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
@@ -1,302 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2015 Benoit Steiner <benoit.steiner.goog@gmail.com>
5
- //
6
- // This Source Code Form is subject to the terms of the Mozilla
7
- // Public License v. 2.0. If a copy of the MPL was not distributed
8
- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
9
-
10
- #ifndef EIGEN_CXX11_TENSOR_TENSOR_GENERATOR_H
11
- #define EIGEN_CXX11_TENSOR_TENSOR_GENERATOR_H
12
-
13
- namespace Eigen {
14
-
15
- /** \class TensorGeneratorOp
16
- * \ingroup CXX11_Tensor_Module
17
- *
18
- * \brief Tensor generator class.
19
- *
20
- *
21
- */
22
- namespace internal {
23
- template<typename Generator, typename XprType>
24
- struct traits<TensorGeneratorOp<Generator, XprType> > : public traits<XprType>
25
- {
26
- typedef typename XprType::Scalar Scalar;
27
- typedef traits<XprType> XprTraits;
28
- typedef typename XprTraits::StorageKind StorageKind;
29
- typedef typename XprTraits::Index Index;
30
- typedef typename XprType::Nested Nested;
31
- typedef typename remove_reference<Nested>::type _Nested;
32
- static const int NumDimensions = XprTraits::NumDimensions;
33
- static const int Layout = XprTraits::Layout;
34
- typedef typename XprTraits::PointerType PointerType;
35
- };
36
-
37
- template<typename Generator, typename XprType>
38
- struct eval<TensorGeneratorOp<Generator, XprType>, Eigen::Dense>
39
- {
40
- typedef const TensorGeneratorOp<Generator, XprType>& type;
41
- };
42
-
43
- template<typename Generator, typename XprType>
44
- struct nested<TensorGeneratorOp<Generator, XprType>, 1, typename eval<TensorGeneratorOp<Generator, XprType> >::type>
45
- {
46
- typedef TensorGeneratorOp<Generator, XprType> type;
47
- };
48
-
49
- } // end namespace internal
50
-
51
-
52
-
53
- template<typename Generator, typename XprType>
54
- class TensorGeneratorOp : public TensorBase<TensorGeneratorOp<Generator, XprType>, ReadOnlyAccessors>
55
- {
56
- public:
57
- typedef typename Eigen::internal::traits<TensorGeneratorOp>::Scalar Scalar;
58
- typedef typename Eigen::NumTraits<Scalar>::Real RealScalar;
59
- typedef typename XprType::CoeffReturnType CoeffReturnType;
60
- typedef typename Eigen::internal::nested<TensorGeneratorOp>::type Nested;
61
- typedef typename Eigen::internal::traits<TensorGeneratorOp>::StorageKind StorageKind;
62
- typedef typename Eigen::internal::traits<TensorGeneratorOp>::Index Index;
63
-
64
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorGeneratorOp(const XprType& expr, const Generator& generator)
65
- : m_xpr(expr), m_generator(generator) {}
66
-
67
- EIGEN_DEVICE_FUNC
68
- const Generator& generator() const { return m_generator; }
69
-
70
- EIGEN_DEVICE_FUNC
71
- const typename internal::remove_all<typename XprType::Nested>::type&
72
- expression() const { return m_xpr; }
73
-
74
- protected:
75
- typename XprType::Nested m_xpr;
76
- const Generator m_generator;
77
- };
78
-
79
-
80
- // Eval as rvalue
81
- template<typename Generator, typename ArgType, typename Device>
82
- struct TensorEvaluator<const TensorGeneratorOp<Generator, ArgType>, Device>
83
- {
84
- typedef TensorGeneratorOp<Generator, ArgType> XprType;
85
- typedef typename XprType::Index Index;
86
- typedef typename TensorEvaluator<ArgType, Device>::Dimensions Dimensions;
87
- static const int NumDims = internal::array_size<Dimensions>::value;
88
- typedef typename XprType::Scalar Scalar;
89
- typedef typename XprType::CoeffReturnType CoeffReturnType;
90
- typedef typename PacketType<CoeffReturnType, Device>::type PacketReturnType;
91
- typedef StorageMemory<CoeffReturnType, Device> Storage;
92
- typedef typename Storage::Type EvaluatorPointerType;
93
- enum {
94
- IsAligned = false,
95
- PacketAccess = (PacketType<CoeffReturnType, Device>::size > 1),
