Merged with trunk + minor changes

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/relaxed-witness@2094 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 6b23778cbe43e7697cd325039e843758a263d927

72 files changed, 2999 insertions, 445 deletions

diff --git a/src/Bottleneck_distance/benchmark/CMakeLists.txt b/src/Bottleneck_distance/benchmark/CMakeLists.txt
index f70dd8ff..355e8d31 100644
--- a/src/Bottleneck_distance/benchmark/CMakeLists.txt
+++ b/src/Bottleneck_distance/benchmark/CMakeLists.txt
@@ -6,8 +6,6 @@ project(Bottleneck_distance_benchmark)
 # cmake -DCGAL_DIR=~/workspace/CGAL-4.8 ../../..
 if(CGAL_FOUND)
   if (NOT CGAL_VERSION VERSION_LESS 4.8.0)
-    if (EIGEN3_FOUND)
-      add_executable ( bottleneck_chrono bottleneck_chrono.cpp )
-    endif()
+    add_executable ( bottleneck_chrono bottleneck_chrono.cpp )
   endif ()
 endif()
diff --git a/src/Bottleneck_distance/concept/Persistence_diagram.h b/src/Bottleneck_distance/concept/Persistence_diagram.h
index 2706716b..b157f22a 100644
--- a/src/Bottleneck_distance/concept/Persistence_diagram.h
+++ b/src/Bottleneck_distance/concept/Persistence_diagram.h
@@ -25,24 +25,25 @@
 
 namespace Gudhi {
 
-namespace bottleneck_distance {
+namespace persistence_diagram {
 
-/** \brief Concept of Diagram_point. std::get<0>(point) must return the birth of the corresponding component and std::get<1>(point) its death.
+/** \brief Concept of point in a persistence diagram. std::get<0>(point) must return the birth of the corresponding component and std::get<1>(point) its death.
+ * Both should be convertible to `double`.
  * A valid implementation of this concept is std::pair<double,double>.
  * Death should be larger than birth, death can be std::numeric_limits<double>::infinity() for components which stay alive.
  *
  * \ingroup bottleneck_distance
  */
-typename Diagram_point;
+struct DiagramPoint{};
 
-/** \brief Concept of persistence diagram. It's a range of Diagram_point.
+/** \brief Concept of persistence diagram. It is a range of `DiagramPoint`.
  * std::begin(diagram) and std::end(diagram) must return corresponding iterators.
  *
  * \ingroup bottleneck_distance
  */
-typename Persistence_Diagram;
+struct PersistenceDiagram{};
 
-}  // namespace bottleneck_distance
+}  // namespace persistence_diagram
 
 }  // namespace Gudhi
 
diff --git a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h
index 21187f9c..5223678d 100644
--- a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h
+++ b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h
@@ -26,7 +26,7 @@
 // needs namespace for Doxygen to link on classes
 namespace Gudhi {
 // needs namespace for Doxygen to link on classes
-namespace bottleneck_distance {
+namespace persistence_diagram {
 
 /**  \defgroup bottleneck_distance Bottleneck distance
  * 
@@ -35,7 +35,7 @@ namespace bottleneck_distance {
  * 
  * \section bottleneckdefinition Definition
  * 
- * The bottleneck distance measures the similarity between two persistence diagrams. It's the shortest distance b for which there exists a perfect matching between
+ * The bottleneck distance measures the similarity between two persistence diagrams. It is the shortest distance b for which there exists a perfect matching between
  * the points of the two diagrams (completed with all the points on the diagonal in order to ignore cardinality mismatchs) such that
  * any couple of matched points are at distance at most b.
  *
@@ -44,7 +44,7 @@ namespace bottleneck_distance {
  */
 /** @} */  // end defgroup bottleneck_distance
 
-}  // namespace bottleneck_distance
+}  // namespace persistence_diagram
 
 }  // namespace Gudhi
 
diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt
index c66623e9..b36d0f34 100644
--- a/src/Bottleneck_distance/example/CMakeLists.txt
+++ b/src/Bottleneck_distance/example/CMakeLists.txt
@@ -5,11 +5,18 @@ project(Bottleneck_distance_examples)
 # cmake -DCGAL_DIR=~/workspace/CGAL-4.8 ../../..
 if(CGAL_FOUND)
   if (NOT CGAL_VERSION VERSION_LESS 4.8.0)
-    if (EIGEN3_FOUND)
-      add_executable (bottleneck_read_file_example bottleneck_read_file_example.cpp)
-      add_executable (bottleneck_basic_example bottleneck_basic_example.cpp)
+    add_executable (bottleneck_read_file_example bottleneck_read_file_example.cpp)
+    add_executable (bottleneck_basic_example bottleneck_basic_example.cpp)
+
+    add_test(bottleneck_basic_example ${CMAKE_CURRENT_BINARY_DIR}/bottleneck_basic_example)
+
+    add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp)
+    target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+    if (TBB_FOUND)
+      target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES})
+    endif(TBB_FOUND)
+    add_test(alpha_rips_persistence_bottleneck_distance ${CMAKE_CURRENT_BINARY_DIR}/alpha_rips_persistence_bottleneck_distance
+        ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -r 0.15 -m 0.12 -d 3 -p 3)
 
-      add_test(bottleneck_basic_example ${CMAKE_CURRENT_BINARY_DIR}/bottleneck_basic_example)
-    endif()
   endif ()
 endif()
diff --git a/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp b/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp
new file mode 100644
index 00000000..6e9be97b
--- /dev/null
+++ b/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp
@@ -0,0 +1,190 @@
+/*    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) 2017  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/Alpha_complex.h>
+#include <gudhi/Rips_complex.h>
+#include <gudhi/distance_functions.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Persistent_cohomology.h>
+#include <gudhi/Points_off_io.h>
+#include <gudhi/Bottleneck.h>
+
+#include <CGAL/Epick_d.h>
+
+#include <boost/program_options.hpp>
+
+#include <string>
+#include <vector>
+#include <limits>  // infinity
+#include <utility>  // for pair
+#include <algorithm>  // for transform
+
+
+// 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 Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
+using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp >;
+using Kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >;
+using Point_d = Kernel::Point_d;
+using Points_off_reader = Gudhi::Points_off_reader<Point_d>;
+
+void program_options(int argc, char * argv[]
+                     , std::string & off_file_points
+                     , Filtration_value & threshold
+                     , int & dim_max
+                     , int & p
+                     , Filtration_value & min_persistence);
+
+static inline std::pair<double, double> compute_root_square (std::pair<double, double> input) {
+  return std::make_pair(std::sqrt(input.first), std::sqrt(input.second));
+}
+
+int main(int argc, char * argv[]) {
+  std::string off_file_points;
+  Filtration_value threshold;
+  int dim_max;
+  int p;
+  Filtration_value min_persistence;
+
+  program_options(argc, argv, off_file_points, threshold, dim_max, p, min_persistence);
+
+  Points_off_reader off_reader(off_file_points);
+
+  // --------------------------------------------
+  // Rips persistence
+  // --------------------------------------------
+  Rips_complex rips_complex(off_reader.get_point_cloud(), threshold, Euclidean_distance());
+
+  // Construct the Rips complex in a Simplex Tree
+  Simplex_tree rips_stree;
+
+  rips_complex.create_complex(rips_stree, dim_max);
+  std::cout << "The Rips complex contains " << rips_stree.num_simplices() << " simplices and has dimension "
+            << rips_stree.dimension() << " \n";
+
+  // Sort the simplices in the order of the filtration
+  rips_stree.initialize_filtration();
+
+  // Compute the persistence diagram of the complex
+  Persistent_cohomology rips_pcoh(rips_stree);
+  // initializes the coefficient field for homology
+  rips_pcoh.init_coefficients(p);
+  rips_pcoh.compute_persistent_cohomology(min_persistence);
+
+  // rips_pcoh.output_diagram();
+
+  // --------------------------------------------
+  // Alpha persistence
+  // --------------------------------------------
+  Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex(off_reader.get_point_cloud());
+
+  Simplex_tree alpha_stree;
+  alpha_complex.create_complex(alpha_stree, threshold * threshold);
+  std::cout << "The Alpha complex contains " << alpha_stree.num_simplices() << " simplices and has dimension "
+            << alpha_stree.dimension() << " \n";
+
+  // Sort the simplices in the order of the filtration
+  alpha_stree.initialize_filtration();
+
+  // Compute the persistence diagram of the complex
+  Persistent_cohomology alpha_pcoh(alpha_stree);
+  // initializes the coefficient field for homology
+  alpha_pcoh.init_coefficients(p);
+  alpha_pcoh.compute_persistent_cohomology(min_persistence * min_persistence);
+
+  // alpha_pcoh.output_diagram();
+
+  // --------------------------------------------
+  // Bottleneck distance between both persistence
+  // --------------------------------------------
+  double max_b_distance {};
+  for (int dim = 0; dim < dim_max; dim ++) {
+    std::vector< std::pair< Filtration_value , Filtration_value > > rips_intervals;
+    std::vector< std::pair< Filtration_value , Filtration_value > > alpha_intervals;
+    rips_intervals = rips_pcoh.intervals_in_dimension(dim);
+    alpha_intervals = alpha_pcoh.intervals_in_dimension(dim);
+    std::transform(alpha_intervals.begin(), alpha_intervals.end(), alpha_intervals.begin(), compute_root_square);
+
+    double bottleneck_distance = Gudhi::persistence_diagram::bottleneck_distance(rips_intervals, alpha_intervals);
+    std::cout << "In dimension " << dim << ", bottleneck distance = " << bottleneck_distance << std::endl;
+    if (bottleneck_distance > max_b_distance)
+      max_b_distance = bottleneck_distance;
+  }
+  std::cout << "================================================================================" << std::endl;
+  std::cout << "Bottleneck distance is " << max_b_distance << std::endl;
+
+  return 0;
+}
+
+void program_options(int argc, char * argv[]
+                     , std::string & off_file_points
+                     , 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")
+      ("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;
+    std::abort();
+  }
+}
diff --git a/src/Bottleneck_distance/example/bottleneck_basic_example.cpp b/src/Bottleneck_distance/example/bottleneck_basic_example.cpp
index 91a7302f..d0ca4e20 100644
--- a/src/Bottleneck_distance/example/bottleneck_basic_example.cpp
+++ b/src/Bottleneck_distance/example/bottleneck_basic_example.cpp
@@ -21,10 +21,13 @@
  */
 
 #include <gudhi/Bottleneck.h>
+
 #include <iostream>
+#include <vector>
+#include <utility>  // for pair
+#include <limits>  // for numeric_limits
 
 int main() {
-
   std::vector< std::pair<double, double> > v1, v2;
 
   v1.emplace_back(2.7, 3.7);
@@ -44,5 +47,4 @@ int main() {
   b = Gudhi::persistence_diagram::bottleneck_distance(v1, v2, 0.1);
 
   std::cout << "Approx bottleneck distance = " << b << std::endl;
-
 }
diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
index 4c74b66e..bde05825 100644
--- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
+++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
@@ -24,6 +24,8 @@
 
 #include <gudhi/Bottleneck.h>
 #include <iostream>
+#include <vector>
+#include <utility>  // for pair
 #include <fstream>
 #include <sstream>
 #include <string>
diff --git a/src/Bottleneck_distance/include/gudhi/Bottleneck.h b/src/Bottleneck_distance/include/gudhi/Bottleneck.h
index 2b7e4767..b90a0ee0 100644
--- a/src/Bottleneck_distance/include/gudhi/Bottleneck.h
+++ b/src/Bottleneck_distance/include/gudhi/Bottleneck.h
@@ -24,6 +24,11 @@
 #define BOTTLENECK_H_
 
 #include <gudhi/Graph_matching.h>
+
+#include <vector>
+#include <algorithm>  // for max
+#include <limits>  // for numeric_limits
+
 #include <cmath>
 
 namespace Gudhi {
@@ -41,7 +46,7 @@ double bottleneck_distance_approx(Persistence_graph& g, double e) {
     if (step <= b_lower_bound || step >= b_upper_bound)  // Avoid precision problem
       break;
     m.set_r(step);
-    while (m.multi_augment());  // compute a maximum matching (in the graph corresponding to the current r)
+    while (m.multi_augment()) {};  // compute a maximum matching (in the graph corresponding to the current r)
     if (m.perfect()) {
       m = biggest_unperfect;
       b_upper_bound = step;
@@ -63,7 +68,7 @@ double bottleneck_distance_exact(Persistence_graph& g) {
   while (lower_bound_i != upper_bound_i) {
     long step = lower_bound_i + static_cast<long> ((upper_bound_i - lower_bound_i - 1) / alpha);
     m.set_r(sd.at(step));
-    while (m.multi_augment());  // compute a maximum matching (in the graph corresponding to the current r)
+    while (m.multi_augment()) {};  // compute a maximum matching (in the graph corresponding to the current r)
     if (m.perfect()) {
       m = biggest_unperfect;
       upper_bound_i = step;
@@ -75,11 +80,22 @@ double bottleneck_distance_exact(Persistence_graph& g) {
   return sd.at(lower_bound_i);
 }
 
-/** \brief Function to use in order to compute the Bottleneck distance between two persistence diagrams (see concepts).
- * If the last parameter e is not 0, you get an additive e-approximation, which is a lot faster to compute whatever is
- * e.
- * Thus, by default, e is a very small positive double, actually the smallest double possible such that the
- * floating-point inaccuracies don't lead to a failure of the algorithm.
+/** \brief Function to compute the Bottleneck distance between two persistence diagrams.
+ *
+ * \tparam Persistence_diagram1,Persistence_diagram2
+ * models of the concept `PersistenceDiagram`.
+ * \param[in] e
+ * \parblock
+ * If `e` is 0, this uses an expensive algorithm to compute the exact distance.
+ *
+ * If `e` is not 0, it asks for an additive `e`-approximation, and currently
+ * also allows a small multiplicative error (the last 2 or 3 bits of the
+ * mantissa may be wrong). This version of the algorithm takes advantage of the
+ * limited precision of `double` and is usually a lot faster to compute,
+ * whatever the value of `e`.
+ *
+ * Thus, by default, `e` is the smallest positive double.
+ * \endparblock
  *
  * \ingroup bottleneck_distance
  */
diff --git a/src/Bottleneck_distance/include/gudhi/Graph_matching.h b/src/Bottleneck_distance/include/gudhi/Graph_matching.h
index 253c89b4..e1708c5b 100644
--- a/src/Bottleneck_distance/include/gudhi/Graph_matching.h
+++ b/src/Bottleneck_distance/include/gudhi/Graph_matching.h
@@ -25,6 +25,9 @@
 
 #include <gudhi/Neighbors_finder.h>
 
+#include <vector>
+#include <list>
+
 namespace Gudhi {
 
 namespace persistence_diagram {
diff --git a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h
index 96ece360..cd5486f8 100644
--- a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h
+++ b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h
@@ -34,6 +34,7 @@
 #include <gudhi/Internal_point.h>
 
 #include <unordered_set>
+#include <vector>
 
 namespace Gudhi {
 
diff --git a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h
index 3a4a5fec..c7695112 100644
--- a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h
+++ b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h
@@ -23,9 +23,11 @@
 #ifndef PERSISTENCE_GRAPH_H_
 #define PERSISTENCE_GRAPH_H_
 
+#include <gudhi/Internal_point.h>
+
 #include <vector>
 #include <algorithm>
-#include <gudhi/Internal_point.h>
+#include <limits>  // for numeric_limits
 
 namespace Gudhi {
 
@@ -38,7 +40,7 @@ namespace persistence_diagram {
  */
 class Persistence_graph {
  public:
-  /** \internal \brief Constructor taking 2 Persistence_Diagrams (concept) as parameters. */
+  /** \internal \brief Constructor taking 2 PersistenceDiagrams (concept) as parameters. */
   template<typename Persistence_diagram1, typename Persistence_diagram2>
   Persistence_graph(const Persistence_diagram1& diag1, const Persistence_diagram2& diag2, double e);
   /** \internal \brief Is the given point from U the projection of a point in V ? */
@@ -92,10 +94,12 @@ Persistence_graph::Persistence_graph(const Persistence_diagram1 &diag1,
     swap(u, v);
   std::sort(u_alive.begin(), u_alive.end());
   std::sort(v_alive.begin(), v_alive.end());
-  if (u_alive.size() != v_alive.size())
+  if (u_alive.size() != v_alive.size()) {
     b_alive = std::numeric_limits<double>::infinity();
-  else for (auto it_u = u_alive.cbegin(), it_v = v_alive.cbegin(); it_u != u_alive.cend(); ++it_u, ++it_v)
+  } else {
+    for (auto it_u = u_alive.cbegin(), it_v = v_alive.cbegin(); it_u != u_alive.cend(); ++it_u, ++it_v)
       b_alive = std::max(b_alive, std::fabs(*it_u - *it_v));
+  }
 }
 
 inline bool Persistence_graph::on_the_u_diagonal(int u_point_index) const {
diff --git a/src/Bottleneck_distance/test/CMakeLists.txt b/src/Bottleneck_distance/test/CMakeLists.txt
index a6979d3c..6c8f112d 100644
--- a/src/Bottleneck_distance/test/CMakeLists.txt
+++ b/src/Bottleneck_distance/test/CMakeLists.txt
@@ -15,14 +15,12 @@ endif()
 # cmake -DCGAL_DIR=~/workspace/CGAL-4.8 ../../..
 if(CGAL_FOUND)
   if (NOT CGAL_VERSION VERSION_LESS 4.8.0)
-    if (EIGEN3_FOUND)
-      add_executable ( bottleneckUT bottleneck_unit_test.cpp )
-      target_link_libraries(bottleneckUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+    add_executable ( bottleneckUT bottleneck_unit_test.cpp )
+    target_link_libraries(bottleneckUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 
-      # Unitary tests
-      add_test(NAME bottleneckUT COMMAND ${CMAKE_CURRENT_BINARY_DIR}/bottleneckUT
-        # XML format for Jenkins xUnit plugin 
-        --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/bottleneckUT.xml --log_level=test_suite --report_level=no)
-    endif()
+    # Unitary tests
+    add_test(NAME bottleneckUT COMMAND ${CMAKE_CURRENT_BINARY_DIR}/bottleneckUT
+      # XML format for Jenkins xUnit plugin
+      --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/bottleneckUT.xml --log_level=test_suite --report_level=no)
   endif ()
 endif()
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 1fa62e35..eb349052 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -112,6 +112,7 @@ else()
   add_subdirectory(example/Bitmap_cubical_complex)
   add_subdirectory(example/Witness_complex)
   add_subdirectory(example/Alpha_complex)
+  add_subdirectory(example/Rips_complex)
   add_subdirectory(example/Spatial_searching)
   add_subdirectory(example/Subsampling)
   add_subdirectory(example/Tangential_complex)
diff --git a/src/Doxyfile b/src/Doxyfile
index 71aa038d..a41c6d6f 100644
--- a/src/Doxyfile
+++ b/src/Doxyfile
@@ -500,7 +500,7 @@ HIDE_SCOPE_NAMES       = NO
 # the files that are included by a file in the documentation of that file.
 # The default value is: YES.
 
