merge from trunk

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/sparserips-python@3935 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 81f81cb6b39ece77718c8b03d408a90789946c0f

55 files changed, 1290 insertions, 707 deletions

diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt
index 6811d7e1..ebaddd47 100644
--- a/CMakeGUDHIVersion.txt
+++ b/CMakeGUDHIVersion.txt
@@ -1,5 +1,5 @@
 set (GUDHI_MAJOR_VERSION 2)
-set (GUDHI_MINOR_VERSION 2)
+set (GUDHI_MINOR_VERSION 3)
 set (GUDHI_PATCH_VERSION 0)
 set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION})
 
diff --git a/CMakeLists.txt b/CMakeLists.txt
index afacede9..76e5b528 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -6,6 +6,10 @@ include(CMakeGUDHIVersion.txt)
 
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/src/cmake/modules/")
 
+# Reset cache
+set(GUDHI_MODULES "" CACHE INTERNAL "GUDHI_MODULES")
+set(GUDHI_MISSING_MODULES "" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+
 # This variable is used by Cython CMakeLists.txt and by GUDHI_third_party_libraries to know its path
 set(GUDHI_CYTHON_PATH "src/cython")
 
@@ -13,8 +17,6 @@ set(GUDHI_CYTHON_PATH "src/cython")
 include(GUDHI_third_party_libraries NO_POLICY_SCOPE)
 
 include(GUDHI_compilation_flags)
-# Only for dev version
-add_cxx_compiler_flag("-pedantic")
 
 # Add your new module in the list, order is not important
 include(GUDHI_modules)
@@ -37,8 +39,6 @@ add_gudhi_module(Tangential_complex)
 add_gudhi_module(Witness_complex)
 add_gudhi_module(Nerve_GIC)
 
-message("++ GUDHI_MODULES list is:\"${GUDHI_MODULES}\"")
-
 # Include module CMake subdirectories
 # GUDHI_SUB_DIRECTORIES is managed in CMAKE_MODULE_PATH/GUDHI_modules.cmake
 foreach(GUDHI_MODULE ${GUDHI_MODULES})
@@ -54,9 +54,15 @@ add_subdirectory(src/GudhUI)
 if (WITH_GUDHI_PYTHON)
   # specific for cython module
   add_subdirectory(${GUDHI_CYTHON_PATH})
+else()
+  message("++ Python module will not be compiled because WITH_GUDHI_PYTHON is set to OFF")
+  set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python")
 endif()
 
