sequenzo 0.1.17__cp311-cp311-win_amd64.whl → 0.1.19__cp311-cp311-win_amd64.whl

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  1. sequenzo/__init__.py +64 -8
  2. sequenzo/big_data/clara/clara.py +1 -1
  3. sequenzo/big_data/clara/utils/get_weighted_diss.c +154 -154
  4. sequenzo/big_data/clara/utils/get_weighted_diss.cp311-win_amd64.pyd +0 -0
  5. sequenzo/clustering/KMedoids.py +39 -0
  6. sequenzo/clustering/clustering_c_code.cp311-win_amd64.pyd +0 -0
  7. sequenzo/clustering/hierarchical_clustering.py +304 -8
  8. sequenzo/define_sequence_data.py +44 -3
  9. sequenzo/dissimilarity_measures/c_code.cp311-win_amd64.pyd +0 -0
  10. sequenzo/dissimilarity_measures/get_distance_matrix.py +1 -2
  11. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  12. sequenzo/dissimilarity_measures/src/DHDdistance.cpp +13 -37
  13. sequenzo/dissimilarity_measures/src/LCPdistance.cpp +13 -37
  14. sequenzo/dissimilarity_measures/src/OMdistance.cpp +12 -47
  15. sequenzo/dissimilarity_measures/src/OMspellDistance.cpp +103 -67
  16. sequenzo/dissimilarity_measures/src/dp_utils.h +160 -0
  17. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_arithmetic.hpp +41 -16
  18. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_complex.hpp +4 -0
  19. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_details.hpp +7 -0
  20. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_logical.hpp +10 -0
  21. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_math.hpp +127 -43
  22. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_memory.hpp +30 -2
  23. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_swizzle.hpp +174 -0
  24. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_trigo.hpp +14 -5
  25. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx.hpp +111 -54
  26. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx2.hpp +131 -9
  27. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512bw.hpp +11 -113
  28. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512dq.hpp +39 -7
  29. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512f.hpp +336 -30
  30. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi.hpp +9 -37
  31. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi2.hpp +58 -0
  32. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common.hpp +1 -0
  33. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common_fwd.hpp +35 -2
  34. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_constants.hpp +3 -1
  35. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_emulated.hpp +17 -0
  36. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx.hpp +13 -0
  37. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_sse.hpp +18 -0
  38. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma4.hpp +13 -0
  39. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_isa.hpp +8 -0
  40. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon.hpp +363 -34
  41. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon64.hpp +7 -0
  42. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_rvv.hpp +13 -0
  43. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_scalar.hpp +41 -4
  44. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse2.hpp +252 -16
  45. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse3.hpp +9 -0
  46. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_ssse3.hpp +12 -1
  47. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sve.hpp +7 -0
  48. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_vsx.hpp +892 -0
  49. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_wasm.hpp +78 -1
  50. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_arch.hpp +3 -1
  51. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_config.hpp +13 -2
  52. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_cpuid.hpp +5 -0
  53. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_inline.hpp +5 -1
  54. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_all_registers.hpp +2 -0
  55. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_api.hpp +64 -1
  56. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch.hpp +36 -0
  57. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_rvv_register.hpp +40 -31
  58. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_traits.hpp +8 -0
  59. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_vsx_register.hpp +77 -0
  60. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/xsimd.hpp +6 -0
  61. sequenzo/dissimilarity_measures/src/xsimd/test/test_basic_math.cpp +6 -0
  62. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch.cpp +54 -2
  63. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_bool.cpp +8 -0
  64. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_cast.cpp +11 -4
  65. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_complex.cpp +18 -0
  66. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_int.cpp +8 -14
  67. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_manip.cpp +216 -173
  68. sequenzo/dissimilarity_measures/src/xsimd/test/test_load_store.cpp +6 -0
  69. sequenzo/dissimilarity_measures/src/xsimd/test/test_memory.cpp +1 -1
  70. sequenzo/dissimilarity_measures/src/xsimd/test/test_power.cpp +7 -4
  71. sequenzo/dissimilarity_measures/src/xsimd/test/test_select.cpp +6 -2
  72. sequenzo/dissimilarity_measures/src/xsimd/test/test_shuffle.cpp +32 -18
  73. sequenzo/dissimilarity_measures/src/xsimd/test/test_utils.hpp +21 -24
  74. sequenzo/dissimilarity_measures/src/xsimd/test/test_xsimd_api.cpp +69 -9
  75. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +154 -154
  76. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cp311-win_amd64.pyd +0 -0
  77. sequenzo/dissimilarity_measures/utils/seqconc.c +154 -154
  78. sequenzo/dissimilarity_measures/utils/seqconc.cp311-win_amd64.pyd +0 -0
  79. sequenzo/dissimilarity_measures/utils/seqdss.c +154 -154
  80. sequenzo/dissimilarity_measures/utils/seqdss.cp311-win_amd64.pyd +0 -0
  81. sequenzo/dissimilarity_measures/utils/seqdur.c +154 -154
  82. sequenzo/dissimilarity_measures/utils/seqdur.cp311-win_amd64.pyd +0 -0
  83. sequenzo/dissimilarity_measures/utils/seqlength.c +154 -154
  84. sequenzo/dissimilarity_measures/utils/seqlength.cp311-win_amd64.pyd +0 -0
  85. sequenzo/multidomain/cat.py +0 -53
  86. sequenzo/multidomain/idcd.py +0 -1
  87. sequenzo/openmp_setup.py +233 -0
  88. sequenzo/sequence_characteristics/__init__.py +4 -0
  89. sequenzo/sequence_characteristics/complexity_index.py +17 -57
  90. sequenzo/sequence_characteristics/overall_cross_sectional_entropy.py +177 -111
  91. sequenzo/sequence_characteristics/plot_characteristics.py +30 -11
  92. sequenzo/sequence_characteristics/simple_characteristics.py +1 -0
  93. sequenzo/sequence_characteristics/state_frequencies_and_entropy_per_sequence.py +9 -3
  94. sequenzo/sequence_characteristics/turbulence.py +47 -67
  95. sequenzo/sequence_characteristics/variance_of_spell_durations.py +19 -9
  96. sequenzo/sequence_characteristics/within_sequence_entropy.py +5 -58
  97. sequenzo/visualization/plot_sequence_index.py +58 -35
  98. sequenzo/visualization/plot_state_distribution.py +57 -36
  99. sequenzo/visualization/plot_transition_matrix.py +21 -22
  100. sequenzo/with_event_history_analysis/__init__.py +35 -0
  101. sequenzo/with_event_history_analysis/sequence_analysis_multi_state_model.py +850 -0
