Delete all files in order to incorporate upstream's move to git.

9 files changed, 0 insertions, 1177 deletions

diff --git a/example/Persistent_cohomology/CMakeLists.txt b/example/Persistent_cohomology/CMakeLists.txt
deleted file mode 100644
index 0f731519..00000000
--- a/example/Persistent_cohomology/CMakeLists.txt
+++ /dev/null
@@ -1,69 +0,0 @@
-project(Persistent_cohomology_examples)
-
-add_executable(plain_homology plain_homology.cpp)
-
-add_executable(persistence_from_simple_simplex_tree persistence_from_simple_simplex_tree.cpp)
-
-add_executable(rips_persistence_step_by_step rips_persistence_step_by_step.cpp)
-target_link_libraries(rips_persistence_step_by_step ${Boost_PROGRAM_OPTIONS_LIBRARY})
-
-add_executable(rips_persistence_via_boundary_matrix rips_persistence_via_boundary_matrix.cpp)
-target_link_libraries(rips_persistence_via_boundary_matrix ${Boost_PROGRAM_OPTIONS_LIBRARY})
-
-add_executable(persistence_from_file persistence_from_file.cpp)
-target_link_libraries(persistence_from_file ${Boost_PROGRAM_OPTIONS_LIBRARY})
-
-if (TBB_FOUND)
-  target_link_libraries(plain_homology ${TBB_LIBRARIES})
-  target_link_libraries(persistence_from_simple_simplex_tree ${TBB_LIBRARIES})
-  target_link_libraries(rips_persistence_step_by_step ${TBB_LIBRARIES})
-  target_link_libraries(rips_persistence_via_boundary_matrix ${TBB_LIBRARIES})
-  target_link_libraries(persistence_from_file ${TBB_LIBRARIES})
-endif()
-
-add_test(NAME Persistent_cohomology_example_plain_homology COMMAND $<TARGET_FILE:plain_homology>)
-add_test(NAME Persistent_cohomology_example_from_simple_simplex_tree COMMAND $<TARGET_FILE:persistence_from_simple_simplex_tree>
-    "1" "0")
-add_test(NAME Persistent_cohomology_example_from_rips_step_by_step_on_tore_3D COMMAND $<TARGET_FILE:rips_persistence_step_by_step>
-    "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3")
-add_test(NAME Persistent_cohomology_example_via_boundary_matrix COMMAND $<TARGET_FILE:rips_persistence_via_boundary_matrix>
-    "${CMAKE_SOURCE_DIR}/data/points/Kl.off" "-r" "0.16" "-d" "3" "-p" "3" "-m" "100")
-add_test(NAME Persistent_cohomology_example_from_file_3_2_0 COMMAND $<TARGET_FILE:persistence_from_file>
-    "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc" "-p" "2" "-m" "0")
-add_test(NAME Persistent_cohomology_example_from_file_3_3_100 COMMAND $<TARGET_FILE:persistence_from_file>
-    "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc" "-p" "3" "-m" "100")
-
-install(TARGETS plain_homology DESTINATION bin)
-install(TARGETS persistence_from_simple_simplex_tree DESTINATION bin)
-install(TARGETS rips_persistence_step_by_step DESTINATION bin)
-install(TARGETS rips_persistence_via_boundary_matrix DESTINATION bin)
-install(TARGETS persistence_from_file DESTINATION bin)
-
-if(GMP_FOUND)
-   if(GMPXX_FOUND)
-      add_executable(rips_multifield_persistence rips_multifield_persistence.cpp )
-      target_link_libraries(rips_multifield_persistence
-          ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
-      if (TBB_FOUND)
-        target_link_libraries(rips_multifield_persistence ${TBB_LIBRARIES})
-      endif(TBB_FOUND)
-      add_test(NAME Persistent_cohomology_example_multifield_2_71 COMMAND $<TARGET_FILE:rips_multifield_persistence>
-          "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "2" "-q" "71")
-      install(TARGETS rips_multifield_persistence DESTINATION bin)
-   endif(GMPXX_FOUND)
-endif(GMP_FOUND)
-
-if(CGAL_FOUND)
-  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
-    add_executable(custom_persistence_sort custom_persistence_sort.cpp)
-    target_link_libraries(custom_persistence_sort ${CGAL_LIBRARY})
-
-    if (TBB_FOUND)
-      target_link_libraries(custom_persistence_sort ${TBB_LIBRARIES})
-    endif(TBB_FOUND)
-    add_test(NAME Persistent_cohomology_example_custom_persistence_sort COMMAND $<TARGET_FILE:custom_persistence_sort>)
-
-    install(TARGETS custom_persistence_sort DESTINATION bin)
-
-  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
-endif(CGAL_FOUND)
diff --git a/example/Persistent_cohomology/README b/example/Persistent_cohomology/README
deleted file mode 100644
index f39d9584..00000000
--- a/example/Persistent_cohomology/README
+++ /dev/null
@@ -1,67 +0,0 @@
-To build the examples, run in a Terminal:
-
-cd /path-to-examples/
-cmake .
-make
-
-***********************************************************************************************************************
-Example of use of RIPS:
-
-Computation of the persistent homology with Z/2Z and Z/3Z coefficients simultaneously of the Rips complex 
-on points sampling a 3D torus:
-
-./rips_multifield_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.12 -d 3 -p 2 -q 3
-
-output:
-6  0 0 inf 
-6  1 0.0983494 inf 
-6  1 0.104347 inf 
-6  2 0.138335 inf 
-6  0 0 0.122545 
-6  0 0 0.121171 
-6  0 0 0.120964 
-6  0 0 0.12057 
-6  0 0 0.12047 
-6  0 0 0.120414 
-
-Every line is of this format: p1*...*pr   dim b d
-where
- 	p1*...*pr is the product of prime numbers pi such that the homology feature exists in homology with Z/piZ coefficients. 
