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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@@ -67,6 +67,64 @@ namespace xsimd
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{
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return _mm512_maskz_expand_epi8(mask.mask(), self);
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}
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// rotl
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template <class A, class T, class = typename std::enable_if<std::is_integral<T>::value, void>::type>
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XSIMD_INLINE batch<T, A> rotl(batch<T, A> const& self, int32_t other, requires_arch<avx512vbmi2>) noexcept
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{
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XSIMD_IF_CONSTEXPR(sizeof(T) == 2)
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{
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return _mm512_shldv_epi16(self, self, _mm512_set1_epi16(static_cast<uint16_t>(other)));
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}
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else
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{
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return rotl(self, other, avx512bw {});
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}
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}
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template <size_t count, class A, class T, class = typename std::enable_if<std::is_integral<T>::value, void>::type>
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XSIMD_INLINE batch<T, A> rotl(batch<T, A> const& self, requires_arch<avx512vbmi2>) noexcept
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{
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constexpr auto bits = std::numeric_limits<T>::digits + std::numeric_limits<T>::is_signed;
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static_assert(count < bits, "Count must be less than the number of bits in T");
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XSIMD_IF_CONSTEXPR(sizeof(T) == 2)
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{
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return _mm512_shldi_epi16(self, self, count);
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}
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else
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{
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return rotl<count>(self, avx512bw {});
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}
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}
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// rotr
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template <class A, class T, class = typename std::enable_if<std::is_integral<T>::value, void>::type>
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XSIMD_INLINE batch<T, A> rotr(batch<T, A> const& self, int32_t other, requires_arch<avx512vbmi2>) noexcept
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{
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XSIMD_IF_CONSTEXPR(sizeof(T) == 2)
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{
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return _mm512_shrdv_epi16(self, self, _mm512_set1_epi16(static_cast<uint16_t>(other)));
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}
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else
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{
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return rotr(self, other, avx512bw {});
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}
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}
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template <size_t count, class A, class T, class = typename std::enable_if<std::is_integral<T>::value, void>::type>
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XSIMD_INLINE batch<T, A> rotr(batch<T, A> const& self, requires_arch<avx512vbmi2>) noexcept
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{
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constexpr auto bits = std::numeric_limits<T>::digits + std::numeric_limits<T>::is_signed;
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static_assert(count < bits, "count must be less than the number of bits in T");
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XSIMD_IF_CONSTEXPR(sizeof(T) == 2)
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{
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return _mm512_shrdi_epi16(self, self, count);
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}
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else
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{
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return rotr<count>(self, avx512bw {});
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}
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}
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}
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}
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@@ -3,6 +3,7 @@
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* Martin Renou *
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* Copyright (c) QuantStack *
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* Copyright (c) Serge Guelton *
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* Copyright (c) Marco Barbone *
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* *
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* Distributed under the terms of the BSD 3-Clause License. *
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* *
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@@ -25,8 +26,12 @@ namespace xsimd
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XSIMD_INLINE batch<T, A> abs(batch<T, A> const& self, requires_arch<common>) noexcept;
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template <class A, class T, class = typename std::enable_if<std::is_integral<T>::value, void>::type>
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XSIMD_INLINE batch<T, A> bitwise_lshift(batch<T, A> const& self, batch<T, A> const& other, requires_arch<common>) noexcept;
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template <size_t shift, class A, class T, class = typename std::enable_if<std::is_integral<T>::value, void>::type>
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XSIMD_INLINE batch<T, A> bitwise_lshift(batch<T, A> const& self, requires_arch<common>) noexcept;
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template <class A, class T, class = typename std::enable_if<std::is_integral<T>::value, void>::type>