  102. sequenzo/with_event_history_analysis/sequence_history_analysis.py +283 -0
  103. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/METADATA +48 -14
  104. sequenzo-0.1.19.dist-info/RECORD +272 -0
  105. sequenzo/dissimilarity_measures/setup.py +0 -35
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  170. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  171. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  172. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  173. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  174. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  175. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  176. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  177. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  178. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  179. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  180. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  181. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  182. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  183. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  184. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  185. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  186. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  187. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  188. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  189. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  190. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  191. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  192. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  193. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  194. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  195. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  196. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  197. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  198. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  199. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  200. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  201. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  202. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  203. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  204. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  205. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  206. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  207. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  208. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  209. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  210. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  211. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  212. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  213. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
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  413. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LevenbergMarquardt.h +0 -396
  414. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixExponential.h +0 -441
  415. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixFunction.h +0 -569
  416. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixLogarithm.h +0 -373
  417. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixPower.h +0 -705
  418. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixSquareRoot.h +0 -368
  419. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/StemFunction.h +0 -117
  420. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MoreVectorization/MathFunctions.h +0 -95
  421. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/HybridNonLinearSolver.h +0 -601
  422. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/LevenbergMarquardt.h +0 -657
  423. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/chkder.h +0 -66
  424. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/covar.h +0 -70
  425. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/dogleg.h +0 -107
  426. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/fdjac1.h +0 -79
  427. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/lmpar.h +0 -298
  428. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/qrsolv.h +0 -91
  429. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/r1mpyq.h +0 -30
  430. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/r1updt.h +0 -99
  431. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/rwupdt.h +0 -49
  432. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NumericalDiff/NumericalDiff.h +0 -130
  433. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/Companion.h +0 -280
  434. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/PolynomialSolver.h +0 -428
  435. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/PolynomialUtils.h +0 -143
  436. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineInplaceLU.h +0 -352
  437. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineMatrix.h +0 -862
  438. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineMatrixBase.h +0 -212
  439. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineProduct.h +0 -295
  440. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineStorage.h +0 -259
  441. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineUtil.h +0 -89
  442. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/BlockOfDynamicSparseMatrix.h +0 -122
  443. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/BlockSparseMatrix.h +0 -1079
  444. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/DynamicSparseMatrix.h +0 -404
  445. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/MarketIO.h +0 -282
  446. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h +0 -247
  447. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/RandomSetter.h +0 -349
  448. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsArrayAPI.h +0 -286
  449. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsBFloat16.h +0 -68
  450. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsFunctors.h +0 -357
  451. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsHalf.h +0 -66
  452. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsImpl.h +0 -1959
  453. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsPacketMath.h +0 -118
  454. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/HipVectorCompatibility.h +0 -67
  455. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsArrayAPI.h +0 -167
  456. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsBFloat16.h +0 -58
  457. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsFunctors.h +0 -330
  458. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsHalf.h +0 -58
  459. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsImpl.h +0 -2045
  460. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsPacketMath.h +0 -79
  461. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/BesselFunctions.h +0 -46
  462. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/SpecialFunctions.h +0 -16
  463. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/BesselFunctions.h +0 -46
  464. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/SpecialFunctions.h +0 -16
  465. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/GPU/SpecialFunctions.h +0 -369
