merge from trunk

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/farthest_distance@2244 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 7d261d59dae839dd5de8f6a03c5a167d015f7d85

188 files changed, 12717 insertions, 1266 deletions

diff --git a/src/Alpha_complex/concept/Simplicial_complex_for_alpha.h b/src/Alpha_complex/concept/SimplicialComplexForAlpha.h
index 2b8bff94..2b8bff94 100644
--- a/src/Alpha_complex/concept/Simplicial_complex_for_alpha.h
+++ b/src/Alpha_complex/concept/SimplicialComplexForAlpha.h
diff --git a/src/Alpha_complex/doc/COPYRIGHT b/src/Alpha_complex/doc/COPYRIGHT
new file mode 100644
index 00000000..dbad2380
--- /dev/null
+++ b/src/Alpha_complex/doc/COPYRIGHT
@@ -0,0 +1,19 @@
+The files of this directory are 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) 2015  INRIA
+
+This program is free software: you can redistribute it and/or modify it under
+the terms of the GNU General Public License as published by the Free Software
+Foundation, either version 3 of the License, or (at your option) any later
+version.
+
+This program is distributed in the hope that it will be useful, but WITHOUT
+ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along with
+this program.  If not, see <http://www.gnu.org/licenses/>.
diff --git a/src/Alpha_complex/example/Alpha_complex_from_off.cpp b/src/Alpha_complex/example/Alpha_complex_from_off.cpp
index 32bef1cd..d411e90a 100644
--- a/src/Alpha_complex/example/Alpha_complex_from_off.cpp
+++ b/src/Alpha_complex/example/Alpha_complex_from_off.cpp
@@ -17,13 +17,13 @@ void usage(int nbArgs, char * const progName) {
 int main(int argc, char **argv) {
   if ((argc != 3) && (argc != 4)) usage(argc, (argv[0] - 1));
 
-  std::string off_file_name(argv[1]);
-  double alpha_square_max_value = atof(argv[2]);
+  std::string off_file_name {argv[1]};
+  double alpha_square_max_value {atof(argv[2])};
 
   // ----------------------------------------------------------------------------
   // Init of an alpha complex from an OFF file
   // ----------------------------------------------------------------------------
-  typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel;
+  using Kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >;
   Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_name);
 
   std::streambuf* streambufffer;
diff --git a/src/Alpha_complex/example/Alpha_complex_from_points.cpp b/src/Alpha_complex/example/Alpha_complex_from_points.cpp
index 491b7e6d..c19f7cc8 100644
--- a/src/Alpha_complex/example/Alpha_complex_from_points.cpp
+++ b/src/Alpha_complex/example/Alpha_complex_from_points.cpp
@@ -9,9 +9,9 @@
 #include <vector>
 #include <limits>  // for numeric limits
 
-typedef CGAL::Epick_d< CGAL::Dimension_tag<2> > Kernel;
-typedef Kernel::Point_d Point;
-typedef std::vector<Point> Vector_of_points;
+using Kernel = CGAL::Epick_d< CGAL::Dimension_tag<2> >;
+using Point = Kernel::Point_d;
+using Vector_of_points = std::vector<Point>;
 
 void usage(int nbArgs, char * const progName) {
   std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n";
@@ -24,7 +24,7 @@ int main(int argc, char **argv) {
   if ((argc != 1) && (argc != 2)) usage(argc, (argv[0] - 1));
 
   // Delaunay complex if alpha_square_max_value is not given by the user.
-  double alpha_square_max_value = std::numeric_limits<double>::infinity();
+  double alpha_square_max_value {std::numeric_limits<double>::infinity()};
   if (argc == 2)
     alpha_square_max_value = atof(argv[1]);
 
diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt
index 71a95d61..b9bcdb55 100644
--- a/src/Alpha_complex/example/CMakeLists.txt
+++ b/src/Alpha_complex/example/CMakeLists.txt
@@ -2,32 +2,28 @@ cmake_minimum_required(VERSION 2.6)
 project(Alpha_complex_examples)
 
 # need CGAL 4.7
-# cmake -DCGAL_DIR=~/workspace/CGAL-4.7-Ic-41 ../../..
-if(CGAL_FOUND)
-  if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
-    if (EIGEN3_FOUND)
-      add_executable ( alphapoints Alpha_complex_from_points.cpp )
-      target_link_libraries(alphapoints  ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY})
-      add_executable ( alphaoffreader Alpha_complex_from_off.cpp )
-      target_link_libraries(alphaoffreader  ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY})
-      if (TBB_FOUND)
-        target_link_libraries(alphapoints ${TBB_LIBRARIES})
-        target_link_libraries(alphaoffreader ${TBB_LIBRARIES})
-      endif()
+# cmake -DCGAL_DIR=~/workspace/CGAL-4.7 ..
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
+  add_executable ( alphapoints Alpha_complex_from_points.cpp )
+  target_link_libraries(alphapoints  ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY})
+  add_executable ( alphaoffreader Alpha_complex_from_off.cpp )
+  target_link_libraries(alphaoffreader  ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY})
+  if (TBB_FOUND)
+    target_link_libraries(alphapoints ${TBB_LIBRARIES})
+    target_link_libraries(alphaoffreader ${TBB_LIBRARIES})
+  endif()
 
-      add_test(alphapoints ${CMAKE_CURRENT_BINARY_DIR}/alphapoints)
-      # Do not forget to copy test files in current binary dir
-      file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
-      add_test(alphaoffreader_doc_60 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader alphacomplexdoc.off 60.0 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt)
-      add_test(alphaoffreader_doc_32 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader alphacomplexdoc.off 32.0 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt)
-      if (DIFF_PATH)
-        # Do not forget to copy test results files in current binary dir
-        file(COPY "alphaoffreader_for_doc_32.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
-        file(COPY "alphaoffreader_for_doc_60.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+  add_test(alphapoints ${CMAKE_CURRENT_BINARY_DIR}/alphapoints)
+  # Do not forget to copy test files in current binary dir
+  file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+  add_test(alphaoffreader_doc_60 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader alphacomplexdoc.off 60.0 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt)
+  add_test(alphaoffreader_doc_32 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader alphacomplexdoc.off 32.0 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt)
+  if (DIFF_PATH)
+    # Do not forget to copy test results files in current binary dir
+    file(COPY "alphaoffreader_for_doc_32.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+    file(COPY "alphaoffreader_for_doc_60.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 
-        add_test(alphaoffreader_doc_60_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_60.txt)
-        add_test(alphaoffreader_doc_32_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_32.txt)
-      endif()
-    endif(EIGEN3_FOUND)
-  endif(NOT CGAL_VERSION VERSION_LESS 4.7.0)
-endif(CGAL_FOUND)
+    add_test(alphaoffreader_doc_60_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_60.txt)
+    add_test(alphaoffreader_doc_32_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_32.txt)
+  endif()
+endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt
index efc0565f..32091196 100644
--- a/src/Alpha_complex/test/CMakeLists.txt
+++ b/src/Alpha_complex/test/CMakeLists.txt
@@ -10,23 +10,19 @@ if (GPROF_PATH)
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
 endif()
 
-if(CGAL_FOUND)
-  if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
-    if (EIGEN3_FOUND)
-      add_executable ( AlphaComplexUT Alpha_complex_unit_test.cpp )
-      target_link_libraries(AlphaComplexUT  ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
-      if (TBB_FOUND)
-        target_link_libraries(AlphaComplexUT ${TBB_LIBRARIES})
-      endif()
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
+  add_executable ( AlphaComplexUT Alpha_complex_unit_test.cpp )
+  target_link_libraries(AlphaComplexUT  ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+  if (TBB_FOUND)
+    target_link_libraries(AlphaComplexUT ${TBB_LIBRARIES})
+  endif()
 
-      # Do not forget to copy test files in current binary dir
-      file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+  # Do not forget to copy test files in current binary dir
+  file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 
-      add_test(AlphaComplexUT ${CMAKE_CURRENT_BINARY_DIR}/AlphaComplexUT
-      # XML format for Jenkins xUnit plugin 
-      --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/AlphaComplexUT.xml --log_level=test_suite --report_level=no)
+  add_test(AlphaComplexUT ${CMAKE_CURRENT_BINARY_DIR}/AlphaComplexUT
+  # XML format for Jenkins xUnit plugin
+  --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/AlphaComplexUT.xml --log_level=test_suite --report_level=no)
 
-    endif(EIGEN3_FOUND)
-  endif (NOT CGAL_VERSION VERSION_LESS 4.7.0)
-endif(CGAL_FOUND)
+endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
 
diff --git a/src/Bitmap_cubical_complex/doc/COPYRIGHT b/src/Bitmap_cubical_complex/doc/COPYRIGHT
new file mode 100644
index 00000000..bcd46b23
--- /dev/null
+++ b/src/Bitmap_cubical_complex/doc/COPYRIGHT
@@ -0,0 +1,19 @@
+The files of this directory are 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
+
+Copyright (C) 2015  INRIA
+
+This program is free software: you can redistribute it and/or modify it under
+the terms of the GNU General Public License as published by the Free Software
+Foundation, either version 3 of the License, or (at your option) any later
+version.
+
+This program is distributed in the hope that it will be useful, but WITHOUT
+ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along with
+this program.  If not, see <http://www.gnu.org/licenses/>.
diff --git a/src/Bottleneck_distance/benchmark/CMakeLists.txt b/src/Bottleneck_distance/benchmark/CMakeLists.txt
index 355e8d31..170081ce 100644
--- a/src/Bottleneck_distance/benchmark/CMakeLists.txt
+++ b/src/Bottleneck_distance/benchmark/CMakeLists.txt
@@ -1,11 +1,9 @@
 cmake_minimum_required(VERSION 2.6)
 project(Bottleneck_distance_benchmark)
 
-
-# requires CGAL 4.8
-# cmake -DCGAL_DIR=~/workspace/CGAL-4.8 ../../..
-if(CGAL_FOUND)
-  if (NOT CGAL_VERSION VERSION_LESS 4.8.0)
-    add_executable ( bottleneck_chrono bottleneck_chrono.cpp )
-  endif ()
-endif()
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  add_executable ( bottleneck_chrono bottleneck_chrono.cpp )
+  if (TBB_FOUND)
+    target_link_libraries(bottleneck_chrono ${TBB_LIBRARIES})
+  endif(TBB_FOUND)
+endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Bottleneck_distance/doc/COPYRIGHT b/src/Bottleneck_distance/doc/COPYRIGHT
new file mode 100644
index 00000000..179740a6
--- /dev/null
+++ b/src/Bottleneck_distance/doc/COPYRIGHT
@@ -0,0 +1,19 @@
+The files of this directory are part of the Gudhi Library. The Gudhi library
+(Geometric Understanding in Higher Dimensions) is a generic C++ library for
+computational topology.
+
+Author(s):       François Godi
+
+Copyright (C) 2015  INRIA
+
+This program is free software: you can redistribute it and/or modify it under
+the terms of the GNU General Public License as published by the Free Software
+Foundation, either version 3 of the License, or (at your option) any later
+version.
+
+This program is distributed in the hope that it will be useful, but WITHOUT
+ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along with
+this program.  If not, see <http://www.gnu.org/licenses/>.
diff --git a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h
index 5223678d..3998fe8d 100644
--- a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h
+++ b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h
@@ -35,9 +35,9 @@ namespace persistence_diagram {
  * 
  * \section bottleneckdefinition Definition
  * 
- * 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.
+ * 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.
  *
  * \image html perturb_pd.png On this picture, the red edges represent the matching. The bottleneck distance is the length of the longest edge.
  *
diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt
index b36d0f34..b0a19f8b 100644
--- a/src/Bottleneck_distance/example/CMakeLists.txt
+++ b/src/Bottleneck_distance/example/CMakeLists.txt
@@ -1,22 +1,20 @@
 cmake_minimum_required(VERSION 2.6)
 project(Bottleneck_distance_examples)
 
-# requires CGAL 4.8
-# cmake -DCGAL_DIR=~/workspace/CGAL-4.8 ../../..
-if(CGAL_FOUND)
-  if (NOT CGAL_VERSION VERSION_LESS 4.8.0)
-    add_executable (bottleneck_read_file_example bottleneck_read_file_example.cpp)
-    add_executable (bottleneck_basic_example bottleneck_basic_example.cpp)
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  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_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_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(bottleneck_read_file_example ${TBB_LIBRARIES})
+    target_link_libraries(bottleneck_basic_example ${TBB_LIBRARIES})
+    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)
 
-  endif ()
-endif()
+endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp b/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp
index 6e9be97b..fd9f0858 100644
--- a/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp
+++ b/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp
@@ -56,7 +56,7 @@ void program_options(int argc, char * argv[]
                      , int & p
                      , Filtration_value & min_persistence);
 
-static inline std::pair<double, double> compute_root_square (std::pair<double, double> input) {
+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));
 }
 
diff --git a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h
index c7695112..44f4b827 100644
--- a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h
+++ b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h
@@ -25,6 +25,10 @@
 
 #include <gudhi/Internal_point.h>
 
+#ifdef GUDHI_USE_TBB
+#include <tbb/parallel_sort.h>
+#endif
+
 #include <vector>
 #include <algorithm>
 #include <limits>  // for numeric_limits
@@ -144,7 +148,11 @@ inline std::vector<double> Persistence_graph::sorted_distances() const {
     for (int v_point_index = 0; v_point_index < size(); ++v_point_index)
       distances.push_back(distance(u_point_index, v_point_index));
   }
+#ifdef GUDHI_USE_TBB
+  tbb::parallel_sort(distances.begin(), distances.end());
+#else
   std::sort(distances.begin(), distances.end());
+#endif
   return distances;
 }
 
diff --git a/src/Bottleneck_distance/test/CMakeLists.txt b/src/Bottleneck_distance/test/CMakeLists.txt
index 6c8f112d..3d8e1f95 100644
--- a/src/Bottleneck_distance/test/CMakeLists.txt
+++ b/src/Bottleneck_distance/test/CMakeLists.txt
@@ -11,16 +11,15 @@ if (GPROF_PATH)
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
 endif()
 
-# requires CGAL 4.8
-# cmake -DCGAL_DIR=~/workspace/CGAL-4.8 ../../..
-if(CGAL_FOUND)
-  if (NOT CGAL_VERSION VERSION_LESS 4.8.0)
-    add_executable ( bottleneckUT bottleneck_unit_test.cpp )
-    target_link_libraries(bottleneckUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  add_executable ( bottleneckUT bottleneck_unit_test.cpp )
+  target_link_libraries(bottleneckUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+  if (TBB_FOUND)
+    target_link_libraries(bottleneckUT ${TBB_LIBRARIES})
+  endif(TBB_FOUND)
 
-    # 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()
+  # 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 (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index eb349052..4fa73662 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -9,148 +9,85 @@ enable_testing()
 
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/modules/")
 
-find_package(Boost REQUIRED COMPONENTS system filesystem program_options chrono timer date_time REQUIRED)
+# For "make doxygen"
+set(GUDHI_USER_VERSION_DIR ${CMAKE_SOURCE_DIR})
+include(${CMAKE_MODULE_PATH}/GUDHI_doxygen_target.txt)
 
-if(NOT Boost_FOUND)
-  message(FATAL_ERROR "NOTICE: This program requires Boost and will not be compiled.")
+# For third parties libraries management - To be done last as CGAL updates CMAKE_MODULE_PATH
+include("${CMAKE_MODULE_PATH}/GUDHI_third_party_libraries.txt")
+
+if(MSVC)
+  # Turn off some VC++ warnings
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4267 /wd4668 /wd4311 /wd4800 /wd4820 /wd4503 /wd4244 /wd4345 /wd4996 /wd4396 /wd4018")
 else()
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Wall -pedantic")
+endif()
 
-  # For "make doxygen"
-  set(GUDHI_USER_VERSION_DIR ${CMAKE_SOURCE_DIR})
-  include(${CMAKE_MODULE_PATH}/GUDHI_doxygen_target.txt)
-
-  find_package(GMP)
-  if(GMP_FOUND)
-    message(STATUS "GMP_LIBRARIES = ${GMP_LIBRARIES}")
-    INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR})
-    find_package(GMPXX)
-    if(GMPXX_FOUND)
-      message(STATUS "GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}")
-      INCLUDE_DIRECTORIES(${GMPXX_INCLUDE_DIR})
-    endif()
-  endif()
-
-  # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CMAKE_CXX_FLAGS are overwritten.
-  # cf. http://doc.cgal.org/latest/Manual/installation.html#title40
-  # A workaround is to include(${CGAL_USE_FILE}) before adding "-std=c++11".
-  # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html 
-  # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html
-  # but it implies to use cmake version 3.1 at least.
-
-  # find CGAL in QUIET mode for cmake to be less verbose when CGAL is not found.
-  find_package(CGAL QUIET)
-  # Only CGAL versions > 4.4 supports what Gudhi uses from CGAL
-  if (CGAL_VERSION VERSION_LESS 4.4.0 AND CGAL_FOUND)
-    message("CGAL version ${CGAL_VERSION} is considered too old to be used by Gudhi.")
-    unset(CGAL_FOUND)
-  endif(CGAL_VERSION VERSION_LESS 4.4.0 AND CGAL_FOUND)
-  if(CGAL_FOUND)
-    message(STATUS "CGAL version: ${CGAL_VERSION}.")
-    include( ${CGAL_USE_FILE} )
-    
-    if (NOT CGAL_VERSION VERSION_LESS 4.8.0)
-      include_directories(BEFORE "include/gudhi_patches")
-    endif()
-  endif()
-  
-  if(MSVC)
-    # Turn off some VC++ warnings
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4267 /wd4668 /wd4311 /wd4800 /wd4820 /wd4503 /wd4244 /wd4345 /wd4996 /wd4396 /wd4018")
-  else()
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Wall -pedantic")
-  endif()
-
-  if(CMAKE_BUILD_TYPE MATCHES Debug)
-    message("++ Debug compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_DEBUG}")
-  else()
-    message("++ Release compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_RELEASE}")
-  endif()
-
-  set(Boost_USE_STATIC_LIBS        ON)
-  set(Boost_USE_MULTITHREADED      ON)
-  set(Boost_USE_STATIC_RUNTIME    OFF)
-
-  # Find TBB package for parallel sort - not mandatory, just optional.
-  set(TBB_FIND_QUIETLY ON)
-  find_package(TBB)
-  if (TBB_FOUND)
-    include(${TBB_USE_FILE})
-    message("TBB found in ${TBB_LIBRARY_DIRS}")
-    add_definitions(-DGUDHI_USE_TBB)
-  endif()
-
-  find_package(Eigen3 3.1.0)
-  if (EIGEN3_FOUND)
-    message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
-    include( ${EIGEN3_USE_FILE} )
-    #include_directories (BEFORE "../../include")
-  endif (EIGEN3_FOUND)
-
-  # BOOST ISSUE result_of vs C++11
-  add_definitions(-DBOOST_RESULT_OF_USE_DECLTYPE)
-  # BOOST ISSUE with Libraries name resolution under Windows
-  add_definitions(-DBOOST_ALL_NO_LIB)
-
-  INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
-  LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
-
-  if (DEBUG_TRACES)
-    message(STATUS "DEBUG_TRACES are activated")
-    # For programs to be more verbose
-    add_definitions(-DDEBUG_TRACES)
-  endif()
-
-  #---------------------------------------------------------------------------------------
-  # Gudhi compilation part
-  include_directories(include)
-
-  add_subdirectory(example/common)
-  add_subdirectory(example/Simplex_tree)                   
-  add_subdirectory(example/Persistent_cohomology)                   
-  add_subdirectory(example/Skeleton_blocker)                   
-  add_subdirectory(example/Contraction)                   
-  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)
-  add_subdirectory(example/Bottleneck_distance)
-
-  # data points generator
-  add_subdirectory(data/points/generator)
-
-  # Please let GudhUI in last compilation position as QT is known to modify CMAKE_CXX_FLAGS
-  # GudhUI
-  add_subdirectory(GudhUI)
-  #---------------------------------------------------------------------------------------
-
-  #---------------------------------------------------------------------------------------
-  # GUDHIConfig.cmake
-  # Export the package for use from the build-tree
-  # (this registers the build-tree with a global CMake-registry)
-  export(PACKAGE GUDHI)
-
-  message("++ make install will install ${PROJECT_NAME} in the following directory : ${CMAKE_INSTALL_PREFIX}")
-  # Create the GUDHIConfig.cmake and GUDHIConfigVersion files
-  set(CONF_INCLUDE_DIRS "${CMAKE_INSTALL_PREFIX}/include")
-  configure_file(GUDHIConfig.cmake.in "${PROJECT_BINARY_DIR}/GUDHIConfig.cmake" @ONLY)
-  configure_file(GUDHIConfigVersion.cmake.in "${PROJECT_BINARY_DIR}/GUDHIConfigVersion.cmake" @ONLY)
-
-  #---------------------------------------------------------------------------------------
-
-  #---------------------------------------------------------------------------------------
-  # Gudhi installation part
-
-  # Install the GUDHIConfig.cmake and GUDHIConfigVersion.cmake
-  install(FILES
-    "${PROJECT_BINARY_DIR}/GUDHIConfig.cmake"
-    "${PROJECT_BINARY_DIR}/GUDHIConfigVersion.cmake"
-    DESTINATION share/gudhi)
-
-  # install the include file on "make install"
-  install(DIRECTORY include/gudhi DESTINATION include)
-  #---------------------------------------------------------------------------------------
-
-endif()  
+if(CMAKE_BUILD_TYPE MATCHES Debug)
+  message("++ Debug compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_DEBUG}")
+else()
+  message("++ Release compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_RELEASE}")
+endif()
+
+if (DEBUG_TRACES)
+  message(STATUS "DEBUG_TRACES are activated")
+  # For programs to be more verbose
+  add_definitions(-DDEBUG_TRACES)
+endif()
+
+#---------------------------------------------------------------------------------------
+# Gudhi compilation part
+include_directories(include)
+
+add_subdirectory(example/common)
+add_subdirectory(example/Simplex_tree)
+add_subdirectory(example/Persistent_cohomology)
+add_subdirectory(example/Skeleton_blocker)
+add_subdirectory(example/Contraction)
+add_subdirectory(example/Bitmap_cubical_complex)
+add_subdirectory(example/Witness_complex)
+add_subdirectory(example/Alpha_complex)
+add_subdirectory(example/Rips_complex)
+add_subdirectory(example/Spatial_searching)
+add_subdirectory(example/Subsampling)
+add_subdirectory(example/Tangential_complex)
+add_subdirectory(example/Bottleneck_distance)
+
+# data points generator
+add_subdirectory(data/points/generator)
+
+# Please let GudhUI in last compilation position as QT is known to modify CMAKE_CXX_FLAGS
+# GudhUI
+add_subdirectory(GudhUI)
+
+# This variable is used by Cython CMakeLists.txt to know its path
+set(GUDHI_CYTHON_PATH "cython")
+add_subdirectory(${GUDHI_CYTHON_PATH})
+#---------------------------------------------------------------------------------------
+
+#---------------------------------------------------------------------------------------
+# GUDHIConfig.cmake
+# Export the package for use from the build-tree
+# (this registers the build-tree with a global CMake-registry)
+export(PACKAGE GUDHI)
+
+message("++ make install will install ${PROJECT_NAME} in the following directory : ${CMAKE_INSTALL_PREFIX}")
+# Create the GUDHIConfig.cmake and GUDHIConfigVersion files
+set(CONF_INCLUDE_DIRS "${CMAKE_INSTALL_PREFIX}/include")
+configure_file(GUDHIConfig.cmake.in "${PROJECT_BINARY_DIR}/GUDHIConfig.cmake" @ONLY)
+configure_file(GUDHIConfigVersion.cmake.in "${PROJECT_BINARY_DIR}/GUDHIConfigVersion.cmake" @ONLY)
+
+#---------------------------------------------------------------------------------------
+
+#---------------------------------------------------------------------------------------
+# Gudhi installation part
+
+# Install the GUDHIConfig.cmake and GUDHIConfigVersion.cmake
+install(FILES
+  "${PROJECT_BINARY_DIR}/GUDHIConfig.cmake"
+  "${PROJECT_BINARY_DIR}/GUDHIConfigVersion.cmake"
+  DESTINATION share/gudhi)
+
+# install the include file on "make install"
+install(DIRECTORY include/gudhi DESTINATION include)
+#---------------------------------------------------------------------------------------
diff --git a/src/Contraction/doc/COPYRIGHT b/src/Contraction/doc/COPYRIGHT
new file mode 100644
index 00000000..1de850d7
--- /dev/null
+++ b/src/Contraction/doc/COPYRIGHT
@@ -0,0 +1,18 @@
+The files of this directory are part of the Gudhi Library. The Gudhi library
+(Geometric Understanding in Higher Dimensions) is a generic C++ library for
+computational topology.
+
+Author(s):       David Salinas
+Copyright (C) 2015  INRIA
+
+This program is free software: you can redistribute it and/or modify it under
+the terms of the GNU General Public License as published by the Free Software
+Foundation, either version 3 of the License, or (at your option) any later
+version.
+
+This program is distributed in the hope that it will be useful, but WITHOUT
+ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along with
+this program.  If not, see <http://www.gnu.org/licenses/>.
diff --git a/src/Contraction/example/Garland_heckbert.cpp b/src/Contraction/example/Garland_heckbert.cpp
index 4689519f..8b5a6a6c 100644
--- a/src/Contraction/example/Garland_heckbert.cpp
+++ b/src/Contraction/example/Garland_heckbert.cpp
@@ -35,10 +35,6 @@
 
 #include "Garland_heckbert/Error_quadric.h"
 
-using namespace Gudhi;
-using namespace skeleton_blocker;
-using namespace contraction;
-
 struct Geometry_trait {
   typedef Point_d Point;
 };
@@ -46,7 +42,8 @@ struct Geometry_trait {
 /**
  * The vertex stored in the complex contains a quadric.
  */
-struct Garland_heckbert_traits : public Skeleton_blocker_simple_geometric_traits<Geometry_trait> {
+struct Garland_heckbert_traits
+    : public Gudhi::skeleton_blocker::Skeleton_blocker_simple_geometric_traits<Geometry_trait> {
  public:
   struct Garland_heckbert_vertex : public Simple_geometric_vertex {
     Error_quadric<Geometry_trait::Point> quadric;
@@ -54,19 +51,21 @@ struct Garland_heckbert_traits : public Skeleton_blocker_simple_geometric_traits
   typedef Garland_heckbert_vertex Graph_vertex;
 };
 
-typedef Skeleton_blocker_geometric_complex< Garland_heckbert_traits > Complex;
-typedef Edge_profile<Complex> EdgeProfile;
-typedef Skeleton_blocker_contractor<Complex> Complex_contractor;
+using Complex = Gudhi::skeleton_blocker::Skeleton_blocker_geometric_complex< Garland_heckbert_traits >;
+using EdgeProfile = Gudhi::contraction::Edge_profile<Complex>;
+using Complex_contractor = Gudhi::contraction::Skeleton_blocker_contractor<Complex>;
 
 /**
  * How the new vertex is placed after an edge collapse : here it is placed at
  * the point minimizing the cost of the quadric.
  */
 class GH_placement : public Gudhi::contraction::Placement_policy<EdgeProfile> {
+  Complex& complex_;
+
  public:
   typedef Gudhi::contraction::Placement_policy<EdgeProfile>::Placement_type Placement_type;
 
-  GH_placement(Complex& complex) { }
+  GH_placement(Complex& complex) : complex_(complex) { (void)complex_; }
 
   Placement_type operator()(const EdgeProfile& profile) const override {
     auto sum_quad(profile.v0().quadric);
@@ -85,10 +84,12 @@ class GH_placement : public Gudhi::contraction::Placement_policy<EdgeProfile> {
  * which expresses a squared distances with triangles planes.
  */
 class GH_cost : public Gudhi::contraction::Cost_policy<EdgeProfile> {
+  Complex& complex_;
+
  public:
   typedef Gudhi::contraction::Cost_policy<EdgeProfile>::Cost_type Cost_type;
 
-  GH_cost(Complex& complex) { }
+  GH_cost(Complex& complex) : complex_(complex) { (void)complex_; }
 
   Cost_type operator()(EdgeProfile const& profile, boost::optional<Point> const& new_point) const override {
     Cost_type res;
@@ -107,8 +108,10 @@ class GH_cost : public Gudhi::contraction::Cost_policy<EdgeProfile> {
  * and we update them when contracting an edge (the quadric become the sum of both quadrics).
  */
 class GH_visitor : public Gudhi::contraction::Contraction_visitor<EdgeProfile> {
+  Complex& complex_;
+
  public:
-  GH_visitor(Complex& complex) { }
+  GH_visitor(Complex& complex) : complex_(complex) { (void)complex_; }
 
   // Compute quadrics for every vertex v
   // The quadric of v consists in the sum of quadric
@@ -147,7 +150,7 @@ int main(int argc, char *argv[]) {
   typedef Complex::Vertex_handle Vertex_handle;
 
   // load the points
-  Skeleton_blocker_off_reader<Complex> off_reader(argv[1], complex);
+  Gudhi::skeleton_blocker::Skeleton_blocker_off_reader<Complex> off_reader(argv[1], complex);
   if (!off_reader.is_valid()) {
     std::cerr << "Unable to read file:" << argv[1] << std::endl;
     return EXIT_FAILURE;
@@ -168,7 +171,7 @@ int main(int argc, char *argv[]) {
   Complex_contractor contractor(complex,
                                 new GH_cost(complex),
                                 new GH_placement(complex),
-                                contraction::make_link_valid_contraction<EdgeProfile>(),
+                                Gudhi::contraction::make_link_valid_contraction<EdgeProfile>(),
                                 new GH_visitor(complex));
 
   std::cout << "Contract " << num_contractions << " edges" << std::endl;
@@ -180,7 +183,7 @@ int main(int argc, char *argv[]) {
       complex.num_triangles() << " triangles." << std::endl;
 
   // write simplified complex
-  Skeleton_blocker_off_writer<Complex> off_writer(argv[2], complex);
+  Gudhi::skeleton_blocker::Skeleton_blocker_off_writer<Complex> off_writer(argv[2], complex);
 
   return EXIT_SUCCESS;
 }
diff --git a/src/Contraction/example/Garland_heckbert/Error_quadric.h b/src/Contraction/example/Garland_heckbert/Error_quadric.h
index 076f1be0..e7dafaa0 100644
--- a/src/Contraction/example/Garland_heckbert/Error_quadric.h
+++ b/src/Contraction/example/Garland_heckbert/Error_quadric.h
@@ -21,8 +21,8 @@
  * 
  */
 
-#ifndef ERROR_QUADRIC_H_
-#define ERROR_QUADRIC_H_
+#ifndef GARLAND_HECKBERT_ERROR_QUADRIC_H_
+#define GARLAND_HECKBERT_ERROR_QUADRIC_H_
 
 #include <boost/optional/optional.hpp>
 
@@ -179,4 +179,4 @@ template <typename Point> class Error_quadric {
   }
 };
 
-#endif  // ERROR_QUADRIC_H_
+#endif  // GARLAND_HECKBERT_ERROR_QUADRIC_H_
diff --git a/src/Contraction/example/Rips_contraction.cpp b/src/Contraction/example/Rips_contraction.cpp
index 7f19e239..8289b1d3 100644
--- a/src/Contraction/example/Rips_contraction.cpp
+++ b/src/Contraction/example/Rips_contraction.cpp
@@ -27,19 +27,15 @@
 #include <boost/timer/timer.hpp>
 #include <iostream>
 
-using namespace Gudhi;
-using namespace skeleton_blocker;
-using namespace contraction;
-
 struct Geometry_trait {
   typedef Point_d Point;
 };
 
-typedef Geometry_trait::Point Point;
-typedef Skeleton_blocker_simple_geometric_traits<Geometry_trait> Complex_geometric_traits;
-typedef Skeleton_blocker_geometric_complex< Complex_geometric_traits > Complex;
-typedef Edge_profile<Complex> Profile;
-typedef Skeleton_blocker_contractor<Complex> Complex_contractor;
+using Complex_geometric_traits = Gudhi::skeleton_blocker::Skeleton_blocker_simple_geometric_traits<Geometry_trait>;
+using Complex = Gudhi::skeleton_blocker::Skeleton_blocker_geometric_complex< Complex_geometric_traits >;
+using Profile = Gudhi::contraction::Edge_profile<Complex>;
+using Complex_contractor = Gudhi::contraction::Skeleton_blocker_contractor<Complex>;
+
 
 template<typename ComplexType>
 void build_rips(ComplexType& complex, double offset) {
@@ -62,7 +58,7 @@ int main(int argc, char *argv[]) {
   Complex complex;
 
   // load only the points
-  Skeleton_blocker_off_reader<Complex> off_reader(argv[1], complex, true);
+  Gudhi::skeleton_blocker::Skeleton_blocker_off_reader<Complex> off_reader(argv[1], complex, true);
   if (!off_reader.is_valid()) {
     std::cerr << "Unable to read file:" << argv[1] << std::endl;
     return EXIT_FAILURE;
@@ -79,10 +75,10 @@ int main(int argc, char *argv[]) {
       complex.num_edges() << " edges" << std::endl;
 
   Complex_contractor contractor(complex,
-                                new Edge_length_cost<Profile>,
-                                contraction::make_first_vertex_placement<Profile>(),
-                                contraction::make_link_valid_contraction<Profile>(),
-                                contraction::make_remove_popable_blockers_visitor<Profile>());
+                                new Gudhi::contraction::Edge_length_cost<Profile>,
+                                Gudhi::contraction::make_first_vertex_placement<Profile>(),
+                                Gudhi::contraction::make_link_valid_contraction<Profile>(),
+                                Gudhi::contraction::make_remove_popable_blockers_visitor<Profile>());
   contractor.contract_edges();
 
   std::cout << "Counting final number of simplices \n";
diff --git a/src/Doxyfile b/src/Doxyfile
index a41c6d6f..d2d0a447 100644
--- a/src/Doxyfile
+++ b/src/Doxyfile
@@ -38,7 +38,7 @@ PROJECT_NAME           = "GUDHI"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = "1.3.1"
+PROJECT_NUMBER         = "2.0.0"
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
@@ -781,10 +781,10 @@ RECURSIVE              = YES
 # run.
 
 EXCLUDE                = data/ \
-	                     example/ \
-	                     GudhUI/  \
-                             cmake/   \
-                             debian/  \
+	                     example/    \
+	                     GudhUI/     \
+                             cmake/      \
+                             src/cython/ \
                              include/gudhi_patches/
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
diff --git a/src/GudhUI/CMakeLists.txt b/src/GudhUI/CMakeLists.txt
index d3a52b60..ca2e47c1 100644
--- a/src/GudhUI/CMakeLists.txt
+++ b/src/GudhUI/CMakeLists.txt
@@ -1,11 +1,13 @@
 cmake_minimum_required(VERSION 2.8)
 project(GudhUI)
 
-find_package(CGAL COMPONENTS Qt5)
 find_package(Qt5 COMPONENTS Widgets Xml OpenGL)
 find_package(QGLViewer)
 find_package(OpenGL)
 
+if (CGAL_VERSION VERSION_EQUAL 4.8.0)
+  message(ERROR " GudhUI does not compile with CGAL 4.8.0. 4.8.1, 4.8.2 and 4.9 are OK.")
+endif()
 
 if (NOT CGAL_FOUND)
   message(ERROR " GudhUI requires CGAL and will not be compiled.")
@@ -25,7 +27,7 @@ endif()
 
 
 
-if ( CGAL_FOUND AND Qt5_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND )
+if ( CGAL_FOUND AND Qt5_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND AND NOT CGAL_VERSION VERSION_EQUAL 4.8.0)
 
   set(CMAKE_AUTOMOC ON)
   set(CMAKE_AUTOUIC ON)
diff --git a/src/GudhUI/utils/Critical_points.h b/src/GudhUI/utils/Critical_points.h
index b88293e9..2a18e079 100644
--- a/src/GudhUI/utils/Critical_points.h
+++ b/src/GudhUI/utils/Critical_points.h
@@ -105,6 +105,9 @@ template<typename SkBlComplex> class Critical_points {
     if (link.empty())
       return 0;
 
+    Edge_contractor<Complex> contractor(link, link.num_vertices() - 1);
+    (void)contractor;
+
     if (link.num_connected_components() > 1)
       // one than more CC -> not contractible
       return 0;
diff --git a/src/GudhUI/utils/Is_manifold.h b/src/GudhUI/utils/Is_manifold.h
index 6dd7898e..d0974463 100644
--- a/src/GudhUI/utils/Is_manifold.h
+++ b/src/GudhUI/utils/Is_manifold.h
@@ -76,6 +76,8 @@ template<typename SkBlComplex> class Is_manifold {
 
   bool is_k_sphere(Vertex_handle v, int k) {
     auto link = input_complex_.link(v);
+    Edge_contractor<Complex> contractor(link, link.num_vertices() - 1);
+    (void)contractor;
     return (is_sphere_simplex(link) == k);
   }
 
diff --git a/src/GudhUI/utils/Vertex_collapsor.h b/src/GudhUI/utils/Vertex_collapsor.h
index 3f0e7ffd..568dab2f 100644
--- a/src/GudhUI/utils/Vertex_collapsor.h
+++ b/src/GudhUI/utils/Vertex_collapsor.h
@@ -80,6 +80,8 @@ template<typename SkBlComplex> class Vertex_collapsor {
     if (link.empty()) return false;
     if (link.is_cone()) return true;
     if (link.num_connected_components() > 1) return false;
+    Edge_contractor<Complex> contractor(link, link.num_vertices() - 1);
+    (void)contractor;
     return (link.num_vertices() == 1);
   }
 };
diff --git a/src/Persistent_cohomology/doc/COPYRIGHT b/src/Persistent_cohomology/doc/COPYRIGHT
new file mode 100644
index 00000000..34345bef
--- /dev/null
+++ b/src/Persistent_cohomology/doc/COPYRIGHT
@@ -0,0 +1,19 @@
+The files of this directory are 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) 2015  INRIA
+
+This program is free software: you can redistribute it and/or modify it under
+the terms of the GNU General Public License as published by the Free Software
+Foundation, either version 3 of the License, or (at your option) any later
+version.
+
+This program is distributed in the hope that it will be useful, but WITHOUT
+ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along with
+this program.  If not, see <http://www.gnu.org/licenses/>.
diff --git a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h
index 40dd3f93..e17e5926 100644
--- a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h
+++ b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h
@@ -172,6 +172,28 @@ Persistent_cohomology/alpha_complex_3d_persistence.cpp</a> computes the persiste
 2  1 0.0934117 1.00003 
 2  2 0.56444 1.03938 \endcode
 
+\li <a href="_persistent_cohomology_2exact_alpha_complex_3d_persistence_8cpp-example.html">
+Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp</a> computes the persistent homology with
+\f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file.
+Here, as CGAL computes the exact values, it is slower, but it is necessary when points are on a grid
+for instance.
+\code $> ./exact_alpha_complex_3d_persistence ../../data/points/sphere3D_pts_on_grid.off 2 0.1 \endcode
+\code Simplex_tree dim: 3
+2  0 0 inf
+2  2 0.0002 0.2028 \endcode
+
+\li <a href="_persistent_cohomology_2weighted_alpha_complex_3d_persistence_8cpp-example.html">
+Persistent_cohomology/weighted_alpha_complex_3d_persistence.cpp</a> computes the persistent homology with
+\f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the weighted alpha complex on points sampling from an OFF file
+and a weights file.
+\code $> ./weighted_alpha_complex_3d_persistence ../../data/points/tore3D_300.off
+../../data/points/tore3D_300.weights 2 0.45 \endcode
+\code Simplex_tree dim: 3
+2  -0 0 inf
+2  1 0.0682162 1.0001
+2  1 0.0934117 1.00003
+2  2 0.56444 1.03938 \endcode
+
 \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html">
 Persistent_cohomology/alpha_complex_persistence.cpp</a> computes the persistent homology with
 \f$\mathbb{Z}/p\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file.
diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index 38d7e9a9..a6b698c3 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -1,10 +1,6 @@
 cmake_minimum_required(VERSION 2.6)
 project(Persistent_cohomology_examples)
 
-# problem with Visual Studio link on Boost program_options
-add_definitions( -DBOOST_ALL_NO_LIB )
-add_definitions( -DBOOST_ALL_DYN_LINK )
-
 add_executable(plain_homology plain_homology.cpp)
 target_link_libraries(plain_homology ${Boost_SYSTEM_LIBRARY})
 
@@ -38,53 +34,73 @@ 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_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)
+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)
    
 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})
+      target_link_libraries(rips_multifield_persistence
+          ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
       if (TBB_FOUND)
         target_link_libraries(rips_multifield_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/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2 -q 71)
+   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)
 
 if(CGAL_FOUND)
   add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp)
   target_link_libraries(alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+  add_executable(exact_alpha_complex_3d_persistence exact_alpha_complex_3d_persistence.cpp)
+  target_link_libraries(exact_alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+  add_executable(weighted_alpha_complex_3d_persistence weighted_alpha_complex_3d_persistence.cpp)
+  target_link_libraries(weighted_alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
 
   if (TBB_FOUND)
     target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES})
+    target_link_libraries(exact_alpha_complex_3d_persistence ${TBB_LIBRARIES})
+    target_link_libraries(weighted_alpha_complex_3d_persistence ${TBB_LIBRARIES})
   endif(TBB_FOUND)
-  add_test(alpha_complex_3d_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_complex_3d_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off 2 0.45)
-
-
-  if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
-    if (EIGEN3_FOUND)
-      add_executable (alpha_complex_persistence alpha_complex_persistence.cpp)
-      target_link_libraries(alpha_complex_persistence  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
-
-      add_executable(periodic_alpha_complex_3d_persistence periodic_alpha_complex_3d_persistence.cpp)
-      target_link_libraries(periodic_alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
-
-      add_executable(custom_persistence_sort custom_persistence_sort.cpp)
-      target_link_libraries(custom_persistence_sort ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
-
-      if (TBB_FOUND)
-        target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES})
-        target_link_libraries(periodic_alpha_complex_3d_persistence ${TBB_LIBRARIES})
-        target_link_libraries(custom_persistence_sort ${TBB_LIBRARIES})
-      endif(TBB_FOUND)
-      add_test(alpha_complex_persistence_2_0_45 ${CMAKE_CURRENT_BINARY_DIR}/alpha_complex_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -m 0.45 -p 2)
-      add_test(periodic_alpha_complex_3d_persistence_2_0 ${CMAKE_CURRENT_BINARY_DIR}/periodic_alpha_complex_3d_persistence ${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off ${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt 2 0)
-      add_test(custom_persistence_sort ${CMAKE_CURRENT_BINARY_DIR}/custom_persistence_sort)
-    endif(EIGEN3_FOUND)
-  endif (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+  add_test(alpha_complex_3d_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_complex_3d_persistence
+      ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off 2 0.45)
+  add_test(exact_alpha_complex_3d_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/exact_alpha_complex_3d_persistence
+      ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off 2 0.45)
+  add_test(weighted_alpha_complex_3d_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/weighted_alpha_complex_3d_persistence
+      ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.weights 2 0.45)
+
+
+  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
+    add_executable (alpha_complex_persistence alpha_complex_persistence.cpp)
+    target_link_libraries(alpha_complex_persistence
+        ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+
+    add_executable(periodic_alpha_complex_3d_persistence periodic_alpha_complex_3d_persistence.cpp)
+    target_link_libraries(periodic_alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+
+    add_executable(custom_persistence_sort custom_persistence_sort.cpp)
+    target_link_libraries(custom_persistence_sort ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+
+    if (TBB_FOUND)
+      target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES})
+      target_link_libraries(periodic_alpha_complex_3d_persistence ${TBB_LIBRARIES})
+      target_link_libraries(custom_persistence_sort ${TBB_LIBRARIES})
+    endif(TBB_FOUND)
+    add_test(alpha_complex_persistence_2_0_45 ${CMAKE_CURRENT_BINARY_DIR}/alpha_complex_persistence
+        ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -m 0.45 -p 2)
+    add_test(periodic_alpha_complex_3d_persistence_2_0 ${CMAKE_CURRENT_BINARY_DIR}/periodic_alpha_complex_3d_persistence
+        ${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off ${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt 2 0)
+    add_test(custom_persistence_sort ${CMAKE_CURRENT_BINARY_DIR}/custom_persistence_sort)
+  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
 endif(CGAL_FOUND)
diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_helper.h b/src/Persistent_cohomology/example/alpha_complex_3d_helper.h
new file mode 100644
index 00000000..7865e4ec
--- /dev/null
+++ b/src/Persistent_cohomology/example/alpha_complex_3d_helper.h
@@ -0,0 +1,76 @@
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       Vincent Rouvreau
+ *
+ *    Copyright (C) 2014  INRIA 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/>.
+ */
+
+#ifndef ALPHA_COMPLEX_3D_HELPER_H_
+#define ALPHA_COMPLEX_3D_HELPER_H_
+
+template<class Vertex_list, class Cell_handle>
+Vertex_list from_cell(const Cell_handle& ch) {
+  Vertex_list the_list;
+  for (auto i = 0; i < 4; i++) {
+#ifdef DEBUG_TRACES
+    std::cout << "from cell[" << i << "]=" << ch->vertex(i)->point() << std::endl;
+#endif  // DEBUG_TRACES
+    the_list.push_back(ch->vertex(i));
+  }
+  return the_list;
+}
+
+template<class Vertex_list, class Facet>
+Vertex_list from_facet(const Facet& fct) {
+  Vertex_list the_list;
+  for (auto i = 0; i < 4; i++) {
+    if (fct.second != i) {
+#ifdef DEBUG_TRACES
+      std::cout << "from facet=[" << i << "]" << fct.first->vertex(i)->point() << std::endl;
+#endif  // DEBUG_TRACES
+      the_list.push_back(fct.first->vertex(i));
+    }
+  }
+  return the_list;
+}
+
+template<class Vertex_list, class Edge_3>
+Vertex_list from_edge(const Edge_3& edg) {
+  Vertex_list the_list;
+  for (auto i = 0; i < 4; i++) {
+    if ((edg.second == i) || (edg.third == i)) {
+#ifdef DEBUG_TRACES
+      std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl;
+#endif  // DEBUG_TRACES
+      the_list.push_back(edg.first->vertex(i));
+    }
+  }
+  return the_list;
+}
+
+template<class Vertex_list, class Vertex_handle>
+Vertex_list from_vertex(const Vertex_handle& vh) {
+  Vertex_list the_list;
+#ifdef DEBUG_TRACES
+  std::cout << "from vertex=" << vh->point() << std::endl;
+#endif  // DEBUG_TRACES
+  the_list.push_back(vh);
+  return the_list;
+}
+
+#endif  // ALPHA_COMPLEX_3D_HELPER_H_
diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
index 978dc942..fd227b82 100644
--- a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
@@ -20,10 +20,11 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
+#include <boost/variant.hpp>
+
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Persistent_cohomology.h>
 #include <gudhi/Points_3D_off_io.h>
-#include <boost/variant.hpp>
 
 #include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
 #include <CGAL/Delaunay_triangulation_3.h>
@@ -39,85 +40,42 @@
 #include <list>
 #include <vector>
 
+#include "alpha_complex_3d_helper.h"
+
 // Alpha_shape_3 templates type definitions
-typedef CGAL::Exact_predicates_inexact_constructions_kernel Kernel;
-typedef CGAL::Alpha_shape_vertex_base_3<Kernel> Vb;
-typedef CGAL::Alpha_shape_cell_base_3<Kernel> Fb;
-typedef CGAL::Triangulation_data_structure_3<Vb, Fb> Tds;
-typedef CGAL::Delaunay_triangulation_3<Kernel, Tds> Triangulation_3;
-typedef CGAL::Alpha_shape_3<Triangulation_3> Alpha_shape_3;
+using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel;
+using Vb = CGAL::Alpha_shape_vertex_base_3<Kernel>;
+using Fb = CGAL::Alpha_shape_cell_base_3<Kernel>;
+using Tds = CGAL::Triangulation_data_structure_3<Vb, Fb>;
+using Triangulation_3 = CGAL::Delaunay_triangulation_3<Kernel, Tds>;
+using Alpha_shape_3 = CGAL::Alpha_shape_3<Triangulation_3>;
 
 // From file type definition
-typedef Kernel::Point_3 Point_3;
+using Point_3 = Kernel::Point_3;
 
 // filtration with alpha values needed type definition
-typedef Alpha_shape_3::FT Alpha_value_type;
-typedef CGAL::Object Object;
-typedef CGAL::Dispatch_output_iterator<
-CGAL::cpp11::tuple<Object, Alpha_value_type>,
-CGAL::cpp11::tuple<std::back_insert_iterator< std::vector<Object> >,
-    std::back_insert_iterator< std::vector<Alpha_value_type> > > > Dispatch;
-typedef Alpha_shape_3::Cell_handle Cell_handle;
-typedef Alpha_shape_3::Facet Facet;
-typedef Alpha_shape_3::Edge Edge_3;
-typedef std::list<Alpha_shape_3::Vertex_handle> Vertex_list;
+using Alpha_value_type = Alpha_shape_3::FT;
+using Object = CGAL::Object;
+using Dispatch = CGAL::Dispatch_output_iterator<
+          CGAL::cpp11::tuple<Object, Alpha_value_type>,
+          CGAL::cpp11::tuple<std::back_insert_iterator< std::vector<Object> >,
+          std::back_insert_iterator< std::vector<Alpha_value_type> > > >;
+using Cell_handle = Alpha_shape_3::Cell_handle;
+using Facet = Alpha_shape_3::Facet;
+using Edge_3 = Alpha_shape_3::Edge;
+using Vertex_handle = Alpha_shape_3::Vertex_handle;
+using Vertex_list = std::list<Alpha_shape_3::Vertex_handle>;
 
 // 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;
-typedef std::vector< Simplex_tree_vertex > Simplex_tree_vector_vertex;
-typedef Gudhi::persistent_cohomology::Persistent_cohomology< ST, Gudhi::persistent_cohomology::Field_Zp > PCOH;
-
-Vertex_list from(const Cell_handle& ch) {
-  Vertex_list the_list;
-  for (auto i = 0; i < 4; i++) {
-#ifdef DEBUG_TRACES
-    std::cout << "from cell[" << i << "]=" << ch->vertex(i)->point() << std::endl;
-#endif  // DEBUG_TRACES
-    the_list.push_back(ch->vertex(i));
-  }
-  return the_list;
-}
-
-Vertex_list from(const Facet& fct) {
-  Vertex_list the_list;
-  for (auto i = 0; i < 4; i++) {
-    if (fct.second != i) {
-#ifdef DEBUG_TRACES
-      std::cout << "from facet=[" << i << "]" << fct.first->vertex(i)->point() << std::endl;
-#endif  // DEBUG_TRACES
-      the_list.push_back(fct.first->vertex(i));
-    }
-  }
-  return the_list;
-}
-
-Vertex_list from(const Edge_3& edg) {
-  Vertex_list the_list;
-  for (auto i = 0; i < 4; i++) {
-    if ((edg.second == i) || (edg.third == i)) {
-#ifdef DEBUG_TRACES
-      std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl;
-#endif  // DEBUG_TRACES
-      the_list.push_back(edg.first->vertex(i));
-    }
-  }
-  return the_list;
-}
-
-Vertex_list from(const Alpha_shape_3::Vertex_handle& vh) {
-  Vertex_list the_list;
-#ifdef DEBUG_TRACES
-  std::cout << "from vertex=" << vh->point() << std::endl;
-#endif  // DEBUG_TRACES
-  the_list.push_back(vh);
-  return the_list;
-}
-
-void usage(char * const progName) {
+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>;
+using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >;
+using PCOH = Gudhi::persistent_cohomology::Persistent_cohomology< ST, Gudhi::persistent_cohomology::Field_Zp >;
+
+void usage(const std::string& progName) {
   std::cerr << "Usage: " << progName <<
       " path_to_file_graph coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
   exit(-1);
@@ -185,30 +143,29 @@ int main(int argc, char * const argv[]) {
   for (auto object_iterator : the_objects) {
     // Retrieve Alpha shape vertex list from object
     if (const Cell_handle * cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
-      vertex_list = from(*cell);
+      vertex_list = from_cell<Vertex_list, Cell_handle>(*cell);
       count_cells++;
       if (dim_max < 3) {
         // Cell is of dim 3
         dim_max = 3;
       }
     } else if (const Facet * facet = CGAL::object_cast<Facet>(&object_iterator)) {
-      vertex_list = from(*facet);
+      vertex_list = from_facet<Vertex_list, Facet>(*facet);
       count_facets++;
       if (dim_max < 2) {
         // Facet is of dim 2
         dim_max = 2;
       }
     } else if (const Edge_3 * edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
-      vertex_list = from(*edge);
+      vertex_list = from_edge<Vertex_list, Edge_3>(*edge);
       count_edges++;
       if (dim_max < 1) {
         // Edge_3 is of dim 1
         dim_max = 1;
       }
-    } else if (const Alpha_shape_3::Vertex_handle * vertex =
-               CGAL::object_cast<Alpha_shape_3::Vertex_handle>(&object_iterator)) {
+    } else if (const Vertex_handle * vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) {
       count_vertices++;
-      vertex_list = from(*vertex);
+      vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex);
     }
     // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex
     Simplex_tree_vector_vertex the_simplex_tree;
diff --git a/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp
new file mode 100644
index 00000000..8a335075
--- /dev/null
+++ b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp
@@ -0,0 +1,245 @@
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       Vincent Rouvreau
+ *
+ *    Copyright (C) 2014  INRIA 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/>.
+ */
+
+#include <boost/variant.hpp>
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Persistent_cohomology.h>
+#include <gudhi/Points_3D_off_io.h>
+
+#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
+#include <CGAL/Delaunay_triangulation_3.h>
+#include <CGAL/Alpha_shape_3.h>
+#include <CGAL/iterator.h>
+
+#include <fstream>
+#include <cmath>
+#include <string>
+#include <tuple>
+#include <map>
+#include <utility>
+#include <list>
+#include <vector>
+
+#include "alpha_complex_3d_helper.h"
+
+// Alpha_shape_3 templates type definitions
+using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel;
+using Exact_tag = CGAL::Tag_true;
+using Vb = CGAL::Alpha_shape_vertex_base_3<Kernel, CGAL::Default, Exact_tag>;
+using Fb = CGAL::Alpha_shape_cell_base_3<Kernel, CGAL::Default, Exact_tag>;
+using Tds = CGAL::Triangulation_data_structure_3<Vb, Fb>;
+using Triangulation_3 = CGAL::Delaunay_triangulation_3<Kernel, Tds>;
+using Alpha_shape_3 = CGAL::Alpha_shape_3<Triangulation_3, Exact_tag>;
+
+// From file type definition
+using Point_3 = Kernel::Point_3;
+
+// filtration with alpha values needed type definition
+using Alpha_value_type = Alpha_shape_3::FT;
+using Object = CGAL::Object;
+using Dispatch = CGAL::Dispatch_output_iterator<
+          CGAL::cpp11::tuple<Object, Alpha_value_type>,
+          CGAL::cpp11::tuple<std::back_insert_iterator< std::vector<Object> >,
+          std::back_insert_iterator< std::vector<Alpha_value_type> > > >;
+using Cell_handle = Alpha_shape_3::Cell_handle;
+using Facet = Alpha_shape_3::Facet;
+using Edge_3 = Alpha_shape_3::Edge;
+using Vertex_handle = Alpha_shape_3::Vertex_handle;
+using Vertex_list = std::list<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>;
+using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >;
+using PCOH = Gudhi::persistent_cohomology::Persistent_cohomology< ST, Gudhi::persistent_cohomology::Field_Zp >;
+
+void usage(char * const progName) {
+  std::cerr << "Usage: " << progName <<
+      " path_to_file_graph coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
+  exit(-1);
+}
+
+int main(int argc, char * const argv[]) {
+  // program args management
+  if (argc != 4) {
+    std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n";
+    usage(argv[0]);
+  }
+
+  int coeff_field_characteristic = atoi(argv[2]);
+
+  Filtration_value min_persistence = 0.0;
+  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]);
+  }
+
+  // Read points from file
+  std::string offInputFile(argv[1]);
+  // Read the OFF file (input file name given as parameter) and triangulate points
+  Gudhi::Points_3D_off_reader<Point_3> off_reader(offInputFile);
+  // Check the read operation was correct
+  if (!off_reader.is_valid()) {
+    std::cerr << "Unable to read file " << offInputFile << std::endl;
+    usage(argv[0]);
+  }
+
+  // Retrieve the triangulation
+  std::vector<Point_3> lp = off_reader.get_point_cloud();
+
+  // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode.
+  Alpha_shape_3 as(lp.begin(), lp.end(), 0, Alpha_shape_3::GENERAL);
+#ifdef DEBUG_TRACES
+  std::cout << "Alpha shape computed in GENERAL mode" << std::endl;
+#endif  // DEBUG_TRACES
+
+  // filtration with alpha values from alpha shape
+  std::vector<Object> the_objects;
+  std::vector<Alpha_value_type> the_alpha_values;
+
+  Dispatch disp = CGAL::dispatch_output<Object, Alpha_value_type>(std::back_inserter(the_objects),
+                                                                  std::back_inserter(the_alpha_values));
+
+  as.filtration_with_alpha_values(disp);
+#ifdef DEBUG_TRACES
+  std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl;
+#endif  // DEBUG_TRACES
+
+  Alpha_shape_3::size_type count_vertices = 0;
+  Alpha_shape_3::size_type count_edges = 0;
+  Alpha_shape_3::size_type count_facets = 0;
+  Alpha_shape_3::size_type count_cells = 0;
+
+  // Loop on objects vector
+  Vertex_list vertex_list;
+  ST simplex_tree;
+  Alpha_shape_simplex_tree_map map_cgal_simplex_tree;
+  std::vector<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin();
+  int dim_max = 0;
+  Filtration_value filtration_max = 0.0;
+  for (auto object_iterator : the_objects) {
+    // Retrieve Alpha shape vertex list from object
+    if (const Cell_handle * cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
+      vertex_list = from_cell<Vertex_list, Cell_handle>(*cell);
+      count_cells++;
+      if (dim_max < 3) {
+        // Cell is of dim 3
+        dim_max = 3;
+      }
+    } else if (const Facet * facet = CGAL::object_cast<Facet>(&object_iterator)) {
+      vertex_list = from_facet<Vertex_list, Facet>(*facet);
+      count_facets++;
+      if (dim_max < 2) {
+        // Facet is of dim 2
+        dim_max = 2;
+      }
+    } else if (const Edge_3 * edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
+      vertex_list = from_edge<Vertex_list, Edge_3>(*edge);
+      count_edges++;
+      if (dim_max < 1) {
+        // Edge_3 is of dim 1
+        dim_max = 1;
+      }
+    } else if (const Vertex_handle * vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) {
+      count_vertices++;
+      vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex);
+    }
+    // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex
+    Simplex_tree_vector_vertex the_simplex_tree;
+    for (auto the_alpha_shape_vertex : vertex_list) {
+      Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex);
+      if (the_map_iterator == map_cgal_simplex_tree.end()) {
+        // alpha shape not found
+        Simplex_tree_vertex vertex = map_cgal_simplex_tree.size();
+#ifdef DEBUG_TRACES
+        std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl;
+#endif  // DEBUG_TRACES
+        the_simplex_tree.push_back(vertex);
+        map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex));
+      } else {
+        // alpha shape found
+        Simplex_tree_vertex vertex = the_map_iterator->second;
+#ifdef DEBUG_TRACES
+        std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl;
+#endif  // DEBUG_TRACES
+        the_simplex_tree.push_back(vertex);
+      }
+    }
+    // Construction of the simplex_tree
+    // you can also use the_alpha_value_iterator->exact()
+    Filtration_value filtr = /*std::sqrt*/CGAL::to_double(the_alpha_value_iterator->exact());
+#ifdef DEBUG_TRACES
+    std::cout << "filtration = " << filtr << std::endl;
+#endif  // DEBUG_TRACES
+    if (filtr > filtration_max) {
+      filtration_max = filtr;
+    }
+    simplex_tree.insert_simplex(the_simplex_tree, filtr);
+    if (the_alpha_value_iterator != the_alpha_values.end())
+      ++the_alpha_value_iterator;
+    else
+      std::cout << "This shall not happen" << std::endl;
+  }
+  simplex_tree.set_filtration(filtration_max);
+  simplex_tree.set_dimension(dim_max);
+
+#ifdef DEBUG_TRACES
+  std::cout << "vertices \t\t" << count_vertices << std::endl;
+  std::cout << "edges \t\t" << count_edges << std::endl;
+  std::cout << "facets \t\t" << count_facets << std::endl;
+  std::cout << "cells \t\t" << count_cells << std::endl;
+
+
+  std::cout << "Information of the Simplex Tree: " << std::endl;
+  std::cout << "  Number of vertices = " << simplex_tree.num_vertices() << " ";
+  std::cout << "  Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl;
+  std::cout << "  Dimension = " << simplex_tree.dimension() << " ";
+  std::cout << "  filtration = " << simplex_tree.filtration() << std::endl << std::endl;
+#endif  // DEBUG_TRACES
+
+#ifdef DEBUG_TRACES
+  std::cout << "Iterator on vertices: " << std::endl;
+  for (auto vertex : simplex_tree.complex_vertex_range()) {
+    std::cout << vertex << " ";
+  }
+#endif  // DEBUG_TRACES
+
+  // Sort the simplices in the order of the filtration
+  simplex_tree.initialize_filtration();
+
+  std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl;
+  // Compute the persistence diagram of the complex
+  PCOH pcoh(simplex_tree);
+  // initializes the coefficient field for homology
+  pcoh.init_coefficients(coeff_field_characteristic);
+
+  pcoh.compute_persistent_cohomology(min_persistence);
+
+  pcoh.output_diagram();
+
+  return 0;
+}
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 dbc42706..8928cfc2 100644
--- a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
@@ -20,10 +20,11 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
+#include <boost/variant.hpp>
+
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Persistent_cohomology.h>
 #include <gudhi/Points_3D_off_io.h>
-#include <boost/variant.hpp>
 
