nmatrix 0.0.9 → 0.1.0.rc1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (101) hide show
  1. checksums.yaml +4 -4
  2. data/Gemfile +1 -0
  3. data/History.txt +95 -1
  4. data/LICENSE.txt +2 -2
  5. data/README.rdoc +24 -26
  6. data/Rakefile +32 -16
  7. data/ext/nmatrix/data/complex.h +2 -2
  8. data/ext/nmatrix/data/data.cpp +27 -51
  9. data/ext/nmatrix/data/data.h +92 -4
  10. data/ext/nmatrix/data/meta.h +2 -2
  11. data/ext/nmatrix/data/rational.h +2 -2
  12. data/ext/nmatrix/data/ruby_object.h +2 -2
  13. data/ext/nmatrix/extconf.rb +87 -86
  14. data/ext/nmatrix/math.cpp +45 -40
  15. data/ext/nmatrix/math/asum.h +3 -3
  16. data/ext/nmatrix/math/geev.h +2 -2
  17. data/ext/nmatrix/math/gemm.h +6 -2
  18. data/ext/nmatrix/math/gemv.h +6 -2
  19. data/ext/nmatrix/math/ger.h +2 -2
  20. data/ext/nmatrix/math/gesdd.h +2 -2
  21. data/ext/nmatrix/math/gesvd.h +2 -2
  22. data/ext/nmatrix/math/getf2.h +2 -2
  23. data/ext/nmatrix/math/getrf.h +2 -2
  24. data/ext/nmatrix/math/getri.h +2 -2
  25. data/ext/nmatrix/math/getrs.h +7 -3
  26. data/ext/nmatrix/math/idamax.h +2 -2
  27. data/ext/nmatrix/math/inc.h +12 -6
  28. data/ext/nmatrix/math/laswp.h +2 -2
  29. data/ext/nmatrix/math/long_dtype.h +2 -2
  30. data/ext/nmatrix/math/math.h +16 -10
  31. data/ext/nmatrix/math/nrm2.h +3 -3
  32. data/ext/nmatrix/math/potrs.h +7 -3
  33. data/ext/nmatrix/math/rot.h +2 -2
  34. data/ext/nmatrix/math/rotg.h +2 -2
  35. data/ext/nmatrix/math/scal.h +2 -2
  36. data/ext/nmatrix/math/swap.h +2 -2
  37. data/ext/nmatrix/math/trsm.h +7 -3
  38. data/ext/nmatrix/nm_memory.h +60 -0
  39. data/ext/nmatrix/nmatrix.cpp +13 -47
  40. data/ext/nmatrix/nmatrix.h +37 -12
  41. data/ext/nmatrix/ruby_constants.cpp +4 -2
  42. data/ext/nmatrix/ruby_constants.h +4 -2
  43. data/ext/nmatrix/ruby_nmatrix.c +937 -170
  44. data/ext/nmatrix/storage/common.cpp +2 -2
  45. data/ext/nmatrix/storage/common.h +2 -2
  46. data/ext/nmatrix/storage/{dense.cpp → dense/dense.cpp} +253 -100
  47. data/ext/nmatrix/storage/{dense.h → dense/dense.h} +6 -5
  48. data/ext/nmatrix/storage/{list.cpp → list/list.cpp} +517 -98
  49. data/ext/nmatrix/storage/{list.h → list/list.h} +13 -6
  50. data/ext/nmatrix/storage/storage.cpp +48 -19
  51. data/ext/nmatrix/storage/storage.h +4 -4
  52. data/ext/nmatrix/storage/yale/class.h +112 -43
  53. data/ext/nmatrix/storage/yale/iterators/base.h +2 -2
  54. data/ext/nmatrix/storage/yale/iterators/iterator.h +2 -2
  55. data/ext/nmatrix/storage/yale/iterators/row.h +2 -2
  56. data/ext/nmatrix/storage/yale/iterators/row_stored.h +2 -2
  57. data/ext/nmatrix/storage/yale/iterators/row_stored_nd.h +4 -3
  58. data/ext/nmatrix/storage/yale/iterators/stored_diagonal.h +2 -2
  59. data/ext/nmatrix/storage/yale/math/transpose.h +2 -2
  60. data/ext/nmatrix/storage/yale/yale.cpp +343 -52
  61. data/ext/nmatrix/storage/yale/yale.h +7 -3
  62. data/ext/nmatrix/types.h +2 -2
  63. data/ext/nmatrix/util/io.cpp +5 -5
  64. data/ext/nmatrix/util/io.h +2 -2
  65. data/ext/nmatrix/util/sl_list.cpp +40 -27
  66. data/ext/nmatrix/util/sl_list.h +3 -3
  67. data/ext/nmatrix/util/util.h +2 -2
  68. data/lib/nmatrix.rb +2 -2
  69. data/lib/nmatrix/blas.rb +2 -2
  70. data/lib/nmatrix/enumerate.rb +17 -6
  71. data/lib/nmatrix/io/market.rb +2 -3
  72. data/lib/nmatrix/io/mat5_reader.rb +2 -2
  73. data/lib/nmatrix/io/mat_reader.rb +2 -2
  74. data/lib/nmatrix/lapack.rb +46 -46
  75. data/lib/nmatrix/math.rb +213 -20
  76. data/lib/nmatrix/monkeys.rb +24 -2
  77. data/lib/nmatrix/nmatrix.rb +394 -9
  78. data/lib/nmatrix/nvector.rb +2 -64
  79. data/lib/nmatrix/rspec.rb +2 -2
  80. data/lib/nmatrix/shortcuts.rb +14 -61
  81. data/lib/nmatrix/version.rb +11 -3
  82. data/lib/nmatrix/yale_functions.rb +4 -4
  83. data/nmatrix.gemspec +2 -7
  84. data/scripts/mac-brew-gcc.sh +11 -8
  85. data/scripts/mac-mavericks-brew-gcc.sh +22 -0
  86. data/spec/00_nmatrix_spec.rb +116 -7
  87. data/spec/01_enum_spec.rb +17 -3
  88. data/spec/02_slice_spec.rb +11 -3
  89. data/spec/blas_spec.rb +5 -2
  90. data/spec/elementwise_spec.rb +5 -2
  91. data/spec/io_spec.rb +27 -17
  92. data/spec/lapack_spec.rb +157 -9
  93. data/spec/math_spec.rb +95 -4
  94. data/spec/nmatrix_yale_spec.rb +21 -26
  95. data/spec/rspec_monkeys.rb +27 -0
  96. data/spec/rspec_spec.rb +2 -2
  97. data/spec/shortcuts_spec.rb +5 -10
  98. data/spec/slice_set_spec.rb +6 -2
  99. data/spec/spec_helper.rb +3 -2
  100. data/spec/stat_spec.rb +174 -158
  101. metadata +15 -15
@@ -9,8 +9,8 @@
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  //
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  // == Copyright Information
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  //