  466. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/BesselFunctions.h +0 -54
  467. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/SpecialFunctions.h +0 -34
  468. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/Spline.h +0 -507
  469. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFitting.h +0 -431
  470. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFwd.h +0 -93
  471. sequenzo/dissimilarity_measures/src/eigen/unsupported/test/matrix_functions.h +0 -67
  472. sequenzo-0.1.17.dist-info/RECORD +0 -631
  473. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/WHEEL +0 -0
  474. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/licenses/LICENSE +0 -0
  475. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/top_level.txt +0 -0
@@ -1,409 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
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- // Copyright (C) 2014 Benoit Steiner <benoit.steiner.goog@gmail.com>
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- //
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- // This Source Code Form is subject to the terms of the Mozilla
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- // Public License v. 2.0. If a copy of the MPL was not distributed
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- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
9
-
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- #if defined(EIGEN_USE_THREADS) && !defined(EIGEN_CXX11_TENSOR_TENSOR_DEVICE_THREAD_POOL_H)
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- #define EIGEN_CXX11_TENSOR_TENSOR_DEVICE_THREAD_POOL_H
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-
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- namespace Eigen {
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-
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- // Runs an arbitrary function and then calls Notify() on the passed in
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- // Notification.
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- template <typename Function, typename... Args> struct FunctionWrapperWithNotification
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- {
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- static void run(Notification* n, Function f, Args... args) {
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- f(args...);
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- if (n) {
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- n->Notify();
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- }
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- }
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- };
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-
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- template <typename Function, typename... Args> struct FunctionWrapperWithBarrier
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- {
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- static void run(Barrier* b, Function f, Args... args) {
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- f(args...);
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- if (b) {
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- b->Notify();
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- }
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- }
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- };
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-
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- template <typename SyncType>
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- static EIGEN_STRONG_INLINE void wait_until_ready(SyncType* n) {
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- if (n) {
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- n->Wait();
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- }
42
- }
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-
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- // An abstract interface to a device specific memory allocator.
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- class Allocator {
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- public:
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- virtual ~Allocator() {}
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- virtual void* allocate(size_t num_bytes) const = 0;
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- virtual void deallocate(void* buffer) const = 0;
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- };
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-
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- // Build a thread pool device on top the an existing pool of threads.
53
- struct ThreadPoolDevice {
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- // The ownership of the thread pool remains with the caller.
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- ThreadPoolDevice(ThreadPoolInterface* pool, int num_cores, Allocator* allocator = nullptr)
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- : pool_(pool), num_threads_(num_cores), allocator_(allocator) { }
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-
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- EIGEN_STRONG_INLINE void* allocate(size_t num_bytes) const {
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- return allocator_ ? allocator_->allocate(num_bytes)
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- : internal::aligned_malloc(num_bytes);
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- }
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-
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- EIGEN_STRONG_INLINE void deallocate(void* buffer) const {
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- if (allocator_) {
65
- allocator_->deallocate(buffer);
66
- } else {
67
- internal::aligned_free(buffer);
68
- }
69
- }
70
-
71
- EIGEN_STRONG_INLINE void* allocate_temp(size_t num_bytes) const {
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- return allocate(num_bytes);
73
- }
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-
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- EIGEN_STRONG_INLINE void deallocate_temp(void* buffer) const {
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- deallocate(buffer);
77
- }
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-
79
- template<typename Type>
80
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Type get(Type data) const {
81
- return data;
82
- }
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-
84
- EIGEN_STRONG_INLINE void memcpy(void* dst, const void* src, size_t n) const {
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- #ifdef __ANDROID__
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- ::memcpy(dst, src, n);
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- #else
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- // TODO(rmlarsen): Align blocks on cache lines.
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- // We have observed that going beyond 4 threads usually just wastes
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- // CPU cycles due to the threads competing for memory bandwidth, so we
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- // statically schedule at most 4 block copies here.
