eigen::eigen_assert_exception()); \
301
- }
302
-
303
- #ifdef EIGEN_EXCEPTIONS
304
- #define VERIFY_RAISES_ASSERT(a) { \
305
- Eigen::no_more_assert = false; \
306
- Eigen::report_on_cerr_on_assert_failure = false; \
307
- try { \
308
- a; \
309
- VERIFY(Eigen::should_raise_an_assert && # a); \
310
- } \
311
- catch (Eigen::eigen_assert_exception&) { VERIFY(true); } \
312
- Eigen::report_on_cerr_on_assert_failure = true; \
313
- }
314
- #endif // EIGEN_EXCEPTIONS
315
- #endif // EIGEN_DEBUG_ASSERTS
316
-
317
- #if defined(TEST_CHECK_STATIC_ASSERTIONS) && defined(EIGEN_EXCEPTIONS)
318
- #define EIGEN_STATIC_ASSERT(a,MSG) \
319
- if( (!Eigen::internal::copy_bool(a)) && (!no_more_assert) )\
320
- { \
321
- Eigen::no_more_assert = true; \
322
- if(report_on_cerr_on_assert_failure) \
323
- eigen_plain_assert((a) && #MSG); \
324
- else \
325
- EIGEN_THROW_X(Eigen::eigen_static_assert_exception()); \
326
- }
327
- #define VERIFY_RAISES_STATIC_ASSERT(a) { \
328
- Eigen::no_more_assert = false; \
329
- Eigen::report_on_cerr_on_assert_failure = false; \
330
- try { \
331
- a; \
332
- VERIFY(Eigen::should_raise_an_assert && # a); \
333
- } \
334
- catch (Eigen::eigen_static_assert_exception&) { VERIFY(true); } \
335
- Eigen::report_on_cerr_on_assert_failure = true; \
336
- }
337
- #endif // TEST_CHECK_STATIC_ASSERTIONS
338
-
339
- #ifndef VERIFY_RAISES_ASSERT
340
- #define VERIFY_RAISES_ASSERT(a) \
341
- std::cout << "Can't VERIFY_RAISES_ASSERT( " #a " ) with exceptions disabled\n";
342
- #endif
343
- #ifndef VERIFY_RAISES_STATIC_ASSERT
344
- #define VERIFY_RAISES_STATIC_ASSERT(a) \
345
- std::cout << "Can't VERIFY_RAISES_STATIC_ASSERT( " #a " ) with exceptions disabled\n";
346
- #endif
347
-
348
- #if !defined(__CUDACC__) && !defined(__HIPCC__) && !defined(SYCL_DEVICE_ONLY)
349
- #define EIGEN_USE_CUSTOM_ASSERT
350
- #endif
351
-
352
- #else // EIGEN_NO_ASSERTION_CHECKING
353
-
354
- #define VERIFY_RAISES_ASSERT(a) {}
355
- #define VERIFY_RAISES_STATIC_ASSERT(a) {}
356
-
357
- #endif // EIGEN_NO_ASSERTION_CHECKING
358
-
359
- #define EIGEN_INTERNAL_DEBUGGING
360
- #include <Eigen/QR> // required for createRandomPIMatrixOfRank
361
-
362
- inline void verify_impl(bool condition, const char *testname, const char *file, int line, const char *condition_as_string)
363
- {
364
- if (!condition)
365
- {
366
- if(Eigen::g_test_level>0)
367
- std::cerr << "WARNING: ";
368
- std::cerr << "Test " << testname << " failed in " << file << " (" << line << ")"
369
- << std::endl << " " << condition_as_string << std::endl;
370
- std::cerr << "Stack:\n";
371
- const int test_stack_size = static_cast<int>(Eigen::g_test_stack.size());
372
- for(int i=test_stack_size-1; i>=0; --i)
373
- std::cerr << " - " << Eigen::g_test_stack[i] << "\n";
374
- std::cerr << "\n";
375
- if(Eigen::g_test_level==0)