 # For "make user_version" - Requires GUDHI_modules to be performed
 include(GUDHI_user_version_target)
 # For "make doxygen" - Requires GUDHI_USER_VERSION_DIR to be set - Done in GUDHI_user_version_target for dev version
 include(GUDHI_doxygen_target)
+
+message("++ GUDHI_MODULES list is:\"${GUDHI_MODULES}\"")
+message("++ GUDHI_MISSING_MODULES list is:\"${GUDHI_MISSING_MODULES}\"")
diff --git a/data/points/human.COPYRIGHT b/data/points/human.COPYRIGHT
new file mode 100644
index 00000000..cb9bdb59
--- /dev/null
+++ b/data/points/human.COPYRIGHT
@@ -0,0 +1,77 @@
+The human.off point cloud is available at this webpage :
+http://segeval.cs.princeton.edu/
+
+LICENSE
+=======
+
+AIM@SHAPE General License for Shapes
+Applicable terms
+----------------
+
+This is the general AIM@SHAPE license applicable to models in the
+Shape Repository. It should be noted that each model is a
+representation of, and is distinct from, a shape, whether physical or
+imaginary. While the shape may be subject to its own terms, the terms
+governing the model you are about to download are described herein.
+
+For some models, the owners have defined specific licenses. The terms
+and conditions laid down in these licenses are in addition to the
+terms prescribed here, and are to be adhered to strictly when using
+such models.
+
+Acknowledgements
+----------------
+
+When including models from the Shape Repository in your website or
+research work, or when using them for other purposes allowed by the
+terms described herein, the AIM@SHAPE project and the model owner must
+be acknowledged as the sources of the models, for example with the
+phrase, "... model is provided courtesy of <model_owner> by the
+AIM@SHAPE Shape Repository."
+
+Information on <model_owner> is present in the accompanying metadata
+files and, where present, owner licenses.
+
+Metadata
+--------
+
+Each model is accompanied by its metadata file. Please keep this file
+with the model as it contains important information about the
+model. Please let us know if you find any errors in the metadata.
+
+(Im)proper use
+--------------
+
+Some models in the Shape Repository represent artifacts of religious,
+cultural and/or historical significance, e.g. the Max Planck
+model. Such models have been entrusted to the Shape Repository under
+the hope that they will be used respectfully and
+conscientiously. Please refrain from conducting experiments on them
+that may be rash or insensitive to people's feelings. Such experiments
+include, but are not limited to, morphing, animation, boolean
+operations, simulations of burning, breaking, exploding and melting.
+
+Models in the Shape Repository are made freely available for research
+and non-commercial purposes only. Use of these models for commercial
+purposes is permitted only after the express approval of the Shape
+Repository and the onwner has been obtained. Please contact us using
+the webform on our site in this regard.
+
+
+CITATION
+========
+
+If you use any part of this benchmark, please cite:
+Xiaobai Chen, Aleksey Golovinskiy, and Thomas Funkhouser,
+A Benchmark for 3D Mesh Segmentation
+ACM Transactions on Graphics (Proc. SIGGRAPH), 28(3), 2009.
+
+@article{Chen:2009:ABF,
+  author = "Xiaobai Chen and Aleksey Golovinskiy and Thomas Funkhouser",
+  title = "A Benchmark for {3D} Mesh Segmentation",
+  journal = "ACM Transactions on Graphics (Proc. SIGGRAPH)",
+  year = "2009",
+  month = aug,
+  volume = "28",
+  number = "3"
+}
\ No newline at end of file
diff --git a/scripts/create_gudhi_version.sh b/scripts/create_gudhi_version.sh
new file mode 100755
index 00000000..f2a9233f
--- /dev/null
+++ b/scripts/create_gudhi_version.sh
@@ -0,0 +1,66 @@
+#!/bin/bash
+
+login="vrouvrea"
+version="2.3.0"
+cgaldir="/home/vincent/workspace/CGAL-4.11-HO/build"
+cpucount=7
+
+
+# We start from scripts dir in the dev branch
+cd ..
+RELATIVEURL=`svn info . |grep -F "Relative URL:" | awk '{print $NF}'`
+
+if [ "$RELATIVEURL" != "^/trunk" ]
+then
+echo "Script must be launched in trunk and not in $RELATIVEURL"
+exit
+fi
+
+rm -rf build; mkdir build; cd build; cmake  -DCMAKE_BUILD_TYPE=Debug -DDEBUG_TRACES=ON -DCGAL_DIR=${cgaldir} -DWITH_GUDHI_EXAMPLE=ON -DWITH_GUDHI_BENCHMARK=ON -DPython_ADDITIONAL_VERSIONS=3 ..
+cmake  -DCMAKE_BUILD_TYPE=Debug .
+
+CURRENTDIRECTORY=`pwd`
+export PYTHONPATH=$CURRENTDIRECTORY/src/cython:$PYTHONPATH
+
+make -j ${cpucount} all test
+
+cd ..
+svn st | grep -v GUDHIVersion.cmake | grep "^\?" | awk "{print \$2}" | xargs rm -rf
+
+svn copy svn+ssh://${login}@scm.gforge.inria.fr/svnroot/gudhi/trunk svn+ssh://${login}@scm.gforge.inria.fr/svnroot/gudhi/tags/gudhi-release-${version} \
+  -m "Creating a tag of Gudhi release version ${version}."
+
+cd build
+make user_version
+
+userversiondir=`find . -type d -name "*_GUDHI_${version}" | sed 's/\.\///g'`
+echo "User version directory = ${userversiondir}"
+
+tar -czvf ${userversiondir}.tar.gz ${userversiondir}
+
+userdocdir=${userversiondir/GUDHI/GUDHI_DOC}
+echo "User documentation directory = ${userdocdir}"
+mkdir ${userdocdir}
+make doxygen
+
+cp -R ${userversiondir}/doc/html ${userdocdir}/cpp
+cd ${userversiondir}
+rm -rf build; mkdir build; cd build; cmake  -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=./installed -DCGAL_DIR=${cgaldir} -DWITH_GUDHI_EXAMPLE=ON -DPython_ADDITIONAL_VERSIONS=3 ..
+
+CURRENTDIRECTORY=`pwd`
+export PYTHONPATH=$CURRENTDIRECTORY/cython:$PYTHONPATH
+
+make sphinx
+
+cp -R cython/sphinx ../../${userdocdir}/python
+cd ../..
+tar -czvf ${userdocdir}.tar.gz ${userdocdir}
+
+cd ${userversiondir}/build
+make -j ${cpucount} all test install
+
+cd ../..
+actualdir=`pwd`
+echo "Library is available at ${actualdir}/${userversiondir}.tar.gz"
+sha256sum ${userversiondir}.tar.gz
+echo "Documentation is available at ${actualdir}/${userdocdir}.tar.gz"
diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp
index 8cda0b70..6e603155 100644
--- a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp
@@ -266,6 +266,6 @@ void program_options(int argc, char *argv[], std::string &off_file_points, std::
 