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- const size_t kMinBlockSize = 32768;
93
- const size_t num_threads = CostModel::numThreads(n, TensorOpCost(1.0, 1.0, 0), 4);
94
- if (n <= kMinBlockSize || num_threads < 2) {
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- ::memcpy(dst, src, n);
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- } else {
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- const char* src_ptr = static_cast<const char*>(src);
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- char* dst_ptr = static_cast<char*>(dst);
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- const size_t blocksize = (n + (num_threads - 1)) / num_threads;
100
- Barrier barrier(static_cast<int>(num_threads - 1));
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- // Launch the last 3 blocks on worker threads.
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- for (size_t i = 1; i < num_threads; ++i) {
103
- enqueue_with_barrier(&barrier, [n, i, src_ptr, dst_ptr, blocksize] {
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- ::memcpy(dst_ptr + i * blocksize, src_ptr + i * blocksize,
105
- numext::mini(blocksize, n - (i * blocksize)));
106
- });
107
- }
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- // Launch the first block on the main thread.
109
- ::memcpy(dst_ptr, src_ptr, blocksize);
110
- barrier.Wait();
111
- }
112
- #endif
113
- }
114
- EIGEN_STRONG_INLINE void memcpyHostToDevice(void* dst, const void* src, size_t n) const {
115
- memcpy(dst, src, n);
116
- }
117
- EIGEN_STRONG_INLINE void memcpyDeviceToHost(void* dst, const void* src, size_t n) const {
118
- memcpy(dst, src, n);
119
- }
120
-
121
- EIGEN_STRONG_INLINE void memset(void* buffer, int c, size_t n) const {
122
- ::memset(buffer, c, n);
123
- }
124
-
125
- EIGEN_STRONG_INLINE int numThreads() const {
126
- return num_threads_;
127
- }
128
-
129
- // Number of theads available in the underlying thread pool. This number can
130
- // be different from the value returned by numThreads().
131
- EIGEN_STRONG_INLINE int numThreadsInPool() const {
132
- return pool_->NumThreads();
133
- }
134
-
135
- EIGEN_STRONG_INLINE size_t firstLevelCacheSize() const {
136
- return l1CacheSize();
137
- }
138
-
139
- EIGEN_STRONG_INLINE size_t lastLevelCacheSize() const {
140
- // The l3 cache size is shared between all the cores.
141
- return l3CacheSize() / num_threads_;
142
- }
143
-
144
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE int majorDeviceVersion() const {
145
- // Should return an enum that encodes the ISA supported by the CPU
146
- return 1;
147
- }
148
-
149
- template <class Function, class... Args>
150
- EIGEN_STRONG_INLINE Notification* enqueue(Function&& f,
151
- Args&&... args) const {
152
- Notification* n = new Notification();
153
- pool_->Schedule(
154
- std::bind(&FunctionWrapperWithNotification<Function, Args...>::run, n,
155
- std::move(f), args...));
156
- return n;
157
- }
158
-
159
- template <class Function, class... Args>
160
- EIGEN_STRONG_INLINE void enqueue_with_barrier(Barrier* b, Function&& f,
161
- Args&&... args) const {
162
- pool_->Schedule(
163
- std::bind(&FunctionWrapperWithBarrier<Function, Args...>::run, b,
164
- std::move(f), args...));
165
- }
166
-
167
- template <class Function, class... Args>
168
- EIGEN_STRONG_INLINE void enqueueNoNotification(Function&& f,
169
- Args&&... args) const {
170
- if (sizeof...(args) > 0) {
171
- pool_->Schedule(std::bind(std::move(f), args...));
172
- } else {
173
- pool_->Schedule(std::move(f));
174
- }
175
- }
176
-
177
- // Returns a logical thread index between 0 and pool_->NumThreads() - 1 if
178
- // called from one of the threads in pool_. Returns -1 otherwise.
179
- EIGEN_STRONG_INLINE int currentThreadId() const {
180
- return pool_->CurrentThreadId();
181
- }
182
-
183
- // WARNING: This function is synchronous and will block the calling thread.
184
- //
185
- // Synchronous parallelFor executes f with [0, n) arguments in parallel and
186
- // waits for completion. F accepts a half-open interval [first, last). Block
187
- // size is chosen based on the iteration cost and resulting parallel
188
- // efficiency. If block_align is not nullptr, it is called to round up the
189
- // block size.
190
- void parallelFor(Index n, const TensorOpCost& cost,
191
- std::function<Index(Index)> block_align,
192
- std::function<void(Index, Index)> f) const {
193
- if (EIGEN_PREDICT_FALSE(n <= 0)){
194
- return;
195
- // Compute small problems directly in the caller thread.