-SHOW_INCLUDE_FILES     = YES
+SHOW_INCLUDE_FILES     = NO
 
 # If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
 # grouped member an include statement to the documentation, telling the reader
@@ -784,7 +784,8 @@ EXCLUDE                = data/ \
 	                     example/ \
 	                     GudhUI/  \
                              cmake/   \
-                             debian/
+                             debian/  \
+                             include/gudhi_patches/
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded
@@ -846,6 +847,7 @@ IMAGE_PATH             = doc/Skeleton_blocker/ \
 	doc/Persistent_cohomology/ \
 	doc/Witness_complex/ \
 	doc/Bitmap_cubical_complex/ \
+	doc/Rips_complex/ \
 	doc/Subsampling/ \
 	doc/Spatial_searching/ \
 	doc/Tangential_complex/ \
@@ -2151,7 +2153,7 @@ TEMPLATE_RELATIONS     = YES
 # The default value is: YES.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-INCLUDE_GRAPH          = YES
+INCLUDE_GRAPH          = NO
 
 # If the INCLUDED_BY_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are
 # set to YES then doxygen will generate a graph for each documented file showing
@@ -2160,7 +2162,7 @@ INCLUDE_GRAPH          = YES
 # The default value is: YES.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-INCLUDED_BY_GRAPH      = YES
+INCLUDED_BY_GRAPH      = NO
 
 # If the CALL_GRAPH tag is set to YES then doxygen will generate a call
 # dependency graph for every global function or class method.
diff --git a/src/GudhUI/CMakeLists.txt b/src/GudhUI/CMakeLists.txt
index a43294ea..d3a52b60 100644
--- a/src/GudhUI/CMakeLists.txt
+++ b/src/GudhUI/CMakeLists.txt
@@ -1,46 +1,40 @@
 cmake_minimum_required(VERSION 2.8)
 project(GudhUI)
 
-find_package(Qt4)
+find_package(CGAL COMPONENTS Qt5)
+find_package(Qt5 COMPONENTS Widgets Xml OpenGL)
 find_package(QGLViewer)
 find_package(OpenGL)
 
-if ( CGAL_FOUND AND QT4_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND )
-  set( QT_USE_QTXML    TRUE )
-  set( QT_USE_QTMAIN   TRUE )
-  set( QT_USE_QTSCRIPT  TRUE )
-  set( QT_USE_QTOPENGL  TRUE )
-  SET(Boost_USE_STATIC_LIBS ON)
-  SET(Boost_USE_MULTITHREAD OFF)
 
-  include(${QT_USE_FILE})
+if (NOT CGAL_FOUND)
+  message(ERROR " GudhUI requires CGAL and will not be compiled.")
+endif()
+
+if (NOT Qt5_FOUND)
+  message(ERROR " GudhUI requires Qt5 and will not be compiled.")
+endif()
+
+if (NOT OPENGL_FOUND)
+  message(ERROR " GudhUI requires OpenGL and will not be compiled.")
+endif()
+
+if (NOT QGLVIEWER_FOUND)
+  message(ERROR " GudhUI requires QGLViewer and will not be compiled.")
+endif()
+
+
 
+if ( CGAL_FOUND AND Qt5_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND )
+
+  set(CMAKE_AUTOMOC ON)
+  set(CMAKE_AUTOUIC ON)
+  set(CMAKE_INCLUDE_CURRENT_DIR ON)
+
+  SET(Boost_USE_STATIC_LIBS ON)
+  SET(Boost_USE_MULTITHREAD OFF)
   include_directories (${QGLVIEWER_INCLUDE_DIR})
-  include_directories(.)	
  
-  # qt : ui file, created wih Qt Designer ###############
-  set(CMAKE_CURRENT_BINARY_DIR "${CMAKE_CURRENT_SOURCE_DIR}/gui")
-  qt4_wrap_ui( uis 
-    gui/main_window.ui
-    gui/MenuEdgeContraction.ui
-    gui/KNearestNeighborsMenu.ui
-    gui/UniformNeighborsMenu.ui
-    gui/PersistenceMenu.ui
-  )	
-
-  set(CMAKE_CURRENT_BINARY_DIR "${CMAKE_CURRENT_SOURCE_DIR}/gui")
-  qt4_automoc(
-    gui/MainWindow.cpp
-    gui/Menu_k_nearest_neighbors.cpp
-    gui/Menu_uniform_neighbors.cpp
-    gui/Menu_edge_contraction.cpp
-    gui/Menu_persistence.cpp    
-  )
-	
-  set(CMAKE_CURRENT_BINARY_DIR "${CMAKE_CURRENT_SOURCE_DIR}/view") 
-  qt4_automoc(view/Viewer_instructor.cpp		
-    view/Viewer.cpp
-  )	
   #####################################################################
 
   add_executable  ( GudhUI 
@@ -52,10 +46,9 @@ if ( CGAL_FOUND AND QT4_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND )
     gui/Menu_persistence.cpp
     view/Viewer_instructor.cpp				
     view/Viewer.cpp
-    ${uis}  
   )	
-	
-  target_link_libraries( GudhUI ${QT_LIBRARIES} ${QGLVIEWER_LIBRARIES} )
+  target_link_libraries( GudhUI Qt5::Widgets Qt5::Xml Qt5::OpenGL )
+  target_link_libraries( GudhUI ${QGLVIEWER_LIBRARIES} )
   target_link_libraries( GudhUI ${OPENGL_gl_LIBRARY} ${OPENGL_glu_LIBRARY} )	
 if (TBB_FOUND)
   target_link_libraries( GudhUI ${TBB_LIBRARIES})
@@ -64,5 +57,5 @@ endif()
 ###############################################################################
 
 else()
-  message(STATUS "NOTICE: GudhUI requires CGAL, the QGLViewer, OpenGL and Qt4, and will not be compiled.")
+  message(STATUS "NOTICE: GudhUI requires CGAL, the QGLViewer, OpenGL and Qt5, and will not be compiled.")
 endif()
diff --git a/src/GudhUI/gui/MainWindow.h b/src/GudhUI/gui/MainWindow.h
index 3fe0d720..15664dcb 100644
--- a/src/GudhUI/gui/MainWindow.h
+++ b/src/GudhUI/gui/MainWindow.h
@@ -23,9 +23,6 @@
 #ifndef GUI_MAINWINDOW_H_
 #define GUI_MAINWINDOW_H_
 
-// Workaround for moc-qt4 not parsing boost headers
-#include <CGAL/config.h>
-
 // Workaround https://svn.boost.org/trac/boost/ticket/12534
 #include <boost/container/flat_map.hpp>
 
diff --git a/src/GudhUI/gui/Menu_edge_contraction.h b/src/GudhUI/gui/Menu_edge_contraction.h
index 08f0bf67..2d5640e8 100644
--- a/src/GudhUI/gui/Menu_edge_contraction.h
+++ b/src/GudhUI/gui/Menu_edge_contraction.h
@@ -23,11 +23,8 @@
 #ifndef GUI_MENU_EDGE_CONTRACTION_H_
 #define GUI_MENU_EDGE_CONTRACTION_H_
 
-// Workaround for moc-qt4 not parsing boost headers
-#include <CGAL/config.h>
-
 #include "gui/MainWindow.h"
-#include "gui/ui_MenuEdgeContraction.h"
+#include "ui_MenuEdgeContraction.h"
 
 #include "model/Model.h"
 
diff --git a/src/GudhUI/gui/Menu_k_nearest_neighbors.h b/src/GudhUI/gui/Menu_k_nearest_neighbors.h
index 8088b768..77303b67 100644
--- a/src/GudhUI/gui/Menu_k_nearest_neighbors.h
+++ b/src/GudhUI/gui/Menu_k_nearest_neighbors.h
@@ -24,7 +24,7 @@
 #define GUI_MENU_K_NEAREST_NEIGHBORS_H_
 
 #include <QMainWindow>
-#include "gui/ui_KNearestNeighborsMenu.h"
+#include "ui_KNearestNeighborsMenu.h"
 
 class QWidget;
 
diff --git a/src/GudhUI/gui/Menu_persistence.h b/src/GudhUI/gui/Menu_persistence.h
index 8c4df158..1a2a2408 100644
--- a/src/GudhUI/gui/Menu_persistence.h
+++ b/src/GudhUI/gui/Menu_persistence.h
@@ -25,7 +25,7 @@
 #define GUI_MENU_PERSISTENCE_H_
 
 #include <QMainWindow>
-#include "gui/ui_PersistenceMenu.h"
+#include "ui_PersistenceMenu.h"
 
 class QWidget;
 
diff --git a/src/GudhUI/gui/Menu_uniform_neighbors.h b/src/GudhUI/gui/Menu_uniform_neighbors.h
index 0b6f65fe..61316966 100644
--- a/src/GudhUI/gui/Menu_uniform_neighbors.h
+++ b/src/GudhUI/gui/Menu_uniform_neighbors.h
@@ -25,7 +25,7 @@
 #define GUI_MENU_UNIFORM_NEIGHBORS_H_
 
 #include <QMainWindow>
-#include "gui/ui_UniformNeighborsMenu.h"
+#include "ui_UniformNeighborsMenu.h"
 
 class Menu_uniform_neighbors : public QDialog, public Ui::UniformMenu {
   Q_OBJECT
diff --git a/src/GudhUI/utils/Persistence_compute.h b/src/GudhUI/utils/Persistence_compute.h
index 97165490..2dc03c8e 100644
--- a/src/GudhUI/utils/Persistence_compute.h
+++ b/src/GudhUI/utils/Persistence_compute.h
@@ -29,6 +29,7 @@
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/distance_functions.h>
 #include <gudhi/Persistent_cohomology.h>
+#include <gudhi/Rips_complex.h>
 
 #include <vector>
 
@@ -69,21 +70,23 @@ template<typename SkBlComplex> class Persistence_compute {
       points.emplace_back(std::move(pt_to_add));
     }
 
+    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 Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp>;
 
-    Graph_t prox_graph = compute_proximity_graph(points, params.threshold, euclidean_distance<Point_t>);
-    Gudhi::Simplex_tree<> st;
-    st.insert_graph(prox_graph);
-    st.expansion(params.max_dim);
+    Rips_complex rips_complex(points, params.threshold, Euclidean_distance());
 
-    Gudhi::persistent_cohomology::Persistent_cohomology< Gudhi::Simplex_tree<>,
-        Gudhi::persistent_cohomology::Field_Zp > pcoh(st);
+    Simplex_tree st;
+    rips_complex.create_complex(st, params.max_dim);
+    Persistent_cohomology pcoh(st);
     // initializes the coefficient field for homology
     pcoh.init_coefficients(params.p);
     // put params.min_pers
     pcoh.compute_persistent_cohomology(params.min_pers);
     stream << "persistence: \n";
     stream << "p dimension birth death: \n";
-
     pcoh.output_diagram(stream);
   }
 };
diff --git a/src/GudhUI/view/Viewer.h b/src/GudhUI/view/Viewer.h
index 319c8e04..797ddc53 100644
--- a/src/GudhUI/view/Viewer.h
+++ b/src/GudhUI/view/Viewer.h
@@ -24,9 +24,6 @@
 #ifndef VIEW_VIEWER_H_
 #define VIEW_VIEWER_H_
 
-// Workaround for moc-qt4 not parsing boost headers
-#include <CGAL/config.h>
-
 #include <QGLViewer/qglviewer.h>
 
 #include <vector>
diff --git a/src/GudhUI/view/Viewer_instructor.h b/src/GudhUI/view/Viewer_instructor.h
index 1da28009..05c5c1fc 100644
--- a/src/GudhUI/view/Viewer_instructor.h
+++ b/src/GudhUI/view/Viewer_instructor.h
@@ -26,9 +26,6 @@
 
 // todo do a viewer instructor that have directely a pointer to a QGLviewer and buffer ot not triangles
 
-// Workaround for moc-qt4 not parsing boost headers
-#include <CGAL/config.h>
-
 #include <QFileDialog>
 #include <QKeyEvent>
 #include <QGLViewer/camera.h>
diff --git a/src/Persistent_cohomology/benchmark/CMakeLists.txt b/src/Persistent_cohomology/benchmark/CMakeLists.txt
new file mode 100644
index 00000000..ea792c89
--- /dev/null
+++ b/src/Persistent_cohomology/benchmark/CMakeLists.txt
@@ -0,0 +1,14 @@
+cmake_minimum_required(VERSION 2.6)
+project(Persistent_cohomology_benchmark)
+
+  
+if(GMP_FOUND)
+   if(GMPXX_FOUND)
+      add_executable ( performance_rips_persistence EXCLUDE_FROM_ALL performance_rips_persistence.cpp )
+      target_link_libraries(performance_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
+      if (TBB_FOUND)
+        target_link_libraries(performance_rips_persistence ${TBB_LIBRARIES})
+      endif(TBB_FOUND)
+      file(COPY "${CMAKE_SOURCE_DIR}/data/points/Kl.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+   endif(GMPXX_FOUND)
+endif(GMP_FOUND)
diff --git a/src/Persistent_cohomology/example/performance_rips_persistence.cpp b/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp
index b4d282ac..ba752999 100644
--- a/src/Persistent_cohomology/example/performance_rips_persistence.cpp
+++ b/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp
@@ -20,20 +20,26 @@
  *    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/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/Hasse_complex.h>
+#include <gudhi/Points_off_io.h>
 
 #include <chrono>
 #include <string>
 #include <vector>
 
-using namespace Gudhi;
-using namespace Gudhi::persistent_cohomology;
+// 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 Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
+using Multi_field = Gudhi::persistent_cohomology::Multi_field;
+using Point = std::vector<double>;
+using Points_off_reader = Gudhi::Points_off_reader<Point>;
 
 /* Compute the persistent homology of the complex cpx with coefficients in Z/pZ. */
 template< typename FilteredComplex>
@@ -66,33 +72,29 @@ int main(int argc, char * argv[]) {
   int elapsed_sec;
   {
 
-  std::string filepoints = "../../../data/points/Kl.txt";
+  std::string off_file_points = "Kl.off";
   Filtration_value threshold = 0.27;
   int dim_max = 3;
   int p = 2;
   int q = 1223;
 
-  // Extract the points from the file filepoints
-  typedef std::vector<double> Point_t;
-  std::vector< Point_t > points;
-  read_points(filepoints, points);
+  // Extract the points from the file off_file_points
+  Points_off_reader off_reader(off_file_points);
 
   // Compute the proximity graph of the points
   start = std::chrono::system_clock::now();
-  Graph_t prox_graph = compute_proximity_graph(points, threshold
-                                               , euclidean_distance<Point_t>);
+  Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Euclidean_distance());
   end = std::chrono::system_clock::now();
   elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
   std::cout << "Compute Rips graph in " << elapsed_sec << " ms.\n";
 
   // Construct the Rips complex in a Simplex Tree
-  Simplex_tree<Simplex_tree_options_fast_persistence> st;
+  Simplex_tree st;
   start = std::chrono::system_clock::now();
 
   // insert the proximity graph in the simplex tree
-  st.insert_graph(prox_graph);
   // expand the graph until dimension dim_max
-  st.expansion(dim_max);
+  rips_complex_from_file.create_complex(st, dim_max);
 
   end = std::chrono::system_clock::now();
   elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
@@ -120,7 +122,7 @@ int main(int argc, char * argv[]) {
 
   // Convert the simplex tree into a hasse diagram
   start = std::chrono::system_clock::now();
-  Hasse_complex<> hcpx(st);
+  Gudhi::Hasse_complex<> hcpx(st);
   end = std::chrono::system_clock::now();
   elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
   std::cout << "Convert the simplex tree into a Hasse diagram in " << elapsed_sec << " ms.\n";
@@ -152,7 +154,7 @@ timing_persistence(FilteredComplex & cpx
   int elapsed_sec;
   {
   start = std::chrono::system_clock::now();
-  Persistent_cohomology< FilteredComplex, Field_Zp > pcoh(cpx);
+  Gudhi::persistent_cohomology::Persistent_cohomology< FilteredComplex, Field_Zp > pcoh(cpx);
   end = std::chrono::system_clock::now();
   elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
   std::cout << "  Initialize pcoh in " << elapsed_sec << " ms.\n";
@@ -186,7 +188,7 @@ timing_persistence(FilteredComplex & cpx
   int elapsed_sec;
   {
   start = std::chrono::system_clock::now();
-  Persistent_cohomology< FilteredComplex, Multi_field > pcoh(cpx);
+  Gudhi::persistent_cohomology::Persistent_cohomology< FilteredComplex, Multi_field > pcoh(cpx);
   end = std::chrono::system_clock::now();
   elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
   std::cout << "  Initialize pcoh in " << elapsed_sec << " ms.\n";
diff --git a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h
index 433cfd3e..40dd3f93 100644
--- a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h
+++ b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h
@@ -144,17 +144,23 @@ namespace persistent_cohomology {
 We provide several example files: run these examples with -h for details on their use, and read the README file.
 
 \li <a href="_persistent_cohomology_2rips_persistence_8cpp-example.html">
-Persistent_cohomology/rips_persistence.cpp</a> computes the Rips complex of a point cloud and its persistence diagram.
+Persistent_cohomology/rips_persistence.cpp</a> computes the Rips complex of a point cloud and outputs its persistence
+diagram.
+\code $> ./rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3 \endcode
+\code The complex contains 177838 simplices 
+   and has dimension 3 
+3  0 0 inf 
+3  1 0.0983494 inf 
+3  1 0.104347 inf 
+3  2 0.138335 inf \endcode
 
 \li <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html">
-Persistent_cohomology/rips_multifield_persistence.cpp</a> computes the Rips complex of a point cloud and its
+Persistent_cohomology/rips_multifield_persistence.cpp</a> computes the Rips complex of a point cloud and outputs its
 persistence diagram with a family of field coefficients.
 
-\li <a href="_persistent_cohomology_2performance_rips_persistence_8cpp-example.html">
-Persistent_cohomology/performance_rips_persistence.cpp</a> provides timings for the construction of the Rips complex
-on a set of points sampling a Klein bottle in \f$\mathbb{R}^5\f$ with a simplex tree, its conversion to a 
-Hasse diagram and the computation of persistent homology and multi-field persistent homology for the 
-different representations.
+\li <a href="_persistent_cohomology_2rips_distance_matrix_persistence_8cpp-example.html">
+Persistent_cohomology/rips_distance_matrix_persistence.cpp</a> computes the Rips complex of a distance matrix and
+outputs its persistence diagram.
 
 \li <a href="_persistent_cohomology_2alpha_complex_3d_persistence_8cpp-example.html">
 Persistent_cohomology/alpha_complex_3d_persistence.cpp</a> computes the persistent homology with
diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index 758bd6b1..38d7e9a9 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -11,9 +11,15 @@ target_link_libraries(plain_homology ${Boost_SYSTEM_LIBRARY})
 add_executable(persistence_from_simple_simplex_tree persistence_from_simple_simplex_tree.cpp)
 target_link_libraries(persistence_from_simple_simplex_tree ${Boost_SYSTEM_LIBRARY})
 
+add_executable(rips_distance_matrix_persistence rips_distance_matrix_persistence.cpp)
+target_link_libraries(rips_distance_matrix_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+
 add_executable(rips_persistence rips_persistence.cpp)
 target_link_libraries(rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
 
+add_executable(rips_persistence_step_by_step rips_persistence_step_by_step.cpp)
+target_link_libraries(rips_persistence_step_by_step ${Boost_SYSTEM_LIBRARY} ${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_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
 
@@ -23,15 +29,19 @@ target_link_libraries(persistence_from_file ${Boost_SYSTEM_LIBRARY} ${Boost_PROG
 if (TBB_FOUND)
   target_link_libraries(plain_homology ${TBB_LIBRARIES})
   target_link_libraries(persistence_from_simple_simplex_tree ${TBB_LIBRARIES})
+  target_link_libraries(rips_distance_matrix_persistence ${TBB_LIBRARIES})
   target_link_libraries(rips_persistence ${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(plain_homology ${CMAKE_CURRENT_BINARY_DIR}/plain_homology)
 add_test(persistence_from_simple_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_simple_simplex_tree 1 0)
-add_test(rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.16 -d 3 -p 3 -m 100)
-add_test(rips_persistence_via_boundary_matrix_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence_via_boundary_matrix ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.16 -d 3 -p 3 -m 100)
+add_test(rips_distance_matrix ${CMAKE_CURRENT_BINARY_DIR}/rips_distance_matrix_persistence ${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv -r 1.0 -d 3 -p 3 -m 0)
+add_test(rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3)
+add_test(rips_persistence_step_by_step_3 ${CMAKE_CURRENT_BINARY_DIR}/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(rips_persistence_via_boundary_matrix_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence_via_boundary_matrix ${CMAKE_SOURCE_DIR}/data/points/Kl.off -r 0.16 -d 3 -p 3 -m 100)
 add_test(persistence_from_file_3_2_0 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc -p 2 -m 0)
 add_test(persistence_from_file_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc -p 3 -m 100)
    
@@ -39,14 +49,10 @@ if(GMP_FOUND)
    if(GMPXX_FOUND)
       add_executable(rips_multifield_persistence rips_multifield_persistence.cpp )
       target_link_libraries(rips_multifield_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
-      add_executable ( performance_rips_persistence performance_rips_persistence.cpp )
-      target_link_libraries(performance_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
       if (TBB_FOUND)
         target_link_libraries(rips_multifield_persistence ${TBB_LIBRARIES})
-        target_link_libraries(performance_rips_persistence ${TBB_LIBRARIES})
       endif(TBB_FOUND)
-
-   add_test(rips_multifield_persistence_2_71 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.2 -d 3 -p 2 -q 71 -m 100)
+   add_test(rips_multifield_persistence_2_71 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2 -q 71)
    endif(GMPXX_FOUND)
 endif(GMP_FOUND)
 
diff --git a/src/Persistent_cohomology/example/README b/src/Persistent_cohomology/example/README
index 7803e5ab..2ac79398 100644
--- a/src/Persistent_cohomology/example/README
+++ b/src/Persistent_cohomology/example/README
@@ -10,13 +10,13 @@ Example of use of RIPS:
 Computation of the persistent homology with Z/2Z coefficients of the Rips complex on points 
 sampling a Klein bottle:
 