376
- abort();
377
- }
378
- }
379
-
380
- #define VERIFY(a) ::verify_impl(a, g_test_stack.back().c_str(), __FILE__, __LINE__, EIGEN_MAKESTRING(a))
381
-
382
- #define VERIFY_GE(a, b) ::verify_impl(a >= b, g_test_stack.back().c_str(), __FILE__, __LINE__, EIGEN_MAKESTRING(a >= b))
383
- #define VERIFY_LE(a, b) ::verify_impl(a <= b, g_test_stack.back().c_str(), __FILE__, __LINE__, EIGEN_MAKESTRING(a <= b))
384
-
385
-
386
- #define VERIFY_IS_EQUAL(a, b) VERIFY(test_is_equal(a, b, true))
387
- #define VERIFY_IS_NOT_EQUAL(a, b) VERIFY(test_is_equal(a, b, false))
388
- #define VERIFY_IS_APPROX(a, b) VERIFY(verifyIsApprox(a, b))
389
- #define VERIFY_IS_NOT_APPROX(a, b) VERIFY(!test_isApprox(a, b))
390
- #define VERIFY_IS_MUCH_SMALLER_THAN(a, b) VERIFY(test_isMuchSmallerThan(a, b))
391
- #define VERIFY_IS_NOT_MUCH_SMALLER_THAN(a, b) VERIFY(!test_isMuchSmallerThan(a, b))
392
- #define VERIFY_IS_APPROX_OR_LESS_THAN(a, b) VERIFY(test_isApproxOrLessThan(a, b))
393
- #define VERIFY_IS_NOT_APPROX_OR_LESS_THAN(a, b) VERIFY(!test_isApproxOrLessThan(a, b))
394
-
395
- #define VERIFY_IS_UNITARY(a) VERIFY(test_isUnitary(a))
396
-
397
- #define STATIC_CHECK(COND) EIGEN_STATIC_ASSERT( (COND) , EIGEN_INTERNAL_ERROR_PLEASE_FILE_A_BUG_REPORT )
398
-
399
- #define CALL_SUBTEST(FUNC) do { \
400
- g_test_stack.push_back(EIGEN_MAKESTRING(FUNC)); \
401
- FUNC; \
402
- g_test_stack.pop_back(); \
403
- } while (0)
404
-
405
-
406
- namespace Eigen {
407
-
408
- template<typename T1,typename T2>
409
- typename internal::enable_if<internal::is_same<T1,T2>::value,bool>::type
410
- is_same_type(const T1&, const T2&)
411
- {
412
- return true;
413
- }
414
-
415
- template<typename T> inline typename NumTraits<T>::Real test_precision() { return NumTraits<T>::dummy_precision(); }
416
- template<> inline float test_precision<float>() { return 1e-3f; }
417
- template<> inline double test_precision<double>() { return 1e-6; }
418
- template<> inline long double test_precision<long double>() { return 1e-6l; }
419
- template<> inline float test_precision<std::complex<float> >() { return test_precision<float>(); }
420
- template<> inline double test_precision<std::complex<double> >() { return test_precision<double>(); }
421
- template<> inline long double test_precision<std::complex<long double> >() { return test_precision<long double>(); }
422
-
423
- #define EIGEN_TEST_SCALAR_TEST_OVERLOAD(TYPE) \
424
- inline bool test_isApprox(TYPE a, TYPE b) \
425
- { return internal::isApprox(a, b, test_precision<TYPE>()); } \
426
- inline bool test_isMuchSmallerThan(TYPE a, TYPE b) \
427
- { return internal::isMuchSmallerThan(a, b, test_precision<TYPE>()); } \
428
- inline bool test_isApproxOrLessThan(TYPE a, TYPE b) \
429
- { return internal::isApproxOrLessThan(a, b, test_precision<TYPE>()); }
430