196
- } else if (n == 1 || numThreads() == 1 ||
197
- CostModel::numThreads(n, cost, static_cast<int>(numThreads())) == 1) {
198
- f(0, n);
199
- return;
200
- }
201
-
202
- // Compute block size and total count of blocks.
203
- ParallelForBlock block = CalculateParallelForBlock(n, cost, block_align);
204
-
205
- // Recursively divide size into halves until we reach block_size.
206
- // Division code rounds mid to block_size, so we are guaranteed to get
207
- // block_count leaves that do actual computations.
208
- Barrier barrier(static_cast<unsigned int>(block.count));
209
- std::function<void(Index, Index)> handleRange;
210
- handleRange = [=, &handleRange, &barrier, &f](Index firstIdx,
211
- Index lastIdx) {
212
- while (lastIdx - firstIdx > block.size) {
213
- // Split into halves and schedule the second half on a different thread.
214
- const Index midIdx = firstIdx + divup((lastIdx - firstIdx) / 2, block.size) * block.size;
215
- pool_->Schedule([=, &handleRange]() { handleRange(midIdx, lastIdx); });
216
- lastIdx = midIdx;
217
- }
218
- // Single block or less, execute directly.
219
- f(firstIdx, lastIdx);
220
- barrier.Notify();
221
- };
222
-
223
- if (block.count <= numThreads()) {
224
- // Avoid a thread hop by running the root of the tree and one block on the
225
- // main thread.
226
- handleRange(0, n);
227
- } else {
228
- // Execute the root in the thread pool to avoid running work on more than
229
- // numThreads() threads.
230
- pool_->Schedule([=, &handleRange]() { handleRange(0, n); });
231
- }
232
-
233
- barrier.Wait();
234
- }
235
-
236
- // Convenience wrapper for parallelFor that does not align blocks.
237
- void parallelFor(Index n, const TensorOpCost& cost,
238
- std::function<void(Index, Index)> f) const {
239
- parallelFor(n, cost, nullptr, std::move(f));
240
- }
241
-
242
- // WARNING: This function is asynchronous and will not block the calling thread.
243
- //
244
- // Asynchronous parallelFor executes f with [0, n) arguments in parallel
245
- // without waiting for completion. When the last block finished, it will call
246
- // 'done' callback. F accepts a half-open interval [first, last). Block size
247
- // is chosen based on the iteration cost and resulting parallel efficiency. If
248
- // block_align is not nullptr, it is called to round up the block size.
249
- void parallelForAsync(Index n, const TensorOpCost& cost,
250
- std::function<Index(Index)> block_align,
251
- std::function<void(Index, Index)> f,
252
- std::function<void()> done) const {
253
- // Compute small problems directly in the caller thread.
254
- if (n <= 1 || numThreads() == 1 ||
255
- CostModel::numThreads(n, cost, static_cast<int>(numThreads())) == 1) {
256
- f(0, n);
257
- done();
258
- return;
259
- }
260
-
261
- // Compute block size and total count of blocks.
262
- ParallelForBlock block = CalculateParallelForBlock(n, cost, block_align);
263
-
264
- ParallelForAsyncContext* const ctx =
265
- new ParallelForAsyncContext(block.count, std::move(f), std::move(done));
266
-
267
- // Recursively divide size into halves until we reach block_size.
268
- // Division code rounds mid to block_size, so we are guaranteed to get
269
- // block_count leaves that do actual computations.
270
- ctx->handle_range = [this, ctx, block](Index firstIdx, Index lastIdx) {
271
- while (lastIdx - firstIdx > block.size) {
272
- // Split into halves and schedule the second half on a different thread.
273
- const Index midIdx = firstIdx + divup((lastIdx - firstIdx) / 2, block.size) * block.size;
274
- pool_->Schedule(
275
- [ctx, midIdx, lastIdx]() { ctx->handle_range(midIdx, lastIdx); });
276
- lastIdx = midIdx;
277
- }
278
-
279
- // Single block or less, execute directly.
280
- ctx->f(firstIdx, lastIdx);
281
-
282
- // Delete async context if it was the last block.
283
- if (ctx->count.fetch_sub(1) == 1) delete ctx;
284
- };
285
-
286
- if (block.count <= numThreads()) {
287
- // Avoid a thread hop by running the root of the tree and one block on the
288
- // main thread.
289
- ctx->handle_range(0, n);
290
- } else {
291
- // Execute the root in the thread pool to avoid running work on more than
292
- // numThreads() threads.
293
- pool_->Schedule([ctx, n]() { ctx->handle_range(0, n); });
294
- }
295
- }
296
-
297
- // Convenience wrapper for parallelForAsync that does not align blocks.