-./rips_persistence ../../data/points/Kl.txt -r 0.25 -d 3 -p 2 -m 100
+./rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2
 
 output:
-210  0 0 inf
-210  1 0.0702103 inf
-2  1 0.0702103 inf
-2  2 0.159992 inf
+2  0 0 inf 
+2  1 0.0983494 inf 
+2  1 0.104347 inf 
+2  2 0.138335 inf 
 
 
 Every line is of this format: p1*...*pr   dim b d
@@ -29,31 +29,45 @@ where
 
 with Z/3Z coefficients:
 
-./rips_persistence ../../data/points/Kl.txt -r 0.25 -d 3 -p 3 -m 100
+./rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3
 
 output:
-3  0 0 inf
-3  1 0.0702103 inf
+3  0 0 inf 
+3  1 0.0983494 inf 
+3  1 0.104347 inf 
+3  2 0.138335 inf 
 
 and the computation with Z/2Z and Z/3Z coefficients simultaneously:
 
-./rips_multifield_persistence ../../data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 3 -m 100
+./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 0.0702103 inf
-2  1 0.0702103 inf
-2  2 0.159992 inf
+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 
 
 and finally the computation with all Z/pZ for 2 <= p <= 71 (20 first prime numbers):
 
- ./rips_multifield_persistence ../../data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 71 -m 100
+ ./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 0.0702103 inf
-2  1 0.0702103 inf
-2  2 0.159992 inf
+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 ALPHA:
diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
index 48fbb91a..978dc942 100644
--- a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2014  INRIA Saclay (France)
+ *    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
@@ -64,6 +64,7 @@ typedef std::list<Alpha_shape_3::Vertex_handle> Vertex_list;
 
 // gudhi type definition
 typedef Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence> ST;
+typedef ST::Filtration_value Filtration_value;
 typedef ST::Vertex_handle Simplex_tree_vertex;
 typedef std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex > Alpha_shape_simplex_tree_map;
 typedef std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex> Alpha_shape_simplex_tree_pair;
@@ -132,7 +133,7 @@ int main(int argc, char * const argv[]) {
   int coeff_field_characteristic = atoi(argv[2]);
 
   Filtration_value min_persistence = 0.0;
-  int returnedScanValue = sscanf(argv[3], "%lf", &min_persistence);
+  int returnedScanValue = sscanf(argv[3], "%f", &min_persistence);
   if ((returnedScanValue == EOF) || (min_persistence < -1.0)) {
     std::cerr << "Error: " << argv[3] << " is not correct\n";
     usage(argv[0]);
diff --git a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp
index 2412569a..9e84e91f 100644
--- a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp
+++ b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp
@@ -11,6 +11,9 @@
 #include <string>
 #include <limits>  // for numeric_limits
 
+using Simplex_tree = Gudhi::Simplex_tree<>;
+using Filtration_value = Simplex_tree::Filtration_value;
+
 void program_options(int argc, char * argv[]
                      , std::string & off_file_points
                      , std::string & output_file_diag
@@ -34,7 +37,7 @@ int main(int argc, char **argv) {
   using Kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >;
   Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_points);
 
-  Gudhi::Simplex_tree<> simplex;
+  Simplex_tree simplex;
   if (alpha_complex_from_file.create_complex(simplex, alpha_square_max_value)) {
     // ----------------------------------------------------------------------------
     // Display information about the alpha complex
@@ -48,7 +51,7 @@ int main(int argc, char **argv) {
 
     std::cout << "Simplex_tree dim: " << simplex.dimension() << std::endl;
     // Compute the persistence diagram of the complex
-    Gudhi::persistent_cohomology::Persistent_cohomology< Gudhi::Simplex_tree<>,
+    Gudhi::persistent_cohomology::Persistent_cohomology< Simplex_tree,
         Gudhi::persistent_cohomology::Field_Zp > pcoh(simplex);
     // initializes the coefficient field for homology
     pcoh.init_coefficients(coeff_field_characteristic);
diff --git a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
index a199fea1..dbc42706 100644
--- a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2014  INRIA Saclay (France)
+ *    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
@@ -39,6 +39,7 @@
 #include <utility>
 #include <list>
 #include <vector>
+#include <cstdlib>
 
 // Traits
 using K = CGAL::Exact_predicates_inexact_constructions_kernel;
@@ -70,6 +71,7 @@ using Vertex_list = std::list<Alpha_shape_3::Vertex_handle>;
 
 // gudhi type definition
 using ST = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
+using Filtration_value = ST::Filtration_value;
 using Simplex_tree_vertex = ST::Vertex_handle;
 using Alpha_shape_simplex_tree_map = std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex >;
 using Alpha_shape_simplex_tree_pair = std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>;
@@ -136,19 +138,8 @@ int main(int argc, char * const argv[]) {
     usage(argv[0]);
   }
 
-  int coeff_field_characteristic = 0;
-  int returnedScanValue = sscanf(argv[3], "%d", &coeff_field_characteristic);
-  if ((returnedScanValue == EOF) || (coeff_field_characteristic <= 0)) {
-    std::cerr << "Error: " << argv[3] << " is not correct\n";
-    usage(argv[0]);
-  }
-
-  Filtration_value min_persistence = 0.0;
-  returnedScanValue = sscanf(argv[4], "%lf", &min_persistence);
-  if ((returnedScanValue == EOF) || (min_persistence < -1.0)) {
-    std::cerr << "Error: " << argv[4] << " is not correct\n";
-    usage(argv[0]);
-  }
+  int coeff_field_characteristic = atoi(argv[3]);
+  Filtration_value min_persistence = strtof(argv[4], nullptr);
 
   // Read points from file
   std::string offInputFile(argv[1]);
diff --git a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp
index ba772f04..7ca9410a 100644
--- a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp
+++ b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
+ *    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
@@ -29,13 +29,12 @@
 #include <utility>
 #include <vector>
 
-using namespace Gudhi;
-using namespace Gudhi::persistent_cohomology;
-
-typedef std::vector< Vertex_handle > typeVectorVertex;
-typedef std::pair<typeVectorVertex, Filtration_value> typeSimplex;
-typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool;
-typedef Simplex_tree<> typeST;
+// 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";
@@ -66,7 +65,7 @@ int main(int argc, char * const argv[]) {
   // TEST OF INSERTION
   std::cout << "********************************************************************" << std::endl;
   std::cout << "TEST OF INSERTION" << std::endl;
-  typeST st;
+  Simplex_tree st;
 
   // ++ FIRST
   std::cout << "   - INSERT (0,1,2)" << std::endl;
@@ -166,7 +165,7 @@ int main(int argc, char * const argv[]) {
   std::cout << "**************************************************************" << std::endl;
 
   // Compute the persistence diagram of the complex
-  persistent_cohomology::Persistent_cohomology< Simplex_tree<>, Field_Zp > pcoh(st);
+  Persistent_cohomology pcoh(st);
   // initializes the coefficient field for homology
   pcoh.init_coefficients(coeff_field_characteristic);
 
diff --git a/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp b/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp
new file mode 100644
index 00000000..8517e7f6
--- /dev/null
+++ b/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp
@@ -0,0 +1,144 @@
+/*    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):       Pawel Dlotko, Vincent Rouvreau
+ *
+ *    Copyright (C) 2016  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/Simplex_tree.h>
+#include <gudhi/Persistent_cohomology.h>
+#include <gudhi/reader_utils.h>
+
+#include <boost/program_options.hpp>
+
+#include <string>
+#include <vector>
+#include <limits>  // infinity
+
+// 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 Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
+using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp >;
+using Distance_matrix = std::vector<std::vector<Filtration_value>>;
+
+void program_options(int argc, char * argv[]
+                     , std::string & csv_matrix_file
+                     , std::string & filediag
+                     , Filtration_value & threshold
+                     , int & dim_max
+                     , int & p
+                     , Filtration_value & min_persistence);
+
+int main(int argc, char * argv[]) {
+  std::string csv_matrix_file;
+  std::string filediag;
+  Filtration_value threshold;
+  int dim_max;
+  int p;
+  Filtration_value min_persistence;
+
+  program_options(argc, argv, csv_matrix_file, filediag, threshold, dim_max, p, min_persistence);
+
+  Distance_matrix distances = read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_matrix_file);
+  Rips_complex rips_complex_from_file(distances, threshold);
+
+  // 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(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 & csv_matrix_file
+                     , 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>(&csv_matrix_file),
+       "Name of file containing a distance matrix. Can be square or lower triangular matrix. Separator is ';'.");
+
+  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 distance matrix.\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;
+    std::abort();
+  }
+}
diff --git a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
index c5cd775d..7674b5a5 100644
--- a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Clément Maria
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
+ *    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
@@ -20,26 +20,29 @@
  *    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/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>
 
-using namespace Gudhi;
-using namespace Gudhi::persistent_cohomology;
-
-typedef int Vertex_handle;
-typedef double Filtration_value;
+// 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 & filepoints
+                     , std::string & off_file_points
                      , std::string & filediag
                      , Filtration_value & threshold
                      , int & dim_max
@@ -48,7 +51,7 @@ void program_options(int argc, char * argv[]
                      , Filtration_value & min_persistence);
 
 int main(int argc, char * argv[]) {
-  std::string filepoints;
+  std::string off_file_points;
   std::string filediag;
   Filtration_value threshold;
   int dim_max;
@@ -56,33 +59,26 @@ int main(int argc, char * argv[]) {
   int max_p;
   Filtration_value min_persistence;
 
-  program_options(argc, argv, filepoints, filediag, threshold, dim_max, min_p, max_p, min_persistence);
-
-  // Extract the points from the file filepoints
-  typedef std::vector<double> Point_t;
-  std::vector< Point_t > points;
-  read_points(filepoints, points);
+  program_options(argc, argv, off_file_points, filediag, threshold, dim_max, min_p, max_p, min_persistence);
 
-  // Compute the proximity graph of the points
-  Graph_t prox_graph = compute_proximity_graph(points, threshold
-                                               , euclidean_distance<Point_t>);
+  Points_off_reader off_reader(off_file_points);
+  Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Euclidean_distance());
 
   // Construct the Rips complex in a Simplex Tree
-  typedef Simplex_tree<Simplex_tree_options_fast_persistence> ST;
-  ST 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);
+  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
-  st.initialize_filtration();
+  simplex_tree.initialize_filtration();
 
   // Compute the persistence diagram of the complex
-  Persistent_cohomology<ST, Multi_field > pcoh(st);
+  Persistent_cohomology pcoh(simplex_tree);
   // initializes the coefficient field for homology
   pcoh.init_coefficients(min_p, max_p);
-  // compute persistent homology, disgarding persistent features of life shorter than min_persistence
+
   pcoh.compute_persistent_cohomology(min_persistence);
 
   // Output the diagram in filediag
@@ -98,7 +94,7 @@ int main(int argc, char * argv[]) {
 }
 
 void program_options(int argc, char * argv[]
-                     , std::string & filepoints
+                     , std::string & off_file_points
                      , std::string & filediag
                      , Filtration_value & threshold
                      , int & dim_max
@@ -108,8 +104,8 @@ void program_options(int argc, char * argv[]
   namespace po = boost::program_options;
   po::options_description hidden("Hidden options");
   hidden.add_options()
-      ("input-file", po::value<std::string>(&filepoints),
-       "Name of file containing a point set. Format is one point per line:   X1 ... Xd \n");
+      ("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()
diff --git a/src/Persistent_cohomology/example/rips_persistence.cpp b/src/Persistent_cohomology/example/rips_persistence.cpp
index cab49395..c6378de7 100644
--- a/src/Persistent_cohomology/example/rips_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_persistence.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Clément Maria
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
+ *    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
@@ -20,11 +20,11 @@
  *    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/Rips_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>
 
@@ -32,14 +32,17 @@
 #include <vector>
 #include <limits>  // infinity
 
-using namespace Gudhi;
-using namespace Gudhi::persistent_cohomology;
-
-typedef int Vertex_handle;
-typedef double Filtration_value;
+// 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 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 & filepoints
+                     , std::string & off_file_points
                      , std::string & filediag
                      , Filtration_value & threshold
                      , int & dim_max
@@ -47,40 +50,30 @@ void program_options(int argc, char * argv[]
                      , Filtration_value & min_persistence);
 
 int main(int argc, char * argv[]) {
-  std::string filepoints;
+  std::string off_file_points;
   std::string filediag;
   Filtration_value threshold;
   int dim_max;
   int p;
   Filtration_value min_persistence;
 
-  program_options(argc, argv, filepoints, filediag, threshold, dim_max, p, min_persistence);
-
-  // Extract the points from the file filepoints
-  typedef std::vector<double> Point_t;
-  std::vector< Point_t > points;
-  read_points(filepoints, points);
+  program_options(argc, argv, off_file_points, filediag, threshold, dim_max, p, min_persistence);
 
-  // Compute the proximity graph of the points
-  Graph_t prox_graph = compute_proximity_graph(points, threshold
-                                               , euclidean_distance<Point_t>);
+  Points_off_reader off_reader(off_file_points);
+  Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Euclidean_distance());
 
   // Construct the Rips complex in a Simplex Tree
-  typedef Simplex_tree<Simplex_tree_options_fast_persistence> ST;
-  ST 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);
+  Simplex_tree simplex_tree;
 
-  std::cout << "The complex contains " << st.num_simplices() << " simplices \n";
-  std::cout << "   and has dimension " << st.dimension() << " \n";
+  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
-  st.initialize_filtration();
+  simplex_tree.initialize_filtration();
 
   // Compute the persistence diagram of the complex
-  persistent_cohomology::Persistent_cohomology<ST, Field_Zp > pcoh(st);
+  Persistent_cohomology pcoh(simplex_tree);
   // initializes the coefficient field for homology
   pcoh.init_coefficients(p);
 
@@ -99,7 +92,7 @@ int main(int argc, char * argv[]) {
 }
 
 void program_options(int argc, char * argv[]
-                     , std::string & filepoints
+                     , std::string & off_file_points
                      , std::string & filediag
                      , Filtration_value & threshold
                      , int & dim_max
@@ -108,15 +101,16 @@ void program_options(int argc, char * argv[]
   namespace po = boost::program_options;
   po::options_description hidden("Hidden options");
   hidden.add_options()
-      ("input-file", po::value<std::string>(&filepoints),
-       "Name of file containing a point set. Format is one point per line:   X1 ... Xd ");
+      ("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()),
+      ("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.")
diff --git a/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp b/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp
new file mode 100644
index 00000000..b159c62e
--- /dev/null
+++ b/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp
@@ -0,0 +1,217 @@
+/*    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 Sophia Antipolis-Méditerranée (France)
+ *
+ *    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 Graph_t = boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS
+, boost::property < vertex_filtration_t, Filtration_value >
+, boost::property < edge_filtration_t, Filtration_value >
+>;
+using Edge_t = std::pair< Vertex_handle, Vertex_handle >;
+
+template< typename InputPointRange, typename Distance >
+Graph_t compute_proximity_graph(InputPointRange &points, Filtration_value threshold, Distance distance);
+
+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
+  Graph_t prox_graph = compute_proximity_graph(off_reader.get_point_cloud(), threshold
+                                               , 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;
+    std::abort();
+  }
+}
+
+/** Output the proximity graph of the points.
+ *
+ * If points contains n elements, the proximity graph is the graph
+ * with n vertices, and an edge [u,v] iff the distance function between
+ * points u and v is smaller than threshold.
+ *
+ * The type PointCloud furnishes .begin() and .end() methods, that return
+ * iterators with value_type Point.
+ */
+template< typename InputPointRange, typename Distance >
+Graph_t compute_proximity_graph(InputPointRange &points, Filtration_value threshold, Distance distance) {
+  std::vector< Edge_t > edges;
+  std::vector< Filtration_value > edges_fil;
+
+  Vertex_handle idx_u, idx_v;
+  Filtration_value fil;
+  idx_u = 0;
+  for (auto it_u = points.begin(); it_u != points.end(); ++it_u) {
+    idx_v = idx_u + 1;
+    for (auto it_v = it_u + 1; it_v != points.end(); ++it_v, ++idx_v) {
+      fil = distance(*it_u, *it_v);
+      if (fil <= threshold) {
+        edges.emplace_back(idx_u, idx_v);
+        edges_fil.push_back(fil);
+      }
+    }
+    ++idx_u;
+  }
+
+  Graph_t skel_graph(edges.begin()
+                     , edges.end()
+                     , edges_fil.begin()
+                     , idx_u);  // number of points labeled from 0 to idx_u-1
+
+  auto vertex_prop = boost::get(vertex_filtration_t(), skel_graph);
+
+  boost::graph_traits<Graph_t>::vertex_iterator vi, vi_end;
+  for (std::tie(vi, vi_end) = boost::vertices(skel_graph);
+       vi != vi_end; ++vi) {
+    boost::put(vertex_prop, *vi, 0.);
+  }
+
+  return skel_graph;
+}
diff --git a/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp b/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp
index 4c6656f5..63da9847 100644
--- a/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp
+++ b/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp
@@ -4,8 +4,7 @@
  *
  *    Author(s):       Clément Maria, Marc Glisse
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France),
- *                  2015  INRIA Saclay Île de France)
+ *    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
@@ -21,12 +20,12 @@
  *    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 <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>
 
@@ -44,14 +43,16 @@
 //                                                            //
 ////////////////////////////////////////////////////////////////
 
-using namespace Gudhi;
-using namespace Gudhi::persistent_cohomology;
-
-typedef int Vertex_handle;
-typedef double Filtration_value;
+// 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 & filepoints
+                     , std::string & off_file_points
                      , std::string & filediag
                      , Filtration_value & threshold
                      , int & dim_max
@@ -59,30 +60,21 @@ void program_options(int argc, char * argv[]
                      , Filtration_value & min_persistence);
 
 int main(int argc, char * argv[]) {
-  std::string filepoints;
+  std::string off_file_points;
   std::string filediag;
   Filtration_value threshold;
   int dim_max;
   int p;
   Filtration_value min_persistence;
 
-  program_options(argc, argv, filepoints, filediag, threshold, dim_max, p, min_persistence);
-
-  // Extract the points from the file filepoints
-  typedef std::vector<double> Point_t;
-  std::vector< Point_t > points;
-  read_points(filepoints, points);
+  program_options(argc, argv, off_file_points, filediag, threshold, dim_max, p, min_persistence);
 
-  // Compute the proximity graph of the points
-  Graph_t prox_graph = compute_proximity_graph(points, threshold
-                                               , euclidean_distance<Point_t>);
+  Points_off_reader off_reader(off_file_points);
+  Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Euclidean_distance());
 
   // Construct the Rips complex in a Simplex Tree
-  Simplex_tree<>& st = *new Simplex_tree<>;
-  // insert the proximity graph in the simplex tree
-  st.insert_graph(prox_graph);
-  // expand the graph until dimension dim_max
-  st.expansion(dim_max);
+  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";
@@ -99,7 +91,7 @@ int main(int argc, char * argv[]) {
     st.assign_key(sh, count++);
 
   // Convert to a more convenient representation.
-  Hasse_complex<> hcpx(st);
+  Gudhi::Hasse_complex<> hcpx(st);
 
 #ifdef GUDHI_USE_TBB
   ts.terminate();
@@ -109,7 +101,7 @@ int main(int argc, char * argv[]) {
   delete &st;
 
   // Compute the persistence diagram of the complex
-  persistent_cohomology::Persistent_cohomology< Hasse_complex<>, Field_Zp > pcoh(hcpx);
+  Gudhi::persistent_cohomology::Persistent_cohomology< Gudhi::Hasse_complex<>, Field_Zp > pcoh(hcpx);
   // initializes the coefficient field for homology
   pcoh.init_coefficients(p);
 
@@ -126,7 +118,7 @@ int main(int argc, char * argv[]) {
 }
 
 void program_options(int argc, char * argv[]
-                     , std::string & filepoints
+                     , std::string & off_file_points
                      , std::string & filediag
                      , Filtration_value & threshold
                      , int & dim_max
@@ -135,7 +127,7 @@ void program_options(int argc, char * argv[]
   namespace po = boost::program_options;
   po::options_description hidden("Hidden options");
   hidden.add_options()
-      ("input-file", po::value<std::string>(&filepoints),
+      ("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);
diff --git a/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp b/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp
index 703682e1..1a6e3296 100644
--- a/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp
+++ b/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp
@@ -21,7 +21,7 @@ using namespace boost::unit_test;
 
 typedef Simplex_tree<> typeST;
 
