sequenzo 0.1.17__cp312-cp312-macosx_10_13_universal2.whl → 0.1.19__cp312-cp312-macosx_10_13_universal2.whl
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- sequenzo/__init__.py +64 -8
- sequenzo/big_data/clara/clara.py +1 -1
- sequenzo/big_data/clara/utils/get_weighted_diss.c +155 -155
- sequenzo/big_data/clara/utils/get_weighted_diss.cpython-312-darwin.so +0 -0
- sequenzo/clustering/KMedoids.py +39 -0
- sequenzo/clustering/hierarchical_clustering.py +304 -8
- sequenzo/define_sequence_data.py +44 -3
- sequenzo/dissimilarity_measures/c_code.cpython-312-darwin.so +0 -0
- sequenzo/dissimilarity_measures/get_distance_matrix.py +1 -2
- sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
- sequenzo/dissimilarity_measures/src/DHDdistance.cpp +13 -37
- sequenzo/dissimilarity_measures/src/LCPdistance.cpp +13 -37
- sequenzo/dissimilarity_measures/src/OMdistance.cpp +12 -47
- sequenzo/dissimilarity_measures/src/OMspellDistance.cpp +103 -67
- sequenzo/dissimilarity_measures/src/dp_utils.h +160 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_arithmetic.hpp +41 -16
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_complex.hpp +4 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_details.hpp +7 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_logical.hpp +10 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_math.hpp +127 -43
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_memory.hpp +30 -2
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_swizzle.hpp +174 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_trigo.hpp +14 -5
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx.hpp +111 -54
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx2.hpp +131 -9
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512bw.hpp +11 -113
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512dq.hpp +39 -7
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512f.hpp +336 -30
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi.hpp +9 -37
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi2.hpp +58 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common.hpp +1 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common_fwd.hpp +35 -2
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_constants.hpp +3 -1
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_emulated.hpp +17 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx.hpp +13 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_sse.hpp +18 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma4.hpp +13 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_isa.hpp +8 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon.hpp +363 -34
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon64.hpp +7 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_rvv.hpp +13 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_scalar.hpp +41 -4
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse2.hpp +252 -16
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse3.hpp +9 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_ssse3.hpp +12 -1
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sve.hpp +7 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_vsx.hpp +892 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_wasm.hpp +78 -1
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_arch.hpp +3 -1
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_config.hpp +13 -2
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_cpuid.hpp +5 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_inline.hpp +5 -1
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_all_registers.hpp +2 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_api.hpp +64 -1
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch.hpp +36 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_rvv_register.hpp +40 -31
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_traits.hpp +8 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_vsx_register.hpp +77 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/xsimd.hpp +6 -0
- sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +155 -155
- sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cpython-312-darwin.so +0 -0
- sequenzo/dissimilarity_measures/utils/seqconc.c +155 -155
- sequenzo/dissimilarity_measures/utils/seqconc.cpython-312-darwin.so +0 -0
- sequenzo/dissimilarity_measures/utils/seqdss.c +155 -155
- sequenzo/dissimilarity_measures/utils/seqdss.cpython-312-darwin.so +0 -0
- sequenzo/dissimilarity_measures/utils/seqdur.c +155 -155
- sequenzo/dissimilarity_measures/utils/seqdur.cpython-312-darwin.so +0 -0
- sequenzo/dissimilarity_measures/utils/seqlength.c +155 -155
- sequenzo/dissimilarity_measures/utils/seqlength.cpython-312-darwin.so +0 -0
- sequenzo/multidomain/cat.py +0 -53
- sequenzo/multidomain/idcd.py +0 -1
- sequenzo/openmp_setup.py +233 -0
- sequenzo/sequence_characteristics/__init__.py +4 -0
- sequenzo/sequence_characteristics/complexity_index.py +17 -57
- sequenzo/sequence_characteristics/overall_cross_sectional_entropy.py +177 -111
- sequenzo/sequence_characteristics/plot_characteristics.py +30 -11
- sequenzo/sequence_characteristics/simple_characteristics.py +1 -0
- sequenzo/sequence_characteristics/state_frequencies_and_entropy_per_sequence.py +9 -3
- sequenzo/sequence_characteristics/turbulence.py +47 -67
- sequenzo/sequence_characteristics/variance_of_spell_durations.py +19 -9
- sequenzo/sequence_characteristics/within_sequence_entropy.py +5 -58
- sequenzo/visualization/plot_sequence_index.py +58 -35
- sequenzo/visualization/plot_state_distribution.py +57 -36
- sequenzo/visualization/plot_transition_matrix.py +21 -22
- sequenzo/with_event_history_analysis/__init__.py +35 -0
- sequenzo/with_event_history_analysis/sequence_analysis_multi_state_model.py +850 -0
- sequenzo/with_event_history_analysis/sequence_history_analysis.py +283 -0
- {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/METADATA +48 -14
- sequenzo-0.1.19.dist-info/RECORD +215 -0
- sequenzo/dissimilarity_measures/setup.py +0 -35
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_relax_snode.h +0 -83
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseQR/SparseQR.h +0 -758
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdDeque.h +0 -116
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdList.h +0 -106
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdVector.h +0 -131
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/details.h +0 -84
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SuperLUSupport/SuperLUSupport.h +0 -1025
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/UmfPackSupport/UmfPackSupport.h +0 -642
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Image.h +0 -82
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Kernel.h +0 -79
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/RealSvd2x2.h +0 -55
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/blas.h +0 -440
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapack.h +0 -152
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke.h +0 -16292
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// This file is part of Eigen, a lightweight C++ template library
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// for linear algebra.