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- // SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
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- // NMatrix is Copyright (c) 2013, Ruby Science Foundation
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+ // SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
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+ // NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
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  //
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  // Please see LICENSE.txt for additional copyright notices.
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  //
@@ -86,7 +86,7 @@ inline ReturnDType asum(const int N, const DType* X, const int incX) {
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  }
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- #ifdef HAVE_CBLAS_H
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+ #if defined HAVE_CBLAS_H || defined HAVE_ATLAS_CBLAS_H
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  template <>
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  inline float asum(const int N, const float* X, const int incX) {
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  return cblas_sasum(N, X, incX);
@@ -9,8 +9,8 @@
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  //
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  // == Copyright Information
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  //
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- // SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
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- // NMatrix is Copyright (c) 2013, Ruby Science Foundation
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+ // SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
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+ // NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
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  //
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  // Please see LICENSE.txt for additional copyright notices.
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  //
@@ -9,8 +9,8 @@
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  //
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  // == Copyright Information
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  //
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- // SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
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- // NMatrix is Copyright (c) 2013, Ruby Science Foundation
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+ // SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
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+ // NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
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  //
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  // Please see LICENSE.txt for additional copyright notices.
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  //
@@ -31,7 +31,11 @@
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  # define GEMM_H
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  extern "C" { // These need to be in an extern "C" block or you'll get all kinds of undefined symbol errors.
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+ #if defined HAVE_CBLAS_H
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  #include <cblas.h>
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+ #elif defined HAVE_ATLAS_CBLAS_H
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+ #include <atlas/cblas.h>
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+ #endif
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  }
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@@ -9,8 +9,8 @@
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  //
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  // == Copyright Information
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  //
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- // SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
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- // NMatrix is Copyright (c) 2013, Ruby Science Foundation
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+ // SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
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+ // NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
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  //
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  // Please see LICENSE.txt for additional copyright notices.