298
- void parallelForAsync(Index n, const TensorOpCost& cost,
299
- std::function<void(Index, Index)> f,
300
- std::function<void()> done) const {
301
- parallelForAsync(n, cost, nullptr, std::move(f), std::move(done));
302
- }
303
-
304
- // Thread pool accessor.
305
- ThreadPoolInterface* getPool() const { return pool_; }
306
-
307
- // Allocator accessor.
308
- Allocator* allocator() const { return allocator_; }
309
-
310
- private:
311
- typedef TensorCostModel<ThreadPoolDevice> CostModel;
312
-
313
- // For parallelForAsync we must keep passed in closures on the heap, and
314
- // delete them only after `done` callback finished.
315
- struct ParallelForAsyncContext {
316
- ParallelForAsyncContext(Index block_count,
317
- std::function<void(Index, Index)> block_f,
318
- std::function<void()> done_callback)
319
- : count(block_count),
320
- f(std::move(block_f)),
321
- done(std::move(done_callback)) {}
322
- ~ParallelForAsyncContext() { done(); }
323
-
324
- std::atomic<Index> count;
325
- std::function<void(Index, Index)> f;
326
- std::function<void()> done;
327
-
328
- std::function<void(Index, Index)> handle_range;
329
- };
330
-
331
- struct ParallelForBlock {
332
- Index size; // block size
333
- Index count; // number of blocks
334
- };
335
-
336
- // Calculates block size based on (1) the iteration cost and (2) parallel
337
- // efficiency. We want blocks to be not too small to mitigate parallelization
338
- // overheads; not too large to mitigate tail effect and potential load
339
- // imbalance and we also want number of blocks to be evenly dividable across
340
- // threads.
341
- ParallelForBlock CalculateParallelForBlock(
342
- const Index n, const TensorOpCost& cost,
343
- std::function<Index(Index)> block_align) const {
344
- const double block_size_f = 1.0 / CostModel::taskSize(1, cost);
345
- const Index max_oversharding_factor = 4;
346
- Index block_size = numext::mini(
347
- n, numext::maxi<Index>(
348
- divup<Index>(n, max_oversharding_factor * numThreads()),
349
- block_size_f));
350
- const Index max_block_size = numext::mini(n, 2 * block_size);
351
-
352
- if (block_align) {
353
- Index new_block_size = block_align(block_size);
354
- eigen_assert(new_block_size >= block_size);
355
- block_size = numext::mini(n, new_block_size);
356
- }
357
-
358
- Index block_count = divup(n, block_size);
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-
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- // Calculate parallel efficiency as fraction of total CPU time used for
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- // computations:
362
- double max_efficiency =
363
- static_cast<double>(block_count) /
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- (divup<int>(block_count, numThreads()) * numThreads());
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-
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- // Now try to increase block size up to max_block_size as long as it
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- // doesn't decrease parallel efficiency.
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- for (Index prev_block_count = block_count;
369
- max_efficiency < 1.0 && prev_block_count > 1;) {
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- // This is the next block size that divides size into a smaller number
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- // of blocks than the current block_size.
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- Index coarser_block_size = divup(n, prev_block_count - 1);
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- if (block_align) {
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- Index new_block_size = block_align(coarser_block_size);
375
- eigen_assert(new_block_size >= coarser_block_size);
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- coarser_block_size = numext::mini(n, new_block_size);
377
- }
378
- if (coarser_block_size > max_block_size) {
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- break; // Reached max block size. Stop.
380
- }
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- // Recalculate parallel efficiency.
382
- const Index coarser_block_count = divup(n, coarser_block_size);
383
- eigen_assert(coarser_block_count < prev_block_count);
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- prev_block_count = coarser_block_count;
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- const double coarser_efficiency =
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- static_cast<double>(coarser_block_count) /
387
- (divup<int>(coarser_block_count, numThreads()) * numThreads());
388
- if (coarser_efficiency + 0.01 >= max_efficiency) {
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- // Taking it.
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- block_size = coarser_block_size;
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- block_count = coarser_block_count;
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- if (max_efficiency < coarser_efficiency) {
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- max_efficiency = coarser_efficiency;
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- }
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- }
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- }
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-
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- return {block_size, block_count};
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- }
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-
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- ThreadPoolInterface* pool_;
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- int num_threads_;
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- Allocator* allocator_;
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- };
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-
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-
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- } // end namespace Eigen
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-
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- #endif // EIGEN_CXX11_TENSOR_TENSOR_DEVICE_THREAD_POOL_H
@@ -1,236 +0,0 @@
1
- // 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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-
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- #ifndef EIGEN_CXX11_TENSOR_TENSOR_DIMENSION_LIST_H
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- #define EIGEN_CXX11_TENSOR_TENSOR_DIMENSION_LIST_H
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-
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- namespace Eigen {
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-
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- /** \internal
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- *
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- * \class TensorDimensionList
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- * \ingroup CXX11_Tensor_Module
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- *
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- * \brief Special case of tensor index list used to list all the dimensions of a tensor of rank n.