 #include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
 #include <CGAL/Periodic_3_Delaunay_triangulation_traits_3.h>
@@ -41,6 +42,8 @@
 #include <vector>
 #include <cstdlib>
 
+#include "alpha_complex_3d_helper.h"
+
 // Traits
 using K = CGAL::Exact_predicates_inexact_constructions_kernel;
 using PK = CGAL::Periodic_3_Delaunay_triangulation_traits_3<K>;
@@ -67,6 +70,7 @@ using Dispatch = CGAL::Dispatch_output_iterator<
 using Cell_handle = Alpha_shape_3::Cell_handle;
 using Facet = Alpha_shape_3::Facet;
 using Edge_3 = Alpha_shape_3::Edge;
+using Vertex_handle = Alpha_shape_3::Vertex_handle;
 using Vertex_list = std::list<Alpha_shape_3::Vertex_handle>;
 
 // gudhi type definition
@@ -79,52 +83,6 @@ using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >;
 using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<
     ST, Gudhi::persistent_cohomology::Field_Zp >;
 
-Vertex_list from(const Cell_handle& ch) {
-  Vertex_list the_list;
-  for (auto i = 0; i < 4; i++) {
-#ifdef DEBUG_TRACES
-    std::cout << "from cell[" << i << "]=" << ch->vertex(i)->point() << std::endl;
-#endif  // DEBUG_TRACES
-    the_list.push_back(ch->vertex(i));
-  }
-  return the_list;
-}
-
-Vertex_list from(const Facet& fct) {
-  Vertex_list the_list;
-  for (auto i = 0; i < 4; i++) {
-    if (fct.second != i) {
-#ifdef DEBUG_TRACES
-      std::cout << "from facet=[" << i << "]" << fct.first->vertex(i)->point() << std::endl;
-#endif  // DEBUG_TRACES
-      the_list.push_back(fct.first->vertex(i));
-    }
-  }
-  return the_list;
-}
-
-Vertex_list from(const Edge_3& edg) {
-  Vertex_list the_list;
-  for (auto i = 0; i < 4; i++) {
-    if ((edg.second == i) || (edg.third == i)) {
-#ifdef DEBUG_TRACES
-      std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl;
-#endif  // DEBUG_TRACES
-      the_list.push_back(edg.first->vertex(i));
-    }
-  }
-  return the_list;
-}
-
-Vertex_list from(const Alpha_shape_3::Vertex_handle& vh) {
-  Vertex_list the_list;
-#ifdef DEBUG_TRACES
-  std::cout << "from vertex=" << vh->point() << std::endl;
-#endif  // DEBUG_TRACES
-  the_list.push_back(vh);
-  return the_list;
-}
-
 void usage(char * const progName) {
   std::cerr << "Usage: " << progName <<
       " path_to_file_graph path_to_iso_cuboid_3_file coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
@@ -203,21 +161,21 @@ int main(int argc, char * const argv[]) {
   for (auto object_iterator : the_objects) {
     // Retrieve Alpha shape vertex list from object
     if (const Cell_handle * cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
-      vertex_list = from(*cell);
+      vertex_list = from_cell<Vertex_list, Cell_handle>(*cell);
       count_cells++;
       if (dim_max < 3) {
         // Cell is of dim 3
         dim_max = 3;
       }
     } else if (const Facet * facet = CGAL::object_cast<Facet>(&object_iterator)) {
-      vertex_list = from(*facet);
+      vertex_list = from_facet<Vertex_list, Facet>(*facet);
       count_facets++;
       if (dim_max < 2) {
         // Facet is of dim 2
         dim_max = 2;
       }
     } else if (const Edge_3 * edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
-      vertex_list = from(*edge);
+      vertex_list = from_edge<Vertex_list, Edge_3>(*edge);
       count_edges++;
       if (dim_max < 1) {
         // Edge_3 is of dim 1
@@ -226,7 +184,7 @@ int main(int argc, char * const argv[]) {
     } else if (const Alpha_shape_3::Vertex_handle * vertex =
                CGAL::object_cast<Alpha_shape_3::Vertex_handle>(&object_iterator)) {
       count_vertices++;
-      vertex_list = from(*vertex);
+      vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex);
     }
     // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex
     Simplex_tree_vector_vertex the_simplex_tree;
diff --git a/src/Persistent_cohomology/example/plain_homology.cpp b/src/Persistent_cohomology/example/plain_homology.cpp
index ae82c817..50f692f2 100644
--- a/src/Persistent_cohomology/example/plain_homology.cpp
+++ b/src/Persistent_cohomology/example/plain_homology.cpp
@@ -27,13 +27,11 @@
 #include <vector>
 #include <cstdint>  // for std::uint8_t
 
-using namespace Gudhi;
-
 /* We could perfectly well use the default Simplex_tree<> (which uses
  * Simplex_tree_options_full_featured), the following simply demonstrates
  * how to save on storage by not storing a filtration value.  */
 
-struct MyOptions : Simplex_tree_options_full_featured {
+struct MyOptions : Gudhi::Simplex_tree_options_full_featured {
   // Implicitly use 0 as filtration value for all simplices
   static const bool store_filtration = false;
   // The persistence algorithm needs this
@@ -43,7 +41,10 @@ struct MyOptions : Simplex_tree_options_full_featured {
   // Maximum number of simplices to compute persistence is 2^8 - 1 = 255. One is reserved for null_key
   typedef std::uint8_t Simplex_key;
 };
-typedef Simplex_tree<MyOptions> ST;
+
+using ST = Gudhi::Simplex_tree<MyOptions>;
+using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
+using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<ST, Field_Zp>;
 
 int main() {
   ST st;
@@ -70,7 +71,7 @@ int main() {
   st.initialize_filtration();
 
   // Class for homology computation
-  persistent_cohomology::Persistent_cohomology<ST, persistent_cohomology::Field_Zp> pcoh(st);
+  Persistent_cohomology pcoh(st);
 
   // Initialize the coefficient field Z/2Z for homology
   pcoh.init_coefficients(2);
diff --git a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp
new file mode 100644
index 00000000..34b90933
--- /dev/null
+++ b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp
@@ -0,0 +1,263 @@
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       Vincent Rouvreau
+ *
+ *    Copyright (C) 2014  INRIA
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include <boost/variant.hpp>
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Persistent_cohomology.h>
+#include <gudhi/Points_3D_off_io.h>
+
+#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
+#include <CGAL/Regular_triangulation_euclidean_traits_3.h>
+#include <CGAL/Regular_triangulation_3.h>
+#include <CGAL/Alpha_shape_3.h>
+#include <CGAL/iterator.h>
+
+#include <fstream>
+#include <cmath>
+#include <string>
+#include <tuple>
+#include <map>
+#include <utility>
+#include <list>
+#include <vector>
+#include <cstdlib>
+
+#include "alpha_complex_3d_helper.h"
+
+// Traits
+using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel;
+using Gt = CGAL::Regular_triangulation_euclidean_traits_3<Kernel>;
+using Vb = CGAL::Alpha_shape_vertex_base_3<Gt>;
+using Fb = CGAL::Alpha_shape_cell_base_3<Gt>;
+using Tds = CGAL::Triangulation_data_structure_3<Vb, Fb>;
+using Triangulation_3 = CGAL::Regular_triangulation_3<Gt, Tds>;
+using Alpha_shape_3 = CGAL::Alpha_shape_3<Triangulation_3>;
+
+// From file type definition
+using Point_3 = Gt::Bare_point;
+using Weighted_point_3 = Gt::Weighted_point;
+
+// filtration with alpha values needed type definition
+using Alpha_value_type = Alpha_shape_3::FT;
+using Object = CGAL::Object;
+using Dispatch = CGAL::Dispatch_output_iterator<
+          CGAL::cpp11::tuple<Object, Alpha_value_type>,
+          CGAL::cpp11::tuple<std::back_insert_iterator< std::vector<Object> >,
+          std::back_insert_iterator< std::vector<Alpha_value_type> > > >;
+using Cell_handle = Alpha_shape_3::Cell_handle;
+using Facet = Alpha_shape_3::Facet;
+using Edge_3 = Alpha_shape_3::Edge;
+using Vertex_handle = Alpha_shape_3::Vertex_handle;
+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>;
+using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >;
+using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<
+    ST, Gudhi::persistent_cohomology::Field_Zp >;
+
+void usage(char * const progName) {
+  std::cerr << "Usage: " << progName <<
+      " path_to_file_graph path_to_weight_file coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
+  exit(-1);
+}
+
+int main(int argc, char * const argv[]) {
+  // program args management
+  if (argc != 5) {
+    std::cerr << "Error: Number of arguments (" << argc << ") 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]);
+  // Read the OFF file (input file name given as parameter) and triangulate points
+  Gudhi::Points_3D_off_reader<Point_3> off_reader(offInputFile);
+  // Check the read operation was correct
+  if (!off_reader.is_valid()) {
+    std::cerr << "Unable to read file " << offInputFile << std::endl;
+    usage(argv[0]);
+  }
+
+  // Retrieve the triangulation
+  std::vector<Point_3> lp = off_reader.get_point_cloud();
+
+  // Read weights information from file
+  std::ifstream weights_ifstr(argv[2]);
+  std::vector<Weighted_point_3> wp;
+  if (weights_ifstr.good()) {
+    double weight = 0.0;
+    std::size_t index = 0;
+    // Attempt read the weight in a double format, return false if it fails
+    while ((weights_ifstr >> weight) && (index < lp.size())) {
+      wp.push_back(Weighted_point_3(lp[index], weight));
+      index++;
+    }
+    if (index != lp.size()) {
+      std::cerr << "Bad number of weights in file " << argv[2] << std::endl;
+      usage(argv[0]);
+    }
+  } else {
+    std::cerr << "Unable to read file " << argv[2] << std::endl;
+    usage(argv[0]);
+  }
+
+  // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode.
+  Alpha_shape_3 as(lp.begin(), lp.end(), 0, Alpha_shape_3::GENERAL);
+#ifdef DEBUG_TRACES
+  std::cout << "Alpha shape computed in GENERAL mode" << std::endl;
+#endif  // DEBUG_TRACES
+
+  // filtration with alpha values from alpha shape
+  std::vector<Object> the_objects;
+  std::vector<Alpha_value_type> the_alpha_values;
+
+  Dispatch disp = CGAL::dispatch_output<Object, Alpha_value_type>(std::back_inserter(the_objects),
+                                                                  std::back_inserter(the_alpha_values));
+
+  as.filtration_with_alpha_values(disp);
+#ifdef DEBUG_TRACES
+  std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl;
+#endif  // DEBUG_TRACES
+
+  Alpha_shape_3::size_type count_vertices = 0;
+  Alpha_shape_3::size_type count_edges = 0;
+  Alpha_shape_3::size_type count_facets = 0;
+  Alpha_shape_3::size_type count_cells = 0;
+
+  // Loop on objects vector
+  Vertex_list vertex_list;
+  ST simplex_tree;
+  Alpha_shape_simplex_tree_map map_cgal_simplex_tree;
+  std::vector<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin();
+  int dim_max = 0;
+  Filtration_value filtration_max = 0.0;
+  for (auto object_iterator : the_objects) {
+    // Retrieve Alpha shape vertex list from object
+    if (const Cell_handle * cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
+      vertex_list = from_cell<Vertex_list, Cell_handle>(*cell);
+      count_cells++;
+      if (dim_max < 3) {
+        // Cell is of dim 3
+        dim_max = 3;
+      }
+    } else if (const Facet * facet = CGAL::object_cast<Facet>(&object_iterator)) {
+      vertex_list = from_facet<Vertex_list, Facet>(*facet);
+      count_facets++;
+      if (dim_max < 2) {
+        // Facet is of dim 2
+        dim_max = 2;
+      }
+    } else if (const Edge_3 * edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
+      vertex_list = from_edge<Vertex_list, Edge_3>(*edge);
+      count_edges++;
+      if (dim_max < 1) {
+        // Edge_3 is of dim 1
+        dim_max = 1;
+      }
+    } else if (const Alpha_shape_3::Vertex_handle * vertex =
+               CGAL::object_cast<Alpha_shape_3::Vertex_handle>(&object_iterator)) {
+      count_vertices++;
+      vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex);
+    }
+    // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex
+    Simplex_tree_vector_vertex the_simplex_tree;
+    for (auto the_alpha_shape_vertex : vertex_list) {
+      Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex);
+      if (the_map_iterator == map_cgal_simplex_tree.end()) {
+        // alpha shape not found
+        Simplex_tree_vertex vertex = map_cgal_simplex_tree.size();
+#ifdef DEBUG_TRACES
+        std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl;
+#endif  // DEBUG_TRACES
+        the_simplex_tree.push_back(vertex);
+        map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex));
+      } else {
+        // alpha shape found
+        Simplex_tree_vertex vertex = the_map_iterator->second;
+#ifdef DEBUG_TRACES
+        std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl;
+#endif  // DEBUG_TRACES
+        the_simplex_tree.push_back(vertex);
+      }
+    }
+    // Construction of the simplex_tree
+    Filtration_value filtr = /*std::sqrt*/(*the_alpha_value_iterator);
+#ifdef DEBUG_TRACES
+    std::cout << "filtration = " << filtr << std::endl;
+#endif  // DEBUG_TRACES
+    if (filtr > filtration_max) {
+      filtration_max = filtr;
+    }
+    simplex_tree.insert_simplex(the_simplex_tree, filtr);
+    if (the_alpha_value_iterator != the_alpha_values.end())
+      ++the_alpha_value_iterator;
+    else
+      std::cout << "This shall not happen" << std::endl;
+  }
+  simplex_tree.set_filtration(filtration_max);
+  simplex_tree.set_dimension(dim_max);
+
+#ifdef DEBUG_TRACES
+  std::cout << "vertices \t\t" << count_vertices << std::endl;
+  std::cout << "edges \t\t" << count_edges << std::endl;
+  std::cout << "facets \t\t" << count_facets << std::endl;
+  std::cout << "cells \t\t" << count_cells << std::endl;
+
+
+  std::cout << "Information of the Simplex Tree: " << std::endl;
+  std::cout << "  Number of vertices = " << simplex_tree.num_vertices() << " ";
+  std::cout << "  Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl;
+  std::cout << "  Dimension = " << simplex_tree.dimension() << " ";
+  std::cout << "  filtration = " << simplex_tree.filtration() << std::endl << std::endl;
+#endif  // DEBUG_TRACES
+
+#ifdef DEBUG_TRACES
+  std::cout << "Iterator on vertices: " << std::endl;
+  for (auto vertex : simplex_tree.complex_vertex_range()) {
+    std::cout << vertex << " ";
+  }
+#endif  // DEBUG_TRACES
+
+  // Sort the simplices in the order of the filtration
+  simplex_tree.initialize_filtration();
+
+  std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl;
+  // Compute the persistence diagram of the complex
+  Persistent_cohomology pcoh(simplex_tree, true);
+  // initializes the coefficient field for homology
+  pcoh.init_coefficients(coeff_field_characteristic);
+
+  pcoh.compute_persistent_cohomology(min_persistence);
+
+  pcoh.output_diagram();
+
+  return 0;
+}
diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
index b3339b7d..672fda48 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
@@ -603,7 +603,7 @@ class Persistent_cohomology {
    */
   std::vector<int> betti_numbers() const {
     // Init Betti numbers vector with zeros until Simplicial complex dimension
-    std::vector<int> betti_numbers(cpx_->dimension(), 0);
+    std::vector<int> betti_numbers(dim_max_, 0);
 
     for (auto pair : persistent_pairs_) {
       // Count never ended persistence intervals
@@ -642,8 +642,7 @@ class Persistent_cohomology {
    */
   std::vector<int> persistent_betti_numbers(Filtration_value from, Filtration_value to) const {
     // Init Betti numbers vector with zeros until Simplicial complex dimension
-    std::vector<int> betti_numbers(cpx_->dimension(), 0);
-
+    std::vector<int> betti_numbers(dim_max_, 0);
     for (auto pair : persistent_pairs_) {
       // Count persistence intervals that covers the given interval
       // null_simplex test : if the function is called with to=+infinity, we still get something useful. And it will
diff --git a/src/Rips_complex/concept/Simplicial_complex_for_rips.h b/src/Rips_complex/concept/SimplicialComplexForRips.h
index 7dab0615..7dab0615 100644
--- a/src/Rips_complex/concept/Simplicial_complex_for_rips.h
+++ b/src/Rips_complex/concept/SimplicialComplexForRips.h
diff --git a/src/Rips_complex/doc/COPYRIGHT b/src/Rips_complex/doc/COPYRIGHT
new file mode 100644
index 00000000..594b7d03
--- /dev/null
+++ b/src/Rips_complex/doc/COPYRIGHT
@@ -0,0 +1,19 @@
+The files of this directory are 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) 2015  INRIA
+
+This program is free software: you can redistribute it and/or modify it under
+the terms of the GNU General Public License as published by the Free Software
+Foundation, either version 3 of the License, or (at your option) any later
+version.
+
+This program is distributed in the hope that it will be useful, but WITHOUT
+ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along with
+this program.  If not, see <http://www.gnu.org/licenses/>.
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
index ef3a9d13..7ae8126f 100644
--- 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
@@ -1,5 +1,5 @@
 #include <gudhi/Rips_complex.h>
-// to construct Rips_complex from a OFF file of points
+// to construct Rips_complex from a csv file representing a distance matrix
 #include <gudhi/reader_utils.h>
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/distance_functions.h>
diff --git a/src/Simplex_tree/doc/COPYRIGHT b/src/Simplex_tree/doc/COPYRIGHT
new file mode 100644
index 00000000..34345bef
--- /dev/null
+++ b/src/Simplex_tree/doc/COPYRIGHT
@@ -0,0 +1,19 @@
+The files of this directory are 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) 2015  INRIA
+
+This program is free software: you can redistribute it and/or modify it under
+the terms of the GNU General Public License as published by the Free Software
+Foundation, either version 3 of the License, or (at your option) any later
+version.
+
+This program is distributed in the hope that it will be useful, but WITHOUT
+ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along with
+this program.  If not, see <http://www.gnu.org/licenses/>.
diff --git a/src/Simplex_tree/example/mini_simplex_tree.cpp b/src/Simplex_tree/example/mini_simplex_tree.cpp
index 7e48aaaf..ad99df23 100644
--- a/src/Simplex_tree/example/mini_simplex_tree.cpp
+++ b/src/Simplex_tree/example/mini_simplex_tree.cpp
@@ -24,19 +24,18 @@
 #include <iostream>
 #include <initializer_list>
 
-using namespace Gudhi;
-
-struct MyOptions : Simplex_tree_options_full_featured {
+struct MyOptions : Gudhi::Simplex_tree_options_full_featured {
   // Not doing persistence, so we don't need those
   static const bool store_key = false;
   static const bool store_filtration = false;
   // I have few vertices
   typedef short Vertex_handle;
 };
-typedef Simplex_tree<MyOptions> ST;
+
+using ST = Gudhi::Simplex_tree<MyOptions>;
 
 // Dictionary should be private, but for now this is the easiest way.
-static_assert(sizeof(ST::Dictionary::value_type) < sizeof(Simplex_tree<>::Dictionary::value_type),
+static_assert(sizeof(ST::Dictionary::value_type) < sizeof(Gudhi::Simplex_tree<>::Dictionary::value_type),
     "Not storing the filtration and key should save some space");
 
 int main() {
diff --git a/src/Skeleton_blocker/doc/COPYRIGHT b/src/Skeleton_blocker/doc/COPYRIGHT
new file mode 100644
index 00000000..1de850d7
--- /dev/null
+++ b/src/Skeleton_blocker/doc/COPYRIGHT
@@ -0,0 +1,18 @@
+The files of this directory are part of the Gudhi Library. The Gudhi library
+(Geometric Understanding in Higher Dimensions) is a generic C++ library for
+computational topology.
+
+Author(s):       David Salinas
+Copyright (C) 2015  INRIA
+
+This program is free software: you can redistribute it and/or modify it under
+the terms of the GNU General Public License as published by the Free Software
+Foundation, either version 3 of the License, or (at your option) any later
+version.
+
+This program is distributed in the hope that it will be useful, but WITHOUT
+ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along with
+this program.  If not, see <http://www.gnu.org/licenses/>.
diff --git a/src/Spatial_searching/test/CMakeLists.txt b/src/Spatial_searching/test/CMakeLists.txt
index 2c685c72..bdc95e4a 100644
--- a/src/Spatial_searching/test/CMakeLists.txt
+++ b/src/Spatial_searching/test/CMakeLists.txt
@@ -10,16 +10,12 @@ if (GPROF_PATH)
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
 endif()
 
-if(CGAL_FOUND)
-  if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-    if (EIGEN3_FOUND)
-      add_executable( Spatial_searching_test_Kd_tree_search test_Kd_tree_search.cpp )
-      target_link_libraries(Spatial_searching_test_Kd_tree_search 
-        ${CGAL_LIBRARY} ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  add_executable( Spatial_searching_test_Kd_tree_search test_Kd_tree_search.cpp )
+  target_link_libraries(Spatial_searching_test_Kd_tree_search
+    ${CGAL_LIBRARY} ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 
-      add_test(Spatial_searching_test_Kd_tree_search ${CMAKE_CURRENT_BINARY_DIR}/Spatial_searching_test_Kd_tree_search
-      # XML format for Jenkins xUnit plugin 
-      --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Spatial_searching_UT.xml --log_level=test_suite --report_level=no)
-    endif()
-  endif ()
-endif()
+  add_test(Spatial_searching_test_Kd_tree_search ${CMAKE_CURRENT_BINARY_DIR}/Spatial_searching_test_Kd_tree_search
+  # XML format for Jenkins xUnit plugin
+  --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Spatial_searching_UT.xml --log_level=test_suite --report_level=no)
+endif ()
diff --git a/src/Subsampling/example/CMakeLists.txt b/src/Subsampling/example/CMakeLists.txt
index 0fd3335c..bb043297 100644
--- a/src/Subsampling/example/CMakeLists.txt
+++ b/src/Subsampling/example/CMakeLists.txt
@@ -1,21 +1,17 @@
 cmake_minimum_required(VERSION 2.6)
 project(Subsampling_examples)
 
-if(CGAL_FOUND)
-  if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-    if (EIGEN3_FOUND)
-      add_executable(Subsampling_example_pick_n_random_points example_pick_n_random_points.cpp)
-      add_executable(Subsampling_example_choose_n_farthest_points example_choose_n_farthest_points.cpp)
-      add_executable(Subsampling_example_custom_kernel example_custom_kernel.cpp)
-      add_executable(Subsampling_example_sparsify_point_set example_sparsify_point_set.cpp)
-      target_link_libraries(Subsampling_example_sparsify_point_set ${CGAL_LIBRARY})
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  add_executable(Subsampling_example_pick_n_random_points example_pick_n_random_points.cpp)
+  add_executable(Subsampling_example_choose_n_farthest_points example_choose_n_farthest_points.cpp)
+  add_executable(Subsampling_example_custom_kernel example_custom_kernel.cpp)
+  add_executable(Subsampling_example_sparsify_point_set example_sparsify_point_set.cpp)
+  target_link_libraries(Subsampling_example_sparsify_point_set ${CGAL_LIBRARY})
 
-      add_test(Subsampling_example_pick_n_random_points
-               ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_example_pick_n_random_points)
-      add_test(Subsampling_example_choose_n_farthest_points
-               ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_example_choose_n_farthest_points)
-      add_test(Subsampling_example_sparsify_point_set
-               ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_example_sparsify_point_set)
-    endif()
-  endif ()
-endif()
+  add_test(Subsampling_example_pick_n_random_points
+           ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_example_pick_n_random_points)
+  add_test(Subsampling_example_choose_n_farthest_points
+           ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_example_choose_n_farthest_points)
+  add_test(Subsampling_example_sparsify_point_set
+           ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_example_sparsify_point_set)
+endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Subsampling/test/CMakeLists.txt b/src/Subsampling/test/CMakeLists.txt
index 3a2fb649..5517fe9d 100644
--- a/src/Subsampling/test/CMakeLists.txt
+++ b/src/Subsampling/test/CMakeLists.txt
@@ -10,29 +10,25 @@ if (GPROF_PATH)
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
 endif()
 
-if(CGAL_FOUND)
-  if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-    if (EIGEN3_FOUND)
-      add_executable( Subsampling_test_pick_n_random_points test_pick_n_random_points.cpp )
-      target_link_libraries(Subsampling_test_pick_n_random_points ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  add_executable( Subsampling_test_pick_n_random_points test_pick_n_random_points.cpp )
+  target_link_libraries(Subsampling_test_pick_n_random_points ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 
-      add_executable( Subsampling_test_choose_n_farthest_points test_choose_n_farthest_points.cpp )
-      target_link_libraries(Subsampling_test_choose_n_farthest_points ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+  add_executable( Subsampling_test_choose_n_farthest_points test_choose_n_farthest_points.cpp )
+  target_link_libraries(Subsampling_test_choose_n_farthest_points ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 
-      add_executable(Subsampling_test_sparsify_point_set test_sparsify_point_set.cpp)
-      target_link_libraries(Subsampling_test_sparsify_point_set ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+  add_executable(Subsampling_test_sparsify_point_set test_sparsify_point_set.cpp)
+  target_link_libraries(Subsampling_test_sparsify_point_set ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 
-      add_test(Subsampling_test_pick_n_random_points ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_test_pick_n_random_points
-      # XML format for Jenkins xUnit plugin 
-      --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Subsampling_test_pick_n_random_points_UT.xml --log_level=test_suite --report_level=no)
+  add_test(Subsampling_test_pick_n_random_points ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_test_pick_n_random_points
+  # XML format for Jenkins xUnit plugin
+  --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Subsampling_test_pick_n_random_points_UT.xml --log_level=test_suite --report_level=no)
 
-      add_test(Subsampling_test_choose_n_farthest_points ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_test_choose_n_farthest_points
-      # XML format for Jenkins xUnit plugin 
-      --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Subsampling_test_choose_n_farthest_points_UT.xml --log_level=test_suite --report_level=no)
+  add_test(Subsampling_test_choose_n_farthest_points ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_test_choose_n_farthest_points
+  # XML format for Jenkins xUnit plugin
+  --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Subsampling_test_choose_n_farthest_points_UT.xml --log_level=test_suite --report_level=no)
 
-      add_test(Subsampling_test_sparsify_point_set ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_test_sparsify_point_set
-      # XML format for Jenkins xUnit plugin 
-      --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Subsampling_test_sparsify_point_set_UT.xml --log_level=test_suite --report_level=no)
-    endif()
-  endif ()
-endif()
+  add_test(Subsampling_test_sparsify_point_set ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_test_sparsify_point_set
+  # XML format for Jenkins xUnit plugin
+  --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Subsampling_test_sparsify_point_set_UT.xml --log_level=test_suite --report_level=no)
+endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Tangential_complex/benchmark/CMakeLists.txt b/src/Tangential_complex/benchmark/CMakeLists.txt
index 788c2b4d..ef772be8 100644
--- a/src/Tangential_complex/benchmark/CMakeLists.txt
+++ b/src/Tangential_complex/benchmark/CMakeLists.txt
@@ -1,17 +1,11 @@
 cmake_minimum_required(VERSION 2.6)
 project(Tangential_complex_benchmark)
 
-# need CGAL 4.8
-if(CGAL_FOUND)
-  if (NOT CGAL_VERSION VERSION_LESS 4.8.0)
-    if (EIGEN3_FOUND)
-      add_executable(Tangential_complex_benchmark benchmark_tc.cpp)
-      target_link_libraries(Tangential_complex_benchmark 
-        ${Boost_DATE_TIME_LIBRARY} ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
-      if (TBB_FOUND)
-        target_link_libraries(Tangential_complex_benchmark ${TBB_LIBRARIES})
-      endif(TBB_FOUND)
-    endif(EIGEN3_FOUND)
-  endif (NOT CGAL_VERSION VERSION_LESS 4.8.0)
-endif(CGAL_FOUND)
-
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  add_executable(Tangential_complex_benchmark benchmark_tc.cpp)
+  target_link_libraries(Tangential_complex_benchmark
+    ${Boost_DATE_TIME_LIBRARY} ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+  if (TBB_FOUND)
+    target_link_libraries(Tangential_complex_benchmark ${TBB_LIBRARIES})
+  endif(TBB_FOUND)
+endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Tangential_complex/doc/COPYRIGHT b/src/Tangential_complex/doc/COPYRIGHT
new file mode 100644
index 00000000..c4df0f64
--- /dev/null
+++ b/src/Tangential_complex/doc/COPYRIGHT
@@ -0,0 +1,19 @@
+The files of this directory are part of the Gudhi Library. The Gudhi library
+(Geometric Understanding in Higher Dimensions) is a generic C++ library for
+computational topology.
+
+Author(s):       Clement Jamin
+
+Copyright (C) 2015  INRIA
+
+This program is free software: you can redistribute it and/or modify it under
+the terms of the GNU General Public License as published by the Free Software
+Foundation, either version 3 of the License, or (at your option) any later
+version.
+
+This program is distributed in the hope that it will be useful, but WITHOUT
+ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along with
+this program.  If not, see <http://www.gnu.org/licenses/>.
diff --git a/src/Tangential_complex/example/CMakeLists.txt b/src/Tangential_complex/example/CMakeLists.txt
index a75ccd5b..47a56e3b 100644
--- a/src/Tangential_complex/example/CMakeLists.txt
+++ b/src/Tangential_complex/example/CMakeLists.txt
@@ -1,23 +1,19 @@
 cmake_minimum_required(VERSION 2.6)
 project(Tangential_complex_examples)
 
-if(CGAL_FOUND)
-  if (NOT CGAL_VERSION VERSION_LESS 4.8.0)
-    if (EIGEN3_FOUND)
-      add_executable( Tangential_complex_example_basic example_basic.cpp )
-      target_link_libraries(Tangential_complex_example_basic ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY})
-      add_executable( Tangential_complex_example_with_perturb example_with_perturb.cpp )
-      target_link_libraries(Tangential_complex_example_with_perturb ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY})
-      if (TBB_FOUND)
-        target_link_libraries(Tangential_complex_example_basic ${TBB_LIBRARIES})
-        target_link_libraries(Tangential_complex_example_with_perturb ${TBB_LIBRARIES})
-      endif(TBB_FOUND)
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  add_executable( Tangential_complex_example_basic example_basic.cpp )
+  target_link_libraries(Tangential_complex_example_basic ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY})
+  add_executable( Tangential_complex_example_with_perturb example_with_perturb.cpp )
+  target_link_libraries(Tangential_complex_example_with_perturb ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY})
+  if (TBB_FOUND)
+    target_link_libraries(Tangential_complex_example_basic ${TBB_LIBRARIES})
+    target_link_libraries(Tangential_complex_example_with_perturb ${TBB_LIBRARIES})
+  endif(TBB_FOUND)
 
-      add_test(Tangential_complex_example_basic
-               ${CMAKE_CURRENT_BINARY_DIR}/Tangential_complex_example_basic)
+  add_test(Tangential_complex_example_basic
+           ${CMAKE_CURRENT_BINARY_DIR}/Tangential_complex_example_basic)
 
-      add_test(Tangential_complex_example_with_perturb
-               ${CMAKE_CURRENT_BINARY_DIR}/Tangential_complex_example_with_perturb)
-    endif(EIGEN3_FOUND)
-  endif(NOT CGAL_VERSION VERSION_LESS 4.8.0)
-endif(CGAL_FOUND)
+  add_test(Tangential_complex_example_with_perturb
+           ${CMAKE_CURRENT_BINARY_DIR}/Tangential_complex_example_with_perturb)
+endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Tangential_complex/test/CMakeLists.txt b/src/Tangential_complex/test/CMakeLists.txt
index 075028c8..b2bf5dd7 100644
--- a/src/Tangential_complex/test/CMakeLists.txt
+++ b/src/Tangential_complex/test/CMakeLists.txt
@@ -10,22 +10,14 @@ if (GPROF_PATH)
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
 endif()
 
-if(CGAL_FOUND)
-  if (NOT CGAL_VERSION VERSION_LESS 4.8.0)
-    if (EIGEN3_FOUND)
-      message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
-      include( ${EIGEN3_USE_FILE} )
-      include_directories (BEFORE "../../include")
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  add_executable( Tangential_complex_test_TC test_tangential_complex.cpp )
+  target_link_libraries(Tangential_complex_test_TC ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY} ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+  if (TBB_FOUND)
+    target_link_libraries(Tangential_complex_test_TC ${TBB_LIBRARIES})
+  endif()
+  add_test(Tangential_complex_test_TC ${CMAKE_CURRENT_BINARY_DIR}/Tangential_complex_test_TC
+  # XML format for Jenkins xUnit plugin
+  --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Tangential_complex_UT.xml --log_level=test_suite --report_level=no)
 
-      add_executable( Tangential_complex_test_TC test_tangential_complex.cpp )
-      target_link_libraries(Tangential_complex_test_TC ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY} ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
-      if (TBB_FOUND)
-        target_link_libraries(Tangential_complex_test_TC ${TBB_LIBRARIES})
-      endif()
-      add_test(Tangential_complex_test_TC ${CMAKE_CURRENT_BINARY_DIR}/Tangential_complex_test_TC
-      # XML format for Jenkins xUnit plugin 
-      --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Tangential_complex_UT.xml --log_level=test_suite --report_level=no)
-
-    endif()
-  endif ()
-endif()
\ No newline at end of file
+endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Witness_complex/concept/Simplicial_complex_for_witness.h b/src/Witness_complex/concept/SimplicialComplexForWitness.h
index caaf0db6..d78cc83f 100644
--- a/src/Witness_complex/concept/Simplicial_complex_for_witness.h
+++ b/src/Witness_complex/concept/SimplicialComplexForWitness.h
@@ -27,57 +27,70 @@ namespace Gudhi {
 
 namespace witness_complex {
 
-/** \brief The concept Simplicial_Complex describes the requirements 
+/** \brief The concept SimplicialComplexForWitness describes the requirements 
  * for a type to implement a simplicial complex, 
- * used for example to build a 'Witness_complex'. 
+ * used for example to build a Witness_complex or Strong_witness_complex. 
  */
 struct SimplicialComplexForWitness {
   /** Handle to specify a simplex. */
   typedef unspecified Simplex_handle;
-  /** Handle to specify a vertex. Must be a non-negative integer. */
-  typedef unspecified Vertex_handle;
+  // /** Handle to specify a vertex. Must be a non-negative integer. */
+  // typedef unspecified Vertex_handle;
 
-  /** Returns a Simplex_hanlde that is different from all simplex handles 
+  /** \brief Returns a Simplex_hanlde that is different from all simplex handles 
    * of the simplices. */
   Simplex_handle null_simplex();
 
-  /** \brief Iterator over the simplices of the complex,
-   * in an arbitrary order.
-   *
-   * 'value_type' must be 'Simplex_handle'.*/
-  typedef unspecified Complex_simplex_range;
-
-  /**
-   * \brief Returns a range over all the simplices of a
-   * complex.
+  /** Returns the number of vertices in the simplicial complex
    */
-  Complex_simplex_range complex_simplex_range();
-
-  /** \brief Iterator over vertices of a simplex.
-   *
-   * 'value type' must be 'Vertex_handle'.*/
-  typedef unspecified Simplex_vertex_range;
-
-  /** \brief Returns a range over vertices of a given
-   *  simplex. */
-  Simplex_vertex_range simplex_vertex_range(Simplex_handle const & simplex);
-
+  std::size_t num_vertices();
+  
   /** \brief Return type of an insertion of a simplex
    */
   typedef unspecified Insertion_result_type;
 
   /** \brief Inserts a simplex with vertices from a given range
    *  'vertex_range' in the simplicial complex.
+   *  The function is only used in Witness_complex class
+   *  and by construction, it is not necessary to check if 
+   *  the faces are in the simplicial complex before insertion. 
+   *  The simplex is given the filtration value 'filtration'.
+   *  Filtration_value should be convertible from double.
+   *  The return type is not used.
    *  */
   template< typedef Input_vertex_range >
-  Insertion_result_type insert_simplex(Input_vertex_range const & vertex_range);
+  Insertion_result_type insert_simplex(Input_vertex_range const & vertex_range, Filtration_value filtration);
 
+  /** \brief Inserts a simplex and all its faces
+   *  with vertices from a given range
+   *  'vertex_range' in the simplicial complex.
+   *  The function is only used in Strong_witness_complex class.
+   *  All inserted simplices are given the filtration
+   *  value 'filtration'.
+   *  Filtration_value should be convertible from double.
+   *  The return type is not used.
+   */
+
+  template< typedef Input_vertex_range,
+            typedef Filtration_value>
+  Insertion_result_type insert_simplex_and_subfaces(Input_vertex_range const & vertex_range, Filtration_value filtration);
+  
   /** \brief Finds a simplex with vertices given by a range
    *
    * If a simplex exists, its Simplex_handle is returned.
    * Otherwise null_simplex() is returned. */
   template< typedef Input_vertex_range >
   Simplex_handle find(Input_vertex_range const & vertex_range);
+
+  /** \brief Sets the dimension of the simplicial complex to 
+   * 'dimension'.
+   */
+  void set_dimension(int dimension);
+
+  /** \brief Returns the filtration of the simplex given by
+   *  the simplex handle 'sh'.
+   */
+  double filtration(Simplex_handle sh);
 };
 
 }  // namespace witness_complex
diff --git a/src/Witness_complex/doc/COPYRIGHT b/src/Witness_complex/doc/COPYRIGHT
new file mode 100644
index 00000000..7d032c87
--- /dev/null
+++ b/src/Witness_complex/doc/COPYRIGHT
@@ -0,0 +1,19 @@
+The files of this directory are part of the Gudhi Library. The Gudhi library
+(Geometric Understanding in Higher Dimensions) is a generic C++ library for
+computational topology.
+
+Author(s):       Siargey Kachanovich
+
+Copyright (C) 2015  INRIA
+
+This program is free software: you can redistribute it and/or modify it under
+the terms of the GNU General Public License as published by the Free Software
+Foundation, either version 3 of the License, or (at your option) any later
+version.
+
+This program is distributed in the hope that it will be useful, but WITHOUT
+ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along with
+this program.  If not, see <http://www.gnu.org/licenses/>.
diff --git a/src/Witness_complex/doc/Witness_complex_doc.h b/src/Witness_complex/doc/Witness_complex_doc.h
index 60dfd27b..171a185f 100644
--- a/src/Witness_complex/doc/Witness_complex_doc.h
+++ b/src/Witness_complex/doc/Witness_complex_doc.h
@@ -8,31 +8,106 @@
 
    \image html "Witness_complex_representation.png" "Witness complex representation"
 
-   \section Definitions
+   \section witnessdefinitions Definitions
 
-   Witness complex \f$ Wit(W,L) \f$  is a simplicial complex defined on two sets of points in \f$\mathbb{R}^D\f$:
+   Witness complex is a simplicial complex defined on two sets of points in \f$\mathbb{R}^D\f$:
 
    \li \f$W\f$ set of **witnesses** and 
-   \li \f$L \subseteq W\f$ set of **landmarks**.
+   \li \f$L\f$ set of **landmarks**.
 
-   The simplices are based on landmarks
-   and a simplex belongs to the witness complex if and only if it is witnessed, that is:
+   Even though often the set of landmarks \f$L\f$ is a subset of the set of witnesses \f$ W\f$, it is not a requirement for the current implementation.
 
-   \f$ \sigma \subset L \f$ is witnessed if there exists a point \f$w \in W\f$ such that 
-   w is closer to the vertices of \f$ \sigma \f$ than other points in \f$ L \f$ and all of its faces are witnessed as well. 
- 
-   The data structure is described in \cite boissonnatmariasimplextreealgorithmica .
+   Landmarks are the vertices of the simplicial complex
+   and witnesses help to decide on which simplices are inserted via a predicate "is witnessed".
 
-   \section Implementation
+   De Silva and Carlsson in their paper \cite de2004topological differentiate **weak witnessing** and **strong witnessing**:
 
-   The principal class of this module is Gudhi::Witness_complex.
+   - *weak*:   \f$ \sigma \subset L \f$ is witnessed by \f$ w \in W\f$ if \f$ \forall l \in \sigma,\ \forall l' \in \mathbf{L \setminus \sigma},\ d(w,l) \leq d(w,l') \f$
+   - *strong*: \f$ \sigma \subset L \f$ is witnessed by \f$ w \in W\f$ if \f$ \forall l \in \sigma,\ \forall l' \in \mathbf{L},\ d(w,l) \leq d(w,l') \f$
 
-   In both cases, the constructor for this class takes a {witness}x{closest_landmarks} table, where each row represents a witness and consists of landmarks sorted by distance to this witness.
-   This table can be constructed by two additional classes Landmark_choice_by_furthest_point and Landmark_choice_by_random_point also included in the module.
+   where \f$ d(.,.) \f$ is a distance function.
 
-   *\image html "bench_Cy8.png" "Running time as function on number of landmarks" width=10cm
-   *\image html "bench_sphere.png" "Running time as function on number of witnesses for |L|=300" width=10cm
+   Both definitions can be relaxed by a real value \f$\alpha\f$:
+
+   - *weak*:   \f$ \sigma \subset L \f$ is \f$\alpha\f$-witnessed by \f$ w \in W\f$ if \f$ \forall l \in \sigma,\ \forall l' \in \mathbf{L \setminus \sigma},\ d(w,l)^2 \leq d(w,l')^2 + \alpha^2 \f$
+   - *strong*: \f$ \sigma \subset L \f$ is \f$\alpha\f$-witnessed by \f$ w \in W\f$ if \f$ \forall l \in \sigma,\ \forall l' \in \mathbf{L},\ d(w,l)^2 \leq d(w,l')^2 + \alpha^2 \f$
+
+   which leads to definitions of **weak relaxed witness complex** (or just relaxed witness complex for short) and **strong relaxed witness complex** respectively.
+
+   \image html "swit.svg" "Strongly witnessed simplex"
+
+   In particular case of 0-relaxation, weak complex corresponds to **witness complex** introduced in \cite de2004topological, whereas 0-relaxed strong witness complex consists of just vertices and is not very interesting.
+   Hence for small relaxation weak version is preferable.
+   However, to capture the homotopy type (for example using Gudhi::persistent_cohomology::Persistent_cohomology) it is often necessary to work with higher filtration values. In this case strong relaxed witness complex is faster to compute and offers similar results.
+
+   \section witnessimplementation Implementation
    
+   The two complexes described above are implemented in the corresponding classes 
+   - Gudhi::witness_complex::Witness_complex
+   - Gudhi::witness_complex::Euclidean_witness_complex
+   - Gudhi::witness_complex::Strong_witness_complex
+   - Gudhi::witness_complex::Euclidean_strong_witness_complex
+
+   The construction of the Euclidean versions of complexes follow the same scheme:
+   1. Construct a search tree on landmarks (for that Gudhi::spatial_searching::Kd_tree_search is used internally).
+   2. Construct lists of nearest landmarks for each witness (special structure Gudhi::witness_complex::Active_witness is used internally).
+   3. Construct the witness complex for nearest landmark lists.
+
+   In the non-Euclidean classes, the lists of nearest landmarks are supposed to be given as input.
+
+   The constructors take on the steps 1 and 2, while the function 'create_complex' executes the step 3.
+
+   \section witnessexample1 Example 1: Constructing weak relaxed witness complex from an off file
+
+   Let's start with a simple example, which reads an off point file and computes a weak witness complex.
+
+   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{.cpp}
+   
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Euclidean_witness_complex.h>
+#include <gudhi/pick_n_random_points.h>
+#include <gudhi/Points_off_io.h>
+
+#include <CGAL/Epick_d.h>
+
+#include <string>
+#include <vector>
+
+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< Point_d > Point_vector;
+
+int main(int argc, char * const argv[]) {
+  std::string file_name = argv[1];
+  int nbL = atoi(argv[2]), lim_dim = atoi(argv[4]);
+  double alpha2 = atof(argv[3]);
+  Gudhi::Simplex_tree<> simplex_tree;
+
+  // Read the point file
+  Point_vector point_vector, landmarks;
+  Gudhi::Points_off_reader<Point_d> off_reader(file_name);
+  point_vector = Point_vector(off_reader.get_point_cloud());
+
+  // Choose landmarks
+  Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks));
+
+  // Compute witness complex
+  Witness_complex witness_complex(landmarks,
+                                  point_vector);
+
+  witness_complex.create_complex(simplex_tree, alpha2, lim_dim);
+}
+
+   
+   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+   \section witnessexample2 Example2: Computing persistence using strong relaxed witness complex
+
+   Here is an example of constructing a strong witness complex filtration and computing persistence on it:
+
+   \include Witness_complex/example_strong_witness_persistence.cpp
 
    \copyright GNU General Public License v3.
 
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diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt
index 857ec819..549a85be 100644
--- a/src/Witness_complex/example/CMakeLists.txt
+++ b/src/Witness_complex/example/CMakeLists.txt
@@ -1,17 +1,44 @@
 cmake_minimum_required(VERSION 2.6)
 project(Witness_complex_examples)
 
-# A simple example
-   add_executable( witness_complex_from_file witness_complex_from_file.cpp )
-   add_test( witness_complex_from_bunny ${CMAKE_CURRENT_BINARY_DIR}/witness_complex_from_file
-             ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.off 100)   
-
-if(CGAL_FOUND)
-  if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
-    if (EIGEN3_FOUND)
-      add_executable ( witness_complex_sphere witness_complex_sphere.cpp )
-      target_link_libraries(witness_complex_sphere ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
-      add_test( witness_complex_sphere_10 ${CMAKE_CURRENT_BINARY_DIR}/witness_complex_sphere 10)   
-    endif(EIGEN3_FOUND)
-  endif (NOT CGAL_VERSION VERSION_LESS 4.6.0)
+add_executable ( Witness_complex_example_nearest_landmark_table example_nearest_landmark_table.cpp )
+target_link_libraries(Witness_complex_example_nearest_landmark_table ${Boost_SYSTEM_LIBRARY})
+if (TBB_FOUND)
+  target_link_libraries(Witness_complex_example_nearest_landmark_table ${TBB_LIBRARIES})
 endif()
+add_test(Witness_complex_test_nearest_landmark_table Witness_complex_example_nearest_landmark_table)
+
+# CGAL and Eigen3 are required for Euclidean version of Witness
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
+  add_executable( Witness_complex_example_off example_witness_complex_off.cpp )
+  target_link_libraries(Witness_complex_example_off ${Boost_SYSTEM_LIBRARY})
+  add_executable( Witness_complex_example_strong_off example_strong_witness_complex_off.cpp )
+  target_link_libraries(Witness_complex_example_strong_off ${Boost_SYSTEM_LIBRARY})
+  add_executable ( Witness_complex_example_sphere example_witness_complex_sphere.cpp )
+  target_link_libraries(Witness_complex_example_sphere ${Boost_SYSTEM_LIBRARY})
+
+  add_executable ( Witness_complex_example_witness_persistence example_witness_complex_persistence.cpp )
+  target_link_libraries(Witness_complex_example_witness_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+
+  add_executable ( Witness_complex_example_strong_witness_persistence example_strong_witness_persistence.cpp )
+  target_link_libraries(Witness_complex_example_strong_witness_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+
+  if (TBB_FOUND)
+    target_link_libraries(Witness_complex_example_witness_persistence ${TBB_LIBRARIES})
+    target_link_libraries(Witness_complex_example_strong_witness_persistence ${TBB_LIBRARIES})
+  endif()
+
+  add_test(Witness_complex_off_test_torus
+           ${CMAKE_CURRENT_BINARY_DIR}/Witness_complex_example_off
+           ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off 20 1.0 3)
+  add_test(Witness_complex_strong_off_test_torus
+           ${CMAKE_CURRENT_BINARY_DIR}/Witness_complex_example_strong_off
+           ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off 20 1.0 3)
+  add_test(Witness_complex_test_sphere_10 Witness_complex_example_sphere 10)
+  add_test(Witness_complex_test_torus_persistence
+           ${CMAKE_CURRENT_BINARY_DIR}/Witness_complex_example_witness_persistence
+           ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -l 20 -a 0.5)
+  add_test(Witness_complex_strong_test_torus_persistence
+           ${CMAKE_CURRENT_BINARY_DIR}/Witness_complex_example_strong_witness_persistence
+           ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -l 20 -a 0.5)
+endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
diff --git a/src/Witness_complex/example/example_nearest_landmark_table.cpp b/src/Witness_complex/example/example_nearest_landmark_table.cpp
new file mode 100644
index 00000000..b8594212
--- /dev/null
+++ b/src/Witness_complex/example/example_nearest_landmark_table.cpp
@@ -0,0 +1,69 @@
+/*    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):       Siargey Kachanovich
+ *
+ *    Copyright (C) 2016  INRIA (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_PARAMETER_MAX_ARITY 12
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Witness_complex.h>
+#include <gudhi/Persistent_cohomology.h>
+
+#include <iostream>
+#include <fstream>
+#include <utility>
+#include <string>
+#include <vector>
+
+int main(int argc, char * const argv[]) {
+  using Nearest_landmark_range = std::vector<std::pair<std::size_t, double>>;
+  using Nearest_landmark_table = std::vector<Nearest_landmark_range>;
+  using Witness_complex = Gudhi::witness_complex::Witness_complex<Nearest_landmark_table>;
+  using Simplex_tree = Gudhi::Simplex_tree<>;
+  using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
+  using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp>;
+
+  Simplex_tree simplex_tree;
+  Nearest_landmark_table nlt;
+
+  // Example contains 5 witnesses and 5 landmarks
+  Nearest_landmark_range w0 = {std::make_pair(0, 0), std::make_pair(1, 1), std::make_pair(2, 2),
+                               std::make_pair(3, 3), std::make_pair(4, 4)}; nlt.push_back(w0);
+  Nearest_landmark_range w1 = {std::make_pair(1, 0), std::make_pair(2, 1), std::make_pair(3, 2),
+                               std::make_pair(4, 3), std::make_pair(0, 4)}; nlt.push_back(w1);
+  Nearest_landmark_range w2 = {std::make_pair(2, 0), std::make_pair(3, 1), std::make_pair(4, 2),
+                               std::make_pair(0, 3), std::make_pair(1, 4)}; nlt.push_back(w2);
+  Nearest_landmark_range w3 = {std::make_pair(3, 0), std::make_pair(4, 1), std::make_pair(0, 2),
+                               std::make_pair(1, 3), std::make_pair(2, 4)}; nlt.push_back(w3);
+  Nearest_landmark_range w4 = {std::make_pair(4, 0), std::make_pair(0, 1), std::make_pair(1, 2),
+                               std::make_pair(2, 3), std::make_pair(3, 4)}; nlt.push_back(w4);
+
+  Witness_complex witness_complex(nlt);
+  witness_complex.create_complex(simplex_tree, 4.1);
+
+  std::cout << "Number of simplices: " << simplex_tree.num_simplices() << std::endl;
+
+  Persistent_cohomology pcoh(simplex_tree);
+  // initializes the coefficient field for homology
+  pcoh.init_coefficients(11);
+
+  pcoh.compute_persistent_cohomology(-0.1);
+  pcoh.output_diagram();
+}
diff --git a/src/Witness_complex/example/witness_complex_from_file.cpp b/src/Witness_complex/example/example_strong_witness_complex_off.cpp
index 5dd18d0a..0ee9ee90 100644
--- a/src/Witness_complex/example/witness_complex_from_file.cpp
+++ b/src/Witness_complex/example/example_strong_witness_complex_off.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Siargey Kachanovich
  *
- *    Copyright (C) 2015  INRIA
+ *    Copyright (C) 2016  INRIA (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
@@ -20,15 +20,12 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <sys/types.h>
-#include <sys/stat.h>
-
-#include <gudhi/Points_off_io.h>
 #include <gudhi/Simplex_tree.h>
-#include <gudhi/Witness_complex.h>
-#include <gudhi/Construct_closest_landmark_table.h>
+#include <gudhi/Euclidean_strong_witness_complex.h>
 #include <gudhi/pick_n_random_points.h>
-#include <gudhi/reader_utils.h>
+#include <gudhi/Points_off_io.h>
+
+#include <CGAL/Epick_d.h>
 
 #include <iostream>
 #include <fstream>
@@ -36,49 +33,47 @@
 #include <string>
 #include <vector>
 
-typedef Gudhi::Simplex_tree<> Simplex_tree;
-typedef std::vector< Simplex_tree::Vertex_handle > typeVectorVertex;
-typedef std::vector< std::vector <double> > Point_Vector;
+using K = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>;
+using Point_d = typename K::Point_d;
+using Witness_complex = Gudhi::witness_complex::Euclidean_strong_witness_complex<K>;
+using Point_vector = std::vector<Point_d>;
 
 int main(int argc, char * const argv[]) {
-  if (argc != 3) {
+  if (argc != 5) {
     std::cerr << "Usage: " << argv[0]
-        << " path_to_point_file.off nbL \n";
+        << " path_to_point_file number_of_landmarks max_squared_alpha limit_dimension\n";
     return 0;
   }
 
-  std::string off_file_name = argv[1];
-  int nbL = atoi(argv[2]);
+  std::string file_name = argv[1];
+  int nbL = atoi(argv[2]), lim_dim = atoi(argv[4]);
+  double alpha2 = atof(argv[3]);
   clock_t start, end;
+  Gudhi::Simplex_tree<> simplex_tree;
 
-  // Construct the Simplex Tree
-  Simplex_tree simplex_tree;
-
-  // Read the OFF file (input file name given as parameter) and triangulate points
-  Gudhi::Points_off_reader<std::vector <double>> off_reader(off_file_name);
-  // Check the read operation was correct
-  if (!off_reader.is_valid()) {
-    std::cerr << "Unable to read file " << off_file_name << std::endl;
-  }
   // Read the point file
-  Point_Vector point_vector = off_reader.get_point_cloud();
+  Point_vector point_vector, landmarks;
+  Gudhi::Points_off_reader<Point_d> off_reader(file_name);
+  if (!off_reader.is_valid()) {
+      std::cerr << "Strong witness complex - Unable to read file " << file_name << "\n";
+      exit(-1);  // ----- >>
+    }
+  point_vector = Point_vector(off_reader.get_point_cloud());
+
   std::cout << "Successfully read " << point_vector.size() << " points.\n";
-  std::cout << "Ambient dimension is " << point_vector[0].size() << ".\n";
+  std::cout << "Ambient dimension is " << point_vector[0].dimension() << ".\n";
 
   // Choose landmarks
-  start = clock();
-  std::vector<std::vector< int > > knn;
-  Point_Vector landmarks;
-  Gudhi::subsampling::pick_n_random_points(point_vector, 100, std::back_inserter(landmarks));
-  Gudhi::witness_complex::construct_closest_landmark_table<Simplex_tree::Filtration_value>(point_vector, landmarks, knn);
-  end = clock();
-  std::cout << "Landmark choice for " << nbL << " landmarks took "
-      << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n";
+  Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks));
 
   // Compute witness complex
   start = clock();
-  Gudhi::witness_complex::witness_complex(knn, nbL, point_vector[0].size(), simplex_tree);
+  Witness_complex witness_complex(landmarks,
+                                  point_vector);
+
+  witness_complex.create_complex(simplex_tree, alpha2, lim_dim);
   end = clock();
-  std::cout << "Witness complex took "
+  std::cout << "Strong witness complex took "
       << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n";
+  std::cout << "Number of simplices is: " << simplex_tree.num_simplices() << "\n";
 }
diff --git a/src/Witness_complex/example/example_strong_witness_persistence.cpp b/src/Witness_complex/example/example_strong_witness_persistence.cpp
new file mode 100644
index 00000000..f786fe7b
--- /dev/null
+++ b/src/Witness_complex/example/example_strong_witness_persistence.cpp
@@ -0,0 +1,171 @@
+/*    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):       Siargey Kachanovich
+ *
+ *    Copyright (C) 2016  INRIA (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/Simplex_tree.h>
+#include <gudhi/Euclidean_strong_witness_complex.h>
+#include <gudhi/Persistent_cohomology.h>
+#include <gudhi/Points_off_io.h>
+#include <gudhi/pick_n_random_points.h>
+
+#include <boost/program_options.hpp>
+
+#include <CGAL/Epick_d.h>
+
+#include <string>
+#include <vector>
+#include <limits>  // infinity
+
+using K = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>;
+using Point_d = K::Point_d;
+
+using Point_vector = std::vector<Point_d>;
+using Strong_witness_complex = Gudhi::witness_complex::Euclidean_strong_witness_complex<K>;
+using SimplexTree = Gudhi::Simplex_tree<>;
+
+using Filtration_value = SimplexTree::Filtration_value;
+
+using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
+using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<SimplexTree, Field_Zp>;
+
+void program_options(int argc, char * argv[]
+                     , int & nbL
+                     , std::string & file_name
+                     , std::string & filediag
+                     , Filtration_value & max_squared_alpha
+                     , int & p
+                     , int & dim_max
+                     , Filtration_value & min_persistence);
+
+int main(int argc, char * argv[]) {
+  std::string file_name;
+  std::string filediag;
+  Filtration_value max_squared_alpha;
+  int p, nbL, lim_d;
+  Filtration_value min_persistence;
+  SimplexTree simplex_tree;
+
+  program_options(argc, argv, nbL, file_name, filediag, max_squared_alpha, p, lim_d, min_persistence);
+
+  // Extract the points from the file file_name
+  Point_vector witnesses, landmarks;
+  Gudhi::Points_off_reader<Point_d> off_reader(file_name);
+  if (!off_reader.is_valid()) {
+      std::cerr << "Witness complex - Unable to read file " << file_name << "\n";
+      exit(-1);  // ----- >>
+  }
+  witnesses = Point_vector(off_reader.get_point_cloud());
+  std::cout << "Successfully read " << witnesses.size() << " points.\n";
+  std::cout << "Ambient dimension is " << witnesses[0].dimension() << ".\n";
+
+  // Choose landmarks from witnesses
+  Gudhi::subsampling::pick_n_random_points(witnesses, nbL, std::back_inserter(landmarks));
+
+  // Compute witness complex
+  Strong_witness_complex strong_witness_complex(landmarks,
+                                                witnesses);
+
+  strong_witness_complex.create_complex(simplex_tree, max_squared_alpha, lim_d);
+
+  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[]
+                     , int & nbL
+                     , std::string & file_name
+                     , std::string & filediag
+                     , Filtration_value & max_squared_alpha
+                     , int & p
+                     , int & dim_max
+                     , Filtration_value & min_persistence) {
+  namespace po = boost::program_options;
+
+  po::options_description hidden("Hidden options");
+  hidden.add_options()
+      ("input-file", po::value<std::string>(&file_name),
+      "Name of file containing a point set in off format.");
+
+  po::options_description visible("Allowed options", 100);
+  Filtration_value default_alpha = std::numeric_limits<Filtration_value>::infinity();
+  visible.add_options()
+      ("help,h", "produce help message")
+      ("landmarks,l", po::value<int>(&nbL),
+       "Number of landmarks to choose from the point cloud.")
+      ("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-sq-alpha,a", po::value<Filtration_value>(&max_squared_alpha)->default_value(default_alpha),
+       "Maximal squared relaxation parameter.")
+      ("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)->default_value(0),
+       "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals")
+      ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(std::numeric_limits<int>::max()),
+       "Maximal dimension of the strong witness complex we want to compute.");
+
+  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 Strong witness 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/Witness_complex/example/example_witness_complex_off.cpp b/src/Witness_complex/example/example_witness_complex_off.cpp
new file mode 100644
index 00000000..b36dac0d
--- /dev/null
+++ b/src/Witness_complex/example/example_witness_complex_off.cpp
@@ -0,0 +1,60 @@
+#include <sys/types.h>
+#include <sys/stat.h>
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Euclidean_witness_complex.h>
+#include <gudhi/pick_n_random_points.h>
+#include <gudhi/Points_off_io.h>
+
+#include <CGAL/Epick_d.h>
+
+#include <iostream>
+#include <fstream>
+#include <ctime>
+#include <string>
+#include <vector>
+
+using K = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>;
+using Point_d = K::Point_d;
+using Witness_complex = Gudhi::witness_complex::Euclidean_witness_complex<K>;
+using Point_vector = std::vector< Point_d >;
+
+int main(int argc, char * const argv[]) {
+  if (argc != 5) {
+    std::cerr << "Usage: " << argv[0]
+        << " path_to_point_file number_of_landmarks max_squared_alpha limit_dimension\n";
+    return 0;
+  }
+
+  std::string file_name = argv[1];
+  int nbL = atoi(argv[2]), lim_dim = atoi(argv[4]);
+  double alpha2 = atof(argv[3]);
+  clock_t start, end;
+  Gudhi::Simplex_tree<> simplex_tree;
+
+  // Read the point file
+  Point_vector point_vector, landmarks;
+  Gudhi::Points_off_reader<Point_d> off_reader(file_name);
+  if (!off_reader.is_valid()) {
+      std::cerr << "Witness complex - Unable to read file " << file_name << "\n";
+      exit(-1);  // ----- >>
+    }
+  point_vector = Point_vector(off_reader.get_point_cloud());
+
+  std::cout << "Successfully read " << point_vector.size() << " points.\n";
+  std::cout << "Ambient dimension is " << point_vector[0].dimension() << ".\n";
+
+  // Choose landmarks
+  Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks));
+
+  // Compute witness complex
+  start = clock();
+  Witness_complex witness_complex(landmarks,
+                                  point_vector);
+
+  witness_complex.create_complex(simplex_tree, alpha2, lim_dim);
+  end = clock();
+  std::cout << "Witness complex took "
+      << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n";
+  std::cout << "Number of simplices is: " << simplex_tree.num_simplices() << "\n";
+}
diff --git a/src/Witness_complex/example/example_witness_complex_persistence.cpp b/src/Witness_complex/example/example_witness_complex_persistence.cpp
new file mode 100644
index 00000000..a1146922
--- /dev/null
+++ b/src/Witness_complex/example/example_witness_complex_persistence.cpp
@@ -0,0 +1,171 @@
+/*    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):       Siargey Kachanovich
+ *
+ *    Copyright (C) 2016  INRIA (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/Simplex_tree.h>
+#include <gudhi/Euclidean_witness_complex.h>
+#include <gudhi/Persistent_cohomology.h>
+#include <gudhi/Points_off_io.h>
+#include <gudhi/pick_n_random_points.h>
+
+#include <boost/program_options.hpp>
+
+#include <CGAL/Epick_d.h>
+
+#include <string>
+#include <vector>
+#include <limits>  // infinity
+
+using K = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>;
+using Point_d = K::Point_d;
+
+using Point_vector = std::vector<Point_d>;
+using Witness_complex = Gudhi::witness_complex::Euclidean_witness_complex<K>;
+using SimplexTree = Gudhi::Simplex_tree<>;
+
+using Filtration_value = SimplexTree::Filtration_value;
+
+using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
+using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<SimplexTree, Field_Zp>;
+
+void program_options(int argc, char * argv[]
+                     , int & nbL
+                     , std::string & file_name
+                     , std::string & filediag
+                     , Filtration_value & max_squared_alpha
+                     , int & p
+                     , int & dim_max
+                     , Filtration_value & min_persistence);
+
+int main(int argc, char * argv[]) {
+  std::string file_name;
+  std::string filediag;
+  Filtration_value max_squared_alpha;
+  int p, nbL, lim_d;
+  Filtration_value min_persistence;
+  SimplexTree simplex_tree;
+
+  program_options(argc, argv, nbL, file_name, filediag, max_squared_alpha, p, lim_d, min_persistence);
+
+  // Extract the points from the file file_name
+  Point_vector witnesses, landmarks;
+  Gudhi::Points_off_reader<Point_d> off_reader(file_name);
+  if (!off_reader.is_valid()) {
+      std::cerr << "Witness complex - Unable to read file " << file_name << "\n";
+      exit(-1);  // ----- >>
+  }
+  witnesses = Point_vector(off_reader.get_point_cloud());
+  std::cout << "Successfully read " << witnesses.size() << " points.\n";
+  std::cout << "Ambient dimension is " << witnesses[0].dimension() << ".\n";
+
+  // Choose landmarks from witnesses
+  Gudhi::subsampling::pick_n_random_points(witnesses, nbL, std::back_inserter(landmarks));
+
+  // Compute witness complex
+  Witness_complex witness_complex(landmarks,
+                                  witnesses);
+
+  witness_complex.create_complex(simplex_tree, max_squared_alpha, lim_d);
+
+  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[]
+                     , int & nbL
+                     , std::string & file_name
+                     , std::string & filediag
+                     , Filtration_value & max_squared_alpha
+                     , int & p
+                     , int & dim_max
+                     , Filtration_value & min_persistence) {
+  namespace po = boost::program_options;
+
+  po::options_description hidden("Hidden options");
+  hidden.add_options()
+      ("input-file", po::value<std::string>(&file_name),
+      "Name of file containing a point set in off format.");
+
+  Filtration_value default_alpha = std::numeric_limits<Filtration_value>::infinity();
+  po::options_description visible("Allowed options", 100);
+  visible.add_options()
+      ("help,h", "produce help message")
+      ("landmarks,l", po::value<int>(&nbL),
+       "Number of landmarks to choose from the point cloud.")
+      ("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-sq-alpha,a", po::value<Filtration_value>(&max_squared_alpha)->default_value(default_alpha),
+       "Maximal squared relaxation parameter.")
+      ("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)->default_value(0),
+       "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals")
+      ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(std::numeric_limits<int>::max()),
+       "Maximal dimension of the weak witness complex we want to compute.");
+
+  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 Weak witness 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/Witness_complex/example/witness_complex_sphere.cpp b/src/Witness_complex/example/example_witness_complex_sphere.cpp
index 60e02225..124fd99b 100644
--- a/src/Witness_complex/example/witness_complex_sphere.cpp
+++ b/src/Witness_complex/example/example_witness_complex_sphere.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Siargey Kachanovich
  *
- *    Copyright (C) 2015  INRIA
+ *    Copyright (C) 2016  INRIA (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
@@ -19,18 +19,16 @@
  *    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_PARAMETER_MAX_ARITY 12
-
 
