sequenzo 0.1.18__cp312-cp312-win_amd64.whl → 0.1.20__cp312-cp312-win_amd64.whl

sequenzo/dissimilarity_measures/src/eigen/bench/BenchTimer.h

@@ -1,199 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2008-2010 Gael Guennebaud <gael.guennebaud@inria.fr>
-// Copyright (C) 2009 Benoit Jacob <jacob.benoit.1@gmail.com>
-//
-// This Source Code Form is subject to the terms of the Mozilla
-// Public License v. 2.0. If a copy of the MPL was not distributed
-// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
-
-#ifndef EIGEN_BENCH_TIMERR_H
-#define EIGEN_BENCH_TIMERR_H
-
-#if defined(_WIN32) || defined(__CYGWIN__)
-# ifndef NOMINMAX
-#   define NOMINMAX
-#   define EIGEN_BT_UNDEF_NOMINMAX
-# endif
-# ifndef WIN32_LEAN_AND_MEAN
-#   define WIN32_LEAN_AND_MEAN
-#   define EIGEN_BT_UNDEF_WIN32_LEAN_AND_MEAN
-# endif
-# include <windows.h>
-#elif defined(__APPLE__)
-#include <mach/mach_time.h>
-#else
-# include <unistd.h>
-#endif
-
-static void escape(void *p) {
-#if EIGEN_COMP_GNUC || EIGEN_COMP_CLANG
-  asm volatile("" : : "g"(p) : "memory");
-#endif
-}
-
-static void clobber() {
-#if EIGEN_COMP_GNUC || EIGEN_COMP_CLANG
-  asm volatile("" : : : "memory");
-#endif
-}
-
-#include <Eigen/Core>
-
-namespace Eigen
-{
-
-enum {
-  CPU_TIMER = 0,
-  REAL_TIMER = 1
-};
-
-/** Elapsed time timer keeping the best try.
-  *
-  * On POSIX platforms we use clock_gettime with CLOCK_PROCESS_CPUTIME_ID.
-  * On Windows we use QueryPerformanceCounter
-  *
-  * Important: on linux, you must link with -lrt
-  */
-class BenchTimer
-{
-public:
-
-  BenchTimer()
-  {
-#if defined(_WIN32) || defined(__CYGWIN__)
-    LARGE_INTEGER freq;
-    QueryPerformanceFrequency(&freq);
-    m_frequency = (double)freq.QuadPart;
-#endif
-    reset();
-  }
-
-  ~BenchTimer() {}
-
-  inline void reset()
-  {
-    m_bests.fill(1e9);
-    m_worsts.fill(0);
-    m_totals.setZero();
-  }
-  inline void start()
-  {
-    m_starts[CPU_TIMER]  = getCpuTime();
-    m_starts[REAL_TIMER] = getRealTime();
-  }
-  inline void stop()
-  {
-    m_times[CPU_TIMER] = getCpuTime() - m_starts[CPU_TIMER];
-    m_times[REAL_TIMER] = getRealTime() - m_starts[REAL_TIMER];
-    #if EIGEN_VERSION_AT_LEAST(2,90,0)
-    m_bests = m_bests.cwiseMin(m_times);
-    m_worsts = m_worsts.cwiseMax(m_times);
-    #else
-    m_bests(0) = std::min(m_bests(0),m_times(0));
-    m_bests(1) = std::min(m_bests(1),m_times(1));