-	dim is the dimension of the homological feature,
-    b and d are respectively the birth and death of the feature and
-
-and the computation with all Z/pZ for 2 <= p <= 71 (20 first prime numbers):
-
- ./rips_multifield_persistence ../../data/points/Kl.off -r 0.25 -m 0.5 -d 3 -p 2 -q 71
-
-output:
-557940830126698960967415390  0 0 inf 
-557940830126698960967415390  1 0.0983494 inf 
-557940830126698960967415390  1 0.104347 inf 
-557940830126698960967415390  2 0.138335 inf 
-557940830126698960967415390  0 0 0.122545 
-557940830126698960967415390  0 0 0.121171 
-557940830126698960967415390  0 0 0.120964 
-557940830126698960967415390  0 0 0.12057 
-557940830126698960967415390  0 0 0.12047 
-557940830126698960967415390  0 0 0.120414 
-
-***********************************************************************************************************************
-Example of use of PLAIN HOMOLOGY:
-
-This example computes the plain homology of the following simplicial complex without filtration values:
-  /* Complex to build. */
-  /*    1   3          */
-  /*    o---o          */
-  /*   /X\ /           */
-  /*  o---o   o        */
-  /*  2   0   4        */
-
-./plain_homology 
-
-output:
-2  0 0 inf 
-2  0 0 inf 
-2  1 0 inf 
-
-Here we retrieve the 2 entities {0,1,2,3} and {4} (Betti numbers[0] = 2) and the hole in {0,1,3} (Betti numbers[1] = 1)
diff --git a/example/Persistent_cohomology/custom_persistence_sort.cpp b/example/Persistent_cohomology/custom_persistence_sort.cpp
deleted file mode 100644
index 35366144..00000000
--- a/example/Persistent_cohomology/custom_persistence_sort.cpp
+++ /dev/null
@@ -1,137 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Vincent Rouvreau
- *
- *    Copyright (C) 2014 Inria
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#include <CGAL/Epick_d.h>
-#include <CGAL/point_generators_d.h>
-#include <CGAL/algorithm.h>
-#include <CGAL/assertions.h>
-
-#include <gudhi/Alpha_complex.h>
-#include <gudhi/Persistent_cohomology.h>
-// to construct a simplex_tree from alpha complex
-#include <gudhi/Simplex_tree.h>
-
-#include <iostream>
-#include <iterator>
-#include <vector>
-#include <fstream>  // for std::ofstream
-#include <algorithm>  // for std::sort
-
-
-using Kernel = CGAL::Epick_d< CGAL::Dimension_tag<3> >;
-using Point = Kernel::Point_d;
-using Alpha_complex = Gudhi::alpha_complex::Alpha_complex<Kernel>;
-using Simplex_tree = Gudhi::Simplex_tree<>;
-using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology< Simplex_tree,
-      Gudhi::persistent_cohomology::Field_Zp >;
-
-std::vector<Point> random_points() {
-  // Instanciate a random point generator
-  CGAL::Random rng(0);
-
-  // Generate "points_number" random points in a vector
-  std::vector<Point> points;
-
-  // Generates 1000 random 3D points on a sphere of radius 4.0
-  CGAL::Random_points_on_sphere_d<Point> rand_outside(3, 4.0, rng);
-  CGAL::cpp11::copy_n(rand_outside, 1000, std::back_inserter(points));
-  // Generates 2000 random 3D points in a sphere of radius 3.0
-  CGAL::Random_points_in_ball_d<Point> rand_inside(3, 3.0, rng);
-  CGAL::cpp11::copy_n(rand_inside, 2000, std::back_inserter(points));
-
-  return points;
-}
-
-/*
- * Compare two intervals by dimension, then by length.