-std::string test_rips_persistence(int min_coefficient, int max_coefficient, int min_persistence) {
+std::string test_rips_persistence(int min_coefficient, int max_coefficient, double min_persistence) {
   // file name is given as parameter from CMakeLists.txt
   const std::string inputFile(framework::master_test_suite().argv[1]);
 
@@ -74,7 +74,7 @@ void test_rips_persistence_in_dimension(int min_dimension, int max_dimension) {
   std::cout << "********************************************************************" << std::endl;
   std::cout << "TEST OF RIPS_PERSISTENT_COHOMOLOGY_MULTI_FIELD MIN_DIM=" << min_dimension << " MAX_DIM=" << max_dimension << " MIN_PERS=0" << std::endl;
 
-  std::string str_rips_persistence = test_rips_persistence(min_dimension, max_dimension, static_cast<Filtration_value> (0.0));
+  std::string str_rips_persistence = test_rips_persistence(min_dimension, max_dimension, 0.0);
   std::cout << "str_rips_persistence=" << str_rips_persistence << std::endl;
 
   BOOST_CHECK(str_rips_persistence.find(value0) != std::string::npos); // Check found
diff --git a/src/Rips_complex/concept/Simplicial_complex_for_rips.h b/src/Rips_complex/concept/Simplicial_complex_for_rips.h
new file mode 100644
index 00000000..7dab0615
--- /dev/null
+++ b/src/Rips_complex/concept/Simplicial_complex_for_rips.h
@@ -0,0 +1,54 @@
+/*    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) 2016  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/>.
+ */
+
+#ifndef CONCEPT_RIPS_COMPLEX_SIMPLICIAL_COMPLEX_FOR_RIPS_H_
+#define CONCEPT_RIPS_COMPLEX_SIMPLICIAL_COMPLEX_FOR_RIPS_H_
+
+namespace Gudhi {
+
+namespace rips_complex {
+
+/** \brief The concept SimplicialComplexForRips describes the requirements for a type to implement a simplicial
+ * complex, that can be created from a `Rips_complex`. The only available model for the moment is the `Simplex_tree`.
+ */
+struct SimplicialComplexForRips {
+  /** \brief Type used to store the filtration values of the simplicial complex. */
+  typedef unspecified Filtration_value;
+
+  /** \brief Inserts a given `Gudhi::rips_complex::Rips_complex::OneSkeletonGraph` in the simplicial complex. */
+  template<class OneSkeletonGraph>
+  void insert_graph(const OneSkeletonGraph& skel_graph);
+
+  /** \brief Expands the simplicial complex containing only its one skeleton until a given maximal dimension as
+   * explained in \ref ripsdefinition. */
+  void expansion(int max_dim);
+
+  /** \brief Returns the number of vertices in the simplicial complex. */
+  std::size_t num_vertices();
+
+};
+
+}  // namespace rips_complex
+
+}  // namespace Gudhi
+
+#endif  // CONCEPT_RIPS_COMPLEX_SIMPLICIAL_COMPLEX_FOR_RIPS_H_
diff --git a/src/Rips_complex/doc/Intro_rips_complex.h b/src/Rips_complex/doc/Intro_rips_complex.h
new file mode 100644
index 00000000..8e374c09
--- /dev/null
+++ b/src/Rips_complex/doc/Intro_rips_complex.h
@@ -0,0 +1,158 @@
+/*    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, Pawel Dlotko, Vincent Rouvreau
+ *
+ *    Copyright (C) 2016  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/>.
+ */
+
+#ifndef DOC_RIPS_COMPLEX_INTRO_RIPS_COMPLEX_H_
+#define DOC_RIPS_COMPLEX_INTRO_RIPS_COMPLEX_H_
+
+namespace Gudhi {
+
+namespace rips_complex {
+
+/**  \defgroup rips_complex Rips complex
+ * 
+ * \author    Clément Maria, Pawel Dlotko, Vincent Rouvreau
+ * 
+ * @{
+ * 
+ * \section ripsdefinition Rips complex definition
+ * 
+ * Rips_complex
+ * <a target="_blank" href="https://en.wikipedia.org/wiki/Vietoris%E2%80%93Rips_complex">(Wikipedia)</a> is a
+ * one skeleton graph that allows to construct a
+ * <a target="_blank" href="https://en.wikipedia.org/wiki/Simplicial_complex">simplicial complex</a>
+ * from it.
+ * The input can be a point cloud with a given distance function, or a distance matrix.
+ * 
+ * The filtration value of each edge is computed from a user-given distance function, or directly from the distance
+ * matrix.
+ * 
+ * All edges that have a filtration value strictly greater than a given threshold value are not inserted into
+ * the complex.
+ * 
+ * When creating a simplicial complex from this one skeleton graph, Rips inserts the one skeleton graph into the data
+ * structure, and then expands the simplicial complex when required.
+ *
+ * Vertex name correspond to the index of the point in the given range (aka. the point cloud).
+ * 
+ * \image html "rips_complex_representation.png" "Rips-complex one skeleton graph representation"
+ * 
+ * On this example, as edges (4,5), (4,6) and (5,6) are in the complex, simplex (4,5,6) is added with the filtration
+ * value set with \f$max(filtration(4,5), filtration(4,6), filtration(5,6))\f$.
+ * And so on for simplex (0,1,2,3).
+ * 
+ * If the Rips_complex interfaces are not detailed enough for your need, please refer to
+ * <a href="_persistent_cohomology_2rips_persistence_step_by_step_8cpp-example.html">
+ * rips_persistence_step_by_step.cpp</a> example, where the graph construction over the Simplex_tree is more detailed.
+ *
+ * \section ripspointsdistance Point cloud and distance function
+ * 
+ * \subsection ripspointscloudexample Example from a point cloud and a distance function
+ * 
+ * This example builds the one skeleton graph from the given points, threshold value, and distance function.
+ * Then it creates a `Simplex_tree` with it.
+ * 
+ * Then, it is asked to display information about the simplicial complex.
+ * 
+ * \include Rips_complex/example_one_skeleton_rips_from_points.cpp
+ * 
+ * When launching (Rips maximal distance between 2 points is 12.0, is expanded until dimension 1 - one skeleton graph
+ * in other words):
+ * 
+ * \code $> ./oneskeletonripspoints
+ * \endcode
+ *
+ * the program output is:
+ * 
+ * \include Rips_complex/one_skeleton_rips_for_doc.txt
+ * 
+ * \subsection ripsoffexample Example from OFF file
+ * 
+ * This example builds the Rips_complex from the given points in an OFF file, threshold value, and distance
+ * function.
+ * Then it creates a `Simplex_tree` with it.
+ * 
+ * 
+ * Then, it is asked to display information about the Rips complex.
+ * 
+ * \include Rips_complex/example_rips_complex_from_off_file.cpp
+ * 
+ * When launching:
+ * 
+ * \code $> ./ripsoffreader ../../data/points/alphacomplexdoc.off 12.0 3
+ * \endcode
+ *
+ * the program output is:
+ * 
+ * \include Rips_complex/full_skeleton_rips_for_doc.txt
+ * 
+ * 
+ * 
+ * \section ripsdistancematrix Distance matrix
+ * 
+ * \subsection ripsdistancematrixexample Example from a distance matrix
+ * 
+ * This example builds the one skeleton graph from the given distance matrix and threshold value.
+ * Then it creates a `Simplex_tree` with it.
+ * 
+ * Then, it is asked to display information about the simplicial complex.
+ * 
+ * \include Rips_complex/example_one_skeleton_rips_from_distance_matrix.cpp
+ * 
+ * When launching (Rips maximal distance between 2 points is 1.0, is expanded until dimension 1 - one skeleton graph
+ * with other words):
+ * 
+ * \code $> ./oneskeletonripsdistance
+ * \endcode
+ *
+ * the program output is:
+ * 
+ * \include Rips_complex/one_skeleton_rips_for_doc.txt
+ * 
+ * \subsection ripscsvdistanceexample Example from a distance matrix read in a csv file
+ * 
+ * This example builds the one skeleton graph from the given distance matrix read in a csv file and threshold value.
+ * Then it creates a `Simplex_tree` with it.
+ * 
+ * 
+ * Then, it is asked to display information about the Rips complex.
+ * 
+ * \include Rips_complex/example_rips_complex_from_csv_distance_matrix_file.cpp
+ * 
+ * When launching:
+ * 
+ * \code $> ./ripscsvdistancereader ../../data/distance_matrix/full_square_distance_matrix.csv 1.0 3
+ * \endcode
+ *
+ * the program output is:
+ * 
+ * \include Rips_complex/full_skeleton_rips_for_doc.txt
+ * 
+ * \copyright GNU General Public License v3.                         
+ * \verbatim  Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
+ */
+/** @} */  // end defgroup rips_complex
+
+}  // namespace rips_complex
+
+}  // namespace Gudhi
+
+#endif  // DOC_RIPS_COMPLEX_INTRO_RIPS_COMPLEX_H_
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diff --git a/src/Rips_complex/doc/rips_complex_representation.png b/src/Rips_complex/doc/rips_complex_representation.png
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diff --git a/src/Rips_complex/doc/rips_one_skeleton.png b/src/Rips_complex/doc/rips_one_skeleton.png
new file mode 100644
index 00000000..1028770e
--- /dev/null
+++ b/src/Rips_complex/doc/rips_one_skeleton.png
diff --git a/src/Rips_complex/example/CMakeLists.txt b/src/Rips_complex/example/CMakeLists.txt
new file mode 100644
index 00000000..070ac710
--- /dev/null
+++ b/src/Rips_complex/example/CMakeLists.txt
@@ -0,0 +1,47 @@
+cmake_minimum_required(VERSION 2.6)
+project(Rips_complex_examples)
+
+# Point cloud
+add_executable ( ripsoffreader example_rips_complex_from_off_file.cpp )
+target_link_libraries(ripsoffreader  ${Boost_SYSTEM_LIBRARY})
+
+add_executable ( oneskeletonripspoints example_one_skeleton_rips_from_points.cpp )
+target_link_libraries(oneskeletonripspoints  ${Boost_SYSTEM_LIBRARY})
+
+# Distance matrix
+add_executable ( oneskeletonripsdistance example_one_skeleton_rips_from_distance_matrix.cpp )
+target_link_libraries(oneskeletonripsdistance  ${Boost_SYSTEM_LIBRARY})
+
+add_executable ( ripscsvdistancereader example_rips_complex_from_csv_distance_matrix_file.cpp )
+target_link_libraries(ripscsvdistancereader  ${Boost_SYSTEM_LIBRARY})
+
+if (TBB_FOUND)
+  target_link_libraries(ripsoffreader ${TBB_LIBRARIES})
+  target_link_libraries(oneskeletonripspoints ${TBB_LIBRARIES})
+  target_link_libraries(oneskeletonripsdistance ${TBB_LIBRARIES})
+  target_link_libraries(ripscsvdistancereader ${TBB_LIBRARIES})
+endif()
+
+add_test(oneskeletonripspoints ${CMAKE_CURRENT_BINARY_DIR}/oneskeletonripspoints)
+add_test(oneskeletonripsdistance ${CMAKE_CURRENT_BINARY_DIR}/oneskeletonripsdistance)
+
+# Do not forget to copy test files in current binary dir
+file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+add_test(ripsoffreader_doc_12_1 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader alphacomplexdoc.off 12.0 1 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_1.txt)
+add_test(ripsoffreader_doc_12_3 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader alphacomplexdoc.off 12.0 3 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_3.txt)
+
+file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+add_test(ripscsvdistancereader_doc_12_1 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvdistancereader full_square_distance_matrix.csv 12.0 1 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_12_1.txt)
+add_test(ripscsvdistancereader_doc_12_3 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvdistancereader full_square_distance_matrix.csv 12.0 3 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_12_3.txt)
+
+
+if (DIFF_PATH)
+  # Do not forget to copy test results files in current binary dir
+  file(COPY "one_skeleton_rips_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+  file(COPY "full_skeleton_rips_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+
+  add_test(ripsoffreader_doc_12_1_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_1.txt ${CMAKE_CURRENT_BINARY_DIR}/one_skeleton_rips_for_doc.txt)
+  add_test(ripsoffreader_doc_12_3_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_3.txt ${CMAKE_CURRENT_BINARY_DIR}/full_skeleton_rips_for_doc.txt)
+  add_test(ripscsvreader_doc_12_1_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_12_1.txt ${CMAKE_CURRENT_BINARY_DIR}/one_skeleton_rips_for_doc.txt)
+  add_test(ripscsvreader_doc_12_3_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_12_3.txt ${CMAKE_CURRENT_BINARY_DIR}/full_skeleton_rips_for_doc.txt)
+endif()
diff --git a/src/Rips_complex/example/example_one_skeleton_rips_from_distance_matrix.cpp b/src/Rips_complex/example/example_one_skeleton_rips_from_distance_matrix.cpp
new file mode 100644
index 00000000..bbc3c755
--- /dev/null
+++ b/src/Rips_complex/example/example_one_skeleton_rips_from_distance_matrix.cpp
@@ -0,0 +1,58 @@
+#include <gudhi/Rips_complex.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/distance_functions.h>
+
+#include <iostream>
+#include <string>
+#include <vector>
+#include <limits>  // for std::numeric_limits
+
+int main() {
+  // Type definitions
+  using Simplex_tree = Gudhi::Simplex_tree<>;
+  using Filtration_value = Simplex_tree::Filtration_value;
+  using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
+  using Distance_matrix = std::vector<std::vector<Filtration_value>>;
+
+  // User defined distance matrix is:
+  // | 0    0.94 0.77 0.99 0.11  |
+  // | 0.94 0    0.26 0.99 0.39  |
+  // | 0.77 0.26 0    0.28 0.97  |
+  // | 0.99 0.99 0.28 0    0.30  |
+  // | 0.11 0.39 0.97 0.30 0     |
+
+  Distance_matrix distances;
+  distances.push_back({});
+  distances.push_back({0.94});
+  distances.push_back({0.77, 0.26});
+  distances.push_back({0.99, 0.99, 0.28});
+  distances.push_back({0.11, 0.39, 0.97, 0.30});
+
+  // ----------------------------------------------------------------------------
+  // Init of a Rips complex from points
+  // ----------------------------------------------------------------------------
+  double threshold = 1.0;
+  Rips_complex rips_complex_from_points(distances, threshold);
+
+  Simplex_tree stree;
+  rips_complex_from_points.create_complex(stree, 1);
+  // ----------------------------------------------------------------------------
+  // Display information about the one skeleton Rips complex
+  // ----------------------------------------------------------------------------
+  std::cout << "Rips complex is of dimension " << stree.dimension() <<
+               " - " << stree.num_simplices() << " simplices - " <<
+               stree.num_vertices() << " vertices." << std::endl;
+
+  std::cout << "Iterator on Rips complex simplices in the filtration order, with [filtration value]:" <<
+               std::endl;
+  for (auto f_simplex : stree.filtration_simplex_range()) {
+    std::cout << "   ( ";
+    for (auto vertex : stree.simplex_vertex_range(f_simplex)) {
+      std::cout << vertex << " ";
+    }
+    std::cout << ") -> " << "[" << stree.filtration(f_simplex) << "] ";
+    std::cout << std::endl;
+  }
+
+  return 0;
+}
diff --git a/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp b/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp
new file mode 100644
index 00000000..3fd69ebc
--- /dev/null
+++ b/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp
@@ -0,0 +1,52 @@
+#include <gudhi/Rips_complex.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/distance_functions.h>
+
+#include <iostream>
+#include <string>
+#include <vector>
+#include <limits>  // for std::numeric_limits
+
+int main() {
+  // Type definitions
+  using Point = std::vector<double>;
+  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>;
+
+  std::vector<Point> points;
+  points.push_back({1.0, 1.0});
+  points.push_back({7.0, 0.0});
+  points.push_back({4.0, 6.0});
+  points.push_back({9.0, 6.0});
+  points.push_back({0.0, 14.0});
+  points.push_back({2.0, 19.0});
+  points.push_back({9.0, 17.0});
+
+  // ----------------------------------------------------------------------------
+  // Init of a Rips complex from points
+  // ----------------------------------------------------------------------------
+  double threshold = 12.0;
+  Rips_complex rips_complex_from_points(points, threshold, Euclidean_distance());
+
+  Simplex_tree stree;
+  rips_complex_from_points.create_complex(stree, 1);
+  // ----------------------------------------------------------------------------
+  // Display information about the one skeleton Rips complex
+  // ----------------------------------------------------------------------------
+  std::cout << "Rips complex is of dimension " << stree.dimension() <<
+               " - " << stree.num_simplices() << " simplices - " <<
+               stree.num_vertices() << " vertices." << std::endl;
+
+  std::cout << "Iterator on Rips complex simplices in the filtration order, with [filtration value]:" <<
+               std::endl;
+  for (auto f_simplex : stree.filtration_simplex_range()) {
+    std::cout << "   ( ";
+    for (auto vertex : stree.simplex_vertex_range(f_simplex)) {
+      std::cout << vertex << " ";
+    }
+    std::cout << ") -> " << "[" << stree.filtration(f_simplex) << "] ";
+    std::cout << std::endl;
+  }
+  return 0;
+}
diff --git a/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp b/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp
new file mode 100644
index 00000000..ef3a9d13
--- /dev/null
+++ b/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp
@@ -0,0 +1,72 @@
+#include <gudhi/Rips_complex.h>
+// to construct Rips_complex from a OFF file of points
+#include <gudhi/reader_utils.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/distance_functions.h>
+
+#include <iostream>
+#include <string>
+#include <vector>
+
+void usage(int nbArgs, char * const progName) {
+  std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n";
+  std::cerr << "Usage: " << progName << " filename.csv threshold dim_max [ouput_file.txt]\n";
+  std::cerr << "       i.e.: " << progName << " ../../data/distance_matrix/full_square_distance_matrix.csv 1.0 3\n";
+  exit(-1);  // ----- >>
+}
+
+int main(int argc, char **argv) {
+  if ((argc != 4) && (argc != 5)) usage(argc, (argv[0] - 1));
+
+  std::string csv_file_name(argv[1]);
+  double threshold = atof(argv[2]);
+  int dim_max = atoi(argv[3]);
+
+  // Type definitions
+  using Simplex_tree = Gudhi::Simplex_tree<>;
+  using Filtration_value = Simplex_tree::Filtration_value;
+  using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
+  using Distance_matrix = std::vector<std::vector<Filtration_value>>;
+
+  // ----------------------------------------------------------------------------
+  // Init of a Rips complex from a distance matrix in a csv file
+  // Default separator is ';'
+  // ----------------------------------------------------------------------------
+  Distance_matrix distances = read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_file_name);
+  Rips_complex rips_complex_from_file(distances, threshold);
+
+  std::streambuf* streambufffer;
+  std::ofstream ouput_file_stream;
+
+  if (argc == 5) {
+    ouput_file_stream.open(std::string(argv[4]));
+    streambufffer = ouput_file_stream.rdbuf();
+  } else {
+    streambufffer = std::cout.rdbuf();
+  }
+
+  Simplex_tree stree;
+  rips_complex_from_file.create_complex(stree, dim_max);
+  std::ostream output_stream(streambufffer);
+
+  // ----------------------------------------------------------------------------
+  // Display information about the Rips complex
+  // ----------------------------------------------------------------------------
+  output_stream << "Rips complex is of dimension " << stree.dimension() <<
+                   " - " << stree.num_simplices() << " simplices - " <<
+                   stree.num_vertices() << " vertices." << std::endl;
+
+  output_stream << "Iterator on Rips complex simplices in the filtration order, with [filtration value]:" <<
+                   std::endl;
+  for (auto f_simplex : stree.filtration_simplex_range()) {
+    output_stream << "   ( ";
+    for (auto vertex : stree.simplex_vertex_range(f_simplex)) {
+      output_stream << vertex << " ";
+    }
+    output_stream << ") -> " << "[" << stree.filtration(f_simplex) << "] ";
+    output_stream << std::endl;
+  }
+
+  ouput_file_stream.close();
+  return 0;
+}
diff --git a/src/Rips_complex/example/example_rips_complex_from_off_file.cpp b/src/Rips_complex/example/example_rips_complex_from_off_file.cpp
new file mode 100644
index 00000000..a1e4e255
--- /dev/null
+++ b/src/Rips_complex/example/example_rips_complex_from_off_file.cpp
@@ -0,0 +1,71 @@
+#include <gudhi/Rips_complex.h>
+// to construct Rips_complex from a OFF file of points
+#include <gudhi/Points_off_io.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/distance_functions.h>
+
+#include <iostream>
+#include <string>
+#include <vector>
+
+void usage(int nbArgs, char * const progName) {
+  std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n";
+  std::cerr << "Usage: " << progName << " filename.off threshold dim_max [ouput_file.txt]\n";
+  std::cerr << "       i.e.: " << progName << " ../../data/points/alphacomplexdoc.off 60.0\n";
+  exit(-1);  // ----- >>
+}
+
+int main(int argc, char **argv) {
+  if ((argc != 4) && (argc != 5)) usage(argc, (argv[0] - 1));
+
+  std::string off_file_name(argv[1]);
+  double threshold = atof(argv[2]);
+  int dim_max = atoi(argv[3]);
+
+  // Type definitions
+  using Point = std::vector<float>;
+  using Simplex_tree = Gudhi::Simplex_tree<>;
+  using Filtration_value = Simplex_tree::Filtration_value;
+  using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
+
+  // ----------------------------------------------------------------------------
+  // Init of a Rips complex from an OFF file
+  // ----------------------------------------------------------------------------
+  Gudhi::Points_off_reader<Point> off_reader(off_file_name);
+  Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Euclidean_distance());
+
+  std::streambuf* streambufffer;
+  std::ofstream ouput_file_stream;
+
+  if (argc == 5) {
+    ouput_file_stream.open(std::string(argv[4]));
+    streambufffer = ouput_file_stream.rdbuf();
+  } else {
+    streambufffer = std::cout.rdbuf();
+  }
+
+  Simplex_tree stree;
+  rips_complex_from_file.create_complex(stree, dim_max);
+  std::ostream output_stream(streambufffer);
+
+  // ----------------------------------------------------------------------------
+  // Display information about the Rips complex
+  // ----------------------------------------------------------------------------
+  output_stream << "Rips complex is of dimension " << stree.dimension() <<
+                   " - " << stree.num_simplices() << " simplices - " <<
+                   stree.num_vertices() << " vertices." << std::endl;
+
+  output_stream << "Iterator on Rips complex simplices in the filtration order, with [filtration value]:" <<
+                   std::endl;
+  for (auto f_simplex : stree.filtration_simplex_range()) {
+    output_stream << "   ( ";
+    for (auto vertex : stree.simplex_vertex_range(f_simplex)) {
+      output_stream << vertex << " ";
+    }
+    output_stream << ") -> " << "[" << stree.filtration(f_simplex) << "] ";
+    output_stream << std::endl;
+  }
+
+  ouput_file_stream.close();
+  return 0;
+}
diff --git a/src/Rips_complex/example/full_skeleton_rips_for_doc.txt b/src/Rips_complex/example/full_skeleton_rips_for_doc.txt
new file mode 100644
index 00000000..55de4ab8
--- /dev/null
+++ b/src/Rips_complex/example/full_skeleton_rips_for_doc.txt
@@ -0,0 +1,26 @@
+Rips complex is of dimension 3 - 24 simplices - 7 vertices.
+Iterator on Rips complex simplices in the filtration order, with [filtration value]:
+   ( 0 ) -> [0] 
+   ( 1 ) -> [0] 
+   ( 2 ) -> [0] 
+   ( 3 ) -> [0] 
+   ( 4 ) -> [0] 
+   ( 5 ) -> [0] 
+   ( 6 ) -> [0] 
+   ( 3 2 ) -> [5] 
+   ( 5 4 ) -> [5.38516] 
+   ( 2 0 ) -> [5.83095] 
+   ( 1 0 ) -> [6.08276] 
+   ( 3 1 ) -> [6.32456] 
+   ( 2 1 ) -> [6.7082] 
+   ( 2 1 0 ) -> [6.7082] 
+   ( 3 2 1 ) -> [6.7082] 
+   ( 6 5 ) -> [7.28011] 
+   ( 4 2 ) -> [8.94427] 
+   ( 3 0 ) -> [9.43398] 
+   ( 3 1 0 ) -> [9.43398] 
+   ( 3 2 0 ) -> [9.43398] 
+   ( 3 2 1 0 ) -> [9.43398] 
+   ( 6 4 ) -> [9.48683] 
+   ( 6 5 4 ) -> [9.48683] 
+   ( 6 3 ) -> [11] 
diff --git a/src/Rips_complex/example/one_skeleton_rips_for_doc.txt b/src/Rips_complex/example/one_skeleton_rips_for_doc.txt
new file mode 100644
index 00000000..706512a5
--- /dev/null
+++ b/src/Rips_complex/example/one_skeleton_rips_for_doc.txt
@@ -0,0 +1,20 @@
+Rips complex is of dimension 1 - 18 simplices - 7 vertices.
+Iterator on Rips complex simplices in the filtration order, with [filtration value]:
+   ( 0 ) -> [0] 
+   ( 1 ) -> [0] 
+   ( 2 ) -> [0] 
+   ( 3 ) -> [0] 
+   ( 4 ) -> [0] 
+   ( 5 ) -> [0] 