-
431
- EIGEN_TEST_SCALAR_TEST_OVERLOAD(short)
432
- EIGEN_TEST_SCALAR_TEST_OVERLOAD(unsigned short)
433
- EIGEN_TEST_SCALAR_TEST_OVERLOAD(int)
434
- EIGEN_TEST_SCALAR_TEST_OVERLOAD(unsigned int)
435
- EIGEN_TEST_SCALAR_TEST_OVERLOAD(long)
436
- EIGEN_TEST_SCALAR_TEST_OVERLOAD(unsigned long)
437
- #if EIGEN_HAS_CXX11
438
- EIGEN_TEST_SCALAR_TEST_OVERLOAD(long long)
439
- EIGEN_TEST_SCALAR_TEST_OVERLOAD(unsigned long long)
440
- #endif
441
- EIGEN_TEST_SCALAR_TEST_OVERLOAD(float)
442
- EIGEN_TEST_SCALAR_TEST_OVERLOAD(double)
443
- EIGEN_TEST_SCALAR_TEST_OVERLOAD(half)
444
- EIGEN_TEST_SCALAR_TEST_OVERLOAD(bfloat16)
445
-
446
- #undef EIGEN_TEST_SCALAR_TEST_OVERLOAD
447
-
448
- #ifndef EIGEN_TEST_NO_COMPLEX
449
- inline bool test_isApprox(const std::complex<float>& a, const std::complex<float>& b)
450
- { return internal::isApprox(a, b, test_precision<std::complex<float> >()); }
451
- inline bool test_isMuchSmallerThan(const std::complex<float>& a, const std::complex<float>& b)
452
- { return internal::isMuchSmallerThan(a, b, test_precision<std::complex<float> >()); }
453
-
454
- inline bool test_isApprox(const std::complex<double>& a, const std::complex<double>& b)
455
- { return internal::isApprox(a, b, test_precision<std::complex<double> >()); }
456
- inline bool test_isMuchSmallerThan(const std::complex<double>& a, const std::complex<double>& b)
457
- { return internal::isMuchSmallerThan(a, b, test_precision<std::complex<double> >()); }
458
-
459
- #ifndef EIGEN_TEST_NO_LONGDOUBLE
460
- inline bool test_isApprox(const std::complex<long double>& a, const std::complex<long double>& b)
461
- { return internal::isApprox(a, b, test_precision<std::complex<long double> >()); }
462
- inline bool test_isMuchSmallerThan(const std::complex<long double>& a, const std::complex<long double>& b)
463
- { return internal::isMuchSmallerThan(a, b, test_precision<std::complex<long double> >()); }
464
- #endif
465
- #endif
466
-
467
- #ifndef EIGEN_TEST_NO_LONGDOUBLE
468
- inline bool test_isApprox(const long double& a, const long double& b)
469
- {
470
- bool ret = internal::isApprox(a, b, test_precision<long double>());
471
- if (!ret) std::cerr
472
- << std::endl << " actual = " << a
473
- << std::endl << " expected = " << b << std::endl << std::endl;
474
- return ret;
475
- }
476
-
477
- inline bool test_isMuchSmallerThan(const long double& a, const long double& b)
478
- { return internal::isMuchSmallerThan(a, b, test_precision<long double>()); }
479
- inline bool test_isApproxOrLessThan(const long double& a, const long double& b)
480
- { return internal::isApproxOrLessThan(a, b, test_precision<long double>()); }
481
- #endif // EIGEN_TEST_NO_LONGDOUBLE
482
-
483
- // test_relative_error returns the relative difference between a and b as a real scalar as used in isApprox.