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XSIMD_INLINE batch<T, A> bitwise_rshift(batch<T, A> const& self, batch<T, A> const& other, requires_arch<common>) noexcept;
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template <size_t shift, class A, class T, class = typename std::enable_if<std::is_integral<T>::value, void>::type>
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XSIMD_INLINE batch<T, A> bitwise_rshift(batch<T, A> const& self, requires_arch<common>) noexcept;
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template <class A, class T>
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XSIMD_INLINE batch_bool<T, A> gt(batch<T, A> const& self, batch<T, A> const& other, requires_arch<common>) noexcept;
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template <class A, class T, class = typename std::enable_if<std::is_integral<T>::value, void>::type>
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@@ -35,9 +40,37 @@ namespace xsimd
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XSIMD_INLINE batch<T, A> sadd(batch<T, A> const& self, batch<T, A> const& other, requires_arch<common>) noexcept;
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template <class A, class T, class = typename std::enable_if<std::is_integral<T>::value, void>::type>
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XSIMD_INLINE batch<T, A> ssub(batch<T, A> const& self, batch<T, A> const& other, requires_arch<common>) noexcept;
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-
template <class A, class T, class = typename std::enable_if<std::
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-
XSIMD_INLINE T
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template <class A, class T, class = typename std::enable_if<std::is_scalar<T>::value, void>::type>
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XSIMD_INLINE T reduce_add(batch<T, A> const& self, requires_arch<common>) noexcept;
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template <class A, class T, class = typename std::enable_if<std::is_scalar<T>::value, void>::type>
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XSIMD_INLINE T reduce_mul(batch<T, A> const& self, requires_arch<common>) noexcept;
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template <class A, class T, class STy>
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XSIMD_INLINE batch<T, A> rotl(batch<T, A> const& self, STy other, requires_arch<common>) noexcept;
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template <size_t count, class A, class T>
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XSIMD_INLINE batch<T, A> rotl(batch<T, A> const& self, requires_arch<common>) noexcept;
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template <class A, class T, class STy>
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XSIMD_INLINE batch<T, A> rotr(batch<T, A> const& self, STy other, requires_arch<common>) noexcept;
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template <size_t count, class A, class T>
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XSIMD_INLINE batch<T, A> rotr(batch<T, A> const& self, requires_arch<common>) noexcept;
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// Forward declarations for pack-level helpers
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namespace detail
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{
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template <typename T, T... Vs>
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XSIMD_INLINE constexpr bool is_identity() noexcept;
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template <typename T, class A, T... Vs>
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XSIMD_INLINE constexpr bool is_identity(batch_constant<T, A, Vs...>) noexcept;
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template <typename T, class A, T... Vs>
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XSIMD_INLINE constexpr bool is_all_different(batch_constant<T, A, Vs...>) noexcept;
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template <typename T, class A, T... Vs>
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XSIMD_INLINE constexpr bool is_dup_lo(batch_constant<T, A, Vs...>) noexcept;
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template <typename T, class A, T... Vs>
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XSIMD_INLINE constexpr bool is_dup_hi(batch_constant<T, A, Vs...>) noexcept;
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template <typename T, class A, T... Vs>
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XSIMD_INLINE constexpr bool is_cross_lane(batch_constant<T, A, Vs...>) noexcept;
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template <typename T, class A, T... Vs>
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XSIMD_INLINE constexpr bool no_duplicates(batch_constant<T, A, Vs...>) noexcept;
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}
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}
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}
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@@ -61,7 +61,10 @@ namespace xsimd
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#pragma GCC push_options
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#pragma GCC optimize("signed-zeros")
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#endif
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#ifndef __FAST_MATH__
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XSIMD_DEFINE_CONSTANT(infinity, (std::numeric_limits<float>::infinity()), (std::numeric_limits<double>::infinity()))
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XSIMD_DEFINE_CONSTANT(minusinfinity, (-infinity<float>()), (-infinity<double>()))
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#endif
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XSIMD_DEFINE_CONSTANT(invlog_2, 1.442695040888963407359924681001892137426645954152986f, 1.442695040888963407359924681001892137426645954152986)
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XSIMD_DEFINE_CONSTANT_HEX(invlog_2hi, 0x3fb8b000, 0x3ff7154765200000)
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XSIMD_DEFINE_CONSTANT_HEX(invlog_2lo, 0xb9389ad4, 0x3de705fc2eefa200)
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@@ -83,7 +86,6 @@ namespace xsimd
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XSIMD_DEFINE_CONSTANT(minlog, -88.3762626647949f, -708.3964185322641)
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XSIMD_DEFINE_CONSTANT(minlog2, -127.0f, -1023.)