-#include <sys/types.h>
-#include <sys/stat.h>
+#define BOOST_PARAMETER_MAX_ARITY 12
 
 #include <gudhi/Simplex_tree.h>
-#include <gudhi/Witness_complex.h>
-#include <gudhi/Construct_closest_landmark_table.h>
+#include <gudhi/Euclidean_witness_complex.h>
 #include <gudhi/pick_n_random_points.h>
 #include <gudhi/reader_utils.h>
 
+#include <CGAL/Epick_d.h>
+
 #include <iostream>
 #include <fstream>
 #include <ctime>
@@ -40,8 +38,6 @@
 
 #include "generators.h"
 
-typedef Gudhi::Simplex_tree<> Simplex_tree;
-
 /** Write a gnuplot readable file.
  *  Data range is a random access range of pairs (arg, value)
  */
@@ -54,6 +50,9 @@ void write_data(Data_range & data, std::string filename) {
 }
 
 int main(int argc, char * const argv[]) {
+  using Kernel = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>;
+  using Witness_complex = Gudhi::witness_complex::Euclidean_witness_complex<Kernel>;
+
   if (argc != 2) {
     std::cerr << "Usage: " << argv[0]
         << " number_of_landmarks \n";
@@ -61,15 +60,14 @@ int main(int argc, char * const argv[]) {
   }
 
   int number_of_landmarks = atoi(argv[1]);
-  clock_t start, end;
-
-  // Construct the Simplex Tree
-  Simplex_tree simplex_tree;
 
   std::vector< std::pair<int, double> > l_time;
 
-  // Read the point file
+  // Generate points
   for (int nbP = 500; nbP < 10000; nbP += 500) {
+    clock_t start, end;
+    // Construct the Simplex Tree
+    Gudhi::Simplex_tree<> simplex_tree;
     Point_Vector point_vector, landmarks;
     generate_points_sphere(point_vector, nbP, 4);
     std::cout << "Successfully generated " << point_vector.size() << " points.\n";
@@ -77,12 +75,12 @@ int main(int argc, char * const argv[]) {
 
     // Choose landmarks
     start = clock();
-    std::vector<std::vector< int > > knn;
-    Gudhi::subsampling::pick_n_random_points(point_vector, 100, std::back_inserter(landmarks));
-    Gudhi::witness_complex::construct_closest_landmark_table<Simplex_tree::Filtration_value>(point_vector, landmarks, knn);
+    Gudhi::subsampling::pick_n_random_points(point_vector, number_of_landmarks, std::back_inserter(landmarks));
 
     // Compute witness complex
-    Gudhi::witness_complex::witness_complex(knn, number_of_landmarks, point_vector[0].size(), simplex_tree);
+    Witness_complex witness_complex(landmarks,
+                                    point_vector);
+    witness_complex.create_complex(simplex_tree, 0);
     end = clock();
     double time = static_cast<double>(end - start) / CLOCKS_PER_SEC;
     std::cout << "Witness complex for " << number_of_landmarks << " landmarks took "
diff --git a/src/Witness_complex/example/generators.h b/src/Witness_complex/example/generators.h
index ac445261..7df43db5 100644
--- a/src/Witness_complex/example/generators.h
+++ b/src/Witness_complex/example/generators.h
@@ -25,17 +25,19 @@
 
 #include <CGAL/Epick_d.h>
 #include <CGAL/point_generators_d.h>
+#include <CGAL/Random.h>
 
 #include <fstream>
 #include <string>
 #include <vector>
+#include <cmath>
 
-typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K;
-typedef K::FT FT;
-typedef K::Point_d Point_d;
-typedef std::vector<Point_d> Point_Vector;
-typedef CGAL::Random_points_in_cube_d<Point_d> Random_cube_iterator;
-typedef CGAL::Random_points_in_ball_d<Point_d> Random_point_iterator;
+using K = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>;
+using FT = K::FT;
+using Point_d = K::Point_d;
+using Point_Vector = std::vector<Point_d>;
+using Random_cube_iterator = CGAL::Random_points_in_cube_d<Point_d>;
+using Random_point_iterator = CGAL::Random_points_in_ball_d<Point_d>;
 
 /**
  * \brief Rock age method of reading off file
@@ -144,4 +146,21 @@ void generate_points_sphere(Point_Vector& W, int nbP, int dim) {
     W.push_back(*rp++);
 }
 
+/** \brief Generate nbP points on a (flat) d-torus embedded in R^{2d}
+ *
+ */
+void generate_points_torus(Point_Vector& W, int nbP, int dim) {
+  CGAL::Random rand;
+  const double pi = std::acos(-1);
+  for (int i = 0; i < nbP; i++) {
+    std::vector<FT> point;
+    for (int j = 0; j < dim; j++) {
+      double alpha = rand.uniform_real(static_cast<double>(0), 2*pi);
+      point.push_back(sin(alpha));
+      point.push_back(cos(alpha));
+    }
+    W.push_back(Point_d(point));
+  }
+}
+
 #endif  // EXAMPLE_WITNESS_COMPLEX_GENERATORS_H_
diff --git a/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h b/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h
new file mode 100644
index 00000000..d41a6811
--- /dev/null
+++ b/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h
@@ -0,0 +1,67 @@
+/*    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):       Siargey Kachanovich
+ *
+ *    Copyright (C) 2016  INRIA (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/>.
+ */
+
+#ifndef ACTIVE_WITNESS_ACTIVE_WITNESS_H_
+#define ACTIVE_WITNESS_ACTIVE_WITNESS_H_
+
+#include <gudhi/Active_witness/Active_witness_iterator.h>
+#include <list>
+
+namespace Gudhi {
+
+namespace witness_complex {
+
+  /* \class Active_witness
+   *  \brief Class representing a list of nearest neighbors to a given witness.
+   *  \details Every element is a pair of a landmark identifier and the squared distance to it.
+  */
+template< typename Id_distance_pair,
+          typename INS_range >
+class Active_witness {
+ public:
+  typedef Active_witness<Id_distance_pair, INS_range> ActiveWitness;
+  typedef typename INS_range::iterator INS_iterator;
+  typedef Active_witness_iterator< ActiveWitness, Id_distance_pair, INS_iterator > iterator;
+  typedef typename std::list<Id_distance_pair> Table;
+
+  Table nearest_landmark_table_;
+  INS_range    search_range_;
+  INS_iterator iterator_next_;
+  INS_iterator iterator_end_;
+
+  Active_witness(const INS_range& search_range)
+    : search_range_(search_range), iterator_next_(search_range_.begin()), iterator_end_(search_range_.end()) {
+  }
+
+  iterator begin() {
+    return iterator(this, nearest_landmark_table_.begin());
+  }
+
+  iterator end() {
+    return iterator(this);
+  }
+};
+
+}  // namespace witness_complex
+}  // namespace Gudhi
+
+#endif  // ACTIVE_WITNESS_ACTIVE_WITNESS_H_
diff --git a/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h b/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h
new file mode 100644
index 00000000..0a05173a
--- /dev/null
+++ b/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h
@@ -0,0 +1,108 @@
+/*    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):       Siargey Kachanovich
+ *
+ *    Copyright (C) 2016  INRIA (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/>.
+ */
+
+#ifndef ACTIVE_WITNESS_ACTIVE_WITNESS_ITERATOR_H_
+#define ACTIVE_WITNESS_ACTIVE_WITNESS_ITERATOR_H_
+
+#include <boost/iterator/iterator_facade.hpp>
+#include <list>
+
+namespace Gudhi {
+
+namespace witness_complex {
+
+/* \brief Iterator in the nearest landmark list.
+ *  \details After the iterator reaches the end of the list,
+ *          the list is augmented by a (nearest landmark, distance) pair if possible.
+ *          If all the landmarks are present in the list, iterator returns the specific end value
+ *          of the corresponding 'Active_witness' object.
+ */
+template< typename Active_witness,
+          typename Id_distance_pair,
+          typename INS_iterator >
+class Active_witness_iterator
+  : public boost::iterator_facade< Active_witness_iterator <Active_witness, Id_distance_pair, INS_iterator>,
+                                   Id_distance_pair const,
+                                   boost::forward_traversal_tag,
+                                   Id_distance_pair const> {
+  friend class boost::iterator_core_access;
+
+  typedef typename std::list<Id_distance_pair>::iterator Pair_iterator;
+  typedef typename Gudhi::witness_complex::Active_witness_iterator<Active_witness,
+                                                                   Id_distance_pair,
+                                                                   INS_iterator> Iterator;
+
+  Active_witness *aw_;
+  Pair_iterator lh_;  // landmark handle
+  bool is_end_;  // true only if the pointer is end and there are no more neighbors to add
+
+ public:
+  Active_witness_iterator(Active_witness* aw)
+    : aw_(aw), lh_(aw_->nearest_landmark_table_.end()), is_end_(true) {
+  }
+
+  Active_witness_iterator(Active_witness* aw, const Pair_iterator& lh)
+    : aw_(aw), lh_(lh) {
+    is_end_ = false;
+    if (lh_ == aw_->nearest_landmark_table_.end()) {
+      if (aw_->iterator_next_ == aw_->iterator_end_) {
+        is_end_ = true;
+      } else {
+        aw_->nearest_landmark_table_.push_back(*aw_->iterator_next_);
+        lh_ = --aw_->nearest_landmark_table_.end();
+        ++(aw_->iterator_next_);
+      }
+    }
+  }
+
+ private :
+  Id_distance_pair& dereference() const {
+    return *lh_;
+  }
+
+  bool equal(const Iterator& other) const {
+    return (is_end_ == other.is_end_) || (lh_ == other.lh_);
+  }
+
+  void increment() {
+    // the neighbor search can't be at the end iterator of a list
+    GUDHI_CHECK(!is_end_ && lh_ != aw_->nearest_landmark_table_.end(),
+                std::logic_error("Wrong active witness increment."));
+    // if the id of the current landmark is the same as the last one
+
+    lh_++;
+    if (lh_ == aw_->nearest_landmark_table_.end()) {
+      if (aw_->iterator_next_ == aw_->iterator_end_) {
+        is_end_ = true;
+      } else {
+        aw_->nearest_landmark_table_.push_back(*aw_->iterator_next_);
+        lh_ = std::prev(aw_->nearest_landmark_table_.end());
+        ++(aw_->iterator_next_);
+      }
+    }
+  }
+};
+
+}  // namespace witness_complex
+}  // namespace Gudhi
+
+#endif  // ACTIVE_WITNESS_ACTIVE_WITNESS_ITERATOR_H_
diff --git a/src/Witness_complex/include/gudhi/Construct_closest_landmark_table.h b/src/Witness_complex/include/gudhi/Construct_closest_landmark_table.h
deleted file mode 100644
index a8cdd096..00000000
--- a/src/Witness_complex/include/gudhi/Construct_closest_landmark_table.h
+++ /dev/null
@@ -1,92 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Siargey Kachanovich
- *
- *    Copyright (C) 2015  INRIA
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#ifndef CONSTRUCT_CLOSEST_LANDMARK_TABLE_H_
-#define CONSTRUCT_CLOSEST_LANDMARK_TABLE_H_
-
-#include <boost/range/size.hpp>
-
-#include <queue>  // for priority_queue<>
-#include <utility>  // for pair<>
-#include <iterator>
-#include <vector>
-#include <set>
-
-namespace Gudhi {
-
-namespace witness_complex {
-
-  /**
-   *  \ingroup witness_complex
-   * \brief Construct the closest landmark tables for all witnesses.
-   *  \details Output a table 'knn', each line of which represents a witness and
-   *   consists of landmarks sorted by
-   *   euclidean distance from the corresponding witness.
-   *
-   *  The type WitnessContainer is a random access range and
-   *  the type LandmarkContainer is a range.
-   *  The type KNearestNeighbors can be seen as 
-   *  Witness_range<Closest_landmark_range<Vertex_handle>>, where
-   *  Witness_range and Closest_landmark_range are random access ranges and
-   *  Vertex_handle is the label type of a vertex in a simplicial complex.
-   *  Closest_landmark_range needs to have push_back operation.
-   */
-
-  template <typename FiltrationValue,
-            typename WitnessContainer,
-            typename LandmarkContainer,
-            typename KNearestNeighbours>
-  void construct_closest_landmark_table(WitnessContainer const &points,
-                                        LandmarkContainer const &landmarks,
-                                        KNearestNeighbours &knn) {
-    int nbP = boost::size(points);
-    assert(nbP >= boost::size(landmarks));
-
-    int dim = boost::size(*std::begin(points));
-    typedef std::pair<double, int> dist_i;
-    typedef bool (*comp)(dist_i, dist_i);
-    knn = KNearestNeighbours(nbP);
-    for (int points_i = 0; points_i < nbP; points_i++) {
-      std::priority_queue<dist_i, std::vector<dist_i>, comp> l_heap([](dist_i j1, dist_i j2) {
-          return j1.first > j2.first;
-        });
-      typename LandmarkContainer::const_iterator landmarks_it;
-      int landmarks_i = 0;
-      for (landmarks_it = landmarks.begin(), landmarks_i = 0; landmarks_it != landmarks.end();
-           ++landmarks_it, landmarks_i++) {
-        dist_i dist = std::make_pair(Euclidean_distance()(points[points_i], *landmarks_it),
-                                     landmarks_i);
-        l_heap.push(dist);
-      }
-      for (int i = 0; i < dim + 1; i++) {
-        dist_i dist = l_heap.top();
-        knn[points_i].push_back(dist.second);
-        l_heap.pop();
-      }
-    }
-  }
-
-}  // namespace witness_complex
-
-}  // namespace Gudhi
-
-#endif  // CONSTRUCT_CLOSEST_LANDMARK_TABLE_H_
diff --git a/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h b/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h
new file mode 100644
index 00000000..fb669ef8
--- /dev/null
+++ b/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h
@@ -0,0 +1,104 @@
+/*    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):       Siargey Kachanovich
+ *
+ *    Copyright (C) 2015  INRIA (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/>.
+ */
+
+#ifndef EUCLIDEAN_STRONG_WITNESS_COMPLEX_H_
+#define EUCLIDEAN_STRONG_WITNESS_COMPLEX_H_
+
+#include <gudhi/Strong_witness_complex.h>
+#include <gudhi/Active_witness/Active_witness.h>
+#include <gudhi/Kd_tree_search.h>
+
+#include <utility>
+#include <vector>
+
+namespace Gudhi {
+
+namespace witness_complex {
+
+/**
+ *  \private
+ * \class Euclidean_strong_witness_complex
+ * \brief Constructs strong witness complex for given sets of witnesses and landmarks in Euclidean space.
+ * \ingroup witness_complex
+ *
+ * \tparam Kernel_ requires a <a target="_blank"
+ * href="http://doc.cgal.org/latest/Kernel_d/classCGAL_1_1Epick__d.html">CGAL::Epick_d</a> class.
+ */
+template< class Kernel_ >
+class Euclidean_strong_witness_complex
+    : public Strong_witness_complex<std::vector<typename Gudhi::spatial_searching::Kd_tree_search<Kernel_,
+                                                                                                  std::vector<typename Kernel_::Point_d>>::INS_range>> {
+ private:
+  typedef Kernel_                                                                      K;
+  typedef typename K::Point_d                                                          Point_d;
+  typedef std::vector<Point_d>                                                         Point_range;
+  typedef Gudhi::spatial_searching::Kd_tree_search<Kernel_, Point_range>               Kd_tree;
+  typedef typename Kd_tree::INS_range                                                  Nearest_landmark_range;
+  typedef typename std::vector<Nearest_landmark_range>                                 Nearest_landmark_table;
+
+  typedef typename Nearest_landmark_range::Point_with_transformed_distance Id_distance_pair;
+  typedef typename Id_distance_pair::first_type Landmark_id;
+  typedef Landmark_id Vertex_handle;
+
+ private:
+  Point_range                         landmarks_;
+  Kd_tree                             landmark_tree_;
+  using Strong_witness_complex<Nearest_landmark_table>::nearest_landmark_table_;
+
+ public:
+  /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+  /* @name Constructor
+   */
+
+  //@{
+
+  /**
+   *  \brief Initializes member variables before constructing simplicial complex.
+   *  \details Records landmarks from the range 'landmarks' into a 
+   *           table internally, as well as witnesses from the range 'witnesses'.
+   *           Both ranges should have value_type Kernel_::Point_d.
+   */
+  template< typename LandmarkRange,
+            typename WitnessRange >
+  Euclidean_strong_witness_complex(const LandmarkRange & landmarks,
+                                   const WitnessRange &  witnesses)
+    : landmarks_(std::begin(landmarks), std::end(landmarks)), landmark_tree_(landmarks_) {
+    nearest_landmark_table_.reserve(boost::size(witnesses));
+    for (auto w : witnesses)
+      nearest_landmark_table_.push_back(landmark_tree_.query_incremental_nearest_neighbors(w));
+  }
+
+  /** \brief Returns the point corresponding to the given vertex.
+   */
+  template <typename Vertex_handle>
+  Point_d get_point(Vertex_handle vertex) const {
+    return landmarks_[vertex];
+  }
+
+  //@}
+};
+
+}  // namespace witness_complex
+
+}  // namespace Gudhi
+
+#endif  // EUCLIDEAN_STRONG_WITNESS_COMPLEX_H_
diff --git a/src/Witness_complex/include/gudhi/Euclidean_witness_complex.h b/src/Witness_complex/include/gudhi/Euclidean_witness_complex.h
new file mode 100644
index 00000000..6afe9a5d
--- /dev/null
+++ b/src/Witness_complex/include/gudhi/Euclidean_witness_complex.h
@@ -0,0 +1,106 @@
+/*    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):       Siargey Kachanovich
+ *
+ *    Copyright (C) 2015  INRIA (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/>.
+ */
+
+#ifndef EUCLIDEAN_WITNESS_COMPLEX_H_
+#define EUCLIDEAN_WITNESS_COMPLEX_H_
+
+#include <gudhi/Witness_complex.h>
+#include <gudhi/Active_witness/Active_witness.h>
+#include <gudhi/Kd_tree_search.h>
+
+#include <utility>
+#include <vector>
+#include <list>
+#include <limits>
+
+namespace Gudhi {
+
+namespace witness_complex {
+
+/**
+ * \private
+ * \class Euclidean_witness_complex
+ * \brief Constructs (weak) witness complex for given sets of witnesses and landmarks in Euclidean space.
+ * \ingroup witness_complex
+ *
+ * \tparam Kernel_ requires a <a target="_blank"
+ * href="http://doc.cgal.org/latest/Kernel_d/classCGAL_1_1Epick__d.html">CGAL::Epick_d</a> class.
+ */
+template< class Kernel_ >
+class Euclidean_witness_complex
+    : public Witness_complex<std::vector<typename Gudhi::spatial_searching::Kd_tree_search<Kernel_,
+                                         std::vector<typename Kernel_::Point_d>>::INS_range>> {
+ private:
+  typedef Kernel_                                                                      K;
+  typedef typename K::Point_d                                                          Point_d;
+  typedef std::vector<Point_d>                                                         Point_range;
+  typedef Gudhi::spatial_searching::Kd_tree_search<Kernel_, Point_range>               Kd_tree;
+  typedef typename Kd_tree::INS_range                                                  Nearest_landmark_range;
+  typedef typename std::vector<Nearest_landmark_range>                                 Nearest_landmark_table;
+
+  typedef typename Nearest_landmark_range::Point_with_transformed_distance Id_distance_pair;
+  typedef typename Id_distance_pair::first_type Landmark_id;
+  typedef Landmark_id Vertex_handle;
+
+ private:
+  Point_range                         landmarks_;
+  Kd_tree                             landmark_tree_;
+  using Witness_complex<Nearest_landmark_table>::nearest_landmark_table_;
+
+ public:
+  /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+  /* @name Constructor
+   */
+
+  //@{
+
+  /**
+   *  \brief Initializes member variables before constructing simplicial complex.
+   *  \details Records landmarks from the range 'landmarks' into a 
+   *           table internally, as well as witnesses from the range 'witnesses'.
+   *           Both ranges should have value_type Kernel_::Point_d.
+   */
+  template< typename LandmarkRange,
+            typename WitnessRange >
+  Euclidean_witness_complex(const LandmarkRange & landmarks,
+                            const WitnessRange &  witnesses)
+    : landmarks_(std::begin(landmarks), std::end(landmarks)), landmark_tree_(landmarks) {
+    nearest_landmark_table_.reserve(boost::size(witnesses));
+    for (auto w : witnesses)
+      nearest_landmark_table_.push_back(landmark_tree_.query_incremental_nearest_neighbors(w));
+  }
+
+  /** \brief Returns the point corresponding to the given vertex.
+   *  @param[in] vertex Vertex handle of the point to retrieve.
+   */
+  Point_d get_point(Vertex_handle vertex) const {
+    return landmarks_[vertex];
+  }
+
+  //@}
+};
+
+}  // namespace witness_complex
+
+}  // namespace Gudhi
+
+#endif  // EUCLIDEAN_WITNESS_COMPLEX_H_
diff --git a/src/Witness_complex/include/gudhi/Strong_witness_complex.h b/src/Witness_complex/include/gudhi/Strong_witness_complex.h
new file mode 100644
index 00000000..a973ddb7
--- /dev/null
+++ b/src/Witness_complex/include/gudhi/Strong_witness_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):       Siargey Kachanovich
+ *
+ *    Copyright (C) 2015  INRIA (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/>.
+ */
+
+#ifndef STRONG_WITNESS_COMPLEX_H_
+#define STRONG_WITNESS_COMPLEX_H_
+
+#include <gudhi/Active_witness/Active_witness.h>
+
+#include <utility>
+#include <vector>
+#include <list>
+#include <limits>
+
+namespace Gudhi {
+
+namespace witness_complex {
+
+/* \private
+ * \class Strong_witness_complex
+ * \brief Constructs strong witness complex for a given table of nearest landmarks with respect to witnesses.
+ * \ingroup witness_complex
+ *
+ * \tparam Nearest_landmark_table_ needs to be a range of a range of pairs of nearest landmarks and distances.
+ *         The class Nearest_landmark_table_::value_type must be a copiable range.
+ *         The range of pairs must admit a member type 'iterator'. The dereference type 
+ *         of the pair range iterator needs to be 'std::pair<std::size_t, double>'.
+ */
+template< class Nearest_landmark_table_ >
+class Strong_witness_complex {
+ private:
+  typedef typename Nearest_landmark_table_::value_type               Nearest_landmark_range;
+  typedef std::size_t                                                Witness_id;
+  typedef std::size_t                                                Landmark_id;
+  typedef std::pair<Landmark_id, double>                             Id_distance_pair;
+  typedef Active_witness<Id_distance_pair, Nearest_landmark_range>   ActiveWitness;
+  typedef std::list< ActiveWitness >                                 ActiveWitnessList;
+  typedef std::vector< Landmark_id >                                 typeVectorVertex;
+  typedef std::vector<Nearest_landmark_range>                        Nearest_landmark_table_internal;
+  typedef Landmark_id Vertex_handle;
+
+ protected:
+  Nearest_landmark_table_internal              nearest_landmark_table_;
+
+ public:
+  /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+  /* @name Constructor
+   */
+
+  //@{
+
+  Strong_witness_complex() {
+  }
+
+  /**
+   *  \brief Initializes member variables before constructing simplicial complex.
+   *  \details Records nearest landmark table.
+   *  @param[in] nearest_landmark_table needs to be a range of a range of pairs of nearest landmarks and distances.
+   *         The class Nearest_landmark_table_::value_type must be a copiable range.
+   *         The range of pairs must admit a member type 'iterator'. The dereference type 
+   *         of the pair range iterator needs to be 'std::pair<std::size_t, double>'.
+   */
+  Strong_witness_complex(Nearest_landmark_table_ const & nearest_landmark_table)
+    : nearest_landmark_table_(std::begin(nearest_landmark_table), std::end(nearest_landmark_table)) {
+  }
+
+  /** \brief Outputs the strong witness complex of relaxation 'max_alpha_square' 
+   *         in a simplicial complex data structure.
+   *  \details The function returns true if the construction is successful and false otherwise.
+   *  @param[out] complex Simplicial complex data structure, which is a model of
+   *              SimplicialComplexForWitness concept.
+   *  @param[in] max_alpha_square Maximal squared relaxation parameter.
+   *  @param[in] limit_dimension Represents the maximal dimension of the simplicial complex
+   *         (default value = no limit).
+   */
+  template < typename SimplicialComplexForWitness >
+  bool create_complex(SimplicialComplexForWitness& complex,
+                      double  max_alpha_square,
+                      Landmark_id limit_dimension = std::numeric_limits<Landmark_id>::max()) const {
+    Landmark_id complex_dim = 0;
+    if (complex.num_vertices() > 0) {
+      std::cerr << "Strong witness complex cannot create complex - complex is not empty.\n";
+      return false;
+    }
+    if (max_alpha_square < 0) {
+      std::cerr << "Strong witness complex cannot create complex - squared relaxation parameter must be "
+                << "non-negative.\n";
+      return false;
+    }
+    if (limit_dimension < 0) {
+      std::cerr << "Strong witness complex cannot create complex - limit dimension must be non-negative.\n";
+      return false;
+    }
+    for (auto w : nearest_landmark_table_) {
+      ActiveWitness aw(w);
+      typeVectorVertex simplex;
+      typename ActiveWitness::iterator aw_it = aw.begin();
+      float lim_dist2 = aw.begin()->second + max_alpha_square;
+      while ((Landmark_id)simplex.size() <= limit_dimension && aw_it != aw.end() && aw_it->second < lim_dist2) {
+        simplex.push_back(aw_it->first);
+        complex.insert_simplex_and_subfaces(simplex, aw_it->second - aw.begin()->second);
+        aw_it++;
+      }
+      // continue inserting limD-faces of the following simplices
+      typeVectorVertex& vertices = simplex;  // 'simplex' now will be called vertices
+      while (aw_it != aw.end() && aw_it->second < lim_dist2) {
+        typeVectorVertex facet = {};
+        add_all_faces_of_dimension(limit_dimension, vertices, vertices.begin(), aw_it,
+                                   aw_it->second - aw.begin()->second, facet, complex);
+        vertices.push_back(aw_it->first);
+        aw_it++;
+      }
+      if ((Landmark_id)simplex.size() - 1 > complex_dim)
+        complex_dim = simplex.size() - 1;
+    }
+    complex.set_dimension(complex_dim);
+    return true;
+  }
+
+ private:
+    /* \brief Adds recursively all the faces of a certain dimension dim-1 witnessed by the same witness.
+     * Iterator is needed to know until how far we can take landmarks to form simplexes.
+     * simplex is the prefix of the simplexes to insert.
+     * The landmark pointed by aw_it is added to all formed simplices.
+     */
+  template < typename SimplicialComplexForWitness >
+  void add_all_faces_of_dimension(Landmark_id dim,
+                                  typeVectorVertex& vertices,
+                                  typename typeVectorVertex::iterator curr_it,
+                                  typename ActiveWitness::iterator aw_it,
+                                  double filtration_value,
+                                  typeVectorVertex& simplex,
+                                  SimplicialComplexForWitness& sc) const {
+    if (dim > 0) {
+      while (curr_it != vertices.end()) {
+        simplex.push_back(*curr_it);
+        ++curr_it;
+        add_all_faces_of_dimension(dim-1,
+                                   vertices,
+                                   curr_it,
+                                   aw_it,
+                                   filtration_value,
+                                   simplex,
+                                   sc);
+        simplex.pop_back();
+        add_all_faces_of_dimension(dim,
+                                   vertices,
+                                   curr_it,
+                                   aw_it,
+                                   filtration_value,
+                                   simplex,
+                                   sc);
+      }
+    } else if (dim == 0) {
+      simplex.push_back(aw_it->first);
+      sc.insert_simplex_and_subfaces(simplex, filtration_value);
+      simplex.pop_back();
+    }
+  }
+  //@}
+};
+
+}  // namespace witness_complex
+
+}  // namespace Gudhi
+
+#endif  // STRONG_WITNESS_COMPLEX_H_
diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h
index 1eb126f1..63f03687 100644
--- a/src/Witness_complex/include/gudhi/Witness_complex.h
+++ b/src/Witness_complex/include/gudhi/Witness_complex.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Siargey Kachanovich
  *
- *    Copyright (C) 2015  INRIA Sophia Antipolis-Méditerranée (France)
+ *    Copyright (C) 2015  INRIA (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
@@ -23,64 +23,44 @@
 #ifndef WITNESS_COMPLEX_H_
 #define WITNESS_COMPLEX_H_
 
-// Needed for the adjacency graph in bad link search
-#include <boost/graph/graph_traits.hpp>
-#include <boost/graph/adjacency_list.hpp>
-#include <boost/graph/connected_components.hpp>
+#include <gudhi/Active_witness/Active_witness.h>
+#include <gudhi/Witness_complex/all_faces_in.h>
 
-#include <boost/range/size.hpp>
-
-#include <gudhi/distance_functions.h>
-
-#include <algorithm>
 #include <utility>
 #include <vector>
 #include <list>
-#include <set>
-#include <queue>
 #include <limits>
-#include <ctime>
-#include <iostream>
 
 namespace Gudhi {
 
 namespace witness_complex {
 
-// /*
-//  *  \private
-//     \class Witness_complex
-//     \brief Constructs the witness complex for the given set of witnesses and landmarks.
-//     \ingroup witness_complex
-//  */
-template< class SimplicialComplex>
+/**
+ * \private
+ * \class Witness_complex
+ * \brief Constructs (weak) witness complex for a given table of nearest landmarks with respect to witnesses.
+ * \ingroup witness_complex
+ *
+ * \tparam Nearest_landmark_table_ needs to be a range of a range of pairs of nearest landmarks and distances.
+ *         The class Nearest_landmark_table_::value_type must be a copiable range.
+ *         The range of pairs must admit a member type 'iterator'. The dereference type 
+ *         of the pair range iterator needs to be 'std::pair<std::size_t, double>'.
+*/
+template< class Nearest_landmark_table_ >
 class Witness_complex {
  private:
-  struct Active_witness {
-    int witness_id;
-    int landmark_id;
-
-    Active_witness(int witness_id_, int landmark_id_)
-        : witness_id(witness_id_),
-        landmark_id(landmark_id_) { }
-  };
-
- private:
-  typedef typename SimplicialComplex::Simplex_handle Simplex_handle;
-  typedef typename SimplicialComplex::Vertex_handle Vertex_handle;
-
-  typedef std::vector< double > Point_t;
-  typedef std::vector< Point_t > Point_Vector;
-
-  typedef std::vector< Vertex_handle > typeVectorVertex;
-  typedef std::pair< Simplex_handle, bool > typePairSimplexBool;
-
-  typedef int Witness_id;
-  typedef int Landmark_id;
-  typedef std::list< Vertex_handle > ActiveWitnessList;
-
- private:
-  int nbL_;  // Number of landmarks
-  SimplicialComplex& sc_;  // Simplicial complex
+  typedef typename Nearest_landmark_table_::value_type               Nearest_landmark_range;
+  typedef std::size_t                                                Witness_id;
+  typedef std::size_t                                                Landmark_id;
+  typedef std::pair<Landmark_id, double>                             Id_distance_pair;
+  typedef Active_witness<Id_distance_pair, Nearest_landmark_range>   ActiveWitness;
+  typedef std::list< ActiveWitness >                                 ActiveWitnessList;
+  typedef std::vector< Landmark_id >                                 typeVectorVertex;
+  typedef std::vector<Nearest_landmark_range>                        Nearest_landmark_table_internal;
+  typedef Landmark_id Vertex_handle;
+
+ protected:
+  Nearest_landmark_table_internal              nearest_landmark_table_;
 
  public:
   /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
@@ -89,174 +69,136 @@ class Witness_complex {
 
   //@{
 
-  // Witness_range<Closest_landmark_range<Vertex_handle>>
+  Witness_complex() {
+  }
 
-  /*
-   *  \brief Iterative construction of the witness complex.
-   *  \details The witness complex is written in sc_ basing on a matrix knn of
-   *  nearest neighbours of the form {witnesses}x{landmarks}.
-   *
-   *  The type KNearestNeighbors can be seen as 
-   *  Witness_range<Closest_landmark_range<Vertex_handle>>, where
-   *  Witness_range and Closest_landmark_range are random access ranges.
-   *
-   *  Constructor takes into account at most (dim+1) 
-   *  first landmarks from each landmark range to construct simplices.
-   *
-   *  Landmarks are supposed to be in [0,nbL_-1]
+  /**
+   *  \brief Initializes member variables before constructing simplicial complex.
+   *  \details Records nearest landmark table.
+   *  @param[in] nearest_landmark_table needs to be a range of a range of pairs of nearest landmarks and distances.
+   *         The class Nearest_landmark_table_::value_type must be a copiable range.
+   *         The range of pairs must admit a member type 'iterator'. The dereference type 
+   *         of the pair range iterator needs to be 'std::pair<std::size_t, double>'.
    */
-  template< typename KNearestNeighbors >
-  Witness_complex(KNearestNeighbors const & knn,
-                  int nbL,
-                  int dim,
-                  SimplicialComplex & sc) : nbL_(nbL), sc_(sc) {
-    // Construction of the active witness list
-    int nbW = boost::size(knn);
-    typeVectorVertex vv;
-    int counter = 0;
-    /* The list of still useful witnesses
-     * it will diminuish in the course of iterations
-     */
-    ActiveWitnessList active_w;  // = new ActiveWitnessList();
-    for (Vertex_handle i = 0; i != nbL_; ++i) {
-      // initial fill of 0-dimensional simplices
-      // by doing it we don't assume that landmarks are necessarily witnesses themselves anymore
-      counter++;
-      vv = {i};
-      sc_.insert_simplex(vv);
-      // TODO(SK) Error if not inserted : normally no need here though
+
+  Witness_complex(Nearest_landmark_table_ const & nearest_landmark_table)
+    : nearest_landmark_table_(std::begin(nearest_landmark_table), std::end(nearest_landmark_table)) {
+  }
+
+  /** \brief Outputs the (weak) witness complex of relaxation 'max_alpha_square'
+   *         in a simplicial complex data structure.
+   *  \details The function returns true if the construction is successful and false otherwise.
+   *  @param[out] complex Simplicial complex data structure compatible which is a model of
+   *              SimplicialComplexForWitness concept.
+   *  @param[in] max_alpha_square Maximal squared relaxation parameter.
+   *  @param[in] limit_dimension Represents the maximal dimension of the simplicial complex
+   *         (default value = no limit).
+   */
+  template < typename SimplicialComplexForWitness >
+  bool create_complex(SimplicialComplexForWitness& complex,
+                      double  max_alpha_square,
+                      std::size_t limit_dimension = std::numeric_limits<std::size_t>::max()) const {
+    if (complex.num_vertices() > 0) {
+      std::cerr << "Witness complex cannot create complex - complex is not empty.\n";
+      return false;
     }
-    int k = 1; /* current dimension in iterative construction */
-    for (int i = 0; i != nbW; ++i)
-      active_w.push_back(i);
-    while (!active_w.empty() && k < dim) {
-      typename ActiveWitnessList::iterator it = active_w.begin();
-      while (it != active_w.end()) {
-        typeVectorVertex simplex_vector;
-        /* THE INSERTION: Checking if all the subfaces are in the simplex tree*/
-        bool ok = all_faces_in(knn, *it, k);
-        if (ok) {
-          for (int i = 0; i != k + 1; ++i)
-            simplex_vector.push_back(knn[*it][i]);
-          sc_.insert_simplex(simplex_vector);
-          // TODO(SK) Error if not inserted : normally no need here though
-          ++it;
-        } else {
-          active_w.erase(it++);  // First increase the iterator and then erase the previous element
-        }
+    if (max_alpha_square < 0) {
+      std::cerr << "Witness complex cannot create complex - squared relaxation parameter must be non-negative.\n";
+      return false;
+    }
+    if (limit_dimension < 0) {
+      std::cerr << "Witness complex cannot create complex - limit dimension must be non-negative.\n";
+      return false;
+    }
+    ActiveWitnessList active_witnesses;
+    Landmark_id k = 0; /* current dimension in iterative construction */
+    for (auto w : nearest_landmark_table_)
+      active_witnesses.push_back(ActiveWitness(w));
+    while (!active_witnesses.empty() && k <= limit_dimension) {
+      typename ActiveWitnessList::iterator aw_it = active_witnesses.begin();
+      std::vector<Landmark_id> simplex;
+      simplex.reserve(k+1);
+      while (aw_it != active_witnesses.end()) {
+        bool ok = add_all_faces_of_dimension(k,
+                                             max_alpha_square,
+                                             std::numeric_limits<double>::infinity(),
+                                             aw_it->begin(),
+                                             simplex,
+                                             complex,
+                                             aw_it->end());
+        assert(simplex.empty());
+        if (!ok)
+          active_witnesses.erase(aw_it++);  // First increase the iterator and then erase the previous element
+        else
+          aw_it++;
       }
       k++;
     }
+    complex.set_dimension(k-1);
+    return true;
   }
 
   //@}
 
  private:
-  /* \brief Check if the facets of the k-dimensional simplex witnessed 
-   *  by witness witness_id are already in the complex.
-   *  inserted_vertex is the handle of the (k+1)-th vertex witnessed by witness_id
+  /* \brief Adds recursively all the faces of a certain dimension dim witnessed by the same witness.
+   * Iterator is needed to know until how far we can take landmarks to form simplexes.
+   * simplex is the prefix of the simplexes to insert.
+   * The output value indicates if the witness rests active or not.
    */
-  template <typename KNearestNeighbors>
-  bool all_faces_in(KNearestNeighbors const &knn, int witness_id, int k) {
-    std::vector< Vertex_handle > facet;
-    // CHECK ALL THE FACETS
-    for (int i = 0; i != k + 1; ++i) {
-      facet = {};
-      for (int j = 0; j != k + 1; ++j) {
-        if (j != i) {
-          facet.push_back(knn[witness_id][j]);
+  template < typename SimplicialComplexForWitness >
+  bool add_all_faces_of_dimension(int dim,
+                                  double alpha2,
+                                  double norelax_dist2,
+                                  typename ActiveWitness::iterator curr_l,
+                                  std::vector<Landmark_id>& simplex,
+                                  SimplicialComplexForWitness& sc,
+                                  typename ActiveWitness::iterator end) const {
+    if (curr_l == end)
+      return false;
+    bool will_be_active = false;
+    typename ActiveWitness::iterator l_it = curr_l;
+    if (dim > 0) {
+      for (; l_it != end && l_it->second - alpha2 <= norelax_dist2; ++l_it) {
+        simplex.push_back(l_it->first);
+        if (sc.find(simplex) != sc.null_simplex()) {
+          typename ActiveWitness::iterator next_it = l_it;
+          will_be_active = add_all_faces_of_dimension(dim-1,
+                                                      alpha2,
+                                                      norelax_dist2,
+                                                      ++next_it,
+                                                      simplex,
+                                                      sc,
+                                                      end) || will_be_active;
         }
-      }  // endfor
-      if (sc_.find(facet) == sc_.null_simplex())
-        return false;
-    }  // endfor
-    return true;
-  }
-
-  template <typename T>
-  static void print_vector(const std::vector<T>& v) {
-    std::cout << "[";
-    if (!v.empty()) {
-      std::cout << *(v.begin());
-      for (auto it = v.begin() + 1; it != v.end(); ++it) {
-        std::cout << ",";
-        std::cout << *it;
+        assert(!simplex.empty());
+        simplex.pop_back();
+        // If norelax_dist is infinity, change to first omitted distance
+        if (l_it->second <= norelax_dist2)
+          norelax_dist2 = l_it->second;
       }
-    }
-    std::cout << "]";
-  }
-
- public:
-  // /*
-  //  *  \brief Verification if every simplex in the complex is witnessed by witnesses in knn.
-  //  *  \param print_output =true will print the witnesses for each simplex
-  //  *  \remark Added for debugging purposes.
-  //  */
-  template< class KNearestNeighbors >
-  bool is_witness_complex(KNearestNeighbors const & knn, bool print_output) {
-    for (Simplex_handle sh : sc_.complex_simplex_range()) {
-      bool is_witnessed = false;
-      typeVectorVertex simplex;
-      int nbV = 0;  // number of verticed in the simplex
-      for (Vertex_handle v : sc_.simplex_vertex_range(sh))
-        simplex.push_back(v);
-      nbV = simplex.size();
-      for (typeVectorVertex w : knn) {
-        bool has_vertices = true;
-        for (Vertex_handle v : simplex)
-          if (std::find(w.begin(), w.begin() + nbV, v) == w.begin() + nbV) {
-            has_vertices = false;
-          }
-        if (has_vertices) {
-          is_witnessed = true;
-          if (print_output) {
-            std::cout << "The simplex ";
-            print_vector(simplex);
-            std::cout << " is witnessed by the witness ";
-            print_vector(w);
-            std::cout << std::endl;
-          }
-          break;
-        }
-      }
-      if (!is_witnessed) {
-        if (print_output) {
-          std::cout << "The following simplex is not witnessed ";
-          print_vector(simplex);
-          std::cout << std::endl;
+    } else if (dim == 0) {
+      for (; l_it != end && l_it->second - alpha2 <= norelax_dist2; ++l_it) {
+        simplex.push_back(l_it->first);
+        double filtration_value = 0;
+        // if norelax_dist is infinite, relaxation is 0.
+        if (l_it->second > norelax_dist2)
+          filtration_value = l_it->second - norelax_dist2;
+        if (all_faces_in(simplex, &filtration_value, sc)) {
+          will_be_active = true;
+          sc.insert_simplex(simplex, filtration_value);
         }
-        assert(is_witnessed);
-        return false;
+        assert(!simplex.empty());
+        simplex.pop_back();
+        // If norelax_dist is infinity, change to first omitted distance
+        if (l_it->second < norelax_dist2)
+          norelax_dist2 = l_it->second;
       }
     }
-    return true;
+    return will_be_active;
   }
 };
 
-  /**
-   *  \ingroup witness_complex
-   *  \brief Iterative construction of the witness complex.
-   *  \details The witness complex is written in simplicial complex sc_
-   *   basing on a matrix knn of
-   *  nearest neighbours of the form {witnesses}x{landmarks}.
-   *
-   *  The type KNearestNeighbors can be seen as
-   *  Witness_range<Closest_landmark_range<Vertex_handle>>, where
-   *  Witness_range and Closest_landmark_range are random access ranges.
-   *
-   *  Procedure takes into account at most (dim+1)
-   *  first landmarks from each landmark range to construct simplices.
-   *
-   *  Landmarks are supposed to be in [0,nbL_-1]
-   */
-  template <class KNearestNeighbors, class SimplicialComplexForWitness>
-  void witness_complex(KNearestNeighbors const & knn,
-                       int nbL,
-                       int dim,
-                       SimplicialComplexForWitness & sc) {
-    Witness_complex<SimplicialComplexForWitness>(knn, nbL, dim, sc);
-  }
-
 }  // namespace witness_complex
 
 }  // namespace Gudhi
diff --git a/src/Witness_complex/include/gudhi/Witness_complex/all_faces_in.h b/src/Witness_complex/include/gudhi/Witness_complex/all_faces_in.h
new file mode 100644
index 00000000..b68d75a1
--- /dev/null
+++ b/src/Witness_complex/include/gudhi/Witness_complex/all_faces_in.h
@@ -0,0 +1,55 @@
+/*    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):       Siargey Kachanovich
+ *
+ *    Copyright (C) 2015  INRIA (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/>.
+ */
+
+#ifndef WITNESS_COMPLEX_ALL_FACES_IN_H_
+#define WITNESS_COMPLEX_ALL_FACES_IN_H_
+
+/* \brief Check if the facets of the k-dimensional simplex witnessed 
+ *  by witness witness_id are already in the complex.
+ *  inserted_vertex is the handle of the (k+1)-th vertex witnessed by witness_id
+ */
+template < typename SimplicialComplexForWitness,
+           typename Simplex >
+  bool all_faces_in(Simplex& simplex,
+                    double* filtration_value,
+                    SimplicialComplexForWitness& sc) {
+    typedef typename SimplicialComplexForWitness::Simplex_handle Simplex_handle;
+
+    if (simplex.size() == 1)
+      return true;                  /* Add vertices unconditionally */
+
+    Simplex facet;
+    for (typename Simplex::iterator not_it = simplex.begin(); not_it != simplex.end(); ++not_it) {
+        facet.clear();
+        for (typename Simplex::iterator it = simplex.begin(); it != simplex.end(); ++it)
+          if (it != not_it)
+            facet.push_back(*it);
+        Simplex_handle facet_sh = sc.find(facet);
+        if (facet_sh == sc.null_simplex())
+          return false;
+        else if (sc.filtration(facet_sh) > *filtration_value)
+          *filtration_value = sc.filtration(facet_sh);
+      }
+    return true;
+  }
+
+#endif  // WITNESS_COMPLEX_ALL_FACES_IN_H_
diff --git a/src/Witness_complex/test/CMakeLists.txt b/src/Witness_complex/test/CMakeLists.txt
index bb55b0f1..e73f9c3a 100644
--- a/src/Witness_complex/test/CMakeLists.txt
+++ b/src/Witness_complex/test/CMakeLists.txt
@@ -10,21 +10,29 @@ if (GPROF_PATH)
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
 endif()
 
-add_executable ( simple_witness_complexUT simple_witness_complex.cpp )
-target_link_libraries(simple_witness_complexUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+add_executable ( Witness_complex_test_simple_witness_complex test_simple_witness_complex.cpp )
+target_link_libraries(Witness_complex_test_simple_witness_complex ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+if (TBB_FOUND)
+  target_link_libraries(Witness_complex_test_simple_witness_complex ${TBB_LIBRARIES})
+endif(TBB_FOUND)
 
 # Unitary tests definition and xml result file generation
-add_test(NAME simple_witness_complexUT
-  COMMAND ${CMAKE_CURRENT_BINARY_DIR}/simple_witness_complexUT 
+add_test(NAME simple_witness_complex
+  COMMAND ${CMAKE_CURRENT_BINARY_DIR}/Witness_complex_test_simple_witness_complex 
     # XML format for Jenkins xUnit plugin 
-    --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/simple_witness_complexUT.xml --log_level=test_suite --report_level=no)
+    --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Witness_complex_test_simple_witness_complexUT.xml --log_level=test_suite --report_level=no)
 
-add_executable ( witness_complex_pointsUT witness_complex_points.cpp )
-target_link_libraries(witness_complex_pointsUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
-
-# Unitary tests definition and xml result file generation
-add_test(NAME witness_complex_pointsUT
-  COMMAND ${CMAKE_CURRENT_BINARY_DIR}/witness_complex_pointsUT 
-    # XML format for Jenkins xUnit plugin 
-    --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/witness_complex_pointsUT.xml --log_level=test_suite --report_level=no)
+# CGAL and Eigen3 are required for Euclidean version of Witness
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
+  add_executable ( Witness_complex_test_euclidean_simple_witness_complex test_euclidean_simple_witness_complex.cpp )
+  target_link_libraries(Witness_complex_test_euclidean_simple_witness_complex ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+  if (TBB_FOUND)
+    target_link_libraries(Witness_complex_test_euclidean_simple_witness_complex ${TBB_LIBRARIES})
+  endif(TBB_FOUND)
 
+  # Unitary tests definition and xml result file generation
+  add_test(NAME euclidean_simple_witness_complex
+    COMMAND ${CMAKE_CURRENT_BINARY_DIR}/Witness_complex_test_euclidean_simple_witness_complex
+      # XML format for Jenkins xUnit plugin
+      --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Witness_complex_test_euclidean_simple_witness_complexUT.xml --log_level=test_suite --report_level=no)
+endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
diff --git a/src/Witness_complex/test/simple_witness_complex.cpp b/src/Witness_complex/test/simple_witness_complex.cpp
deleted file mode 100644
index 6be39f58..00000000
--- a/src/Witness_complex/test/simple_witness_complex.cpp
+++ /dev/null
@@ -1,59 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Siargey Kachanovich
- *
- *    Copyright (C) 2016  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/>.
- */
-
-#define BOOST_TEST_DYN_LINK
-#define BOOST_TEST_MODULE "simple_witness_complex"
-#include <boost/test/unit_test.hpp>
-#include <boost/mpl/list.hpp>
-
-#include <gudhi/Simplex_tree.h>
-#include <gudhi/Witness_complex.h>
-
-#include <iostream>
-#include <ctime>
-#include <vector>
-
-typedef Gudhi::Simplex_tree<> Simplex_tree;
-typedef std::vector< Simplex_tree::Vertex_handle > typeVectorVertex;
-typedef Gudhi::witness_complex::Witness_complex<Simplex_tree> WitnessComplex;
-
-BOOST_AUTO_TEST_CASE(simple_witness_complex) {
-  Simplex_tree complex;
-  std::vector< typeVectorVertex > knn;
-
-  knn.push_back({1, 0, 5, 2, 6, 3, 4});
-  knn.push_back({2, 6, 4, 5, 0, 1, 3});
-  knn.push_back({3, 4, 2, 1, 5, 6, 0});
-  knn.push_back({4, 2, 1, 3, 5, 6, 0});
-  knn.push_back({5, 1, 6, 0, 2, 3, 4});
-  knn.push_back({6, 0, 5, 2, 1, 3, 4});
-  knn.push_back({0, 5, 6, 1, 2, 3, 4});
-  knn.push_back({2, 6, 4, 5, 3, 1, 0});
-  knn.push_back({1, 2, 5, 4, 3, 6, 0});
-  knn.push_back({3, 4, 0, 6, 5, 1, 2});
-  knn.push_back({5, 0, 1, 3, 6, 2, 4});
-  knn.push_back({5, 6, 1, 0, 2, 3, 4});
-  knn.push_back({1, 6, 0, 5, 2, 3, 4});
-  WitnessComplex witnessComplex(knn, 7, 7, complex);
-
-  BOOST_CHECK(witnessComplex.is_witness_complex(knn, false));
-}
diff --git a/src/Witness_complex/test/test_euclidean_simple_witness_complex.cpp b/src/Witness_complex/test/test_euclidean_simple_witness_complex.cpp
new file mode 100644
index 00000000..62fd1157
--- /dev/null
+++ b/src/Witness_complex/test/test_euclidean_simple_witness_complex.cpp
@@ -0,0 +1,135 @@
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "euclidean_simple_witness_complex"
+#include <boost/test/unit_test.hpp>
+#include <boost/mpl/list.hpp>
+
+#include <CGAL/Epick_d.h>
+
+#include <gudhi/Simplex_tree.h>
+
+#include <gudhi/Witness_complex.h>
+#include <gudhi/Euclidean_witness_complex.h>
+#include <gudhi/Strong_witness_complex.h>
+#include <gudhi/Euclidean_strong_witness_complex.h>
+
+#include <gudhi/Kd_tree_search.h>
+
+#include <iostream>
+#include <ctime>
+#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;
+typedef typename Kernel::Point_d Point_d;
+typedef Gudhi::witness_complex::Euclidean_witness_complex<Kernel> EuclideanWitnessComplex;
+typedef Gudhi::witness_complex::Euclidean_strong_witness_complex<Kernel> EuclideanStrongWitnessComplex;
+
+typedef std::vector<Point_d> Point_range;
+typedef Gudhi::spatial_searching::Kd_tree_search<Kernel, Point_range> Kd_tree;
+typedef Kd_tree::INS_range Nearest_landmark_range;
+typedef std::vector<Nearest_landmark_range> Nearest_landmark_table;
+typedef Gudhi::witness_complex::Witness_complex<Nearest_landmark_table> WitnessComplex;
+typedef Gudhi::witness_complex::Strong_witness_complex<Nearest_landmark_table> StrongWitnessComplex;
+
+
+/* All landmarks and witnesses are taken on the grid in the following manner.
+   LWLWL
+   WW.WW
+   L...L
+   WW.WW
+   LWLWL
+
+   Witness complex consists of 8 vertices, 12 edges and 4 triangles
+ */
+
+BOOST_AUTO_TEST_CASE(simple_witness_complex) {
+  Simplex_tree complex, relaxed_complex, strong_relaxed_complex, strong_relaxed_complex2;
+  Simplex_tree complex_ne, relaxed_complex_ne, strong_relaxed_complex_ne, strong_relaxed_complex2_ne;
+
+  Point_range witnesses, landmarks;
+
+  landmarks.push_back(Point_d(std::vector<FT>{-2,-2}));
+  landmarks.push_back(Point_d(std::vector<FT>{-2, 0}));
+  landmarks.push_back(Point_d(std::vector<FT>{-2, 2}));
+  landmarks.push_back(Point_d(std::vector<FT>{ 0,-2}));
+  landmarks.push_back(Point_d(std::vector<FT>{ 0, 2}));
+  landmarks.push_back(Point_d(std::vector<FT>{ 2,-2}));
+  landmarks.push_back(Point_d(std::vector<FT>{ 2, 0}));
+  landmarks.push_back(Point_d(std::vector<FT>{ 2, 2}));
+  witnesses.push_back(Point_d(std::vector<FT>{-2,-1}));
+  witnesses.push_back(Point_d(std::vector<FT>{-2, 1}));
+  witnesses.push_back(Point_d(std::vector<FT>{-1,-2}));
+  witnesses.push_back(Point_d(std::vector<FT>{-1,-1}));
+  witnesses.push_back(Point_d(std::vector<FT>{-1, 1}));
+  witnesses.push_back(Point_d(std::vector<FT>{-1, 2}));
+  witnesses.push_back(Point_d(std::vector<FT>{ 1,-2}));
+  witnesses.push_back(Point_d(std::vector<FT>{ 1,-1}));
+  witnesses.push_back(Point_d(std::vector<FT>{ 1, 1}));
+  witnesses.push_back(Point_d(std::vector<FT>{ 1, 2}));
+  witnesses.push_back(Point_d(std::vector<FT>{ 2,-1}));
+  witnesses.push_back(Point_d(std::vector<FT>{ 2, 1}));
+
+  Kd_tree landmark_tree(landmarks);
+  Nearest_landmark_table nearest_landmark_table;
+  for (auto w: witnesses)
+    nearest_landmark_table.push_back(landmark_tree.query_incremental_nearest_neighbors(w));
+
+  // Weak witness complex: Euclidean version
+  EuclideanWitnessComplex eucl_witness_complex(landmarks,
+                                               witnesses);
+  eucl_witness_complex.create_complex(complex, 0);
+
+  std::cout << "complex.num_simplices() = " << complex.num_simplices() << std::endl;
+  BOOST_CHECK(complex.num_simplices() == 24);
+
+  eucl_witness_complex.create_complex(relaxed_complex, 8.01);
+
+  std::cout << "relaxed_complex.num_simplices() = " << relaxed_complex.num_simplices() << std::endl;
+  BOOST_CHECK(relaxed_complex.num_simplices() == 239);
+  // The corner simplex {0,2,5,7} and its cofaces are missing.
+
+  // Weak witness complex: non-Euclidean version
+  WitnessComplex witness_complex(nearest_landmark_table);
+  witness_complex.create_complex(complex_ne, 0);
+
+  std::cout << "complex.num_simplices() = " << complex_ne.num_simplices() << std::endl;
+  BOOST_CHECK(complex_ne.num_simplices() == 24);
+
+  witness_complex.create_complex(relaxed_complex_ne, 8.01);
+
+  std::cout << "relaxed_complex.num_simplices() = " << relaxed_complex_ne.num_simplices() << std::endl;
+  BOOST_CHECK(relaxed_complex_ne.num_simplices() == 239);
+
+
+  // Strong complex : Euclidean version
+  EuclideanStrongWitnessComplex eucl_strong_witness_complex(landmarks,
+                                                            witnesses);
+
+  eucl_strong_witness_complex.create_complex(strong_relaxed_complex, 9.1);
+  eucl_strong_witness_complex.create_complex(strong_relaxed_complex2, 9.1, 2);
+
+  std::cout << "strong_relaxed_complex.num_simplices() = " << strong_relaxed_complex.num_simplices() << std::endl;
+  BOOST_CHECK(strong_relaxed_complex.num_simplices() == 239);
+
+  std::cout << "strong_relaxed_complex2.num_simplices() = " << strong_relaxed_complex2.num_simplices() << std::endl;
+  BOOST_CHECK(strong_relaxed_complex2.num_simplices() == 92);
+
+
+  // Strong complex : non-Euclidean version
+  StrongWitnessComplex strong_witness_complex(nearest_landmark_table);
+
+  strong_witness_complex.create_complex(strong_relaxed_complex_ne, 9.1);
+  strong_witness_complex.create_complex(strong_relaxed_complex2_ne, 9.1, 2);
+
+  std::cout << "strong_relaxed_complex.num_simplices() = " << strong_relaxed_complex_ne.num_simplices() << std::endl;
+  BOOST_CHECK(strong_relaxed_complex_ne.num_simplices() == 239);
+
+  std::cout << "strong_relaxed_complex2.num_simplices() = " << strong_relaxed_complex2_ne.num_simplices() << std::endl;
+  BOOST_CHECK(strong_relaxed_complex2_ne.num_simplices() == 92);
+
+
+  // 8 vertices, 28 edges, 56 triangles
+}
diff --git a/src/Witness_complex/test/test_simple_witness_complex.cpp b/src/Witness_complex/test/test_simple_witness_complex.cpp
new file mode 100644
index 00000000..9e3509d3
--- /dev/null
+++ b/src/Witness_complex/test/test_simple_witness_complex.cpp
@@ -0,0 +1,53 @@
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "simple_witness_complex"
+#include <boost/test/unit_test.hpp>
+#include <boost/mpl/list.hpp>
+
+#include <gudhi/Simplex_tree.h>
+
+#include <gudhi/Witness_complex.h>
+
+#include <iostream>
+#include <vector>
+#include <utility>
+
+
+BOOST_AUTO_TEST_CASE(simple_witness_complex) {
+  using Nearest_landmark_range = std::vector<std::pair<std::size_t, double>>;
+  using Nearest_landmark_table = std::vector<Nearest_landmark_range>;
+  using Witness_complex = Gudhi::witness_complex::Witness_complex<Nearest_landmark_table>;
+  using Simplex_tree = Gudhi::Simplex_tree<>;
+
+  Simplex_tree stree;
+  Nearest_landmark_table nlt;
+
+  // Example contains 5 witnesses and 5 landmarks
+  Nearest_landmark_range w0 = {std::make_pair(0, 0), std::make_pair(1, 1), std::make_pair(2, 2),
+                               std::make_pair(3, 3), std::make_pair(4, 4)}; nlt.push_back(w0);
+  Nearest_landmark_range w1 = {std::make_pair(1, 0), std::make_pair(2, 1), std::make_pair(3, 2),
+                               std::make_pair(4, 3), std::make_pair(0, 4)}; nlt.push_back(w1);
+  Nearest_landmark_range w2 = {std::make_pair(2, 0), std::make_pair(3, 1), std::make_pair(4, 2),
+                               std::make_pair(0, 3), std::make_pair(1, 4)}; nlt.push_back(w2);
+  Nearest_landmark_range w3 = {std::make_pair(3, 0), std::make_pair(4, 1), std::make_pair(0, 2),
+                               std::make_pair(1, 3), std::make_pair(2, 4)}; nlt.push_back(w3);
+  Nearest_landmark_range w4 = {std::make_pair(4, 0), std::make_pair(0, 1), std::make_pair(1, 2),
+                               std::make_pair(2, 3), std::make_pair(3, 4)}; nlt.push_back(w4);
+
+  Witness_complex witness_complex(nlt);
+  BOOST_CHECK(witness_complex.create_complex(stree, 4.1));
+
+  std::cout << "Number of simplices: " << stree.num_simplices() << std::endl;
+  BOOST_CHECK(stree.num_simplices() == 31);
+
+  // Check when complex not empty
+  BOOST_CHECK(!witness_complex.create_complex(stree, 4.1));
+
+  // Check when max_alpha_square negative
+  Simplex_tree stree2;
+  BOOST_CHECK(!witness_complex.create_complex(stree2, -0.02));
+
+  witness_complex.create_complex(stree2, 4.1, 2);
+  std::cout << "Number of simplices: " << stree2.num_simplices() << std::endl;
+  BOOST_CHECK(stree2.num_simplices() == 25);
+
+}
diff --git a/src/Witness_complex/test/witness_complex_points.cpp b/src/Witness_complex/test/witness_complex_points.cpp
deleted file mode 100644
index 92f53417..00000000
--- a/src/Witness_complex/test/witness_complex_points.cpp
+++ /dev/null
@@ -1,58 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Siargey Kachanovich
- *
- *    Copyright (C) 2016  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/>.
- */
-
-#define BOOST_TEST_DYN_LINK
-#define BOOST_TEST_MODULE "witness_complex_points"
-#include <boost/test/unit_test.hpp>
-#include <boost/mpl/list.hpp>
-
-#include <gudhi/Simplex_tree.h>
-#include <gudhi/Witness_complex.h>
-#include <gudhi/Construct_closest_landmark_table.h>
-#include <gudhi/pick_n_random_points.h>
-
-#include <iostream>
-#include <vector>
-
-typedef std::vector<double> Point;
-typedef Gudhi::Simplex_tree<> Simplex_tree;
-typedef std::vector< Simplex_tree::Vertex_handle > typeVectorVertex;
-typedef Gudhi::witness_complex::Witness_complex<Simplex_tree> WitnessComplex;
-
-BOOST_AUTO_TEST_CASE(witness_complex_points) {
-  std::vector< typeVectorVertex > knn;
-  std::vector< Point > points, landmarks;
-  // Add grid points as witnesses
-  for (double i = 0; i < 10; i += 1.0)
-    for (double j = 0; j < 10; j += 1.0)
-      for (double k = 0; k < 10; k += 1.0)
-        points.push_back(Point({i, j, k}));
-
-  bool b_print_output = false;
-  // First test: random choice
-  Simplex_tree complex1;
-  Gudhi::subsampling::pick_n_random_points(points, 100, std::back_inserter(landmarks));
-  Gudhi::witness_complex::construct_closest_landmark_table<Simplex_tree::Filtration_value>(points, landmarks, knn);
-  assert(!knn.empty());
-  WitnessComplex witnessComplex1(knn, 100, 3, complex1);
-  BOOST_CHECK(witnessComplex1.is_witness_complex(knn, b_print_output));
-}
diff --git a/src/cmake/modules/FindGMPXX.cmake b/src/cmake/modules/FindGMPXX.cmake
index 277e4b19..dda302c0 100644
--- a/src/cmake/modules/FindGMPXX.cmake
+++ b/src/cmake/modules/FindGMPXX.cmake
@@ -33,6 +33,10 @@ if(GMP_FOUND)
                DOC "Path to the GMPXX library"
                )
 