484
- template<typename T1,typename T2>
485
- typename NumTraits<typename T1::RealScalar>::NonInteger test_relative_error(const EigenBase<T1> &a, const EigenBase<T2> &b)
486
- {
487
- using std::sqrt;
488
- typedef typename NumTraits<typename T1::RealScalar>::NonInteger RealScalar;
489
- typename internal::nested_eval<T1,2>::type ea(a.derived());
490
- typename internal::nested_eval<T2,2>::type eb(b.derived());
491
- return sqrt(RealScalar((ea-eb).cwiseAbs2().sum()) / RealScalar((std::min)(eb.cwiseAbs2().sum(),ea.cwiseAbs2().sum())));
492
- }
493
-
494
- template<typename T1,typename T2>
495
- typename T1::RealScalar test_relative_error(const T1 &a, const T2 &b, const typename T1::Coefficients* = 0)
496
- {
497
- return test_relative_error(a.coeffs(), b.coeffs());
498
- }
499
-
500
- template<typename T1,typename T2>
501
- typename T1::Scalar test_relative_error(const T1 &a, const T2 &b, const typename T1::MatrixType* = 0)
502
- {
503
- return test_relative_error(a.matrix(), b.matrix());
504
- }
505
-
506
- template<typename S, int D>
507
- S test_relative_error(const Translation<S,D> &a, const Translation<S,D> &b)
508
- {
509
- return test_relative_error(a.vector(), b.vector());
510
- }
511
-
512
- template <typename S, int D, int O>
513
- S test_relative_error(const ParametrizedLine<S,D,O> &a, const ParametrizedLine<S,D,O> &b)
514
- {
515
- return (std::max)(test_relative_error(a.origin(), b.origin()), test_relative_error(a.origin(), b.origin()));
516
- }
517
-
518
- template <typename S, int D>
519
- S test_relative_error(const AlignedBox<S,D> &a, const AlignedBox<S,D> &b)
520
- {
521
- return (std::max)(test_relative_error((a.min)(), (b.min)()), test_relative_error((a.max)(), (b.max)()));
522
- }
523
-
524
- template<typename Derived> class SparseMatrixBase;
525
- template<typename T1,typename T2>
526
- typename T1::RealScalar test_relative_error(const MatrixBase<T1> &a, const SparseMatrixBase<T2> &b)
527
- {
528
- return test_relative_error(a,b.toDense());
529
- }
530
-
531
- template<typename Derived> class SparseMatrixBase;
532
- template<typename T1,typename T2>
533
- typename T1::RealScalar test_relative_error(const SparseMatrixBase<T1> &a, const MatrixBase<T2> &b)
534
- {
535
- return test_relative_error(a.toDense(),b);
536
- }
537
-
538
- template<typename Derived> class SparseMatrixBase;
539
- template<typename T1,typename T2>
540
- typename T1::RealScalar test_relative_error(const SparseMatrixBase<T1> &a, const SparseMatrixBase<T2> &b)
541
- {
542
- return test_relative_error(a.toDense(),b.toDense());
543
- }
544
-
545
- template<typename T1,typename T2>
546
- typename NumTraits<typename NumTraits<T1>::Real>::NonInteger test_relative_error(const T1 &a, const T2 &b, typename internal::enable_if<internal::is_arithmetic<typename NumTraits<T1>::Real>::value, T1>::type* = 0)
547
- {
548
- typedef typename NumTraits<typename NumTraits<T1>::Real>::NonInteger RealScalar;
549
- return numext::sqrt(RealScalar(numext::abs2(a-b))/(numext::mini)(RealScalar(numext::abs2(a)),RealScalar(numext::abs2(b))));
550
- }
551
-
552
- template<typename T>
553
- T test_relative_error(const Rotation2D<T> &a, const Rotation2D<T> &b)
554
- {
555
- return test_relative_error(a.angle(), b.angle());
556
- }
557
-
558
- template<typename T>
559
- T test_relative_error(const AngleAxis<T> &a, const AngleAxis<T> &b)
560
- {
561
- return (std::max)(test_relative_error(a.angle(), b.angle()), test_relative_error(a.axis(), b.axis()));
562
- }
563
-
564
- template<typename Type1, typename Type2>
565
- inline bool test_isApprox(const Type1& a, const Type2& b, typename Type1::Scalar* = 0) // Enabled for Eigen's type only
566
- {
567
- return a.isApprox(b, test_precision<typename Type1::Scalar>());
568
- }
569
-
570
- // get_test_precision is a small wrapper to test_precision allowing to return the scalar precision for either scalars or expressions
571
- template<typename T>
572
- typename NumTraits<typename T::Scalar>::Real get_test_precision(const T&, const typename T::Scalar* = 0)
573
- {
574
- return test_precision<typename NumTraits<typename T::Scalar>::Real>();
575
- }
576
-
577
- template<typename T>
578
- typename NumTraits<T>::Real get_test_precision(const T&,typename internal::enable_if<internal::is_arithmetic<typename NumTraits<T>::Real>::value, T>::type* = 0)
579
- {
580
- return test_precision<typename NumTraits<T>::Real>();
581
- }
582
-
583
- // verifyIsApprox is a wrapper to test_isApprox that outputs the relative difference magnitude if the test fails.
