sequenzo 0.1.18__cp310-cp310-win_amd64.whl → 0.1.20__cp310-cp310-win_amd64.whl

sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/c_interface_base.h

@@ -1,73 +0,0 @@
-
-#ifndef BTL_C_INTERFACE_BASE_H
-#define BTL_C_INTERFACE_BASE_H
-
-#include "utilities.h"
-#include <vector>
-
-template<class real> class c_interface_base
-{
-
-public:
-
-  typedef real                      real_type;
-  typedef std::vector<real>         stl_vector;
-  typedef std::vector<stl_vector >  stl_matrix;
-
-  typedef real* gene_matrix;
-  typedef real* gene_vector;
-
-  static void free_matrix(gene_matrix & A, int /*N*/){
-    delete[] A;
-  }
-
-  static void free_vector(gene_vector & B){
-    delete[] B;
-  }
-
-  static inline void matrix_from_stl(gene_matrix & A, stl_matrix & A_stl){
-    int N = A_stl.size();
-    A = new real[N*N];
-    for (int j=0;j<N;j++)
-      for (int i=0;i<N;i++)
-        A[i+N*j] = A_stl[j][i];
-  }
-
-  static inline void vector_from_stl(gene_vector & B, stl_vector & B_stl){
-    int N = B_stl.size();
-    B = new real[N];
-    for (int i=0;i<N;i++)
-      B[i] = B_stl[i];
-  }
-
-  static inline void vector_to_stl(gene_vector & B, stl_vector & B_stl){
-    int N = B_stl.size();
-    for (int i=0;i<N;i++)
-      B_stl[i] = B[i];
-  }
-
-  static inline void matrix_to_stl(gene_matrix & A, stl_matrix & A_stl){
-    int N = A_stl.size();
-    for (int j=0;j<N;j++){
-      A_stl[j].resize(N);
-      for (int i=0;i<N;i++)
-        A_stl[j][i] = A[i+N*j];
-    }
-  }
-
-  static inline void copy_vector(const gene_vector & source, gene_vector & cible, int N){
-    for (int i=0;i<N;i++)
-      cible[i]=source[i];
-  }
-
-  static inline void copy_matrix(const gene_matrix & source, gene_matrix & cible, int N){
-    for (int j=0;j<N;j++){
-      for (int i=0;i<N;i++){
-        cible[i+N*j] = source[i+N*j];
-      }
-    }
-  }
-
-};
-
-#endif

sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemm_common.h

@@ -1,67 +0,0 @@
-#include <iostream>
-#include <fstream>
-#include <vector>
-#include <string>
-#include "eigen_src/Eigen/Core"
-#include "../BenchTimer.h"
-using namespace Eigen;
-
-#ifndef SCALAR
-#error SCALAR must be defined
-#endif
-
-typedef SCALAR Scalar;
-
-typedef Matrix<Scalar,Dynamic,Dynamic> Mat;
-
-template<typename Func>
-EIGEN_DONT_INLINE
-double bench(long m, long n, long k, const Func& f)
-{
-  Mat A(m,k);
-  Mat B(k,n);
-  Mat C(m,n);
-  A.setRandom();
-  B.setRandom();
-  C.setZero();
-  
-  BenchTimer t;
-  
-  double up = 1e8*4/sizeof(Scalar);
-  double tm0 = 4, tm1 = 10;
-  if(NumTraits<Scalar>::IsComplex)
-  {
-    up /= 4;
-    tm0 = 2;
-    tm1 = 4;
-  }
-  
-  double flops = 2. * m * n * k;
-  long rep = std::max(1., std::min(100., up/flops) );
-  long tries = std::max(tm0, std::min(tm1, up/flops) );
-  
-  BENCH(t, tries, rep, f(A,B,C));
-  
-  return 1e-9 * rep * flops / t.best();
-}
-
-template<typename Func>
-int main_gemm(int argc, char **argv, const Func& f)
-{
-  std::vector<double> results;
-  
-  std::string filename = std::string("gemm_settings.txt");
-  if(argc>1)
-    filename = std::string(argv[1]);
-  std::ifstream settings(filename);
-  long m, n, k;
-  while(settings >> m >> n >> k)
-  {
-    //std::cerr << "  Testing " << m << " " << n << " " << k << std::endl;
-    results.push_back( bench(m, n, k, f) );
-  }
-  
-  std::cout << RowVectorXd::Map(results.data(), results.size());
-  
-  return 0;
-}

sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemv_common.h

@@ -1,69 +0,0 @@
-#include <iostream>
-#include <fstream>
-#include <vector>
-#include <string>
-#include <functional>
-#include "eigen_src/Eigen/Core"
-#include "../BenchTimer.h"
-using namespace Eigen;
-
-#ifndef SCALAR
-#error SCALAR must be defined
-#endif
-
-typedef SCALAR Scalar;
-
-typedef Matrix<Scalar,Dynamic,Dynamic> Mat;
-typedef Matrix<Scalar,Dynamic,1>       Vec;
-
-template<typename Func>
-EIGEN_DONT_INLINE
-double bench(long m, long n, Func &f)
-{
-  Mat A(m,n);
-  Vec B(n);
-  Vec C(m);
-  A.setRandom();
-  B.setRandom();
-  C.setRandom();
-
-  BenchTimer t;
-
-  double up = 1e8/sizeof(Scalar);
-  double tm0 = 4, tm1 = 10;
-  if(NumTraits<Scalar>::IsComplex)
-  {
-    up /= 4;
-    tm0 = 2;
-    tm1 = 4;
-  }
-
-  double flops = 2. * m * n;
-  long rep = std::max(1., std::min(100., up/flops) );
-  long tries = std::max(tm0, std::min(tm1, up/flops) );
-
-  BENCH(t, tries, rep, f(A,B,C));
-
-  return 1e-9 * rep * flops / t.best();
-}
-
-template<typename Func>
-int main_gemv(int argc, char **argv, Func& f)
-{
-  std::vector<double> results;
-
-  std::string filename = std::string("gemv_settings.txt");
-  if(argc>1)
-    filename = std::string(argv[1]);
-  std::ifstream settings(filename);
-  long m, n;
-  while(settings >> m >> n)
-  {
-    //std::cerr << "  Testing " << m << " " << n << std::endl;
-    results.push_back( bench(m, n, f) );
-  }
-
-  std::cout << RowVectorXd::Map(results.data(), results.size());
-
-  return 0;
-}