96
- BlockAccess = true,
97
- PreferBlockAccess = true,
98
- Layout = TensorEvaluator<ArgType, Device>::Layout,
99
- CoordAccess = false, // to be implemented
100
- RawAccess = false
101
- };
102
-
103
- typedef internal::TensorIntDivisor<Index> IndexDivisor;
104
-
105
- //===- Tensor block evaluation strategy (see TensorBlock.h) -------------===//
106
- typedef internal::TensorBlockDescriptor<NumDims, Index> TensorBlockDesc;
107
- typedef internal::TensorBlockScratchAllocator<Device> TensorBlockScratch;
108
-
109
- typedef typename internal::TensorMaterializedBlock<CoeffReturnType, NumDims,
110
- Layout, Index>
111
- TensorBlock;
112
- //===--------------------------------------------------------------------===//
113
-
114
- EIGEN_STRONG_INLINE TensorEvaluator(const XprType& op, const Device& device)
115
- : m_device(device), m_generator(op.generator())
116
- {
117
- TensorEvaluator<ArgType, Device> argImpl(op.expression(), device);
118
- m_dimensions = argImpl.dimensions();
119
-
120
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
121
- m_strides[0] = 1;
122
- EIGEN_UNROLL_LOOP
123
- for (int i = 1; i < NumDims; ++i) {
124
- m_strides[i] = m_strides[i - 1] * m_dimensions[i - 1];
125
- if (m_strides[i] != 0) m_fast_strides[i] = IndexDivisor(m_strides[i]);
126
- }
127
- } else {
128
- m_strides[NumDims - 1] = 1;
129
- EIGEN_UNROLL_LOOP
130
- for (int i = NumDims - 2; i >= 0; --i) {
131
- m_strides[i] = m_strides[i + 1] * m_dimensions[i + 1];
132
- if (m_strides[i] != 0) m_fast_strides[i] = IndexDivisor(m_strides[i]);
133
- }
134
- }
135
- }
136
-
137
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Dimensions& dimensions() const { return m_dimensions; }
138
-
139
- EIGEN_STRONG_INLINE bool evalSubExprsIfNeeded(EvaluatorPointerType /*data*/) {
140
- return true;
141
- }
142
- EIGEN_STRONG_INLINE void cleanup() {
143
- }
144
-
145
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE CoeffReturnType coeff(Index index) const
146
- {
147
- array<Index, NumDims> coords;
148
- extract_coordinates(index, coords);
149
- return m_generator(coords);
150
- }
151
-
152
- template<int LoadMode>
153
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE PacketReturnType packet(Index index) const
154
- {
155
- const int packetSize = PacketType<CoeffReturnType, Device>::size;
156
- EIGEN_STATIC_ASSERT((packetSize > 1), YOU_MADE_A_PROGRAMMING_MISTAKE)
157
- eigen_assert(index+packetSize-1 < dimensions().TotalSize());
158
-
159
- EIGEN_ALIGN_MAX typename internal::remove_const<CoeffReturnType>::type values[packetSize];
160
- for (int i = 0; i < packetSize; ++i) {
161
- values[i] = coeff(index+i);
162
- }
163
- PacketReturnType rslt = internal::pload<PacketReturnType>(values);
164
- return rslt;
165
- }
166
-
167
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
168
- internal::TensorBlockResourceRequirements getResourceRequirements() const {
169
- const size_t target_size = m_device.firstLevelCacheSize();
170
- // TODO(ezhulenev): Generator should have a cost.
171
- return internal::TensorBlockResourceRequirements::skewed<Scalar>(
172
- target_size);
173
- }
174
-
175
- struct BlockIteratorState {
176
- Index stride;
177
- Index span;
178
- Index size;
179
- Index count;
180
- };
181
-
182
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorBlock
183
- block(TensorBlockDesc& desc, TensorBlockScratch& scratch,
184
- bool /*root_of_expr_ast*/ = false) const {
185
- static const bool is_col_major =
186
- static_cast<int>(Layout) == static_cast<int>(ColMajor);
187
-
188
- // Compute spatial coordinates for the first block element.
189
- array<Index, NumDims> coords;
190
- extract_coordinates(desc.offset(), coords);
191
- array<Index, NumDims> initial_coords = coords;
192
-
193
- // Offset in the output block buffer.