- */
-struct cmp_intervals_by_dim_then_length {
-  explicit cmp_intervals_by_dim_then_length(Simplex_tree * sc)
-      : sc_(sc) { }
-
-  template<typename Persistent_interval>
-  bool operator()(const Persistent_interval & p1, const Persistent_interval & p2) {
-    if (sc_->dimension(get < 0 > (p1)) == sc_->dimension(get < 0 > (p2)))
-      return (sc_->filtration(get < 1 > (p1)) - sc_->filtration(get < 0 > (p1))
-              > sc_->filtration(get < 1 > (p2)) - sc_->filtration(get < 0 > (p2)));
-    else
-      return (sc_->dimension(get < 0 > (p1)) > sc_->dimension(get < 0 > (p2)));
-  }
-  Simplex_tree* sc_;
-};
-
-int main(int argc, char **argv) {
-  std::vector<Point> points = random_points();
-
-  std::cout << "Points size=" << points.size() << std::endl;
-  // Alpha complex persistence computation from generated points
-  Alpha_complex alpha_complex_from_points(points);
-  std::cout << "alpha_complex_from_points" << std::endl;
-
-  Simplex_tree simplex;
-  std::cout << "simplex" << std::endl;
-  if (alpha_complex_from_points.create_complex(simplex, 0.6)) {
-    std::cout << "simplex" << std::endl;
-    // ----------------------------------------------------------------------------
-    // Display information about the alpha complex
-    // ----------------------------------------------------------------------------
-    std::cout << "Simplicial complex is of dimension " << simplex.dimension() <<
-        " - " << simplex.num_simplices() << " simplices - " <<
-        simplex.num_vertices() << " vertices." << std::endl;
-
-    // Sort the simplices in the order of the filtration
-    simplex.initialize_filtration();
-
-    std::cout << "Simplex_tree dim: " << simplex.dimension() << std::endl;
-
-    Persistent_cohomology pcoh(simplex);
-
-    // initializes the coefficient field for homology - Z/3Z
-    pcoh.init_coefficients(3);
-    pcoh.compute_persistent_cohomology(0.2);
-
-    // Custom sort and output persistence
-    cmp_intervals_by_dim_then_length cmp(&simplex);
-    auto persistent_pairs = pcoh.get_persistent_pairs();
-    std::sort(std::begin(persistent_pairs), std::end(persistent_pairs), cmp);
-    for (auto pair : persistent_pairs) {
-      std::cout << simplex.dimension(get<0>(pair)) << " "
-            << simplex.filtration(get<0>(pair)) << " "
-            << simplex.filtration(get<1>(pair)) << std::endl;
-    }
-
-    // Persistent Betti numbers
-    std::cout << "The persistent Betti numbers in interval [0.40, 0.41] are : ";
-    for (int dim = 0; dim < simplex.dimension(); dim++)
-      std::cout << "b" << dim << " = " << pcoh.persistent_betti_number(dim, 0.40, 0.41) << " ; ";
-    std::cout << std::endl;
-
-    // Betti numbers
-    std::vector<int> betti_numbers = pcoh.betti_numbers();
-    std::cout << "The Betti numbers are : ";
-    for (std::size_t i = 0; i < betti_numbers.size(); i++)
-      std::cout << "b" << i << " = " << betti_numbers[i] << " ; ";
-    std::cout << std::endl;
-  }
-  return 0;
-}
-
diff --git a/example/Persistent_cohomology/persistence_from_file.cpp b/example/Persistent_cohomology/persistence_from_file.cpp
deleted file mode 100644
index 53456919..00000000
--- a/example/Persistent_cohomology/persistence_from_file.cpp
+++ /dev/null
@@ -1,143 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library 
- *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
- *    library for computational topology.
- *
- *    Author(s):       Vincent Rouvreau
- *
- *    Copyright (C) 2014 Inria
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#include <gudhi/reader_utils.h>
-#include <gudhi/graph_simplicial_complex.h>
-#include <gudhi/distance_functions.h>
-#include <gudhi/Simplex_tree.h>
-#include <gudhi/Persistent_cohomology.h>
-
-#include <boost/program_options.hpp>
-
-#include <string>
-
-using namespace Gudhi;
-using namespace Gudhi::persistent_cohomology;
-
-typedef int Vertex_handle;
-typedef double Filtration_value;
-
-void program_options(int argc, char * argv[]
-                     , std::string & simplex_tree_file
-                     , std::string & output_file
-                     , int & p
-                     , Filtration_value & min_persistence);
-
-int main(int argc, char * argv[]) {
-  std::string simplex_tree_file;
-  std::string output_file;
-  int p;
-  Filtration_value min_persistence;
-
-  program_options(argc, argv, simplex_tree_file, output_file, p, min_persistence);
-
-  std::cout << "Simplex_tree from file=" << simplex_tree_file.c_str() << " - output_file=" << output_file.c_str()
-      << std::endl;
-  std::cout << "     - p=" << p << " - min_persistence=" << min_persistence << std::endl;
-
-  // Read the list of simplices from a file.
-  Simplex_tree<> simplex_tree;
-
-  std::ifstream simplex_tree_stream(simplex_tree_file);
-  simplex_tree_stream >> simplex_tree;
-
-  std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices" << std::endl;
-  std::cout << "   - dimension " << simplex_tree.dimension() << std::endl;
-
-  /*
-  std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl;
-  for( auto f_simplex : simplex_tree.filtration_simplex_range() )
-  { std::cout << "   " << "[" << simplex_tree.filtration(f_simplex) << "] ";
-  for( auto vertex : simplex_tree.simplex_vertex_range(f_simplex) )
-  { std::cout << vertex << " "; }
-  std::cout << std::endl;
-  }*/
-
-  // Sort the simplices in the order of the filtration
-  simplex_tree.initialize_filtration();
-
-  // Compute the persistence diagram of the complex
-  Persistent_cohomology< Simplex_tree<>, Field_Zp > pcoh(simplex_tree);
-  // initializes the coefficient field for homology
-  pcoh.init_coefficients(p);
-
-  pcoh.compute_persistent_cohomology(min_persistence);
-
-  // Output the diagram in output_file
-  if (output_file.empty()) {
-    pcoh.output_diagram();
-  } else {
-    std::ofstream out(output_file);
-    pcoh.output_diagram(out);
-    out.close();
-  }
-
-  return 0;
-}
-
-void program_options(int argc, char * argv[]
-                     , std::string & simplex_tree_file
-                     , std::string & output_file
-                     , int & p
-                     , Filtration_value & min_persistence) {
-  namespace po = boost::program_options;
-  po::options_description hidden("Hidden options");
-  hidden.add_options()
-      ("input-file", po::value<std::string>(&simplex_tree_file),
-       "Name of file containing a simplex set. Format is one simplex per line (cf. reader_utils.h - read_simplex): Dim1 X11 X12 ... X1d Fil1  ");
-
-  po::options_description visible("Allowed options", 100);
-  visible.add_options()
-      ("help,h", "produce help message")
-      ("output-file,o", po::value<std::string>(&output_file)->default_value(std::string()),
-       "Name of file in which the persistence diagram is written. Default print in std::cout")
-      ("field-charac,p", po::value<int>(&p)->default_value(11),
-       "Characteristic p of the coefficient field Z/pZ for computing homology.")