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  //
@@ -31,7 +31,11 @@
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  # define GEMV_H
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  extern "C" { // These need to be in an extern "C" block or you'll get all kinds of undefined symbol errors.
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+ #if defined HAVE_CBLAS_H
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  #include <cblas.h>
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+ #elif defined HAVE_ATLAS_CBLAS_H
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+ #include <atlas/cblas.h>
38
+ #endif
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  }
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@@ -9,8 +9,8 @@
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  //
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  // == Copyright Information
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  //
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- // SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
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- // NMatrix is Copyright (c) 2013, Ruby Science Foundation
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+ // SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
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+ // NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
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  //
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  // Please see LICENSE.txt for additional copyright notices.
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  //
@@ -9,8 +9,8 @@
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  //
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  // == Copyright Information
11
11
  //
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- // SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
13
- // NMatrix is Copyright (c) 2013, Ruby Science Foundation
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+ // SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
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+ // NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
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  //
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  // Please see LICENSE.txt for additional copyright notices.
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  //
@@ -9,8 +9,8 @@
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  //
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  // == Copyright Information
11
11
  //
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- // SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
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- // NMatrix is Copyright (c) 2013, Ruby Science Foundation
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+ // SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
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+ // NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
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  //
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  // Please see LICENSE.txt for additional copyright notices.
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  //
@@ -9,8 +9,8 @@
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  //
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  // == Copyright Information
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  //
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- // SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
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- // NMatrix is Copyright (c) 2013, Ruby Science Foundation
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+ // SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
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+ // NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
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  //
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  // Please see LICENSE.txt for additional copyright notices.
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  //
@@ -9,8 +9,8 @@
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  //
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  // == Copyright Information
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11
  //
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- // SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
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- // NMatrix is Copyright (c) 2013, Ruby Science Foundation
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+ // SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
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+ // NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
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  //
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  // Please see LICENSE.txt for additional copyright notices.
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  //
@@ -9,8 +9,8 @@
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  //
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  // == Copyright Information
11
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  //
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- // SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
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- // NMatrix is Copyright (c) 2013, Ruby Science Foundation
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+ // SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
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+ // NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
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  //
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  // Please see LICENSE.txt for additional copyright notices.
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  //
@@ -9,8 +9,8 @@
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  //
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  // == Copyright Information
11
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  //
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- // SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
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- // NMatrix is Copyright (c) 2013, Ruby Science Foundation
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+ // SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
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+ // NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
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  //
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  // Please see LICENSE.txt for additional copyright notices.
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  //
@@ -60,7 +60,11 @@
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  #define GETRS_H
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62
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  extern "C" {
63
+ #if defined HAVE_CBLAS_H
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  #include <cblas.h>
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+ #elif defined HAVE_ATLAS_CBLAS_H
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+ #include <atlas/cblas.h>
67
+ #endif
64
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  }
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66
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  namespace nm { namespace math {
@@ -122,4 +126,4 @@ inline int clapack_getrs(const enum CBLAS_ORDER order, const enum CBLAS_TRANSPOS
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  } } // end nm::math
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- #endif // GETRS_H
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+ #endif // GETRS_H
@@ -9,8 +9,8 @@
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  //
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  // == Copyright Information
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  //
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- // SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
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- // NMatrix is Copyright (c) 2013, Ruby Science Foundation
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+ // SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
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+ // NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
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  //
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  // Please see LICENSE.txt for additional copyright notices.
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  //
@@ -9,8 +9,8 @@
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  //
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  // == Copyright Information
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  //
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- // SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
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- // NMatrix is Copyright (c) 2013, Ruby Science Foundation
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+ // SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
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+ // NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
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  //
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  //
@@ -31,11 +31,17 @@
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  extern "C" { // These need to be in an extern "C" block or you'll get all kinds of undefined symbol errors.