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//
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// Copyright (C) 2015 Benoit Steiner <benoit.steiner.goog@gmail.com>
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//
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// This Source Code Form is subject to the terms of the Mozilla
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// Public License v. 2.0. If a copy of the MPL was not distributed
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// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
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#ifndef EIGEN_CXX11_TENSOR_TENSOR_META_H
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#define EIGEN_CXX11_TENSOR_TENSOR_META_H
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namespace Eigen {
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template<bool cond> struct Cond {};
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template<typename T1, typename T2> EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE
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const T1& choose(Cond<true>, const T1& first, const T2&) {
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return first;
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}
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template<typename T1, typename T2> EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE
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const T2& choose(Cond<false>, const T1&, const T2& second) {
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return second;
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}
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template <typename T, typename X, typename Y>
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EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE
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T divup(const X x, const Y y) {
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return static_cast<T>((x + y - 1) / y);
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}
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template <typename T>
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EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE
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T divup(const T x, const T y) {
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return static_cast<T>((x + y - 1) / y);
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}
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template <size_t n> struct max_n_1 {
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static const size_t size = n;
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};
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template <> struct max_n_1<0> {
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static const size_t size = 1;
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};
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// Default packet types
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template <typename Scalar, typename Device>
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struct PacketType : internal::packet_traits<Scalar> {
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typedef typename internal::packet_traits<Scalar>::type type;
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};
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// For CUDA packet types when using a GpuDevice
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#if defined(EIGEN_USE_GPU) && defined(EIGEN_HAS_GPU_FP16)
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typedef ulonglong2 Packet4h2;
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template<>
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struct PacketType<half, GpuDevice> {
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typedef Packet4h2 type;
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static const int size = 8;
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enum {
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HasAdd = 1,
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HasSub = 1,
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HasMul = 1,
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HasNegate = 1,
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HasAbs = 1,
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HasArg = 0,
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HasAbs2 = 0,
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HasMin = 1,
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HasMax = 1,
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HasConj = 0,
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HasSetLinear = 0,
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HasBlend = 0,
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HasDiv = 1,
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HasSqrt = 1,
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HasRsqrt = 1,
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HasExp = 1,
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HasExpm1 = 0,
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HasLog = 1,
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HasLog1p = 0,
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HasLog10 = 0,
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HasPow = 1,
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};
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};
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#endif
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#if defined(EIGEN_USE_SYCL)
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namespace TensorSycl {
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namespace internal {
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template <typename Index, Index A, Index B> struct PlusOp {
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static constexpr Index Value = A + B;
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};
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template <typename Index, Index A, Index B> struct DivOp {
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static constexpr Index Value = A / B;
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};
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template <typename Index, Index start, Index end, Index step,
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template <class Indx, Indx...> class StepOp>
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struct static_for {
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template <typename UnaryOperator>
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static EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void loop(UnaryOperator op) {
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op(start);
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static_for<Index, StepOp<Index, start, step>::Value, end, step,
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StepOp>::loop(op);
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}
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};
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template <typename Index, Index end, Index step,
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template <class Indx, Indx...> class StepOp>
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struct static_for<Index, end, end, step, StepOp> {
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template <typename UnaryOperator>
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static EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void loop(UnaryOperator) {}
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};
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template <typename OutScalar, typename Device, bool Vectorizable>
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struct Vectorise {
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static const int PacketSize = 1;
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typedef OutScalar PacketReturnType;
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};
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template <typename OutScalar, typename Device>
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struct Vectorise<OutScalar, Device, true> {
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static const int PacketSize = Eigen::PacketType<OutScalar, Device>::size;
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typedef typename Eigen::PacketType<OutScalar, Device>::type PacketReturnType;
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};
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static EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE Index roundUp(Index x, Index y) {
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return ((((x) + (y)-1) / (y)) * (y));
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}
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} // namespace internal
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} // namespace TensorSycl
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template <>
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struct PacketType<half, SyclDevice> {
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typedef half type;
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static const int size = 1;
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enum {
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HasAdd = 0,
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HasSub = 0,
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HasMul = 0,
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HasNegate = 0,
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HasAbs = 0,
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HasArg = 0,
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HasAbs2 = 0,
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HasMin = 0,
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HasMax = 0,
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HasConj = 0,
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HasSetLinear = 0,
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HasBlend = 0
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};
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};