-      ("min-persistence,m", po::value<Filtration_value>(&min_persistence),
-       "Minimal lifetime of homology feature to be recorded. Default is 0");
-
-  po::positional_options_description pos;
-  pos.add("input-file", 1);
-
-  po::options_description all;
-  all.add(visible).add(hidden);
-
-  po::variables_map vm;
-  po::store(po::command_line_parser(argc, argv).
-            options(all).positional(pos).run(), vm);
-  po::notify(vm);
-
-  if (vm.count("help") || !vm.count("input-file")) {
-    std::cout << std::endl;
-    std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
-    std::cout << "of a Rips complex defined on a set of input points.\n \n";
-    std::cout << "The output diagram contains one bar per line, written with the convention: \n";
-    std::cout << "   p   dim b d \n";
-    std::cout << "where dim is the dimension of the homological feature,\n";
-    std::cout << "b and d are respectively the birth and death of the feature and \n";
-    std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
-
-    std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
-    std::cout << visible << std::endl;
-    exit(-1);
-  }
-}
diff --git a/example/Persistent_cohomology/persistence_from_simple_simplex_tree.cpp b/example/Persistent_cohomology/persistence_from_simple_simplex_tree.cpp
deleted file mode 100644
index ffccfd86..00000000
--- a/example/Persistent_cohomology/persistence_from_simple_simplex_tree.cpp
+++ /dev/null
@@ -1,175 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Vincent Rouvreau
- *
- *    Copyright (C) 2014 Inria
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#include <gudhi/graph_simplicial_complex.h>
-#include <gudhi/Simplex_tree.h>
-#include <gudhi/Persistent_cohomology.h>
-
-#include <iostream>
-#include <ctime>
-#include <utility>
-#include <vector>
-
-// Types definition
-using Simplex_tree = Gudhi::Simplex_tree<>;
-using Filtration_value = Simplex_tree::Filtration_value;
-using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
-using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp >;
-using typeVectorVertex = std::vector< Simplex_tree::Vertex_handle >;
-
-void usage(char * const progName) {
-  std::cerr << "Usage: " << progName << " coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
-  exit(-1);
-}
-
-int main(int argc, char * const argv[]) {
-  // program args management
-  if (argc != 3) {
-    std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n";
-    usage(argv[0]);
-  }
-
-  int coeff_field_characteristic = 0;
-  int returnedScanValue = sscanf(argv[1], "%d", &coeff_field_characteristic);
-  if ((returnedScanValue == EOF) || (coeff_field_characteristic <= 0)) {
-    std::cerr << "Error: " << argv[1] << " is not correct\n";
-    usage(argv[0]);
-  }
-
-  Filtration_value min_persistence = 0.0;
-  returnedScanValue = sscanf(argv[2], "%lf", &min_persistence);
-  if ((returnedScanValue == EOF) || (min_persistence < -1.0)) {
-    std::cerr << "Error: " << argv[2] << " is not correct\n";
-    usage(argv[0]);
-  }
-
-  // TEST OF INSERTION
-  std::cout << "********************************************************************" << std::endl;
-  std::cout << "TEST OF INSERTION" << std::endl;
-  Simplex_tree st;
-
-  // ++ FIRST
-  std::cout << "   - INSERT (0,1,2)" << std::endl;
-  typeVectorVertex SimplexVector = {0, 1, 2};
-  st.insert_simplex_and_subfaces(SimplexVector, 0.3);
-
-  // ++ SECOND
-  std::cout << "   - INSERT 3" << std::endl;
-  SimplexVector = {3};
-  st.insert_simplex_and_subfaces(SimplexVector, 0.1);
-
-  // ++ THIRD
-  std::cout << "   - INSERT (0,3)" << std::endl;
-  SimplexVector = {0, 3};
-  st.insert_simplex_and_subfaces(SimplexVector, 0.2);
-
-  // ++ FOURTH
-  std::cout << "   - INSERT (0,1) (already inserted)" << std::endl;
-  SimplexVector = {0, 1};
-  st.insert_simplex_and_subfaces(SimplexVector, 0.2);
-
-  // ++ FIFTH
-  std::cout << "   - INSERT (3,4,5)" << std::endl;
-  SimplexVector = {3, 4, 5};
-  st.insert_simplex_and_subfaces(SimplexVector, 0.3);
-
-  // ++ SIXTH
-  std::cout << "   - INSERT (0,1,6,7)" << std::endl;
-  SimplexVector = {0, 1, 6, 7};
-  st.insert_simplex_and_subfaces(SimplexVector, 0.4);
-
-  // ++ SEVENTH
-  std::cout << "   - INSERT (4,5,8,9)" << std::endl;
-  SimplexVector = {4, 5, 8, 9};
-  st.insert_simplex_and_subfaces(SimplexVector, 0.4);
-
-  // ++ EIGHTH
-  std::cout << "   - INSERT (9,10,11)" << std::endl;
-  SimplexVector = {9, 10, 11};
-  st.insert_simplex_and_subfaces(SimplexVector, 0.3);
-
-  // ++ NINETH
-  std::cout << "   - INSERT (2,10,12)" << std::endl;
-  SimplexVector = {2, 10, 12};
-  st.insert_simplex_and_subfaces(SimplexVector, 0.3);
-
-  // ++ TENTH
-  std::cout << "   - INSERT (11,6)" << std::endl;