+   ( 6 ) -> [0] 
+   ( 3 2 ) -> [5] 
+   ( 5 4 ) -> [5.38516] 
+   ( 2 0 ) -> [5.83095] 
+   ( 1 0 ) -> [6.08276] 
+   ( 3 1 ) -> [6.32456] 
+   ( 2 1 ) -> [6.7082] 
+   ( 6 5 ) -> [7.28011] 
+   ( 4 2 ) -> [8.94427] 
+   ( 3 0 ) -> [9.43398] 
+   ( 6 4 ) -> [9.48683] 
+   ( 6 3 ) -> [11] 
diff --git a/src/Rips_complex/include/gudhi/Rips_complex.h b/src/Rips_complex/include/gudhi/Rips_complex.h
new file mode 100644
index 00000000..1e4b76a7
--- /dev/null
+++ b/src/Rips_complex/include/gudhi/Rips_complex.h
@@ -0,0 +1,185 @@
+/*    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, Pawel Dlotko, Vincent Rouvreau
+ *
+ *    Copyright (C) 2016  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/>.
+ */
+
+#ifndef RIPS_COMPLEX_H_
+#define RIPS_COMPLEX_H_
+
+#include <gudhi/Debug_utils.h>
+#include <gudhi/graph_simplicial_complex.h>
+
+#include <boost/graph/adjacency_list.hpp>
+
+#include <iostream>
+#include <vector>
+#include <map>
+#include <string>
+#include <limits>  // for numeric_limits
+#include <utility>  // for pair<>
+
+
+namespace Gudhi {
+
+namespace rips_complex {
+
+/**
+ * \class Rips_complex
+ * \brief Rips complex data structure.
+ * 
+ * \ingroup rips_complex
+ * 
+ * \details
+ * The data structure is a one skeleton graph, or Rips graph, containing edges when the edge length is less or equal
+ * to a given threshold. Edge length is computed from a user given point cloud with a given distance function, or a
+ * distance matrix.
+ * 
+ * \tparam Filtration_value is the type used to store the filtration values of the simplicial complex.
+ */
+template<typename Filtration_value>
+class Rips_complex {
+ public:
+  /**
+   * \brief Type of the one skeleton graph stored inside the Rips complex structure.
+   */
+  typedef typename boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS
+  , boost::property < vertex_filtration_t, Filtration_value >
+  , boost::property < edge_filtration_t, Filtration_value >> OneSkeletonGraph;
+
+ private:
+  typedef int Vertex_handle;
+
+ public:
+  /** \brief Rips_complex constructor from a list of points.
+   *
+   * @param[in] points Range of points.
+   * @param[in] threshold Rips value.
+   * @param[in] distance distance function that returns a `Filtration_value` from 2 given points.
+   * 
+   * \tparam ForwardPointRange must be a range for which `std::begin` and `std::end` return input iterators on a
+   * point.
+   *
+   * \tparam Distance furnishes `operator()(const Point& p1, const Point& p2)`, where
+   * `Point` is a point from the `ForwardPointRange`, and that returns a `Filtration_value`.
+   */
+  template<typename ForwardPointRange, typename Distance >
+  Rips_complex(const ForwardPointRange& points, Filtration_value threshold, Distance distance) {
+    compute_proximity_graph(points, threshold, distance);
+  }
+
+  /** \brief Rips_complex constructor from a distance matrix.
+   *
+   * @param[in] distance_matrix Range of distances.
+   * @param[in] threshold Rips value.
+   * 
+   * \tparam DistanceMatrix must have a `size()` method and on which `distance_matrix[i][j]` returns
+   * the distance between points \f$i\f$ and \f$j\f$ as long as \f$ 0 \leqslant i < j \leqslant
+   * distance\_matrix.size().\f$
+   */
+  template<typename DistanceMatrix>
+  Rips_complex(const DistanceMatrix& distance_matrix, Filtration_value threshold) {
+    compute_proximity_graph(boost::irange((size_t)0, distance_matrix.size()), threshold,
+                            [&](size_t i, size_t j){return distance_matrix[j][i];});
+  }
+
+  /** \brief Initializes the simplicial complex from the Rips graph and expands it until a given maximal
+   * dimension.
+   *
+   * \tparam SimplicialComplexForRips must meet `SimplicialComplexForRips` concept.
+   * 
+   * @param[in] complex SimplicialComplexForRips to be created.
+   * @param[in] dim_max graph expansion for Rips until this given maximal dimension.
+   * @exception std::invalid_argument In debug mode, if `complex.num_vertices()` does not return 0.
+   *
+   */
+  template <typename SimplicialComplexForRips>
+  void create_complex(SimplicialComplexForRips& complex, int dim_max) {
+    GUDHI_CHECK(complex.num_vertices() == 0,
+                std::invalid_argument("Rips_complex::create_complex - simplicial complex is not empty"));
+
+    // insert the proximity graph in the simplicial complex
+    complex.insert_graph(rips_skeleton_graph_);
+    // expand the graph until dimension dim_max
+    complex.expansion(dim_max);
+  }
+
+ private:
+  /** \brief Computes the proximity graph of the points.
+   *
+   * If points contains n elements, the proximity graph is the graph with n vertices, and an edge [u,v] iff the
+   * distance function between points u and v is smaller than threshold.
+   *
+   * \tparam ForwardPointRange furnishes `.begin()` and `.end()`
+   * methods.
+   *
+   * \tparam Distance furnishes `operator()(const Point& p1, const Point& p2)`, where
+   * `Point` is a point from the `ForwardPointRange`, and that returns a `Filtration_value`.
+   */
+  template< typename ForwardPointRange, typename Distance >
+  void compute_proximity_graph(const ForwardPointRange& points, Filtration_value threshold,
+               Distance distance) {
+    std::vector< std::pair< Vertex_handle, Vertex_handle > > edges;
+    std::vector< Filtration_value > edges_fil;
+
+    // Compute the proximity graph of the points.
+    // If points contains n elements, the proximity graph is the graph with n vertices, and an edge [u,v] iff the
+    // distance function between points u and v is smaller than threshold.
+    // --------------------------------------------------------------------------------------------
+    // Creates the vector of edges and its filtration values (returned by distance function)
+    Vertex_handle idx_u = 0;
+    for (auto it_u = std::begin(points); it_u != std::end(points); ++it_u, ++idx_u) {
+      Vertex_handle idx_v = idx_u + 1;
+      for (auto it_v = it_u + 1; it_v != std::end(points); ++it_v, ++idx_v) {
+        Filtration_value fil = distance(*it_u, *it_v);
+        if (fil <= threshold) {
+          edges.emplace_back(idx_u, idx_v);
+          edges_fil.push_back(fil);
+        }
+      }
+    }
+
+    // --------------------------------------------------------------------------------------------
+    // Creates the proximity graph from edges and sets the property with the filtration value.
+    // Number of points is labeled from 0 to idx_u-1
+    // --------------------------------------------------------------------------------------------
+    // Do not use : rips_skeleton_graph_ = OneSkeletonGraph(...) -> deep copy of the graph (boost graph is not
+    // move-enabled)
+    rips_skeleton_graph_.~OneSkeletonGraph();
+    new(&rips_skeleton_graph_)OneSkeletonGraph(edges.begin(), edges.end(), edges_fil.begin(), idx_u);
+
+    auto vertex_prop = boost::get(vertex_filtration_t(), rips_skeleton_graph_);
+
+    using vertex_iterator = typename boost::graph_traits<OneSkeletonGraph>::vertex_iterator;
+    vertex_iterator vi, vi_end;
+    for (std::tie(vi, vi_end) = boost::vertices(rips_skeleton_graph_);
+         vi != vi_end; ++vi) {
+      boost::put(vertex_prop, *vi, 0.);
+    }
+  }
+
+ private:
+  OneSkeletonGraph rips_skeleton_graph_;
+};
+
+}  // namespace rips_complex
+
+}  // namespace Gudhi
+
+#endif  // RIPS_COMPLEX_H_
diff --git a/src/Rips_complex/test/CMakeLists.txt b/src/Rips_complex/test/CMakeLists.txt
new file mode 100644
index 00000000..87bad2ed
--- /dev/null
+++ b/src/Rips_complex/test/CMakeLists.txt
@@ -0,0 +1,25 @@
+cmake_minimum_required(VERSION 2.6)
+project(Rips_complex_tests)
+
+if (GCOVR_PATH)
+  # for gcovr to make coverage reports - Corbera Jenkins plugin
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
+endif()
+if (GPROF_PATH)
+  # for gprof to make coverage reports - Jenkins
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
+endif()
+
+add_executable ( rips_complex_UT test_rips_complex.cpp )
+target_link_libraries(rips_complex_UT  ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+if (TBB_FOUND)
+  target_link_libraries(rips_complex_UT ${TBB_LIBRARIES})
+endif()
+
+# Do not forget to copy test files in current binary dir
+file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+
+add_test(rips_complex_UT ${CMAKE_CURRENT_BINARY_DIR}/rips_complex_UT
+         # XML format for Jenkins xUnit plugin 
+         --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/rips_complex_UT.xml --log_level=test_suite --report_level=no)
diff --git a/src/Rips_complex/test/README b/src/Rips_complex/test/README
new file mode 100644
index 00000000..28236b52
--- /dev/null
+++ b/src/Rips_complex/test/README
@@ -0,0 +1,12 @@
+To compile:
+***********
+
+cmake .
+make
+
+To launch with details:
+***********************
+
+./rips_complex_UT --report_level=detailed --log_level=all 
+
+   ==> echo $? returns 0 in case of success (non-zero otherwise)
diff --git a/src/Rips_complex/test/test_rips_complex.cpp b/src/Rips_complex/test/test_rips_complex.cpp
new file mode 100644
index 00000000..ae68ba0d
--- /dev/null
+++ b/src/Rips_complex/test/test_rips_complex.cpp
@@ -0,0 +1,353 @@
+/*    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) 2016  INRIA Saclay (France)
+ *
+ *    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/>.
+ */
+
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "rips_complex"
+#include <boost/test/unit_test.hpp>
+
+#include <cmath>  // float comparison
+#include <limits>
+#include <string>
+#include <vector>
+#include <algorithm>    // std::max
+
+#include <gudhi/Rips_complex.h>
+// to construct Rips_complex from a OFF file of points
+#include <gudhi/Points_off_io.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/distance_functions.h>
+#include <gudhi/reader_utils.h>
+
+// Type definitions
+using Point = std::vector<double>;
+using Simplex_tree = Gudhi::Simplex_tree<>;
+using Filtration_value = Simplex_tree::Filtration_value;
+using Rips_complex = Gudhi::rips_complex::Rips_complex<Simplex_tree::Filtration_value>;
+using Distance_matrix = std::vector<std::vector<Filtration_value>>;
+
+bool are_almost_the_same(float a, float b) {
+  return std::fabs(a - b) < std::numeric_limits<float>::epsilon();
+}
+
+BOOST_AUTO_TEST_CASE(RIPS_DOC_OFF_file) {
+  // ----------------------------------------------------------------------------
+  //
+  // Init of a Rips complex from a OFF file
+  //
+  // ----------------------------------------------------------------------------
+  std::string off_file_name("alphacomplexdoc.off");
+  double rips_threshold = 12.0;
+  std::cout << "========== OFF FILE NAME = " << off_file_name << " - Rips threshold=" <<
+      rips_threshold << "==========" << std::endl;
+
+  Gudhi::Points_off_reader<Point> off_reader(off_file_name);
+  Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), rips_threshold, Euclidean_distance());
+
+  const int DIMENSION_1 = 1;
+  Simplex_tree st;
+  rips_complex_from_file.create_complex(st, DIMENSION_1);
+  std::cout << "st.dimension()=" << st.dimension() << std::endl;
+  BOOST_CHECK(st.dimension() == DIMENSION_1);
+
+  const int NUMBER_OF_VERTICES = 7;
+  std::cout << "st.num_vertices()=" << st.num_vertices() << std::endl;
+  BOOST_CHECK(st.num_vertices() == NUMBER_OF_VERTICES);
+
+  std::cout << "st.num_simplices()=" << st.num_simplices() << std::endl;
+  BOOST_CHECK(st.num_simplices() == 18);
+
+  // Check filtration values of vertices is 0.0
+  for (auto f_simplex : st.skeleton_simplex_range(0)) {
+    BOOST_CHECK(st.filtration(f_simplex) == 0.0);
+  }
+
+  // Check filtration values of edges
+  for (auto f_simplex : st.skeleton_simplex_range(DIMENSION_1)) {
+    if (DIMENSION_1 == st.dimension(f_simplex)) {
+      std::vector<Point> vp;
+      std::cout << "vertex = (";
+      for (auto vertex : st.simplex_vertex_range(f_simplex)) {
+        std::cout << vertex << ",";
+        vp.push_back(off_reader.get_point_cloud().at(vertex));
+      }
+      std::cout << ") - distance =" << Euclidean_distance()(vp.at(0), vp.at(1)) <<
+          " - filtration =" << st.filtration(f_simplex) << std::endl;
+      BOOST_CHECK(vp.size() == 2);
+      BOOST_CHECK(are_almost_the_same(st.filtration(f_simplex), Euclidean_distance()(vp.at(0), vp.at(1))));
+    }
+  }
+
+  const int DIMENSION_2 = 2;
+  Simplex_tree st2;
+  rips_complex_from_file.create_complex(st2, DIMENSION_2);
+  std::cout << "st2.dimension()=" << st2.dimension() << std::endl;
+  BOOST_CHECK(st2.dimension() == DIMENSION_2);
+  
+  std::cout << "st2.num_vertices()=" << st2.num_vertices() << std::endl;
+  BOOST_CHECK(st2.num_vertices() == NUMBER_OF_VERTICES);
+
+  std::cout << "st2.num_simplices()=" << st2.num_simplices() << std::endl;
+  BOOST_CHECK(st2.num_simplices() == 23);
+
+  Simplex_tree::Filtration_value f01 = st2.filtration(st2.find({0, 1}));
+  Simplex_tree::Filtration_value f02 = st2.filtration(st2.find({0, 2}));
+  Simplex_tree::Filtration_value f12 = st2.filtration(st2.find({1, 2}));
+  Simplex_tree::Filtration_value f012 = st2.filtration(st2.find({0, 1, 2}));
+  std::cout << "f012= " << f012 << " | f01= " << f01 << " - f02= " << f02 << " - f12= " << f12 << std::endl;
+  BOOST_CHECK(are_almost_the_same(f012, std::max(f01, std::max(f02,f12))));
+  
+  Simplex_tree::Filtration_value f45 = st2.filtration(st2.find({4, 5}));
+  Simplex_tree::Filtration_value f56 = st2.filtration(st2.find({5, 6}));
+  Simplex_tree::Filtration_value f46 = st2.filtration(st2.find({4, 6}));
+  Simplex_tree::Filtration_value f456 = st2.filtration(st2.find({4, 5, 6}));
+  std::cout << "f456= " << f456 << " | f45= " << f45 << " - f56= " << f56 << " - f46= " << f46 << std::endl;
+  BOOST_CHECK(are_almost_the_same(f456, std::max(f45, std::max(f56,f46))));
+
+  const int DIMENSION_3 = 3;
+  Simplex_tree st3;
+  rips_complex_from_file.create_complex(st3, DIMENSION_3);
+  std::cout << "st3.dimension()=" << st3.dimension() << std::endl;
+  BOOST_CHECK(st3.dimension() == DIMENSION_3);
+  
+  std::cout << "st3.num_vertices()=" << st3.num_vertices() << std::endl;
+  BOOST_CHECK(st3.num_vertices() == NUMBER_OF_VERTICES);
+
+  std::cout << "st3.num_simplices()=" << st3.num_simplices() << std::endl;
+  BOOST_CHECK(st3.num_simplices() == 24);
+
+  Simplex_tree::Filtration_value f123 = st3.filtration(st3.find({1, 2, 3}));
+  Simplex_tree::Filtration_value f013 = st3.filtration(st3.find({0, 1, 3}));
+  Simplex_tree::Filtration_value f023 = st3.filtration(st3.find({0, 2, 3}));
+  Simplex_tree::Filtration_value f0123 = st3.filtration(st3.find({0, 1, 2, 3}));
+  std::cout << "f0123= " << f0123 << " | f012= " << f012 << " - f123= " << f123 << " - f013= " << f013 <<
+      " - f023= " << f023 << std::endl;
+  BOOST_CHECK(are_almost_the_same(f0123, std::max(f012, std::max(f123, std::max(f013, f023)))));
+
+}
+
+using Vector_of_points = std::vector<Point>;
+
+bool is_point_in_list(Vector_of_points points_list, Point point) {
+  for (auto& point_in_list : points_list) {
+    if (point_in_list == point) {
+      return true;  // point found
+    }
+  }
+  return false;  // point not found
+}
+
+class Custom_square_euclidean_distance {
+ public:
+  template< typename Point >
+  auto operator()(const Point& p1, const Point& p2) -> typename Point::value_type {
+    auto it1 = p1.begin();
+    auto it2 = p2.begin();
+    typename Point::value_type dist = 0.;
+    for (; it1 != p1.end(); ++it1, ++it2) {
+      typename Point::value_type tmp = (*it1) - (*it2);
+      dist += tmp*tmp;
+    }
+    return dist;
+  }
+};
+
+BOOST_AUTO_TEST_CASE(Rips_complex_from_points) {
+  // ----------------------------------------------------------------------------
+  // Init of a list of points
+  // ----------------------------------------------------------------------------
+  Vector_of_points points;
+  std::vector<double> coords = { 0.0, 0.0, 0.0, 1.0 };
+  points.push_back(Point(coords.begin(), coords.end()));
+  coords = { 0.0, 0.0, 1.0, 0.0 };
+  points.push_back(Point(coords.begin(), coords.end()));
+  coords = { 0.0, 1.0, 0.0, 0.0 };
+  points.push_back(Point(coords.begin(), coords.end()));
+  coords = { 1.0, 0.0, 0.0, 0.0 };
+  points.push_back(Point(coords.begin(), coords.end()));
+
+  // ----------------------------------------------------------------------------
+  // Init of a Rips complex from the list of points
+  // ----------------------------------------------------------------------------
+  Rips_complex rips_complex_from_points(points, 2.0, Custom_square_euclidean_distance());
+
+  std::cout << "========== Rips_complex_from_points ==========" << std::endl;
+  Simplex_tree st;
+  const int DIMENSION = 3;
+  rips_complex_from_points.create_complex(st, DIMENSION);
+
+  // Another way to check num_simplices
+  std::cout << "Iterator on Rips complex simplices in the filtration order, with [filtration value]:" << std::endl;
+  int num_simplices = 0;
+  for (auto f_simplex : st.filtration_simplex_range()) {
+    num_simplices++;
+    std::cout << "   ( ";
+    for (auto vertex : st.simplex_vertex_range(f_simplex)) {
+      std::cout << vertex << " ";
+    }
+    std::cout << ") -> " << "[" << st.filtration(f_simplex) << "] ";
+    std::cout << std::endl;
+  }
+  BOOST_CHECK(num_simplices == 15);
+  std::cout << "st.num_simplices()=" << st.num_simplices() << std::endl;
+  BOOST_CHECK(st.num_simplices() == 15);
+
+  std::cout << "st.dimension()=" << st.dimension() << std::endl;
+  BOOST_CHECK(st.dimension() == DIMENSION);
+  std::cout << "st.num_vertices()=" << st.num_vertices() << std::endl;
+  BOOST_CHECK(st.num_vertices() == 4);
+
+  for (auto f_simplex : st.filtration_simplex_range()) {
+    std::cout << "dimension(" << st.dimension(f_simplex) << ") - f = " << st.filtration(f_simplex) << std::endl;
+    switch (st.dimension(f_simplex)) {
+      case 0:
+        BOOST_CHECK(are_almost_the_same(st.filtration(f_simplex), 0.0));
+        break;
+      case 1:
+      case 2:
+      case 3:
+        BOOST_CHECK(are_almost_the_same(st.filtration(f_simplex), 2.0));
+        break;
+      default:
+        BOOST_CHECK(false);  // Shall not happen
+        break;
+    }
+  }
+}
+
+BOOST_AUTO_TEST_CASE(Rips_doc_csv_file) {
+  // ----------------------------------------------------------------------------
+  //
+  // Init of a Rips complex from a OFF file
+  //
+  // ----------------------------------------------------------------------------
+  std::string csv_file_name("full_square_distance_matrix.csv");
+  double rips_threshold = 12.0;
+  std::cout << "========== CSV FILE NAME = " << csv_file_name << " - Rips threshold=" <<
+      rips_threshold << "==========" << std::endl;
+
+  Distance_matrix distances = read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_file_name);
+  Rips_complex rips_complex_from_file(distances, rips_threshold);
+
+  const int DIMENSION_1 = 1;
+  Simplex_tree st;
+  rips_complex_from_file.create_complex(st, DIMENSION_1);
+  std::cout << "st.dimension()=" << st.dimension() << std::endl;
+  BOOST_CHECK(st.dimension() == DIMENSION_1);
+
+  const int NUMBER_OF_VERTICES = 7;
+  std::cout << "st.num_vertices()=" << st.num_vertices() << std::endl;
+  BOOST_CHECK(st.num_vertices() == NUMBER_OF_VERTICES);
+
+  std::cout << "st.num_simplices()=" << st.num_simplices() << std::endl;
+  BOOST_CHECK(st.num_simplices() == 18);
+
+  // Check filtration values of vertices is 0.0
+  for (auto f_simplex : st.skeleton_simplex_range(0)) {
+    BOOST_CHECK(st.filtration(f_simplex) == 0.0);
+  }
+
+  // Check filtration values of edges
+  for (auto f_simplex : st.skeleton_simplex_range(DIMENSION_1)) {
+    if (DIMENSION_1 == st.dimension(f_simplex)) {
+      std::vector<Simplex_tree::Vertex_handle> vvh;
+      std::cout << "vertex = (";
+      for (auto vertex : st.simplex_vertex_range(f_simplex)) {
+        std::cout << vertex << ",";
+        vvh.push_back(vertex);
+      }
+      std::cout << ") - filtration =" << st.filtration(f_simplex) << std::endl;
+      BOOST_CHECK(vvh.size() == 2);
+      BOOST_CHECK(are_almost_the_same(st.filtration(f_simplex), distances[vvh.at(0)][vvh.at(1)]));
+    }
+  }
+
+  const int DIMENSION_2 = 2;
+  Simplex_tree st2;
+  rips_complex_from_file.create_complex(st2, DIMENSION_2);
+  std::cout << "st2.dimension()=" << st2.dimension() << std::endl;
+  BOOST_CHECK(st2.dimension() == DIMENSION_2);
+  
+  std::cout << "st2.num_vertices()=" << st2.num_vertices() << std::endl;
+  BOOST_CHECK(st2.num_vertices() == NUMBER_OF_VERTICES);
+
+  std::cout << "st2.num_simplices()=" << st2.num_simplices() << std::endl;
+  BOOST_CHECK(st2.num_simplices() == 23);
+
+  Simplex_tree::Filtration_value f01 = st2.filtration(st2.find({0, 1}));
+  Simplex_tree::Filtration_value f02 = st2.filtration(st2.find({0, 2}));
+  Simplex_tree::Filtration_value f12 = st2.filtration(st2.find({1, 2}));
+  Simplex_tree::Filtration_value f012 = st2.filtration(st2.find({0, 1, 2}));
+  std::cout << "f012= " << f012 << " | f01= " << f01 << " - f02= " << f02 << " - f12= " << f12 << std::endl;
+  BOOST_CHECK(are_almost_the_same(f012, std::max(f01, std::max(f02,f12))));
+  
+  Simplex_tree::Filtration_value f45 = st2.filtration(st2.find({4, 5}));
+  Simplex_tree::Filtration_value f56 = st2.filtration(st2.find({5, 6}));
+  Simplex_tree::Filtration_value f46 = st2.filtration(st2.find({4, 6}));
+  Simplex_tree::Filtration_value f456 = st2.filtration(st2.find({4, 5, 6}));
+  std::cout << "f456= " << f456 << " | f45= " << f45 << " - f56= " << f56 << " - f46= " << f46 << std::endl;
+  BOOST_CHECK(are_almost_the_same(f456, std::max(f45, std::max(f56,f46))));
+
+  const int DIMENSION_3 = 3;
+  Simplex_tree st3;
+  rips_complex_from_file.create_complex(st3, DIMENSION_3);
+  std::cout << "st3.dimension()=" << st3.dimension() << std::endl;
+  BOOST_CHECK(st3.dimension() == DIMENSION_3);
+  
+  std::cout << "st3.num_vertices()=" << st3.num_vertices() << std::endl;
+  BOOST_CHECK(st3.num_vertices() == NUMBER_OF_VERTICES);
+
+  std::cout << "st3.num_simplices()=" << st3.num_simplices() << std::endl;
+  BOOST_CHECK(st3.num_simplices() == 24);
+
+  Simplex_tree::Filtration_value f123 = st3.filtration(st3.find({1, 2, 3}));
+  Simplex_tree::Filtration_value f013 = st3.filtration(st3.find({0, 1, 3}));
+  Simplex_tree::Filtration_value f023 = st3.filtration(st3.find({0, 2, 3}));
+  Simplex_tree::Filtration_value f0123 = st3.filtration(st3.find({0, 1, 2, 3}));
+  std::cout << "f0123= " << f0123 << " | f012= " << f012 << " - f123= " << f123 << " - f013= " << f013 <<
+      " - f023= " << f023 << std::endl;
+  BOOST_CHECK(are_almost_the_same(f0123, std::max(f012, std::max(f123, std::max(f013, f023)))));
+
+}
+
+#ifdef GUDHI_DEBUG
+BOOST_AUTO_TEST_CASE(Rips_create_complex_throw) {
+  // ----------------------------------------------------------------------------
+  //
+  // Init of a Rips complex from a OFF file
+  //
+  // ----------------------------------------------------------------------------
+  std::string off_file_name("alphacomplexdoc.off");
+  double rips_threshold = 12.0;
+  std::cout << "========== OFF FILE NAME = " << off_file_name << " - Rips threshold=" <<
+      rips_threshold << "==========" << std::endl;
+
+  Gudhi::Points_off_reader<Point> off_reader(off_file_name);
+  Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), rips_threshold, Euclidean_distance());
+
+  Simplex_tree stree;
+  std::vector<int> simplex = {0, 1, 2};
+  stree.insert_simplex_and_subfaces(simplex);
+  std::cout << "Check exception throw in debug mode" << std::endl;
+  // throw excpt because stree is not empty
+  BOOST_CHECK_THROW (rips_complex_from_file.create_complex(stree, 1), std::invalid_argument);
+}
+#endif
diff --git a/src/Simplex_tree/example/simple_simplex_tree.cpp b/src/Simplex_tree/example/simple_simplex_tree.cpp
index 5146b906..60f9a35e 100644
--- a/src/Simplex_tree/example/simple_simplex_tree.cpp
+++ b/src/Simplex_tree/example/simple_simplex_tree.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
+ *    Copyright (C) 2014
  *
  *    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
@@ -27,10 +27,11 @@
 #include <utility>  // for pair
 #include <vector>
 