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template <typename Scalar>
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struct PacketType<Scalar, SyclDevice> : internal::default_packet_traits {
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typedef Scalar type;
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typedef Scalar half;
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enum {
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Vectorizable = 0,
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size = 1,
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AlignedOnScalar = 0,
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HasHalfPacket = 0
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};
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enum {
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HasAdd = 0,
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HasSub = 0,
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HasMul = 0,
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HasNegate = 0,
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HasAbs = 0,
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HasAbs2 = 0,
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HasMin = 0,
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HasMax = 0,
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HasConj = 0,
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HasSetLinear = 0
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};
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};
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template <typename Scalar>
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struct PacketType<Scalar, const SyclDevice> : PacketType<Scalar, SyclDevice>{};
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#ifndef EIGEN_DONT_VECTORIZE_SYCL
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#define PACKET_TYPE(CVQual, Type, val, lengths, DEV)\
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template<> struct PacketType<CVQual Type, DEV> : internal::sycl_packet_traits<val, lengths> \
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{\
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typedef typename internal::packet_traits<Type>::type type;\
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typedef typename internal::packet_traits<Type>::half half;\
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};
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PACKET_TYPE(const, float, 1, 4, SyclDevice)
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PACKET_TYPE(, float, 1, 4, SyclDevice)
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PACKET_TYPE(const, float, 1, 4, const SyclDevice)
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PACKET_TYPE(, float, 1, 4, const SyclDevice)
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PACKET_TYPE(const, double, 0, 2, SyclDevice)
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PACKET_TYPE(, double, 0, 2, SyclDevice)
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PACKET_TYPE(const, double, 0, 2, const SyclDevice)
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PACKET_TYPE(, double, 0, 2, const SyclDevice)
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#undef PACKET_TYPE
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template<> struct PacketType<half, const SyclDevice>: PacketType<half, SyclDevice>{};
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template<> struct PacketType<const half, const SyclDevice>: PacketType<half, SyclDevice>{};
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#endif
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#endif
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// Tuple mimics std::pair but works on e.g. nvcc.
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template <typename U, typename V> struct Tuple {
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public:
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U first;
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V second;
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typedef U first_type;
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typedef V second_type;
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EIGEN_CONSTEXPR EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
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Tuple() : first(), second() {}
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EIGEN_CONSTEXPR EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
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Tuple(const U& f, const V& s) : first(f), second(s) {}
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EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
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void swap(Tuple& rhs) {
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using numext::swap;
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swap(first, rhs.first);
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swap(second, rhs.second);
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}
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};
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template <typename U, typename V>
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EIGEN_CONSTEXPR EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
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bool operator==(const Tuple<U, V>& x, const Tuple<U, V>& y) {
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return (x.first == y.first && x.second == y.second);
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}
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template <typename U, typename V>
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EIGEN_CONSTEXPR EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
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bool operator!=(const Tuple<U, V>& x, const Tuple<U, V>& y) {
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return !(x == y);
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}
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// Can't use std::pairs on cuda devices
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template <typename Idx> struct IndexPair {
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EIGEN_CONSTEXPR EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE IndexPair() : first(0), second(0) {}
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EIGEN_CONSTEXPR EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE IndexPair(Idx f, Idx s) : first(f), second(s) {}
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EIGEN_DEVICE_FUNC void set(IndexPair<Idx> val) {
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first = val.first;
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second = val.second;
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}
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Idx first;
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Idx second;
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};
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#ifdef EIGEN_HAS_SFINAE
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namespace internal {
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template<typename IndexType, typename Index, Index... Is>
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EIGEN_CONSTEXPR EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
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array<Index, sizeof...(Is)> customIndices2Array(IndexType& idx, numeric_list<Index, Is...>) {
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return { idx[Is]... };
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}
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template<typename IndexType, typename Index>
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EIGEN_CONSTEXPR EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
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array<Index, 0> customIndices2Array(IndexType&, numeric_list<Index>) {
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return array<Index, 0>();
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}
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/** Make an array (for index/dimensions) out of a custom index */
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template<typename Index, std::size_t NumIndices, typename IndexType>
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EIGEN_CONSTEXPR EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
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array<Index, NumIndices> customIndices2Array(IndexType& idx) {
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return customIndices2Array(idx, typename gen_numeric_list<Index, NumIndices>::type{});
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}
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template <typename B, typename D>
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struct is_base_of
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{
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typedef char (&yes)[1];
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typedef char (&no)[2];
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template <typename BB, typename DD>
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struct Host
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{
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operator BB*() const;
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operator DD*();
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};
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template<typename T>
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static yes check(D*, T);
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static no check(B*, int);
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static const bool value = sizeof(check(Host<B,D>(), int())) == sizeof(yes);
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};
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}
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#endif
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} // namespace Eigen
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#endif // EIGEN_CXX11_TENSOR_TENSOR_META_H
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