+  if ( GMPXX_LIBRARIES )
+    get_filename_component(GMPXX_LIBRARIES_DIR ${GMPXX_LIBRARIES} PATH CACHE )
+  endif()
+
   include(FindPackageHandleStandardArgs)
 
   find_package_handle_standard_args(GMPXX "DEFAULT_MSG" GMPXX_LIBRARIES GMPXX_INCLUDE_DIR )
diff --git a/src/cmake/modules/GUDHI_third_party_libraries.txt b/src/cmake/modules/GUDHI_third_party_libraries.txt
new file mode 100644
index 00000000..75f73537
--- /dev/null
+++ b/src/cmake/modules/GUDHI_third_party_libraries.txt
@@ -0,0 +1,107 @@
+# This files manage third party libraries required by GUDHI
+
+find_package(Boost REQUIRED COMPONENTS system filesystem unit_test_framework chrono timer date_time program_options thread REQUIRED)
+
+if(NOT Boost_FOUND)
+  message(FATAL_ERROR "NOTICE: This program requires Boost and will not be compiled.")
+endif(NOT Boost_FOUND)
+
+find_package(GMP)
+if(GMP_FOUND)
+  message(STATUS "GMP_LIBRARIES = ${GMP_LIBRARIES}")
+  INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR})
+  find_package(GMPXX)
+  if(GMPXX_FOUND)
+    message(STATUS "GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}")
+    INCLUDE_DIRECTORIES(${GMPXX_INCLUDE_DIR})
+  endif()
+endif()
+
+# In CMakeLists.txt, when include(${CGAL_USE_FILE}), CMAKE_CXX_FLAGS are overwritten.
+# cf. http://doc.cgal.org/latest/Manual/installation.html#title40
+# A workaround is to include(${CGAL_USE_FILE}) before adding "-std=c++11".
+# A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html
+# or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html
+# but it implies to use cmake version 3.1 at least.
+find_package(CGAL)
+
+# Only CGAL versions > 4.4 supports what Gudhi uses from CGAL
+if (CGAL_VERSION VERSION_LESS 4.4.0)
+  message("CGAL version ${CGAL_VERSION} is considered too old to be used by Gudhi.")
+  unset(CGAL_FOUND)
+endif()
+if(CGAL_FOUND)
+  message(STATUS "CGAL version: ${CGAL_VERSION}.")
+  include( ${CGAL_USE_FILE} )
+
+  if (NOT CGAL_VERSION VERSION_LESS 4.8.0)
+    # HACK to detect CGAL version 4.8.0
+    # CGAL version 4.8, 4.8.1 and 4.8.2 are identified as version 4.8.1000)
+    # cf. https://github.com/CGAL/cgal/issues/1559
+    # Limit the HACK between CGAL versions 4.8 and 4.9 because of file read
+    if (NOT CGAL_VERSION VERSION_GREATER 4.9.0)
+      foreach(CGAL_INCLUDE_DIR ${CGAL_INCLUDE_DIRS})
+        if (EXISTS "${CGAL_INCLUDE_DIR}/CGAL/version.h")
+          FILE(READ "${CGAL_INCLUDE_DIR}/CGAL/version.h" contents)
+          STRING(REGEX REPLACE "\n" ";" contents "${contents}")
+          foreach(Line ${contents})
+            if("${Line}" STREQUAL "#define CGAL_VERSION 4.8")
+              set(CGAL_VERSION 4.8.0)
+              message (">>>>> HACK CGAL version to ${CGAL_VERSION}")
+            endif("${Line}" STREQUAL "#define CGAL_VERSION 4.8")
+          endforeach(Line ${contents})
+        endif (EXISTS "${CGAL_INCLUDE_DIR}/CGAL/version.h")
+      endforeach(CGAL_INCLUDE_DIR ${CGAL_INCLUDE_DIRS})
+    endif(NOT CGAL_VERSION VERSION_GREATER 4.9.0)
+
+    # For dev version
+    include_directories(BEFORE "src/common/include/gudhi_patches")
+    # For user version
+    include_directories(BEFORE "include/gudhi_patches")
+  endif()
+endif()
+
+# Find TBB package for parallel sort - not mandatory, just optional.
+set(TBB_FIND_QUIETLY ON)
+find_package(TBB)
+if (TBB_FOUND)
+  include(${TBB_USE_FILE})
+  message("TBB found in ${TBB_LIBRARY_DIRS}")
+  add_definitions(-DGUDHI_USE_TBB)
+endif()
+
+set(CGAL_WITH_EIGEN3_VERSION 0.0.0)
+find_package(Eigen3 3.1.0)
+if (EIGEN3_FOUND)
+  message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
+  include( ${EIGEN3_USE_FILE} )
+  set(CGAL_WITH_EIGEN3_VERSION ${CGAL_VERSION})
+endif (EIGEN3_FOUND)
+
+# Required programs for unitary tests purpose
+FIND_PROGRAM( GCOVR_PATH gcovr )
+if (GCOVR_PATH)
+  message("gcovr found in ${GCOVR_PATH}")
+endif()
+# Required programs for unitary tests purpose
+FIND_PROGRAM( GPROF_PATH gprof )
+if (GPROF_PATH)
+  message("gprof found in ${GPROF_PATH}")
+endif()
+FIND_PROGRAM( DIFF_PATH diff )
+if (DIFF_PATH)
+  message("diff found in ${DIFF_PATH}")
+endif()
+
+# BOOST ISSUE result_of vs C++11
+add_definitions(-DBOOST_RESULT_OF_USE_DECLTYPE)
+# BOOST ISSUE with Libraries name resolution under Windows
+add_definitions(-DBOOST_ALL_NO_LIB)
+# problem with Visual Studio link on Boost program_options
+add_definitions( -DBOOST_ALL_DYN_LINK )
+
+INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
+LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
+
+message(STATUS "boost include dirs:" ${Boost_INCLUDE_DIRS})
+message(STATUS "boost library dirs:" ${Boost_LIBRARY_DIRS})
diff --git a/src/cmake/modules/GUDHI_user_version_target.txt b/src/cmake/modules/GUDHI_user_version_target.txt
index 6332b065..13fccd32 100644
--- a/src/cmake/modules/GUDHI_user_version_target.txt
+++ b/src/cmake/modules/GUDHI_user_version_target.txt
@@ -1,8 +1,6 @@
 # Some functionnalities requires CMake 2.8.11 minimum
 if (NOT CMAKE_VERSION VERSION_LESS 2.8.11)
 
-  string(TIMESTAMP DATE_AND_TIME "%Y-%m-%d-%H-%M-%S")
-  
   # Definition of the custom target user_version
   add_custom_target(user_version)
   
@@ -11,6 +9,7 @@ if (NOT CMAKE_VERSION VERSION_LESS 2.8.11)
     set(GUDHI_USER_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/${USER_VERSION_DIR})
   else()
     # set the GUDHI_USER_VERSION_DIR with timestamp and Gudhi version number
+    string(TIMESTAMP DATE_AND_TIME "%Y-%m-%d-%H-%M-%S")
     set(GUDHI_USER_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/${DATE_AND_TIME}_GUDHI_${GUDHI_VERSION})
   endif()
 
@@ -21,6 +20,8 @@ if (NOT CMAKE_VERSION VERSION_LESS 2.8.11)
                      COMMENT "user_version creation in ${GUDHI_USER_VERSION_DIR}")
   
   add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                     copy ${CMAKE_SOURCE_DIR}/Conventions.txt ${GUDHI_USER_VERSION_DIR}/Conventions.txt)
+  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
                      copy ${CMAKE_SOURCE_DIR}/README ${GUDHI_USER_VERSION_DIR}/README)
   add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
                      copy ${CMAKE_SOURCE_DIR}/COPYING ${GUDHI_USER_VERSION_DIR}/COPYING)
@@ -40,76 +41,53 @@ 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}/biblio ${GUDHI_USER_VERSION_DIR}/biblio)
   add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                     copy_directory ${CMAKE_SOURCE_DIR}/src/cython ${GUDHI_USER_VERSION_DIR}/cython)
+  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
                      copy_directory ${CMAKE_SOURCE_DIR}/data ${GUDHI_USER_VERSION_DIR}/data)
   add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
                      copy_directory ${CMAKE_SOURCE_DIR}/src/cmake ${GUDHI_USER_VERSION_DIR}/cmake)
   add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                     copy_directory ${CMAKE_SOURCE_DIR}/src/debian ${GUDHI_USER_VERSION_DIR}/debian)
-  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;Rips_complex;Simplex_tree;Skeleton_blocker;Spatial_searching;Subsampling;Tangential_complex;Witness_complex")
-  
+  set(GUDHI_DIRECTORIES "doc;example;concept")
+  set(GUDHI_INCLUDE_DIRECTORIES "include/gudhi;include/gudhi_patches")
+
   foreach(GUDHI_MODULE ${GUDHI_MODULES})
-    # doc files
-    file(GLOB GUDHI_DOC_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/doc/*)
-  
-    foreach(GUDHI_DOC_FILE ${GUDHI_DOC_FILES})
-      get_filename_component(GUDHI_DOC_FILE_NAME ${GUDHI_DOC_FILE} NAME)
-      # GUDHI_DOC_FILE can be a file or a directory
-      if(IS_DIRECTORY ${GUDHI_DOC_FILE})
-        add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                           copy_directory ${GUDHI_DOC_FILE} ${GUDHI_USER_VERSION_DIR}/doc/${GUDHI_MODULE}/${GUDHI_DOC_FILE_NAME})
-      else()
-        add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                           copy ${GUDHI_DOC_FILE} ${GUDHI_USER_VERSION_DIR}/doc/${GUDHI_MODULE}/${GUDHI_DOC_FILE_NAME})
-      endif()
-    endforeach()
-  
-    # example files
-    file(GLOB GUDHI_EXAMPLE_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/example/*)
-  
-    foreach(GUDHI_EXAMPLE_FILE ${GUDHI_EXAMPLE_FILES})
-      get_filename_component(GUDHI_EXAMPLE_FILE_NAME ${GUDHI_EXAMPLE_FILE} NAME)
-      # GUDHI_EXAMPLE_FILE can be a file or a directory
-      if(IS_DIRECTORY ${GUDHI_EXAMPLE_FILE})
-        add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                           copy_directory ${GUDHI_EXAMPLE_FILE} ${GUDHI_USER_VERSION_DIR}/example/${GUDHI_MODULE}/${GUDHI_EXAMPLE_FILE_NAME})
-      else()
-        add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                           copy ${GUDHI_EXAMPLE_FILE} ${GUDHI_USER_VERSION_DIR}/example/${GUDHI_MODULE}/${GUDHI_EXAMPLE_FILE_NAME})
-      endif()
-    endforeach()
-  
-    # 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} ${GUDHI_USER_VERSION_DIR}/include/gudhi/${GUDHI_INCLUDE_FILE_NAME})
-      else()
-        add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                           copy ${GUDHI_INCLUDE_FILE} ${GUDHI_USER_VERSION_DIR}/include/gudhi/${GUDHI_INCLUDE_FILE_NAME})
-      endif()
-    endforeach()
-  
-    # concept files
-    file(GLOB GUDHI_CONCEPT_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/concept/*.h)
-  
-    foreach(GUDHI_CONCEPT_FILE ${GUDHI_CONCEPT_FILES})
-      get_filename_component(GUDHI_CONCEPT_FILE_NAME ${GUDHI_CONCEPT_FILE} NAME)
-      # GUDHI_CONCEPT_FILE can be a file or a directory
-      if(IS_DIRECTORY ${GUDHI_CONCEPT_FILE})
-        add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                           copy_directory ${GUDHI_CONCEPT_FILE} ${GUDHI_USER_VERSION_DIR}/concept/${GUDHI_MODULE}/${GUDHI_CONCEPT_FILE_NAME})
-      else()
-        add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                           copy ${GUDHI_CONCEPT_FILE} ${GUDHI_USER_VERSION_DIR}/concept/${GUDHI_MODULE}/${GUDHI_CONCEPT_FILE_NAME})
-      endif()
-    endforeach()
-  endforeach()
+    foreach(GUDHI_DIRECTORY ${GUDHI_DIRECTORIES})
+      # Find files
+      file(GLOB GUDHI_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/${GUDHI_DIRECTORY}/*)
+
+      foreach(GUDHI_FILE ${GUDHI_FILES})
+        get_filename_component(GUDHI_FILE_NAME ${GUDHI_FILE} NAME)
+        # GUDHI_FILE can be a file or a directory
+        if(IS_DIRECTORY ${GUDHI_FILE})
+          add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                             copy_directory ${GUDHI_FILE} ${GUDHI_USER_VERSION_DIR}/${GUDHI_DIRECTORY}/${GUDHI_MODULE}/${GUDHI_FILE_NAME})
+        else()
+          add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                             copy ${GUDHI_FILE} ${GUDHI_USER_VERSION_DIR}/${GUDHI_DIRECTORY}/${GUDHI_MODULE}/${GUDHI_FILE_NAME})
+        endif()
+      endforeach()
+    endforeach(GUDHI_DIRECTORY ${GUDHI_DIRECTORIES})
+
+    foreach(GUDHI_INCLUDE_DIRECTORY ${GUDHI_INCLUDE_DIRECTORIES})
+      # include files
+      file(GLOB GUDHI_INCLUDE_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/${GUDHI_INCLUDE_DIRECTORY}/*)
+
+      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} ${GUDHI_USER_VERSION_DIR}/${GUDHI_INCLUDE_DIRECTORY}/${GUDHI_INCLUDE_FILE_NAME})
+        else()
+          add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                             copy ${GUDHI_INCLUDE_FILE} ${GUDHI_USER_VERSION_DIR}/${GUDHI_INCLUDE_DIRECTORY}/${GUDHI_INCLUDE_FILE_NAME})
+        endif()
+      endforeach()
+    endforeach(GUDHI_INCLUDE_DIRECTORY ${GUDHI_INCLUDE_DIRECTORIES})
+
+  endforeach(GUDHI_MODULE ${GUDHI_MODULES})
 
 endif()
diff --git a/src/common/doc/header.html b/src/common/doc/header.html
index a6f3ed9c..94e641b2 100644
--- a/src/common/doc/header.html
+++ b/src/common/doc/header.html
@@ -9,7 +9,7 @@
 <!--BEGIN PROJECT_NAME--><title>$projectname: $title</title><!--END PROJECT_NAME-->
 <!--BEGIN !PROJECT_NAME--><title>$title</title><!--END !PROJECT_NAME-->
 <!-- GUDHI website css for header BEGIN -->
-<link rel="stylesheet" type="text/css" href="http://gudhi.gforge.inria.fr/assets/css/styles_feeling_responsive.css" />
+<link rel="stylesheet" type="text/css" href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/gudhi-doc-2.0.0/assets/css/styles_feeling_responsive.css" />
 <!-- GUDHI website css for header END -->
 <link href="$relpath^tabs.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="$relpath^jquery.js"></script>
@@ -25,6 +25,13 @@ $extrastylesheet
 <!-- GUDHI website header BEGIN -->
 <div id="navigation" class="sticky">
   <nav class="top-bar" role="navigation" data-topbar>
+    <ul class="title-area">
+      <li class="name">
+      <h1 class="show-for-small-only"><a href="http://gudhi.gforge.inria.fr" class="icon-tree"> GUDHI C++ library</a></h1>
+    </li>
+       <!-- Remove the class "menu-icon" to get rid of menu icon. Take out "Menu" to just have icon alone -->
+      <li class="toggle-topbar menu-icon"><a href="#"><span>Navigation</span></a></li>
+    </ul>
     <section class="top-bar-section">
       <ul class="right">
               <li class="divider"></li>
@@ -37,7 +44,7 @@ $extrastylesheet
                 <a href="#">Project</a>
                   <ul class="dropdown">
                       <li><a href="http://gudhi.gforge.inria.fr/people/">People</a></li>
-                      <li><a href="http://gudhi.gforge.inria.fr/getinvolved/">Get involved</a></li>
+                      <li><a href="http://gudhi.gforge.inria.fr/keepintouch/">Keep in touch</a></li>
                       <li><a href="http://gudhi.gforge.inria.fr/partners/">Partners and Funding</a></li>
                       <li><a href="http://gudhi.gforge.inria.fr/relatedprojects/">Related projects</a></li>
                       <li><a href="http://gudhi.gforge.inria.fr/theyaretalkingaboutus/">They are talking about us</a></li>
@@ -49,11 +56,18 @@ $extrastylesheet
                   <ul class="dropdown">
                       <li><a href="http://gudhi.gforge.inria.fr/licensing/">Licensing</a></li>
                       <li><a href="https://gforge.inria.fr/frs/?group_id=3865" target="_blank">Get the sources</a></li>
-                      <li><a href="http://gudhi.gforge.inria.fr/doc/latest/installation.html">Installation manual</a></li>
                   </ul>
               </li>
               <li class="divider"></li>
-              <li><a href="http://gudhi.gforge.inria.fr/doc/latest/">Documentation</a></li>
+              <li class="has-dropdown">
+                <a href="#">Documentation</a>
+                  <ul class="dropdown">
+                      <li><a href="http://gudhi.gforge.inria.fr/doc/latest/">C++ documentation</a></li>
+                      <li><a href="http://gudhi.gforge.inria.fr/doc/latest/installation.html">C++ installation manual</a></li>
+                      <li><a href="http://gudhi.gforge.inria.fr/cython/latest/">Cython documentation</a></li>
+                      <li><a href="http://gudhi.gforge.inria.fr/cython/latest/installation.html">Cython installation manual</a></li>
+                  </ul>
+              </li>
               <li class="divider"></li>
               <li><a href="http://gudhi.gforge.inria.fr/interfaces/">Interfaces</a></li>
               <li class="divider"></li>
@@ -62,7 +76,7 @@ $extrastylesheet
   </nav>
 </div><!-- /#navigation -->
 <!-- GUDHI website header BEGIN -->
-    
+
 <div id="top"><!-- do not remove this div, it is closed by doxygen! -->
 
 <!--BEGIN TITLEAREA-->
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index 60c9cd07..e6f29fa8 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -3,7 +3,9 @@
  * \image html "Gudhi_banner.png" "" width=20cm
  * 
  * \section Introduction Introduction
- * The Gudhi library (Geometry Understanding in Higher Dimensions) is a generic open source C++ library for
+ * The GUDHI library (Geometry Understanding in Higher Dimensions) is a generic open source
+ * <a class="el" target="_blank" href="http://gudhi.gforge.inria.fr/doc/latest/">C++ library</a>, with a
+ * <a class="el" target="_blank" href="http://gudhi.gforge.inria.fr/cython/latest/">Cython interface</a>, for
  * Computational Topology and Topological Data Analysis
  * (<a class="el" target="_blank" href="https://en.wikipedia.org/wiki/Topological_data_analysis">TDA</a>).
  * The GUDHI library intends  to help the development of new algorithmic solutions in TDA and their transfer to
@@ -62,7 +64,7 @@
   <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>Introduced in:</b> GUDHI 2.0.0<br>
       <b>Copyright:</b> GPL v3<br>
     </td>
     <td width="75%">
@@ -118,8 +120,9 @@
   <tr>
     <td width="25%">
       <b>Author:</b> Cl&eacute;ment Jamin<br>
-      <b>Introduced in:</b> GUDHI 1.4.0<br>
+      <b>Introduced in:</b> GUDHI 2.0.0<br>
       <b>Copyright:</b> GPL v3<br>
+      <b>Requires:</b> \ref cgal &ge; 4.8.1 and \ref eigen3
     </td>
     <td width="75%">
     A Tangential Delaunay complex is a <a target="_blank" href="https://en.wikipedia.org/wiki/Simplicial_complex">simplicial complex</a>
@@ -139,6 +142,7 @@
       <b>Author:</b> Siargey Kachanovich<br>
       <b>Introduced in:</b> GUDHI 1.3.0<br>
       <b>Copyright:</b> GPL v3<br>
+      <b>Euclidean version requires:</b> \ref cgal &ge; 4.6.0 and \ref eigen3
     </td>
     <td width="75%">
     Witness complex \f$ Wit(W,L) \f$  is a simplicial complex defined on two sets of points in \f$\mathbb{R}^D\f$.
@@ -155,9 +159,9 @@
   <tr>
     <td width="25%">
       <b>Author:</b> Fran&ccedil;ois Godi<br>
-      <b>Introduced in:</b> GUDHI 1.4.0<br>
+      <b>Introduced in:</b> GUDHI 2.0.0<br>
       <b>Copyright:</b> GPL v3<br>
-      <b>Requires:</b> \ref cgal &ge; 4.8.0 and \ref eigen3
+      <b>Requires:</b> \ref cgal &ge; 4.8.1 and \ref eigen3
     </td>
     <td width="75%">
     Bottleneck distance measures the similarity between two persistence diagrams. 
@@ -211,11 +215,11 @@
 </table>
 */
 
-/*! \page installation Gudhi installation
+/*! \page installation GUDHI installation
  *  \tableofcontents
- * As Gudhi is a header only library, there is no need to install the library.
+ * As GUDHI is a header only library, there is no need to install the library.
  * 
- * Examples of Gudhi headers inclusion can be found in \ref demos.
+ * Examples of GUDHI headers inclusion can be found in \ref demos.
  * 
  * \section compiling Compiling
  * The library uses c++11 and requires <a target="_blank" href="http://www.boost.org/">Boost</a> with version 1.48.0 or
@@ -234,6 +238,15 @@ make \endverbatim
  * To test your build, run the following command in a terminal:
  * \verbatim  make test \endverbatim
  * 
+ * \subsection documentationgeneration Documentation
+ * To generate the documentation, <a target="_blank" href="http://www.doxygen.org/">Doxygen</a> is required.
+ * Run the following command in a terminal:
+\verbatim
+make doxygen
+# Documentation will be generated in the folder YYYY-MM-DD-hh-mm-ss_GUDHI_X.Y.Z/doc/html/
+# You can customize the directory name by calling `cmake -DUSER_VERSION_DIR=/my/custom/folder`
+\endverbatim
+ *
  * \section optionallibrary Optional third-party library
  * \subsection gmp GMP
  * The multi-field persistent homology algorithm requires GMP which is a free library for arbitrary-precision
@@ -249,6 +262,10 @@ make \endverbatim
  * \subsection cgal CGAL
  * The \ref alpha_complex data structure, \ref bottleneck_distance, and few examples requires CGAL, which is a C++
  * library which provides easy access to efficient and reliable geometric algorithms.
+ *
+ * \note There is no need to install CGAL, you can just <CODE>cmake . && make</CODE> CGAL (or even
+ * <CODE>cmake -DCGAL_HEADER_ONLY=ON .</CODE> for CGAL version &ge; 4.8.0), thereafter you will be able to compile
+ * GUDHI by calling <CODE>cmake -DCGAL_DIR=/your/path/to/CGAL-X.Y .. && make</CODE>
  * 
  * Having CGAL version 4.4.0 or higher installed is recommended. The procedure to install this library according to
  * your operating system is detailed here http://doc.cgal.org/latest/Manual/installation.html
@@ -257,6 +274,10 @@ make \endverbatim
  * Library</a> (CGAL \cite cgal:eb-15b) and will not be built if CGAL is not installed:
  * \li <a href="_persistent_cohomology_2alpha_complex_3d_persistence_8cpp-example.html">
  * Persistent_cohomology/alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2exact_alpha_complex_3d_persistence_8cpp-example.html">
+ * Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2weighted_alpha_complex_3d_persistence_8cpp-example.html">
+ * Persistent_cohomology/weighted_alpha_complex_3d_persistence.cpp</a>
  * \li <a href="_simplex_tree_2example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html">
  * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp</a>
  * 
@@ -276,11 +297,27 @@ make \endverbatim
  * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html">
  * Persistent_cohomology/custom_persistence_sort.cpp</a>
  * 
- * The following example requires CGAL version &ge; 4.8.0:
- * \li <a href="_bottleneck_distance_2_bottleneck_basic_example_8cpp-example.html">
+ * The following example requires CGAL version &ge; 4.8.1:
+ * \li <a href="_bottleneck_distance_2alpha_rips_persistence_bottleneck_distance_8cpp-example.html">
+ * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a>
+ * \li <a href="_bottleneck_distance_2bottleneck_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">
+ * \li <a href="_bottleneck_distance_2bottleneck_read_file_example_8cpp-example.html">
  * Bottleneck_distance/bottleneck_read_file_example.cpp</a>
+ * \li <a href="_spatial_searching_2example_spatial_searching_8cpp-example.html">
+ * Spatial_searching/example_spatial_searching.cpp</a>
+ * \li <a href="_subsampling_2example_choose_n_farthest_points_8cpp-example.html">
+ * Subsampling/example_choose_n_farthest_points.cpp</a>
+ * \li <a href="_subsampling_2example_custom_kernel_8cpp-example.html">
+ * Subsampling/example_custom_kernel.cpp</a>
+ * \li <a href="_subsampling_2example_pick_n_random_points_8cpp-example.html">
+ * Subsampling/example_pick_n_random_points.cpp</a>
+ * \li <a href="_subsampling_2example_sparsify_point_set_8cpp-example.html">
+ * Subsampling/example_sparsify_point_set.cpp</a>
+ * \li <a href="_tangential_complex_2example_basic_8cpp-example.html">
+ * Tangential_complex/example_basic.cpp</a>
+ * \li <a href="_tangential_complex_2example_with_perturb_8cpp-example.html">
+ * Tangential_complex/example_with_perturb.cpp</a>
  *
  * \subsection eigen3 Eigen3
  * The \ref alpha_complex data structure and few examples requires
@@ -348,6 +385,10 @@ make \endverbatim
  * 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_2exact_alpha_complex_3d_persistence_8cpp-example.html">
+ * Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2weighted_alpha_complex_3d_persistence_8cpp-example.html">
+ * Persistent_cohomology/weighted_alpha_complex_3d_persistence.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">
@@ -361,7 +402,7 @@ make \endverbatim
  * Please help us improving the quality of the GUDHI library. You may report bugs or suggestions to:
  * \verbatim  Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
  * 
- * Gudhi is open to external contributions. If you want to join our development team, please contact us.
+ * GUDHI is open to external contributions. If you want to join our development team, please contact us.
  * 
 */
 
@@ -376,10 +417,11 @@ make \endverbatim
  * \verbinclude  biblio/how_to_cite_gudhi.bib
 */
 
-// List of Gudhi examples - Doxygen needs at least a file tag to analyse comments
+// List of GUDHI examples - Doxygen needs at least a file tag to analyse comments
 /*! @file Examples
  * @example Alpha_complex/Alpha_complex_from_off.cpp
  * @example Alpha_complex/Alpha_complex_from_points.cpp
+ * @example Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp
  * @example Bottleneck_distance/bottleneck_basic_example.cpp
  * @example Bottleneck_distance/bottleneck_read_file_example.cpp
  * @example Bitmap_cubical_complex/Bitmap_cubical_complex.cpp
@@ -392,6 +434,8 @@ 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/exact_alpha_complex_3d_persistence.cpp
+ * @example Persistent_cohomology/weighted_alpha_complex_3d_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
@@ -410,9 +454,18 @@ make \endverbatim
  * @example Skeleton_blocker/Skeleton_blocker_from_simplices.cpp
  * @example Skeleton_blocker/Skeleton_blocker_iteration.cpp
  * @example Skeleton_blocker/Skeleton_blocker_link.cpp
+ * @example Spatial_searching/example_spatial_searching.cpp
+ * @example Subsampling/example_choose_n_farthest_points.cpp
+ * @example Subsampling/example_custom_kernel.cpp
+ * @example Subsampling/example_pick_n_random_points.cpp
+ * @example Subsampling/example_sparsify_point_set.cpp
  * @example Tangential_complex/example_basic.cpp
  * @example Tangential_complex/example_with_perturb.cpp
- * @example Witness_complex/witness_complex_from_file.cpp
- * @example Witness_complex/witness_complex_sphere.cpp
+ * @example Witness_complex/example_nearest_landmark_table.cpp
+ * @example Witness_complex/example_strong_witness_complex_off.cpp
+ * @example Witness_complex/example_strong_witness_persistence.cpp
+ * @example Witness_complex/example_witness_complex_off.cpp
+ * @example Witness_complex/example_witness_complex_persistence.cpp
+ * @example Witness_complex/example_witness_complex_sphere.cpp
  */
 
diff --git a/src/common/example/CMakeLists.txt b/src/common/example/CMakeLists.txt
index b0c6d69a..61c94391 100644
--- a/src/common/example/CMakeLists.txt
+++ b/src/common/example/CMakeLists.txt
@@ -10,12 +10,10 @@ if(CGAL_FOUND)
   target_link_libraries(cgal_3D_off_reader  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
   add_test(cgal_3D_off_reader ${CMAKE_CURRENT_BINARY_DIR}/cgal_3D_off_reader ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
 
-  # need CGAL 4.7
-  if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
-    if (EIGEN3_FOUND)
-      add_executable ( cgal_off_reader example_CGAL_points_off_reader.cpp )
-      target_link_libraries(cgal_off_reader  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
-      add_test(cgal_off_reader ${CMAKE_CURRENT_BINARY_DIR}/cgal_off_reader ${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off)
-    endif(EIGEN3_FOUND)
-  endif (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+  # need CGAL 4.7and Eigen3
+  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
+    add_executable ( cgal_off_reader example_CGAL_points_off_reader.cpp )
+    target_link_libraries(cgal_off_reader  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+    add_test(cgal_off_reader ${CMAKE_CURRENT_BINARY_DIR}/cgal_off_reader ${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off)
+  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
 endif()
diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h
index 5891ef0e..22747637 100644
--- a/src/common/include/gudhi/distance_functions.h
+++ b/src/common/include/gudhi/distance_functions.h
@@ -24,6 +24,8 @@
 #define DISTANCE_FUNCTIONS_H_
 
 #include <cmath>  // for std::sqrt
+#include <type_traits>  // for std::decay
+#include <iterator>  // for std::begin, std::end
 