194
- Index offset = 0;
195
-
196
- // Initialize output block iterator state. Dimension in this array are
197
- // always in inner_most -> outer_most order (col major layout).
198
- array<BlockIteratorState, NumDims> it;
199
- for (int i = 0; i < NumDims; ++i) {
200
- const int dim = is_col_major ? i : NumDims - 1 - i;
201
- it[i].size = desc.dimension(dim);
202
- it[i].stride = i == 0 ? 1 : (it[i - 1].size * it[i - 1].stride);
203
- it[i].span = it[i].stride * (it[i].size - 1);
204
- it[i].count = 0;
205
- }
206
- eigen_assert(it[0].stride == 1);
207
-
208
- // Prepare storage for the materialized generator result.
209
- const typename TensorBlock::Storage block_storage =
210
- TensorBlock::prepareStorage(desc, scratch);
211
-
212
- CoeffReturnType* block_buffer = block_storage.data();
213
-
214
- static const int packet_size = PacketType<CoeffReturnType, Device>::size;
215
-
216
- static const int inner_dim = is_col_major ? 0 : NumDims - 1;
217
- const Index inner_dim_size = it[0].size;
218
- const Index inner_dim_vectorized = inner_dim_size - packet_size;
219
-
220
- while (it[NumDims - 1].count < it[NumDims - 1].size) {
221
- Index i = 0;
222
- // Generate data for the vectorized part of the inner-most dimension.
223
- for (; i <= inner_dim_vectorized; i += packet_size) {
224
- for (Index j = 0; j < packet_size; ++j) {
225
- array<Index, NumDims> j_coords = coords; // Break loop dependence.
226
- j_coords[inner_dim] += j;
227
- *(block_buffer + offset + i + j) = m_generator(j_coords);
228
- }
229
- coords[inner_dim] += packet_size;
230
- }
231
- // Finalize non-vectorized part of the inner-most dimension.
232
- for (; i < inner_dim_size; ++i) {
233
- *(block_buffer + offset + i) = m_generator(coords);
234
- coords[inner_dim]++;
235
- }
236
- coords[inner_dim] = initial_coords[inner_dim];
237
-
238
- // For the 1d tensor we need to generate only one inner-most dimension.
239
- if (NumDims == 1) break;
240
-
241
- // Update offset.
242
- for (i = 1; i < NumDims; ++i) {
243
- if (++it[i].count < it[i].size) {
244
- offset += it[i].stride;
245
- coords[is_col_major ? i : NumDims - 1 - i]++;
246
- break;
247
- }
248
- if (i != NumDims - 1) it[i].count = 0;
249
- coords[is_col_major ? i : NumDims - 1 - i] =
250
- initial_coords[is_col_major ? i : NumDims - 1 - i];
251
- offset -= it[i].span;
252
- }
253
- }
254
-
255
- return block_storage.AsTensorMaterializedBlock();
256
- }
257
-
258
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorOpCost
259
- costPerCoeff(bool) const {
260
- // TODO(rmlarsen): This is just a placeholder. Define interface to make
261
- // generators return their cost.
262
- return TensorOpCost(0, 0, TensorOpCost::AddCost<Scalar>() +
263
- TensorOpCost::MulCost<Scalar>());
264
- }
265
-
266
- EIGEN_DEVICE_FUNC EvaluatorPointerType data() const { return NULL; }
267
-
268
- #ifdef EIGEN_USE_SYCL
269
- // binding placeholder accessors to a command group handler for SYCL
270
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void bind(cl::sycl::handler&) const {}
271
- #endif
272
-
273
- protected:
274
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
275
- void extract_coordinates(Index index, array<Index, NumDims>& coords) const {
276
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
277
- for (int i = NumDims - 1; i > 0; --i) {
278
- const Index idx = index / m_fast_strides[i];
279
- index -= idx * m_strides[i];
280
- coords[i] = idx;
281
- }
282
- coords[0] = index;
283
- } else {
284
- for (int i = 0; i < NumDims - 1; ++i) {
285
- const Index idx = index / m_fast_strides[i];
286
- index -= idx * m_strides[i];
287
- coords[i] = idx;
288
- }
289
- coords[NumDims-1] = index;
290
- }
291
- }
292
-
293
- const Device EIGEN_DEVICE_REF m_device;
294
- Dimensions m_dimensions;
295
- array<Index, NumDims> m_strides;
296
- array<IndexDivisor, NumDims> m_fast_strides;
297
- Generator m_generator;
298
- };
299
-
300
- } // end namespace Eigen
301
-
302
- #endif // EIGEN_CXX11_TENSOR_TENSOR_GENERATOR_H
@@ -1,33 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2016 Eugene Brevdo <ebrevdo@gmail.com>
5
- //
6
- // This Source Code Form is subject to the terms of the Mozilla
7
- // Public License v. 2.0. If a copy of the MPL was not distributed
8
- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
9
-
10
- #ifndef EIGEN_CXX11_TENSOR_TENSOR_GLOBAL_FUNCTIONS_H
11
- #define EIGEN_CXX11_TENSOR_TENSOR_GLOBAL_FUNCTIONS_H
12
-
13
- namespace Eigen {
14
-
15
- /** \cpp11 \returns an expression of the coefficient-wise betainc(\a x, \a a, \a b) to the given tensors.