584
- template<typename Type1, typename Type2>
585
- inline bool verifyIsApprox(const Type1& a, const Type2& b)
586
- {
587
- bool ret = test_isApprox(a,b);
588
- if(!ret)
589
- {
590
- std::cerr << "Difference too large wrt tolerance " << get_test_precision(a) << ", relative error is: " << test_relative_error(a,b) << std::endl;
591
- }
592
- return ret;
593
- }
594
-
595
- // The idea behind this function is to compare the two scalars a and b where
596
- // the scalar ref is a hint about the expected order of magnitude of a and b.
597
- // WARNING: the scalar a and b must be positive
598
- // Therefore, if for some reason a and b are very small compared to ref,
599
- // we won't issue a false negative.
600
- // This test could be: abs(a-b) <= eps * ref
601
- // However, it seems that simply comparing a+ref and b+ref is more sensitive to true error.
602
- template<typename Scalar,typename ScalarRef>
603
- inline bool test_isApproxWithRef(const Scalar& a, const Scalar& b, const ScalarRef& ref)
604
- {
605
- return test_isApprox(a+ref, b+ref);
606
- }
607
-
608
- template<typename Derived1, typename Derived2>
609
- inline bool test_isMuchSmallerThan(const MatrixBase<Derived1>& m1,
610
- const MatrixBase<Derived2>& m2)
611
- {
612
- return m1.isMuchSmallerThan(m2, test_precision<typename internal::traits<Derived1>::Scalar>());
613
- }
614
-
615
- template<typename Derived>
616
- inline bool test_isMuchSmallerThan(const MatrixBase<Derived>& m,
617
- const typename NumTraits<typename internal::traits<Derived>::Scalar>::Real& s)
618
- {
619
- return m.isMuchSmallerThan(s, test_precision<typename internal::traits<Derived>::Scalar>());
620
- }
621
-
622
- template<typename Derived>
623
- inline bool test_isUnitary(const MatrixBase<Derived>& m)
624
- {
625
- return m.isUnitary(test_precision<typename internal::traits<Derived>::Scalar>());
626
- }
627
-
628
- // Forward declaration to avoid ICC warning
629
- template<typename T, typename U>
630
- bool test_is_equal(const T& actual, const U& expected, bool expect_equal=true);
631
-
632
- template<typename T, typename U>
633
- bool test_is_equal(const T& actual, const U& expected, bool expect_equal)
634
- {
635
- if ((actual==expected) == expect_equal)
636
- return true;
637
- // false:
638
- std::cerr
639
- << "\n actual = " << actual
640
- << "\n expected " << (expect_equal ? "= " : "!=") << expected << "\n\n";
641
- return false;
642
- }
643
-
644
- /** Creates a random Partial Isometry matrix of given rank.
645
- *
646
- * A partial isometry is a matrix all of whose singular values are either 0 or 1.
647
- * This is very useful to test rank-revealing algorithms.