 /** @file
  * @brief Global distance functions
@@ -34,7 +36,7 @@
 class Euclidean_distance {
  public:
   template< typename Point >
-  auto operator()(const Point& p1, const Point& p2) -> typename std::decay<decltype(*std::begin(p1))>::type {
+  auto operator()(const Point& p1, const Point& p2) const -> typename std::decay<decltype(*std::begin(p1))>::type {
     auto it1 = p1.begin();
     auto it2 = p2.begin();
     typename Point::value_type dist = 0.;
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
new file mode 100644
index 00000000..2131505d
--- /dev/null
+++ b/src/cython/CMakeLists.txt
@@ -0,0 +1,225 @@
+cmake_minimum_required(VERSION 2.8)
+project(Cython)
+
+macro( find_the_lib placeholder THE_LIBS )
+  set (THE_LIB_WE_FOUND "NO")
+  foreach(THE_LIB ${THE_LIBS})
+    if(EXISTS ${THE_LIB})
+      get_filename_component(THE_LIB_WE ${THE_LIB} NAME_WE)
+      if (NOT THE_LIB_WE_FOUND)
+        set (THE_LIB_WE_FOUND "YES")
+        set(returnValue "${THE_LIB_WE}")
+      endif(NOT THE_LIB_WE_FOUND)
+    endif(EXISTS ${THE_LIB})
+  endforeach(THE_LIB ${THE_LIBS})
+endmacro( find_the_lib )
+
+FIND_PROGRAM( PYTHON_PATH python )
+FIND_PROGRAM( CYTHON_PATH cython )
+
+if(PYTHON_PATH AND CYTHON_PATH)
+  find_package(Boost REQUIRED COMPONENTS system REQUIRED)
+
+  if(NOT Boost_FOUND)
+    message(FATAL_ERROR "NOTICE: This demo requires Boost and will not be compiled.")
+  else(NOT Boost_FOUND)
+
+    set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_RESULT_OF_USE_DECLTYPE', ")
+    set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ")
+    set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ")
+    if(WIN32)
+      set( returnValue "" )
+      find_the_lib (${returnValue} ${Boost_SYSTEM_LIBRARY})
+      set(BOOST_SYSTEM_LIB_NAME ${returnValue})
+    else()
+        set(BOOST_SYSTEM_LIB_NAME "boost_system")
+        endif()
+    set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'${BOOST_SYSTEM_LIB_NAME}', ")
+
+    # Gudhi and CGAL compilation option
+    if(MSVC)
+      set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'/fp:strict', ")
+    else(MSVC)
+      set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-std=c++11', ")
+    endif(MSVC)
+    if(CMAKE_COMPILER_IS_GNUCXX)
+      set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-frounding-math', ")
+    endif(CMAKE_COMPILER_IS_GNUCXX)
+    if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
+      set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-fp-model strict', ")
+    endif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
+    if (DEBUG_TRACES)
+      # For programs to be more verbose
+      set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DDEBUG_TRACES', ")
+    endif()
+  
+    find_package(Eigen3 3.1.0)
+    
+    if (EIGEN3_FOUND)
+      # No problem, even if no CGAL found
+      set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ")
+    endif (EIGEN3_FOUND)
+    
+    # Copy recursively include, cython, example, doc and test repositories before packages finding
+    # Some tests and doc files are removed in case some packages are not found
+    file(COPY include DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+    file(COPY cython DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+    file(COPY example DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+    file(COPY test DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+    file(COPY doc DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+    # Developper version for doc images
+    file(GLOB GUDHI_DEV_DOC_IMAGES "${CMAKE_SOURCE_DIR}/src/*/doc/*.png")
+    file(COPY ${GUDHI_DEV_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img")
+    file(GLOB GUDHI_DEV_DOC_IMAGES "${CMAKE_SOURCE_DIR}/src/*/doc/*.svg")
+    file(COPY ${GUDHI_DEV_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img")
+    # User version for doc images
+    file(GLOB GUDHI_USER_DOC_IMAGES "${CMAKE_SOURCE_DIR}/doc/*/*.png")
+    file(COPY ${GUDHI_USER_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img")
+    file(GLOB GUDHI_USER_DOC_IMAGES "${CMAKE_SOURCE_DIR}/doc/*/*.svg")
+    file(COPY ${GUDHI_USER_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img")
+    # Biblio
+    file(GLOB GUDHI_BIB_FILES "${CMAKE_SOURCE_DIR}/biblio/*.bib")
+    file(COPY ${GUDHI_BIB_FILES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
+    # Cubical complex perseus doc example
+    file(GLOB GUDHI_CUBICAL_PERSEUS_FILES "${CMAKE_SOURCE_DIR}/data/bitmap/*cubicalcomplexdoc.txt")
+    file(COPY ${GUDHI_CUBICAL_PERSEUS_FILES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
+    file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
+    file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
+    # Persistence graphical tools examples
+    file(COPY "${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
+    file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
+
+    if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+      # If CGAL_VERSION >= 4.8.1, include subsampling
+      set(GUDHI_CYTHON_SUBSAMPLING "include 'cython/subsampling.pyx'")
+      set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include 'cython/tangential_complex.pyx'")
+      set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include 'cython/bottleneck_distance.pyx'")
+    else (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+      # Remove subsampling unitary tests
+      file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_subsampling.py)
+      file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_ref.rst")
+      file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_sum.rst")
+      file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_user.rst")
+      # Remove tangential complex and bottleneck unitary tests
+      file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_tangential_complex.py)
+      file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_bottleneck_distance.py)
+      file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/bottleneck_distance_ref.rst")
+      file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/bottleneck_distance_sum.rst")
+      file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/bottleneck_distance_user.rst")
+      file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_ref.rst")
+      file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_sum.rst")
+      file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_user.rst")
+    endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+    if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+      # If CGAL_VERSION >= 4.7.0, include alpha
+      set(GUDHI_CYTHON_ALPHA_COMPLEX "include 'cython/alpha_complex.pyx'")
+    else (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+      # Remove alpha complex unitary tests
+      file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_alpha_complex.py)
+      file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/alpha_complex_ref.rst")
+      file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/alpha_complex_sum.rst")
+      file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/alpha_complex_user.rst")
+    endif (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+    if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
+      # If CGAL_VERSION >= 4.6.0, include euclidean versions of witness complex
+      set(GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX
+          "include 'cython/euclidean_witness_complex.pyx'\ninclude 'cython/euclidean_strong_witness_complex.pyx'\n")
+    else (NOT CGAL_VERSION VERSION_LESS 4.6.0)
+      # Remove alpha complex unitary tests
+      file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_euclidean_witness_complex.py)
+      file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/euclidean_witness_complex_ref.rst")
+      file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/euclidean_strong_witness_complex_ref.rst")
+    endif (NOT CGAL_VERSION VERSION_LESS 4.6.0)
+
+    if(CGAL_FOUND)
+      # Add CGAL compilation args
+      if(CGAL_HEADER_ONLY)
+        set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ")
+      else(CGAL_HEADER_ONLY)
+        if(WIN32)
+          set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'CGAL-vc140-mt-4.7', ")
+        else(WIN32)
+          set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'CGAL', ")
+        endif(WIN32)
+        set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ")
+      endif(CGAL_HEADER_ONLY)
+      # GMP and GMPXX are not required, but if present, CGAL will link with them.
+      if(GMP_FOUND)
+        set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMP', ")
+        if(WIN32)
+          set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'libgmp-10', ")
+        else(WIN32)
+          set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'gmp', ")
+        endif(WIN32)
+          set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMP_LIBRARIES_DIR}', ")
+        if(GMPXX_FOUND)
+          set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMPXX', ")
+          set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'gmpxx', ")
+          set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMPXX_LIBRARIES_DIR}', ")
+        endif(GMPXX_FOUND)
+      endif(GMP_FOUND)
+    endif(CGAL_FOUND)
+
+    # Specific for Mac
+    if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+        set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-mmacosx-version-min=10.9', ")
+        set(GUDHI_CYTHON_EXTRA_LINK_ARGS "${GUDHI_CYTHON_EXTRA_LINK_ARGS}'-mmacosx-version-min=10.9', ")
+    endif(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+
+    # Loop on INCLUDE_DIRECTORIES PROPERTY
+    get_property(GUDHI_INCLUDE_DIRECTORIES DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY INCLUDE_DIRECTORIES)
+    foreach(GUDHI_INCLUDE_DIRECTORY ${GUDHI_INCLUDE_DIRECTORIES})
+      set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${GUDHI_INCLUDE_DIRECTORY}', ")
+    endforeach()
+    set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${CMAKE_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/include', ")
+
+    if (TBB_FOUND)
+      set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DGUDHI_USE_TBB', ")
+      set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'tbb', 'tbbmalloc', ")
+      set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${TBB_LIBRARY_DIRS}', ")
+      set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${TBB_INCLUDE_DIRS}', ")
+    endif()
+
+    # Generate cythonize_gudhi.py file to cythonize Gudhi
+    configure_file(cythonize_gudhi.py.in "${CMAKE_CURRENT_BINARY_DIR}/cythonize_gudhi.py" @ONLY)
+    # Generate gudhi.pyx - Gudhi cython file 
+    configure_file(gudhi.pyx.in "${CMAKE_CURRENT_BINARY_DIR}/gudhi.pyx" @ONLY)
+    
+    add_custom_command(
+        OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
+        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+        COMMAND python "${CMAKE_CURRENT_BINARY_DIR}/cythonize_gudhi.py" "build_ext" "--inplace")
+    
+    add_custom_target(cython ALL DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
+                      COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/ to your PYTHONPATH before using examples or tests")
+  
+    if(UNIX)
+        set( ENV{PYTHONPATH} $ENV{PYTHONPATH}:${CMAKE_CURRENT_BINARY_DIR}/ )
+    endif(UNIX)
+
+    # Unitary tests are available through py.test
+    find_program( PYTEST_PATH py.test )
+    if(PYTEST_PATH)
+      add_test(
+          NAME gudhi_cython_py_test
+          WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+          COMMAND ${PYTEST_PATH})
+      set_tests_properties(gudhi_cython_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+    endif(PYTEST_PATH)
+  
+    # Documentation generation is available through sphinx
+    find_program( SPHINX_PATH sphinx-build )
+    if(SPHINX_PATH)
+      if (UNIX)
+        add_custom_target(sphinx
+            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc
+            DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
+            COMMAND make html doctest)
+      else (UNIX)
+        add_custom_target(sphinx
+            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc
+            COMMAND make.bat html)
+      endif (UNIX)
+    endif(SPHINX_PATH)
+  endif(NOT Boost_FOUND)
+endif(PYTHON_PATH AND CYTHON_PATH)
diff --git a/src/cython/CONVENTIONS b/src/cython/CONVENTIONS
new file mode 100644
index 00000000..804e97f3
--- /dev/null
+++ b/src/cython/CONVENTIONS
@@ -0,0 +1,9 @@
+Gudhi is following PEP8 conventions.
+
+Please refer to:
+https://www.python.org/dev/peps/pep-0008/
+
+A summary:
+ - modules (filenames) should have short, all-lowercase names, and they can contain underscores.
+ - packages (directories) should have short, all-lowercase names, preferably without underscores.
+ - classes should use the CapWords convention.
\ No newline at end of file
diff --git a/src/cython/README b/src/cython/README
new file mode 100644
index 00000000..7d2c4491
--- /dev/null
+++ b/src/cython/README
@@ -0,0 +1,3 @@
+
+If you do not want to install the package, just launch the following command to help Python to find the compiled package :
+$> export PYTHONPATH=`pwd`:$PYTHONPATH
diff --git a/src/cython/cython/alpha_complex.pyx b/src/cython/cython/alpha_complex.pyx
new file mode 100644
index 00000000..da537c2e
--- /dev/null
+++ b/src/cython/cython/alpha_complex.pyx
@@ -0,0 +1,121 @@
+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.utility cimport pair
+from libcpp.string cimport string
+from libcpp cimport bool
+import os
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+cdef extern from "Alpha_complex_interface.h" namespace "Gudhi":
+    cdef cppclass Alpha_complex_interface "Gudhi::alpha_complex::Alpha_complex_interface":
+        Alpha_complex_interface(vector[vector[double]] points)
+        # bool from_file is a workaround for cython to find the correct signature
+        Alpha_complex_interface(string off_file, bool from_file)
+        vector[double] get_point(int vertex)
+        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square)
+
+# AlphaComplex python interface
+cdef class AlphaComplex:
+    """AlphaComplex is a simplicial complex constructed from the finite cells
+    of a Delaunay Triangulation.
+
+    The filtration value of each simplex is computed as the square of the
+    circumradius of the simplex if the circumsphere is empty (the simplex is
+    then said to be Gabriel), and as the minimum of the filtration values of
+    the codimension 1 cofaces that make it not Gabriel otherwise.
+
+    All simplices that have a filtration value strictly greater than a given
+    alpha squared value are not inserted into the complex.
+
+    .. note::
+
+        When Alpha_complex is constructed with an infinite value of alpha, the
+        complex is a Delaunay complex.
+
+    """
+
+    cdef Alpha_complex_interface * thisptr
+
+    # Fake constructor that does nothing but documenting the constructor
+    def __init__(self, points=None, off_file=''):
+        """AlphaComplex constructor.
+
+        :param points: A list of points in d-Dimension.
+        :type points: list of list of double
+
+        Or
+
+        :param off_file: An OFF file style name.
+        :type off_file: string
+        """
+
+    # The real cython constructor
+    def __cinit__(self, points=None, off_file=''):
+        if off_file is not '':
+            if os.path.isfile(off_file):
+                self.thisptr = new Alpha_complex_interface(off_file, True)
+            else:
+                print("file " + off_file + " not found.")
+        else:
+            if points is None:
+                # Empty Alpha construction
+                points=[]
+            self.thisptr = new Alpha_complex_interface(points)
+                
+
+    def __dealloc__(self):
+        if self.thisptr != NULL:
+            del self.thisptr
+
+    def __is_defined(self):
+        """Returns true if AlphaComplex pointer is not NULL.
+         """
+        return self.thisptr != NULL
+
+    def get_point(self, vertex):
+        """This function returns the point corresponding to a given vertex.
+
+        :param vertex: The vertex.
+        :type vertex: int
+        :rtype: list of float
+        :returns: the point.
+        """
+        cdef vector[double] point = self.thisptr.get_point(vertex)
+        return point
+
+    def create_simplex_tree(self, max_alpha_square=float('inf')):
+        """
+        :param max_alpha_square: The maximum alpha square threshold the
+            simplices shall not exceed. Default is set to infinity.
+        :type max_alpha_square: float
+        :returns: A simplex tree created from the Delaunay Triangulation.
+        :rtype: SimplexTree
+        """
+        simplex_tree = SimplexTree()
+        self.thisptr.create_simplex_tree(simplex_tree.thisptr, max_alpha_square)
+        return simplex_tree
diff --git a/src/cython/cython/bottleneck_distance.pyx b/src/cython/cython/bottleneck_distance.pyx
new file mode 100644
index 00000000..ee3e6ef9
--- /dev/null
+++ b/src/cython/cython/bottleneck_distance.pyx
@@ -0,0 +1,59 @@
+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.utility cimport pair
+import os
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+cdef extern from "Bottleneck_distance_interface.h" namespace "Gudhi::persistence_diagram":
+    double bottleneck(vector[pair[double, double]], vector[pair[double, double]], double)
+    double bottleneck(vector[pair[double, double]], vector[pair[double, double]])
+
+def bottleneck_distance(diagram_1, diagram_2, e=0.0):
+    """This function returns the point corresponding to a given vertex.
+
+    :param diagram_1: The first diagram.
+    :type diagram_1: vector[pair[double, double]]
+    :param diagram_2: The second diagram.
+    :type diagram_2: vector[pair[double, double]]
+    :param e: 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.
+    :type e: float
+    :rtype: float
+    :returns: the bottleneck distance.
+    """
+    if e is 0.0:
+        return bottleneck(diagram_1, diagram_2)
+    else:
+        return bottleneck(diagram_1, diagram_2, e)
diff --git a/src/cython/cython/cubical_complex.pyx b/src/cython/cython/cubical_complex.pyx
new file mode 100644
index 00000000..e1344f49
--- /dev/null
+++ b/src/cython/cython/cubical_complex.pyx
@@ -0,0 +1,197 @@
+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.utility cimport pair
+from libcpp.string cimport string
+from libcpp cimport bool
+import os
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+cdef extern from "Cubical_complex_interface.h" namespace "Gudhi":
+    cdef cppclass Bitmap_cubical_complex_base_interface "Gudhi::Cubical_complex::Cubical_complex_interface<>":
+        Bitmap_cubical_complex_base_interface(vector[unsigned] dimensions, vector[double] top_dimensional_cells)
+        Bitmap_cubical_complex_base_interface(string perseus_file)
+        int num_simplices()
+        int dimension()
+
+cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi":
+    cdef cppclass Cubical_complex_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Cubical_complex::Cubical_complex_interface<>>":
+        Cubical_complex_persistence_interface(Bitmap_cubical_complex_base_interface * st, bool persistence_dim_max)
+        vector[pair[int, pair[double, double]]] get_persistence(int homology_coeff_field, double min_persistence)
+        vector[int] betti_numbers()
+        vector[int] persistent_betti_numbers(double from_value, double to_value)
+        vector[pair[double,double]] intervals_in_dimension(int dimension)
+
+# CubicalComplex python interface
+cdef class CubicalComplex:
+    """The CubicalComplex is an example of a structured complex useful in
+    computational mathematics (specially rigorous numerics) and image
+    analysis.
+    """
+    cdef Bitmap_cubical_complex_base_interface * thisptr
+
+    cdef Cubical_complex_persistence_interface * pcohptr
+
+    # Fake constructor that does nothing but documenting the constructor
+    def __init__(self, dimensions=None, top_dimensional_cells=None,
+                  perseus_file=''):
+        """CubicalComplex constructor from dimensions and
+        top_dimensional_cells or from a perseus file style name.
+
+        :param dimensions: A list of number of top dimensional cells.
+        :type dimensions: list of int
+        :param top_dimensional_cells: A list of top dimensional cells.
+        :type top_dimensional_cells: list of double
+
+        Or
+
+        :param perseus_file: A perseus file style name.
+        :type perseus_file: string
+        """
+
+    # The real cython constructor
+    def __cinit__(self, dimensions=None, top_dimensional_cells=None,
+                  perseus_file=''):
+        if (dimensions is not None) and (top_dimensional_cells is not None) and (perseus_file is ''):
+            self.thisptr = new Bitmap_cubical_complex_base_interface(dimensions, top_dimensional_cells)
+        elif (dimensions is None) and (top_dimensional_cells is None) and (perseus_file is not ''):
+            if os.path.isfile(perseus_file):
+                self.thisptr = new Bitmap_cubical_complex_base_interface(perseus_file)
+            else:
+                print("file " + perseus_file + " not found.")
+        else:
+            print("CubicalComplex can be constructed from dimensions and "
+              "top_dimensional_cells or from a perseus file style name.")
+
+    def __dealloc__(self):
+        if self.thisptr != NULL:
+            del self.thisptr
+        if self.pcohptr != NULL:
+            del self.pcohptr
+
+    def __is_defined(self):
+        """Returns true if CubicalComplex pointer is not NULL.
+         """
+        return self.thisptr != NULL
+
+    def __is_persistence_defined(self):
+        """Returns true if Persistence pointer is not NULL.
+         """
+        return self.pcohptr != NULL
+
+    def num_simplices(self):
+        """This function returns the number of simplices of the simplicial
+        complex.
+
+        :returns:  int -- the simplicial complex number of simplices.
+        """
+        return self.thisptr.num_simplices()
+
+    def dimension(self):
+        """This function returns the dimension of the simplicial complex.
+
+        :returns:  int -- the simplicial complex dimension.
+        """
+        return self.thisptr.dimension()
+
+    def persistence(self, homology_coeff_field=11, min_persistence=0):
+        """This function returns the persistence of the simplicial complex.
+
+        :param homology_coeff_field: The homology coefficient field. Must be a
+            prime number
+        :type homology_coeff_field: int.
+        :param min_persistence: The minimum persistence value to take into
+            account (strictly greater than min_persistence). Default value is
+            0.0.
+            Sets min_persistence to -1.0 to see all values.
+        :type min_persistence: float.
+        :returns: list of pairs(dimension, pair(birth, death)) -- the
+            persistence of the simplicial complex.
+        """
+        if self.pcohptr != NULL:
+            del self.pcohptr
+        if self.thisptr != NULL:
+            self.pcohptr = new Cubical_complex_persistence_interface(self.thisptr, True)
+        cdef vector[pair[int, pair[double, double]]] persistence_result
+        if self.pcohptr != NULL:
+            persistence_result = self.pcohptr.get_persistence(homology_coeff_field, min_persistence)
+        return persistence_result
+
+    def betti_numbers(self):
+        """This function returns the Betti numbers of the simplicial complex.
+
+        :returns: list of int -- The Betti numbers ([B0, B1, ..., Bn]).
+
+        :note: betti_numbers function requires persistence function to be
+            launched first.
+        """
+        cdef vector[int] bn_result
+        if self.pcohptr != NULL:
+            bn_result = self.pcohptr.betti_numbers()
+        return bn_result
+
+    def persistent_betti_numbers(self, from_value, to_value):
+        """This function returns the persistent Betti numbers of the
+        simplicial complex.
+
+        :param from_value: The persistence birth limit to be added in the
+            numbers (persistent birth <= from_value).
+        :type from_value: float.
+        :param to_value: The persistence death limit to be added in the
+            numbers (persistent death > to_value).
+        :type to_value: float.
+
+        :returns: list of int -- The persistent Betti numbers ([B0, B1, ...,
+            Bn]).
+
+        :note: persistent_betti_numbers function requires persistence
+            function to be launched first.
+        """
+        cdef vector[int] pbn_result
+        if self.pcohptr != NULL:
+            pbn_result = self.pcohptr.persistent_betti_numbers(<double>from_value, <double>to_value)
+        return pbn_result
+
+    def persistence_intervals_in_dimension(self, dimension):
+        """This function returns the persistence intervals of the simplicial
+        complex in a specific dimension.
+
+        :param dimension: The specific dimension.
+        :type from_value: int.
+        :returns: The persistence intervals.
+        :rtype:  list of pair of float
+
+        :note: intervals_in_dim function requires persistence function to be
+            launched first.
+        """
+        cdef vector[pair[double,double]] intervals_result
+        if self.pcohptr != NULL:
+            intervals_result = self.pcohptr.intervals_in_dimension(dimension)
+        else:
+            print("intervals_in_dim function requires persistence function"
+                  " to be launched first.")
+        return intervals_result
diff --git a/src/cython/cython/euclidean_strong_witness_complex.pyx b/src/cython/cython/euclidean_strong_witness_complex.pyx
new file mode 100644
index 00000000..c1523892
--- /dev/null
+++ b/src/cython/cython/euclidean_strong_witness_complex.pyx
@@ -0,0 +1,97 @@
+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.utility cimport pair
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+cdef extern from "Euclidean_strong_witness_complex_interface.h" namespace "Gudhi":
+    cdef cppclass Euclidean_strong_witness_complex_interface "Gudhi::witness_complex::Euclidean_strong_witness_complex_interface":
+        Euclidean_strong_witness_complex_interface(vector[vector[double]] landmarks, vector[vector[double]] witnesses)
+        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square)
+        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square,
+            unsigned limit_dimension)
+        vector[double] get_point(unsigned vertex)
+
+# EuclideanStrongWitnessComplex python interface
+cdef class EuclideanStrongWitnessComplex:
+    """Constructs strong witness complex for given sets of witnesses and
+    landmarks in Euclidean space.
+    """
+
+    cdef Euclidean_strong_witness_complex_interface * thisptr
+
+    # Fake constructor that does nothing but documenting the constructor
+    def __init__(self, landmarks=None, witnesses=None):
+        """WitnessComplex constructor.
+
+        :param landmarks: A list of landmarks (in the point cloud).
+        :type landmarks: list of list of double
+
+        :param witnesses: The point cloud.
+        :type witnesses: list of list of double
+        """
+
+    # The real cython constructor
+    def __cinit__(self, landmarks=None, witnesses=None):
+        if landmarks is not None and witnesses is not None:
+            self.thisptr = new Euclidean_strong_witness_complex_interface(landmarks, witnesses)
+
+    def __dealloc__(self):
+        if self.thisptr != NULL:
+            del self.thisptr
+
+    def __is_defined(self):
+        """Returns true if WitnessComplex pointer is not NULL.
+         """
+        return self.thisptr != NULL
+
+    def create_simplex_tree(self, max_alpha_square, limit_dimension = -1):
+        """
+        :param max_alpha_square: The maximum alpha square threshold the
+            simplices shall not exceed. Default is set to infinity.
+        :type max_alpha_square: float
+        :returns: A simplex tree created from the Delaunay Triangulation.
+        :rtype: SimplexTree
+        """
+        simplex_tree = SimplexTree()
+        if limit_dimension is not -1:
+            self.thisptr.create_simplex_tree(simplex_tree.thisptr, max_alpha_square, limit_dimension)
+        else:
+            self.thisptr.create_simplex_tree(simplex_tree.thisptr, max_alpha_square)
+        return simplex_tree
+
+    def get_point(self, vertex):
+        """This function returns the point corresponding to a given vertex.
+
+        :param vertex: The vertex.
+        :type vertex: int.
+        :returns:  The point.
+        :rtype: list of float
+        """
+        cdef vector[double] point = self.thisptr.get_point(vertex)
+        return point
+
diff --git a/src/cython/cython/euclidean_witness_complex.pyx b/src/cython/cython/euclidean_witness_complex.pyx
new file mode 100644
index 00000000..7c443b6b
--- /dev/null
+++ b/src/cython/cython/euclidean_witness_complex.pyx
@@ -0,0 +1,97 @@
+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.utility cimport pair
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+cdef extern from "Euclidean_witness_complex_interface.h" namespace "Gudhi":
+    cdef cppclass Euclidean_witness_complex_interface "Gudhi::witness_complex::Euclidean_witness_complex_interface":
+        Euclidean_witness_complex_interface(vector[vector[double]] landmarks, vector[vector[double]] witnesses)
+        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square)
+        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square,
+            unsigned limit_dimension)
+        vector[double] get_point(unsigned vertex)
+
+# EuclideanWitnessComplex python interface
+cdef class EuclideanWitnessComplex:
+    """Constructs (weak) witness complex for given sets of witnesses and
+    landmarks in Euclidean space.
+    """
+
+    cdef Euclidean_witness_complex_interface * thisptr
+
+    # Fake constructor that does nothing but documenting the constructor
+    def __init__(self, landmarks=None, witnesses=None):
+        """WitnessComplex constructor.
+
+        :param landmarks: A list of landmarks (in the point cloud).
+        :type landmarks: list of list of double
+
+        :param witnesses: The point cloud.
+        :type witnesses: list of list of double
+        """
+
+    # The real cython constructor
+    def __cinit__(self, landmarks=None, witnesses=None):
+        if landmarks is not None and witnesses is not None:
+            self.thisptr = new Euclidean_witness_complex_interface(landmarks, witnesses)
+
+    def __dealloc__(self):
+        if self.thisptr != NULL:
+            del self.thisptr
+
+    def __is_defined(self):
+        """Returns true if WitnessComplex pointer is not NULL.
+         """
+        return self.thisptr != NULL
+
+    def create_simplex_tree(self, max_alpha_square, limit_dimension = -1):
+        """
+        :param max_alpha_square: The maximum alpha square threshold the
+            simplices shall not exceed. Default is set to infinity.
+        :type max_alpha_square: float
+        :returns: A simplex tree created from the Delaunay Triangulation.
+        :rtype: SimplexTree
+        """
+        simplex_tree = SimplexTree()
+        if limit_dimension is not -1:
+            self.thisptr.create_simplex_tree(simplex_tree.thisptr, max_alpha_square, limit_dimension)
+        else:
+            self.thisptr.create_simplex_tree(simplex_tree.thisptr, max_alpha_square)
+        return simplex_tree
+
+    def get_point(self, vertex):
+        """This function returns the point corresponding to a given vertex.
+
+        :param vertex: The vertex.
+        :type vertex: int.
+        :returns:  The point.
+        :rtype: list of float
+        """
+        cdef vector[double] point = self.thisptr.get_point(vertex)
+        return point
+
diff --git a/src/cython/cython/off_reader.pyx b/src/cython/cython/off_reader.pyx
new file mode 100644
index 00000000..78c37969
--- /dev/null
+++ b/src/cython/cython/off_reader.pyx
@@ -0,0 +1,49 @@
+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.string cimport string
+import os
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+cdef extern from "Off_reader_interface.h" namespace "Gudhi":
+    vector[vector[double]] read_points_from_OFF_file(string off_file)
+
+def read_off(off_file=''):
+    """Read points from OFF file.
+
+    :param off_file: An OFF file style name.
+    :type off_file: string
+
+    :returns:  The point set.
+    :rtype: vector[vector[double]]
+    """
+    if off_file is not '':
+        if os.path.isfile(off_file):
+            return read_points_from_OFF_file(off_file)
+        else:
+            print("file " + off_file + " not found.")
+
diff --git a/src/cython/cython/periodic_cubical_complex.pyx b/src/cython/cython/periodic_cubical_complex.pyx
new file mode 100644
index 00000000..1445d429
--- /dev/null
+++ b/src/cython/cython/periodic_cubical_complex.pyx
@@ -0,0 +1,197 @@
+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.utility cimport pair
+from libcpp.string cimport string
+from libcpp cimport bool
+import os
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+cdef extern from "Cubical_complex_interface.h" namespace "Gudhi":
+    cdef cppclass Periodic_cubical_complex_base_interface "Gudhi::Cubical_complex::Cubical_complex_interface<Gudhi::cubical_complex::Bitmap_cubical_complex_periodic_boundary_conditions_base<double>>":
+        Periodic_cubical_complex_base_interface(vector[unsigned] dimensions, vector[double] top_dimensional_cells)
+        Periodic_cubical_complex_base_interface(string perseus_file)
+        int num_simplices()
+        int dimension()
+
+cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi":
+    cdef cppclass Periodic_cubical_complex_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Cubical_complex::Cubical_complex_interface<Gudhi::cubical_complex::Bitmap_cubical_complex_periodic_boundary_conditions_base<double>>>":
+        Periodic_cubical_complex_persistence_interface(Periodic_cubical_complex_base_interface * st, bool persistence_dim_max)
+        vector[pair[int, pair[double, double]]] get_persistence(int homology_coeff_field, double min_persistence)
+        vector[int] betti_numbers()
+        vector[int] persistent_betti_numbers(double from_value, double to_value)
+        vector[pair[double,double]] intervals_in_dimension(int dimension)
+
+# PeriodicCubicalComplex python interface
+cdef class PeriodicCubicalComplex:
+    """The PeriodicCubicalComplex is an example of a structured complex useful
+    in computational mathematics (specially rigorous numerics) and image
+    analysis.
+    """
+    cdef Periodic_cubical_complex_base_interface * thisptr
+
+    cdef Periodic_cubical_complex_persistence_interface * pcohptr
+
+    # Fake constructor that does nothing but documenting the constructor
+    def __init__(self, dimensions=None, top_dimensional_cells=None,
+                  perseus_file=''):
+        """PeriodicCubicalComplex constructor from dimensions and
+        top_dimensional_cells or from a perseus file style name.
+
+        :param dimensions: A list of number of top dimensional cells.
+        :type dimensions: list of int
+        :param top_dimensional_cells: A list of top dimensional cells.
+        :type top_dimensional_cells: list of double
+
+        Or
+
+        :param perseus_file: A perseus file style name.
+        :type perseus_file: string
+        """
+
+    # The real cython constructor
+    def __cinit__(self, dimensions=None, top_dimensional_cells=None,
+                  perseus_file=''):
+        if (dimensions is not None) and (top_dimensional_cells is not None) and (perseus_file is ''):
+            self.thisptr = new Periodic_cubical_complex_base_interface(dimensions, top_dimensional_cells)
+        elif (dimensions is None) and (top_dimensional_cells is None) and (perseus_file is not ''):
+            if os.path.isfile(perseus_file):
+                self.thisptr = new Periodic_cubical_complex_base_interface(perseus_file)
+            else:
+                print("file " + perseus_file + " not found.")
+        else:
+            print("CubicalComplex can be constructed from dimensions and "
+              "top_dimensional_cells or from a perseus file style name.")
+
+    def __dealloc__(self):
+        if self.thisptr != NULL:
+            del self.thisptr
+        if self.pcohptr != NULL:
+            del self.pcohptr
+
+    def __is_defined(self):
+        """Returns true if PeriodicCubicalComplex pointer is not NULL.
+         """
+        return self.thisptr != NULL
+
+    def __is_persistence_defined(self):
+        """Returns true if Persistence pointer is not NULL.
+         """
+        return self.pcohptr != NULL
+
+    def num_simplices(self):
+        """This function returns the number of simplices of the simplicial
+        complex.
+
+        :returns:  int -- the simplicial complex number of simplices.
+        """
+        return self.thisptr.num_simplices()
+
+    def dimension(self):
+        """This function returns the dimension of the simplicial complex.
+
+        :returns:  int -- the simplicial complex dimension.
+        """
+        return self.thisptr.dimension()
+
+    def persistence(self, homology_coeff_field=11, min_persistence=0):
+        """This function returns the persistence of the simplicial complex.
+
+        :param homology_coeff_field: The homology coefficient field. Must be a
+            prime number
+        :type homology_coeff_field: int.
+        :param min_persistence: The minimum persistence value to take into
+            account (strictly greater than min_persistence). Default value is
+            0.0.
+            Sets min_persistence to -1.0 to see all values.
+        :type min_persistence: float.
+        :returns: list of pairs(dimension, pair(birth, death)) -- the
+            persistence of the simplicial complex.
+        """
+        if self.pcohptr != NULL:
+            del self.pcohptr
+        if self.thisptr != NULL:
+            self.pcohptr = new Periodic_cubical_complex_persistence_interface(self.thisptr, True)
+        cdef vector[pair[int, pair[double, double]]] persistence_result
+        if self.pcohptr != NULL:
+            persistence_result = self.pcohptr.get_persistence(homology_coeff_field, min_persistence)
+        return persistence_result
+
+    def betti_numbers(self):
+        """This function returns the Betti numbers of the simplicial complex.
+
+        :returns: list of int -- The Betti numbers ([B0, B1, ..., Bn]).
+
+        :note: betti_numbers function requires persistence function to be
+            launched first.
+        """
+        cdef vector[int] bn_result
+        if self.pcohptr != NULL:
+            bn_result = self.pcohptr.betti_numbers()
+        return bn_result
+
+    def persistent_betti_numbers(self, from_value, to_value):
+        """This function returns the persistent Betti numbers of the
+        simplicial complex.
+
+        :param from_value: The persistence birth limit to be added in the
+            numbers (persistent birth <= from_value).
+        :type from_value: float.
+        :param to_value: The persistence death limit to be added in the
+            numbers (persistent death > to_value).
+        :type to_value: float.
+
+        :returns: list of int -- The persistent Betti numbers ([B0, B1, ...,
+            Bn]).
+
+        :note: persistent_betti_numbers function requires persistence
+            function to be launched first.
+        """
+        cdef vector[int] pbn_result
+        if self.pcohptr != NULL:
+            pbn_result = self.pcohptr.persistent_betti_numbers(<double>from_value, <double>to_value)
+        return pbn_result
+
+    def persistence_intervals_in_dimension(self, dimension):
+        """This function returns the persistence intervals of the simplicial
+        complex in a specific dimension.
+
+        :param dimension: The specific dimension.
+        :type from_value: int.
+        :returns: The persistence intervals.
+        :rtype:  list of pair of float
+
+        :note: intervals_in_dim function requires persistence function to be
+            launched first.
+        """
+        cdef vector[pair[double,double]] intervals_result
+        if self.pcohptr != NULL:
+            intervals_result = self.pcohptr.intervals_in_dimension(dimension)
+        else:
+            print("intervals_in_dim function requires persistence function"
+                  " to be launched first.")
+        return intervals_result
diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py
new file mode 100755
index 00000000..a984633e
--- /dev/null
+++ b/src/cython/cython/persistence_graphical_tools.py
@@ -0,0 +1,152 @@
+import matplotlib.pyplot as plt
+import numpy as np
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+def __min_birth_max_death(persistence):
+    """This function returns (min_birth, max_death) from the persistence.
+
+    :param persistence: The persistence to plot.
+    :type persistence: list of tuples(dimension, tuple(birth, death)).
+    :returns: (float, float) -- (min_birth, max_death).
+    """
+    # Look for minimum birth date and maximum death date for plot optimisation
+    max_death = 0
+    min_birth = persistence[0][1][0]
+    for interval in reversed(persistence):
+        if float(interval[1][1]) != float('inf'):
+            if float(interval[1][1]) > max_death:
+                max_death = float(interval[1][1])
+        if float(interval[1][0]) > max_death:
+            max_death = float(interval[1][0])
+        if float(interval[1][0]) < min_birth:
+            min_birth = float(interval[1][0])
+    return (min_birth, max_death)
+
+"""
+Only 13 colors for the palette
+"""
+palette = ['#ff0000', '#00ff00', '#0000ff', '#00ffff', '#ff00ff', '#ffff00',
+           '#000000', '#880000', '#008800', '#000088', '#888800', '#880088',
+           '#008888']
+ 
+def show_palette_values(alpha=0.6):
+    """This function shows palette color values in function of the dimension.
+
+    :param alpha: alpha value in [0.0, 1.0] for horizontal bars (default is 0.6).
+    :type alpha: float.
+    :returns: plot -- An horizontal bar plot of dimensions color.
+    """
+    colors = []
+    for color in palette:
+        colors.append(color)
+
+    y_pos = np.arange(len(palette))
+
+    plt.barh(y_pos, y_pos + 1, align='center', alpha=alpha, color=colors)
+    plt.ylabel('Dimension')
+    plt.title('Dimension palette values')
+
+    plt.show()
+
+def plot_persistence_barcode(persistence, alpha=0.6):
+    """This function plots the persistence bar code.
+
+    :param persistence: The persistence to plot.
+    :type persistence: list of tuples(dimension, tuple(birth, death)).
+    :param alpha: alpha value in [0.0, 1.0] for horizontal bars (default is 0.6).
+    :type alpha: float.
+    :returns: plot -- An horizontal bar plot of persistence.
+    """
+    (min_birth, max_death) = __min_birth_max_death(persistence)
+    ind = 0
+    delta = ((max_death - min_birth) / 10.0)
+    # Replace infinity values with max_death + delta for bar code to be more
+    # readable
+    infinity = max_death + delta
+    axis_start = min_birth - delta
+    # Draw horizontal bars in loop
+    for interval in reversed(persistence):
+        if float(interval[1][1]) != float('inf'):
+            # Finite death case
+            plt.barh(ind, (interval[1][1] - interval[1][0]), height=0.8,
+                     left = interval[1][0], alpha=alpha,
+                     color = palette[interval[0]])
+        else:
+            # Infinite death case for diagram to be nicer
+            plt.barh(ind, (infinity - interval[1][0]), height=0.8,
+                     left = interval[1][0], alpha=alpha,
+                     color = palette[interval[0]])
+        ind = ind + 1
+
+    plt.title('Persistence barcode')
+    # Ends plot on infinity value and starts a little bit before min_birth
+    plt.axis([axis_start, infinity, 0, ind])
+    plt.show()
+
+def plot_persistence_diagram(persistence, alpha=0.6):
+    """This function plots the persistence diagram.
+
+    :param persistence: The persistence to plot.
+    :type persistence: list of tuples(dimension, tuple(birth, death)).
+    :param alpha: alpha value in [0.0, 1.0] for points and horizontal infinity line (default is 0.6).
+    :type alpha: float.
+    :returns: plot -- An diagram plot of persistence.
+    """
+    (min_birth, max_death) = __min_birth_max_death(persistence)
+    ind = 0
+    delta = ((max_death - min_birth) / 10.0)
+    # Replace infinity values with max_death + delta for diagram to be more
+    # readable
+    infinity = max_death + delta
+    axis_start = min_birth - delta
+
+    # line display of equation : birth = death
+    x = np.linspace(axis_start, infinity, 1000)
+    # infinity line and text
+    plt.plot(x, x, color='k', linewidth=1.0)
+    plt.plot(x, [infinity] * len(x), linewidth=1.0, color='k', alpha=alpha)
+    plt.text(axis_start, infinity, r'$\infty$', color='k', alpha=alpha)
+
+    # Draw points in loop
+    for interval in reversed(persistence):
+        if float(interval[1][1]) != float('inf'):
+            # Finite death case
+            plt.scatter(interval[1][0], interval[1][1], alpha=alpha,
+                        color = palette[interval[0]])
+        else:
+            # Infinite death case for diagram to be nicer
+            plt.scatter(interval[1][0], infinity, alpha=alpha,
+                        color = palette[interval[0]])
+        ind = ind + 1
+
+    plt.title('Persistence diagram')
+    plt.xlabel('Birth')
+    plt.ylabel('Death')
+    # Ends plot on infinity value and starts a little bit before min_birth
+    plt.axis([axis_start, infinity, axis_start, infinity + delta])
+    plt.show()
diff --git a/src/cython/cython/rips_complex.pyx b/src/cython/cython/rips_complex.pyx
new file mode 100644
index 00000000..6bfb4482
--- /dev/null
+++ b/src/cython/cython/rips_complex.pyx
@@ -0,0 +1,125 @@
+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.utility cimport pair
+from libcpp.string cimport string
+from libcpp cimport bool
+import os
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+cdef extern from "Rips_complex_interface.h" namespace "Gudhi":
+    cdef cppclass Rips_complex_interface "Gudhi::rips_complex::Rips_complex_interface":
+        Rips_complex_interface(vector[vector[double]] values, double threshold, bool euclidean)
+        # bool from_file is a workaround for cython to find the correct signature
+        Rips_complex_interface(string file_name, double threshold, bool euclidean, bool from_file)
+        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, int dim_max)
+
+# RipsComplex python interface
+cdef class RipsComplex:
+    """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.
+    """
+
+    cdef Rips_complex_interface * thisptr
+
+    # Fake constructor that does nothing but documenting the constructor
+    def __init__(self, points=None, off_file='', distance_matrix=None, csv_file='', max_edge_length=float('inf')):
+        """RipsComplex constructor.
+
+        :param max_edge_length: Rips value.
+        :type max_edge_length: int
+
+        :param points: A list of points in d-Dimension.
+        :type points: list of list of double
+
+        Or
+
+        :param off_file: An OFF file style name.
+        :type off_file: string
+
+        Or
+
+        :param distance_matrix: A distance matrix (full square or lower
+        triangular).
+        :type points: list of list of double
+
+        Or
+
+        :param csv_file: A csv file style name containing a full square or a
+        lower triangular distance matrix.
+        :type csv_file: string
+        """
+
+    # The real cython constructor
+    def __cinit__(self, points=None, off_file='', distance_matrix=None, csv_file='', max_edge_length=float('inf')):
+        if off_file is not '':
+            if os.path.isfile(off_file):
+                self.thisptr = new Rips_complex_interface(off_file,
+                                                          max_edge_length,
+                                                          True,
+                                                          True)
+            else:
+                print("file " + off_file + " not found.")
+        elif csv_file is not '':
+            if os.path.isfile(csv_file):
+                self.thisptr = new Rips_complex_interface(csv_file,
+                                                          max_edge_length,
+                                                          False,
+                                                          True)
+            else:
+                print("file " + csv_file + " not found.")
+        elif distance_matrix is not None:
+            self.thisptr = new Rips_complex_interface(distance_matrix, max_edge_length, False)
+        else:
+            if points is None:
+                # Empty Rips construction
+                points=[]
+            self.thisptr = new Rips_complex_interface(points, max_edge_length, True)
+
+
+    def __dealloc__(self):
+        if self.thisptr != NULL:
+            del self.thisptr
+
+    def __is_defined(self):
+        """Returns true if RipsComplex pointer is not NULL.
+         """
+        return self.thisptr != NULL
+
+    def create_simplex_tree(self, max_dimension=1):
+        """
+        :param max_dimension: graph expansion for rips until this given maximal
+            dimension.
+        :type max_dimension: int
+        :returns: A simplex tree created from the Delaunay Triangulation.
+        :rtype: SimplexTree
+        """
+        simplex_tree = SimplexTree()
+        self.thisptr.create_simplex_tree(simplex_tree.thisptr, max_dimension)
+        return simplex_tree
diff --git a/src/cython/cython/simplex_tree.pyx b/src/cython/cython/simplex_tree.pyx
new file mode 100644
index 00000000..148227e1
--- /dev/null
+++ b/src/cython/cython/simplex_tree.pyx
@@ -0,0 +1,427 @@
+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.utility cimport pair
+from libcpp cimport bool
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+cdef extern from "Simplex_tree_interface.h" namespace "Gudhi":
+    cdef cppclass Simplex_tree_options_full_featured:
+        pass
+
+    cdef cppclass Simplex_tree_interface_full_featured "Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_full_featured>":
+        Simplex_tree()
+        double filtration()
+        double simplex_filtration(vector[int] simplex)
+        void set_filtration(double filtration)
+        void initialize_filtration()
+        int num_vertices()
+        int num_simplices()
+        void set_dimension(int dimension)
+        int dimension()
+        bint find_simplex(vector[int] simplex)
+        bint insert_simplex_and_subfaces(vector[int] simplex,
+                                         double filtration)
+        bint insert_simplex(vector[int] simplex, double filtration)
+        vector[pair[vector[int], double]] get_filtered_tree()
+        vector[pair[vector[int], double]] get_skeleton_tree(int dimension)
+        vector[pair[vector[int], double]] get_star(vector[int] simplex)
+        vector[pair[vector[int], double]] get_cofaces(vector[int] simplex,
+                                                          int dimension)
+        void remove_maximal_simplex(vector[int] simplex)
+        void expansion(int max_dim)
+
+cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi":
+    cdef cppclass Simplex_tree_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>>":
+        Simplex_tree_persistence_interface(Simplex_tree_interface_full_featured * st, bool persistence_dim_max)
+        vector[pair[int, pair[double, double]]] get_persistence(int homology_coeff_field, double min_persistence)
+        vector[int] betti_numbers()
+        vector[int] persistent_betti_numbers(double from_value, double to_value)
+        vector[pair[double,double]] intervals_in_dimension(int dimension)
+
+# SimplexTree python interface
+cdef class SimplexTree:
+    """The simplex tree is an efficient and flexible data structure for
+    representing general (filtered) simplicial complexes. The data structure
+    is described in Jean-Daniel Boissonnat and Clément Maria. The Simplex
+    Tree: An Efficient Data Structure for General Simplicial Complexes.
+    Algorithmica, pages 1–22, 2014.
+
+    This class is a filtered, with keys, and non contiguous vertices version
+    of the simplex tree.
+    """
+    cdef Simplex_tree_interface_full_featured * thisptr
+
+    cdef Simplex_tree_persistence_interface * pcohptr
+
+    # Fake constructor that does nothing but documenting the constructor
+    def __init__(self):
+        """SimplexTree constructor.
+        """
+
+    # The real cython constructor
+    def __cinit__(self):
+        self.thisptr = new Simplex_tree_interface_full_featured()
+
+    def __dealloc__(self):
+        if self.thisptr != NULL:
+            del self.thisptr
+        if self.pcohptr != NULL:
+            del self.pcohptr
+
+    def __is_defined(self):
+        """Returns true if SimplexTree pointer is not NULL.
+         """
+        return self.thisptr != NULL
+
+    def __is_persistence_defined(self):
+        """Returns true if Persistence pointer is not NULL.
+         """
+        return self.pcohptr != NULL
+
+    def get_filtration(self):
+        """This function returns the main simplicial complex filtration value.
+
+        :returns:  The simplicial complex filtration value.
+        :rtype:  float
+        """
+        return self.thisptr.filtration()
+
+    def filtration(self, simplex):
+        """This function returns the simplicial complex filtration value for a
+        given N-simplex.
+
+        :param simplex: The N-simplex, represented by a list of vertex.
+        :type simplex: list of int.
+        :returns:  The simplicial complex filtration value.
+        :rtype:  float
+        """
+        return self.thisptr.simplex_filtration(simplex)
+
+    def set_filtration(self, filtration):
+        """This function sets the main simplicial complex filtration value.
+
+        :param filtration: The filtration value.
+        :type filtration: float.
+        """
+        self.thisptr.set_filtration(<double> filtration)
+
+    def initialize_filtration(self):
+        """This function initializes and sorts the simplicial complex
+        filtration vector.
+
+        .. note::
+
+            This function must be launched before persistence, betti_numbers,
+            persistent_betti_numbers or get_filtered_tree after inserting or
+            removing simplices.
+        """
+        self.thisptr.initialize_filtration()
+
+    def num_vertices(self):
+        """This function returns the number of vertices of the simplicial
+        complex.
+
+        :returns:  The simplicial complex number of vertices.
+        :rtype:  int
+        """
+        return self.thisptr.num_vertices()
+
+    def num_simplices(self):
+        """This function returns the number of simplices of the simplicial
+        complex.
+
+        :returns:  the simplicial complex number of simplices.
+        :rtype:  int
+        """
+        return self.thisptr.num_simplices()
+
+    def dimension(self):
+        """This function returns the dimension of the simplicial complex.
+
+        :returns:  the simplicial complex dimension.
+        :rtype:  int
+        """
+        return self.thisptr.dimension()
+
+    def set_dimension(self, dimension):
+        """This function sets the dimension of the simplicial complex.
+
+        insert and remove_maximal_simplex functions do not update dimension
+        value of the `SimplexTree`.
+
+        `AlphaComplex`, `RipsComplex`, `TangentialComplex` and `WitnessComplex`
+        automatically sets the correct dimension in their `create_simplex_tree`
+        functions.
+
+        :param dimension: The new dimension value.
+        :type dimension: int.
+        """
+        self.thisptr.set_dimension(<int>dimension)
+
+    def find(self, simplex):
+        """This function returns if the N-simplex was found in the simplicial
+        complex or not.
+
+        :param simplex: The N-simplex to find, represented by a list of vertex.
+        :type simplex: list of int.
+        :returns:  true if the simplex was found, false otherwise.
+        :rtype:  bool
+        """
+        cdef vector[int] complex
+        for i in simplex:
+            complex.push_back(i)
+        return self.thisptr.find_simplex(complex)
+
+    def insert_simplex(self, simplex, filtration=0.0):
+        """This function inserts the given N-simplex with the given filtration
+        value (default value is '0.0').
+
+        :param simplex: The N-simplex to insert, represented by a list of
+            vertex.
+        :type simplex: list of int.
+        :param filtration: The filtration value of the simplex.
+        :type filtration: float.
+        :returns:  true if the simplex was found, false otherwise.
+        :rtype:  bool
+        """
+        cdef vector[int] complex
+        for i in simplex:
+            complex.push_back(i)
+        return self.thisptr.insert_simplex(complex, <double>filtration)
+
+    def insert_simplex_and_subfaces(self, simplex, filtration=0.0):
+        """This function inserts the given N-simplex and its subfaces with the
+        given filtration value (default value is '0.0').
+
+        :param simplex: The N-simplex to insert, represented by a list of
+            vertex.
+        :type simplex: list of int.
+        :param filtration: The filtration value of the simplex.
+        :type filtration: float.
+        :returns:  true if the simplex was found, false otherwise.
+        :rtype:  bool
+        """
+        cdef vector[int] complex
+        for i in simplex:
+            complex.push_back(i)
+        return self.thisptr.insert_simplex_and_subfaces(complex,
+                                                        <double>filtration)
+
+    def get_filtered_tree(self):
+        """This function returns the tree sorted by increasing filtration
+        values.
+
+        :returns:  The tree sorted by increasing filtration values.
+        :rtype:  list of tuples(simplex, filtration)
+        """
+        cdef vector[pair[vector[int], double]] filtered_tree \
+            = self.thisptr.get_filtered_tree()
+        ct = []
+        for filtered_complex in filtered_tree:
+            v = []
+            for vertex in filtered_complex.first:
+                v.append(vertex)
+            ct.append((v, filtered_complex.second))
+        return ct
+
+    def get_skeleton_tree(self, dimension):
+        """This function returns the tree skeleton of a maximum given
+        dimension.
+
+        :param dimension: The skeleton dimension value.
+        :type dimension: int.
+        :returns:  The skeleton tree of a maximum dimension.
+        :rtype:  list of tuples(simplex, filtration)
+        """
+        cdef vector[pair[vector[int], double]] sk_tree \
+            = self.thisptr.get_skeleton_tree(<int>dimension)
+        ct = []
+        for filtered_complex in sk_tree:
+            v = []
+            for vertex in filtered_complex.first:
+                v.append(vertex)
+            ct.append((v, filtered_complex.second))
+        return ct
+
+    def get_star(self, simplex):
+        """This function returns the stars of a given N-simplex.
+
+        :param simplex: The N-simplex, represented by a list of vertex.
+        :type simplex: list of int.
+        :returns:  The star tree of a simplex.
+        :rtype:  list of tuples(simplex, filtration)
+        """
+        cdef vector[int] complex
+        for i in simplex:
+            complex.push_back(i)
+        cdef vector[pair[vector[int], double]] stars \
+            = self.thisptr.get_star(complex)
+        ct = []
+        for filtered_complex in stars:
+            v = []
+            for vertex in filtered_complex.first:
+                v.append(vertex)
+            ct.append((v, filtered_complex.second))
+        return ct
+
+    def get_cofaces(self, simplex, codimension):
+        """This function returns the cofaces of a given N-simplex with a
+        given codimension.
+
+        :param simplex: The N-simplex, represented by a list of vertex.
+        :type simplex: list of int.
+        :param codimension: The codimension. If codimension = 0, all cofaces
+            are returned (equivalent of get_star function)
+        :type codimension: int.
+        :returns:  The coface tree of a simplex.
+        :rtype:  list of tuples(simplex, filtration)
+        """
+        cdef vector[int] complex
+        for i in simplex:
+            complex.push_back(i)
+        cdef vector[pair[vector[int], double]] cofaces \
+            = self.thisptr.get_cofaces(complex, <int>codimension)
+        ct = []
+        for filtered_complex in cofaces:
+            v = []
+            for vertex in filtered_complex.first:
+                v.append(vertex)
+            ct.append((v, filtered_complex.second))
+        return ct
+
+    def remove_maximal_simplex(self, simplex):
+        """This function removes a given maximal N-simplex from the simplicial
+        complex.
+
+        :param simplex: The N-simplex, represented by a list of vertex.
+        :type simplex: list of int.
+        """
+        self.thisptr.remove_maximal_simplex(simplex)
+
+    def expansion(self, max_dim):
+        """Expands the Simplex_tree containing only its one skeleton
+        until dimension max_dim.
+
+        The expanded simplicial complex until dimension :math:`d`
+        attached to a graph :math:`G` is the maximal simplicial complex of
+        dimension at most :math:`d` admitting the graph :math:`G` as
+        :math:`1`-skeleton.
+        The filtration value assigned to a simplex is the maximal filtration
+        value of one of its edges.
+
+        The Simplex_tree must contain no simplex of dimension bigger than
+        1 when calling the method.
+
+        :param max_dim: The maximal dimension.
+        :type max_dim: int.
+        """
+        self.thisptr.expansion(max_dim)
+
+    def persistence(self, homology_coeff_field=11, min_persistence=0, persistence_dim_max = False):
+        """This function returns the persistence of the simplicial complex.
+
+        :param homology_coeff_field: The homology coefficient field. Must be a
+            prime number
+        :type homology_coeff_field: int.
+        :param min_persistence: The minimum persistence value to take into
+            account (strictly greater than min_persistence). Default value is
+            0.0.
+            Sets min_persistence to -1.0 to see all values.
+        :type min_persistence: float.
+        :returns: The persistence of the simplicial complex.
+        :rtype:  list of pairs(dimension, pair(birth, death))
+        """
+        if self.pcohptr != NULL:
+            del self.pcohptr
+        self.pcohptr = new Simplex_tree_persistence_interface(self.thisptr, persistence_dim_max)
+        cdef vector[pair[int, pair[double, double]]] persistence_result
+        if self.pcohptr != NULL:
+            persistence_result = self.pcohptr.get_persistence(homology_coeff_field, min_persistence)
+        return persistence_result
+
+    def betti_numbers(self):
+        """This function returns the Betti numbers of the simplicial complex.
+
+        :returns: The Betti numbers ([B0, B1, ..., Bn]).
+        :rtype:  list of int
+
+        :note: betti_numbers function requires persistence function to be
+            launched first.
+        """
+        cdef vector[int] bn_result
+        if self.pcohptr != NULL:
+            bn_result = self.pcohptr.betti_numbers()
+        else:
+            print("betti_numbers function requires persistence function"
+                  " to be launched first.")
+        return bn_result
+
+    def persistent_betti_numbers(self, from_value, to_value):
+        """This function returns the persistent Betti numbers of the
+        simplicial complex.
+
+        :param from_value: The persistence birth limit to be added in the
+            numbers (persistent birth <= from_value).
+        :type from_value: float.
+        :param to_value: The persistence death limit to be added in the
+            numbers (persistent death > to_value).
+        :type to_value: float.
+
+        :returns: The persistent Betti numbers ([B0, B1, ..., Bn]).
+        :rtype:  list of int
+
+        :note: persistent_betti_numbers function requires persistence
+            function to be launched first.
+        """
+        cdef vector[int] pbn_result
+        if self.pcohptr != NULL:
+            pbn_result = self.pcohptr.persistent_betti_numbers(<double>from_value, <double>to_value)
+        else:
+            print("persistent_betti_numbers function requires persistence function"
+                  " to be launched first.")
+        return pbn_result
+
+    def persistence_intervals_in_dimension(self, dimension):
+        """This function returns the persistence intervals of the simplicial
+        complex in a specific dimension.
+
+        :param dimension: The specific dimension.
+        :type from_value: int.
+        :returns: The persistence intervals.
+        :rtype:  list of pair of float
+
+        :note: intervals_in_dim function requires persistence function to be
+            launched first.
+        """
+        cdef vector[pair[double,double]] intervals_result
+        if self.pcohptr != NULL:
+            intervals_result = self.pcohptr.intervals_in_dimension(dimension)
+        else:
+            print("intervals_in_dim function requires persistence function"
+                  " to be launched first.")
+        return intervals_result
diff --git a/src/cython/cython/strong_witness_complex.pyx b/src/cython/cython/strong_witness_complex.pyx
new file mode 100644
index 00000000..770b46f5
--- /dev/null
+++ b/src/cython/cython/strong_witness_complex.pyx
@@ -0,0 +1,81 @@
+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.utility cimport pair
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+cdef extern from "Strong_witness_complex_interface.h" namespace "Gudhi":
+    cdef cppclass Strong_witness_complex_interface "Gudhi::witness_complex::Strong_witness_complex_interface":
+        Strong_witness_complex_interface(vector[vector[pair[size_t, double]]] nearest_landmark_table)
+        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square)
+        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square,
+            unsigned limit_dimension)
+
+# StrongWitnessComplex python interface
+cdef class StrongWitnessComplex:
+    """Constructs (strong) witness complex for a given table of nearest
+    landmarks with respect to witnesses.
+    """
+
+    cdef Strong_witness_complex_interface * thisptr
+
+    # Fake constructor that does nothing but documenting the constructor
+    def __init__(self, nearest_landmark_table=None):
+        """StrongWitnessComplex constructor.
+
+        :param nearest_landmark_table: A list of nearest landmark.
+        :type nearest_landmark_table: list of list of pair of unsigned and double
+        """
+
+    # The real cython constructor
+    def __cinit__(self, nearest_landmark_table=None):
+        if nearest_landmark_table is not None:
+            self.thisptr = new Strong_witness_complex_interface(nearest_landmark_table)
+
+    def __dealloc__(self):
+        if self.thisptr != NULL:
+            del self.thisptr
+
+    def __is_defined(self):
+        """Returns true if StrongWitnessComplex pointer is not NULL.
+         """
+        return self.thisptr != NULL
+
+    def create_simplex_tree(self, max_alpha_square, limit_dimension = -1):
+        """
+        :param max_alpha_square: The maximum alpha square threshold the
+            simplices shall not exceed. Default is set to infinity.
+        :type max_alpha_square: float
+        :returns: A simplex tree created from the Delaunay Triangulation.
+        :rtype: SimplexTree
+        """
+        simplex_tree = SimplexTree()
+        if limit_dimension is not -1:
+            self.thisptr.create_simplex_tree(simplex_tree.thisptr, max_alpha_square, limit_dimension)
+        else:
+            self.thisptr.create_simplex_tree(simplex_tree.thisptr, max_alpha_square)
+        return simplex_tree
diff --git a/src/cython/cython/subsampling.pyx b/src/cython/cython/subsampling.pyx
new file mode 100644
index 00000000..a25d196d
--- /dev/null
+++ b/src/cython/cython/subsampling.pyx
@@ -0,0 +1,139 @@
+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.string cimport string
+from libcpp cimport bool
+import os
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+cdef extern from "Subsampling_interface.h" namespace "Gudhi::subsampling":
+    vector[vector[double]] subsampling_n_farthest_points(vector[vector[double]] points, unsigned nb_points)
+    vector[vector[double]] subsampling_n_farthest_points(vector[vector[double]] points, unsigned nb_points, unsigned starting_point)
+    vector[vector[double]] subsampling_n_farthest_points_from_file(string off_file, unsigned nb_points)
+    vector[vector[double]] subsampling_n_farthest_points_from_file(string off_file, unsigned nb_points, unsigned starting_point)
+    vector[vector[double]] subsampling_n_random_points(vector[vector[double]] points, unsigned nb_points)
+    vector[vector[double]] subsampling_n_random_points_from_file(string off_file, unsigned nb_points)
+    vector[vector[double]] subsampling_sparsify_points(vector[vector[double]] points, double min_squared_dist)
+    vector[vector[double]] subsampling_sparsify_points_from_file(string off_file, double min_squared_dist)
+
+def choose_n_farthest_points(points=None, off_file='', nb_points=0, starting_point = ''):
+    """Subsample by a greedy strategy of iteratively adding the farthest point
+    from the current chosen point set to the subsampling.
+    The iteration starts with the landmark `starting point`.
+
+    :param points: The input point set.
+    :type points: vector[vector[double]].
+
+    Or
+
+    :param off_file: An OFF file style name.
+    :type off_file: string
+
+    :param nb_points: Number of points of the subsample.
+    :type nb_points: unsigned.
+    :param starting_point: The iteration starts with the landmark `starting \
+    point`,which is the index of the poit to start with. If not set, this \
+    index is choosen randomly.
+    :type starting_point: unsigned.
+    :returns:  The subsample point set.
+    :rtype: vector[vector[double]]
+    """
+    if off_file is not '':
+        if os.path.isfile(off_file):
+            if starting_point is '':
+                return subsampling_n_farthest_points_from_file(off_file,
+                                                               nb_points)
+            else:
+                return subsampling_n_farthest_points_from_file(off_file,