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XSIMD_DEFINE_CONSTANT(minlog10, -37.89999771118164f, -308.2547155599167)
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-
XSIMD_DEFINE_CONSTANT(minusinfinity, (-infinity<float>()), (-infinity<double>()))
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XSIMD_DEFINE_CONSTANT_HEX(nan, 0xffffffff, 0xffffffffffffffff)
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XSIMD_DEFINE_CONSTANT_HEX(oneosqrteps, 0x453504f3, 0x4190000000000000)
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XSIMD_DEFINE_CONSTANT_HEX(oneotwoeps, 0x4a800000, 0x4320000000000000)
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@@ -230,6 +230,13 @@ namespace xsimd
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return r;
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}
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// first
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template <class A, class T, size_t N = 8 * sizeof(T) * batch<T, A>::size>
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T XSIMD_INLINE first(batch<T, A> const& self, requires_arch<emulated<N>>) noexcept
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{
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return self.data[0];
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}
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#if 0
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// count
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template <class A, class T, size_t N = 8 * sizeof(T) * batch<T, A>::size>
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@@ -594,6 +601,16 @@ namespace xsimd
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{ return xsimd::min(x, y); });
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}
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+
// reduce_mul
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605
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template <class A, class T, size_t N = 8 * sizeof(T) * batch<T, A>::size>
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606
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+
XSIMD_INLINE T reduce_mul(batch<T, A> const& self, requires_arch<emulated<N>>) noexcept
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607
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{
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608
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constexpr size_t size = batch<T, A>::size;
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609
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+
std::array<T, size> buffer;
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610
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+
self.store_unaligned(buffer.data());
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611
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+
return std::accumulate(buffer.begin() + 1, buffer.end(), *buffer.begin(), std::multiplies<T>());
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612
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+
}
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613
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+
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// rsqrt
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598
615
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template <class A, class T, size_t N = 8 * sizeof(T) * batch<T, A>::size>
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599
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XSIMD_INLINE batch<T, A> rsqrt(batch<T, A> const& self, requires_arch<emulated<N>>) noexcept
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@@ -73,6 +73,19 @@ namespace xsimd
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return _mm256_fmsub_pd(x, y, z);
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}
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+
// fmas
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template <class A>
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XSIMD_INLINE batch<float, A> fmas(batch<float, A> const& x, batch<float, A> const& y, batch<float, A> const& z, requires_arch<fma3<avx>>) noexcept
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79
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{
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return _mm256_fmaddsub_ps(x, y, z);
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}
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+
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template <class A>
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XSIMD_INLINE batch<double, A> fmas(batch<double, A> const& x, batch<double, A> const& y, batch<double, A> const& z, requires_arch<fma3<avx>>) noexcept
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85
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+
{
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86
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+
return _mm256_fmaddsub_pd(x, y, z);
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}
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}
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}
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@@ -71,6 +71,24 @@ namespace xsimd
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{
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72
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return _mm_fmsub_pd(x, y, z);
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}
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74
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+
// fms
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75
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+
template <class A>
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76
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XSIMD_INLINE batch<float, A> fmas(batch<float, A> const& x,
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batch<float, A> const& y,
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+
batch<float, A> const& z,
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requires_arch<fma3<sse4_2>>) noexcept
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{
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return _mm_fmaddsub_ps(x, y, z);
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+
}
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83
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+
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84
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+
template <class A>
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85
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XSIMD_INLINE batch<double, A> fmas(batch<double, A> const& x,
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86
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+
batch<double, A> const& y,
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87
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+
batch<double, A> const& z,
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requires_arch<fma3<sse4_2>>) noexcept
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{
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90
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return _mm_fmaddsub_pd(x, y, z);
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+
}
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}
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@@ -72,6 +72,19 @@ namespace xsimd
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{
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73
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return _mm_msub_pd(x, y, z);
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74
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}
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75
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+
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76
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+
// fmas
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77
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+
template <class A>
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78
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+
XSIMD_INLINE batch<float, A> fmas(batch<float, A> const& x, batch<float, A> const& y, batch<float, A> const& z, requires_arch<fma4>) noexcept
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79
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+
{
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+
return _mm_maddsub_ps(x, y, z);
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+
}
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82
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+
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83
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+
template <class A>
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84
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XSIMD_INLINE batch<double, A> fmas(batch<double, A> const& x, batch<double, A> const& y, batch<double, A> const& z, requires_arch<fma4>) noexcept
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85
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+
{
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+
return _mm_maddsub_pd(x, y, z);
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+
}
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}
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}
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@@ -72,6 +72,10 @@
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#include "./xsimd_avx512f.hpp"
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#endif
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74
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75
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+
#if XSIMD_WITH_AVX512DQ
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+
#include "./xsimd_avx512dq.hpp"
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+
#endif
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+
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#if XSIMD_WITH_AVX512BW
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#include "./xsimd_avx512bw.hpp"
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#endif
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@@ -128,6 +132,10 @@
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#include "./xsimd_wasm.hpp"
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#endif
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+
#if XSIMD_WITH_VSX
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#include "./xsimd_vsx.hpp"
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+
#endif
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138
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+
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// Must come last to have access to all conversion specializations.
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#include "./xsimd_common.hpp"
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