16
- *
17
- * This function computes the regularized incomplete beta function (integral).
18
- *
19
- */
20
- template <typename ADerived, typename BDerived, typename XDerived>
21
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const
22
- TensorCwiseTernaryOp<internal::scalar_betainc_op<typename XDerived::Scalar>,
23
- const ADerived, const BDerived, const XDerived>
24
- betainc(const ADerived& a, const BDerived& b, const XDerived& x) {
25
- return TensorCwiseTernaryOp<
26
- internal::scalar_betainc_op<typename XDerived::Scalar>, const ADerived,
27
- const BDerived, const XDerived>(
28
- a, b, x, internal::scalar_betainc_op<typename XDerived::Scalar>());
29
- }
30
-
31
- } // end namespace Eigen
32
-
33
- #endif // EIGEN_CXX11_TENSOR_TENSOR_GLOBAL_FUNCTIONS_H
@@ -1,99 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2014 Benoit Steiner <benoit.steiner.goog@gmail.com>
5
- // Copyright (C) 2018 Deven Desai <deven.desai.amd@gmail.com>
6
- //
7
- // 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
9
- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
10
-
11
- #if defined(EIGEN_USE_GPU) && !defined(EIGEN_CXX11_TENSOR_GPU_HIP_CUDA_DEFINES_H)
12
- #define EIGEN_CXX11_TENSOR_GPU_HIP_CUDA_DEFINES_H
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-
14
- // Note that we are using EIGEN_USE_HIP here instead of EIGEN_HIPCC...this is by design
15
- // There is code in the Tensorflow codebase that will define EIGEN_USE_GPU, but
16
- // for some reason gets sent to the gcc/host compiler instead of the gpu/nvcc/hipcc compiler
17
- // When compiling such files, gcc will end up trying to pick up the CUDA headers by
18
- // default (see the code within "unsupported/Eigen/CXX11/Tensor" that is guarded by EIGEN_USE_GPU)
19
- // This will obviously not work when trying to compile tensorflow on a system with no CUDA
20
- // To work around this issue for HIP systems (and leave the default behaviour intact), the
21
- // HIP tensorflow build defines EIGEN_USE_HIP when compiling all source files, and
22
- // "unsupported/Eigen/CXX11/Tensor" has been updated to use HIP header when EIGEN_USE_HIP is
23
- // defined. In continuation of that requirement, the guard here needs to be EIGEN_USE_HIP as well
24
-
25
- #if defined(EIGEN_USE_HIP)
26
-
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- #define gpuStream_t hipStream_t
28
- #define gpuDeviceProp_t hipDeviceProp_t
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- #define gpuError_t hipError_t
30
- #define gpuSuccess hipSuccess
31
- #define gpuErrorNotReady hipErrorNotReady
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- #define gpuGetDeviceCount hipGetDeviceCount
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- #define gpuGetLastError hipGetLastError
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- #define gpuPeekAtLastError hipPeekAtLastError
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- #define gpuGetErrorName hipGetErrorName
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- #define gpuGetErrorString hipGetErrorString
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- #define gpuGetDeviceProperties hipGetDeviceProperties
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- #define gpuStreamDefault hipStreamDefault
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- #define gpuGetDevice hipGetDevice
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- #define gpuSetDevice hipSetDevice
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- #define gpuMalloc hipMalloc
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- #define gpuFree hipFree
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- #define gpuMemsetAsync hipMemsetAsync
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- #define gpuMemcpyAsync hipMemcpyAsync
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- #define gpuMemcpyDeviceToDevice hipMemcpyDeviceToDevice