-using namespace Gudhi;
-
-typedef std::vector< Vertex_handle > typeVectorVertex;
-typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool;
+using Simplex_tree = Gudhi::Simplex_tree<>;
+using Vertex_handle = Simplex_tree::Vertex_handle;
+using Filtration_value = Simplex_tree::Filtration_value;
+using typeVectorVertex = std::vector< Vertex_handle >;
+using typePairSimplexBool = std::pair< Simplex_tree::Simplex_handle, bool >;
 
 int main(int argc, char * const argv[]) {
   const Filtration_value FIRST_FILTRATION_VALUE = 0.1;
@@ -42,7 +43,7 @@ int main(int argc, char * const argv[]) {
   std::cout << "********************************************************************" << std::endl;
   std::cout << "EXAMPLE OF SIMPLE INSERTION" << std::endl;
   // Construct the Simplex Tree
-  Simplex_tree<> simplexTree;
+  Simplex_tree simplexTree;
 
   /* Simplex to be inserted:  */
   /*    1                     */
@@ -212,7 +213,7 @@ int main(int argc, char * const argv[]) {
   // ------------------------------------------------------------------------------------------------------------------
   // Find in the simplex_tree
   // ------------------------------------------------------------------------------------------------------------------
-  Simplex_tree<>::Simplex_handle simplexFound = simplexTree.find(secondSimplexVector);
+  Simplex_tree::Simplex_handle simplexFound = simplexTree.find(secondSimplexVector);
   std::cout << "**************IS THE SIMPLEX {1} IN THE SIMPLEX TREE ?\n";
   if (simplexFound != simplexTree.null_simplex())
     std::cout << "***+ YES IT IS!\n";
diff --git a/src/Simplex_tree/example/simplex_tree_from_cliques_of_graph.cpp b/src/Simplex_tree/example/simplex_tree_from_cliques_of_graph.cpp
index 58085014..d1b8b2de 100644
--- a/src/Simplex_tree/example/simplex_tree_from_cliques_of_graph.cpp
+++ b/src/Simplex_tree/example/simplex_tree_from_cliques_of_graph.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Clément Maria
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
+ *    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
@@ -26,9 +26,16 @@
 #include <iostream>
 #include <ctime>
 #include <string>
+#include <utility>  // for std::pair
 
 using namespace Gudhi;
 
+typedef int Vertex_handle;
+typedef double Filtration_value;
+typedef boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS,
+                                boost::property < vertex_filtration_t, Filtration_value >,
+                                boost::property < edge_filtration_t, Filtration_value > > Graph_t;
+
 int main(int argc, char * const argv[]) {
   if (argc != 3) {
     std::cerr << "Usage: " << argv[0]
@@ -43,7 +50,7 @@ int main(int argc, char * const argv[]) {
   Simplex_tree<> st;
 
   start = clock();
-  auto g = read_graph(filegraph);
+  auto g = read_graph<Graph_t, Filtration_value, Vertex_handle>(filegraph);
   // insert the graph in the simplex tree as 1-skeleton
   st.insert_graph(g);
   end = clock();
diff --git a/src/Simplex_tree/test/simplex_tree_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
index 28bf202b..b06d7ec9 100644
--- a/src/Simplex_tree/test/simplex_tree_unit_test.cpp
+++ b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
@@ -1,4 +1,5 @@
 #include <iostream>
+#include <fstream>
 #include <string>
 #include <algorithm>
 #include <utility> // std::pair, std::make_pair
@@ -19,19 +20,19 @@ using namespace Gudhi;
 
 typedef boost::mpl::list<Simplex_tree<>, Simplex_tree<Simplex_tree_options_fast_persistence>> list_of_tested_variants;
 
-const Vertex_handle DEFAULT_VERTEX_HANDLE = (const Vertex_handle) - 1;
-const Filtration_value DEFAULT_FILTRATION_VALUE = (const Filtration_value) 0.0;
 
 template<class typeST>
 void test_empty_simplex_tree(typeST& tst) {
-  BOOST_CHECK(tst.null_vertex() == DEFAULT_VERTEX_HANDLE);
-  BOOST_CHECK(tst.filtration() == DEFAULT_FILTRATION_VALUE);
+  typedef typename typeST::Vertex_handle Vertex_handle;
+  const Vertex_handle DEFAULT_VERTEX_VALUE = Vertex_handle(- 1);
+  BOOST_CHECK(tst.null_vertex() == DEFAULT_VERTEX_VALUE);
+  BOOST_CHECK(tst.filtration() == 0.0);
   BOOST_CHECK(tst.num_vertices() == (size_t) 0);
   BOOST_CHECK(tst.num_simplices() == (size_t) 0);
   typename typeST::Siblings* STRoot = tst.root();
   BOOST_CHECK(STRoot != nullptr);
   BOOST_CHECK(STRoot->oncles() == nullptr);
-  BOOST_CHECK(STRoot->parent() == DEFAULT_VERTEX_HANDLE);
+  BOOST_CHECK(STRoot->parent() == DEFAULT_VERTEX_VALUE);
   BOOST_CHECK(tst.dimension() == -1);
 }
 
@@ -59,7 +60,7 @@ void test_iterators_on_empty_simplex_tree(typeST& tst) {
 
 BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_when_empty, typeST, list_of_tested_variants) {
   typedef std::pair<typename typeST::Simplex_handle, bool> typePairSimplexBool;
-  typedef std::vector<Vertex_handle> typeVectorVertex;
+  typedef std::vector<typename typeST::Vertex_handle> typeVectorVertex;
 
   std::cout << "********************************************************************" << std::endl;
   std::cout << "TEST OF DEFAULT CONSTRUCTOR" << std::endl;
@@ -72,8 +73,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_when_empty, typeST, list_of_tested_va
   std::cout << "TEST OF EMPTY INSERTION" << std::endl;
   typeVectorVertex simplexVectorEmpty;
   BOOST_CHECK(simplexVectorEmpty.empty() == true);
-  typePairSimplexBool returnEmptyValue = st.insert_simplex(simplexVectorEmpty,
-                                                           DEFAULT_FILTRATION_VALUE);
+  typePairSimplexBool returnEmptyValue = st.insert_simplex(simplexVectorEmpty, 0.0);
   BOOST_CHECK(returnEmptyValue.first == typename typeST::Simplex_handle(nullptr));
   BOOST_CHECK(returnEmptyValue.second == true);
 
@@ -141,12 +141,13 @@ void test_simplex_tree_contains(typeST& simplexTree, typeSimplex& simplex, int p
 template<class typeST, class typePairSimplexBool>
 void test_simplex_tree_insert_returns_true(const typePairSimplexBool& returnValue) {
   BOOST_CHECK(returnValue.second == true);
-  typename typeST::Simplex_handle shReturned = returnValue.first; // Simplex_handle = boost::container::flat_map< Vertex_handle, Node >::iterator
+  // Simplex_handle = boost::container::flat_map< typeST::Vertex_handle, Node >::iterator
+  typename typeST::Simplex_handle shReturned = returnValue.first;
   BOOST_CHECK(shReturned != typename typeST::Simplex_handle(nullptr));
 }
 
 // Global variables
-Filtration_value max_fil = DEFAULT_FILTRATION_VALUE;
+double max_fil = 0.0;
 int dim_max = -1;
 
 template<class typeST, class Filtration_value>
@@ -179,8 +180,9 @@ void set_and_test_simplex_tree_dim_fil(typeST& simplexTree, int vectorSize, cons
 }
 
 BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_insertion, typeST, list_of_tested_variants) {
+  typedef typename typeST::Filtration_value Filtration_value;
   typedef std::pair<typename typeST::Simplex_handle, bool> typePairSimplexBool;
-  typedef std::vector<Vertex_handle> typeVectorVertex;
+  typedef std::vector<typename typeST::Vertex_handle> typeVectorVertex;
   typedef std::pair<typeVectorVertex, Filtration_value> typeSimplex;
   const Filtration_value FIRST_FILTRATION_VALUE = 0.1;
   const Filtration_value SECOND_FILTRATION_VALUE = 0.2;
@@ -188,7 +190,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_insertion, typeST, list_of_tested_var
   const Filtration_value FOURTH_FILTRATION_VALUE = 0.4;
   // reset since we run the test several times
   dim_max = -1;
-  max_fil = DEFAULT_FILTRATION_VALUE;
+  max_fil = 0.0;
 
   // TEST OF INSERTION
   std::cout << "********************************************************************" << std::endl;
@@ -303,7 +305,8 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_insertion, typeST, list_of_tested_var
   returnValue = st.insert_simplex(tenthSimplex.first, tenthSimplex.second);
 