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+ #if defined HAVE_CBLAS_H
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+ #elif defined HAVE_ATLAS_CBLAS_H
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+ #include <atlas/cblas.h>
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+ #endif
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+ #elif defined HAVE_ATLAS_CLAPACK_H
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+ #include <atlas/clapack.h>
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+ #endif
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+ #endif // INC_H
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  // == Copyright Information
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  //
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- // SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
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- // NMatrix is Copyright (c) 2013, Ruby Science Foundation
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+ // SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
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+ // NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
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@@ -9,8 +9,8 @@
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  // == Copyright Information
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  //
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- // SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
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- // NMatrix is Copyright (c) 2013, Ruby Science Foundation
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+ // SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
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+ // NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
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  //
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- // SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
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- // NMatrix is Copyright (c) 2013, Ruby Science Foundation
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+ // SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
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+ // NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
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@@ -69,11 +69,17 @@
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  extern "C" { // These need to be in an extern "C" block or you'll get all kinds of undefined symbol errors.
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+ #if defined HAVE_CBLAS_H
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+ #endif
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  inline int potrf(const enum CBLAS_ORDER order, const enum CBLAS_UPLO uplo, const int N, DType* A, const int lda) {
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  inline int potrf(const enum CBLAS_ORDER order, const enum CBLAS_UPLO uplo, const int N, float* A, const int lda) {
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@@ -928,7 +934,7 @@ inline void lauum(const enum CBLAS_ORDER order, const enum CBLAS_UPLO uplo, cons
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933
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@@ -1019,7 +1025,7 @@ inline int potri(const enum CBLAS_ORDER order, const enum CBLAS_UPLO uplo, const
1019
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@@ -9,8 +9,8 @@
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  // == Copyright Information
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  //
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- // SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
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- // NMatrix is Copyright (c) 2013, Ruby Science Foundation
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+ // SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
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+ // NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
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@@ -98,7 +98,7 @@ ReturnDType nrm2(const int N, const DType* X, const int incX) {
98
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103
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@@ -9,8 +9,8 @@
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  //
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- // SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
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- // NMatrix is Copyright (c) 2013, Ruby Science Foundation
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+ // SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
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+ // NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
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  //
@@ -60,7 +60,11 @@
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62
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63
+ #if defined HAVE_CBLAS_H
63
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65
+ #elif defined HAVE_ATLAS_CBLAS_H
66
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67
+ #endif
64
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66
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@@ -122,4 +126,4 @@ inline int clapack_potrs(const enum CBLAS_ORDER order, const enum CBLAS_UPLO upl
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123
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125
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  //
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- // SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
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- // NMatrix is Copyright (c) 2013, Ruby Science Foundation
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+ // SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
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+ // NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
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@@ -9,8 +9,8 @@
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  //
12
- // SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
13
- // NMatrix is Copyright (c) 2013, Ruby Science Foundation
12
+ // SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
13
+ // NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
14
14
  //
15
15
  // Please see LICENSE.txt for additional copyright notices.
16
16
  //
@@ -9,8 +9,8 @@
9
9
  //
10
10
  // == Copyright Information
11
11
  //
12
- // SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
13
- // NMatrix is Copyright (c) 2013, Ruby Science Foundation
12
+ // SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
13
+ // NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
14
14
  //
15
15
  // Please see LICENSE.txt for additional copyright notices.
16
16
  //
@@ -9,8 +9,8 @@
9
9
  //
10
10
  // == Copyright Information
11
11
  //
12
- // SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
13
- // NMatrix is Copyright (c) 2013, Ruby Science Foundation
12
+ // SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
13
+ // NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
14
14
  //
15
15
  // Please see LICENSE.txt for additional copyright notices.
16
16
  //
@@ -9,8 +9,8 @@
9
9
  //
10
10
  // == Copyright Information
11
11
  //
12
- // SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
13
- // NMatrix is Copyright (c) 2013, Ruby Science Foundation
12
+ // SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
13
+ // NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
14
14
  //
15
15
  // Please see LICENSE.txt for additional copyright notices.
16
16
  //
@@ -60,7 +60,11 @@
60
60
 
61
61
 
62
62
  extern "C" {
63
+ #if defined HAVE_CBLAS_H
63
64
  #include <cblas.h>
65
+ #elif defined HAVE_ATLAS_CBLAS_H
66
+ #include <atlas/cblas.h>
67
+ #endif
64
68
  }
65
69
 
66
70
  namespace nm { namespace math {
@@ -380,4 +384,4 @@ inline void trsm(const enum CBLAS_ORDER order, const enum CBLAS_SIDE side, const
380
384
 
381
385
 
382
386
  } } // namespace nm::math
383
- #endif // TRSM_H
387
+ #endif // TRSM_H