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- #define gpuMemcpyDeviceToHost hipMemcpyDeviceToHost
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- #define gpuMemcpyHostToDevice hipMemcpyHostToDevice
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- #define gpuStreamQuery hipStreamQuery
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- #define gpuSharedMemConfig hipSharedMemConfig
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- #define gpuDeviceSetSharedMemConfig hipDeviceSetSharedMemConfig
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- #define gpuStreamSynchronize hipStreamSynchronize
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- #define gpuDeviceSynchronize hipDeviceSynchronize
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- #define gpuMemcpy hipMemcpy
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-
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- #else
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-
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- #define gpuStream_t cudaStream_t
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- #define gpuDeviceProp_t cudaDeviceProp
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- #define gpuError_t cudaError_t
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- #define gpuSuccess cudaSuccess
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- #define gpuErrorNotReady cudaErrorNotReady
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- #define gpuGetDeviceCount cudaGetDeviceCount
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- #define gpuGetLastError cudaGetLastError
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- #define gpuPeekAtLastError cudaPeekAtLastError
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- #define gpuGetErrorName cudaGetErrorName
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- #define gpuGetErrorString cudaGetErrorString
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- #define gpuGetDeviceProperties cudaGetDeviceProperties
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- #define gpuStreamDefault cudaStreamDefault
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- #define gpuGetDevice cudaGetDevice
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- #define gpuSetDevice cudaSetDevice
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- #define gpuMalloc cudaMalloc
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- #define gpuFree cudaFree
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- #define gpuMemsetAsync cudaMemsetAsync
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- #define gpuMemcpyAsync cudaMemcpyAsync
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- #define gpuMemcpyDeviceToDevice cudaMemcpyDeviceToDevice
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- #define gpuMemcpyDeviceToHost cudaMemcpyDeviceToHost
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- #define gpuMemcpyHostToDevice cudaMemcpyHostToDevice
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- #define gpuStreamQuery cudaStreamQuery
79
- #define gpuSharedMemConfig cudaSharedMemConfig
80
- #define gpuDeviceSetSharedMemConfig cudaDeviceSetSharedMemConfig
81
- #define gpuStreamSynchronize cudaStreamSynchronize
82
- #define gpuDeviceSynchronize cudaDeviceSynchronize
83
- #define gpuMemcpy cudaMemcpy
84
-
85
- #endif
86
-
87
- // gpu_assert can be overridden
88
- #ifndef gpu_assert
89
-
90
- #if defined(EIGEN_HIP_DEVICE_COMPILE)
91
- // HIPCC do not support the use of assert on the GPU side.
92
- #define gpu_assert(COND)
93
- #else
94
- #define gpu_assert(COND) assert(COND)
95
- #endif
96
-
97
- #endif // gpu_assert
98
-
99
- #endif // EIGEN_CXX11_TENSOR_GPU_HIP_CUDA_DEFINES_H
@@ -1,44 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2014 Benoit Steiner <benoit.steiner.goog@gmail.com>
5
- // Copyright (C) 2018 Deven Desai <deven.desai.amd@gmail.com>
6
- //
7