-  SimplexVector = {6, 11};
-  st.insert_simplex_and_subfaces(SimplexVector, 0.2);
-
-  // ++ ELEVENTH
-  std::cout << "   - INSERT (13,14,15)" << std::endl;
-  SimplexVector = {13, 14, 15};
-  st.insert_simplex_and_subfaces(SimplexVector, 0.25);
-
-  /* Inserted simplex:         */
-  /*    1   6                  */
-  /*    o---o                  */
-  /*   /X\7/      4       2    */
-  /*  o---o---o---o       o    */
-  /*  2   0   3\X/8\  10 /X\   */
-  /*            o---o---o---o  */
-  /*            5   9\X/    12 */
-  /*                  o---o    */
-  /*                 11   6    */
-  /* In other words:          */
-  /*   A facet [2,1,0]        */
-  /*   An edge [0,3]          */
-  /*   A facet [3,4,5]        */
-  /*   A cell  [0,1,6,7]      */
-  /*   A cell  [4,5,8,9]      */
-  /*   A facet [9,10,11]      */
-  /*   An edge [11,6]         */
-  /*   An edge [10,12,2]      */
-
-
-  std::cout << "The complex contains " << st.num_simplices() << " simplices - " << st.num_vertices() << " vertices "
-      << std::endl;
-  std::cout << "   - dimension " << st.dimension() << std::endl;
-  std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:"
-      << std::endl;
-  std::cout << "**************************************************************" << std::endl;
-  std::cout << "strict graph G { " << std::endl;
-
-  for (auto f_simplex : st.filtration_simplex_range()) {
-    std::cout << "   " << "[" << st.filtration(f_simplex) << "] ";
-    for (auto vertex : st.simplex_vertex_range(f_simplex)) {
-      std::cout << static_cast<int>(vertex) << " -- ";
-    }
-    std::cout << ";" << std::endl;
-  }
-
-  std::cout << "}" << std::endl;
-  std::cout << "**************************************************************" << std::endl;
-
-  // Compute the persistence diagram of the complex
-  Persistent_cohomology pcoh(st);
-  // initializes the coefficient field for homology
-  pcoh.init_coefficients(coeff_field_characteristic);
-
-  pcoh.compute_persistent_cohomology(min_persistence);
-
-  // Output the diagram in filediag
-  pcoh.output_diagram();
-  return 0;
-}
diff --git a/example/Persistent_cohomology/plain_homology.cpp b/example/Persistent_cohomology/plain_homology.cpp
deleted file mode 100644
index a2256060..00000000
--- a/example/Persistent_cohomology/plain_homology.cpp
+++ /dev/null
@@ -1,94 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Marc Glisse
- *
- *    Copyright (C) 2015 Inria
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#include <gudhi/Simplex_tree.h>
-#include <gudhi/Persistent_cohomology.h>
-
-#include <iostream>
-#include <vector>
-#include <cstdint>  // for std::uint8_t
-
-/* We could perfectly well use the default Simplex_tree<> (which uses
- * Simplex_tree_options_full_featured), the following simply demonstrates
- * how to save on storage by not storing a filtration value.  */
-
-struct MyOptions : Gudhi::Simplex_tree_options_full_featured {
-  // Implicitly use 0 as filtration value for all simplices
-  static const bool store_filtration = false;
-  // The persistence algorithm needs this
-  static const bool store_key = true;
-  // I have few vertices
-  typedef short Vertex_handle;
-  // Maximum number of simplices to compute persistence is 2^8 - 1 = 255. One is reserved for null_key
-  typedef std::uint8_t Simplex_key;
-};
-
-using ST = Gudhi::Simplex_tree<MyOptions>;
-using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
-using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<ST, Field_Zp>;
-
-int main() {
-  ST st;
-
-  /* Complex to build. */
-  /*    1   3          */
-  /*    o---o          */
-  /*   /X\ /           */
-  /*  o---o   o        */
-  /*  2   0   4        */
-
-  const short triangle012[] = {0, 1, 2};
-  const short edge03[] = {0, 3};
-  const short edge13[] = {1, 3};
-  const short vertex4[] = {4};
-  st.insert_simplex_and_subfaces(triangle012);
-  st.insert_simplex_and_subfaces(edge03);
-  st.insert_simplex(edge13);
-  st.insert_simplex(vertex4);
-
-  // Sort the simplices in the order of the filtration
-  st.initialize_filtration();
-
-  // Class for homology computation
-  Persistent_cohomology pcoh(st);
-
-  // Initialize the coefficient field Z/2Z for homology
-  pcoh.init_coefficients(2);
-
-  // Compute the persistence diagram of the complex
-  pcoh.compute_persistent_cohomology();
-
-  // Print the result. The format is, on each line: 2 dim 0 inf
-  // where 2 represents the field, dim the dimension of the feature.
-  // 2  0 0 inf
-  // 2  0 0 inf
-  // 2  1 0 inf
-  // means that in Z/2Z-homology, the Betti numbers are b0=2 and b1=1.
-  pcoh.output_diagram();
-
-  // Print the Betti numbers are b0=2 and b1=1.