648
- */
649
- // Forward declaration to avoid ICC warning
650
- template<typename MatrixType>
651
- void createRandomPIMatrixOfRank(Index desired_rank, Index rows, Index cols, MatrixType& m);
652
- template<typename MatrixType>
653
- void createRandomPIMatrixOfRank(Index desired_rank, Index rows, Index cols, MatrixType& m)
654
- {
655
- typedef typename internal::traits<MatrixType>::Scalar Scalar;
656
- enum { Rows = MatrixType::RowsAtCompileTime, Cols = MatrixType::ColsAtCompileTime };
657
-
658
- typedef Matrix<Scalar, Dynamic, 1> VectorType;
659
- typedef Matrix<Scalar, Rows, Rows> MatrixAType;
660
- typedef Matrix<Scalar, Cols, Cols> MatrixBType;
661
-
662
- if(desired_rank == 0)
663
- {
664
- m.setZero(rows,cols);
665
- return;
666
- }
667
-
668
- if(desired_rank == 1)
669
- {
670
- // here we normalize the vectors to get a partial isometry
671
- m = VectorType::Random(rows).normalized() * VectorType::Random(cols).normalized().transpose();
672
- return;
673
- }
674
-
675
- MatrixAType a = MatrixAType::Random(rows,rows);
676
- MatrixType d = MatrixType::Identity(rows,cols);
677
- MatrixBType b = MatrixBType::Random(cols,cols);
678
-
679
- // set the diagonal such that only desired_rank non-zero entries reamain
680
- const Index diag_size = (std::min)(d.rows(),d.cols());
681
- if(diag_size != desired_rank)
682
- d.diagonal().segment(desired_rank, diag_size-desired_rank) = VectorType::Zero(diag_size-desired_rank);
683
-
684
- HouseholderQR<MatrixAType> qra(a);
685
- HouseholderQR<MatrixBType> qrb(b);
686
- m = qra.householderQ() * d * qrb.householderQ();
687
- }
688
-
689
- // Forward declaration to avoid ICC warning
690
- template<typename PermutationVectorType>
691
- void randomPermutationVector(PermutationVectorType& v, Index size);
692
- template<typename PermutationVectorType>
693
- void randomPermutationVector(PermutationVectorType& v, Index size)
694
- {
695
- typedef typename PermutationVectorType::Scalar Scalar;
696
- v.resize(size);
697
- for(Index i = 0; i < size; ++i) v(i) = Scalar(i);
698
- if(size == 1) return;
699
- for(Index n = 0; n < 3 * size; ++n)
700
- {
701
- Index i = internal::random<Index>(0, size-1);
702
- Index j;
703
- do j = internal::random<Index>(0, size-1); while(j==i);
704
- std::swap(v(i), v(j));
705
- }
706
- }
707
-
708
- template<typename T> bool isNotNaN(const T& x)
709
- {
710
- return x==x;
711
- }
712
-
713
- template<typename T> bool isPlusInf(const T& x)
714
- {
715
- return x > NumTraits<T>::highest();
716
- }
717
-
718
- template<typename T> bool isMinusInf(const T& x)
719
- {
720
- return x < NumTraits<T>::lowest();
721
- }
722
-
723
- } // end namespace Eigen
724
-
725
- template<typename T> struct GetDifferentType;
726
-
727
- template<> struct GetDifferentType<float> { typedef double type; };
728
- template<> struct GetDifferentType<double> { typedef float type; };
729
- template<typename T> struct GetDifferentType<std::complex<T> >
730
- { typedef std::complex<typename GetDifferentType<T>::type> type; };
731
-
732
- // Forward declaration to avoid ICC warning
733
- template<typename T> std::string type_name();
734
- template<typename T> std::string type_name() { return "other"; }
735
- template<> std::string type_name<float>() { return "float"; }
736
- template<> std::string type_name<double>() { return "double"; }
737
- template<> std::string type_name<long double>() { return "long double"; }
738
- template<> std::string type_name<int>() { return "int"; }
739
- template<> std::string type_name<std::complex<float> >() { return "complex<float>"; }
740
- template<> std::string type_name<std::complex<double> >() { return "complex<double>"; }
741
- template<> std::string type_name<std::complex<long double> >() { return "complex<long double>"; }
742
- template<> std::string type_name<std::complex<int> >() { return "complex<int>"; }
743
-
744
- using namespace Eigen;