- // This Source Code Form is subject to the terms of the Mozilla
8
- // Public License v. 2.0. If a copy of the MPL was not distributed
9
- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
10
-
11
- #if defined(EIGEN_CXX11_TENSOR_GPU_HIP_CUDA_DEFINES_H)
12
-
13
- #ifndef EIGEN_PERMANENTLY_ENABLE_GPU_HIP_CUDA_DEFINES
14
-
15
- #undef gpuStream_t
16
- #undef gpuDeviceProp_t
17
- #undef gpuError_t
18
- #undef gpuSuccess
19
- #undef gpuErrorNotReady
20
- #undef gpuGetDeviceCount
21
- #undef gpuGetErrorString
22
- #undef gpuGetDeviceProperties
23
- #undef gpuStreamDefault
24
- #undef gpuGetDevice
25
- #undef gpuSetDevice
26
- #undef gpuMalloc
27
- #undef gpuFree
28
- #undef gpuMemsetAsync
29
- #undef gpuMemcpyAsync
30
- #undef gpuMemcpyDeviceToDevice
31
- #undef gpuMemcpyDeviceToHost
32
- #undef gpuMemcpyHostToDevice
33
- #undef gpuStreamQuery
34
- #undef gpuSharedMemConfig
35
- #undef gpuDeviceSetSharedMemConfig
36
- #undef gpuStreamSynchronize
37
- #undef gpuDeviceSynchronize
38
- #undef gpuMemcpy
39
-
40
- #endif // EIGEN_PERMANENTLY_ENABLE_GPU_HIP_CUDA_DEFINES
41
-
42
- #undef EIGEN_CXX11_TENSOR_GPU_HIP_CUDA_DEFINES_H
43
-
44
- #endif // EIGEN_CXX11_TENSOR_GPU_HIP_CUDA_DEFINES_H
@@ -1,79 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2014 Benoit Steiner <benoit.steiner.goog@gmail.com>
5
- //
6
- // This Source Code Form is subject to the terms of the Mozilla
7
- // Public License v. 2.0. If a copy of the MPL was not distributed
8
- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
9
-
10
- #ifndef EIGEN_CXX11_TENSOR_TENSOR_IO_H
11
- #define EIGEN_CXX11_TENSOR_TENSOR_IO_H
12
-
13
- namespace Eigen {
14
-
15
- namespace internal {
16
-
17
- // Print the tensor as a 2d matrix
18
- template <typename Tensor, int Rank>
19
- struct TensorPrinter {
20
- static void run (std::ostream& os, const Tensor& tensor) {
21
- typedef typename internal::remove_const<typename Tensor::Scalar>::type Scalar;
22
- typedef typename Tensor::Index Index;
23
- const Index total_size = internal::array_prod(tensor.dimensions());
24
- if (total_size > 0) {
25
- const Index first_dim = Eigen::internal::array_get<0>(tensor.dimensions());
26
- static const int layout = Tensor::Layout;
27
- Map<const Array<Scalar, Dynamic, Dynamic, layout> > matrix(const_cast<Scalar*>(tensor.data()), first_dim, total_size/first_dim);
28
- os << matrix;
29
- }
30
- }
31
- };
32
-
33
-
34
- // Print the tensor as a vector
35
- template <typename Tensor>
36
- struct TensorPrinter<Tensor, 1> {
37
- static void run (std::ostream& os, const Tensor& tensor) {
38
- typedef typename internal::remove_const<typename Tensor::Scalar>::type Scalar;
39
- typedef typename Tensor::Index Index;
40
- const Index total_size = internal::array_prod(tensor.dimensions());
41
- if (total_size > 0) {
42
- Map<const Array<Scalar, Dynamic, 1> > array(const_cast<Scalar*>(tensor.data()), total_size);
43
- os << array;
44
- }
45
- }
46
- };
47
-
48
-
49
- // Print the tensor as a scalar
50
- template <typename Tensor>
51
- struct TensorPrinter<Tensor, 0> {
52
- static void run (std::ostream& os, const Tensor& tensor) {
53
- os << tensor.coeff(0);
54
- }
55
- };
56
- }
57
-
58
- template <typename T>
59
- std::ostream& operator << (std::ostream& os, const TensorBase<T, ReadOnlyAccessors>& expr) {
60
- typedef TensorEvaluator<const TensorForcedEvalOp<const T>, DefaultDevice> Evaluator;
61
- typedef typename Evaluator::Dimensions Dimensions;
62
-
63
- // Evaluate the expression if needed
64
- TensorForcedEvalOp<const T> eval = expr.eval();
65
- Evaluator tensor(eval, DefaultDevice());
66
- tensor.evalSubExprsIfNeeded(NULL);
67
-
68
- // Print the result
69
- static const int rank = internal::array_size<Dimensions>::value;
70
- internal::TensorPrinter<Evaluator, rank>::run(os, tensor);
71
-
72
- // Cleanup.
73
- tensor.cleanup();
74
- return os;
75
- }
76
-
77
- } // end namespace Eigen
78
-
79
- #endif // EIGEN_CXX11_TENSOR_TENSOR_IO_H