-    m_worsts(0) = std::max(m_worsts(0),m_times(0));
-    m_worsts(1) = std::max(m_worsts(1),m_times(1));
-    #endif
-    m_totals += m_times;
-  }
-
-  /** Return the elapsed time in seconds between the last start/stop pair
-    */
-  inline double value(int TIMER = CPU_TIMER) const
-  {
-    return m_times[TIMER];
-  }
-
-  /** Return the best elapsed time in seconds
-    */
-  inline double best(int TIMER = CPU_TIMER) const
-  {
-    return m_bests[TIMER];
-  }
-
-  /** Return the worst elapsed time in seconds
-    */
-  inline double worst(int TIMER = CPU_TIMER) const
-  {
-    return m_worsts[TIMER];
-  }
-
-  /** Return the total elapsed time in seconds.
-    */
-  inline double total(int TIMER = CPU_TIMER) const
-  {
-    return m_totals[TIMER];
-  }
-
-  inline double getCpuTime() const
-  {
-#ifdef _WIN32
-    LARGE_INTEGER query_ticks;
-    QueryPerformanceCounter(&query_ticks);
-    return query_ticks.QuadPart/m_frequency;
-#elif __APPLE__
-    return double(mach_absolute_time())*1e-9;
-#else
-    timespec ts;
-    clock_gettime(CLOCK_PROCESS_CPUTIME_ID, &ts);
-    return double(ts.tv_sec) + 1e-9 * double(ts.tv_nsec);
-#endif
-  }
-
-  inline double getRealTime() const
-  {
-#ifdef _WIN32
-    SYSTEMTIME st;
-    GetSystemTime(&st);
-    return (double)st.wSecond + 1.e-3 * (double)st.wMilliseconds;
-#elif __APPLE__
-    return double(mach_absolute_time())*1e-9;
-#else
-    timespec ts;
-    clock_gettime(CLOCK_REALTIME, &ts);
-    return double(ts.tv_sec) + 1e-9 * double(ts.tv_nsec);
-#endif
-  }
-
-protected:
-#if defined(_WIN32) || defined(__CYGWIN__)
-  double m_frequency;
-#endif
-  Vector2d m_starts;
-  Vector2d m_times;
-  Vector2d m_bests;
-  Vector2d m_worsts;
-  Vector2d m_totals;
-
-public:
-  EIGEN_MAKE_ALIGNED_OPERATOR_NEW
-};
-
-#define BENCH(TIMER,TRIES,REP,CODE) { \
-    TIMER.reset(); \
-    for(int uglyvarname1=0; uglyvarname1<TRIES; ++uglyvarname1){ \
-      TIMER.start(); \
-      for(int uglyvarname2=0; uglyvarname2<REP; ++uglyvarname2){ \
-        CODE; \
-      } \
-      TIMER.stop(); \
-      clobber(); \
-    } \
-  }
-
-}
-
-// clean #defined tokens
-#ifdef EIGEN_BT_UNDEF_NOMINMAX
-# undef EIGEN_BT_UNDEF_NOMINMAX
-# undef NOMINMAX
-#endif
-
-#ifdef EIGEN_BT_UNDEF_WIN32_LEAN_AND_MEAN
-# undef EIGEN_BT_UNDEF_WIN32_LEAN_AND_MEAN
-# undef WIN32_LEAN_AND_MEAN
-#endif
-
-#endif // EIGEN_BENCH_TIMERR_H