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- *
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- * \sa Tensor
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- */
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-
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- template <typename Index, std::size_t Rank> struct DimensionList {
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- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE
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- const Index operator[] (const Index i) const { return i; }
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- };
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-
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- namespace internal {
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-
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- template<typename Index, std::size_t Rank> struct array_size<DimensionList<Index, Rank> > {
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- static const size_t value = Rank;
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- };
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- template<typename Index, std::size_t Rank> struct array_size<const DimensionList<Index, Rank> > {
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- static const size_t value = Rank;
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- };
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-
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- template<DenseIndex n, typename Index, std::size_t Rank> const Index array_get(DimensionList<Index, Rank>&) {
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- return n;
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- }
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- template<DenseIndex n, typename Index, std::size_t Rank> const Index array_get(const DimensionList<Index, Rank>&) {
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- return n;
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- }
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-
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-
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- #if EIGEN_HAS_CONSTEXPR
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- template <typename Index, std::size_t Rank>
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- struct index_known_statically_impl<DimensionList<Index, Rank> > {
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- EIGEN_DEVICE_FUNC static constexpr bool run(const DenseIndex) {
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- return true;
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- }
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- };
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- template <typename Index, std::size_t Rank>
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- struct index_known_statically_impl<const DimensionList<Index, Rank> > {
56
- EIGEN_DEVICE_FUNC static constexpr bool run(const DenseIndex) {
57
- return true;
58
- }
59
- };
60
-
61
- template <typename Index, std::size_t Rank>
62
- struct all_indices_known_statically_impl<DimensionList<Index, Rank> > {
63
- EIGEN_DEVICE_FUNC static constexpr bool run() {
64
- return true;
65
- }
66
- };
67
- template <typename Index, std::size_t Rank>
68
- struct all_indices_known_statically_impl<const DimensionList<Index, Rank> > {
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- EIGEN_DEVICE_FUNC static constexpr bool run() {
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- return true;
71
- }
72
- };
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-
74
- template <typename Index, std::size_t Rank>
75
- struct indices_statically_known_to_increase_impl<DimensionList<Index, Rank> > {
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- EIGEN_DEVICE_FUNC static constexpr bool run() {
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- return true;
78
- }
79
- };
80
- template <typename Index, std::size_t Rank>
81
- struct indices_statically_known_to_increase_impl<const DimensionList<Index, Rank> > {
82
- EIGEN_DEVICE_FUNC static constexpr bool run() {
83
- return true;
84
- }
85
- };
86
-
87
- template <typename Index, std::size_t Rank>
88
- struct index_statically_eq_impl<DimensionList<Index, Rank> > {
89
- static constexpr bool run(const DenseIndex i, const DenseIndex value) {
90
- return i == value;
91
- }
92
- };
93
- template <typename Index, std::size_t Rank>
94
- struct index_statically_eq_impl<const DimensionList<Index, Rank> > {
95
- EIGEN_DEVICE_FUNC static constexpr bool run(const DenseIndex i, const DenseIndex value) {
96
- return i == value;
97
- }
98
- };
99
-
100
- template <typename Index, std::size_t Rank>
101
- struct index_statically_ne_impl<DimensionList<Index, Rank> > {
102
- EIGEN_DEVICE_FUNC static constexpr bool run(const DenseIndex i, const DenseIndex value) {
103
- return i != value;
104
- }
105
- };
106
- template <typename Index, std::size_t Rank>
107