+                                                               nb_points,
+                                                               starting_point)
+        else:
+            print("file " + off_file + " not found.")
+    else:
+        if points is None:
+            # Empty points
+            points=[]
+        if starting_point is '':
+            return subsampling_n_farthest_points(points, nb_points)
+        else:
+            return subsampling_n_farthest_points(points, nb_points,
+                                                 starting_point)
+
+def pick_n_random_points(points=None, off_file='', nb_points=0):
+    """Subsample a point set by picking random vertices.
+
+    :param points: The input point set.
+    :type points: vector[vector[double]].
+
+    Or
+
+    :param off_file: An OFF file style name.
+    :type off_file: string
+
+    :param nb_points: Number of points of the subsample.
+    :type nb_points: unsigned.
+    :returns:  The subsample point set.
+    :rtype: vector[vector[double]]
+    """
+    if off_file is not '':
+        if os.path.isfile(off_file):
+            return subsampling_n_random_points_from_file(off_file, nb_points)
+        else:
+            print("file " + off_file + " not found.")
+    else:
+        if points is None:
+            # Empty points
+            points=[]
+        return subsampling_n_random_points(points, nb_points)
+
+def sparsify_point_set(points=None, off_file='', min_squared_dist=0.0):
+    """Subsample a point set by picking random vertices.
+
+    :param points: The input point set.
+    :type points: vector[vector[double]].
+
+    Or
+
+    :param off_file: An OFF file style name.
+    :type off_file: string
+
+    :param min_squared_dist: Number of points of the subsample.
+    :type min_squared_dist: unsigned.
+    :returns:  The subsample point set.
+    :rtype: vector[vector[double]]
+    """
+    if off_file is not '':
+        if os.path.isfile(off_file):
+            return subsampling_sparsify_points_from_file(off_file,
+                                                         min_squared_dist)
+        else:
+            print("file " + off_file + " not found.")
+    else:
+        if points is None:
+            # Empty points
+            points=[]
+        return subsampling_sparsify_points(points, min_squared_dist)
diff --git a/src/cython/cython/tangential_complex.pyx b/src/cython/cython/tangential_complex.pyx
new file mode 100644
index 00000000..52bd8111
--- /dev/null
+++ b/src/cython/cython/tangential_complex.pyx
@@ -0,0 +1,151 @@
+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.utility cimport pair
+from libcpp.string cimport string
+from libcpp cimport bool
+import os
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+cdef extern from "Tangential_complex_interface.h" namespace "Gudhi":
+    cdef cppclass Tangential_complex_interface "Gudhi::tangential_complex::Tangential_complex_interface":
+        Tangential_complex_interface(vector[vector[double]] points)
+        # bool from_file is a workaround for cython to find the correct signature
+        Tangential_complex_interface(string off_file, bool from_file)
+        vector[double] get_point(unsigned vertex)
+        unsigned number_of_vertices()
+        unsigned number_of_simplices()
+        unsigned number_of_inconsistent_simplices()
+        unsigned number_of_inconsistent_stars()
+        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree)
+        void fix_inconsistencies_using_perturbation(double max_perturb, double time_limit)
+
+# TangentialComplex python interface
+cdef class TangentialComplex:
+    """The class Tangential_complex represents a tangential complex. After the
+    computation of the complex, an optional post-processing called perturbation
+    can be run to attempt to remove inconsistencies.
+    """
+
+    cdef Tangential_complex_interface * thisptr
+
+    # Fake constructor that does nothing but documenting the constructor
+    def __init__(self, points=None, off_file=''):
+        """TangentialComplex constructor.
+
+        :param points: A list of points in d-Dimension.
+        :type points: list of list of double
+
+        Or
+
+        :param off_file: An OFF file style name.
+        :type off_file: string
+        """
+
+    # The real cython constructor
+    def __cinit__(self, points=None, off_file=''):
+        if off_file is not '':
+            if os.path.isfile(off_file):
+                self.thisptr = new Tangential_complex_interface(off_file, True)
+            else:
+                print("file " + off_file + " not found.")
+        else:
+            if points is None:
+                # Empty tangential construction
+                points=[]
+            self.thisptr = new Tangential_complex_interface(points)
+                
+
+    def __dealloc__(self):
+        if self.thisptr != NULL:
+            del self.thisptr
+
+    def __is_defined(self):
+        """Returns true if TangentialComplex pointer is not NULL.
+         """
+        return self.thisptr != NULL
+
+    def get_point(self, vertex):
+        """This function returns the point corresponding to a given vertex.
+
+        :param vertex: The vertex.
+        :type vertex: int.
+        :returns:  The point.
+        :rtype: list of float
+        """
+        cdef vector[double] point = self.thisptr.get_point(vertex)
+        return point
+
+    def num_vertices(self):
+        """
+        :returns:  The number of vertices.
+        :rtype: unsigned
+        """
+        return self.thisptr.number_of_vertices()
+
+    def num_simplices(self):
+        """
+        :returns:  Total number of simplices in stars (including duplicates that appear in several stars).
+        :rtype: unsigned
+        """
+        return self.thisptr.number_of_simplices()
+
+    def num_inconsistent_simplices(self):
+        """
+        :returns:  The number of inconsistent simplices.
+        :rtype: unsigned
+        """
+        return self.thisptr.number_of_inconsistent_simplices()
+
+    def num_inconsistent_stars(self):
+        """
+        :returns:  The number of stars containing at least one inconsistent simplex.
+        :rtype: unsigned
+        """
+        return self.thisptr.number_of_inconsistent_stars()
+
+    def create_simplex_tree(self):
+        """Exports the complex into a simplex tree.
+
+        :returns: A simplex tree created from the complex.
+        :rtype: SimplexTree
+        """
+        simplex_tree = SimplexTree()
+        self.thisptr.create_simplex_tree(simplex_tree.thisptr)
+        return simplex_tree
+
+    def fix_inconsistencies_using_perturbation(self, max_perturb, time_limit=-1.0):
+        """Attempts to fix inconsistencies by perturbing the point positions.
+
+        :param max_perturb: Maximum length of the translations used by the
+            perturbation.
+        :type max_perturb: double
+        :param time_limit: Time limit in seconds. If -1, no time limit is set.
+        :type time_limit: double
+        """
+        self.thisptr.fix_inconsistencies_using_perturbation(max_perturb,
+                                                            time_limit)
diff --git a/src/cython/cython/witness_complex.pyx b/src/cython/cython/witness_complex.pyx
new file mode 100644
index 00000000..96d122bb
--- /dev/null
+++ b/src/cython/cython/witness_complex.pyx
@@ -0,0 +1,81 @@
+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.utility cimport pair
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+cdef extern from "Witness_complex_interface.h" namespace "Gudhi":
+    cdef cppclass Witness_complex_interface "Gudhi::witness_complex::Witness_complex_interface":
+        Witness_complex_interface(vector[vector[pair[size_t, double]]] nearest_landmark_table)
+        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square)
+        void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square,
+            unsigned limit_dimension)
+
+# WitnessComplex python interface
+cdef class WitnessComplex:
+    """Constructs (weak) witness complex for a given table of nearest landmarks
+    with respect to witnesses.
+    """
+
+    cdef Witness_complex_interface * thisptr
+
+    # Fake constructor that does nothing but documenting the constructor
+    def __init__(self, nearest_landmark_table=None):
+        """WitnessComplex constructor.
+
+        :param nearest_landmark_table: A list of nearest landmark.
+        :type nearest_landmark_table: list of list of pair of unsigned and double
+        """
+
+    # The real cython constructor
+    def __cinit__(self, nearest_landmark_table=None):
+        if nearest_landmark_table is not None:
+            self.thisptr = new Witness_complex_interface(nearest_landmark_table)
+
+    def __dealloc__(self):
+        if self.thisptr != NULL:
+            del self.thisptr
+
+    def __is_defined(self):
+        """Returns true if WitnessComplex pointer is not NULL.
+         """
+        return self.thisptr != NULL
+
+    def create_simplex_tree(self, max_alpha_square, limit_dimension = -1):
+        """
+        :param max_alpha_square: The maximum alpha square threshold the
+            simplices shall not exceed. Default is set to infinity.
+        :type max_alpha_square: float
+        :returns: A simplex tree created from the Delaunay Triangulation.
+        :rtype: SimplexTree
+        """
+        simplex_tree = SimplexTree()
+        if limit_dimension is not -1:
+            self.thisptr.create_simplex_tree(simplex_tree.thisptr, max_alpha_square, limit_dimension)
+        else:
+            self.thisptr.create_simplex_tree(simplex_tree.thisptr, max_alpha_square)
+        return simplex_tree
diff --git a/src/cython/cythonize_gudhi.py.in b/src/cython/cythonize_gudhi.py.in
new file mode 100644
index 00000000..5a97e9f3
--- /dev/null
+++ b/src/cython/cythonize_gudhi.py.in
@@ -0,0 +1,48 @@
+from distutils.core import setup, Extension
+from Cython.Build import cythonize
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016  INRIA"
+__license__ = "GPL v3"
+
+gudhi = Extension(
+    "gudhi",
+    sources = ['gudhi.pyx',],
+    language = 'c++',
+    extra_compile_args=[@GUDHI_CYTHON_EXTRA_COMPILE_ARGS@],
+    extra_link_args=[@GUDHI_CYTHON_EXTRA_LINK_ARGS@],
+    libraries=[@GUDHI_CYTHON_LIBRARIES@],
+    library_dirs=[@GUDHI_CYTHON_LIBRARY_DIRS@],
+    include_dirs = [@GUDHI_CYTHON_INCLUDE_DIRS@],
+)
+
+setup(
+    name = 'gudhi',
+    author='Vincent Rouvreau',
+    author_email='gudhi-contact@lists.gforge.inria.fr',
+    version='0.1.0',
+    url='http://gudhi.gforge.inria.fr/',
+    ext_modules = cythonize(gudhi),
+)
diff --git a/src/cython/doc/Makefile b/src/cython/doc/Makefile
new file mode 100644
index 00000000..be3ff7c4
--- /dev/null
+++ b/src/cython/doc/Makefile
@@ -0,0 +1,181 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = _build
+
+# User-friendly check for sphinx-build
+ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
+$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
+endif
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  xml        to make Docutils-native XML files"
+	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	rm -f examples.inc
+	rm -rf $(BUILDDIR)/*
+
+# GUDHI specific : Examples.inc is generated with generate_examples.py (and deleted on clean)
+
+html:
+	./generate_examples.py
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/pouet.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/pouet.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/pouet"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/pouet"
+	@echo "# devhelp"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+latexpdfja:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through platex and dvipdfmx..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+
+xml:
+	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+	@echo
+	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+
+pseudoxml:
+	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+	@echo
+	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
diff --git a/src/cython/doc/_templates/layout.html b/src/cython/doc/_templates/layout.html
new file mode 100644
index 00000000..af0eef64
--- /dev/null
+++ b/src/cython/doc/_templates/layout.html
@@ -0,0 +1,270 @@
+{#
+    basic/layout.html
+    ~~~~~~~~~~~~~~~~~
+
+    Master layout template for Sphinx themes.
+
+    :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
+    :license: BSD, see LICENSE for details.
+#}
+{%- block doctype -%}
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+{%- endblock %}
+{%- set reldelim1 = reldelim1 is not defined and ' &raquo;' or reldelim1 %}
+{%- set reldelim2 = reldelim2 is not defined and ' |' or reldelim2 %}
+{%- set render_sidebar = (not embedded) and (not theme_nosidebar|tobool) and
+                         (sidebars != []) %}
+{%- set url_root = pathto('', 1) %}
+{# XXX necessary? #}
+{%- if url_root == '#' %}{% set url_root = '' %}{% endif %}
+{%- if not embedded and docstitle %}
+  {%- set titlesuffix = " &mdash; "|safe + docstitle|e %}
+{%- else %}
+  {%- set titlesuffix = "" %}
+{%- endif %}
+
+{%- macro relbar() %}
+    <div class="related" role="navigation" aria-label="related navigation">
+      <h3>{{ _('Navigation') }}</h3>
+      <ul>
+        {%- for rellink in rellinks %}
+        <li class="right" {% if loop.first %}style="margin-right: 10px"{% endif %}>
+          <a href="{{ pathto(rellink[0]) }}" title="{{ rellink[1]|striptags|e }}"
+             {{ accesskey(rellink[2]) }}>{{ rellink[3] }}</a>
+          {%- if not loop.first %}{{ reldelim2 }}{% endif %}</li>
+        {%- endfor %}
+        {%- block rootrellink %}
+        <li class="nav-item nav-item-0"><a href="{{ pathto(master_doc) }}">{{ shorttitle|e }}</a>{{ reldelim1 }}</li>
+        {%- endblock %}
+        {%- for parent in parents %}
+          <li class="nav-item nav-item-{{ loop.index }}"><a href="{{ parent.link|e }}" {% if loop.last %}{{ accesskey("U") }}{% endif %}>{{ parent.title }}</a>{{ reldelim1 }}</li>
+        {%- endfor %}
+        {%- block relbaritems %} {% endblock %}
+      </ul>
+    </div>
+{%- endmacro %}
+
+{%- macro sidebar() %}
+      {%- if render_sidebar %}
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+        <div class="sphinxsidebarwrapper">
+          {%- block sidebarlogo %}
+          {%- if logo %}
+            <p class="logo"><a href="{{ pathto(master_doc) }}">
+              <img class="logo" src="{{ pathto('_static/' + logo, 1) }}" alt="Logo"/>
+            </a></p>
+          {%- endif %}
+          {%- endblock %}
+          {%- if sidebars != None %}
+            {#- new style sidebar: explicitly include/exclude templates #}
+            {%- for sidebartemplate in sidebars %}
+            {%- include sidebartemplate %}
+            {%- endfor %}
+          {%- else %}
+            {#- old style sidebars: using blocks -- should be deprecated #}
+            {%- block sidebartoc %}
+<h2><a href="index.html">GUDHI</a></h2>
+<h2><a href="installation.html">GUDHI installation</a></h2>
+<h2><a href="citation.html">Acknowledging the GUDHI library</a></h2>
+<h2><a href="genindex.html">Index</a></h2>
+<h2><a href="examples.html">Examples</a></h2>
+
+            {%- include "localtoc.html" %}
+            {%- endblock %}
+            {%- block sidebarrel %}
+            {%- include "relations.html" %}
+            {%- endblock %}
+            {%- block sidebarsourcelink %}
+            {%- include "sourcelink.html" %}
+            {%- endblock %}
+            {%- if customsidebar %}
+            {%- include customsidebar %}
+            {%- endif %}
+            {%- block sidebarsearch %}
+            {%- include "searchbox.html" %}
+            {%- endblock %}
+          {%- endif %}
+        </div>
+      </div>
+      {%- endif %}
+{%- endmacro %}
+
+{%- macro script() %}
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    '{{ url_root }}',
+        VERSION:     '{{ release|e }}',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '{{ '' if no_search_suffix else file_suffix }}',
+        HAS_SOURCE:  {{ has_source|lower }}
+      };
+    </script>
+    {%- for scriptfile in script_files %}
+    <script type="text/javascript" src="{{ pathto(scriptfile, 1) }}"></script>
+    {%- endfor %}
+{%- endmacro %}
+
+{%- macro css() %}
+<!-- GUDHI website css for header BEGIN -->
+<link rel="stylesheet" type="text/css" href="http://gudhi.gforge.inria.fr/assets/css/styles_feeling_responsive.css" />
+<!-- GUDHI website css for header END -->
+    <link rel="stylesheet" href="{{ pathto('_static/' + style, 1) }}" type="text/css" />
+    <link rel="stylesheet" href="{{ pathto('_static/pygments.css', 1) }}" type="text/css" />
+    {%- for cssfile in css_files %}
+    <link rel="stylesheet" href="{{ pathto(cssfile, 1) }}" type="text/css" />
+    {%- endfor %}
+{%- endmacro %}
+<!-- GUDHI website html class for header BEGIN -->
+<html xmlns="http://www.w3.org/1999/xhtml" class="no-js" lang="en">
+<!-- GUDHI website html class for header END -->
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset={{ encoding }}" />
+    {{ metatags }}
+    {%- block htmltitle %}
+    <title>{{ title|striptags|e }}{{ titlesuffix }}</title>
+    {%- endblock %}
+    {{ css() }}
+    {%- if not embedded %}
+    {{ script() }}
+    {%- if use_opensearch %}
+    <link rel="search" type="application/opensearchdescription+xml"
+          title="{% trans docstitle=docstitle|e %}Search within {{ docstitle }}{% endtrans %}"
+          href="{{ pathto('_static/opensearch.xml', 1) }}"/>
+    {%- endif %}
+    {%- if favicon %}
+    <link rel="shortcut icon" href="{{ pathto('_static/' + favicon, 1) }}"/>
+    {%- endif %}
+    {%- endif %}
+{%- block linktags %}
+    {%- if hasdoc('about') %}
+    <link rel="author" title="{{ _('About these documents') }}" href="{{ pathto('about') }}" />
+    {%- endif %}
+    {%- if hasdoc('genindex') %}
+    <link rel="index" title="{{ _('Index') }}" href="{{ pathto('genindex') }}" />
+    {%- endif %}
+    {%- if hasdoc('search') %}
+    <link rel="search" title="{{ _('Search') }}" href="{{ pathto('search') }}" />
+    {%- endif %}
+    {%- if hasdoc('copyright') %}
+    <link rel="copyright" title="{{ _('Copyright') }}" href="{{ pathto('copyright') }}" />
+    {%- endif %}
+    <link rel="top" title="{{ docstitle|e }}" href="{{ pathto(master_doc) }}" />
+    {%- if parents %}
+    <link rel="up" title="{{ parents[-1].title|striptags|e }}" href="{{ parents[-1].link|e }}" />
+    {%- endif %}
+    {%- if next %}
+    <link rel="next" title="{{ next.title|striptags|e }}" href="{{ next.link|e }}" />
+    {%- endif %}
+    {%- if prev %}
+    <link rel="prev" title="{{ prev.title|striptags|e }}" href="{{ prev.link|e }}" />
+    {%- endif %}
+{%- endblock %}
+{%- block extrahead %} {% endblock %}
+  </head>
+  <body role="document">
+  <!-- GUDHI website header BEGIN -->
+  <div id="navigation" class="sticky">
+    <nav class="top-bar" role="navigation" data-topbar>
+      <ul class="title-area">
+        <li class="name">
+        <h1 class="show-for-small-only"><a href="http://gudhi.gforge.inria.fr" class="icon-tree"> GUDHI C++ library</a></h1>
+      </li>
+         <!-- Remove the class "menu-icon" to get rid of menu icon. Take out "Menu" to just have icon alone -->
+        <li class="toggle-topbar menu-icon"><a href="#"><span>Navigation</span></a></li>
+      </ul>
+      <section class="top-bar-section">
+        <ul class="right">
+                <li class="divider"></li>
+                <li><a href="http://gudhi.gforge.inria.fr/contact/">Contact</a></li>
+        </ul>
+        <ul class="left">
+                <li><a href="http://gudhi.gforge.inria.fr/"> <img src="http://gudhi.gforge.inria.fr/assets/img/home.png" alt="&nbsp;&nbsp;GUDHI">&nbsp;&nbsp;GUDHI </a></li>
+                <li class="divider"></li>
+                <li class="has-dropdown">
+                  <a href="#">Project</a>
+                    <ul class="dropdown">
+                        <li><a href="http://gudhi.gforge.inria.fr/people/">People</a></li>
+                        <li><a href="http://gudhi.gforge.inria.fr/keepintouch/">Keep in touch</a></li>
+                        <li><a href="http://gudhi.gforge.inria.fr/partners/">Partners and Funding</a></li>
+                        <li><a href="http://gudhi.gforge.inria.fr/relatedprojects/">Related projects</a></li>
+                        <li><a href="http://gudhi.gforge.inria.fr/theyaretalkingaboutus/">They are talking about us</a></li>
+                    </ul>
+                </li>
+                <li class="divider"></li>
+                <li class="has-dropdown">
+                  <a href="#">Download</a>
+                    <ul class="dropdown">
+                        <li><a href="http://gudhi.gforge.inria.fr/licensing/">Licensing</a></li>
+                        <li><a href="https://gforge.inria.fr/frs/?group_id=3865" target="_blank">Get the sources</a></li>
+                    </ul>
+                </li>
+                <li class="divider"></li>
+                <li class="has-dropdown">
+                  <a href="#">Documentation</a>
+                    <ul class="dropdown">
+                        <li><a href="http://gudhi.gforge.inria.fr/doc/latest/">C++ documentation</a></li>
+                        <li><a href="http://gudhi.gforge.inria.fr/doc/latest/installation.html">C++ installation manual</a></li>
+                        <li><a href="http://gudhi.gforge.inria.fr/cython/latest/">Cython documentation</a></li>
+                        <li><a href="http://gudhi.gforge.inria.fr/cython/latest/installation.html">Cython installation manual</a></li>
+                    </ul>
+                </li>
+                <li class="divider"></li>
+                <li><a href="http://gudhi.gforge.inria.fr/interfaces/">Interfaces</a></li>
+                <li class="divider"></li>
+        </ul>
+      </section>
+    </nav>
+  </div><!-- /#navigation -->
+  <!-- GUDHI website header BEGIN -->
+
+
+{%- block header %}{% endblock %}
+
+{%- block relbar1 %}{% endblock %}
+
+{%- block content %}
+  {%- block sidebar1 %} {# possible location for sidebar #} {% endblock %}
+
+    <div class="document">
+  {%- block document %}
+      <div class="documentwrapper">
+      {%- if render_sidebar %}
+        <div class="bodywrapper">
+      {%- endif %}
+          <div class="body" role="main">
+            {% block body %} {% endblock %}
+          </div>
+      {%- if render_sidebar %}
+        </div>
+      {%- endif %}
+      </div>
+  {%- endblock %}
+
+  {%- block sidebar2 %}{{ sidebar() }}{% endblock %}
+      <div class="clearer"></div>
+    </div>
+{%- endblock %}
+
+{%- block relbar2 %}{% endblock %}
+
+{%- block footer %}
+    <div class="footer" role="contentinfo">
+    {%- if show_copyright %}
+      {%- if hasdoc('copyright') %}
+        {% trans path=pathto('copyright'), copyright=copyright|e %}&copy; <a href="{{ path }}">Copyright</a> {{ copyright }}.{% endtrans %}
+      {%- else %}
+        {% trans copyright=copyright|e %}&copy; Copyright {{ copyright }}.{% endtrans %}
+      {%- endif %}
+    {%- endif %}
+    {%- if last_updated %}
+      {% trans last_updated=last_updated|e %}Last updated on {{ last_updated }}.{% endtrans %}
+    {%- endif %}
+    {%- if show_sphinx %}
+      {% trans sphinx_version=sphinx_version|e %}Created using <a href="http://sphinx-doc.org/">Sphinx</a> {{ sphinx_version }}.{% endtrans %}
+    {%- endif %}
+    </div>
+{%- endblock %}
+  </body>
+</html>
+
diff --git a/src/cython/doc/alpha_complex_ref.rst b/src/cython/doc/alpha_complex_ref.rst
new file mode 100644
index 00000000..6a122b09
--- /dev/null
+++ b/src/cython/doc/alpha_complex_ref.rst
@@ -0,0 +1,10 @@
+==============================
+Alpha complex reference manual
+==============================
+
+.. autoclass:: gudhi.AlphaComplex
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+   .. automethod:: gudhi.AlphaComplex.__init__
diff --git a/src/cython/doc/alpha_complex_sum.rst b/src/cython/doc/alpha_complex_sum.rst
new file mode 100644
index 00000000..8437e901
--- /dev/null
+++ b/src/cython/doc/alpha_complex_sum.rst
@@ -0,0 +1,22 @@
+=================================================================  ===================================  ===================================
+:Author: Vincent Rouvreau                                          :Introduced in: GUDHI 2.0.0          :Copyright: GPL v3
+:Requires: CGAL :math:`\geq` 4.7.0                                 Eigen3
+=================================================================  ===================================  ===================================
+
++----------------------------------------------------------------+------------------------------------------------------------------------+
+| .. figure::                                                    | Alpha_complex is a simplicial complex constructed from the finite      |
+|      img/alpha_complex_representation.png                      | cells of a Delaunay Triangulation.                                     |
+|      :alt: Alpha complex representation                        |                                                                        |
+|      :figclass: align-center                                   | The filtration value of each simplex is computed as the square of the  |
+|                                                                | circumradius of the simplex if the circumsphere is empty (the simplex  |
+|      Alpha complex representation                              | is then said to be Gabriel), and as the minimum of the filtration      |
+|                                                                | values of the codimension 1 cofaces that make it not Gabriel           |
+|                                                                | otherwise. All simplices that have a filtration value strictly         |
+|                                                                | greater than a given alpha squared value are not inserted into the     |
+|                                                                | complex.                                                               |
+|                                                                |                                                                        |
+|                                                                | This package requires having CGAL version 4.7 or higher (4.8.1 is      |
+|                                                                | advised for better perfomances).                                       |
++----------------------------------------------------------------+------------------------------------------------------------------------+
+| :doc:`alpha_complex_user`                                      | :doc:`alpha_complex_ref`                                               |
++----------------------------------------------------------------+------------------------------------------------------------------------+
diff --git a/src/cython/doc/alpha_complex_user.rst b/src/cython/doc/alpha_complex_user.rst
new file mode 100644
index 00000000..68e53a77
--- /dev/null
+++ b/src/cython/doc/alpha_complex_user.rst
@@ -0,0 +1,205 @@
+=========================
+Alpha complex user manual
+=========================
+Definition
+----------
+
+.. include:: alpha_complex_sum.rst
+
+Alpha_complex is constructing a :doc:`Simplex_tree <simplex_tree_sum>` using
+`Delaunay Triangulation  <http://doc.cgal.org/latest/Triangulation/index.html#Chapter_Triangulations>`_ 
+:cite:`cgal:hdj-t-15b` from `CGAL <http://www.cgal.org/>`_ (the Computational Geometry Algorithms Library
+:cite:`cgal:eb-15b`).
+
+Remarks
+^^^^^^^
+When Alpha_complex is constructed with an infinite value of :math:`\alpha`, the complex is a Delaunay complex.
+
+Example from points
+-------------------
+
+This example builds the Delaunay triangulation from the given points, and initializes the alpha complex with it:
+
+.. testcode::
+
+    import gudhi
+    alpha_complex = gudhi.AlphaComplex(points=[[1, 1], [7, 0], [4, 6], [9, 6], [0, 14], [2, 19], [9, 17]])
+
+    simplex_tree = alpha_complex.create_simplex_tree(max_alpha_square=60.0)
+    result_str = 'Alpha complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \
+        repr(simplex_tree.num_simplices()) + ' simplices - ' + \
+        repr(simplex_tree.num_vertices()) + ' vertices.'
+    print(result_str)
+    for filtered_value in simplex_tree.get_filtered_tree():
+        print(filtered_value)
+
+The output is:
+
+.. testoutput::
+
+   Alpha complex is of dimension 2 - 25 simplices - 7 vertices.
+   ([0], 0.0)
+   ([1], 0.0)
+   ([2], 0.0)
+   ([3], 0.0)
+   ([4], 0.0)
+   ([5], 0.0)
+   ([6], 0.0)
+   ([2, 3], 6.25)
+   ([4, 5], 7.25)
+   ([0, 2], 8.5)
+   ([0, 1], 9.25)
+   ([1, 3], 10.0)
+   ([1, 2], 11.25)
+   ([1, 2, 3], 12.5)
+   ([0, 1, 2], 12.995867768595042)
+   ([5, 6], 13.25)
+   ([2, 4], 20.0)
+   ([4, 6], 22.736686390532547)
+   ([4, 5, 6], 22.736686390532547)
+   ([3, 6], 30.25)
+   ([2, 6], 36.5)
+   ([2, 3, 6], 36.5)
+   ([2, 4, 6], 37.24489795918368)
+   ([0, 4], 59.710743801652896)
+   ([0, 2, 4], 59.710743801652896)
+
+
+Algorithm
+---------
+
+Data structure
+^^^^^^^^^^^^^^
+
+In order to build the alpha complex, first, a Simplex tree is built from the cells of a Delaunay Triangulation.
+(The filtration value is set to NaN, which stands for unknown value):
+
+.. figure::
+    img/alpha_complex_doc.png
+    :figclass: align-center
+    :alt: Simplex tree structure construction example
+
+    Simplex tree structure construction example
+
+Filtration value computation algorithm
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+  **for** i : dimension :math:`\rightarrow` 0 **do**
+    **for all** :math:`\sigma` of dimension i
+      **if** filtration(:math:`\sigma`) is NaN **then**
+        filtration(:math:`\sigma`) = :math:`\alpha^2(\sigma)`
+      **end if**
+
+      *//propagate alpha filtration value*
+
+      **for all** :math:`\tau` face of :math:`\sigma`
+        **if** filtration(:math:`\tau`) is not NaN **then**
+          filtration(:math:`\tau`) = filtration(:math:`\sigma`)
+        **end if**
+      **end for**
+    **end for**
+  **end for**
+  
+  make_filtration_non_decreasing()
+  
+  prune_above_filtration()
+
+Dimension 2
+^^^^^^^^^^^
+
+From the example above, it means the algorithm looks into each triangle ([0,1,2], [0,2,4], [1,2,3], ...),
+computes the filtration value of the triangle, and then propagates the filtration value as described
+here:
+
+.. figure::
+    img/alpha_complex_doc_420.png
+    :figclass: align-center
+    :alt: Filtration value propagation example
+
+    Filtration value propagation example
+
+Dimension 1
+^^^^^^^^^^^
+
+Then, the algorithm looks into each edge ([0,1], [0,2], [1,2], ...),
+computes the filtration value of the edge (in this case, propagation will have no effect).
+
+Dimension 0
+^^^^^^^^^^^
+
+Finally, the algorithm looks into each vertex ([0], [1], [2], [3], [4], [5] and [6]) and
+sets the filtration value (0 in case of a vertex - propagation will have no effect).
+
+Non decreasing filtration values
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+As the squared radii computed by CGAL are an approximation, it might happen that these alpha squared values do not
+quite define a proper filtration (i.e. non-decreasing with respect to inclusion).
+We fix that up by calling `Simplex_tree::make_filtration_non_decreasing()` (cf.
+`C++ version <http://gudhi.gforge.inria.fr/doc/latest/index.html>`_).
+
+Prune above given filtration value
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The simplex tree is pruned from the given maximum alpha squared value (cf. `Simplex_tree::prune_above_filtration()`
+int he `C++ version <http://gudhi.gforge.inria.fr/doc/latest/index.html>`_).
+In the following example, the value is given by the user as argument of the program.
+
+
+Example from OFF file
+^^^^^^^^^^^^^^^^^^^^^
+
+This example builds the Delaunay triangulation from the points given by an OFF file, and initializes the alpha complex
+with it.
+
+
+Then, it is asked to display information about the alpha complex:
+
+.. testcode::
+
+    import gudhi
+    alpha_complex = gudhi.AlphaComplex(off_file='alphacomplexdoc.off')
+    simplex_tree = alpha_complex.create_simplex_tree(max_alpha_square=59.0)
+    result_str = 'Alpha complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \
+        repr(simplex_tree.num_simplices()) + ' simplices - ' + \
+        repr(simplex_tree.num_vertices()) + ' vertices.'
+    print(result_str)
+    for filtered_value in simplex_tree.get_filtered_tree():
+        print(filtered_value)
+
+the program output is:
+
+.. testoutput::
+
+   Alpha complex is of dimension 2 - 23 simplices - 7 vertices.
+   ([0], 0.0)
+   ([1], 0.0)
+   ([2], 0.0)
+   ([3], 0.0)
+   ([4], 0.0)
+   ([5], 0.0)
+   ([6], 0.0)
+   ([2, 3], 6.25)
+   ([4, 5], 7.25)
+   ([0, 2], 8.5)
+   ([0, 1], 9.25)
+   ([1, 3], 10.0)
+   ([1, 2], 11.25)
+   ([1, 2, 3], 12.5)
+   ([0, 1, 2], 12.995867768595042)
+   ([5, 6], 13.25)
+   ([2, 4], 20.0)
+   ([4, 6], 22.736686390532547)
+   ([4, 5, 6], 22.736686390532547)
+   ([3, 6], 30.25)
+   ([2, 6], 36.5)
+   ([2, 3, 6], 36.5)
+   ([2, 4, 6], 37.24489795918368)
+
+==============
+CGAL citations
+==============
+
+.. bibliography:: how_to_cite_cgal.bib
+   :filter: docnames
+   :style: unsrt
diff --git a/src/cython/doc/bottleneck_distance_sum.rst b/src/cython/doc/bottleneck_distance_sum.rst
new file mode 100644
index 00000000..5c475d0d
--- /dev/null
+++ b/src/cython/doc/bottleneck_distance_sum.rst
@@ -0,0 +1,15 @@
+=================================================================  ===================================  ===================================
+:Author: François Godi                                             :Introduced in: GUDHI 2.0.0          :Copyright: GPL v3
+:Requires: CGAL :math:`\geq` 4.8.0
+=================================================================  ===================================  ===================================
+
++-----------------------------------------------------------------+----------------------------------------------------------------------+
+| .. figure::                                                     | Bottleneck distance measures the similarity between two persistence  |
+|      img/perturb_pd.png                                         | diagrams. It's the shortest distance b for which there exists a      |
+|      :figclass: align-center                                    | perfect matching between the points of the two diagrams (+ all the   |
+|                                                                 | diagonal points) such that any couple of matched points are at       |
+|      Bottleneck distance is the length of                       | distance at most b.                                                  |
+|      the longest edge                                           |                                                                      |
++-----------------------------------------------------------------+----------------------------------------------------------------------+
+| :doc:`bottleneck_distance_user`                                 |                                                                      |
++-----------------------------------------------------------------+----------------------------------------------------------------------+
diff --git a/src/cython/doc/bottleneck_distance_user.rst b/src/cython/doc/bottleneck_distance_user.rst
new file mode 100644
index 00000000..3bc170f4
--- /dev/null
+++ b/src/cython/doc/bottleneck_distance_user.rst
@@ -0,0 +1,37 @@
+===============================
+Bottleneck distance user manual
+===============================
+Definition
+----------
+
+.. include:: bottleneck_distance_sum.rst
+
+Function
+--------
+.. autofunction:: gudhi.bottleneck_distance
+
+
+Basic example
+-------------
+
+This example computes the bottleneck distance from 2 persistence diagrams:
+
+.. testcode::
+
+    import gudhi
+
+    diag1 = [[2.7, 3.7],[9.6, 14.],[34.2, 34.974], [3.,float('Inf')]]
+    diag2 = [[2.8, 4.45],[9.5, 14.1],[3.2,float('Inf')]]
+
+    message = "Bottleneck distance approximation=" + repr(gudhi.bottleneck_distance(diag1, diag2, 0.1))
+    print(message)
+
+    message = "Bottleneck distance exact value=" + repr(gudhi.bottleneck_distance(diag1, diag2))
+    print(message)
+
+The output is:
+
+.. testoutput::
+
+    Bottleneck distance approximation=0.8081763781405569
+    Bottleneck distance exact value=0.75
diff --git a/src/cython/doc/citation.rst b/src/cython/doc/citation.rst
new file mode 100644
index 00000000..6cdfb7cc
--- /dev/null
+++ b/src/cython/doc/citation.rst
@@ -0,0 +1,15 @@
+Acknowledging the GUDHI library
+###############################
+
+We kindly ask users to cite the GUDHI library as appropriately as possible in
+their papers, and to mention the use of the GUDHI library on the web pages of
+their projects using GUDHI and provide us with links to these web pages. Feel
+free to contact us in case you have any question or remark on this topic.
+
+We provide GUDHI bibtex entries for the modules of the User and Reference
+Manual, as well as for publications directly related to the GUDHI library.
+
+GUDHI bibtex
+************
+
+.. literalinclude:: how_to_cite_gudhi.bib
diff --git a/src/cython/doc/conf.py b/src/cython/doc/conf.py
new file mode 100755
index 00000000..42bfd59c
--- /dev/null
+++ b/src/cython/doc/conf.py
@@ -0,0 +1,278 @@
+# -*- coding: utf-8 -*-
+#
+# GUDHI documentation build configuration file, created by
+# sphinx-quickstart on Thu Jun 30 09:55:51 2016.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys
+import os
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#sys.path.insert(0, os.path.abspath('.'))
+
+# Path to Gudhi.so from source path
+sys.path.insert(0, os.path.abspath('..'))
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'matplotlib.sphinxext.plot_directive',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.doctest',
+    'sphinx.ext.todo',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.ifconfig',
+    'sphinx.ext.viewcode',
+    'sphinxcontrib.bibtex',
+]
+
+todo_include_todos = True
+# plot option : do not show hyperlinks (Source code, png, hires.png, pdf)
+plot_html_show_source_link = False
+plot_html_show_formats = False
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'GUDHI'
+copyright = u'2016, GUDHI Editorial Board'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = '2.0'
+# The full version, including alpha/beta/rc tags.
+release = '2.0.0'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = ['_build']
+
+# The reST default role (used for this markup: `text`) to use for all
+# documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+# If true, keep warnings as "system message" paragraphs in the built documents.
+#keep_warnings = False
+
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+html_theme = 'classic'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+html_theme_options = {
+     "sidebarbgcolor": "#A1ADCD",
+     "sidebartextcolor": "black",
+     "sidebarlinkcolor": "#334D5C",
+}
+
+# Add any paths that contain custom themes here, relative to this directory.
+#html_theme_path = []
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+#html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo =
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon =
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# Add any extra paths that contain custom files (such as robots.txt or
+# .htaccess) here, relative to this directory. These files are copied
+# directly to the root of the documentation.
+#html_extra_path = []
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {'installation': 'installation.html'}
+
+# If false, no module index is generated.
+#html_domain_indices = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = None
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'GUDHIdoc'
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+# The paper size ('letterpaper' or 'a4paper').
+#'papersize': 'letterpaper',
+
+# The font size ('10pt', '11pt' or '12pt').
+#'pointsize': '10pt',
+
+# Additional stuff for the LaTeX preamble.
+#'preamble': '',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+  ('index', 'GUDHI.tex', u'GUDHI Documentation',
+   u'Vincent Rouvreau', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# If true, show page references after internal links.
+#latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_domain_indices = True
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    ('index', 'gudhi', u'GUDHI Documentation',
+     [u'Vincent Rouvreau'], 1)
+]
+
+# If true, show URL addresses after external links.
+#man_show_urls = False
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+  ('index', 'GUDHI', u'GUDHI Documentation',
+   u'Vincent Rouvreau', 'GUDHI', 'One line description of project.',
+   'Miscellaneous'),
+]
+
+# Documents to append as an appendix to all manuals.
+#texinfo_appendices = []
+
+# If false, no module index is generated.
+#texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#texinfo_show_urls = 'footnote'
+
+# If true, do not generate a @detailmenu in the "Top" node's menu.
+#texinfo_no_detailmenu = False
diff --git a/src/cython/doc/cubical_complex_ref.rst b/src/cython/doc/cubical_complex_ref.rst
new file mode 100644
index 00000000..84aa4223
--- /dev/null
+++ b/src/cython/doc/cubical_complex_ref.rst
@@ -0,0 +1,9 @@
+Cubical complex reference manual
+################################
+
+.. autoclass:: gudhi.CubicalComplex
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+   .. automethod:: gudhi.CubicalComplex.__init__
diff --git a/src/cython/doc/cubical_complex_sum.rst b/src/cython/doc/cubical_complex_sum.rst
new file mode 100644
index 00000000..3ddf6375
--- /dev/null
+++ b/src/cython/doc/cubical_complex_sum.rst
@@ -0,0 +1,15 @@
+=================================================================  ===================================  ===================================
+:Author: Pawel Dlotko                                              :Introduced in: GUDHI 2.0.0          :Copyright: GPL v3
+=================================================================  ===================================  ===================================
+
++-----------------------------------------------------------------+----------------------------------------------------------------------+
+| .. figure::                                                     | The cubical complex is an example of a structured complex useful in  |
+|      img/Cubical_complex_representation.png                     | computational mathematics (specially rigorous numerics) and image    |
+|      :alt: Cubical complex representation                       | analysis.                                                            |
+|      :figclass: align-center                                    |                                                                      |
+|                                                                 |                                                                      |
+|      Cubical complex representation                             |                                                                      |
++-----------------------------------------------------------------+----------------------------------------------------------------------+
+| :doc:`cubical_complex_user`                                     | * :doc:`cubical_complex_ref`                                         |
+|                                                                 | * :doc:`periodic_cubical_complex_ref`                                |
++-----------------------------------------------------------------+----------------------------------------------------------------------+
diff --git a/src/cython/doc/cubical_complex_user.rst b/src/cython/doc/cubical_complex_user.rst
new file mode 100644
index 00000000..692acdd9
--- /dev/null
+++ b/src/cython/doc/cubical_complex_user.rst
@@ -0,0 +1,161 @@
+===========================
+Cubical complex user manual
+===========================
+Definition
+----------
+
+=====================================  =====================================  =====================================
+:Author: Pawel Dlotko                  :Introduced in: GUDHI PYTHON 2.0.0     :Copyright: GPL v3
+=====================================  =====================================  =====================================
+
++---------------------------------------------+----------------------------------------------------------------------+
+| :doc:`cubical_complex_user`                 | * :doc:`cubical_complex_ref`                                         |
+|                                             | * :doc:`periodic_cubical_complex_ref`                                |
++---------------------------------------------+----------------------------------------------------------------------+
+
+The cubical complex is an example of a structured complex useful in computational mathematics (specially rigorous
+numerics) and image analysis.
+
+An *elementary interval* is an interval of a form :math:`[n,n+1]`, or :math:`[n,n]`, for :math:`n \in \mathcal{Z}`.
+The first one is called *non-degenerate*, while the second one is a *degenerate* interval. A
+*boundary of a elementary interval* is a chain  :math:`\partial [n,n+1] = [n+1,n+1]-[n,n]` in case of
+non-degenerated elementary interval and :math:`\partial [n,n] = 0` in case of degenerate elementary interval. An
+*elementary cube* :math:`C` is a product of elementary intervals, :math:`C=I_1 \times \ldots \times I_n`.
+*Embedding dimension* of a cube is n, the number of elementary intervals (degenerate or not) in the product.
+A *dimension of a cube* :math:`C=I_1 \times ... \times I_n` is the number of non degenerate elementary
+intervals in the product. A *boundary of a cube* :math:`C=I_1 \times \ldots \times I_n` is a chain obtained
+in the following way:
+
+.. math::
+
+    \partial C = (\partial I_1 \times \ldots \times I_n) + (I_1 \times \partial I_2 \times \ldots \times I_n) +
+    \ldots + (I_1 \times I_2 \times \ldots \times \partial I_n).
+
+A *cubical complex* :math:`\mathcal{K}` is a collection of cubes closed under operation of taking boundary
+(i.e. boundary of every cube from the collection is in the collection). A cube :math:`C` in cubical complex
+:math:`\mathcal{K}` is *maximal* if it is not in a boundary of any other cube in :math:`\mathcal{K}`. A
+*support* of a cube :math:`C` is the set in :math:`\mathbb{R}^n` occupied by :math:`C` (:math:`n` is the embedding
+dimension of :math:`C`).
+
+Cubes may be equipped with a filtration values in which case we have filtered cubical complex. All the cubical
+complexes considered in this implementation are filtered cubical complexes (although, the range of a filtration may
+be a set of two elements).
+
+For further details and theory of cubical complexes, please consult :cite:`kaczynski2004computational` as well as the
+following paper :cite:`peikert2012topological`.
+
+Data structure.
+---------------
+
+The implementation of Cubical complex provides a representation of complexes that occupy a rectangular region in
+:math:`\mathbb{R}^n`. This extra assumption allows for a memory efficient way of storing cubical complexes in a form
+of so called bitmaps. Let
+:math:`R = [b_1,e_1] \times \ldots \times [b_n,e_n]`, for :math:`b_1,...b_n,e_1,...,e_n \in \mathbb{Z}`,
+:math:`b_i \leq d_i` be the considered rectangular region and let :math:`\mathcal{K}` be a filtered
+cubical complex having the rectangle :math:`R` as its support. Note that the structure of the coordinate system gives
+a way a lexicographical ordering of cells of :math:`\mathcal{K}`. This ordering is a base of the presented
+bitmap-based implementation. In this implementation, the whole cubical complex is stored as a vector of the values
+of filtration. This, together with dimension of :math:`\mathcal{K}` and the sizes of :math:`\mathcal{K}` in all
+directions, allows to determine, dimension, neighborhood, boundary and coboundary of every cube
+:math:`C \in \mathcal{K}`.
+
+.. figure::
+    img/Cubical_complex_representation.png
+    :alt: Cubical complex.
+    :figclass: align-center
+
+    Cubical complex.
+
+Note that the cubical complex in the figure above is, in a natural way, a product of one dimensional cubical
+complexes in :math:`\mathbb{R}`. The number of all cubes in each direction is equal :math:`2n+1`, where :math:`n` is
+the number of maximal cubes in the considered direction. Let us consider a cube at the position :math:`k` in the
+bitmap.
+Knowing the sizes of the bitmap, by a series of modulo operation, we can determine which elementary intervals are
+present in the product that gives the cube :math:`C`. In a similar way, we can compute boundary and the coboundary of
+each cube. Further details can be found in the literature.
+
+Input Format.
+-------------
+
+In the current implantation, filtration is given at the maximal cubes, and it is then extended by the lower star
+filtration to all cubes. There are a number of constructors that can be used to construct cubical complex by users
+who want to use the code directly. They can be found in the :doc:`cubical_complex_ref`.
+Currently one input from a text file is used. It uses a format used already in
+`Perseus software <http://www.sas.upenn.edu/~vnanda/perseus/>`_ by Vidit Nanda.
+Below we are providing a description of the format. The first line contains a number d begin the dimension of the
+bitmap (2 in the example below). Next d lines are the numbers of top dimensional cubes in each dimensions (3 and 3
+in the example below). Next, in lexicographical order, the filtration of top dimensional cubes is given (1 4 6 8
+20 4 7 6 5 in the example below).
+
+.. figure::
+    img/exampleBitmap.png
+    :alt: Example of a input data.
+    :figclass: align-center
+
+    Example of a input data.
+
+The input file for the following complex is:
+
+.. literalinclude:: cubicalcomplexdoc.txt
+
+.. centered:: cubicalcomplexdoc.txt
+
+.. testcode::
+
+    import gudhi
+    cubical_complex = gudhi.CubicalComplex(perseus_file='cubicalcomplexdoc.txt')
+    result_str = 'Cubical complex is of dimension ' + repr(cubical_complex.dimension()) + ' - ' + \
+        repr(cubical_complex.num_simplices()) + ' simplices.'
+    print(result_str)
+
+the program output is:
+
+.. testoutput::
+    
+    Cubical complex is of dimension 2 - 49 simplices.
+
+Periodic boundary conditions.
+-----------------------------
+
+Often one would like to impose periodic boundary conditions to the cubical complex (cf.
+:doc:`periodic_cubical_complex_ref`).
+Let :math:`I_1\times ... \times I_n` be a box that is decomposed with a cubical complex :math:`\mathcal{K}`.
+Imposing periodic boundary conditions in the direction i, means that the left and the right side of a complex
+:math:`\mathcal{K}` are considered the same. In particular, if for a bitmap :math:`\mathcal{K}` periodic boundary
+conditions are imposed in all directions, then complex :math:`\mathcal{K}` became n-dimensional torus. One can use
+various constructors from the file Bitmap_cubical_complex_periodic_boundary_conditions_base.h to construct cubical
+complex with periodic boundary conditions. One can also use Perseus style input files. To indicate periodic boundary
+conditions in a given direction, then number of top dimensional cells in this direction have to be multiplied by -1.
+For instance:
+
+.. literalinclude:: periodiccubicalcomplexdoc.txt
+
+.. centered:: periodiccubicalcomplexdoc.txt
+
+Indicate that we have imposed periodic boundary conditions in the direction x, but not in the direction y.
+
+.. testcode::
+
+    import gudhi
+    periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='periodiccubicalcomplexdoc.txt')
+    result_str = 'Periodic cubical complex is of dimension ' + repr(periodic_cc.dimension()) + ' - ' + \
+        repr(periodic_cc.num_simplices()) + ' simplices.'
+    print(result_str)
+
+the program output is:
+
+.. testoutput::
+    
+    Periodic cubical complex is of dimension 2 - 42 simplices.
+
+Examples.
+---------
+
+End user programs are available in cython/example/ folder.
+
+Bibliography
+************
+
+.. bibliography:: bibliography.bib
+   :filter: docnames
+   :style: unsrt
diff --git a/src/cython/doc/euclidean_strong_witness_complex_ref.rst b/src/cython/doc/euclidean_strong_witness_complex_ref.rst
new file mode 100644
index 00000000..bebf0f9a
--- /dev/null
+++ b/src/cython/doc/euclidean_strong_witness_complex_ref.rst
@@ -0,0 +1,10 @@
+=================================================
+Euclidean strong witness complex reference manual
+=================================================
+
+.. autoclass:: gudhi.EuclideanStrongWitnessComplex
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+   .. automethod:: gudhi.EuclideanStrongWitnessComplex.__init__
diff --git a/src/cython/doc/euclidean_witness_complex_ref.rst b/src/cython/doc/euclidean_witness_complex_ref.rst
new file mode 100644
index 00000000..29b8806f
--- /dev/null
+++ b/src/cython/doc/euclidean_witness_complex_ref.rst
@@ -0,0 +1,10 @@
+==========================================
+Euclidean witness complex reference manual
+==========================================
+
+.. autoclass:: gudhi.EuclideanWitnessComplex
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+   .. automethod:: gudhi.EuclideanWitnessComplex.__init__
diff --git a/src/cython/doc/examples.rst b/src/cython/doc/examples.rst
new file mode 100644
index 00000000..a89e0596
--- /dev/null
+++ b/src/cython/doc/examples.rst
@@ -0,0 +1,4 @@
+Examples
+########
+
+.. include:: examples.inc
diff --git a/src/cython/doc/generate_examples.py b/src/cython/doc/generate_examples.py
new file mode 100755
index 00000000..d64d506c
--- /dev/null
+++ b/src/cython/doc/generate_examples.py
@@ -0,0 +1,43 @@
+#!/usr/bin/env python
+
+from os import listdir
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2017 INRIA"
+__license__ = "GPL v3"
+
+"""
+generate_examples.py generates examples.inc to be included in examples.rst.
+Refer to Makefile and make.bat to see if it is correctly launched.
+"""
+
+output_file = open('examples.inc','w')
+
+output_file.write('.. only:: builder_html\n\n')
+
+for file in listdir('../example/'):
+    output_file.write("    * :download:`" + file + " <../example/" + file + ">`\n")
+
+output_file.close()
diff --git a/src/cython/doc/img/graphical_tools_representation.png b/src/cython/doc/img/graphical_tools_representation.png
new file mode 100644
index 00000000..9759f7ba
--- /dev/null
+++ b/src/cython/doc/img/graphical_tools_representation.png
diff --git a/src/cython/doc/index.rst b/src/cython/doc/index.rst
new file mode 100644
index 00000000..fca63d65
--- /dev/null
+++ b/src/cython/doc/index.rst
@@ -0,0 +1,87 @@
+GUDHI documentation
+###################
+
+.. image:: img/Gudhi_banner.png
+   :align: center
+
+Introduction
+************
+
+The Gudhi library (Geometry Understanding in Higher Dimensions) is a generic
+open source `C++ library <http://gudhi.gforge.inria.fr/doc/latest/>`_, with a
+`Cython interface <http://gudhi.gforge.inria.fr/cython/latest/>`_, for
+Computational Topology and Topological Data Analysis
+(`TDA <https://en.wikipedia.org/wiki/Topological_data_analysis>`_).
+The GUDHI library intends to help the development of new algorithmic solutions
+in TDA and their transfer to applications. It provides robust, efficient,
+flexible and easy to use implementations of state-of-the-art algorithms and
+data structures.
+
+The current release of the GUDHI library includes:
+
+* Data structures to represent, construct and manipulate simplicial complexes.
+* Algorithms to compute persistent homology and multi-field persistent homology.
+* Simplication of simplicial complexes by edge contraction.
+
+All data-structures are generic and several of their aspects can be
+parameterized via template classes. We refer to :cite:`gudhilibrary_ICMS14`
+for a detailed description of the design of the library.
+
+Data structures
+***************
+
+Alpha complex
+=============
+
+.. include:: alpha_complex_sum.rst
+
+Cubical complex
+===============
+
+.. include:: cubical_complex_sum.rst
+
+Rips complex
+============
+
+.. include:: rips_complex_sum.rst
+
+Simplex tree
+============
+
+.. include:: simplex_tree_sum.rst
+
+Tangential complex
+==================
+
+.. include:: tangential_complex_sum.rst
+
+Witness complex
+===============
+
+.. include:: witness_complex_sum.rst
+
+
+Toolbox
+*******
+
+Bottleneck distance
+===================
+
+.. include:: bottleneck_distance_sum.rst
+
+Persistence cohomology
+======================
+
+.. include:: persistent_cohomology_sum.rst
+
+Persistence graphical tools
+===========================
+
+.. include:: persistence_graphical_tools_sum.rst
+
+Bibliography
+************
+
+.. bibliography:: bibliography.bib
+   :filter: docnames
+   :style: unsrt
diff --git a/src/cython/doc/installation.rst b/src/cython/doc/installation.rst
new file mode 100644
index 00000000..e7d8c210
--- /dev/null
+++ b/src/cython/doc/installation.rst
@@ -0,0 +1,171 @@
+Installation
+############
+
+Compiling
+*********
+
+The library uses c++11 and requires `Boost <http://www.boost.org/>`_ with version
+1.48.0 or more recent. It is a multi-platform library and compiles on Linux,
+Mac OSX and Visual Studio 2015.
+It also requires cmake to generate makefiles, and cython to compile the
+library.
+
+GUDHI Cythonization
+===================
+
+To build the GUDHI cython module, run the following commands in a terminal:
+
+.. code-block:: bash
+
+    cd /path-to-gudhi/
+    mkdir build
+    cd build/
+    cmake ..
+    make cython
+
+A list of examples is available here.
+
+Test suites
+===========
+
+To test your build, `py.test <http://doc.pytest.org>`_ is required. Run the
+following command in a terminal:
+
+.. code-block:: bash
+
+    cd /path-to-gudhi/build/src/cython
+    # For windows, you have to set PYTHONPATH environment variable
+    export PYTHONPATH='$PYTHONPATH:/path-to-gudhi/build/src/cython'
+    py.test
+
+Documentation
+=============
+
+To build the documentation, `sphinx-doc <http://http://www.sphinx-doc.org>`_ is
+required. Please refer to *conf.py* file to see which
+`sphinx-doc <http://http://www.sphinx-doc.org>`_ modules are required to
+generate the documentation. Run the following commands in a terminal:
+
+.. code-block:: bash
+
+    make sphinx
+
+Optional third-party library
+****************************
+
+CGAL
+====
+
+The :doc:`Alpha complex </alpha_complex_user>`,
+:doc:`Tangential complex </tangential_complex_user>` and
+:doc:`Witness complex </witness_complex_user>` data structures, and
+:doc:`Bottleneck distance </bottleneck_distance_user>` requires CGAL, which is a
+C++ library which provides easy access to efficient and reliable geometric
+algorithms.
+
+Having CGAL version 4.6.0 or higher installed is recommended. The procedure to
+install this library according to your operating system is detailed
+`here <http://doc.cgal.org/latest/Manual/installation.html>`_.
+
+The following examples require the Computational Geometry Algorithms Library:
+
+.. only:: builder_html
+
+    * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>`
+    * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>`
+
+The following example requires CGAL version ≥ 4.7.0:
+
+.. only:: builder_html
+
+    * :download:`alpha_complex_diagram_persistence_from_off_file_example.py <../example/alpha_complex_diagram_persistence_from_off_file_example.py>`
+    * :download:`alpha_complex_from_points_example.py <../example/alpha_complex_from_points_example.py>`
+
+The following example requires CGAL version ≥ 4.8.0:
+
+.. only:: builder_html
+
+    * :download:`bottleneck_basic_example.py <../example/bottleneck_basic_example.py>`
+    * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>`
+
+Eigen3
+======
+
+The :doc:`Alpha complex </alpha_complex_user>`,
+:doc:`Tangential complex </tangential_complex_user>` and
+:doc:`Witness complex </witness_complex_user>` data structures and few
+examples requires `Eigen3 <http://eigen.tuxfamily.org/>`_, a C++ template
+library for linear algebra: matrices, vectors, numerical solvers, and related
+algorithms.
+
+The following examples require the `Eigen3 <http://eigen.tuxfamily.org/>`_:
+
+.. only:: builder_html
+
+    * :download:`alpha_complex_diagram_persistence_from_off_file_example.py <../example/alpha_complex_diagram_persistence_from_off_file_example.py>`
+    * :download:`alpha_complex_from_points_example.py <../example/alpha_complex_from_points_example.py>`
+    * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>`
+    * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>`
+    * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>`
+
+Matplotlib
+==========
+
+The :doc:`persistence graphical tools </persistence_graphical_tools_user>`
+module requires `Matplotlib <http://matplotlib.org>`_, a Python 2D plotting
+library which produces publication quality figures in a variety of hardcopy
+formats and interactive environments across platforms.
+
+The following examples require the `Matplotlib <http://matplotlib.org>`_:
+
+.. only:: builder_html
+
+    * :download:`alpha_complex_diagram_persistence_from_off_file_example.py <../example/alpha_complex_diagram_persistence_from_off_file_example.py>`
+    * :download:`gudhi_graphical_tools_example.py <../example/gudhi_graphical_tools_example.py>`
+    * :download:`periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py <../example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py>`
+    * :download:`rips_complex_diagram_persistence_from_off_file_example.py <../example/rips_complex_diagram_persistence_from_off_file_example.py>`
+    * :download:`rips_persistence_diagram.py <../example/rips_persistence_diagram.py>`
+    * :download:`rips_complex_diagram_persistence_from_distance_matrix_file_example.py <../example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py>`
+    * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>`
+    * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>`
+    * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>`
+
+Numpy
+=====
+
+The :doc:`persistence graphical tools </persistence_graphical_tools_user>`
+module requires `NumPy <http://numpy.org>`_, a fundamental package for
+scientific computing with Python.
+
+The following examples require the `NumPy <http://numpy.org>`_:
+
+.. only:: builder_html
+
+    * :download:`alpha_complex_diagram_persistence_from_off_file_example.py <../example/alpha_complex_diagram_persistence_from_off_file_example.py>`
+    * :download:`gudhi_graphical_tools_example.py <../example/gudhi_graphical_tools_example.py>`
+    * :download:`periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py <../example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py>`
+    * :download:`rips_complex_diagram_persistence_from_off_file_example.py <../example/rips_complex_diagram_persistence_from_off_file_example.py>`
+    * :download:`rips_persistence_diagram.py <../example/rips_persistence_diagram.py>`
+    * :download:`rips_complex_diagram_persistence_from_distance_matrix_file_example.py <../example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py>`
+    * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>`
+    * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>`
+    * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>`
+
+Threading Building Blocks
+=========================
+
+`Intel® TBB <https://www.threadingbuildingblocks.org/>`_ lets you easily write
+parallel C++ programs that take full advantage of multicore performance, that
+are portable and composable, and that have future-proof scalability.
+
+Having Intel® TBB installed is recommended to parallelize and accelerate some
+GUDHI computations.
+
+Bug reports and contributions
+*****************************
+
+Please help us improving the quality of the GUDHI library. You may report bugs or suggestions to:
+
+    Contact: gudhi-users@lists.gforge.inria.fr
+
+GUDHI is open to external contributions. If you want to join our development team, please contact us.
diff --git a/src/cython/doc/make.bat b/src/cython/doc/make.bat
new file mode 100644
index 00000000..ba009a90
--- /dev/null
+++ b/src/cython/doc/make.bat
@@ -0,0 +1,246 @@
+@ECHO OFF

+

+REM Command file for Sphinx documentation

+

+if "%SPHINXBUILD%" == "" (

+	set SPHINXBUILD=sphinx-build

+)

+set BUILDDIR=_build

+set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% .

+set I18NSPHINXOPTS=%SPHINXOPTS% .

+if NOT "%PAPER%" == "" (

+	set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%

+	set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS%

+)

+

+if "%1" == "" goto help

+

+if "%1" == "help" (

+	:help

+	echo.Please use `make ^<target^>` where ^<target^> is one of

+	echo.  html       to make standalone HTML files

+	echo.  dirhtml    to make HTML files named index.html in directories

+	echo.  singlehtml to make a single large HTML file

+	echo.  pickle     to make pickle files

+	echo.  json       to make JSON files

+	echo.  htmlhelp   to make HTML files and a HTML help project

+	echo.  qthelp     to make HTML files and a qthelp project

+	echo.  devhelp    to make HTML files and a Devhelp project

+	echo.  epub       to make an epub

+	echo.  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter

+	echo.  text       to make text files

+	echo.  man        to make manual pages

+	echo.  texinfo    to make Texinfo files

+	echo.  gettext    to make PO message catalogs

+	echo.  changes    to make an overview over all changed/added/deprecated items

+	echo.  xml        to make Docutils-native XML files

+	echo.  pseudoxml  to make pseudoxml-XML files for display purposes

+	echo.  linkcheck  to check all external links for integrity

+	echo.  doctest    to run all doctests embedded in the documentation if enabled

+	goto end

+)

+

+if "%1" == "clean" (

+	del examples.inc

+	for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i

+	del /q /s %BUILDDIR%\*

+	goto end

+)

+

+

+%SPHINXBUILD% 2> nul

+if errorlevel 9009 (

+	echo.

+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx

+	echo.installed, then set the SPHINXBUILD environment variable to point

+	echo.to the full path of the 'sphinx-build' executable. Alternatively you

+	echo.may add the Sphinx directory to PATH.

+	echo.

+	echo.If you don't have Sphinx installed, grab it from

+	echo.http://sphinx-doc.org/

+	exit /b 1

+)

+

+:: GUDHI specific : Examples.inc is generated with generate_examples.py (and deleted on clean)

+

+if "%1" == "html" (

+	generate_examples.py

+	%SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished. The HTML pages are in %BUILDDIR%/html.

+	goto end

+)

+

+if "%1" == "dirhtml" (

+	%SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml.

+	goto end

+)

+

+if "%1" == "singlehtml" (

+	%SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml.

+	goto end

+)

+

+if "%1" == "pickle" (

+	%SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished; now you can process the pickle files.

+	goto end

+)

+

+if "%1" == "json" (

+	%SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished; now you can process the JSON files.

+	goto end

+)

+

+if "%1" == "htmlhelp" (

+	%SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished; now you can run HTML Help Workshop with the ^

+.hhp project file in %BUILDDIR%/htmlhelp.

+	goto end

+)

+

+if "%1" == "qthelp" (

+	%SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished; now you can run "qcollectiongenerator" with the ^

+.qhcp project file in %BUILDDIR%/qthelp, like this:

+	echo.^> qcollectiongenerator %BUILDDIR%\qthelp\pouet.qhcp

+	echo.To view the help file:

+	echo.^> assistant -collectionFile %BUILDDIR%\qthelp\pouet.ghc

+	goto end

+)

+

+if "%1" == "devhelp" (

+	%SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished.

+	goto end

+)

+

+if "%1" == "epub" (

+	%SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished. The epub file is in %BUILDDIR%/epub.

+	goto end

+)

+

+if "%1" == "latex" (

+	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished; the LaTeX files are in %BUILDDIR%/latex.

+	goto end

+)

+

+if "%1" == "latexpdf" (

+	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex

+	cd %BUILDDIR%/latex

+	make all-pdf

+	cd %BUILDDIR%/..

+	echo.

+	echo.Build finished; the PDF files are in %BUILDDIR%/latex.

+	goto end

+)

+

+if "%1" == "latexpdfja" (

+	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex

+	cd %BUILDDIR%/latex

+	make all-pdf-ja

+	cd %BUILDDIR%/..

+	echo.

+	echo.Build finished; the PDF files are in %BUILDDIR%/latex.

+	goto end

+)

+

+if "%1" == "text" (

+	%SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished. The text files are in %BUILDDIR%/text.

+	goto end

+)

+

+if "%1" == "man" (

+	%SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished. The manual pages are in %BUILDDIR%/man.

+	goto end

+)

+

+if "%1" == "texinfo" (

+	%SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo.

+	goto end

+)

+

+if "%1" == "gettext" (

+	%SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished. The message catalogs are in %BUILDDIR%/locale.

+	goto end

+)

+

+if "%1" == "changes" (

+	%SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.The overview file is in %BUILDDIR%/changes.

+	goto end

+)

+

+if "%1" == "linkcheck" (

+	%SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Link check complete; look for any errors in the above output ^

+or in %BUILDDIR%/linkcheck/output.txt.

+	goto end

+)

+

+if "%1" == "doctest" (

+	%SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Testing of doctests in the sources finished, look at the ^

+results in %BUILDDIR%/doctest/output.txt.

+	goto end

+)

+

+if "%1" == "xml" (

+	%SPHINXBUILD% -b xml %ALLSPHINXOPTS% %BUILDDIR%/xml

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished. The XML files are in %BUILDDIR%/xml.

+	goto end

+)

+

+if "%1" == "pseudoxml" (

+	%SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml.

+	goto end

+)

+

+:end

diff --git a/src/cython/doc/periodic_cubical_complex_ref.rst b/src/cython/doc/periodic_cubical_complex_ref.rst
new file mode 100644
index 00000000..c6190a1b
--- /dev/null
+++ b/src/cython/doc/periodic_cubical_complex_ref.rst
@@ -0,0 +1,9 @@
+Periodic cubical complex reference manual
+#########################################
+
+.. autoclass:: gudhi.PeriodicCubicalComplex
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+   .. automethod:: gudhi.PeriodicCubicalComplex.__init__
diff --git a/src/cython/doc/persistence_graphical_tools_ref.rst b/src/cython/doc/persistence_graphical_tools_ref.rst
new file mode 100644
index 00000000..27c2f68a
--- /dev/null
+++ b/src/cython/doc/persistence_graphical_tools_ref.rst
@@ -0,0 +1,8 @@
+============================================
+Persistence graphical tools reference manual
+============================================
+
+.. autofunction:: gudhi.__min_birth_max_death