-  std::cout << std::endl;
-  std::cout << "The Betti numbers are : ";
-  for (int i = 0; i < st.dimension(); i++)
-    std::cout << "b" << i << " = " << pcoh.betti_number(i) << " ; ";
-  std::cout << std::endl;
-}
diff --git a/example/Persistent_cohomology/rips_multifield_persistence.cpp b/example/Persistent_cohomology/rips_multifield_persistence.cpp
deleted file mode 100644
index d6a5bdad..00000000
--- a/example/Persistent_cohomology/rips_multifield_persistence.cpp
+++ /dev/null
@@ -1,154 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library 
- *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
- *    library for computational topology.
- *
- *    Author(s):       Clément Maria
- *
- *    Copyright (C) 2014 Inria
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#include <gudhi/Rips_complex.h>
-#include <gudhi/distance_functions.h>
-#include <gudhi/Simplex_tree.h>
-#include <gudhi/Persistent_cohomology.h>
-#include <gudhi/Persistent_cohomology/Multi_field.h>
-#include <gudhi/Points_off_io.h>
-
-#include <boost/program_options.hpp>
-
-#include <string>
-#include <vector>
-
-// Types definition
-using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
-using Filtration_value = Simplex_tree::Filtration_value;
-using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
-using Multi_field = Gudhi::persistent_cohomology::Multi_field;
-using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Multi_field >;
-using Point = std::vector<double>;
-using Points_off_reader = Gudhi::Points_off_reader<Point>;
-
-void program_options(int argc, char * argv[]
-                     , std::string & off_file_points
-                     , std::string & filediag
-                     , Filtration_value & threshold
-                     , int & dim_max
-                     , int & min_p
-                     , int & max_p
-                     , Filtration_value & min_persistence);
-
-int main(int argc, char * argv[]) {
-  std::string off_file_points;
-  std::string filediag;
-  Filtration_value threshold;
-  int dim_max;
-  int min_p;
-  int max_p;
-  Filtration_value min_persistence;
-
-  program_options(argc, argv, off_file_points, filediag, threshold, dim_max, min_p, max_p, min_persistence);
-
-  Points_off_reader off_reader(off_file_points);
-  Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Gudhi::Euclidean_distance());
-
-  // Construct the Rips complex in a Simplex Tree
-  Simplex_tree simplex_tree;
-
-  rips_complex_from_file.create_complex(simplex_tree, dim_max);
-  std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n";
-  std::cout << "   and has dimension " << simplex_tree.dimension() << " \n";
-
-  // Sort the simplices in the order of the filtration
-  simplex_tree.initialize_filtration();
-
-  // Compute the persistence diagram of the complex
-  Persistent_cohomology pcoh(simplex_tree);
-  // initializes the coefficient field for homology
-  pcoh.init_coefficients(min_p, max_p);
-
-  pcoh.compute_persistent_cohomology(min_persistence);
-
-  // Output the diagram in filediag
-  if (filediag.empty()) {
-    pcoh.output_diagram();
-  } else {
-    std::ofstream out(filediag);
-    pcoh.output_diagram(out);
-    out.close();
-  }
-
-  return 0;
-}
-
-void program_options(int argc, char * argv[]
-                     , std::string & off_file_points
-                     , std::string & filediag
-                     , Filtration_value & threshold
-                     , int & dim_max
-                     , int & min_p
-                     , int & max_p
-                     , Filtration_value & min_persistence) {
-  namespace po = boost::program_options;
-  po::options_description hidden("Hidden options");
-  hidden.add_options()
-      ("input-file", po::value<std::string>(&off_file_points),
-       "Name of an OFF file containing a point set.\n");
-
-  po::options_description visible("Allowed options");
-  visible.add_options()
-      ("help,h", "produce help message")
-      ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
-       "Name of file in which the persistence diagram is written. Default print in std::cout")
-      ("max-edge-length,r", po::value<Filtration_value>(&threshold)->default_value(0),
-       "Maximal length of an edge for the Rips complex construction.")
-      ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
-       "Maximal dimension of the Rips complex we want to compute.")
-      ("min-field-charac,p", po::value<int>(&min_p)->default_value(2),
-       "Minimal characteristic p of the coefficient field Z/pZ.")
-      ("max-field-charac,q", po::value<int>(&max_p)->default_value(1223),
-       "Minimial characteristic q of the coefficient field Z/pZ.")
-      ("min-persistence,m", po::value<Filtration_value>(&min_persistence),
-       "Minimal lifetime of homology feature to be recorded. Default is 0");
-
-  po::positional_options_description pos;
-  pos.add("input-file", 1);
-
-  po::options_description all;
-  all.add(visible).add(hidden);
-
-  po::variables_map vm;
-  po::store(po::command_line_parser(argc, argv).
-            options(all).positional(pos).run(), vm);
-  po::notify(vm);
-
-  if (vm.count("help") || !vm.count("input-file")) {
-    std::cout << std::endl;
-    std::cout << "Compute the persistent homology with various coefficient fields \n";
-    std::cout << "of a Rips complex defined on a set of input points. The coefficient \n";
-    std::cout << "fields are all the Z/rZ for a prime number r contained in the \n";
-    std::cout << "specified range [p,q]\n \n";
-    std::cout << "The output diagram contains one bar per line, written with the convention: \n";
-    std::cout << "   p1*...*pr   dim b d \n";
-    std::cout << "where dim is the dimension of the homological feature,\n";
-    std::cout << "b and d are respectively the birth and death of the feature and \n";
-    std::cout << "p1*...*pr is the product of prime numbers pi such that the homology \n";
-    std::cout << "feature exists in homology with Z/piZ coefficients." << std::endl << std::endl;
-
-    std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
-    std::cout << visible << std::endl;
-    exit(-1);
-  }
-}
diff --git a/example/Persistent_cohomology/rips_persistence_step_by_step.cpp b/example/Persistent_cohomology/rips_persistence_step_by_step.cpp
deleted file mode 100644
index 796cfa3a..00000000
--- a/example/Persistent_cohomology/rips_persistence_step_by_step.cpp
+++ /dev/null
@@ -1,166 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library 
- *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
- *    library for computational topology.