- struct index_statically_ne_impl<const DimensionList<Index, Rank> > {
108
- static constexpr bool run(const DenseIndex i, const DenseIndex value) {
109
- return i != value;
110
- }
111
- };
112
-
113
- template <typename Index, std::size_t Rank>
114
- struct index_statically_gt_impl<DimensionList<Index, Rank> > {
115
- EIGEN_DEVICE_FUNC static constexpr bool run(const DenseIndex i, const DenseIndex value) {
116
- return i > value;
117
- }
118
- };
119
- template <typename Index, std::size_t Rank>
120
- struct index_statically_gt_impl<const DimensionList<Index, Rank> > {
121
- EIGEN_DEVICE_FUNC static constexpr bool run(const DenseIndex i, const DenseIndex value) {
122
- return i > value;
123
- }
124
- };
125
-
126
- template <typename Index, std::size_t Rank>
127
- struct index_statically_lt_impl<DimensionList<Index, Rank> > {
128
- EIGEN_DEVICE_FUNC static constexpr bool run(const DenseIndex i, const DenseIndex value) {
129
- return i < value;
130
- }
131
- };
132
- template <typename Index, std::size_t Rank>
133
- struct index_statically_lt_impl<const DimensionList<Index, Rank> > {
134
- EIGEN_DEVICE_FUNC static constexpr bool run(const DenseIndex i, const DenseIndex value) {
135
- return i < value;
136
- }
137
- };
138
-
139
- #else
140
- template <typename Index, std::size_t Rank>
141
- struct index_known_statically_impl<DimensionList<Index, Rank> > {
142
- EIGEN_DEVICE_FUNC static EIGEN_ALWAYS_INLINE bool run(const DenseIndex) {
143
- return true;
144
- }
145
- };
146
- template <typename Index, std::size_t Rank>
147
- struct index_known_statically_impl<const DimensionList<Index, Rank> > {
148
- EIGEN_DEVICE_FUNC static EIGEN_ALWAYS_INLINE bool run(const DenseIndex) {
149
- return true;
150
- }
151
- };
152
-
153
- template <typename Index, std::size_t Rank>
154
- struct all_indices_known_statically_impl<DimensionList<Index, Rank> > {
155
- EIGEN_DEVICE_FUNC static EIGEN_ALWAYS_INLINE bool run() {
156
- return true;
157
- }
158
- };
159
- template <typename Index, std::size_t Rank>
160
- struct all_indices_known_statically_impl<const DimensionList<Index, Rank> > {
161
- EIGEN_DEVICE_FUNC static EIGEN_ALWAYS_INLINE bool run() {
162
- return true;
163
- }
164
- };
165
-
166
- template <typename Index, std::size_t Rank>
167
- struct indices_statically_known_to_increase_impl<DimensionList<Index, Rank> > {
168
- static EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE bool run() {
169
- return true;
170
- }
171
- };
172
- template <typename Index, std::size_t Rank>
173
- struct indices_statically_known_to_increase_impl<const DimensionList<Index, Rank> > {
174
- static EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE bool run() {
175
- return true;
176
- }
177
- };
178
-
179
- template <typename Index, std::size_t Rank>
180
- struct index_statically_eq_impl<DimensionList<Index, Rank> > {
181
- static EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE bool run(const DenseIndex, const DenseIndex) {
182
- return false;
183
- }
184
- };
185
- template <typename Index, std::size_t Rank>
186
- struct index_statically_eq_impl<const DimensionList<Index, Rank> > {
187
- static EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE bool run(const DenseIndex, const DenseIndex) {
188
- return false;
189
- }
190
- };
191
-
192
- template <typename Index, std::size_t Rank>
193
- struct index_statically_ne_impl<DimensionList<Index, Rank> > {
194
- static EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE bool run(const DenseIndex, const DenseIndex){
195
- return false;
196
- }
197
- };
198
- template <typename Index, std::size_t Rank>
199
- struct index_statically_ne_impl<const DimensionList<Index, Rank> > {
200
- static EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE bool run(const DenseIndex, const DenseIndex) {
201
- return false;
202
- }
203
- };
204
-
205
- template <typename Index, std::size_t Rank>
206
- struct index_statically_gt_impl<DimensionList<Index, Rank> > {
207
- static EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE bool run(const DenseIndex, const DenseIndex) {
208
- return false;
209
- }
210
- };
211
- template <typename Index, std::size_t Rank>
212
- struct index_statically_gt_impl<const DimensionList<Index, Rank> > {
213
- static EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE bool run(const DenseIndex, const DenseIndex) {
214
- return false;
215
- }
216
- };
217
-
218
- template <typename Index, std::size_t Rank>
219
- struct index_statically_lt_impl<DimensionList<Index, Rank> > {
220
- static EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE bool run(const DenseIndex, const DenseIndex) {
221
- return false;
222
- }
223
- };
224
- template <typename Index, std::size_t Rank>
225
- struct index_statically_lt_impl<const DimensionList<Index, Rank> > {
226
- static EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE bool run(const DenseIndex, const DenseIndex) {
227
- return false;
228
- }
229
- };
230
- #endif
231
-
232
- } // end namespace internal
233
- } // end namespace Eigen
234
-
235
-
236
- #endif // EIGEN_CXX11_TENSOR_TENSOR_DIMENSION_LIST_H