+.. autofunction:: gudhi.show_palette_values
+.. autofunction:: gudhi.plot_persistence_barcode
+.. autofunction:: gudhi.plot_persistence_diagram
diff --git a/src/cython/doc/persistence_graphical_tools_sum.rst b/src/cython/doc/persistence_graphical_tools_sum.rst
new file mode 100644
index 00000000..d602daa7
--- /dev/null
+++ b/src/cython/doc/persistence_graphical_tools_sum.rst
@@ -0,0 +1,12 @@
+=================================================================  ===================================  ===================================
+:Author: Vincent Rouvreau                                          :Introduced in: GUDHI 2.0.0          :Copyright: GPL v3
+:Requires: Matplotlib                                              Numpy
+=================================================================  ===================================  ===================================
+
++-----------------------------------------------------------------+-----------------------------------------------------------------------+
+| .. figure::                                                     | These graphical tools comes on top of persistence results and allows  |
+|      img/graphical_tools_representation.png                     | the user to build easily barcode and persistence diagram.             |
+|                                                                 |                                                                       |
++-----------------------------------------------------------------+-----------------------------------------------------------------------+
+|  :doc:`persistence_graphical_tools_user`                        | :doc:`persistence_graphical_tools_ref`                                |
++-----------------------------------------------------------------+-----------------------------------------------------------------------+
diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst
new file mode 100644
index 00000000..f713e971
--- /dev/null
+++ b/src/cython/doc/persistence_graphical_tools_user.rst
@@ -0,0 +1,67 @@
+=======================================
+Persistence graphical tools user manual
+=======================================
+Definition
+----------
+.. include:: persistence_graphical_tools_sum.rst
+
+
+Show palette values
+-------------------
+
+This function is useful to show the color palette values of dimension:
+
+
+.. testcode::
+
+    import gudhi
+    gudhi.show_palette_values(alpha=1.0)
+
+.. plot::
+
+    import gudhi
+    gudhi.show_palette_values(alpha=1.0)
+
+Show persistence as a barcode
+-----------------------------
+
+This function can display the persistence result as a barcode:
+
+.. testcode::
+
+    import gudhi
+    
+    periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt')
+    diag = periodic_cc.persistence()
+    gudhi.plot_persistence_barcode(diag)
+
+.. plot::
+
+    import gudhi
+
+    periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt')
+    diag = periodic_cc.persistence()
+    gudhi.plot_persistence_barcode(diag)
+
+Show persistence as a diagram
+-----------------------------
+
+This function can display the persistence result as a diagram:
+
+.. testcode::
+
+    import gudhi
+    
+    rips_complex = gudhi.RipsComplex(off_file='tore3D_300.off', max_edge_length=2.0)
+    simplex_tree = rips_complex.create_simplex_tree(max_dimension=3)
+    diag = simplex_tree.persistence()
+    gudhi.plot_persistence_diagram(diag)
+
+.. plot::
+
+    import gudhi
+
+    rips_complex = gudhi.RipsComplex(off_file='tore3D_300.off', max_edge_length=2.0)
+    simplex_tree = rips_complex.create_simplex_tree(max_dimension=3)
+    diag = simplex_tree.persistence()
+    gudhi.plot_persistence_diagram(diag)
diff --git a/src/cython/doc/persistent_cohomology_sum.rst b/src/cython/doc/persistent_cohomology_sum.rst
new file mode 100644
index 00000000..d1f79cb4
--- /dev/null
+++ b/src/cython/doc/persistent_cohomology_sum.rst
@@ -0,0 +1,27 @@
+=================================================================  ===================================  ===================================
+:Author: Clément Maria                                             :Introduced in: GUDHI 2.0.0          :Copyright: GPL v3
+=================================================================  ===================================  ===================================
+
++-----------------------------------------------------------------+-----------------------------------------------------------------------+
+| .. figure::                                                     | The theory of homology consists in attaching to a topological space   |
+|      img/3DTorus_poch.png                                       | a sequence of (homology) groups, capturing global topological         |
+|      :figclass: align-center                                    | features like connected components, holes, cavities, etc. Persistent  |
+|                                                                 | homology studies the evolution -- birth, life and death -- of these   |
+|      Rips Persistent Cohomology on a 3D                         | features when the topological space is changing. Consequently, the    |
+|      Torus                                                      | theory is essentially composed of three elements: topological spaces, |
+|                                                                 | their homology groups and an evolution scheme.                        |
+|                                                                 |                                                                       |
+|                                                                 | Computation of persistent cohomology using the algorithm of           |
+|                                                                 | :cite:`DBLP:journals/dcg/SilvaMV11` and                               |
+|                                                                 | :cite:`DBLP:journals/corr/abs-1208-5018` and the Compressed           |
+|                                                                 | Annotation Matrix implementation of                                   |
+|                                                                 | :cite:`DBLP:conf/esa/BoissonnatDM13`.                                 |
+|                                                                 |                                                                       |
++-----------------------------------------------------------------+-----------------------------------------------------------------------+
+|  :doc:`persistent_cohomology_user`                              | Please refer to each data structure that contains persistence         |
+|                                                                 | feature for reference:                                                |
+|                                                                 |                                                                       |
+|                                                                 | * :doc:`simplex_tree_ref`                                             |
+|                                                                 | * :doc:`cubical_complex_ref`                                          |
+|                                                                 | * :doc:`periodic_cubical_complex_ref`                                 |
++-----------------------------------------------------------------+-----------------------------------------------------------------------+
diff --git a/src/cython/doc/persistent_cohomology_user.rst b/src/cython/doc/persistent_cohomology_user.rst
new file mode 100644
index 00000000..69be3b86
--- /dev/null
+++ b/src/cython/doc/persistent_cohomology_user.rst
@@ -0,0 +1,115 @@
+=================================
+Persistent cohomology user manual
+=================================
+Definition
+----------
+=====================================  =====================================  =====================================
+:Author: Clément Maria                 :Introduced in: GUDHI PYTHON 2.0.0     :Copyright: GPL v3
+=====================================  =====================================  =====================================
+
++---------------------------------------------+----------------------------------------------------------------------+
+|  :doc:`persistent_cohomology_user`          | Please refer to each data structure that contains persistence        |
+|                                             | feature for reference:                                               |
+|                                             |                                                                      |
+|                                             | * :doc:`simplex_tree_ref`                                            |
++---------------------------------------------+----------------------------------------------------------------------+
+
+
+Computation of persistent cohomology using the algorithm of :cite:`DBLP:journals/dcg/SilvaMV11` and
+:cite:`DBLP:journals/corr/abs-1208-5018` and the Compressed Annotation Matrix implementation of
+:cite:`DBLP:conf/esa/BoissonnatDM13`.
+     
+The theory of homology consists in attaching to a topological space a sequence of (homology) groups, capturing global
+topological features like connected components, holes, cavities, etc. Persistent homology studies the evolution --
+birth, life and death -- of these features when the topological space is changing. Consequently, the theory is
+essentially composed of three elements:
+
+* topological spaces
+* their homology groups
+* an evolution scheme.
+
+Topological Spaces
+------------------
+
+Topological spaces are represented by simplicial complexes.
+Let :math:`V = \{1, \cdots ,|V|\}` be a set of *vertices*.
+A *simplex* :math:`\sigma` is a subset of vertices :math:`\sigma \subseteq V`.
+A *simplicial complex* :math:`\mathbf{K}` on :math:`V` is a collection of simplices :math:`\{\sigma\}`,
+:math:`\sigma \subseteq V`, such that :math:`\tau \subseteq \sigma \in \mathbf{K} \Rightarrow \tau \in \mathbf{K}`.
+The dimension :math:`n=|\sigma|-1` of :math:`\sigma` is its number of elements minus 1.
+A *filtration* of a simplicial complex is a function :math:`f:\mathbf{K} \rightarrow \mathbb{R}` satisfying
+:math:`f(\tau)\leq f(\sigma)` whenever :math:`\tau \subseteq \sigma`.
+
+Homology
+--------
+
+For a ring :math:`\mathcal{R}`, the group of *n-chains*, denoted :math:`\mathbf{C}_n(\mathbf{K},\mathcal{R})`, of
+:math:`\mathbf{K}` is the group of formal sums of n-simplices with :math:`\mathcal{R}` coefficients. The
+*boundary operator* is a linear operator
+:math:`\partial_n: \mathbf{C}_n(\mathbf{K},\mathcal{R}) \rightarrow \mathbf{C}_{n-1}(\mathbf{K},\mathcal{R})`
+such that :math:`\partial_n \sigma = \partial_n [v_0, \cdots , v_n] = \sum_{i=0}^n (-1)^{i}[v_0,\cdots ,\widehat{v_i}, \cdots,v_n]`,
+where :math:`\widehat{v_i}` means :math:`v_i` is omitted from the list. The chain groups form a sequence:
+
+.. math::
+
+    \cdots \ \ \mathbf{C}_n(\mathbf{K},\mathcal{R}) \xrightarrow{\ \partial_n\ }
+    \mathbf{C}_{n-1}(\mathbf{K},\mathcal{R}) \xrightarrow{\partial_{n-1}} \cdots \xrightarrow{\ \partial_2 \ }
+    \mathbf{C}_1(\mathbf{K},\mathcal{R}) \xrightarrow{\ \partial_1 \ }  \mathbf{C}_0(\mathbf{K},\mathcal{R})
+
+of finitely many groups :math:`\mathbf{C}_n(\mathbf{K},\mathcal{R})` and homomorphisms :math:`\partial_n`, indexed by
+the dimension :math:`n \geq 0`. The boundary operators satisfy the property :math:`\partial_n \circ \partial_{n+1}=0`
+for every :math:`n > 0` and we define the homology groups:
+
+.. math::
+
+    \mathbf{H}_n(\mathbf{K},\mathcal{R}) = \ker \partial_n / \mathrm{im} \  \partial_{n+1}
+
+We refer to :cite:`Munkres-elementsalgtop1984` for an introduction to homology
+theory and to :cite:`DBLP:books/daglib/0025666` for an introduction to persistent homology.
+
+Indexing Scheme
+---------------
+
+"Changing" a simplicial complex consists in applying a simplicial map. An *indexing scheme* is a directed graph
+together with a traversal order, such that two consecutive nodes in the graph are connected by an arrow (either forward
+or backward).
+The nodes represent simplicial complexes and the directed edges simplicial maps.
+
+From the computational point of view, there are two types of indexing schemes of interest in persistent homology:
+    
+* linear ones
+  :math:`\bullet \longrightarrow \bullet \longrightarrow \cdots \longrightarrow \bullet \longrightarrow \bullet`
+  in persistent homology :cite:`DBLP:journals/dcg/ZomorodianC05`,
+* zigzag ones
+  :math:`\bullet \longrightarrow \bullet \longleftarrow \cdots \longrightarrow \bullet \longleftarrow \bullet`
+  in zigzag persistent homology :cite:`DBLP:journals/focm/CarlssonS10`.
+  
+These indexing schemes have a natural left-to-right traversal order, and we describe them with ranges and iterators.
+In the current release of the Gudhi library, only the linear case is implemented.
+
+In the following, we consider the case where the indexing scheme is induced by a filtration.
+
+Ordering the simplices by increasing filtration values (breaking ties so as a simplex appears after its subsimplices of
+same filtration value) provides an indexing scheme.
+
+Examples
+--------
+
+We provide several example files: run these examples with -h for details on their use.
+
+.. only:: builder_html
+
+    * :download:`alpha_complex_diagram_persistence_from_off_file_example.py <../example/alpha_complex_diagram_persistence_from_off_file_example.py>`
+    * :download:`periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py <../example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py>`
+    * :download:`rips_complex_diagram_persistence_from_off_file_example.py <../example/rips_complex_diagram_persistence_from_off_file_example.py>`
+    * :download:`rips_persistence_diagram.py <../example/rips_persistence_diagram.py>`
+    * :download:`rips_complex_diagram_persistence_from_distance_matrix_file_example.py <../example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py>`
+    * :download:`random_cubical_complex_persistence_example.py <../example/random_cubical_complex_persistence_example.py>`
+    * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>`
+
+Bibliography
+************
+
+.. bibliography:: bibliography.bib
+   :filter: docnames
+   :style: unsrt
diff --git a/src/cython/doc/pyplots/barcode_persistence.py b/src/cython/doc/pyplots/barcode_persistence.py
new file mode 100755
index 00000000..c06ac5a7
--- /dev/null
+++ b/src/cython/doc/pyplots/barcode_persistence.py
@@ -0,0 +1,5 @@
+import gudhi
+
+periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='../3d_torus.txt')
+diag = periodic_cc.persistence()
+gudhi.plot_persistence_barcode(diag)
diff --git a/src/cython/doc/pyplots/diagram_persistence.py b/src/cython/doc/pyplots/diagram_persistence.py
new file mode 100755
index 00000000..b4714fe3
--- /dev/null
+++ b/src/cython/doc/pyplots/diagram_persistence.py
@@ -0,0 +1,5 @@
+import gudhi
+
+alpha_complex = gudhi.AlphaComplex(off_file='../tore3D_300.off')
+diag = alpha_complex.persistence()
+gudhi.plot_persistence_diagram(diag)
diff --git a/src/cython/doc/pyplots/show_palette_values.py b/src/cython/doc/pyplots/show_palette_values.py
new file mode 100755
index 00000000..e72a55fd
--- /dev/null
+++ b/src/cython/doc/pyplots/show_palette_values.py
@@ -0,0 +1,2 @@
+import gudhi
+gudhi.show_palette_values(alpha=1.0)
diff --git a/src/cython/doc/rips_complex_ref.rst b/src/cython/doc/rips_complex_ref.rst
new file mode 100644
index 00000000..b17dc4e0
--- /dev/null
+++ b/src/cython/doc/rips_complex_ref.rst
@@ -0,0 +1,10 @@
+=============================
+Rips complex reference manual
+=============================
+
+.. autoclass:: gudhi.RipsComplex
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+   .. automethod:: gudhi.RipsComplex.__init__
diff --git a/src/cython/doc/rips_complex_sum.rst b/src/cython/doc/rips_complex_sum.rst
new file mode 100644
index 00000000..2b65fc19
--- /dev/null
+++ b/src/cython/doc/rips_complex_sum.rst
@@ -0,0 +1,17 @@
+=================================================================  ===================================  ===================================
+:Author: Clément Maria, Pawel Dlotko, Vincent Rouvreau             :Introduced in: GUDHI 2.0.0          :Copyright: GPL v3
+=================================================================  ===================================  ===================================
+
++----------------------------------------------------------------+------------------------------------------------------------------------+
+| .. figure::                                                    | Rips complex is a simplicial complex constructed from a one skeleton   |
+|      img/rips_complex_representation.png                       | graph.                                                                 |
+|      :figclass: align-center                                   |                                                                        |
+|                                                                | The filtration value of each edge is computed from a user-given        |
+|      Rips complex representation                               | distance function and is inserted until a user-given threshold         |
+|                                                                | value.                                                                 |
+|                                                                |                                                                        |
+|                                                                | This complex can be built from a point cloud and a distance function,  |
+|                                                                | or from a distance matrix.                                             |
++----------------------------------------------------------------+------------------------------------------------------------------------+
+| :doc:`rips_complex_user`                                       | :doc:`rips_complex_ref`                                                |
++----------------------------------------------------------------+------------------------------------------------------------------------+
diff --git a/src/cython/doc/rips_complex_user.rst b/src/cython/doc/rips_complex_user.rst
new file mode 100644
index 00000000..027c3bf7
--- /dev/null
+++ b/src/cython/doc/rips_complex_user.rst
@@ -0,0 +1,237 @@
+=========================
+Rips complex user manual
+=========================
+Definition
+----------
+
+=======================================================  =====================================  =====================================
+:Authors: Clément Maria, Pawel Dlotko, Vincent Rouvreau  :Introduced in: GUDHI 2.0.0            :Copyright: GPL v3
+=======================================================  =====================================  =====================================
+
++-------------------------------------------+----------------------------------------------------------------------+
+| :doc:`rips_complex_user`                  | :doc:`rips_complex_ref`                                              |
++-------------------------------------------+----------------------------------------------------------------------+
+
+`Rips complex <https://en.wikipedia.org/wiki/Vietoris%E2%80%93Rips_complex>`_ is a one skeleton graph that allows to
+construct a simplicial complex 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).
+
+.. figure::
+    img/rips_complex_representation.png
+    :align: center
+
+    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 :math:`max(filtration(4,5), filtration(4,6), filtration(5,6))`. And so on for simplex (0,1,2,3).
+
+If the Rips_complex interfaces are not detailed enough for your need, please refer to rips_persistence_step_by_step.cpp
+example, where the graph construction over the Simplex_tree is more detailed.
+
+Point cloud
+-----------
+
+Example from a point cloud
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+This example builds the one skeleton graph from the given points, and max_edge_length value.
+Then it creates a :doc:`Simplex_tree <simplex_tree_ref>` with it.
+
+Finally, it is asked to display information about the simplicial complex.
+
+.. testcode::
+
+    import gudhi
+    rips_complex = gudhi.RipsComplex(points=[[1, 1], [7, 0], [4, 6], [9, 6], [0, 14], [2, 19], [9, 17]],
+        max_edge_length=12.0)
+
+    simplex_tree = rips_complex.create_simplex_tree(max_dimension=1)
+    result_str = 'Rips complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \
+        repr(simplex_tree.num_simplices()) + ' simplices - ' + \
+        repr(simplex_tree.num_vertices()) + ' vertices.'
+    print(result_str)
+    for filtered_value in simplex_tree.get_filtered_tree():
+        print(filtered_value)
+
+When launching (Rips maximal distance between 2 points is 12.0, is expanded
+until dimension 1 - one skeleton graph in other words), the output is:
+
+.. testoutput::
+
+    Rips complex is of dimension 1 - 18 simplices - 7 vertices.
+    ([0], 0.0)
+    ([1], 0.0)
+    ([2], 0.0)
+    ([3], 0.0)
+    ([4], 0.0)
+    ([5], 0.0)
+    ([6], 0.0)
+    ([2, 3], 5.0)
+    ([4, 5], 5.385164807134504)
+    ([0, 2], 5.830951894845301)
+    ([0, 1], 6.082762530298219)
+    ([1, 3], 6.324555320336759)
+    ([1, 2], 6.708203932499369)
+    ([5, 6], 7.280109889280518)
+    ([2, 4], 8.94427190999916)
+    ([0, 3], 9.433981132056603)
+    ([4, 6], 9.486832980505138)
+    ([3, 6], 11.0)
+
+Example from OFF file
+^^^^^^^^^^^^^^^^^^^^^
+
+This example builds the :doc:`Rips_complex <rips_complex_ref>` from the given
+points in an OFF file, and max_edge_length value.
+Then it creates a :doc:`Simplex_tree <simplex_tree_ref>` with it.
+
+Finally, it is asked to display information about the Rips complex.
+
+
+.. testcode::
+
+    import gudhi
+    rips_complex = gudhi.RipsComplex(off_file='alphacomplexdoc.off', max_edge_length=12.0)
+    simplex_tree = rips_complex.create_simplex_tree(max_dimension=1)
+    result_str = 'Rips complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \
+        repr(simplex_tree.num_simplices()) + ' simplices - ' + \
+        repr(simplex_tree.num_vertices()) + ' vertices.'
+    print(result_str)
+    for filtered_value in simplex_tree.get_filtered_tree():
+        print(filtered_value)
+
+the program output is:
+
+.. testoutput::
+
+    Rips complex is of dimension 1 - 18 simplices - 7 vertices.
+    ([0], 0.0)
+    ([1], 0.0)
+    ([2], 0.0)
+    ([3], 0.0)
+    ([4], 0.0)
+    ([5], 0.0)
+    ([6], 0.0)
+    ([2, 3], 5.0)
+    ([4, 5], 5.385164807134504)
+    ([0, 2], 5.830951894845301)
+    ([0, 1], 6.082762530298219)
+    ([1, 3], 6.324555320336759)
+    ([1, 2], 6.708203932499369)
+    ([5, 6], 7.280109889280518)
+    ([2, 4], 8.94427190999916)
+    ([0, 3], 9.433981132056603)
+    ([4, 6], 9.486832980505138)
+    ([3, 6], 11.0)
+
+Distance matrix
+---------------
+
+Example from a distance matrix
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+This example builds the one skeleton graph from the given distance matrix, and max_edge_length value.
+Then it creates a :doc:`Simplex_tree <simplex_tree_ref>` with it.
+
+Finally, it is asked to display information about the simplicial complex.
+
+.. testcode::
+
+    import gudhi
+    rips_complex = gudhi.RipsComplex(distance_matrix=[[],
+                                                      [6.0827625303],
+                                                      [5.8309518948, 6.7082039325],
+                                                      [9.4339811321, 6.3245553203, 5],
+                                                      [13.0384048104, 15.6524758425, 8.94427191, 12.0415945788],
+                                                      [18.0277563773, 19.6468827044, 13.152946438, 14.7648230602, 5.3851648071],
+                                                      [17.88854382, 17.1172427686, 12.0830459736, 11, 9.4868329805, 7.2801098893]],
+                                     max_edge_length=12.0)
+
+    simplex_tree = rips_complex.create_simplex_tree(max_dimension=1)
+    result_str = 'Rips complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \
+        repr(simplex_tree.num_simplices()) + ' simplices - ' + \
+        repr(simplex_tree.num_vertices()) + ' vertices.'
+    print(result_str)
+    for filtered_value in simplex_tree.get_filtered_tree():
+        print(filtered_value)
+
+When launching (Rips maximal distance between 2 points is 12.0, is expanded
+until dimension 1 - one skeleton graph in other words), the output is:
+
+.. testoutput::
+
+    Rips complex is of dimension 1 - 18 simplices - 7 vertices.
+    ([0], 0.0)
+    ([1], 0.0)
+    ([2], 0.0)
+    ([3], 0.0)
+    ([4], 0.0)
+    ([5], 0.0)
+    ([6], 0.0)
+    ([2, 3], 5.0)
+    ([4, 5], 5.3851648071)
+    ([0, 2], 5.8309518948)
+    ([0, 1], 6.0827625303)
+    ([1, 3], 6.3245553203)
+    ([1, 2], 6.7082039325)
+    ([5, 6], 7.2801098893)
+    ([2, 4], 8.94427191)
+    ([0, 3], 9.4339811321)
+    ([4, 6], 9.4868329805)
+    ([3, 6], 11.0)
+
+Example from csv file
+^^^^^^^^^^^^^^^^^^^^^
+
+This example builds the :doc:`Rips_complex <rips_complex_ref>` from the given
+points in an OFF file, and max_edge_length value.
+Then it creates a :doc:`Simplex_tree <simplex_tree_ref>` with it.
+
+Finally, it is asked to display information about the Rips complex.
+
+
+.. testcode::
+
+    import gudhi
+    rips_complex = gudhi.RipsComplex(csv_file='full_square_distance_matrix.csv', max_edge_length=12.0)
+    simplex_tree = rips_complex.create_simplex_tree(max_dimension=1)
+    result_str = 'Rips complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \
+        repr(simplex_tree.num_simplices()) + ' simplices - ' + \
+        repr(simplex_tree.num_vertices()) + ' vertices.'
+    print(result_str)
+    for filtered_value in simplex_tree.get_filtered_tree():
+        print(filtered_value)
+
+the program output is:
+
+.. testoutput::
+
+    Rips complex is of dimension 1 - 18 simplices - 7 vertices.
+    ([0], 0.0)
+    ([1], 0.0)
+    ([2], 0.0)
+    ([3], 0.0)
+    ([4], 0.0)
+    ([5], 0.0)
+    ([6], 0.0)
+    ([2, 3], 5.0)
+    ([4, 5], 5.3851648071)
+    ([0, 2], 5.8309518948)
+    ([0, 1], 6.0827625303)
+    ([1, 3], 6.3245553203)
+    ([1, 2], 6.7082039325)
+    ([5, 6], 7.2801098893)
+    ([2, 4], 8.94427191)
+    ([0, 3], 9.4339811321)
+    ([4, 6], 9.4868329805)
+    ([3, 6], 11.0)
diff --git a/src/cython/doc/simplex_tree_ref.rst b/src/cython/doc/simplex_tree_ref.rst
new file mode 100644
index 00000000..6d196843
--- /dev/null
+++ b/src/cython/doc/simplex_tree_ref.rst
@@ -0,0 +1,10 @@
+=============================
+Simplex tree reference manual
+=============================
+
+.. autoclass:: gudhi.SimplexTree
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+   .. automethod:: gudhi.SimplexTree.__init__
diff --git a/src/cython/doc/simplex_tree_sum.rst b/src/cython/doc/simplex_tree_sum.rst
new file mode 100644
index 00000000..3174fb62
--- /dev/null
+++ b/src/cython/doc/simplex_tree_sum.rst
@@ -0,0 +1,14 @@
+=================================================================  ===================================  ===================================
+:Author: Clément Maria                                             :Introduced in: GUDHI 2.0.0          :Copyright: GPL v3
+=================================================================  ===================================  ===================================
+
++----------------------------------------------------------------+------------------------------------------------------------------------+
+| .. figure::                                                    | The simplex tree is an efficient and flexible data structure for       |
+|      img/Simplex_tree_representation.png                       | representing general (filtered) simplicial complexes.                  |
+|      :alt: Simplex tree representation                         |                                                                        |
+|      :figclass: align-center                                   | The data structure is described in                                     |
+|                                                                | :cite:`boissonnatmariasimplextreealgorithmica`                         |
+|      Simplex tree representation                               |                                                                        |
++----------------------------------------------------------------+------------------------------------------------------------------------+
+| :doc:`simplex_tree_user`                                       | :doc:`simplex_tree_ref`                                                |
++----------------------------------------------------------------+------------------------------------------------------------------------+
diff --git a/src/cython/doc/simplex_tree_user.rst b/src/cython/doc/simplex_tree_user.rst
new file mode 100644
index 00000000..6b55c4e7
--- /dev/null
+++ b/src/cython/doc/simplex_tree_user.rst
@@ -0,0 +1,67 @@
+========================
+Simplex tree user manual
+========================
+Definition
+----------
+
+.. include:: simplex_tree_sum.rst
+
+A simplicial complex :math:`\mathbf{K}` on a set of vertices :math:`V = \{1, \cdots ,|V|\}` is a collection of
+simplices :math:`\{\sigma\}`, :math:`\sigma \subseteq V` such that
+:math:`\tau \subseteq \sigma \in \mathbf{K} \rightarrow \tau \in \mathbf{K}`. The dimension :math:`n=|\sigma|-1` of
+:math:`\sigma` is its number of elements minus `1`.
+
+A filtration of a simplicial complex is a function :math:`f:\mathbf{K} \rightarrow \mathbb{R}` satisfying
+:math:`f(\tau)\leq f(\sigma)` whenever :math:`\tau \subseteq \sigma`. Ordering the simplices by increasing filtration
+values (breaking ties so as a simplex appears after its subsimplices of same filtration value) provides an indexing
+scheme.
+
+
+Implementation
+--------------
+
+There are two implementation of complexes. The first on is the Simplex_tree data structure.
+The simplex tree is an efficient and flexible data structure for representing general (filtered) simplicial complexes.
+The data structure is described in :cite`boissonnatmariasimplextreealgorithmica`.
+
+The second one is the Hasse_complex. The Hasse complex is a data structure representing explicitly all co-dimension 1
+incidence relations in a complex. It is consequently faster when accessing the boundary of a simplex, but is less
+compact and harder to construct from scratch.
+
+Example
+-------
+
+.. testcode::
+
+   import gudhi
+   st = gudhi.SimplexTree()
+   if st.insert_simplex([0, 1]):
+       print("[0, 1] inserted")
+   if st.insert_simplex_and_subfaces([0, 1, 2], filtration=4.0):
+       print("[0, 1, 2] inserted")
+   if st.find([0, 1]):
+       print("[0, 1] found")
+   print("num_vertices=", st.num_vertices())
+   print("num_simplices=", st.num_simplices())
+   print("skeleton_tree(2) =")
+   for sk_value in st.get_skeleton_tree(2):
+       print(sk_value)
+
+
+The output is:
+
+.. testoutput::
+
+   [0, 1] inserted
+   [0, 1, 2] inserted
+   [0, 1] found
+   ('num_vertices=', 3)
+   ('num_simplices=', 7)
+   skeleton_tree(2) =
+   ([0, 1, 2], 4.0)
+   ([0, 1], 0.0)
+   ([0, 2], 4.0)
+   ([0], 0.0)
+   ([1, 2], 4.0)
+   ([1], 4.0)
+   ([2], 4.0)
diff --git a/src/cython/doc/strong_witness_complex_ref.rst b/src/cython/doc/strong_witness_complex_ref.rst
new file mode 100644
index 00000000..4ed4fe46
--- /dev/null
+++ b/src/cython/doc/strong_witness_complex_ref.rst
@@ -0,0 +1,10 @@
+=======================================
+Strong witness complex reference manual
+=======================================
+
+.. autoclass:: gudhi.StrongWitnessComplex
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+   .. automethod:: gudhi.StrongWitnessComplex.__init__
diff --git a/src/cython/doc/tangential_complex_ref.rst b/src/cython/doc/tangential_complex_ref.rst
new file mode 100644
index 00000000..35589475
--- /dev/null
+++ b/src/cython/doc/tangential_complex_ref.rst
@@ -0,0 +1,10 @@
+===================================
+Tangential complex reference manual
+===================================
+
+.. autoclass:: gudhi.TangentialComplex
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+   .. automethod:: gudhi.TangentialComplex.__init__
diff --git a/src/cython/doc/tangential_complex_sum.rst b/src/cython/doc/tangential_complex_sum.rst
new file mode 100644
index 00000000..2b05bc10
--- /dev/null
+++ b/src/cython/doc/tangential_complex_sum.rst
@@ -0,0 +1,15 @@
+=================================================================  ===================================  ===================================
+:Author: Clément Jamin                                             :Introduced in: GUDHI 2.0.0          :Copyright: GPL v3
+:Requires: CGAL :math:`\geq` 4.8.0                                 Eigen3
+=================================================================  ===================================  ===================================
+
++----------------------------------------------------------------+------------------------------------------------------------------------+
+| .. figure::                                                    | A Tangential Delaunay complex is a simplicial complex designed to      |
+|      img/tc_examples.png                                       | reconstruct a :math:`k`-dimensional manifold embedded in :math:`d`-    |
+|      :figclass: align-center                                   | dimensional Euclidean space. The input is a point sample coming from   |
+|                                                                | an unknown manifold. The running time depends only linearly on the     |
+|      **Tangential complex representation**                     | extrinsic dimension :math:`d` and exponentially on the intrinsic       |
+|                                                                | dimension :math:`k`.                                                   |
++----------------------------------------------------------------+------------------------------------------------------------------------+
+| :doc:`tangential_complex_user`                                 | :doc:`tangential_complex_ref`                                          |
++----------------------------------------------------------------+------------------------------------------------------------------------+
diff --git a/src/cython/doc/tangential_complex_user.rst b/src/cython/doc/tangential_complex_user.rst
new file mode 100644
index 00000000..6a7e6e41
--- /dev/null
+++ b/src/cython/doc/tangential_complex_user.rst
@@ -0,0 +1,195 @@
+==============================
+Tangential complex user manual
+==============================
+.. include:: tangential_complex_sum.rst
+
+Definition
+----------
+
+A Tangential Delaunay complex is a simplicial complex designed to reconstruct a
+:math:`k`-dimensional smooth manifold embedded in :math:`d`-dimensional
+Euclidean space. The input is a point sample coming from an unknown manifold,
+which means that the points lie close to a structure of "small" intrinsic
+dimension. The running time depends only linearly on the extrinsic dimension
+:math:`d` and exponentially on the intrinsic dimension :math:`k`.
+
+An extensive description of the Tangential complex can be found in
+:cite:`tangentialcomplex2014`.
+
+What is a Tangential Complex?
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Let us start with the description of the Tangential complex of a simple
+example, with :math:`k = 1` and :math:`d = 2`. The input data is 4 points
+:math:`P` located on a curve embedded in 2D.
+
+.. figure:: img/tc_example_01.png
+    :alt: The input
+    :figclass: align-center
+
+    The input
+
+For each point :math:`p`, estimate its tangent subspace :math:`T_p` (e.g.
+using PCA). 
+
+.. figure:: img/tc_example_02.png
+    :alt: The estimated normals
+    :figclass: align-center
+
+    The estimated normals
+
+
+Let us add the Voronoi diagram of the points in orange. For each point
+:math:`p`, construct its star in the Delaunay triangulation of :math:`P`
+restricted to :math:`T_p`.
+
+.. figure:: img/tc_example_03.png
+    :alt: The Voronoi diagram
+    :figclass: align-center
+
+    The Voronoi diagram
+
+The Tangential Delaunay complex is the union of those stars.
+
+In practice, neither the ambient Voronoi diagram nor the ambient Delaunay
+triangulation is computed. Instead, local :math:`k`-dimensional regular
+triangulations are computed with a limited number of points as we only need the
+star of each point. More details can be found in :cite:`tangentialcomplex2014`.
+
+Inconsistencies
+^^^^^^^^^^^^^^^
+Inconsistencies between the stars can occur. An inconsistency occurs when a
+simplex is not in the star of all its vertices.
+
+Let us take the same example.
+
+.. figure:: img/tc_example_07_before.png
+    :alt: Before
+    :figclass: align-center
+
+    Before
+
+Let us slightly move the tangent subspace :math:`T_q`
+
+.. figure:: img/tc_example_07_after.png
+    :alt: After
+    :figclass: align-center
+
+    After
+
+Now, the star of :math:`Q` contains :math:`QP`, but the star of :math:`P` does
+not contain :math:`QP`. We have an inconsistency.
+
+.. figure:: img/tc_example_08.png
+    :alt: After
+    :figclass: align-center
+
+    After
+
+One way to solve inconsistencies is to randomly perturb the positions of the
+points involved in an inconsistency. In the current implementation, this
+perturbation is done in the tangent subspace of each point. The maximum
+perturbation radius is given as a parameter to the constructor.
+
+In most cases, we recommend to provide a point set where the minimum distance
+between any two points is not too small. This can be achieved using the
+functions provided by the Subsampling module. Then, a good value to start with
+for the maximum perturbation radius would be around half the minimum distance
+between any two points. The Example with perturbation below shows an example of
+such a process.
+
+In most cases, this process is able to dramatically reduce the number of
+inconsistencies, but is not guaranteed to succeed.
+
+Output
+^^^^^^
+The result of the computation is exported as a Simplex_tree. It is the union of
+the stars of all the input points. A vertex in the Simplex Tree is the index of
+the point in the range provided by the user. The point corresponding to a
+vertex can also be obtained through the Tangential_complex::get_point function.
+Note that even if the positions of the points are perturbed, their original
+positions are kept (e.g. Tangential_complex::get_point returns the original
+position of the point).
+
+The result can be obtained after the computation of the Tangential complex
+itself and/or after the perturbation process.
+
+
+Simple example
+--------------
+
+This example builds the Tangential complex of point set read in an OFF file.
+
+.. testcode::
+
+    import gudhi
+    tc = gudhi.TangentialComplex(off_file='alphacomplexdoc.off')
+    result_str = 'Tangential contains ' + repr(tc.num_simplices()) + \
+        ' simplices - ' + repr(tc.num_vertices()) + ' vertices.'
+    print(result_str)
+
+    st = tc.create_simplex_tree()
+    result_str = 'Simplex tree is of dimension ' + repr(st.dimension()) + \
+        ' - ' + repr(st.num_simplices()) + ' simplices - ' + \
+        repr(st.num_vertices()) + ' vertices.'
+    print(result_str)
+    for filtered_value in st.get_filtered_tree():
+        print(filtered_value)
+
+The output is:
+
+.. testoutput::
+
+    Tangential contains 12 simplices - 7 vertices.
+    Simplex tree is of dimension 1 - 15 simplices - 7 vertices.
+    ([0], 0.0)
+    ([1], 0.0)
+    ([0, 1], 0.0)
+    ([2], 0.0)
+    ([0, 2], 0.0)
+    ([1, 2], 0.0)
+    ([3], 0.0)
+    ([1, 3], 0.0)
+    ([4], 0.0)
+    ([2, 4], 0.0)
+    ([5], 0.0)
+    ([4, 5], 0.0)
+    ([6], 0.0)
+    ([3, 6], 0.0)
+    ([5, 6], 0.0)
+
+
+Example with perturbation
+-------------------------
+
+This example builds the Tangential complex of a point set, then tries to solve
+inconsistencies by perturbing the positions of points involved in inconsistent
+simplices.
+
+.. testcode::
+
+   import gudhi
+   tc = gudhi.TangentialComplex(points=[[0.0, 0.0], [1.0, 0.0], [0.0, 1.0], [1.0, 1.0]])
+   result_str = 'Tangential contains ' + repr(tc.num_vertices()) + ' vertices.'
+   print(result_str)
+
+   if tc.num_inconsistent_simplices() > 0:
+       print('Tangential contains inconsistencies.')
+
+   tc.fix_inconsistencies_using_perturbation(10, 60)
+   if tc.num_inconsistent_simplices() == 0:
+       print('Inconsistencies has been fixed.')
+
+The output is:
+
+.. testoutput::
+
+    Tangential contains 4 vertices.
+    Inconsistencies has been fixed.
+
+Bibliography
+************
+
+.. bibliography:: bibliography.bib
+   :filter: docnames
+   :style: unsrt
diff --git a/src/cython/doc/todos.rst b/src/cython/doc/todos.rst
new file mode 100644
index 00000000..78972a4c
--- /dev/null
+++ b/src/cython/doc/todos.rst
@@ -0,0 +1,5 @@
+==========
+To be done
+==========
+
+.. todolist::
diff --git a/src/cython/doc/witness_complex_ref.rst b/src/cython/doc/witness_complex_ref.rst
new file mode 100644
index 00000000..c78760cb
--- /dev/null
+++ b/src/cython/doc/witness_complex_ref.rst
@@ -0,0 +1,10 @@
+================================
+Witness complex reference manual
+================================
+
+.. autoclass:: gudhi.WitnessComplex
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+   .. automethod:: gudhi.WitnessComplex.__init__
diff --git a/src/cython/doc/witness_complex_sum.rst b/src/cython/doc/witness_complex_sum.rst
new file mode 100644
index 00000000..b65522ba
--- /dev/null
+++ b/src/cython/doc/witness_complex_sum.rst
@@ -0,0 +1,17 @@
+=================================================================  ===================================  ===================================
+:Author: Siargey Kachanovich                                       :Introduced in: GUDHI 2.0.0          :Copyright: GPL v3
+:Euclidean version requires: CGAL :math:`\geq` 4.6.0               Eigen3
+=================================================================  ===================================  ===================================
+
++-----------------------------------------------------------------+----------------------------------------------------------------------+
+| .. image::                                                      | Witness complex :math:`Wit(W,L)` is a simplicial complex defined on  |
+|      img/Witness_complex_representation.png                     | two sets of points in :math:`\mathbb{R}^D`.                          |
+|                                                                 |                                                                      |
+|                                                                 | The data structure is described in                                   |
+|                                                                 | :cite:`boissonnatmariasimplextreealgorithmica`.                      |
++-----------------------------------------------------------------+----------------------------------------------------------------------+
+| :doc:`witness_complex_user`                                     | * :doc:`witness_complex_ref`                                         |
+|                                                                 | * :doc:`strong_witness_complex_ref`                                  |
+|                                                                 | * :doc:`euclidean_witness_complex_ref`                               |
+|                                                                 | * :doc:`euclidean_strong_witness_complex_ref`                        |
++-----------------------------------------------------------------+----------------------------------------------------------------------+
diff --git a/src/cython/doc/witness_complex_user.rst b/src/cython/doc/witness_complex_user.rst
new file mode 100644
index 00000000..07945361
--- /dev/null
+++ b/src/cython/doc/witness_complex_user.rst
@@ -0,0 +1,135 @@
+===========================
+Witness complex user manual
+===========================
+Definition
+----------
+
+.. include:: witness_complex_sum.rst
+
+
+Definitions
+-----------
+
+Witness complex is a simplicial complex defined on two sets of points in :math:`\mathbb{R}^D`:
+
+- :math:`W` set of **witnesses** and
+- :math:`L` set of **landmarks**.
+
+Even though often the set of landmarks :math:`L` is a subset of the set of witnesses :math:`W`, it is not a requirement
+for the current implementation.
+
+Landmarks are the vertices of the simplicial complex and witnesses help to decide on which simplices are inserted via a
+predicate "is witnessed".
+
+De Silva and Carlsson in their paper :cite:`de2004topological` differentiate **weak witnessing** and
+**strong witnessing**:
+
+- *weak*:   :math:`\sigma \subset L` is witnessed by :math:`w \in W` if :math:`\forall l \in \sigma,\ \forall l' \in \mathbf{L \setminus \sigma},\ d(w,l) \leq d(w,l')`
+- *strong*: :math:`\sigma \subset L` is witnessed by :math:`w \in W` if :math:`\forall l \in \sigma,\ \forall l' \in \mathbf{L},\ d(w,l) \leq d(w,l')`
+
+where :math:`d(.,.)` is a distance function.
+
+Both definitions can be relaxed by a real value :math:`\alpha`:
+
+- *weak*:   :math:`\sigma \subset L` is :math:`\alpha`-witnessed by :math:`w \in W` if :math:`\forall l \in \sigma,\ \forall l' \in \mathbf{L \setminus \sigma},\ d(w,l)^2 \leq d(w,l')^2 + \alpha^2`
+- *strong*: :math:`\sigma \subset L` is :math:`\alpha`-witnessed by :math:`w \in W` if :math:`\forall l \in \sigma,\ \forall l' \in \mathbf{L},\ d(w,l)^2 \leq d(w,l')^2 + \alpha^2`
+
+which leads to definitions of **weak relaxed witness complex** (or just relaxed witness complex for short) and
+**strong relaxed witness complex** respectively.
+
+.. figure:: img/swit.svg
+    :alt: Strongly witnessed simplex
+    :figclass: align-center
+
+    Strongly witnessed simplex
+
+
+In particular case of 0-relaxation, weak complex corresponds to **witness complex** introduced in
+:cite:`de2004topological`, whereas 0-relaxed strong witness complex consists of just vertices and is not very
+interesting. Hence for small relaxation weak version is preferable.
+However, to capture the homotopy type (for example using Gudhi::persistent_cohomology::Persistent_cohomology) it is
+often necessary to work with higher filtration values. In this case strong relaxed witness complex is faster to compute
+and offers similar results.
+
+Implementation
+--------------
+
+The two complexes described above are implemented in the corresponding classes
+
+- :doc:`witness_complex_ref`
+- :doc:`strong_witness_complex_ref`
+- :doc:`euclidean_witness_complex_ref`
+- :doc:`euclidean_strong_witness_complex_ref`
+
+The construction of the Euclidean versions of complexes follow the same scheme:
+
+1. Construct a search tree on landmarks.
+2. Construct lists of nearest landmarks for each witness.
+3. Construct the witness complex for nearest landmark lists.
+
+In the non-Euclidean classes, the lists of nearest landmarks are supposed to be given as input.
+
+The constructors take on the steps 1 and 2, while the function 'create_complex' executes the step 3.
+
+Constructing weak relaxed witness complex from an off file
+----------------------------------------------------------
+
+Let's start with a simple example, which reads an off point file and computes a weak witness complex.
+
+.. code-block:: python
+
+    import gudhi
+    import argparse
+
+    parser = argparse.ArgumentParser(description='EuclideanWitnessComplex creation from '
+                                     'points read in a OFF file.',
+                                     epilog='Example: '
+                                     'example/witness_complex_diagram_persistence_from_off_file_example.py '
+                                     '-f ../data/points/tore3D_300.off -a 1.0 -n 20 -d 2'
+                                     '- Constructs a alpha complex with the '
+                                     'points from the given OFF file.')
+    parser.add_argument("-f", "--file", type=str, required=True)
+    parser.add_argument("-a", "--max_alpha_square", type=float, required=True)
+    parser.add_argument("-n", "--number_of_landmarks", type=int, required=True)
+    parser.add_argument("-d", "--limit_dimension", type=int, required=True)
+
+    args = parser.parse_args()
+
+    with open(args.file, 'r') as f:
+        first_line = f.readline()
+        if (first_line == 'OFF\n') or (first_line == 'nOFF\n'):
+            print("#####################################################################")
+            print("EuclideanWitnessComplex creation from points read in a OFF file")
+
+            witnesses = gudhi.read_off(off_file=args.file)
+            landmarks = gudhi.pick_n_random_points(points=witnesses, nb_points=args.number_of_landmarks)
+
+            message = "EuclideanWitnessComplex with max_edge_length=" + repr(args.max_alpha_square) + \
+                " - Number of landmarks=" + repr(args.number_of_landmarks)
+            print(message)
+
+            witness_complex = gudhi.EuclideanWitnessComplex(witnesses=witnesses, landmarks=landmarks)
+            simplex_tree = witness_complex.create_simplex_tree(max_alpha_square=args.max_alpha_square,
+                limit_dimension=args.limit_dimension)
+
+            message = "Number of simplices=" + repr(simplex_tree.num_simplices())
+            print(message)
+        else:
+            print(args.file, "is not a valid OFF file")
+
+        f.close()
+
+
+Example2: Computing persistence using strong relaxed witness complex
+--------------------------------------------------------------------
+
+Here is an example of constructing a strong witness complex filtration and computing persistence on it:
+
+* :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py>`
+
+Bibliography
+************
+
+.. bibliography:: bibliography.bib
+   :filter: docnames
+   :style: unsrt
diff --git a/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py
new file mode 100755
index 00000000..adedc7d2
--- /dev/null
+++ b/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py
@@ -0,0 +1,70 @@
+#!/usr/bin/env python
+
+import gudhi
+import argparse
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+parser = argparse.ArgumentParser(description='AlphaComplex creation from '
+                                 'points read in a OFF file.',
+                                 epilog='Example: '
+                                 'example/alpha_complex_diagram_persistence_from_off_file_example.py '
+                                 '-f ../data/points/tore3D_300.off -a 0.6'
+                                 '- Constructs a alpha complex with the '
+                                 'points from the given OFF file.')
+parser.add_argument("-f", "--file", type=str, required=True)
+parser.add_argument("-a", "--max_alpha_square", type=float, default=0.5)
+parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
+
+args = parser.parse_args()
+
+with open(args.file, 'r') as f:
+    first_line = f.readline()
+    if (first_line == 'OFF\n') or (first_line == 'nOFF\n'):
+        print("#####################################################################")
+        print("AlphaComplex creation from points read in a OFF file")
+        
+        message = "AlphaComplex with max_edge_length=" + repr(args.max_alpha_square)
+        print(message)
+        
+        alpha_complex = gudhi.AlphaComplex(off_file=args.file)
+        simplex_tree = alpha_complex.create_simplex_tree(max_alpha_square=args.max_alpha_square)
+    
+        message = "Number of simplices=" + repr(simplex_tree.num_simplices())
+        print(message)
+        
+        diag = simplex_tree.persistence()
+    
+        print("betti_numbers()=")
+        print(simplex_tree.betti_numbers())
+    
+        if args.no_diagram == False:
+            gudhi.plot_persistence_diagram(diag)
+    else:
+        print(args.file, "is not a valid OFF file")
+
+    f.close()
diff --git a/src/cython/example/alpha_complex_from_points_example.py b/src/cython/example/alpha_complex_from_points_example.py
new file mode 100755
index 00000000..688edb65
--- /dev/null
+++ b/src/cython/example/alpha_complex_from_points_example.py
@@ -0,0 +1,67 @@
+#!/usr/bin/env python
+
+from gudhi import AlphaComplex, SimplexTree
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+print("#####################################################################")
+print("AlphaComplex creation from points")
+alpha_complex = AlphaComplex(points=[[0, 0], [1, 0], [0, 1], [1, 1]])
+simplex_tree = alpha_complex.create_simplex_tree(max_alpha_square=60.0)
+
+if simplex_tree.find([0, 1]):
+    print("[0, 1] Found !!")
+else:
+    print("[0, 1] Not found...")
+
+if simplex_tree.find([4]):
+    print("[4] Found !!")
+else:
+    print("[4] Not found...")
+
+if simplex_tree.insert([0, 1, 2], filtration=4.0):
+    print("[0, 1, 2] Inserted !!")
+else:
+    print("[0, 1, 2] Not inserted...")
+
+if simplex_tree.insert([0, 1, 4], filtration=4.0):
+    print("[0, 1, 4] Inserted !!")
+else:
+    print("[0, 1, 4] Not inserted...")
+
+if simplex_tree.find([4]):
+    print("[4] Found !!")
+else:
+    print("[4] Not found...")
+
+print("dimension=", simplex_tree.dimension())
+print("filtered_tree=", simplex_tree.get_filtered_tree())
+print("star([0])=", simplex_tree.get_star([0]))
+print("coface([0], 1)=", simplex_tree.get_cofaces([0], 1))
+
+print("point[0]=", alpha_complex.get_point(0))
+print("point[5]=", alpha_complex.get_point(5))
diff --git a/src/cython/example/alpha_rips_persistence_bottleneck_distance.py b/src/cython/example/alpha_rips_persistence_bottleneck_distance.py
new file mode 100755
index 00000000..ab5fc1e9
--- /dev/null
+++ b/src/cython/example/alpha_rips_persistence_bottleneck_distance.py
@@ -0,0 +1,100 @@
+#!/usr/bin/env python
+
+import gudhi
+import argparse
+import math
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+parser = argparse.ArgumentParser(description='AlphaComplex and RipsComplex '
+                                 'persistence creation from points read in '
+                                 'a OFF file. Bottleneck distance computation'
+                                 ' on each dimension',
+                                 epilog='Example: '
+                                 'example/alpha_rips_persistence_bottleneck_distance.py '
+                                 '-f ../data/points/tore3D_1307.off -t 0.15 -d 3')
+parser.add_argument("-f", "--file", type=str, required=True)
+parser.add_argument("-t", "--threshold", type=float, default=0.5)
+parser.add_argument("-d", "--max_dimension", type=int, default=1)
+
+args = parser.parse_args()
+with open(args.file, 'r') as f:
+    first_line = f.readline()
+    if (first_line == 'OFF\n') or (first_line == 'nOFF\n'):
+        print("#####################################################################")
+        print("RipsComplex creation from points read in a OFF file")
+
+        message = "RipsComplex with max_edge_length=" + repr(args.threshold)
+        print(message)
+
+        rips_complex = gudhi.RipsComplex(off_file=args.file,
+                                         max_edge_length=args.threshold)
+
+        rips_stree = rips_complex.create_simplex_tree(max_dimension=args.max_dimension)
+
+        message = "Number of simplices=" + repr(rips_stree.num_simplices())
+        print(message)
+
+        rips_diag = rips_stree.persistence()
+
+        print("#####################################################################")
+        print("AlphaComplex creation from points read in a OFF file")
+
+        message = "AlphaComplex with max_edge_length=" + repr(args.threshold)
+        print(message)
+
+        alpha_complex = gudhi.AlphaComplex(off_file=args.file)
+        alpha_stree = alpha_complex.create_simplex_tree(max_alpha_square=(args.threshold * args.threshold))
+
+        message = "Number of simplices=" + repr(alpha_stree.num_simplices())
+        print(message)
+
+        alpha_diag = alpha_stree.persistence()
+
+        max_b_distance = 0.0
+        for dim in range(args.max_dimension):
+            # Alpha persistence values needs to be transform because filtration
+            # values are alpha square values
+            funcs = [math.sqrt, math.sqrt]
+            alpha_intervals = []
+            for interval in alpha_stree.persistence_intervals_in_dimension(dim):
+                alpha_intervals.append(map(lambda func,value: func(value), funcs, interval))
+
+            rips_intervals = rips_stree.persistence_intervals_in_dimension(dim)
+            bottleneck_distance = gudhi.bottleneck_distance(rips_intervals, alpha_intervals)
+            message = "In dimension " + repr(dim) + ", bottleneck distance = " + repr(bottleneck_distance)
+            print(message)
+            max_b_distance = max(bottleneck_distance, max_b_distance)
+
+        print("================================================================================")
+        message = "Bottleneck distance is " + repr(max_b_distance)
+        print(message)
+
+    else:
+        print(args.file, "is not a valid OFF file")
+
+    f.close()
diff --git a/src/cython/example/bottleneck_basic_example.py b/src/cython/example/bottleneck_basic_example.py
new file mode 100755
index 00000000..31cecb29
--- /dev/null
+++ b/src/cython/example/bottleneck_basic_example.py
@@ -0,0 +1,48 @@
+#!/usr/bin/env python
+
+import gudhi
+
+"""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):       Francois Godi, 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/>.
+"""
+
+__author__ = "Francois Godi, Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+import gudhi
+
+diag1 = [[2.7, 3.7],[9.6, 14.],[34.2, 34.974], [3.,float('Inf')]]
+
+diag2 = [[2.8, 4.45],[9.5, 14.1],[3.2,float('Inf')]]
+
+message = "diag1=" + repr(diag1)
+print(message)
+
+message = "diag2=" + repr(diag2)
+print(message)
+
+message = "Bottleneck distance approximation=" + repr(gudhi.bottleneck_distance(diag1, diag2, 0.1))
+print(message)
+
+message = "Bottleneck distance exact value=" + repr(gudhi.bottleneck_distance(diag1, diag2))
+print(message)
+
diff --git a/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
new file mode 100755
index 00000000..2474fc87
--- /dev/null
+++ b/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
@@ -0,0 +1,78 @@
+#!/usr/bin/env python
+
+import gudhi
+import argparse
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+parser = argparse.ArgumentParser(description='EuclideanStrongWitnessComplex creation from '
+                                 'points read in a OFF file.',
+                                 epilog='Example: '
+                                 'example/witness_complex_diagram_persistence_from_off_file_example.py '
+                                 '-f ../data/points/tore3D_300.off -a 1.0 -n 20 -d 2'
+                                 '- Constructs a strong witness complex with the '
+                                 'points from the given OFF file.')
+parser.add_argument("-f", "--file", type=str, required=True)
+parser.add_argument("-a", "--max_alpha_square", type=float, required=True)
+parser.add_argument("-n", "--number_of_landmarks", type=int, required=True)
+parser.add_argument("-d", "--limit_dimension", type=int, required=True)
+parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
+
+args = parser.parse_args()
+
+with open(args.file, 'r') as f:
+    first_line = f.readline()
+    if (first_line == 'OFF\n') or (first_line == 'nOFF\n'):
+        print("#####################################################################")
+        print("EuclideanStrongWitnessComplex creation from points read in a OFF file")
+
+        witnesses = gudhi.read_off(off_file=args.file)
+        landmarks = gudhi.pick_n_random_points(points=witnesses, nb_points=args.number_of_landmarks)
+
+        message = "EuclideanStrongWitnessComplex with max_edge_length=" + repr(args.max_alpha_square) + \
+            " - Number of landmarks=" + repr(args.number_of_landmarks)
+        print(message)
+
+        witness_complex = gudhi.EuclideanStrongWitnessComplex(witnesses=witnesses, landmarks=landmarks)
+        simplex_tree = witness_complex.create_simplex_tree(max_alpha_square=args.max_alpha_square,
+            limit_dimension=args.limit_dimension)
+
+        message = "Number of simplices=" + repr(simplex_tree.num_simplices())
+        print(message)
+
+        diag = simplex_tree.persistence()
+
+        print("betti_numbers()=")
+        print(simplex_tree.betti_numbers())
+
+        if args.no_diagram == False:
+            gudhi.plot_persistence_diagram(diag)
+
+    else:
+        print(args.file, "is not a valid OFF file")
+
+    f.close()
diff --git a/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
new file mode 100755
index 00000000..5a75417b
--- /dev/null
+++ b/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
@@ -0,0 +1,78 @@
+#!/usr/bin/env python
+
+import gudhi
+import argparse
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+parser = argparse.ArgumentParser(description='EuclideanWitnessComplex creation from '
+                                 'points read in a OFF file.',
+                                 epilog='Example: '
+                                 'example/witness_complex_diagram_persistence_from_off_file_example.py '
+                                 '-f ../data/points/tore3D_300.off -a 1.0 -n 20 -d 2'
+                                 '- Constructs a weak witness complex with the '
+                                 'points from the given OFF file.')
+parser.add_argument("-f", "--file", type=str, required=True)
+parser.add_argument("-a", "--max_alpha_square", type=float, required=True)
+parser.add_argument("-n", "--number_of_landmarks", type=int, required=True)
+parser.add_argument("-d", "--limit_dimension", type=int, required=True)
+parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
+
+args = parser.parse_args()
+
+with open(args.file, 'r') as f:
+    first_line = f.readline()
+    if (first_line == 'OFF\n') or (first_line == 'nOFF\n'):
+        print("#####################################################################")
+        print("EuclideanWitnessComplex creation from points read in a OFF file")
+
+        witnesses = gudhi.read_off(off_file=args.file)
+        landmarks = gudhi.pick_n_random_points(points=witnesses, nb_points=args.number_of_landmarks)
+
+        message = "EuclideanWitnessComplex with max_edge_length=" + repr(args.max_alpha_square) + \
+            " - Number of landmarks=" + repr(args.number_of_landmarks)
+        print(message)
+
+        witness_complex = gudhi.EuclideanWitnessComplex(witnesses=witnesses, landmarks=landmarks)
+        simplex_tree = witness_complex.create_simplex_tree(max_alpha_square=args.max_alpha_square,
+            limit_dimension=args.limit_dimension)
+
+        message = "Number of simplices=" + repr(simplex_tree.num_simplices())
+        print(message)
+
+        diag = simplex_tree.persistence()
+
+        print("betti_numbers()=")
+        print(simplex_tree.betti_numbers())
+
+        if args.no_diagram == False:
+            gudhi.plot_persistence_diagram(diag)
+
+    else:
+        print(args.file, "is not a valid OFF file")
+
+    f.close()
diff --git a/src/cython/example/gudhi_graphical_tools_example.py b/src/cython/example/gudhi_graphical_tools_example.py
new file mode 100755
index 00000000..bc3b16ec
--- /dev/null
+++ b/src/cython/example/gudhi_graphical_tools_example.py
@@ -0,0 +1,47 @@
+#!/usr/bin/env python
+
+import gudhi
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+print("#####################################################################")
+print("Show palette colors values for dimension")
+
+gudhi.show_palette_values()
+
+print("#####################################################################")
+print("Show barcode persistence example")
+
+persistence = [(2, (1.0, float('inf'))), (1, (1.4142135623730951, float('inf'))),
+               (1, (1.4142135623730951, float('inf'))), (0, (0.0, float('inf'))),
+               (0, (0.0, 1.0)), (0, (0.0, 1.0)), (0, (0.0, 1.0))]
+gudhi.plot_persistence_barcode(persistence)
+
+print("#####################################################################")
+print("Show diagram persistence example")
+
+gudhi.plot_persistence_diagram(persistence)
diff --git a/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py b/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py
new file mode 100755
index 00000000..db530161
--- /dev/null
+++ b/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py
@@ -0,0 +1,76 @@
+#!/usr/bin/env python
+
+import gudhi
+import argparse
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+def is_file_perseus(file):
+    num_lines = open(file).read().count('\n')
+    try:
+        f = open(file)
+        num_dim = int(f.readline())
+        coeff = 1
+        for dim in range(0, num_dim):
+            try:
+                line = int(f.readline())
+                coeff *= abs(line)
+            except ValueError:
+                return False
+        if num_lines == (1 + num_dim + coeff):
+            return True
+        else:
+            return False
+    except ValueError:
+        return False
+
+parser = argparse.ArgumentParser(description='Periodic cubical complex from a '
+                                 'perseus file style name.',
+                                 epilog='Example: '
+                                 './periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py'
+                                 ' -f ../data/bitmap/CubicalTwoSphere.txt')
+
+parser.add_argument("-f", "--file", type=str, required=True)
+parser.add_argument('--no-barcode', default=False, action='store_true' , help='Flag for not to display the barcodes')
+
+args = parser.parse_args()
+
+if is_file_perseus(args.file):
+    print("#####################################################################")
+    print("PeriodicCubicalComplex creation")
+    periodic_cubical_complex = gudhi.PeriodicCubicalComplex(perseus_file=args.file)
+
+    print("persistence(homology_coeff_field=3, min_persistence=0)=")
+    diag = periodic_cubical_complex.persistence(homology_coeff_field=3, min_persistence=0)
+    print(diag)
+
+    print("betti_numbers()=")
+    print(periodic_cubical_complex.betti_numbers())
+    if args.no_barcode == False:
+        gudhi.plot_persistence_barcode(diag)
+else:
+    print(args.file, "is not a valid perseus style file")
diff --git a/src/cython/example/random_cubical_complex_persistence_example.py b/src/cython/example/random_cubical_complex_persistence_example.py
new file mode 100755
index 00000000..1c55f777
--- /dev/null
+++ b/src/cython/example/random_cubical_complex_persistence_example.py
@@ -0,0 +1,57 @@
+#!/usr/bin/env python
+
+import gudhi
+import numpy
+import argparse
+import operator
+
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+parser = argparse.ArgumentParser(description='Random cubical complex.',
+                                 epilog='Example: '
+                                 './random_cubical_complex_persistence_example.py'
+                                 ' 10 10 10 - Constructs a random cubical '
+                                 'complex in a dimension [10, 10, 10] (aka. '
+                                 '1000 random top dimensional cells).')
+parser.add_argument('dimension', type=int, nargs="*",
+                    help='Cubical complex dimensions')
+
+args = parser.parse_args()
+dimension_multiplication = reduce(operator.mul, args.dimension, 1)
+
+if dimension_multiplication > 1: 
+    print("#####################################################################")
+    print("CubicalComplex creation")
+    cubical_complex = gudhi.CubicalComplex(dimensions=args.dimension,
+                                           top_dimensional_cells = numpy.random.rand(dimension_multiplication))
+
+    print("persistence(homology_coeff_field=2, min_persistence=0)=")
+    print(cubical_complex.persistence(homology_coeff_field=2, min_persistence=0))
+
+    print("betti_numbers()=")
+    print(cubical_complex.betti_numbers())
\ No newline at end of file
diff --git a/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
new file mode 100755
index 00000000..664eb5c4
--- /dev/null
+++ b/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
@@ -0,0 +1,71 @@
+#!/usr/bin/env python
+
+import gudhi
+import argparse
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+parser = argparse.ArgumentParser(description='RipsComplex creation from '
+                                 'a distance matrix read in a OFF file.',
+                                 epilog='Example: '
+                                 'example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py '
+                                 '-f ../data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3'
+                                 '- Constructs a Rips complex with the '
+                                 'points from the given OFF file.')
+parser.add_argument("-f", "--file", type=str, required=True)
+parser.add_argument("-e", "--max_edge_length", type=float, default=0.5)
+parser.add_argument("-d", "--max_dimension", type=int, default=1)
+parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
+
+args = parser.parse_args()
+
+with open(args.file, 'r') as f:
+    first_line = f.readline()
+    if (first_line == 'OFF\n') or (first_line == 'nOFF\n'):
+        print("#####################################################################")
+        print("RipsComplex creation from distance matrix read in a csv file")
+        
+        message = "RipsComplex with max_edge_length=" + repr(args.max_edge_length)
+        print(message)
+        
+        rips_complex = gudhi.RipsComplex(off_file=args.file, max_edge_length=args.max_edge_length)
+        simplex_tree = rips_complex.create_simplex_tree(max_dimension=args.max_dimension)
+    
+        message = "Number of simplices=" + repr(simplex_tree.num_simplices())
+        print(message)
+        
+        diag = simplex_tree.persistence()
+    
+        print("betti_numbers()=")
+        print(simplex_tree.betti_numbers())
+    
+        if args.no_diagram == False:
+            gudhi.plot_persistence_diagram(diag)
+    else:
+        print(args.file, "is not a valid OFF file")
+
+    f.close()
diff --git a/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py
new file mode 100755
index 00000000..4c21b98e
--- /dev/null
+++ b/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py
@@ -0,0 +1,71 @@
+#!/usr/bin/env python
+
+import gudhi
+import argparse
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+parser = argparse.ArgumentParser(description='RipsComplex creation from '
+                                 'points read in a OFF file.',
+                                 epilog='Example: '