   BOOST_CHECK(returnValue.second == false);
-  typename typeST::Simplex_handle shReturned = returnValue.first; // Simplex_handle = boost::container::flat_map< Vertex_handle, Node >::iterator
+  // Simplex_handle = boost::container::flat_map< typeST::Vertex_handle, Node >::iterator
+  typename typeST::Simplex_handle shReturned = returnValue.first;
   BOOST_CHECK(shReturned == typename typeST::Simplex_handle(nullptr));
   BOOST_CHECK(st.num_vertices() == (size_t) 4); // Not incremented !!
   BOOST_CHECK(st.dimension() == dim_max);
@@ -317,7 +320,8 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_insertion, typeST, list_of_tested_var
   returnValue = st.insert_simplex(eleventhSimplex.first, eleventhSimplex.second);
 
   BOOST_CHECK(returnValue.second == false);
-  shReturned = returnValue.first; // Simplex_handle = boost::container::flat_map< Vertex_handle, Node >::iterator
+  // Simplex_handle = boost::container::flat_map< typeST::Vertex_handle, Node >::iterator
+  shReturned = returnValue.first;
   BOOST_CHECK(shReturned == typename typeST::Simplex_handle(nullptr));
   BOOST_CHECK(st.num_vertices() == (size_t) 4); // Not incremented !!
   BOOST_CHECK(st.dimension() == dim_max);
@@ -375,8 +379,8 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_insertion, typeST, list_of_tested_var
 
 BOOST_AUTO_TEST_CASE_TEMPLATE(NSimplexAndSubfaces_tree_insertion, typeST, list_of_tested_variants) {
   typedef std::pair<typename typeST::Simplex_handle, bool> typePairSimplexBool;
-  typedef std::vector<Vertex_handle> typeVectorVertex;
-  typedef std::pair<typeVectorVertex, Filtration_value> typeSimplex;
+  typedef std::vector<typename typeST::Vertex_handle> typeVectorVertex;
+  typedef std::pair<typeVectorVertex, typename typeST::Filtration_value> typeSimplex;
   std::cout << "********************************************************************" << std::endl;
   std::cout << "TEST OF RECURSIVE INSERTION" << std::endl;
   typeST st;
@@ -394,7 +398,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(NSimplexAndSubfaces_tree_insertion, typeST, list_o
   // Check it is well inserted
   BOOST_CHECK(true == returnValue.second);
   position = 0;
-  std::sort(SimplexVector1.begin(), SimplexVector1.end(), std::greater<Vertex_handle>());
+  std::sort(SimplexVector1.begin(), SimplexVector1.end(), std::greater<typename typeST::Vertex_handle>());
   for (auto vertex : st.simplex_vertex_range(returnValue.first)) {
     // Check returned Simplex_handle
     std::cout << "vertex = " << vertex << " | vector[" << position << "] = " << SimplexVector1[position] << std::endl;
@@ -413,7 +417,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(NSimplexAndSubfaces_tree_insertion, typeST, list_o
   // Check it is well inserted
   BOOST_CHECK(true == returnValue.second);
   position = 0;
-  std::sort(SimplexVector2.begin(), SimplexVector2.end(), std::greater<Vertex_handle>());
+  std::sort(SimplexVector2.begin(), SimplexVector2.end(), std::greater<typename typeST::Vertex_handle>());
   for (auto vertex : st.simplex_vertex_range(returnValue.first)) {
     // Check returned Simplex_handle
     std::cout << "vertex = " << vertex << " | vector[" << position << "] = " << SimplexVector2[position] << std::endl;
@@ -432,7 +436,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(NSimplexAndSubfaces_tree_insertion, typeST, list_o
   // Check it is well inserted
   BOOST_CHECK(true == returnValue.second);
   position = 0;
-  std::sort(SimplexVector3.begin(), SimplexVector3.end(), std::greater<Vertex_handle>());
+  std::sort(SimplexVector3.begin(), SimplexVector3.end(), std::greater<typename typeST::Vertex_handle>());
   for (auto vertex : st.simplex_vertex_range(returnValue.first)) {
     // Check returned Simplex_handle
     std::cout << "vertex = " << vertex << " | vector[" << position << "] = " << SimplexVector3[position] << std::endl;
@@ -462,7 +466,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(NSimplexAndSubfaces_tree_insertion, typeST, list_o
   // Check it is well inserted
   BOOST_CHECK(true == returnValue.second);
   position = 0;
-  std::sort(SimplexVector5.begin(), SimplexVector5.end(), std::greater<Vertex_handle>());
+  std::sort(SimplexVector5.begin(), SimplexVector5.end(), std::greater<typename typeST::Vertex_handle>());
   for (auto vertex : st.simplex_vertex_range(returnValue.first)) {
     // Check returned Simplex_handle
     std::cout << "vertex = " << vertex << " | vector[" << position << "] = " << SimplexVector5[position] << std::endl;
@@ -481,7 +485,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(NSimplexAndSubfaces_tree_insertion, typeST, list_o
   // Check it is well inserted
   BOOST_CHECK(true == returnValue.second);
   position = 0;
-  std::sort(SimplexVector6.begin(), SimplexVector6.end(), std::greater<Vertex_handle>());
+  std::sort(SimplexVector6.begin(), SimplexVector6.end(), std::greater<typename typeST::Vertex_handle>());
   for (auto vertex : st.simplex_vertex_range(returnValue.first)) {
     // Check returned Simplex_handle
     std::cout << "vertex = " << vertex << " | vector[" << position << "] = " << SimplexVector6[position] << std::endl;
@@ -504,12 +508,12 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(NSimplexAndSubfaces_tree_insertion, typeST, list_o
   /*   A facet [3,4,5]        */
   /*   A cell  [0,1,6,7]      */
 
-  typeSimplex simplexPair1 = std::make_pair(SimplexVector1, DEFAULT_FILTRATION_VALUE);
-  typeSimplex simplexPair2 = std::make_pair(SimplexVector2, DEFAULT_FILTRATION_VALUE);
-  typeSimplex simplexPair3 = std::make_pair(SimplexVector3, DEFAULT_FILTRATION_VALUE);
-  typeSimplex simplexPair4 = std::make_pair(SimplexVector4, DEFAULT_FILTRATION_VALUE);
-  typeSimplex simplexPair5 = std::make_pair(SimplexVector5, DEFAULT_FILTRATION_VALUE);
-  typeSimplex simplexPair6 = std::make_pair(SimplexVector6, DEFAULT_FILTRATION_VALUE);
+  typeSimplex simplexPair1 = std::make_pair(SimplexVector1, 0.0);
+  typeSimplex simplexPair2 = std::make_pair(SimplexVector2, 0.0);
+  typeSimplex simplexPair3 = std::make_pair(SimplexVector3, 0.0);
+  typeSimplex simplexPair4 = std::make_pair(SimplexVector4, 0.0);
+  typeSimplex simplexPair5 = std::make_pair(SimplexVector5, 0.0);
+  typeSimplex simplexPair6 = std::make_pair(SimplexVector6, 0.0);
   test_simplex_tree_contains(st, simplexPair1, 6); // (2,1,0) is in position 6
   test_simplex_tree_contains(st, simplexPair2, 7); // (3) is in position 7
   test_simplex_tree_contains(st, simplexPair3, 8); // (3,0) is in position 8
@@ -600,7 +604,7 @@ void test_cofaces(typeST& st, const std::vector<Vertex_handle>& expected, int di
 }
 
 BOOST_AUTO_TEST_CASE_TEMPLATE(coface_on_simplex_tree, typeST, list_of_tested_variants) {
-  typedef std::vector<Vertex_handle> typeVectorVertex;
+  typedef std::vector<typename typeST::Vertex_handle> typeVectorVertex;
   std::cout << "********************************************************************" << std::endl;
   std::cout << "TEST COFACE ALGORITHM" << std::endl;
   typeST st;
@@ -629,7 +633,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(coface_on_simplex_tree, typeST, list_of_tested_var
   // FIXME
   st.set_dimension(3);
 
-  std::vector<Vertex_handle> simplex_result;
+  std::vector<typename typeST::Vertex_handle> simplex_result;
   std::vector<typename typeST::Simplex_handle> result;
   std::cout << "First test - Star of (3):" << std::endl;
 
@@ -649,7 +653,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(coface_on_simplex_tree, typeST, list_of_tested_var
   result.push_back(st.find(simplex_result));
   simplex_result.clear();
 
-  std::vector<Vertex_handle> vertex = {3};
+  std::vector<typename typeST::Vertex_handle> vertex = {3};
   test_cofaces(st, vertex, 0, result);
   vertex.clear();
   result.clear();
@@ -699,7 +703,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(coface_on_simplex_tree, typeST, list_of_tested_var
 }
 
 BOOST_AUTO_TEST_CASE_TEMPLATE(copy_move_on_simplex_tree, typeST, list_of_tested_variants) {
-  typedef std::vector<Vertex_handle> typeVectorVertex;
+  typedef std::vector<typename typeST::Vertex_handle> typeVectorVertex;
   std::cout << "********************************************************************" << std::endl;
   std::cout << "TEST COPY MOVE CONSTRUCTORS" << std::endl;
   typeST st;
@@ -771,12 +775,11 @@ void test_simplex_is_vertex(typeST& st, typename typeST::Simplex_handle sh, type
 
 BOOST_AUTO_TEST_CASE(non_contiguous) {
   typedef Simplex_tree<> typeST;
-  typedef typeST::Vertex_handle Vertex_handle;
   typedef typeST::Simplex_handle Simplex_handle;
   std::cout << "********************************************************************" << std::endl;
   std::cout << "TEST NON-CONTIGUOUS VERTICES" << std::endl;
   typeST st;
-  Vertex_handle e[] = {3,-7};
+  typeST::Vertex_handle e[] = {3,-7};
   std::cout << "Insert" << std::endl;
   st.insert_simplex_and_subfaces(e);
   BOOST_CHECK(st.num_vertices() == 2);
diff --git a/src/Witness_complex/example/example_strong_witness_complex_off.cpp b/src/Witness_complex/example/example_strong_witness_complex_off.cpp
index 61b8bc4a..c9a3b543 100644
--- a/src/Witness_complex/example/example_strong_witness_complex_off.cpp
+++ b/src/Witness_complex/example/example_strong_witness_complex_off.cpp
@@ -17,7 +17,7 @@
 typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K;
 typedef typename K::Point_d Point_d;
 typedef typename Gudhi::witness_complex::Euclidean_strong_witness_complex<K> Witness_complex;
-typedef std::vector< Vertex_handle > typeVectorVertex;
+typedef std::vector< typename Gudhi::Simplex_tree<>::Vertex_handle > typeVectorVertex;
 typedef std::vector< Point_d > Point_vector;
 
 int main(int argc, char * const argv[]) {
diff --git a/src/Witness_complex/example/example_witness_complex_off.cpp b/src/Witness_complex/example/example_witness_complex_off.cpp
index 751d2d4c..38c6bedc 100644
--- a/src/Witness_complex/example/example_witness_complex_off.cpp
+++ b/src/Witness_complex/example/example_witness_complex_off.cpp
@@ -17,7 +17,7 @@
 typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K;
 typedef typename K::Point_d Point_d;
 typedef typename Gudhi::witness_complex::Euclidean_witness_complex<K> Witness_complex;
-typedef std::vector< Vertex_handle > typeVectorVertex;
+typedef std::vector< typename Gudhi::Simplex_tree<>::Vertex_handle > typeVectorVertex;
 typedef std::vector< Point_d > Point_vector;
 
 int main(int argc, char * const argv[]) {
diff --git a/src/Witness_complex/test/test_simple_witness_complex.cpp b/src/Witness_complex/test/test_simple_witness_complex.cpp
index b47ebe4d..bb1df72d 100644
--- a/src/Witness_complex/test/test_simple_witness_complex.cpp
+++ b/src/Witness_complex/test/test_simple_witness_complex.cpp
@@ -19,6 +19,7 @@
 #include <vector>
 
 typedef Gudhi::Simplex_tree<> Simplex_tree;
+typedef typename Simplex_tree::Vertex_handle Vertex_handle;
 typedef std::vector< Vertex_handle > typeVectorVertex;
 typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> Kernel;
 typedef typename Kernel::FT FT;
diff --git a/src/cmake/modules/FindQGLViewer.cmake b/src/cmake/modules/FindQGLViewer.cmake
index 1f3dbc1f..56c1b3cf 100644
--- a/src/cmake/modules/FindQGLViewer.cmake
+++ b/src/cmake/modules/FindQGLViewer.cmake
@@ -15,7 +15,7 @@ find_path(QGLVIEWER_INCLUDE_DIR
          )
 
 find_library(QGLVIEWER_LIBRARY_RELEASE 
-             NAMES qglviewer-qt4 QGLViewer-qt4 qglviewer QGLViewer QGLViewer2
+             NAMES qglviewer-qt5 QGLViewer-qt5 qglviewer QGLViewer QGLViewer2
              PATHS /usr/lib
                    /usr/local/lib
                    ENV QGLVIEWERROOT
diff --git a/src/cmake/modules/GUDHI_user_version_target.txt b/src/cmake/modules/GUDHI_user_version_target.txt
index c91d5659..6332b065 100644
--- a/src/cmake/modules/GUDHI_user_version_target.txt
+++ b/src/cmake/modules/GUDHI_user_version_target.txt
@@ -48,7 +48,7 @@ if (NOT CMAKE_VERSION VERSION_LESS 2.8.11)
   add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
                      copy_directory ${CMAKE_SOURCE_DIR}/src/GudhUI ${GUDHI_USER_VERSION_DIR}/GudhUI)
   
-  set(GUDHI_MODULES "common;Alpha_complex;Bitmap_cubical_complex;Bottleneck_distance;Contraction;Hasse_complex;Persistent_cohomology;Simplex_tree;Skeleton_blocker;Spatial_searching;Subsampling;Tangential_complex;Witness_complex")
+  set(GUDHI_MODULES "common;Alpha_complex;Bitmap_cubical_complex;Bottleneck_distance;Contraction;Hasse_complex;Persistent_cohomology;Rips_complex;Simplex_tree;Skeleton_blocker;Spatial_searching;Subsampling;Tangential_complex;Witness_complex")
   
   foreach(GUDHI_MODULE ${GUDHI_MODULES})
     # doc files
@@ -81,21 +81,21 @@ if (NOT CMAKE_VERSION VERSION_LESS 2.8.11)
       endif()
     endforeach()
   
-    # include files and patches
-    file(GLOB GUDHI_INCLUDE_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/include/*)
+    # include files
+    file(GLOB GUDHI_INCLUDE_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/include/gudhi/*)
   
     foreach(GUDHI_INCLUDE_FILE ${GUDHI_INCLUDE_FILES})
       get_filename_component(GUDHI_INCLUDE_FILE_NAME ${GUDHI_INCLUDE_FILE} NAME)
       # GUDHI_INCLUDE_FILE can be a file or a directory
       if(IS_DIRECTORY ${GUDHI_INCLUDE_FILE})
         add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                           copy_directory ${GUDHI_INCLUDE_FILE} ${GUDHI_USER_VERSION_DIR}/include/${GUDHI_INCLUDE_FILE_NAME})
+                           copy_directory ${GUDHI_INCLUDE_FILE} ${GUDHI_USER_VERSION_DIR}/include/gudhi/${GUDHI_INCLUDE_FILE_NAME})
       else()
         add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                           copy ${GUDHI_INCLUDE_FILE} ${GUDHI_USER_VERSION_DIR}/include/${GUDHI_INCLUDE_FILE_NAME})
+                           copy ${GUDHI_INCLUDE_FILE} ${GUDHI_USER_VERSION_DIR}/include/gudhi/${GUDHI_INCLUDE_FILE_NAME})
       endif()
     endforeach()
-
+  
     # concept files
     file(GLOB GUDHI_CONCEPT_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/concept/*.h)
   
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index 5fb75002..116aba09 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -56,6 +56,24 @@
     <b>User manual:</b> \ref cubical_complex - <b>Reference manual:</b> Gudhi::cubical_complex::Bitmap_cubical_complex
     </td>
  </tr>
+ \subsection RipsComplexDataStructure Rips complex
+ \image html "rips_complex_representation.png" "Rips complex representation"
+<table border="0">
+  <tr>
+    <td width="25%">
+      <b>Author:</b> Cl&eacute;ment Maria, Pawel Dlotko, Vincent Rouvreau<br>
+      <b>Introduced in:</b> GUDHI 1.4.0<br>
+      <b>Copyright:</b> GPL v3<br>
+    </td>
+    <td width="75%">
+    Rips_complex is a simplicial complex constructed from a one skeleton graph.<br>
+    The filtration value of each edge is computed from a user-given distance function and is inserted until a
+    user-given threshold value.<br>
+    This complex can be built from a point cloud and a distance function, or from a distance matrix.<br>
+    <b>User manual:</b> \ref rips_complex - <b>Reference manual:</b> Gudhi::rips_complex::Rips_complex
+    </td>
+ </tr>
+</table>
 </table>
  \subsection SimplexTreeDataStructure Simplex tree
  \image html "Simplex_tree_representation.png" "Simplex tree representation"
@@ -223,8 +241,6 @@ make \endverbatim
  * 
  * The following example requires the <a target="_blank" href="http://gmplib.org/">GNU Multiple Precision Arithmetic
  * Library</a> (GMP) and will not be built if GMP is not installed:
- * \li <a href="_persistent_cohomology_2performance_rips_persistence_8cpp-example.html">
- * Persistent_cohomology/performance_rips_persistence.cpp</a>
  * \li <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html">
  * Persistent_cohomology/rips_multifield_persistence.cpp</a>
  *
@@ -261,9 +277,11 @@ make \endverbatim
  * Persistent_cohomology/custom_persistence_sort.cpp</a>
  * 
  * The following example requires CGAL version &ge; 4.8.0:
- * \li <a href="_bottleneck_distance_2_bottleneck_example_8cpp-example.html">
- * 
- * Bottleneck_distance/bottleneck_example.cpp</a>
+ * \li <a href="_bottleneck_distance_2_bottleneck_basic_example_8cpp-example.html">
+ * Bottleneck_distance/bottleneck_basic_example.cpp</a>
+ * \li <a href="_bottleneck_distance_2_bottleneck_read_file_example_8cpp-example.html">
+ * Bottleneck_distance/bottleneck_read_file_example.cpp</a>
+ *
  * \subsection eigen3 Eigen3
  * The \ref alpha_complex data structure and few examples requires
  * <a target="_blank" href="http://eigen.tuxfamily.org/">Eigen3</a> is a C++ template library for linear algebra:
@@ -275,8 +293,6 @@ make \endverbatim
  * Alpha_complex/Alpha_complex_from_off.cpp</a>
  * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html">
  * Alpha_complex/Alpha_complex_from_points.cpp</a>
- * \li <a href="_bottleneck_distance_2_bottleneck_example_8cpp-example.html">
- * Bottleneck_distance/bottleneck_example.cpp</a>
  * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html">
  * Persistent_cohomology/alpha_complex_persistence.cpp</a>
  * \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html">
@@ -318,22 +334,28 @@ make \endverbatim
  * Persistent_cohomology/alpha_complex_persistence.cpp</a>
  * \li <a href="_persistent_cohomology_2rips_persistence_via_boundary_matrix_8cpp-example.html">
  * Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp</a>
- * \li <a href="_persistent_cohomology_2performance_rips_persistence_8cpp-example.html">
- * Persistent_cohomology/performance_rips_persistence.cpp</a>
  * \li <a href="_persistent_cohomology_2persistence_from_file_8cpp-example.html">
  * Persistent_cohomology/persistence_from_file.cpp</a>
  * \li <a href="_persistent_cohomology_2persistence_from_simple_simplex_tree_8cpp-example.html">
  * Persistent_cohomology/persistence_from_simple_simplex_tree.cpp</a>
  * \li <a href="_persistent_cohomology_2plain_homology_8cpp-example.html">
  * Persistent_cohomology/plain_homology.cpp</a>
+ * \li <a href="_persistent_cohomology_2rips_distance_matrix_persistence_8cpp-example.html">
+ * Persistent_cohomology/rips_distance_matrix_persistence.cpp</a>
  * \li <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html">
  * Persistent_cohomology/rips_multifield_persistence.cpp</a>
  * \li <a href="_persistent_cohomology_2rips_persistence_8cpp-example.html">
  * Persistent_cohomology/rips_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2rips_persistence_step_by_step_8cpp-example.html">
+ * Persistent_cohomology/rips_persistence_step_by_step.cpp</a>
  * \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html">
  * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a>
  * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html">
  * Persistent_cohomology/custom_persistence_sort.cpp</a>
+ * \li <a href="_rips_complex_2example_one_skeleton_rips_from_points_8cpp-example.html">
+ * Rips_complex/example_one_skeleton_rips_from_points.cpp</a>
+ * \li <a href="_rips_complex_2example_rips_complex_from_off_file_8cpp-example.html">
+ * Rips_complex/example_rips_complex_from_off_file.cpp</a>
  * 
  * \section Contributions Bug reports and contributions
  * Please help us improving the quality of the GUDHI library. You may report bugs or suggestions to:
@@ -358,7 +380,8 @@ make \endverbatim
 /*! @file Examples
  * @example Alpha_complex/Alpha_complex_from_off.cpp
  * @example Alpha_complex/Alpha_complex_from_points.cpp
- * @example Bottleneck_distance/bottleneck_example.cpp
+ * @example Bottleneck_distance/bottleneck_basic_example.cpp
+ * @example Bottleneck_distance/bottleneck_read_file_example.cpp
  * @example Bitmap_cubical_complex/Bitmap_cubical_complex.cpp
  * @example Bitmap_cubical_complex/Bitmap_cubical_complex_periodic_boundary_conditions.cpp
  * @example Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp
@@ -369,14 +392,17 @@ make \endverbatim
  * @example Persistent_cohomology/alpha_complex_3d_persistence.cpp
  * @example Persistent_cohomology/alpha_complex_persistence.cpp
  * @example Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp
- * @example Persistent_cohomology/performance_rips_persistence.cpp
  * @example Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp
  * @example Persistent_cohomology/persistence_from_file.cpp
  * @example Persistent_cohomology/persistence_from_simple_simplex_tree.cpp
  * @example Persistent_cohomology/plain_homology.cpp
  * @example Persistent_cohomology/rips_multifield_persistence.cpp
+ * @example Persistent_cohomology/rips_distance_matrix_persistence.cpp
  * @example Persistent_cohomology/rips_persistence.cpp
  * @example Persistent_cohomology/custom_persistence_sort.cpp
+ * @example Persistent_cohomology/rips_persistence_step_by_step.cpp
+ * @example Rips_complex/example_one_skeleton_rips_from_points.cpp
+ * @example Rips_complex/example_rips_complex_from_off_file.cpp
  * @example Simplex_tree/mini_simplex_tree.cpp
  * @example Simplex_tree/simple_simplex_tree.cpp
  * @example Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp
diff --git a/src/common/example/example_CGAL_3D_points_off_reader.cpp b/src/common/example/example_CGAL_3D_points_off_reader.cpp
index d48bb17d..665b7a29 100644
--- a/src/common/example/example_CGAL_3D_points_off_reader.cpp
+++ b/src/common/example/example_CGAL_3D_points_off_reader.cpp
@@ -32,7 +32,7 @@ int main(int argc, char **argv) {
   // Retrieve the triangulation
   std::vector<Point_3> point_cloud = off_reader.get_point_cloud();
 