- *
- *    Author(s):       Clément Maria
- *
- *    Copyright (C) 2014 Inria
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#include <gudhi/graph_simplicial_complex.h>
-#include <gudhi/distance_functions.h>
-#include <gudhi/Simplex_tree.h>
-#include <gudhi/Persistent_cohomology.h>
-#include <gudhi/Points_off_io.h>
-
-#include <boost/program_options.hpp>
-
-#include <string>
-#include <vector>
-#include <limits>  // infinity
-#include <utility>  // for pair
-#include <map>
-
-// ----------------------------------------------------------------------------
-// rips_persistence_step_by_step is an example of each step that is required to
-// build a Rips over a Simplex_tree. Please refer to rips_persistence to see
-// how to do the same thing with the Rips_complex wrapper for less detailed
-// steps.
-// ----------------------------------------------------------------------------
-
-// Types definition
-using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
-using Vertex_handle = Simplex_tree::Vertex_handle;
-using Filtration_value = Simplex_tree::Filtration_value;
-using Proximity_graph = Gudhi::Proximity_graph<Simplex_tree>;
-
-using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
-using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp >;
-using Point = std::vector<double>;
-using Points_off_reader = Gudhi::Points_off_reader<Point>;
-
-void program_options(int argc, char * argv[]
-                     , std::string & off_file_points
-                     , std::string & filediag
-                     , Filtration_value & threshold
-                     , int & dim_max
-                     , int & p
-                     , Filtration_value & min_persistence);
-
-int main(int argc, char * argv[]) {
-  std::string off_file_points;
-  std::string filediag;
-  Filtration_value threshold;
-  int dim_max;
-  int p;
-  Filtration_value min_persistence;
-
-  program_options(argc, argv, off_file_points, filediag, threshold, dim_max, p, min_persistence);
-
-  // Extract the points from the file filepoints
-  Points_off_reader off_reader(off_file_points);
-
-  // Compute the proximity graph of the points
-  Proximity_graph prox_graph = Gudhi::compute_proximity_graph<Simplex_tree>(off_reader.get_point_cloud(),
-                                                                            threshold,
-                                                                            Gudhi::Euclidean_distance());
-
-  // Construct the Rips complex in a Simplex Tree
-  Simplex_tree st;
-  // insert the proximity graph in the simplex tree
-  st.insert_graph(prox_graph);
-  // expand the graph until dimension dim_max
-  st.expansion(dim_max);
-
-  std::cout << "The complex contains " << st.num_simplices() << " simplices \n";
-  std::cout << "   and has dimension " << st.dimension() << " \n";
-
-  // Sort the simplices in the order of the filtration
-  st.initialize_filtration();
-
-  // Compute the persistence diagram of the complex
-  Persistent_cohomology pcoh(st);
-  // initializes the coefficient field for homology
-  pcoh.init_coefficients(p);
-
-  pcoh.compute_persistent_cohomology(min_persistence);
-
-  // Output the diagram in filediag
-  if (filediag.empty()) {
-    pcoh.output_diagram();
-  } else {
-    std::ofstream out(filediag);
-    pcoh.output_diagram(out);
-    out.close();
-  }
-
-  return 0;
-}
-
-void program_options(int argc, char * argv[]
-                     , std::string & off_file_points
-                     , std::string & filediag
-                     , Filtration_value & threshold
-                     , int & dim_max
-                     , int & p
-                     , Filtration_value & min_persistence) {
-  namespace po = boost::program_options;
-  po::options_description hidden("Hidden options");
-  hidden.add_options()
-      ("input-file", po::value<std::string>(&off_file_points),
-       "Name of an OFF file containing a point set.\n");
-
-  po::options_description visible("Allowed options", 100);
-  visible.add_options()
-      ("help,h", "produce help message")
-      ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
-       "Name of file in which the persistence diagram is written. Default print in std::cout")
-      ("max-edge-length,r",
-       po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()),
-       "Maximal length of an edge for the Rips complex construction.")
-      ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
-       "Maximal dimension of the Rips complex we want to compute.")
-      ("field-charac,p", po::value<int>(&p)->default_value(11),
-       "Characteristic p of the coefficient field Z/pZ for computing homology.")
-      ("min-persistence,m", po::value<Filtration_value>(&min_persistence),
-       "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals");
-
-  po::positional_options_description pos;
-  pos.add("input-file", 1);
-
-  po::options_description all;
-  all.add(visible).add(hidden);
-
-  po::variables_map vm;
-  po::store(po::command_line_parser(argc, argv).
-            options(all).positional(pos).run(), vm);
-  po::notify(vm);
-
-  if (vm.count("help") || !vm.count("input-file")) {
-    std::cout << std::endl;
-    std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
-    std::cout << "of a Rips complex defined on a set of input points.\n \n";
-    std::cout << "The output diagram contains one bar per line, written with the convention: \n";
-    std::cout << "   p   dim b d \n";
-    std::cout << "where dim is the dimension of the homological feature,\n";
-    std::cout << "b and d are respectively the birth and death of the feature and \n";
-    std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
-
-    std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
-    std::cout << visible << std::endl;
-    exit(-1);
-  }
-}
diff --git a/example/Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp b/example/Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp
deleted file mode 100644
index 71fc0802..00000000
--- a/example/Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp
+++ /dev/null
@@ -1,172 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library 
- *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
- *    library for computational topology.