sequenzo/dissimilarity_measures/src/eigen/bench/BenchUtil.h

@@ -1,92 +0,0 @@
-
-#ifndef EIGEN_BENCH_UTIL_H
-#define EIGEN_BENCH_UTIL_H
-
-#include <Eigen/Core>
-#include "BenchTimer.h"
-
-using namespace std;
-using namespace Eigen;
-
-#include <boost/preprocessor/repetition/enum_params.hpp>
-#include <boost/preprocessor/repetition.hpp>
-#include <boost/preprocessor/seq.hpp>
-#include <boost/preprocessor/array.hpp>
-#include <boost/preprocessor/arithmetic.hpp>
-#include <boost/preprocessor/comparison.hpp>
-#include <boost/preprocessor/punctuation.hpp>
-#include <boost/preprocessor/punctuation/comma.hpp>
-#include <boost/preprocessor/stringize.hpp>
-
-template<typename MatrixType> void initMatrix_random(MatrixType& mat) __attribute__((noinline));
-template<typename MatrixType> void initMatrix_random(MatrixType& mat)
-{
-  mat.setRandom();// = MatrixType::random(mat.rows(), mat.cols());
-}
-
-template<typename MatrixType> void initMatrix_identity(MatrixType& mat) __attribute__((noinline));
-template<typename MatrixType> void initMatrix_identity(MatrixType& mat)
-{
-  mat.setIdentity();
-}
-
-#ifndef __INTEL_COMPILER
-#define DISABLE_SSE_EXCEPTIONS()  { \
-  int aux; \
-  asm( \
-  "stmxcsr   %[aux]           \n\t" \
-  "orl       $32832, %[aux]   \n\t" \
-  "ldmxcsr   %[aux]           \n\t" \
-  : : [aux] "m" (aux)); \
-}
-#else
-#define DISABLE_SSE_EXCEPTIONS()  
-#endif
-
-#ifdef BENCH_GMM
-#include <gmm/gmm.h>
-template <typename EigenMatrixType, typename GmmMatrixType>
-void eiToGmm(const EigenMatrixType& src, GmmMatrixType& dst)
-{
-  dst.resize(src.rows(),src.cols());
-  for (int j=0; j<src.cols(); ++j)
-    for (int i=0; i<src.rows(); ++i)
-      dst(i,j) = src.coeff(i,j);
-}
-#endif
-
-
-#ifdef BENCH_GSL
-#include <gsl/gsl_matrix.h>
-#include <gsl/gsl_linalg.h>
-#include <gsl/gsl_eigen.h>
-template <typename EigenMatrixType>
-void eiToGsl(const EigenMatrixType& src, gsl_matrix** dst)
-{
-  for (int j=0; j<src.cols(); ++j)
-    for (int i=0; i<src.rows(); ++i)
-      gsl_matrix_set(*dst, i, j, src.coeff(i,j));
-}
-#endif
-
-#ifdef BENCH_UBLAS
-#include <boost/numeric/ublas/matrix.hpp>
-#include <boost/numeric/ublas/vector.hpp>
-template <typename EigenMatrixType, typename UblasMatrixType>
-void eiToUblas(const EigenMatrixType& src, UblasMatrixType& dst)
-{
-  dst.resize(src.rows(),src.cols());
-  for (int j=0; j<src.cols(); ++j)
-    for (int i=0; i<src.rows(); ++i)
-      dst(i,j) = src.coeff(i,j);
-}
-template <typename EigenType, typename UblasType>
-void eiToUblasVec(const EigenType& src, UblasType& dst)
-{
-  dst.resize(src.size());
-  for (int j=0; j<src.size(); ++j)
-      dst[j] = src.coeff(j);
-}
-#endif
-
-#endif // EIGEN_BENCH_UTIL_H

sequenzo/dissimilarity_measures/src/eigen/bench/basicbenchmark.h

@@ -1,63 +0,0 @@
-
-#ifndef EIGEN_BENCH_BASICBENCH_H
-#define EIGEN_BENCH_BASICBENCH_H
-
-enum {LazyEval, EarlyEval, OmpEval};
-
-template<int Mode, typename MatrixType>
-void benchBasic_loop(const MatrixType& I, MatrixType& m, int iterations) __attribute__((noinline));
-
-template<int Mode, typename MatrixType>
-void benchBasic_loop(const MatrixType& I, MatrixType& m, int iterations)
-{
-  for(int a = 0; a < iterations; a++)
-  {
-    if (Mode==LazyEval)
-    {
-      asm("#begin_bench_loop LazyEval");
-      if (MatrixType::SizeAtCompileTime!=Eigen::Dynamic) asm("#fixedsize");
-      m = (I + 0.00005 * (m + m.lazyProduct(m))).eval();
-    }
-    else if (Mode==OmpEval)
-    {
-      asm("#begin_bench_loop OmpEval");
-      if (MatrixType::SizeAtCompileTime!=Eigen::Dynamic) asm("#fixedsize");
-      m = (I + 0.00005 * (m + m.lazyProduct(m))).eval();
-    }
-    else
-    {
-      asm("#begin_bench_loop EarlyEval");
-      if (MatrixType::SizeAtCompileTime!=Eigen::Dynamic) asm("#fixedsize");
-      m = I + 0.00005 * (m + m * m);
-    }
-    asm("#end_bench_loop");
-  }
-}
-
-template<int Mode, typename MatrixType>
-double benchBasic(const MatrixType& mat, int size, int tries) __attribute__((noinline));
-
-template<int Mode, typename MatrixType>
-double benchBasic(const MatrixType& mat, int iterations, int tries)
-{
-  const int rows = mat.rows();
-  const int cols = mat.cols();
-
-  MatrixType I(rows,cols);
-  MatrixType m(rows,cols);
-
-  initMatrix_identity(I);
-
-  Eigen::BenchTimer timer;
-  for(uint t=0; t<tries; ++t)
-  {
-    initMatrix_random(m);
-    timer.start();
-    benchBasic_loop<Mode>(I, m, iterations);
-    timer.stop();
-    cerr << m;
-  }
-  return timer.value();
-};
-
-#endif // EIGEN_BENCH_BASICBENCH_H

sequenzo/dissimilarity_measures/src/eigen/bench/btl/generic_bench/utils/utilities.h