-  int n {0};
+  int n {};
   for (auto point : point_cloud) {
     ++n;
     std::cout << "Point[" << n << "] = (" << point[0] << ", " << point[1] << ", " << point[2] << ")\n";
diff --git a/src/common/example/example_CGAL_points_off_reader.cpp b/src/common/example/example_CGAL_points_off_reader.cpp
index 4522174a..8c6a6b54 100644
--- a/src/common/example/example_CGAL_points_off_reader.cpp
+++ b/src/common/example/example_CGAL_points_off_reader.cpp
@@ -34,7 +34,7 @@ int main(int argc, char **argv) {
   // Retrieve the triangulation
   std::vector<Point_d> point_cloud = off_reader.get_point_cloud();
 
-  int n {0};
+  int n {};
   for (auto point : point_cloud) {
     std::cout << "Point[" << n << "] = ";
     for (std::size_t i {0}; i < point.size(); i++)
diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h
index cd518581..5891ef0e 100644
--- a/src/common/include/gudhi/distance_functions.h
+++ b/src/common/include/gudhi/distance_functions.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Clément Maria
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
+ *    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
@@ -25,19 +25,25 @@
 
 #include <cmath>  // for std::sqrt
 
-/* Compute the Euclidean distance between two Points given
- * by a range of coordinates. The points are assumed to have 
- * the same dimension. */
-template< typename Point >
-double euclidean_distance(Point &p1, Point &p2) {
-  double dist = 0.;
-  auto it1 = p1.begin();
-  auto it2 = p2.begin();
-  for (; it1 != p1.end(); ++it1, ++it2) {
-    double tmp = *it1 - *it2;
-    dist += tmp*tmp;
+/** @file
+ * @brief Global distance functions
+ */
+
+/** @brief Compute the Euclidean distance between two Points given by a range of coordinates. The points are assumed to
+ * have the same dimension. */
+class Euclidean_distance {
+ public:
+  template< typename Point >
+  auto operator()(const Point& p1, const Point& p2) -> typename std::decay<decltype(*std::begin(p1))>::type {
+    auto it1 = p1.begin();
+    auto it2 = p2.begin();
+    typename Point::value_type dist = 0.;
+    for (; it1 != p1.end(); ++it1, ++it2) {
+      typename Point::value_type tmp = (*it1) - (*it2);
+      dist += tmp*tmp;
+    }
+    return std::sqrt(dist);
   }
-  return std::sqrt(dist);
-}
+};
 
 #endif  // DISTANCE_FUNCTIONS_H_
diff --git a/src/common/include/gudhi/graph_simplicial_complex.h b/src/common/include/gudhi/graph_simplicial_complex.h
index 042ef516..5fe7c826 100644
--- a/src/common/include/gudhi/graph_simplicial_complex.h
+++ b/src/common/include/gudhi/graph_simplicial_complex.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Clément Maria
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
+ *    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
@@ -39,61 +39,4 @@ struct vertex_filtration_t {
   typedef boost::vertex_property_tag kind;
 };
 
-typedef int Vertex_handle;
-typedef double Filtration_value;
-typedef boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS
-, boost::property < vertex_filtration_t, Filtration_value >
-, boost::property < edge_filtration_t, Filtration_value >
-> Graph_t;
-typedef std::pair< Vertex_handle, Vertex_handle > Edge_t;
-
-/** \brief Output the proximity graph of the points.
- *
- * If points contains n elements, the proximity graph is the graph 
- * with n vertices, and an edge [u,v] iff the distance function between 
- * points u and v is smaller than threshold.
- *
- * The type PointCloud furnishes .begin() and .end() methods, that return
- * iterators with value_type Point.
- */
-template< typename PointCloud
-, typename Point >
-Graph_t compute_proximity_graph(PointCloud &points
-                                , Filtration_value threshold
-                                , Filtration_value distance(Point p1, Point p2)) {
-  std::vector< Edge_t > edges;
-  std::vector< Filtration_value > edges_fil;
-  std::map< Vertex_handle, Filtration_value > vertices;
-
-  Vertex_handle idx_u, idx_v;
-  Filtration_value fil;
-  idx_u = 0;
-  for (auto it_u = points.begin(); it_u != points.end(); ++it_u) {
-    idx_v = idx_u + 1;
-    for (auto it_v = it_u + 1; it_v != points.end(); ++it_v, ++idx_v) {
-      fil = distance(*it_u, *it_v);
-      if (fil <= threshold) {
-        edges.emplace_back(idx_u, idx_v);
-        edges_fil.push_back(fil);
-      }
-    }
-    ++idx_u;
-  }
-
-  Graph_t skel_graph(edges.begin()
-                     , edges.end()
-                     , edges_fil.begin()
-                     , idx_u);  // number of points labeled from 0 to idx_u-1
-
-  auto vertex_prop = boost::get(vertex_filtration_t(), skel_graph);
-
-  boost::graph_traits<Graph_t>::vertex_iterator vi, vi_end;
-  for (std::tie(vi, vi_end) = boost::vertices(skel_graph);
-       vi != vi_end; ++vi) {
-    boost::put(vertex_prop, *vi, 0.);
-  }
-
-  return skel_graph;
-}
-
 #endif  // GRAPH_SIMPLICIAL_COMPLEX_H_
diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index 899f9df6..97a87edd 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -2,9 +2,9 @@
  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
  *    library for computational topology.
  *
- *    Author(s):       Clément Maria
+ *    Author(s):       Clement Maria, Pawel Dlotko
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
+ *    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
@@ -30,18 +30,25 @@
 #include <iostream>
 #include <fstream>
 #include <map>
-#include <limits>  // for numeric_limits<>
+#include <limits>  // for numeric_limits
 #include <string>
 #include <vector>
+#include <utility>  // for pair
+
+// Keep this file tag for Doxygen to parse the code, otherwise, functions are not documented.
+// It is required for global functions and variables.
+
+/** @file
+ * @brief This file includes common file reader for GUDHI
+ */
 
 /**
- * \brief Read a set of points to turn it
- * into a vector< vector<double> > by filling points
+ * @brief Read a set of points to turn it into a vector< vector<double> > by filling points.
  *
- * File format: 1 point per line
- * X11 X12 ... X1d 
- * X21 X22 ... X2d
- * etc
+ * File format: 1 point per line<br>
+ * X11 X12 ... X1d<br>
+ * X21 X22 ... X2d<br>
+ * etc<br>
  */
 inline void read_points(std::string file_name, std::vector< std::vector< double > > & points) {
   std::ifstream in_file(file_name.c_str(), std::ios::in);
@@ -66,23 +73,29 @@ inline void read_points(std::string file_name, std::vector< std::vector< double
 }
 
 /**
- * \brief Read a graph from a file.
+ * @brief Read a graph from a file.
+ *
+ * \tparam Graph_t Type for the return graph. Must be constructible from iterators on pairs of Vertex_handle
+ * \tparam Filtration_value Type for the value of the read filtration
+ * \tparam Vertex_handle Type for the value of the read vertices
  *
- * File format: 1 simplex per line
- * Dim1 X11 X12 ... X1d Fil1 
- * Dim2 X21 X22 ... X2d Fil2
- * etc
+ * File format: 1 simplex per line<br>
+ * Dim1 X11 X12 ... X1d Fil1<br>
+ * Dim2 X21 X22 ... X2d Fil2<br>
+ * etc<br>
  *
  * The vertices must be labeled from 0 to n-1.
  * Every simplex must appear exactly once.
  * Simplices of dimension more than 1 are ignored.
  */
-inline Graph_t read_graph(std::string file_name) {
+template< typename Graph_t, typename Filtration_value, typename Vertex_handle >
+Graph_t read_graph(std::string file_name) {
   std::ifstream in_(file_name.c_str(), std::ios::in);
   if (!in_.is_open()) {
     std::cerr << "Unable to open file " << file_name << std::endl;
   }
 
+  typedef std::pair< Vertex_handle, Vertex_handle > Edge_t;
   std::vector< Edge_t > edges;
   std::vector< Filtration_value > edges_fil;
   std::map< Vertex_handle, Filtration_value > vertices;
@@ -130,7 +143,7 @@ inline Graph_t read_graph(std::string file_name) {
   Graph_t skel_graph(edges.begin(), edges.end(), edges_fil.begin(), vertices.size());
   auto vertex_prop = boost::get(vertex_filtration_t(), skel_graph);
 
-  boost::graph_traits<Graph_t>::vertex_iterator vi, vi_end;
+  typename boost::graph_traits<Graph_t>::vertex_iterator vi, vi_end;
   auto v_it = vertices.begin();
   for (std::tie(vi, vi_end) = boost::vertices(skel_graph); vi != vi_end; ++vi, ++v_it) {
     boost::put(vertex_prop, *vi, v_it->second);
@@ -140,12 +153,12 @@ inline Graph_t read_graph(std::string file_name) {
 }
 
 /**
- * \brief Read a face from a file.
+ * @brief Read a face from a file.
  *
- * File format: 1 simplex per line
- * Dim1 X11 X12 ... X1d Fil1 
- * Dim2 X21 X22 ... X2d Fil2
- * etc
+ * File format: 1 simplex per line<br>
+ * Dim1 X11 X12 ... X1d Fil1<br>
+ * Dim2 X21 X22 ... X2d Fil2<br>
+ * etc<br>
  *
  * The vertices must be labeled from 0 to n-1.
  * Every simplex must appear exactly once.
@@ -166,18 +179,16 @@ bool read_simplex(std::istream & in_, std::vector< Vertex_handle > & simplex, Fi
 }
 
 /**
- * \brief Read a hasse simplex from a file.
- *
- * File format: 1 simplex per line
- * Dim1 k11 k12 ... k1Dim1 Fil1 
- * Dim2 k21 k22 ... k2Dim2 Fil2
- * etc
- *
- * The key of a simplex is its position in the filtration order
- * and also the number of its row in the file.
- * Dimi ki1 ki2 ... kiDimi Fili means that the ith simplex in the 
- * filtration has dimension Dimi, filtration value fil1 and simplices with 
- * key ki1 ... kiDimi in its boundary.*/
+ * @brief Read a hasse simplex from a file.
+ *
+ * File format: 1 simplex per line<br>
+ * Dim1 k11 k12 ... k1Dim1 Fil1<br>
+ * Dim2 k21 k22 ... k2Dim2 Fil2<br>
+ * etc<br>
+ *
+ * The key of a simplex is its position in the filtration order and also the number of its row in the file.
+ * Dimi ki1 ki2 ... kiDimi Fili means that the ith simplex in the filtration has dimension Dimi, filtration value
+ * fil1 and simplices with key ki1 ... kiDimi in its boundary.*/
 template< typename Simplex_key, typename Filtration_value >
 bool read_hasse_simplex(std::istream & in_, std::vector< Simplex_key > & boundary, Filtration_value & fil) {
   int dim;
@@ -195,4 +206,93 @@ bool read_hasse_simplex(std::istream & in_, std::vector< Simplex_key > & boundar
   return true;
 }
 
+/**
+ * @brief Read a lower triangular distance matrix from a csv file. We assume that the .csv store the whole
+ * (square) matrix.
+ * 
+ * @author Pawel Dlotko
+ *
+ * Square matrix file format:<br>
+ * 0;D12;...;D1j<br>
+ * D21;0;...;D2j<br>
+ * ...<br>
+ * Dj1;Dj2;...;0<br>
+ *
+ * lower matrix file format:<br>
+ * 0<br>
+ * D21;<br>
+ * D31;D32;<br>
+ * ...<br>
+ * Dj1;Dj2;...;Dj(j-1);<br>
+ *
+ **/
+template< typename Filtration_value >
+std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from_csv_file(const std::string& filename,
+                                                                                          const char separator = ';') {
+#ifdef DEBUG_TRACES
+  std::cout << "Using procedure read_lower_triangular_matrix_from_csv_file \n";
+#endif  // DEBUG_TRACES
+  std::vector< std::vector< Filtration_value > > result;
+  std::ifstream in;
+  in.open(filename.c_str());
+  if (!in.is_open()) {
+    return result;
+  }
+
+  std::string line;
+
+  // the first line is emtpy, so we ignore it:
+  std::getline(in, line);
+  std::vector< Filtration_value > values_in_this_line;
+  result.push_back(values_in_this_line);
+
+  int number_of_line = 0;
+
+  // first, read the file line by line to a string:
+  while (std::getline(in, line)) {
+    // if line is empty, break
+    if (line.size() == 0)
+      break;
+
+    // if the last element of a string is comma:
+    if (line[ line.size() - 1 ] == separator) {
+      // then shrink the string by one
+      line.pop_back();
+    }
+
+    // replace all commas with spaces
+    std::replace(line.begin(), line.end(), separator, ' ');
+
+    // put the new line to a stream
+    std::istringstream iss(line);
+    // and now read the doubles.
+
+    int number_of_entry = 0;
+    std::vector< Filtration_value > values_in_this_line;
+    while (iss.good()) {
+      double entry;
+      iss >> entry;
+      if (number_of_entry <= number_of_line) {
+        values_in_this_line.push_back(entry);
+      }
+      ++number_of_entry;
+    }
+    if (!values_in_this_line.empty())result.push_back(values_in_this_line);
+    ++number_of_line;
+  }
+  in.close();
+
+#ifdef DEBUG_TRACES
+  std::cerr << "Here is the matrix we read : \n";
+  for (size_t i = 0; i != result.size(); ++i) {
+    for (size_t j = 0; j != result[i].size(); ++j) {
+      std::cerr << result[i][j] << " ";
+    }
+    std::cerr << std::endl;
+  }
+#endif  // DEBUG_TRACES
+
+  return result;
+}  // read_lower_triangular_matrix_from_csv_file
+
 #endif  // READER_UTILS_H_
diff --git a/src/common/test/CMakeLists.txt b/src/common/test/CMakeLists.txt
index 7ccdb752..baa24539 100644
--- a/src/common/test/CMakeLists.txt
+++ b/src/common/test/CMakeLists.txt
@@ -13,12 +13,21 @@ endif()
 add_executable ( poffreader_UT test_points_off_reader.cpp )
 target_link_libraries(poffreader_UT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 
+add_executable ( distancematrixreader_UT test_distance_matrix_reader.cpp )
+target_link_libraries(distancematrixreader_UT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+
 # Do not forget to copy test files in current binary dir
 file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 
 # Unitary tests
 add_test(poffreader_UT ${CMAKE_CURRENT_BINARY_DIR}/poffreader_UT
          # XML format for Jenkins xUnit plugin 
          --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/poffreader_UT.xml --log_level=test_suite --report_level=no)
 
+add_test(distancematrixreader_UT ${CMAKE_CURRENT_BINARY_DIR}/distancematrixreader_UT
+         # XML format for Jenkins xUnit plugin 
+         --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/distancematrixreader_UT.xml --log_level=test_suite --report_level=no)
+
 
diff --git a/src/common/test/test_distance_matrix_reader.cpp b/src/common/test/test_distance_matrix_reader.cpp
new file mode 100644
index 00000000..95a73bd9
--- /dev/null
+++ b/src/common/test/test_distance_matrix_reader.cpp
@@ -0,0 +1,85 @@
+/*    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) 2016  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 <iostream>
+#include <string>
+#include <vector>
+
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "distance_matrix_reader"
+#include <boost/test/unit_test.hpp>
+
+using Distance_matrix = std::vector<std::vector<double>>;
+
+BOOST_AUTO_TEST_CASE( lower_triangular_distance_matrix )
+{
+  Distance_matrix from_lower_triangular;
+  // Read lower_triangular_distance_matrix.csv file where the separator is a ','
+  from_lower_triangular = read_lower_triangular_matrix_from_csv_file<double>("lower_triangular_distance_matrix.csv",
+                                                                             ',');
+  for (auto& i : from_lower_triangular) {
+    for (auto j : i) {
+      std::cout << j << " ";
+    }
+    std::cout << std::endl;
+  }
+  std::cout << "from_lower_triangular size = " << from_lower_triangular.size() << std::endl;
+  BOOST_CHECK(from_lower_triangular.size() == 5);
+
+  for (std::size_t i = 0; i < from_lower_triangular.size(); i++) {
+    std::cout << "from_lower_triangular[" << i << "] size = " << from_lower_triangular[i].size() << std::endl;
+    BOOST_CHECK(from_lower_triangular[i].size() == i);
+  }
+  std::vector<double> expected = {1};
+  BOOST_CHECK(from_lower_triangular[1] == expected);
+  
+  expected = {2,3};
+  BOOST_CHECK(from_lower_triangular[2] == expected);
+  
+  expected = {4,5,6};
+  BOOST_CHECK(from_lower_triangular[3] == expected);
+  
+  expected = {7,8,9,10};
+  BOOST_CHECK(from_lower_triangular[4] == expected);
+  
+}
+
+BOOST_AUTO_TEST_CASE( full_square_distance_matrix )
+{
+  Distance_matrix from_full_square;
+  // Read full_square_distance_matrix.csv file where the separator is the default one ';'
+  from_full_square = read_lower_triangular_matrix_from_csv_file<double>("full_square_distance_matrix.csv");
+  for (auto& i : from_full_square) {
+    for (auto j : i) {
+      std::cout << j << " ";
+    }
+    std::cout << std::endl;
+  }
+  std::cout << "from_full_square size = " << from_full_square.size() << std::endl;
+  BOOST_CHECK(from_full_square.size() == 7);
+  for (std::size_t i = 0; i < from_full_square.size(); i++) {
+    std::cout << "from_full_square[" << i << "] size = " << from_full_square[i].size() << std::endl;
+    BOOST_CHECK(from_full_square[i].size() == i);
+  }  
+}
diff --git a/src/common/test/test_points_off_reader.cpp b/src/common/test/test_points_off_reader.cpp
index b4f71182..0a78d190 100644
--- a/src/common/test/test_points_off_reader.cpp
+++ b/src/common/test/test_points_off_reader.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2015  INRIA Saclay (France)
+ *    Copyright (C) 2015
  *
  *    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