- *
- *    Author(s):       Clément Maria, Marc Glisse
- *
- *    Copyright (C) 2014 Inria
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#include <gudhi/Simplex_tree.h>
-#include <gudhi/Persistent_cohomology.h>
-#include <gudhi/Rips_complex.h>
-#include <gudhi/Hasse_complex.h>
-#include <gudhi/Points_off_io.h>
-#include <gudhi/distance_functions.h>
-
-#include <boost/program_options.hpp>
-
-#ifdef GUDHI_USE_TBB
-#include <tbb/task_scheduler_init.h>
-#endif
-
-#include <string>
-#include <vector>
-
-////////////////////////////////////////////////////////////////
-//                                                            //
-//  WARNING: persistence computation itself is not parallel,  //
-//  and this uses more memory than rips_persistence.          //
-//                                                            //
-////////////////////////////////////////////////////////////////
-
-// Types definition
-using Simplex_tree = Gudhi::Simplex_tree<>;
-using Filtration_value = Simplex_tree::Filtration_value;
-using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
-using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
-using Point = std::vector<double>;
-using Points_off_reader = Gudhi::Points_off_reader<Point>;
-
-void program_options(int argc, char * argv[]
-                     , std::string & off_file_points
-                     , std::string & filediag
-                     , Filtration_value & threshold
-                     , int & dim_max
-                     , int & p
-                     , Filtration_value & min_persistence);
-
-int main(int argc, char * argv[]) {
-  std::string off_file_points;
-  std::string filediag;
-  Filtration_value threshold;
-  int dim_max;
-  int p;
-  Filtration_value min_persistence;
-
-  program_options(argc, argv, off_file_points, filediag, threshold, dim_max, p, min_persistence);
-
-  Points_off_reader off_reader(off_file_points);
-  Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Gudhi::Euclidean_distance());
-
-  // Construct the Rips complex in a Simplex Tree
-  Simplex_tree& st = *new Simplex_tree;
-  rips_complex_from_file.create_complex(st, dim_max);
-
-  std::cout << "The complex contains " << st.num_simplices() << " simplices \n";
-  std::cout << "   and has dimension " << st.dimension() << " \n";
-
-#ifdef GUDHI_USE_TBB
-  // Unnecessary, but clarifies which operations are parallel.
-  tbb::task_scheduler_init ts;
-#endif
-
-  // Sort the simplices in the order of the filtration
-  st.initialize_filtration();
-  int count = 0;
-  for (auto sh : st.filtration_simplex_range())
-    st.assign_key(sh, count++);
-
-  // Convert to a more convenient representation.
-  Gudhi::Hasse_complex<> hcpx(st);
-
-#ifdef GUDHI_USE_TBB
-  ts.terminate();
-#endif
-
-  // Free some space.
-  delete &st;
-
-  // Compute the persistence diagram of the complex
-  Gudhi::persistent_cohomology::Persistent_cohomology< Gudhi::Hasse_complex<>, Field_Zp > pcoh(hcpx);
-  // initializes the coefficient field for homology
-  pcoh.init_coefficients(p);
-
-  pcoh.compute_persistent_cohomology(min_persistence);
-
-  // Output the diagram in filediag
-  if (filediag.empty()) {
-    pcoh.output_diagram();
-  } else {
-    std::ofstream out(filediag);
-    pcoh.output_diagram(out);
-    out.close();
-  }
-}
-
-void program_options(int argc, char * argv[]
-                     , std::string & off_file_points
-                     , std::string & filediag
-                     , Filtration_value & threshold
-                     , int & dim_max
-                     , int & p
-                     , Filtration_value & min_persistence) {
-  namespace po = boost::program_options;
-  po::options_description hidden("Hidden options");
-  hidden.add_options()
-      ("input-file", po::value<std::string>(&off_file_points),
-       "Name of file containing a point set. Format is one point per line:   X1 ... Xd ");
-
-  po::options_description visible("Allowed options", 100);
-  visible.add_options()
-      ("help,h", "produce help message")
-      ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
-       "Name of file in which the persistence diagram is written. Default print in std::cout")
-      ("max-edge-length,r", po::value<Filtration_value>(&threshold)->default_value(0),
-       "Maximal length of an edge for the Rips complex construction.")
-      ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
-       "Maximal dimension of the Rips complex we want to compute.")
-      ("field-charac,p", po::value<int>(&p)->default_value(11),
-       "Characteristic p of the coefficient field Z/pZ for computing homology.")
-      ("min-persistence,m", po::value<Filtration_value>(&min_persistence),
-       "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals");
-
-  po::positional_options_description pos;
-  pos.add("input-file", 1);
-
-  po::options_description all;
-  all.add(visible).add(hidden);
-
-  po::variables_map vm;
-  po::store(po::command_line_parser(argc, argv).
-            options(all).positional(pos).run(), vm);
-  po::notify(vm);
-
-  if (vm.count("help") || !vm.count("input-file")) {
-    std::cout << std::endl;
-    std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
-    std::cout << "of a Rips complex defined on a set of input points.\n \n";
-    std::cout << "The output diagram contains one bar per line, written with the convention: \n";
-    std::cout << "   p   dim b d \n";
-    std::cout << "where dim is the dimension of the homological feature,\n";
-    std::cout << "b and d are respectively the birth and death of the feature and \n";
-    std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
-
-    std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
-    std::cout << visible << std::endl;
-    exit(-1);
-  }
-}