@@ -1,90 +0,0 @@
-//=============================================================================
-// File      : utilities.h
-// Created   : mar jun 19 13:18:14 CEST 2001
-// Author    : Antoine YESSAYAN, Paul RASCLE, EDF
-// Project   : SALOME
-// Copyright : EDF 2001
-// $Header$
-//=============================================================================
-
-/* ---  Definition macros file to print information if _DEBUG_ is defined --- */
-
-# ifndef UTILITIES_H
-# define UTILITIES_H
-
-# include <stdlib.h>
-//# include <iostream> ok for gcc3.01
-# include <iostream>
-
-/* ---  INFOS is always defined (without _DEBUG_): to be used for warnings, with release version --- */
-
-# define HEREWEARE cout<<flush ; cerr << __FILE__ << " [" << __LINE__ << "] : " << flush ;
-# define INFOS(chain) {HEREWEARE ; cerr << chain << endl ;}
-# define PYSCRIPT(chain) {cout<<flush ; cerr << "---PYSCRIPT--- " << chain << endl ;}
-
-/* --- To print date and time of compilation of current source on stdout --- */
-
-# if defined ( __GNUC__ )
-# define COMPILER		"g++" ;
-# elif defined ( __sun )
-# define COMPILER		"CC" ;
-# elif defined ( __KCC )
-# define COMPILER		"KCC" ;
-# elif defined ( __PGI )
-# define COMPILER		"pgCC" ;
-# else
-# define COMPILER		"undefined" ;
-# endif
-
-# ifdef INFOS_COMPILATION
-# error INFOS_COMPILATION already defined
-# endif
-# define INFOS_COMPILATION	{\
-					cerr << flush;\
-					cout << __FILE__ ;\
-					cout << " [" << __LINE__ << "] : " ;\
-					cout << "COMPILED with " << COMPILER ;\
-					cout << ", " << __DATE__ ; \
-					cout << " at " << __TIME__ << endl ;\
-					cout << "\n\n" ;\
-					cout << flush ;\
-				}
-
-# ifdef _DEBUG_
-
-/* --- the following MACROS are useful at debug time --- */
-
-# define HERE cout<<flush ; cerr << "- Trace " << __FILE__ << " [" << __LINE__ << "] : " << flush ;
-# define SCRUTE(var) HERE ; cerr << #var << "=" << var << endl ;
-# define MESSAGE(chain) {HERE ; cerr << chain << endl ;}
-# define INTERRUPTION(code) HERE ; cerr << "INTERRUPTION return code= " << code << endl ; exit(code) ;
-
-# ifndef ASSERT
-# define ASSERT(condition) if (!(condition)){ HERE ; cerr << "CONDITION " << #condition << " NOT VERIFIED"<< endl ; INTERRUPTION(1) ;}
-# endif /* ASSERT */
-
-#define REPERE cout<<flush ; cerr << "   --------------" << endl << flush ;
-#define BEGIN_OF(chain) {REPERE ; HERE ; cerr << "Begin of: " << chain << endl ; REPERE ; }
-#define END_OF(chain) {REPERE ; HERE ; cerr << "Normal end of: " << chain << endl ; REPERE ; }
-
-
-
-# else /* ifdef _DEBUG_*/
-
-# define HERE
-# define SCRUTE(var)
-# define MESSAGE(chain)
-# define INTERRUPTION(code)
-
-# ifndef ASSERT
-# define ASSERT(condition)
-# endif /* ASSERT */
-
-#define REPERE
-#define BEGIN_OF(chain)
-#define END_OF(chain)
-
-
-# endif /* ifdef _DEBUG_*/
-
-# endif /* ifndef UTILITIES_H */