745
-
746
- inline void set_repeat_from_string(const char *str)
747
- {
748
- errno = 0;
749
- g_repeat = int(strtoul(str, 0, 10));
750
- if(errno || g_repeat <= 0)
751
- {
752
- std::cout << "Invalid repeat value " << str << std::endl;
753
- exit(EXIT_FAILURE);
754
- }
755
- g_has_set_repeat = true;
756
- }
757
-
758
- inline void set_seed_from_string(const char *str)
759
- {
760
- errno = 0;
761
- g_seed = int(strtoul(str, 0, 10));
762
- if(errno || g_seed == 0)
763
- {
764
- std::cout << "Invalid seed value " << str << std::endl;
765
- exit(EXIT_FAILURE);
766
- }
767
- g_has_set_seed = true;
768
- }
769
-
770
- int main(int argc, char *argv[])
771
- {
772
- g_has_set_repeat = false;
773
- g_has_set_seed = false;
774
- bool need_help = false;
775
-
776
- for(int i = 1; i < argc; i++)
777
- {
778
- if(argv[i][0] == 'r')
779
- {
780
- if(g_has_set_repeat)
781
- {
782
- std::cout << "Argument " << argv[i] << " conflicting with a former argument" << std::endl;
783
- return 1;
784
- }
785
- set_repeat_from_string(argv[i]+1);
786
- }
787
- else if(argv[i][0] == 's')
788
- {
789
- if(g_has_set_seed)
790
- {
791
- std::cout << "Argument " << argv[i] << " conflicting with a former argument" << std::endl;
792
- return 1;
793
- }
794
- set_seed_from_string(argv[i]+1);
795
- }
796
- else
797
- {
798
- need_help = true;
799
- }
800
- }
801
-
802
- if(need_help)
803
- {
804
- std::cout << "This test application takes the following optional arguments:" << std::endl;
805
- std::cout << " rN Repeat each test N times (default: " << DEFAULT_REPEAT << ")" << std::endl;
806
- std::cout << " sN Use N as seed for random numbers (default: based on current time)" << std::endl;
807
- std::cout << std::endl;
808
- std::cout << "If defined, the environment variables EIGEN_REPEAT and EIGEN_SEED" << std::endl;
809
- std::cout << "will be used as default values for these parameters." << std::endl;
810
- return 1;
811
- }
812
-
813
- char *env_EIGEN_REPEAT = getenv("EIGEN_REPEAT");
814
- if(!g_has_set_repeat && env_EIGEN_REPEAT)
815
- set_repeat_from_string(env_EIGEN_REPEAT);
816
- char *env_EIGEN_SEED = getenv("EIGEN_SEED");
817
- if(!g_has_set_seed && env_EIGEN_SEED)
818
- set_seed_from_string(env_EIGEN_SEED);
819
-
820
- if(!g_has_set_seed) g_seed = (unsigned int) time(NULL);
821
- if(!g_has_set_repeat) g_repeat = DEFAULT_REPEAT;
822
-
823
- std::cout << "Initializing random number generator with seed " << g_seed << std::endl;
824
- std::stringstream ss;
825
- ss << "Seed: " << g_seed;
826
- g_test_stack.push_back(ss.str());
827
- srand(g_seed);
828
- std::cout << "Repeating each test " << g_repeat << " times" << std::endl;
829
-
830
- VERIFY(EigenTest::all().size()>0);
831
-
832
- for(std::size_t i=0; i<EigenTest::all().size(); ++i)
833
- {
834
- const EigenTest& current_test = *EigenTest::all()[i];
835
- Eigen::g_test_stack.push_back(current_test.name());
836
- current_test();
837
- Eigen::g_test_stack.pop_back();
838
- }
839
-
840
- return 0;
841
- }
842
-
843
- // These warning are disabled here such that they are still ON when parsing Eigen's header files.
844
- #if defined __INTEL_COMPILER
845
- // remark #383: value copied to temporary, reference to temporary used
846
- // -> this warning is raised even for legal usage as: g_test_stack.push_back("foo"); where g_test_stack is a std::vector<std::string>
847
- // remark #1418: external function definition with no prior declaration
848
- // -> this warning is raised for all our test functions. Declaring them static would fix the issue.
849
- // warning #279: controlling expression is constant
850
- // remark #1572: floating-point equality and inequality comparisons are unreliable
851
- #pragma warning disable 279 383 1418 1572
852
- #endif
853
-
854
- #ifdef _MSC_VER
855
- // 4503 - decorated name length exceeded, name was truncated
856
- #pragma warning( disable : 4503)
857
- #endif