+                                 'example/rips_complex_diagram_persistence_from_off_file_example.py '
+                                 '-f ../data/points/tore3D_300.off -a 0.6'
+                                 '- Constructs a Rips complex with the '
+                                 'points from the given OFF file.')
+parser.add_argument("-f", "--file", type=str, required=True)
+parser.add_argument("-e", "--max_edge_length", type=float, default=0.5)
+parser.add_argument("-d", "--max_dimension", type=int, default=1)
+parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
+
+args = parser.parse_args()
+
+with open(args.file, 'r') as f:
+    first_line = f.readline()
+    if (first_line == 'OFF\n') or (first_line == 'nOFF\n'):
+        print("#####################################################################")
+        print("RipsComplex creation from points read in a OFF file")
+        
+        message = "RipsComplex with max_edge_length=" + repr(args.max_edge_length)
+        print(message)
+        
+        rips_complex = gudhi.RipsComplex(off_file=args.file, max_edge_length=args.max_edge_length)
+        simplex_tree = rips_complex.create_simplex_tree(max_dimension=args.max_dimension)
+    
+        message = "Number of simplices=" + repr(simplex_tree.num_simplices())
+        print(message)
+        
+        diag = simplex_tree.persistence()
+    
+        print("betti_numbers()=")
+        print(simplex_tree.betti_numbers())
+    
+        if args.no_diagram == False:
+            gudhi.plot_persistence_diagram(diag)
+    else:
+        print(args.file, "is not a valid OFF file")
+
+    f.close()
diff --git a/src/cython/example/rips_complex_from_points_example.py b/src/cython/example/rips_complex_from_points_example.py
new file mode 100755
index 00000000..9b7fc79d
--- /dev/null
+++ b/src/cython/example/rips_complex_from_points_example.py
@@ -0,0 +1,40 @@
+#!/usr/bin/env python
+
+import gudhi
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+print("#####################################################################")
+print("RipsComplex creation from points")
+rips = gudhi.RipsComplex(points=[[0, 0], [1, 0], [0, 1], [1, 1]],
+                         max_edge_length=42)
+
+simplex_tree = rips.create_simplex_tree(max_dimension=1)
+
+print("filtered_tree=", simplex_tree.get_filtered_tree())
+print("star([0])=", simplex_tree.get_star([0]))
+print("coface([0], 1)=", simplex_tree.get_cofaces([0], 1))
diff --git a/src/cython/example/rips_persistence_diagram.py b/src/cython/example/rips_persistence_diagram.py
new file mode 100755
index 00000000..4e5cd2c8
--- /dev/null
+++ b/src/cython/example/rips_persistence_diagram.py
@@ -0,0 +1,42 @@
+#!/usr/bin/env python
+
+import gudhi
+
+"""This file is part of the Gudhi Library. The Gudhi library
+   (Geometric Understanding in Higher Dimensions) is a generic C++
+   library for computational topology.
+
+   Author(s):       Marc Glisse
+
+   Copyright (C) 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/>.
+"""
+
+__author__ = "Marc Glisse"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+print("#####################################################################")
+print("RipsComplex creation from points")
+rips = gudhi.RipsComplex(points=[[0, 0], [1, 0], [0, 1], [1, 1]],
+                         max_edge_length=42)
+
+simplex_tree = rips.create_simplex_tree(max_dimension=1)
+
+
+diag = simplex_tree.persistence(homology_coeff_field=2, min_persistence=0)
+print("diag=", diag)
+
+gudhi.plot_persistence_diagram(diag)
diff --git a/src/cython/example/simplex_tree_example.py b/src/cython/example/simplex_tree_example.py
new file mode 100755
index 00000000..bf5f17a2
--- /dev/null
+++ b/src/cython/example/simplex_tree_example.py
@@ -0,0 +1,66 @@
+#!/usr/bin/env python
+
+import gudhi
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+print("#####################################################################")
+print("SimplexTree creation from insertion")
+
+st = gudhi.SimplexTree()
+
+if st.insert([0, 1]):
+    print("Inserted !!")
+else:
+    print("Not inserted...")
+
+if st.find([0, 1]):
+    print("Found !!")
+else:
+    print("Not found...")
+
+if st.insert([0, 1, 2], filtration=4.0):
+    print("Inserted !!")
+else:
+    print("Not inserted...")
+
+# FIXME: Remove this line
+st.set_dimension(3)
+print("dimension=", st.dimension())
+
+st.set_filtration(4.0)
+st.initialize_filtration()
+print("filtration=", st.get_filtration())
+print("filtration[1, 2]=", st.filtration([1, 2]))
+print("filtration[4, 2]=", st.filtration([4, 2]))
+
+print("num_simplices=", st.num_simplices())
+print("num_vertices=", st.num_vertices())
+
+print("skeleton_tree[2]=", st.get_skeleton_tree(2))
+print("skeleton_tree[1]=", st.get_skeleton_tree(1))
+print("skeleton_tree[0]=", st.get_skeleton_tree(0))
diff --git a/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py b/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py
new file mode 100755
index 00000000..4845eb47
--- /dev/null
+++ b/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py
@@ -0,0 +1,66 @@
+#!/usr/bin/env python
+
+import gudhi
+import argparse
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+parser = argparse.ArgumentParser(description='TangentialComplex creation from '
+                                 'points read in a OFF file.',
+                                 epilog='Example: '
+                                 'example/tangential_complex_plain_homology_from_off_file_example.py '
+                                 '-f ../data/points/tore3D_300.off'
+                                 '- Constructs a tangential complex with the '
+                                 'points from the given OFF file')
+parser.add_argument("-f", "--file", type=str, required=True)
+parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
+
+args = parser.parse_args()
+
+with open(args.file, 'r') as f:
+    first_line = f.readline()
+    if (first_line == 'OFF\n') or (first_line == 'nOFF\n'):
+        print("#####################################################################")
+        print("TangentialComplex creation from points read in a OFF file")
+        
+        tc = gudhi.TangentialComplex(off_file=args.file)
+        st = tc.create_simplex_tree()
+    
+        message = "Number of simplices=" + repr(st.num_simplices())
+        print(message)
+        
+        diag = st.persistence(persistence_dim_max = True)
+    
+        print("betti_numbers()=")
+        print(st.betti_numbers())
+    
+        if args.no_diagram == False:
+            gudhi.plot_persistence_diagram(diag)
+    else:
+        print(args.file, "is not a valid OFF file")
+
+    f.close()
diff --git a/src/cython/example/witness_complex_from_nearest_landmark_table.py b/src/cython/example/witness_complex_from_nearest_landmark_table.py
new file mode 100755
index 00000000..92ed970b
--- /dev/null
+++ b/src/cython/example/witness_complex_from_nearest_landmark_table.py
@@ -0,0 +1,46 @@
+#!/usr/bin/env python
+
+from gudhi import StrongWitnessComplex, SimplexTree
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+print("#####################################################################")
+print("WitnessComplex creation from nearest landmark table")
+nearest_landmark_table = [[[0, 0], [1, 1], [2, 2], [3, 3], [4, 4]],
+                          [[1, 0], [2, 1], [3, 2], [4, 3], [0, 4]],
+                          [[2, 0], [3, 1], [4, 2], [0, 3], [1, 4]],
+                          [[3, 0], [4, 1], [0, 2], [1, 3], [2, 4]],
+                          [[4, 0], [0, 1], [1, 2], [2, 3], [3, 4]]]
+
+witness_complex = StrongWitnessComplex(nearest_landmark_table=nearest_landmark_table)
+simplex_tree = witness_complex.create_simplex_tree(max_alpha_square=4.1)
+
+message = "Number of simplices: " + repr(simplex_tree.num_simplices())
+print(message)
+
+diag = simplex_tree.persistence(min_persistence=-0.1, homology_coeff_field=11)
+print(diag)
diff --git a/src/cython/gudhi.pyx.in b/src/cython/gudhi.pyx.in
new file mode 100644
index 00000000..34d7c3b5
--- /dev/null
+++ b/src/cython/gudhi.pyx.in
@@ -0,0 +1,39 @@
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016  INRIA"
+__license__ = "GPL v3"
+
+include "cython/off_reader.pyx"
+include "cython/simplex_tree.pyx"
+include "cython/rips_complex.pyx"
+include "cython/cubical_complex.pyx"
+include "cython/periodic_cubical_complex.pyx"
+include "cython/persistence_graphical_tools.py"
+include "cython/witness_complex.pyx"
+include "cython/strong_witness_complex.pyx"
+@GUDHI_CYTHON_ALPHA_COMPLEX@
+@GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX@
+@GUDHI_CYTHON_SUBSAMPLING@
+@GUDHI_CYTHON_TANGENTIAL_COMPLEX@
+@GUDHI_CYTHON_BOTTLENECK_DISTANCE@
diff --git a/src/cython/include/Alpha_complex_interface.h b/src/cython/include/Alpha_complex_interface.h
new file mode 100644
index 00000000..d47db71f
--- /dev/null
+++ b/src/cython/include/Alpha_complex_interface.h
@@ -0,0 +1,82 @@
+/*    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 INCLUDE_ALPHA_COMPLEX_INTERFACE_H_
+#define INCLUDE_ALPHA_COMPLEX_INTERFACE_H_
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Alpha_complex.h>
+#include <CGAL/Epick_d.h>
+
+#include "Simplex_tree_interface.h"
+
+#include <iostream>
+#include <vector>
+#include <string>
+
+namespace Gudhi {
+
+namespace alpha_complex {
+
+class Alpha_complex_interface {
+  using Dynamic_kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >;
+  using Point_d = Dynamic_kernel::Point_d;
+
+ public:
+  Alpha_complex_interface(const std::vector<std::vector<double>>& points) {
+    alpha_complex_ = new Alpha_complex<Dynamic_kernel>(points);
+  }
+
+  Alpha_complex_interface(const std::string& off_file_name, bool from_file = true) {
+    alpha_complex_ = new Alpha_complex<Dynamic_kernel>(off_file_name);
+  }
+
+  ~Alpha_complex_interface() {
+    delete alpha_complex_;
+  }
+
+  std::vector<double> get_point(int vh) {
+    std::vector<double> vd;
+    try {
+      Point_d ph = alpha_complex_->get_point(vh);
+      for (auto coord = ph.cartesian_begin(); coord < ph.cartesian_end(); coord++)
+        vd.push_back(*coord);
+    } catch (std::out_of_range outofrange) {
+      // std::out_of_range is thrown in case not found. Other exceptions must be re-thrown
+    }
+    return vd;
+  }
+
+  void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, double max_alpha_square) {
+    alpha_complex_->create_complex(*simplex_tree, max_alpha_square);
+    simplex_tree->initialize_filtration();
+  }
+
+ private:
+  Alpha_complex<Dynamic_kernel>* alpha_complex_;
+};
+
+}  // namespace alpha_complex
+
+}  // namespace Gudhi
+
+#endif  // INCLUDE_ALPHA_COMPLEX_INTERFACE_H_
diff --git a/src/cython/include/Bottleneck_distance_interface.h b/src/cython/include/Bottleneck_distance_interface.h
new file mode 100644
index 00000000..d5fbf6ea
--- /dev/null
+++ b/src/cython/include/Bottleneck_distance_interface.h
@@ -0,0 +1,53 @@
+/*    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 INCLUDE_BOTTLENECK_DISTANCE_INTERFACE_H_
+#define INCLUDE_BOTTLENECK_DISTANCE_INTERFACE_H_
+
+#include <gudhi/Bottleneck.h>
+
+#include <iostream>
+#include <vector>
+#include <utility>  // for std::pair
+
+namespace Gudhi {
+
+namespace persistence_diagram {
+
+  // bottleneck_distance function renamed for the python function can be called bottleneck_dstance
+  double bottleneck(const std::vector<std::pair<double, double>>& diag1,
+                    const std::vector<std::pair<double, double>>& diag2,
+                    double e) {
+    return bottleneck_distance(diag1, diag2, e);
+  }
+
+  double bottleneck(const std::vector<std::pair<double, double>>& diag1,
+                    const std::vector<std::pair<double, double>>& diag2) {
+    return bottleneck_distance(diag1, diag2);
+  }
+
+}  // namespace persistence_diagram
+
+}  // namespace Gudhi
+
+
+#endif  // INCLUDE_BOTTLENECK_DISTANCE_INTERFACE_H_
diff --git a/src/cython/include/Cubical_complex_interface.h b/src/cython/include/Cubical_complex_interface.h
new file mode 100644
index 00000000..7c0148f1
--- /dev/null
+++ b/src/cython/include/Cubical_complex_interface.h
@@ -0,0 +1,56 @@
+/*    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 INCLUDE_CUBICAL_COMPLEX_INTERFACE_H_
+#define INCLUDE_CUBICAL_COMPLEX_INTERFACE_H_
+
+#include <gudhi/Bitmap_cubical_complex.h>
+#include <gudhi/Bitmap_cubical_complex_base.h>
+#include <gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h>
+
+#include <iostream>
+#include <vector>
+#include <string>
+
+namespace Gudhi {
+
+namespace cubical_complex {
+
+template<typename CubicalComplexOptions = Bitmap_cubical_complex_base<double>>
+class Cubical_complex_interface : public Bitmap_cubical_complex<CubicalComplexOptions> {
+ public:
+  Cubical_complex_interface(const std::vector<unsigned>& dimensions,
+                            const std::vector<double>& top_dimensional_cells)
+  : Bitmap_cubical_complex<CubicalComplexOptions>(dimensions, top_dimensional_cells) {
+  }
+
+  Cubical_complex_interface(const std::string& perseus_file)
+  : Bitmap_cubical_complex<CubicalComplexOptions>(perseus_file.c_str()) {
+  }
+};
+
+}  // namespace cubical_complex
+
+}  // namespace Gudhi
+
+#endif  // INCLUDE_CUBICAL_COMPLEX_INTERFACE_H_
+
diff --git a/src/cython/include/Euclidean_strong_witness_complex_interface.h b/src/cython/include/Euclidean_strong_witness_complex_interface.h
new file mode 100644
index 00000000..b9dd8177
--- /dev/null
+++ b/src/cython/include/Euclidean_strong_witness_complex_interface.h
@@ -0,0 +1,93 @@
+/*    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 INCLUDE_EUCLIDEAN_STRONG_WITNESS_COMPLEX_INTERFACE_H_
+#define INCLUDE_EUCLIDEAN_STRONG_WITNESS_COMPLEX_INTERFACE_H_
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Euclidean_strong_witness_complex.h>
+
+#include "Simplex_tree_interface.h"
+
+#include <CGAL/Epick_d.h>
+
+#include <vector>
+#include <utility>  // std::pair
+#include <iostream>
+#include <cstddef>
+
+namespace Gudhi {
+
+namespace witness_complex {
+
+
+class Euclidean_strong_witness_complex_interface {
+  using Dynamic_kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >;
+  using Point_d = Dynamic_kernel::Point_d;
+
+  typedef typename Simplex_tree<>::Simplex_key Simplex_key;
+
+ public:
+  Euclidean_strong_witness_complex_interface(const std::vector<std::vector<double>>& landmarks,
+                                             const std::vector<std::vector<double>>& witnesses) {
+    landmarks_.reserve(landmarks.size());
+    for (auto& landmark : landmarks)
+      landmarks_.emplace_back(landmark.begin(), landmark.end());
+    witness_complex_ = new Euclidean_strong_witness_complex<Dynamic_kernel>(landmarks_, witnesses);
+  }
+
+  ~Euclidean_strong_witness_complex_interface() {
+    delete witness_complex_;
+  }
+
+  void create_simplex_tree(Gudhi::Simplex_tree<>* simplex_tree, double max_alpha_square,
+                           std::size_t limit_dimension) {
+    witness_complex_->create_complex(*simplex_tree, max_alpha_square, limit_dimension);
+    simplex_tree->initialize_filtration();
+  }
+
+  void create_simplex_tree(Gudhi::Simplex_tree<>* simplex_tree, double max_alpha_square) {
+    witness_complex_->create_complex(*simplex_tree, max_alpha_square);
+    simplex_tree->initialize_filtration();
+  }
+
+  std::vector<double> get_point(unsigned vh) {
+    std::vector<double> vd;
+    if (vh < landmarks_.size()) {
+      Point_d ph = witness_complex_->get_point(vh);
+      for (auto coord = ph.cartesian_begin(); coord < ph.cartesian_end(); coord++)
+        vd.push_back(*coord);
+    }
+    return vd;
+  }
+
+ private:
+  std::vector<Point_d> landmarks_;
+  Euclidean_strong_witness_complex<Dynamic_kernel>* witness_complex_;
+};
+
+}  // namespace witness_complex
+
+}  // namespace Gudhi
+
+#endif  // INCLUDE_EUCLIDEAN_STRONG_WITNESS_COMPLEX_INTERFACE_H_
+
diff --git a/src/cython/include/Euclidean_witness_complex_interface.h b/src/cython/include/Euclidean_witness_complex_interface.h
new file mode 100644
index 00000000..2a09b3b5
--- /dev/null
+++ b/src/cython/include/Euclidean_witness_complex_interface.h
@@ -0,0 +1,92 @@
+/*    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 INCLUDE_EUCLIDEAN_WITNESS_COMPLEX_INTERFACE_H_
+#define INCLUDE_EUCLIDEAN_WITNESS_COMPLEX_INTERFACE_H_
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Euclidean_witness_complex.h>
+
+#include "Simplex_tree_interface.h"
+
+#include <CGAL/Epick_d.h>
+
+#include <vector>
+#include <utility>  // std::pair
+#include <iostream>
+#include <cstddef>
+
+namespace Gudhi {
+
+namespace witness_complex {
+
+
+class Euclidean_witness_complex_interface {
+  using Dynamic_kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >;
+  using Point_d = Dynamic_kernel::Point_d;
+
+  typedef typename Simplex_tree<>::Simplex_key Simplex_key;
+
+ public:
+  Euclidean_witness_complex_interface(const std::vector<std::vector<double>>& landmarks,
+                                      const std::vector<std::vector<double>>& witnesses) {
+    landmarks_.reserve(landmarks.size());
+    for (auto& landmark : landmarks)
+      landmarks_.emplace_back(landmark.begin(), landmark.end());
+    witness_complex_ = new Euclidean_witness_complex<Dynamic_kernel>(landmarks_, witnesses);
+  }
+
+  ~Euclidean_witness_complex_interface() {
+    delete witness_complex_;
+  }
+
+  void create_simplex_tree(Gudhi::Simplex_tree<>* simplex_tree, double max_alpha_square, std::size_t limit_dimension) {
+    witness_complex_->create_complex(*simplex_tree, max_alpha_square, limit_dimension);
+    simplex_tree->initialize_filtration();
+  }
+
+  void create_simplex_tree(Gudhi::Simplex_tree<>* simplex_tree, double max_alpha_square) {
+    witness_complex_->create_complex(*simplex_tree, max_alpha_square);
+    simplex_tree->initialize_filtration();
+  }
+
+  std::vector<double> get_point(unsigned vh) {
+    std::vector<double> vd;
+    if (vh < landmarks_.size()) {
+      Point_d ph = witness_complex_->get_point(vh);
+      for (auto coord = ph.cartesian_begin(); coord < ph.cartesian_end(); coord++)
+        vd.push_back(*coord);
+    }
+    return vd;
+  }
+
+ private:
+  std::vector<Point_d> landmarks_;
+  Euclidean_witness_complex<Dynamic_kernel>* witness_complex_;
+};
+
+}  // namespace witness_complex
+
+}  // namespace Gudhi
+
+#endif  // INCLUDE_EUCLIDEAN_WITNESS_COMPLEX_INTERFACE_H_
+
diff --git a/src/cython/include/Off_reader_interface.h b/src/cython/include/Off_reader_interface.h
new file mode 100644
index 00000000..0ca55500
--- /dev/null
+++ b/src/cython/include/Off_reader_interface.h
@@ -0,0 +1,42 @@
+/*    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 INCLUDE_OFF_READER_INTERFACE_H_
+#define INCLUDE_OFF_READER_INTERFACE_H_
+
+#include <gudhi/Points_off_io.h>
+
+#include <iostream>
+#include <vector>
+#include <string>
+
+namespace Gudhi {
+
+std::vector<std::vector<double>> read_points_from_OFF_file(const std::string& off_file) {
+  Gudhi::Points_off_reader<std::vector<double>> off_reader(off_file);
+  return off_reader.get_point_cloud();
+}
+
+}  // namespace Gudhi
+
+#endif  // INCLUDE_OFF_READER_INTERFACE_H_
+
diff --git a/src/cython/include/Persistent_cohomology_interface.h b/src/cython/include/Persistent_cohomology_interface.h
new file mode 100644
index 00000000..55028fd0
--- /dev/null
+++ b/src/cython/include/Persistent_cohomology_interface.h
@@ -0,0 +1,95 @@
+/*    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 INCLUDE_PERSISTENT_COHOMOLOGY_INTERFACE_H_
+#define INCLUDE_PERSISTENT_COHOMOLOGY_INTERFACE_H_
+
+#include <gudhi/Persistent_cohomology.h>
+
+#include <vector>
+#include <utility>  // for std::pair
+#include <algorithm>  // for sort
+
+namespace Gudhi {
+
+template<class FilteredComplex>
+class Persistent_cohomology_interface : public
+persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomology::Field_Zp> {
+ private:
+  /*
+   * Compare two intervals by dimension, then by length.
+   */
+  struct cmp_intervals_by_dim_then_length {
+    explicit cmp_intervals_by_dim_then_length(FilteredComplex * sc)
+        : sc_(sc) { }
+
+    template<typename Persistent_interval>
+    bool operator()(const Persistent_interval & p1, const Persistent_interval & p2) {
+      if (sc_->dimension(get < 0 > (p1)) == sc_->dimension(get < 0 > (p2)))
+        return (sc_->filtration(get < 1 > (p1)) - sc_->filtration(get < 0 > (p1))
+                > sc_->filtration(get < 1 > (p2)) - sc_->filtration(get < 0 > (p2)));
+      else
+        return (sc_->dimension(get < 0 > (p1)) > sc_->dimension(get < 0 > (p2)));
+    }
+    FilteredComplex* sc_;
+  };
+
+ public:
+  Persistent_cohomology_interface(FilteredComplex* stptr)
+      : persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomology::Field_Zp>(*stptr),
+      stptr_(stptr) { }
+
+  Persistent_cohomology_interface(FilteredComplex* stptr, bool persistence_dim_max)
+      : persistent_cohomology::Persistent_cohomology<FilteredComplex,
+          persistent_cohomology::Field_Zp>(*stptr, persistence_dim_max),
+        stptr_(stptr) { }
+
+  std::vector<std::pair<int, std::pair<double, double>>> get_persistence(int homology_coeff_field,
+                                                                         double min_persistence) {
+    persistent_cohomology::Persistent_cohomology<FilteredComplex,
+      persistent_cohomology::Field_Zp>::init_coefficients(homology_coeff_field);
+    persistent_cohomology::Persistent_cohomology<FilteredComplex,
+      persistent_cohomology::Field_Zp>::compute_persistent_cohomology(min_persistence);
+
+    // Custom sort and output persistence
+    cmp_intervals_by_dim_then_length cmp(stptr_);
+    auto persistent_pairs = persistent_cohomology::Persistent_cohomology<FilteredComplex,
+      persistent_cohomology::Field_Zp>::get_persistent_pairs();
+    std::sort(std::begin(persistent_pairs), std::end(persistent_pairs), cmp);
+
+    std::vector<std::pair<int, std::pair<double, double>>> persistence;
+    for (auto pair : persistent_pairs) {
+      persistence.push_back(std::make_pair(stptr_->dimension(get<0>(pair)),
+                                           std::make_pair(stptr_->filtration(get<0>(pair)),
+                                                          stptr_->filtration(get<1>(pair)))));
+    }
+    return persistence;
+  }
+
+ private:
+  // A copy
+  FilteredComplex* stptr_;
+};
+
+}  // namespace Gudhi
+
+#endif  // INCLUDE_PERSISTENT_COHOMOLOGY_INTERFACE_H_
diff --git a/src/cython/include/Rips_complex_interface.h b/src/cython/include/Rips_complex_interface.h
new file mode 100644
index 00000000..1879bd74
--- /dev/null
+++ b/src/cython/include/Rips_complex_interface.h
@@ -0,0 +1,86 @@
+/*    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 INCLUDE_RIPS_COMPLEX_INTERFACE_H_
+#define INCLUDE_RIPS_COMPLEX_INTERFACE_H_
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Rips_complex.h>
+#include <gudhi/Points_off_io.h>
+#include <gudhi/distance_functions.h>
+#include <gudhi/reader_utils.h>
+
+#include "Simplex_tree_interface.h"
+
+#include <iostream>
+#include <vector>
+#include <utility>  // std::pair
+#include <string>
+
+namespace Gudhi {
+
+namespace rips_complex {
+
+class Rips_complex_interface {
+  using Point_d = std::vector<double>;
+  using Distance_matrix = std::vector<std::vector<Simplex_tree_interface<>::Filtration_value>>;
+
+ public:
+  Rips_complex_interface(const std::vector<std::vector<double>>& values, double threshold, bool euclidean) {
+    if (euclidean) {
+      // Rips construction where values is a vector of points
+      rips_complex_ = new Rips_complex<Simplex_tree_interface<>::Filtration_value>(values, threshold,
+                                                                                   Euclidean_distance());
+    } else {
+      // Rips construction where values is a distance matrix
+      rips_complex_ = new Rips_complex<Simplex_tree_interface<>::Filtration_value>(values, threshold);
+    }
+  }
+
+  Rips_complex_interface(const std::string& file_name, double threshold, bool euclidean, bool from_file = true) {
+    if (euclidean) {
+      // Rips construction where file_name is an OFF file
+      Gudhi::Points_off_reader<Point_d> off_reader(file_name);
+      rips_complex_ = new Rips_complex<Simplex_tree_interface<>::Filtration_value>(off_reader.get_point_cloud(),
+                                                                                   threshold, Euclidean_distance());
+    } else {
+      // Rips construction where values is a distance matrix
+      Distance_matrix distances =
+          read_lower_triangular_matrix_from_csv_file<Simplex_tree_interface<>::Filtration_value>(file_name);
+      rips_complex_ = new Rips_complex<Simplex_tree_interface<>::Filtration_value>(distances, threshold);
+    }
+  }
+
+  void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, int dim_max) {
+    rips_complex_->create_complex(*simplex_tree, dim_max);
+    simplex_tree->initialize_filtration();
+  }
+
+ private:
+  Rips_complex<Simplex_tree_interface<>::Filtration_value>* rips_complex_;
+};
+
+}  // namespace rips_complex
+
+}  // namespace Gudhi
+
+#endif  // INCLUDE_RIPS_COMPLEX_INTERFACE_H_
diff --git a/src/cython/include/Simplex_tree_interface.h b/src/cython/include/Simplex_tree_interface.h
new file mode 100644
index 00000000..4266b3ef
--- /dev/null
+++ b/src/cython/include/Simplex_tree_interface.h
@@ -0,0 +1,149 @@
+/*    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 INCLUDE_SIMPLEX_TREE_INTERFACE_H_
+#define INCLUDE_SIMPLEX_TREE_INTERFACE_H_
+
+#include <gudhi/graph_simplicial_complex.h>
+#include <gudhi/distance_functions.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Points_off_io.h>
+
+#include "Persistent_cohomology_interface.h"
+
+#include <iostream>
+#include <vector>
+#include <utility>  // std::pair
+
+namespace Gudhi {
+
+template<typename SimplexTreeOptions = Simplex_tree_options_full_featured>
+class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
+ public:
+  using Base = Simplex_tree<SimplexTreeOptions>;
+  using Filtration_value = typename Base::Filtration_value;
+  using Vertex_handle = typename Base::Vertex_handle;
+  using Simplex_handle = typename Base::Simplex_handle;
+  using Insertion_result = typename std::pair<Simplex_handle, bool>;
+  using Simplex = std::vector<Vertex_handle>;
+  using Complex = std::vector<std::pair<Simplex, Filtration_value>>;
+
+ public:
+  bool find_simplex(const Simplex& vh) {
+    return (Base::find(vh) != Base::null_simplex());
+  }
+
+  bool insert_simplex(const Simplex& simplex, Filtration_value filtration = 0) {
+    Insertion_result result = Base::insert_simplex(simplex, filtration);
+    Base::initialize_filtration();
+    return (result.second);
+  }
+
+  bool insert_simplex_and_subfaces(const Simplex& simplex, Filtration_value filtration = 0) {
+    Insertion_result result = Base::insert_simplex_and_subfaces(simplex, filtration);
+    Base::initialize_filtration();
+    return (result.second);
+  }
+
+  // Do not interface this function, only used in strong witness interface for complex creation
+  bool insert_simplex(const std::vector<std::size_t>& complex, Filtration_value filtration = 0) {
+    Insertion_result result = Base::insert_simplex(complex, filtration);
+    Base::initialize_filtration();
+    return (result.second);
+  }
+
+  // Do not interface this function, only used in strong witness interface for complex creation
+  bool insert_simplex_and_subfaces(const std::vector<std::size_t>& complex, Filtration_value filtration = 0) {
+    Insertion_result result = Base::insert_simplex_and_subfaces(complex, filtration);
+    Base::initialize_filtration();
+    return (result.second);
+  }
+
+  Filtration_value simplex_filtration(const Simplex& simplex) {
+    return Base::filtration(Base::find(simplex));
+  }
+
+  void remove_maximal_simplex(const Simplex& simplex) {
+    Base::remove_maximal_simplex(Base::find(simplex));
+    Base::initialize_filtration();
+  }
+
+  Complex get_filtered_tree() {
+    Complex filtered_tree;
+    for (auto f_simplex : Base::filtration_simplex_range()) {
+      Simplex simplex;
+      for (auto vertex : Base::simplex_vertex_range(f_simplex)) {
+        simplex.insert(simplex.begin(), vertex);
+      }
+      filtered_tree.push_back(std::make_pair(simplex, Base::filtration(f_simplex)));
+    }
+    return filtered_tree;
+  }
+
+  Complex get_skeleton_tree(int dimension) {
+    Complex skeleton_tree;
+    for (auto f_simplex : Base::skeleton_simplex_range(dimension)) {
+      Simplex simplex;
+      for (auto vertex : Base::simplex_vertex_range(f_simplex)) {
+        simplex.insert(simplex.begin(), vertex);
+      }
+      skeleton_tree.push_back(std::make_pair(simplex, Base::filtration(f_simplex)));
+    }
+    return skeleton_tree;
+  }
+
+  Complex get_star(const Simplex& simplex) {
+    Complex star;
+    for (auto f_simplex : Base::star_simplex_range(Base::find(simplex))) {
+      Simplex simplex_star;
+      for (auto vertex : Base::simplex_vertex_range(f_simplex)) {
+        std::cout << vertex << " ";
+        simplex_star.insert(simplex_star.begin(), vertex);
+      }
+      std::cout << std::endl;
+      star.push_back(std::make_pair(simplex_star, Base::filtration(f_simplex)));
+    }
+    return star;
+  }
+
+  Complex get_cofaces(const Simplex& simplex, int dimension) {
+    Complex cofaces;
+    for (auto f_simplex : Base::cofaces_simplex_range(Base::find(simplex), dimension)) {
+      Simplex simplex_coface;
+      for (auto vertex : Base::simplex_vertex_range(f_simplex)) {
+        std::cout << vertex << " ";
+        simplex_coface.insert(simplex_coface.begin(), vertex);
+      }
+      std::cout << std::endl;
+      cofaces.push_back(std::make_pair(simplex_coface, Base::filtration(f_simplex)));
+    }
+    return cofaces;
+  }
+
+  void create_persistence(Gudhi::Persistent_cohomology_interface<Base>* pcoh) {
+    pcoh = new Gudhi::Persistent_cohomology_interface<Base>(*this);
+  }
+};
+
+}  // namespace Gudhi
+
+#endif  // INCLUDE_SIMPLEX_TREE_INTERFACE_H_
diff --git a/src/cython/include/Strong_witness_complex_interface.h b/src/cython/include/Strong_witness_complex_interface.h
new file mode 100644
index 00000000..d05eaac5
--- /dev/null
+++ b/src/cython/include/Strong_witness_complex_interface.h
@@ -0,0 +1,73 @@
+/*    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 INCLUDE_STRONG_WITNESS_COMPLEX_INTERFACE_H_
+#define INCLUDE_STRONG_WITNESS_COMPLEX_INTERFACE_H_
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Strong_witness_complex.h>
+
+#include "Simplex_tree_interface.h"
+
+#include <vector>
+#include <utility>  // std::pair
+#include <iostream>
+#include <cstddef>
+
+namespace Gudhi {
+
+namespace witness_complex {
+
+class Strong_witness_complex_interface {
+  using Nearest_landmark_range = std::vector<std::pair<std::size_t, double>>;
+  using Nearest_landmark_table = std::vector<Nearest_landmark_range>;
+
+ public:
+  Strong_witness_complex_interface(const Nearest_landmark_table& nlt) {
+    witness_complex_ = new Strong_witness_complex<Nearest_landmark_table>(nlt);
+  }
+
+  ~Strong_witness_complex_interface() {
+    delete witness_complex_;
+  }
+
+  void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, double  max_alpha_square,
+                           std::size_t limit_dimension) {
+    witness_complex_->create_complex(*simplex_tree, max_alpha_square, limit_dimension);
+    simplex_tree->initialize_filtration();
+  }
+
+  void create_simplex_tree(Simplex_tree_interface<>* simplex_tree,
+                           double  max_alpha_square) {
+    witness_complex_->create_complex(*simplex_tree, max_alpha_square);
+    simplex_tree->initialize_filtration();
+  }
+
+ private:
+  Strong_witness_complex<Nearest_landmark_table>* witness_complex_;
+};
+
+}  // namespace witness_complex
+
+}  // namespace Gudhi
+
+#endif  // INCLUDE_STRONG_WITNESS_COMPLEX_INTERFACE_H_
diff --git a/src/cython/include/Subsampling_interface.h b/src/cython/include/Subsampling_interface.h
new file mode 100644
index 00000000..1c6032c0
--- /dev/null
+++ b/src/cython/include/Subsampling_interface.h
@@ -0,0 +1,119 @@
+/*    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 INCLUDE_SUBSAMPLING_INTERFACE_H_
+#define INCLUDE_SUBSAMPLING_INTERFACE_H_
+
+#include <gudhi/choose_n_farthest_points.h>
+#include <gudhi/pick_n_random_points.h>
+#include <gudhi/sparsify_point_set.h>
+#include <gudhi/Points_off_io.h>
+#include <CGAL/Epick_d.h>
+
+#include <iostream>
+#include <vector>
+#include <string>
+
+namespace Gudhi {
+
+namespace subsampling {
+
+using Subsampling_dynamic_kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >;
+using Subsampling_point_d = Subsampling_dynamic_kernel::Point_d;
+using Subsampling_ft = Subsampling_dynamic_kernel::FT;
+
+// ------ choose_n_farthest_points ------
+std::vector<std::vector<double>> subsampling_n_farthest_points(const std::vector<std::vector<double>>& points,
+                                                               unsigned nb_points) {
+  std::vector<std::vector<double>> landmarks;
+  Subsampling_dynamic_kernel k;
+  choose_n_farthest_points(k, points, nb_points, std::back_inserter(landmarks));
+
+  return landmarks;
+}
+
+std::vector<std::vector<double>> subsampling_n_farthest_points(const std::vector<std::vector<double>>& points,
+                                                               unsigned nb_points, unsigned starting_point) {
+  std::vector<std::vector<double>> landmarks;
+  Subsampling_dynamic_kernel k;
+  choose_n_farthest_points(k, points, nb_points, starting_point, std::back_inserter(landmarks));
+
+  return landmarks;
+}
+
+std::vector<std::vector<double>> subsampling_n_farthest_points_from_file(const std::string& off_file,
+                                                                         unsigned nb_points) {
+  Gudhi::Points_off_reader<std::vector<double>> off_reader(off_file);
+  std::vector<std::vector<double>> points = off_reader.get_point_cloud();
+  return subsampling_n_farthest_points(points, nb_points);
+}
+
+std::vector<std::vector<double>> subsampling_n_farthest_points_from_file(const std::string& off_file,
+                                                                         unsigned nb_points, unsigned starting_point) {
+    Gudhi::Points_off_reader<std::vector<double>> off_reader(off_file);
+    std::vector<std::vector<double>> points = off_reader.get_point_cloud();
+    return subsampling_n_farthest_points(points, nb_points, starting_point);
+}
+
+// ------ pick_n_random_points ------
+std::vector<std::vector<double>> subsampling_n_random_points(const std::vector<std::vector<double>>& points,
+                                                             unsigned nb_points) {
+  std::vector<std::vector<double>> landmarks;
+  pick_n_random_points(points, nb_points, std::back_inserter(landmarks));
+
+  return landmarks;
+}
+
+std::vector<std::vector<double>> subsampling_n_random_points_from_file(const std::string& off_file,
+                                                                       unsigned nb_points) {
+  Gudhi::Points_off_reader<std::vector<double>> off_reader(off_file);
+  std::vector<std::vector<double>> points = off_reader.get_point_cloud();
+  return subsampling_n_random_points(points, nb_points);
+}
+
+// ------ sparsify_point_set ------
+std::vector<std::vector<double>> subsampling_sparsify_points(const std::vector<std::vector<double>>& points,
+                                                             double min_squared_dist) {
+  std::vector<Subsampling_point_d> input, output;
+  for (auto point : points)
+      input.push_back(Subsampling_point_d(point.size(), point.begin(), point.end()));
+  Subsampling_dynamic_kernel k;
+  sparsify_point_set(k, input, min_squared_dist, std::back_inserter(output));
+
+  std::vector<std::vector<double>> landmarks;
+  for (auto point : output)
+      landmarks.push_back(std::vector<double>(point.cartesian_begin(), point.cartesian_end()));
+  return landmarks;
+}
+
+std::vector<std::vector<double>> subsampling_sparsify_points_from_file(const std::string& off_file,
+                                                                       double min_squared_dist) {
+  Gudhi::Points_off_reader<std::vector<double>> off_reader(off_file);
+  std::vector<std::vector<double>> points = off_reader.get_point_cloud();
+  return subsampling_sparsify_points(points, min_squared_dist);
+}
+
+}  // namespace subsampling
+
+}  // namespace Gudhi
+
+#endif  // INCLUDE_SUBSAMPLING_INTERFACE_H_
diff --git a/src/cython/include/Tangential_complex_interface.h b/src/cython/include/Tangential_complex_interface.h
new file mode 100644
index 00000000..5e9dc0e4
--- /dev/null
+++ b/src/cython/include/Tangential_complex_interface.h
@@ -0,0 +1,123 @@
+/*    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 INCLUDE_TANGENTIAL_COMPLEX_INTERFACE_H_
+#define INCLUDE_TANGENTIAL_COMPLEX_INTERFACE_H_
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Tangential_complex.h>
+#include <gudhi/Points_off_io.h>
+#include <CGAL/Epick_d.h>
+
+#include "Simplex_tree_interface.h"
+
+#include <vector>
+#include <utility>  // std::pair
+#include <iostream>
+#include <string>
+
+namespace Gudhi {
+
+namespace tangential_complex {
+
+class Tangential_complex_interface {
+  using Dynamic_kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >;
+  using Point_d = Dynamic_kernel::Point_d;
+  using TC = Tangential_complex<Dynamic_kernel, CGAL::Dynamic_dimension_tag, CGAL::Parallel_tag>;
+
+ public:
+  Tangential_complex_interface(const std::vector<std::vector<double>>& points) {
+    Dynamic_kernel k;
+    unsigned intrisic_dim = 0;
+    if (points.size() > 0)
+      intrisic_dim = points[0].size() - 1;
+
+    tangential_complex_ = new TC(points, intrisic_dim, k);
+    tangential_complex_->compute_tangential_complex();
+    num_inconsistencies_ = tangential_complex_->number_of_inconsistent_simplices();
+  }
+
+  Tangential_complex_interface(const std::string& off_file_name, bool from_file = true) {
+    Gudhi::Points_off_reader<Point_d> off_reader(off_file_name);
+    Dynamic_kernel k;
+    unsigned intrisic_dim = 0;
+    std::vector<Point_d> points = off_reader.get_point_cloud();
+    if (points.size() > 0)
+      intrisic_dim = points[0].size() - 1;
+
+    tangential_complex_ = new TC(points, intrisic_dim, k);
+    tangential_complex_->compute_tangential_complex();
+    num_inconsistencies_ = tangential_complex_->number_of_inconsistent_simplices();
+  }
+
+  ~Tangential_complex_interface() {
+    delete tangential_complex_;
+  }
+
+  std::vector<double> get_point(unsigned vh) {
+    std::vector<double> vd;
+    if (vh < tangential_complex_->number_of_vertices()) {
+      Point_d ph = tangential_complex_->get_point(vh);
+      for (auto coord = ph.cartesian_begin(); coord < ph.cartesian_end(); coord++)
+        vd.push_back(*coord);
+    }
+    return vd;
+  }
+
+  unsigned number_of_vertices() {
+    return tangential_complex_->number_of_vertices();
+  }
+
+  unsigned number_of_simplices() {
+    return num_inconsistencies_.num_simplices;
+  }
+
+  unsigned number_of_inconsistent_simplices() {
+    return num_inconsistencies_.num_inconsistent_simplices;
+  }
+
+  unsigned number_of_inconsistent_stars() {
+    return num_inconsistencies_.num_inconsistent_stars;
+  }
+
+  void fix_inconsistencies_using_perturbation(double max_perturb, double time_limit) {
+      tangential_complex_->fix_inconsistencies_using_perturbation(max_perturb, time_limit);
+      num_inconsistencies_ = tangential_complex_->number_of_inconsistent_simplices();
+  }
+
+  void create_simplex_tree(Simplex_tree<>* simplex_tree) {
+    int max_dim = tangential_complex_->create_complex<Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>>(*simplex_tree);
+    // FIXME
+    simplex_tree->set_dimension(max_dim);
+    simplex_tree->initialize_filtration();
+  }
+
+ private:
+  TC* tangential_complex_;
+  TC::Num_inconsistencies num_inconsistencies_;
+};
+
+}  // namespace tangential_complex
+
+}  // namespace Gudhi
+
+#endif  // INCLUDE_TANGENTIAL_COMPLEX_INTERFACE_H_
diff --git a/src/cython/include/Witness_complex_interface.h b/src/cython/include/Witness_complex_interface.h
new file mode 100644
index 00000000..6501cc35
--- /dev/null
+++ b/src/cython/include/Witness_complex_interface.h
@@ -0,0 +1,74 @@
+/*    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 INCLUDE_WITNESS_COMPLEX_INTERFACE_H_
+#define INCLUDE_WITNESS_COMPLEX_INTERFACE_H_
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Witness_complex.h>
+
+#include "Simplex_tree_interface.h"
+
+#include <vector>
+#include <utility>  // std::pair
+#include <iostream>
+#include <cstddef>
+
+namespace Gudhi {
+
+namespace witness_complex {
+
+class Witness_complex_interface {
+  using Nearest_landmark_range = std::vector<std::pair<std::size_t, double>>;
+  using Nearest_landmark_table = std::vector<Nearest_landmark_range>;
+
+ public:
+  Witness_complex_interface(const Nearest_landmark_table& nlt) {
+    witness_complex_ = new Witness_complex<Nearest_landmark_table>(nlt);
+  }
+
+  ~Witness_complex_interface() {
+    delete witness_complex_;
+  }
+
+  void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, double  max_alpha_square,
+                           std::size_t limit_dimension) {
+    witness_complex_->create_complex(*simplex_tree, max_alpha_square, limit_dimension);
+    simplex_tree->initialize_filtration();
+  }
+
+  void create_simplex_tree(Simplex_tree_interface<>* simplex_tree,
+                           double  max_alpha_square) {
+    witness_complex_->create_complex(*simplex_tree, max_alpha_square);
+    simplex_tree->initialize_filtration();
+  }
+
+ private:
+  Witness_complex<Nearest_landmark_table>* witness_complex_;
+};
+
+}  // namespace witness_complex
+
+}  // namespace Gudhi
+
+#endif  // INCLUDE_WITNESS_COMPLEX_INTERFACE_H_
+
diff --git a/src/cython/test/test_alpha_complex.py b/src/cython/test/test_alpha_complex.py
new file mode 100755
index 00000000..2625d529
--- /dev/null
+++ b/src/cython/test/test_alpha_complex.py
@@ -0,0 +1,86 @@
+from gudhi import AlphaComplex, SimplexTree
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+
+def test_empty_alpha():
+    alpha_complex = AlphaComplex(points=[[0,0]])
+    assert alpha_complex.__is_defined() == True
+
+def test_infinite_alpha():
+    point_list = [[0, 0], [1, 0], [0, 1], [1, 1]]
+    alpha_complex = AlphaComplex(points=point_list)
+    assert alpha_complex.__is_defined() == True
+
+    simplex_tree = alpha_complex.create_simplex_tree()
+    assert simplex_tree.__is_persistence_defined() == False
+
+    assert simplex_tree.num_simplices() == 11
+    assert simplex_tree.num_vertices() == 4
+ 
+    assert simplex_tree.get_filtered_tree() == \
+           [([0], 0.0), ([1], 0.0), ([2], 0.0), ([3], 0.0),
+            ([0, 1], 0.25), ([0, 2], 0.25), ([1, 3], 0.25),
+            ([2, 3], 0.25), ([1, 2], 0.5), ([0, 1, 2], 0.5),
+            ([1, 2, 3], 0.5)]
+    assert simplex_tree.get_star([0]) == \
+           [([0], 0.0), ([0, 1], 0.25), ([0, 1, 2], 0.5),
+           ([0, 2], 0.25)]
+    assert simplex_tree.get_cofaces([0], 1) == \
+           [([0, 1], 0.25), ([0, 2], 0.25)]
+ 
+    assert point_list[0] == alpha_complex.get_point(0)
+    assert point_list[1] == alpha_complex.get_point(1)
+    assert point_list[2] == alpha_complex.get_point(2)
+    assert point_list[3] == alpha_complex.get_point(3)
+    assert alpha_complex.get_point(4) == []
+    assert alpha_complex.get_point(125) == []
+
+def test_filtered_alpha():
+    point_list = [[0, 0], [1, 0], [0, 1], [1, 1]]
+    filtered_alpha = AlphaComplex(points=point_list)
+
+    simplex_tree = filtered_alpha.create_simplex_tree(max_alpha_square=0.25)
+
+    assert simplex_tree.num_simplices() == 8
+    assert simplex_tree.num_vertices() == 4
+
+    assert point_list[0] == filtered_alpha.get_point(0)
+    assert point_list[1] == filtered_alpha.get_point(1)
+    assert point_list[2] == filtered_alpha.get_point(2)
+    assert point_list[3] == filtered_alpha.get_point(3)
+    assert filtered_alpha.get_point(4) == []
+    assert filtered_alpha.get_point(125) == []
+
+    assert simplex_tree.get_filtered_tree() == \
+           [([0], 0.0), ([1], 0.0), ([2], 0.0), ([3], 0.0),
+            ([0, 1], 0.25), ([0, 2], 0.25), ([1, 3], 0.25),
+            ([2, 3], 0.25)]
+    assert simplex_tree.get_star([0]) == \
+           [([0], 0.0), ([0, 1], 0.25), ([0, 2], 0.25)]
+    assert simplex_tree.get_cofaces([0], 1) == \
+           [([0, 1], 0.25), ([0, 2], 0.25)]
diff --git a/src/cython/test/test_bottleneck_distance.py b/src/cython/test/test_bottleneck_distance.py
new file mode 100755
index 00000000..3d982d34
--- /dev/null
+++ b/src/cython/test/test_bottleneck_distance.py
@@ -0,0 +1,35 @@
+import gudhi
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+
+def test_basic_bottleneck():
+    diag1 = [[2.7, 3.7],[9.6, 14.],[34.2, 34.974], [3.,float('Inf')]]
+    diag2 = [[2.8, 4.45],[9.5, 14.1],[3.2,float('Inf')]]
+
+    assert(gudhi.bottleneck_distance(diag1, diag2, 0.1) == 0.8081763781405569)
+    assert(gudhi.bottleneck_distance(diag1, diag2) == 0.75)
diff --git a/src/cython/test/test_cubical_complex.py b/src/cython/test/test_cubical_complex.py
new file mode 100755
index 00000000..c8df8089
--- /dev/null
+++ b/src/cython/test/test_cubical_complex.py
@@ -0,0 +1,86 @@
+from gudhi import CubicalComplex
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+
+def test_empty_constructor():
+    # Try to create an empty CubicalComplex
+    cub = CubicalComplex()
+    assert cub.__is_defined() == False
+    assert cub.__is_persistence_defined() == False
+
+def test_non_existing_perseus_file_constructor():
+    # Try to open a non existing file
+    cub = CubicalComplex(perseus_file='pouetpouettralala.toubiloubabdou')
+    assert cub.__is_defined() == False
+    assert cub.__is_persistence_defined() == False
+
+def test_dimension_or_perseus_file_constructor():
+    # Create test file
+    test_file = open('CubicalOneSphere.txt', 'w')
+    test_file.write('2\n3\n3\n0\n0\n0\n0\n100\n0\n0\n0\n0\n')
+    test_file.close()
+    # CubicalComplex can be constructed from dimensions and
+    # top_dimensional_cells OR from a perseus file style name.
+    cub = CubicalComplex(dimensions=[3, 3],
+                         top_dimensional_cells = [1,2,3,4,5,6,7,8,9],
+                         perseus_file='CubicalOneSphere.txt')
+    assert cub.__is_defined() == False
+    assert cub.__is_persistence_defined() == False
+
+    cub = CubicalComplex(top_dimensional_cells = [1,2,3,4,5,6,7,8,9],
+                         perseus_file='CubicalOneSphere.txt')
+    assert cub.__is_defined() == False
+    assert cub.__is_persistence_defined() == False
+
+    cub = CubicalComplex(dimensions=[3, 3],
+                         perseus_file='CubicalOneSphere.txt')
+    assert cub.__is_defined() == False
+    assert cub.__is_persistence_defined() == False
+
+def test_dimension_constructor():
+    cub = CubicalComplex(dimensions=[3, 3],
+                         top_dimensional_cells = [1,2,3,4,5,6,7,8,9])
+    assert cub.__is_defined() == True
+    assert cub.__is_persistence_defined() == False
+    assert cub.persistence() == [(1, (0.0, 100.0)), (0, (0.0, 1.8446744073709552e+19))]
+    assert cub.__is_persistence_defined() == True
+    assert cub.betti_numbers() == [1, 0]
+    assert cub.persistent_betti_numbers(0, 1000) == [0, 0]
+
+def test_dimension_constructor():
+    # Create test file
+    test_file = open('CubicalOneSphere.txt', 'w')
+    test_file.write('2\n3\n3\n0\n0\n0\n0\n100\n0\n0\n0\n0\n')
+    test_file.close()
+    cub = CubicalComplex(perseus_file='CubicalOneSphere.txt')
+    assert cub.__is_defined() == True
+    assert cub.__is_persistence_defined() == False
+    assert cub.persistence() == [(1, (0.0, 100.0)), (0, (0.0, 1.8446744073709552e+19))]
+    assert cub.__is_persistence_defined() == True
+    assert cub.betti_numbers() == [1, 0, 0]
+    assert cub.persistent_betti_numbers(0, 1000) == [1, 0, 0]
diff --git a/src/cython/test/test_euclidean_witness_complex.py b/src/cython/test/test_euclidean_witness_complex.py
new file mode 100755
index 00000000..0947cc09
--- /dev/null
+++ b/src/cython/test/test_euclidean_witness_complex.py
@@ -0,0 +1,71 @@
+import gudhi
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+
+def test_empty_euclidean_witness_complex():
+    euclidean_witness = gudhi.EuclideanWitnessComplex()
+    assert euclidean_witness.__is_defined() == False
+
+def test_witness_complex():
+    point_cloud = [[1.0, 1.0], [7.0, 0.0], [4.0, 6.0], [9.0, 6.0],
+        [0.0, 14.0], [2.0, 19.0], [9.0, 17.0]]
+    landmarks = [[1.0, 1.0], [7.0, 0.0], [4.0, 6.0]]
+    euclidean_witness_complex = gudhi.EuclideanWitnessComplex(landmarks=landmarks, witnesses = point_cloud)
+    simplex_tree = euclidean_witness_complex.create_simplex_tree(max_alpha_square=4.1)
+
+    assert landmarks[0] == euclidean_witness_complex.get_point(0)
+    assert landmarks[1] == euclidean_witness_complex.get_point(1)
+    assert landmarks[2] == euclidean_witness_complex.get_point(2)
+
+    assert simplex_tree.get_filtered_tree() == [([0], 0.0), ([1], 0.0),
+        ([0, 1], 0.0), ([2], 0.0), ([0, 2], 0.0), ([1, 2], 0.0),
+        ([0, 1, 2], 0.0)]
+
+def test_empty_euclidean_strong_witness_complex():
+    euclidean_strong_witness = gudhi.EuclideanStrongWitnessComplex()
+    assert euclidean_strong_witness.__is_defined() == False
+
+def test_strong_witness_complex():
+    point_cloud = [[1.0, 1.0], [7.0, 0.0], [4.0, 6.0], [9.0, 6.0],
+        [0.0, 14.0], [2.0, 19.0], [9.0, 17.0]]
+    landmarks = [[1.0, 1.0], [7.0, 0.0], [4.0, 6.0]]
+    euclidean_strong_witness_complex = gudhi.EuclideanStrongWitnessComplex(landmarks=landmarks, witnesses = point_cloud)
+    simplex_tree = euclidean_strong_witness_complex.create_simplex_tree(max_alpha_square=14.9)
+
+    assert landmarks[0] == euclidean_strong_witness_complex.get_point(0)
+    assert landmarks[1] == euclidean_strong_witness_complex.get_point(1)
+    assert landmarks[2] == euclidean_strong_witness_complex.get_point(2)
+
+    assert simplex_tree.get_filtered_tree() == [([0], 0.0), ([1], 0.0), ([2], 0.0)]
+
+    simplex_tree = euclidean_strong_witness_complex.create_simplex_tree(max_alpha_square=100.0)
+
+    assert simplex_tree.get_filtered_tree() == [([0], 0.0), ([1], 0.0),
+    ([2], 0.0), ([1, 2], 15.0), ([0, 2], 34.0), ([0, 1], 37.0),
+    ([0, 1, 2], 37.0)]
+
diff --git a/src/cython/test/test_rips_complex.py b/src/cython/test/test_rips_complex.py
new file mode 100755
index 00000000..286a645b
--- /dev/null
+++ b/src/cython/test/test_rips_complex.py
@@ -0,0 +1,111 @@
+from gudhi import RipsComplex
+from math import sqrt
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+
+def test_empty_rips():
+    rips_complex = RipsComplex()
+    assert rips_complex.__is_defined() == True
+
+def test_rips_from_points():
+    point_list = [[0, 0], [1, 0], [0, 1], [1, 1]]
+    rips_complex = RipsComplex(points=point_list, max_edge_length=42)
+
+    simplex_tree = rips_complex.create_simplex_tree(max_dimension=1)
+
+    assert simplex_tree.__is_defined() == True
+    assert simplex_tree.__is_persistence_defined() == False
+
+    assert simplex_tree.num_simplices() == 10
+    assert simplex_tree.num_vertices() == 4
+
+    assert simplex_tree.get_filtered_tree() == \
+           [([0], 0.0), ([1], 0.0), ([2], 0.0), ([3], 0.0),
+            ([0, 1], 1.0), ([0, 2], 1.0), ([1, 3], 1.0),
+            ([2, 3], 1.0), ([1, 2], 1.4142135623730951),
+            ([0, 3], 1.4142135623730951)]
+    assert simplex_tree.get_star([0]) == \
+           [([0], 0.0), ([0, 1], 1.0), ([0, 2], 1.0),
+            ([0, 3], 1.4142135623730951)]
+    assert simplex_tree.get_cofaces([0], 1) == \
+           [([0, 1], 1.0), ([0, 2], 1.0),
+            ([0, 3], 1.4142135623730951)]
+
+def test_filtered_rips_from_points():
+    point_list = [[0, 0], [1, 0], [0, 1], [1, 1]]
+    filtered_rips = RipsComplex(points=point_list, max_edge_length=1.0)
+
+    simplex_tree = filtered_rips.create_simplex_tree(max_dimension=1)
+
+    assert simplex_tree.__is_defined() == True
+    assert simplex_tree.__is_persistence_defined() == False
+
+    assert simplex_tree.num_simplices() == 8
+    assert simplex_tree.num_vertices() == 4
+
+def test_rips_from_distance_matrix():
+    distance_matrix = [[0],
+                       [1, 0],
+                       [1, sqrt(2), 0],
+                       [sqrt(2), 1, 1, 0]]
+    rips_complex = RipsComplex(distance_matrix=distance_matrix, max_edge_length=42)
+
+    simplex_tree = rips_complex.create_simplex_tree(max_dimension=1)
+
+    assert simplex_tree.__is_defined() == True
+    assert simplex_tree.__is_persistence_defined() == False
+
+    assert simplex_tree.num_simplices() == 10
+    assert simplex_tree.num_vertices() == 4
+
+    assert simplex_tree.get_filtered_tree() == \
+           [([0], 0.0), ([1], 0.0), ([2], 0.0), ([3], 0.0),
+            ([0, 1], 1.0), ([0, 2], 1.0), ([1, 3], 1.0),
+            ([2, 3], 1.0), ([1, 2], 1.4142135623730951),
+            ([0, 3], 1.4142135623730951)]
+    assert simplex_tree.get_star([0]) == \
+           [([0], 0.0), ([0, 1], 1.0), ([0, 2], 1.0),
+            ([0, 3], 1.4142135623730951)]
+    assert simplex_tree.get_cofaces([0], 1) == \
+           [([0, 1], 1.0), ([0, 2], 1.0),
+            ([0, 3], 1.4142135623730951)]
+
+def test_filtered_rips_from_distance_matrix():
+    distance_matrix = [[0],
+                       [1, 0],
+                       [1, sqrt(2), 0],
+                       [sqrt(2), 1, 1, 0]]
+    filtered_rips = RipsComplex(distance_matrix=distance_matrix, max_edge_length=1.0)
+
+    simplex_tree = filtered_rips.create_simplex_tree(max_dimension=1)
+
+    assert simplex_tree.__is_defined() == True
+    assert simplex_tree.__is_persistence_defined() == False
+
+    assert simplex_tree.num_simplices() == 8
+    assert simplex_tree.num_vertices() == 4
diff --git a/src/cython/test/test_simplex_tree.py b/src/cython/test/test_simplex_tree.py
new file mode 100755
index 00000000..af5b639a
--- /dev/null
+++ b/src/cython/test/test_simplex_tree.py
@@ -0,0 +1,133 @@
+from gudhi import SimplexTree
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+
+def test_insertion():
+    st = SimplexTree()
+    assert st.__is_defined() == True
+    assert st.__is_persistence_defined() == False
+
+    # insert test
+    assert st.insert_simplex([0, 1]) == True
+    assert st.insert_simplex_and_subfaces([0, 1, 2], filtration=4.0) == True
+    # FIXME: Remove this line
+    st.set_dimension(2)
+    assert st.num_simplices() == 7
+    assert st.num_vertices() == 3
+
+    # find test
+    assert st.find([0, 1, 2]) == True
+    assert st.find([0, 1]) == True
+    assert st.find([0, 2]) == True
+    assert st.find([0]) == True
+    assert st.find([1]) == True
+    assert st.find([2]) == True
+    assert st.find([3])    == False
+    assert st.find([0, 3]) == False
+    assert st.find([1, 3]) == False
+    assert st.find([2, 3]) == False
+
+    # filtration test
+    st.set_filtration(5.0)
+    st.initialize_filtration()
+    assert st.get_filtration() == 5.0
+    assert st.filtration([0, 1, 2]) == 4.0
+    assert st.filtration([0, 2]) == 4.0
+    assert st.filtration([1, 2]) == 4.0
+    assert st.filtration([2]) == 4.0
+    assert st.filtration([0, 1]) == 0.0
+    assert st.filtration([0]) == 0.0
+    assert st.filtration([1]) == 4.0
+
+    # skeleton_tree test
+    assert st.get_skeleton_tree(2) == \
+        [([0, 1, 2], 4.0), ([0, 1], 0.0), ([0, 2], 4.0),
+        ([0], 0.0), ([1, 2], 4.0), ([1], 4.0), ([2], 4.0)]
+    assert st.get_skeleton_tree(1) == \
+        [([0, 1], 0.0), ([0, 2], 4.0), ([0], 0.0),
+        ([1, 2], 4.0), ([1], 4.0), ([2], 4.0)]
+    assert st.get_skeleton_tree(0) == \
+        [([0], 0.0), ([1], 4.0), ([2], 4.0)]
+
+    # remove_maximal_simplex test
+    assert st.get_cofaces([0, 1, 2], 1) == []
+    st.remove_maximal_simplex([0, 1, 2])
+    assert st.get_skeleton_tree(2) == \
+        [([0, 1], 0.0), ([0, 2], 4.0), ([0], 0.0),
+        ([1, 2], 4.0), ([1], 4.0), ([2], 4.0)]
+    assert st.find([0, 1, 2]) == False
+    assert st.find([0, 1]) == True
+    assert st.find([0, 2]) == True
+    assert st.find([0]) == True
+    assert st.find([1]) == True
+    assert st.find([2]) == True
+
+    st.initialize_filtration()
+    assert st.persistence() == [(1, (4.0, float('inf'))), (0, (0.0, float('inf')))]
+    assert st.__is_persistence_defined() == True
+    assert st.betti_numbers() == [1, 1]
+    assert st.persistent_betti_numbers(-0.1, 10000.0) == [0, 0]
+    assert st.persistent_betti_numbers(0.0, 10000.0) == [1, 0]
+    assert st.persistent_betti_numbers(3.9, 10000.0) == [1, 0]
+    assert st.persistent_betti_numbers(4.0, 10000.0) == [1, 1]
+    assert st.persistent_betti_numbers(9999.0, 10000.0) == [1, 1]
+
+def test_expansion():
+    st = SimplexTree()
+    assert st.__is_defined() == True
+    assert st.__is_persistence_defined() == False
+
+    # insert test
+    assert st.insert_simplex_and_subfaces([3, 2], 0.1) == True
+    assert st.insert_simplex_and_subfaces([2, 0], 0.2) == True
+    assert st.insert_simplex_and_subfaces([1, 0], 0.3) == True
+    assert st.insert_simplex_and_subfaces([3, 1], 0.4) == True
+    assert st.insert_simplex_and_subfaces([2, 1], 0.5) == True
+    assert st.insert_simplex_and_subfaces([6, 5], 0.6) == True
+    assert st.insert_simplex_and_subfaces([4, 2], 0.7) == True
+    assert st.insert_simplex_and_subfaces([3, 0], 0.8) == True
+    assert st.insert_simplex_and_subfaces([6, 4], 0.9) == True
+    assert st.insert_simplex_and_subfaces([6, 3], 1.0) == True
+
+    assert st.num_vertices() == 7
+    assert st.num_simplices() == 17
+    assert st.get_filtered_tree() == [([2], 0.1), ([3], 0.1), ([2, 3], 0.1),
+    ([0], 0.2), ([0, 2], 0.2), ([1], 0.3), ([0, 1], 0.3), ([1, 3], 0.4),
+    ([1, 2], 0.5), ([5], 0.6), ([6], 0.6), ([5, 6], 0.6), ([4], 0.7),
+    ([2, 4], 0.7), ([0, 3], 0.8), ([4, 6], 0.9), ([3, 6], 1.0)]
+
+    st.expansion(3)
+    assert st.num_vertices() == 7
+    assert st.num_simplices() == 22
+    st.initialize_filtration()
+
+    assert st.get_filtered_tree() == [([2], 0.1), ([3], 0.1), ([2, 3], 0.1),
+    ([0], 0.2), ([0, 2], 0.2), ([1], 0.3), ([0, 1], 0.3), ([1, 3], 0.4),
+    ([1, 2], 0.5), ([0, 1, 2], 0.5), ([1, 2, 3], 0.5), ([5], 0.6), ([6], 0.6),
+    ([5, 6], 0.6), ([4], 0.7), ([2, 4], 0.7), ([0, 3], 0.8), ([0, 1, 3], 0.8),
+    ([0, 2, 3], 0.8), ([0, 1, 2, 3], 0.8), ([4, 6], 0.9), ([3, 6], 1.0)]
diff --git a/src/cython/test/test_subsampling.py b/src/cython/test/test_subsampling.py
new file mode 100755
index 00000000..2caf4ddb
--- /dev/null
+++ b/src/cython/test/test_subsampling.py
@@ -0,0 +1,133 @@
+import gudhi
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+
+def test_write_off_file_for_tests():
+    file = open("subsample.off", "w")
+    file.write("nOFF\n")
+    file.write("2 7 0 0\n")
+    file.write("1.0 1.0\n")
+    file.write("7.0 0.0\n")
+    file.write("4.0 6.0\n")
+    file.write("9.0 6.0\n")
+    file.write("0.0 14.0\n")
+    file.write("2.0 19.0\n")
+    file.write("9.0 17.0\n")
+    file.close()
+
+def test_simple_choose_n_farthest_points_with_a_starting_point():
+    point_set = [[0,1], [0,0], [1,0], [1,1]]
+    i = 0
+    for point in point_set:
+        # The iteration starts with the given starting point
+        sub_set = gudhi.choose_n_farthest_points(points = point_set, nb_points = 1, starting_point = i)
+        assert sub_set[0] == point_set[i]
+        i = i + 1
+
+    # The iteration finds then the farthest
+    sub_set = gudhi.choose_n_farthest_points(points = point_set, nb_points = 2, starting_point = 1)
+    assert sub_set[1] == point_set[3]
+    sub_set = gudhi.choose_n_farthest_points(points = point_set, nb_points = 2, starting_point = 3)
+    assert sub_set[1] == point_set[1]
+    sub_set = gudhi.choose_n_farthest_points(points = point_set, nb_points = 2, starting_point = 0)
+    assert sub_set[1] == point_set[2]
+    sub_set = gudhi.choose_n_farthest_points(points = point_set, nb_points = 2, starting_point = 2)
+    assert sub_set[1] == point_set[0]
+
+    # Test the limits
+    assert gudhi.choose_n_farthest_points(points = [], nb_points = 0, starting_point = 0) == []
+    assert gudhi.choose_n_farthest_points(points = [], nb_points = 1, starting_point = 0) == []
+    assert gudhi.choose_n_farthest_points(points = [], nb_points = 0, starting_point = 1) == []
+    assert gudhi.choose_n_farthest_points(points = [], nb_points = 1, starting_point = 1) == []
+
+    # From off file test
+    for i in range (0, 7):
+        assert len(gudhi.choose_n_farthest_points(off_file = 'subsample.off', nb_points = i, starting_point = i)) == i
+
+def test_simple_choose_n_farthest_points_randomed():
+    point_set = [[0,1], [0,0], [1,0], [1,1]]
+    # Test the limits
+    assert gudhi.choose_n_farthest_points(points = [], nb_points = 0) == []
+    assert gudhi.choose_n_farthest_points(points = [], nb_points = 1) == []
+    assert gudhi.choose_n_farthest_points(points = point_set, nb_points = 0) == []
+
+    # Go furter than point set on purpose
+    for iter in range(1,10):
+        sub_set = gudhi.choose_n_farthest_points(points = point_set, nb_points = iter)
+        for sub in sub_set:
+            found = False
+            for point in point_set:
+                if point == sub:
+                    found = True
+            # Check each sub set point is existing in the point set
+            assert found == True
+
+    # From off file test
+    for i in range (0, 7):
+        assert len(gudhi.choose_n_farthest_points(off_file = 'subsample.off', nb_points = i)) == i
+
+def test_simple_pick_n_random_points():
+    point_set = [[0,1], [0,0], [1,0], [1,1]]
+    # Test the limits
+    assert gudhi.pick_n_random_points(points = [], nb_points = 0) == []
+    assert gudhi.pick_n_random_points(points = [], nb_points = 1) == []
+    assert gudhi.pick_n_random_points(points = point_set, nb_points = 0) == []
+
+    # Go furter than point set on purpose
+    for iter in range(1,10):
+        sub_set = gudhi.pick_n_random_points(points = point_set, nb_points = iter)
+        print(5)
+        for sub in sub_set:
+            found = False
+            for point in point_set:
+                if point == sub:
+                    found = True
+            # Check each sub set point is existing in the point set
+            assert found == True
+
+    # From off file test
+    for i in range (0, 7):
+        assert len(gudhi.pick_n_random_points(off_file = 'subsample.off', nb_points = i)) == i
+
+def test_simple_sparsify_points():
+    point_set = [[0,1], [0,0], [1,0], [1,1]]
+    # Test the limits
+    # assert gudhi.sparsify_point_set(points = [], min_squared_dist = 0.0) == []
+    # assert gudhi.sparsify_point_set(points = [], min_squared_dist = 10.0) == []
+    assert gudhi.sparsify_point_set(points = point_set, min_squared_dist = 0.0) == point_set
+    assert gudhi.sparsify_point_set(points = point_set, min_squared_dist = 1.0) == point_set
+    assert gudhi.sparsify_point_set(points = point_set, min_squared_dist = 2.0) == [[0,1], [1,0]]
+    assert gudhi.sparsify_point_set(points = point_set, min_squared_dist = 2.01) == [[0,1]]
+
+    assert len(gudhi.sparsify_point_set(off_file = 'subsample.off', min_squared_dist = 0.0)) == 7
+    assert len(gudhi.sparsify_point_set(off_file = 'subsample.off', min_squared_dist = 30.0)) == 5
+    assert len(gudhi.sparsify_point_set(off_file = 'subsample.off', min_squared_dist = 40.0)) == 4
+    assert len(gudhi.sparsify_point_set(off_file = 'subsample.off', min_squared_dist = 90.0)) == 3
+    assert len(gudhi.sparsify_point_set(off_file = 'subsample.off', min_squared_dist = 100.0)) == 2
+    assert len(gudhi.sparsify_point_set(off_file = 'subsample.off', min_squared_dist = 325.0)) == 2
+    assert len(gudhi.sparsify_point_set(off_file = 'subsample.off', min_squared_dist = 325.01)) == 1
diff --git a/src/cython/test/test_tangential_complex.py b/src/cython/test/test_tangential_complex.py
new file mode 100755
index 00000000..c191baa4
--- /dev/null
+++ b/src/cython/test/test_tangential_complex.py
@@ -0,0 +1,52 @@
+from gudhi import TangentialComplex, SimplexTree
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+
+def test_tangential():
+    point_list = [[0.0, 0.0], [1.0, 0.0], [0.0, 1.0], [1.0, 1.0]]
+    tc = TangentialComplex(points=point_list)
+    assert tc.__is_defined() == True
+    assert tc.num_vertices() == 4
+
+    st = tc.create_simplex_tree()
+    assert st.__is_defined() == True
+    assert st.__is_persistence_defined() == False
+
+    assert st.num_simplices() == 6
+    assert st.num_vertices() == 4
+ 
+    assert st.get_filtered_tree() == \
+        [([0], 0.0), ([1], 0.0), ([2], 0.0), ([0, 2], 0.0), ([3], 0.0), ([1, 3], 0.0)]
+    assert st.get_cofaces([0], 1) == [([0, 2], 0.0)]
+ 
+    assert point_list[0] == tc.get_point(0)
+    assert point_list[1] == tc.get_point(1)
+    assert point_list[2] == tc.get_point(2)
+    assert point_list[3] == tc.get_point(3)
+    assert tc.get_point(4) == []
+    assert tc.get_point(125) == []
diff --git a/src/cython/test/test_witness_complex.py b/src/cython/test/test_witness_complex.py
new file mode 100755
index 00000000..7d1fb6be
--- /dev/null
+++ b/src/cython/test/test_witness_complex.py
@@ -0,0 +1,62 @@
+from gudhi import WitnessComplex, StrongWitnessComplex, SimplexTree
+
+"""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/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 INRIA"
+__license__ = "GPL v3"
+
+
+def test_empty_witness_complex():
+    witness = WitnessComplex()
+    assert witness.__is_defined() == False
+
+def test_witness_complex():
+    nearest_landmark_table = [[[0, 0], [1, 1], [2, 2], [3, 3], [4, 4]],
+                              [[1, 0], [2, 1], [3, 2], [4, 3], [0, 4]],
+                              [[2, 0], [3, 1], [4, 2], [0, 3], [1, 4]],
+                              [[3, 0], [4, 1], [0, 2], [1, 3], [2, 4]],
+                              [[4, 0], [0, 1], [1, 2], [2, 3], [3, 4]]]
+
+    witness_complex = WitnessComplex(nearest_landmark_table=nearest_landmark_table)
+    simplex_tree = witness_complex.create_simplex_tree(max_alpha_square=4.1)
+    assert simplex_tree.num_vertices() == 5
+    assert simplex_tree.num_simplices() == 31
+    simplex_tree = witness_complex.create_simplex_tree(max_alpha_square=4.1, limit_dimension=2)
+    assert simplex_tree.num_vertices() == 5
+    assert simplex_tree.num_simplices() == 25
+
+def test_strong_witness_complex():
+    nearest_landmark_table = [[[0, 0], [1, 1], [2, 2], [3, 3], [4, 4]],
+                              [[1, 0], [2, 1], [3, 2], [4, 3], [0, 4]],
+                              [[2, 0], [3, 1], [4, 2], [0, 3], [1, 4]],
+                              [[3, 0], [4, 1], [0, 2], [1, 3], [2, 4]],
+                              [[4, 0], [0, 1], [1, 2], [2, 3], [3, 4]]]
+
+    strong_witness_complex = StrongWitnessComplex(nearest_landmark_table=nearest_landmark_table)
+    simplex_tree = strong_witness_complex.create_simplex_tree(max_alpha_square=4.1)
+    assert simplex_tree.num_vertices() == 5
+    assert simplex_tree.num_simplices() == 31
+    simplex_tree = strong_witness_complex.create_simplex_tree(max_alpha_square=4.1, limit_dimension=2)
+    assert simplex_tree.num_vertices() == 5
+    assert simplex_tree.num_simplices() == 25
diff --git a/src/debian/changelog b/src/debian/changelog
deleted file mode 100644
index 32b3f6f9..00000000
--- a/src/debian/changelog
+++ /dev/null
@@ -1,5 +0,0 @@
-gudhi (1.3.0-1) unstable; urgency=low
-
-  * Initial release.
-
- -- Marc Glisse <marc.glisse@inria.fr>  Sat, 26 Mar 2016 10:51:01 +0100
diff --git a/src/debian/compat b/src/debian/compat
deleted file mode 100644
index ec635144..00000000
--- a/src/debian/compat
+++ /dev/null
@@ -1 +0,0 @@
-9
diff --git a/src/debian/control b/src/debian/control
deleted file mode 100644
index 838234a9..00000000
--- a/src/debian/control
+++ /dev/null
@@ -1,26 +0,0 @@
-Source: gudhi
-Priority: optional
-Maintainer: Marc Glisse <marc.glisse@normalesup.org>
-Build-Depends: debhelper (>= 9), cmake, libboost-dev
-Standards-Version: 3.9.6
-Section: libs
-Homepage: http://gudhi.gforge.inria.fr/
-#Vcs-Git: git://anonscm.debian.org/collab-maint/gudhi.git
-#Vcs-Browser: https://anonscm.debian.org/gitweb/?p=collab-maint/gudhi.git;a=summary
-
-Package: libgudhi-dev
-Section: libdevel
-Architecture: all
-Depends: libboost-dev, ${misc:Depends}
-Recommends: libcgal-dev
-Description: Gudhi library for topological data analysis
- The Gudhi library (Geometric Understanding in Higher Dimensions) is a generic
- open source C++ library for Computational Topology and Topological Data
- Analysis (TDA).
- .
- The current release of the GUDHI library includes:
- * Data structures to represent, construct and manipulate simplicial and
- cubical complexes, including alpha-complex, witness complex, Rips complex.
- * Algorithms to compute persistent homology and multi-field persistent
- homology.
- * Simplication of simplicial complexes by edge contraction.
diff --git a/src/debian/copyright b/src/debian/copyright
deleted file mode 100644
index 2e1f88cd..00000000
--- a/src/debian/copyright
+++ /dev/null
@@ -1,28 +0,0 @@
-Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: gudhi
-Upstream-Contact: gudhi-users@lists.gforge.inria.fr
-Source: <url://http://gudhi.gforge.inria.fr/>
-
-Files: *
-Copyright: 2014-2016 Inria Sophia Antipolis-Méditerranée
-           2014-2016 Inria Saclay - Ile de France
-           2014-2016 Université Nice Sophia Antipolis
-License: GPL-3.0+
-
-License: GPL-3.0+
- 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 package 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 <https://www.gnu.org/licenses/>.
- .
- On Debian systems, the complete text of the GNU General
- Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
-
diff --git a/src/debian/docs b/src/debian/docs
deleted file mode 100644
index 878a2ba1..00000000
--- a/src/debian/docs
+++ /dev/null
@@ -1,2 +0,0 @@
-Conventions.txt
-README
diff --git a/src/debian/rules b/src/debian/rules
deleted file mode 100755
index c9b049af..00000000
--- a/src/debian/rules
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/make -f
-# See debhelper(7) (uncomment to enable)
-# output every command that modifies files on the build system.
-#export DH_VERBOSE = 1
-
-# see EXAMPLES in dpkg-buildflags(1) and read /usr/share/dpkg/*
-DPKG_EXPORT_BUILDFLAGS = 1
-include /usr/share/dpkg/default.mk
-
-# see FEATURE AREAS in dpkg-buildflags(1)
-#export DEB_BUILD_MAINT_OPTIONS = hardening=+all
-
-# see ENVIRONMENT in dpkg-buildflags(1)
-# package maintainers to append CFLAGS
-#export DEB_CFLAGS_MAINT_APPEND  = -Wall -pedantic
-# package maintainers to append LDFLAGS
-#export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
-
-
-# main packaging script based on dh7 syntax
-%:
-	dh $@ 
-
-# dh_make generated override targets
-# This is example for Cmake (See https://bugs.debian.org/641051 )
-#override_dh_auto_configure:
-#	dh_auto_configure -- \
-#	-DCMAKE_LIBRARY_PATH=$(DEB_HOST_MULTIARCH)
diff --git a/src/debian/source/format b/src/debian/source/format
deleted file mode 100644
index 163aaf8d..00000000
--- a/src/debian/source/format
+++ /dev/null
@@ -1 +0,0 @@
-3.0 (quilt)