     std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
     std::cout << visible << std::endl;
-    std::abort();
+    exit(-1);
   }
 }
diff --git a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp
index 42390b0e..8e6c40b7 100644
--- a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp
+++ b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp
@@ -133,6 +133,6 @@ void program_options(int argc, char *argv[], std::string &off_file_points, std::
 
     std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
     std::cout << visible << std::endl;
-    std::abort();
+    exit(-1);
   }
 }
diff --git a/src/Alpha_complex/utilities/alphacomplex.md b/src/Alpha_complex/utilities/alphacomplex.md
index 0fe98837..b1a33e4b 100644
--- a/src/Alpha_complex/utilities/alphacomplex.md
+++ b/src/Alpha_complex/utilities/alphacomplex.md
@@ -143,7 +143,7 @@ where
 

 * `<input OFF file>` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html).

 * `<cuboid file>` is the path to the file describing the periodic domain. It must be in the format described

-[here](/doc/latest/fileformats.html#FileFormatsIsoCuboid).

+[here]({{ site.officialurl }}/doc/latest/fileformats.html#FileFormatsIsoCuboid).

 

 **Allowed options**

 

@@ -161,5 +161,5 @@ periodic_alpha_complex_3d_persistence ../../data/points/grid_10_10_10_in_0_1.off
 

 N.B.:

 

-* Cuboid file must be in the format described [here](/doc/latest/fileformats.html#FileFormatsIsoCuboid).

+* Cuboid file must be in the format described [here]({{ site.officialurl }}/doc/latest/fileformats.html#FileFormatsIsoCuboid).

 * Filtration values are alpha square values.

diff --git a/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp
index cbe003ff..61f49bb1 100644
--- a/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp
@@ -260,6 +260,6 @@ void program_options(int argc, char *argv[], std::string &off_file_points, std::
 
     std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
     std::cout << visible << std::endl;
-    std::abort();
+    exit(-1);
   }
 }
diff --git a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp
index 11010701..a261c5a3 100644
--- a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp
@@ -297,6 +297,6 @@ void program_options(int argc, char *argv[], std::string &off_file_points, std::
 
     std::cout << "Usage: " << argv[0] << " [options] input-file cuboid-file" << std::endl << std::endl;
     std::cout << visible << std::endl;
-    std::abort();
+    exit(-1);
   }
 }
diff --git a/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp
index cdeeabfc..aa7ddee2 100644
--- a/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp
@@ -311,6 +311,6 @@ void program_options(int argc, char *argv[], std::string &off_file_points, std::
 
     std::cout << "Usage: " << argv[0] << " [options] input-file weight-file" << std::endl << std::endl;
     std::cout << visible << std::endl;
-    std::abort();
+    exit(-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 1e27887c..2db1ef80 100644
--- a/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp
+++ b/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp
@@ -185,6 +185,6 @@ void program_options(int argc, char * argv[]
 
     std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
     std::cout << visible << std::endl;
-    std::abort();
+    exit(-1);
   }
 }
diff --git a/src/Bottleneck_distance/include/gudhi/Bottleneck.h b/src/Bottleneck_distance/include/gudhi/Bottleneck.h
index b0fc3949..7a553006 100644
--- a/src/Bottleneck_distance/include/gudhi/Bottleneck.h
+++ b/src/Bottleneck_distance/include/gudhi/Bottleneck.h
@@ -36,7 +36,7 @@ namespace Gudhi {
 
 namespace persistence_diagram {
 
-double bottleneck_distance_approx(Persistence_graph& g, double e) {
+inline double bottleneck_distance_approx(Persistence_graph& g, double e) {
   double b_lower_bound = 0.;
   double b_upper_bound = g.diameter_bound();
   const double alpha = std::pow(g.size(), 1. / 5.);
@@ -66,7 +66,7 @@ double bottleneck_distance_approx(Persistence_graph& g, double e) {
   return (b_lower_bound + b_upper_bound) / 2.;
 }
 
-double bottleneck_distance_exact(Persistence_graph& g) {
+inline double bottleneck_distance_exact(Persistence_graph& g) {
   std::vector<double> sd = g.sorted_distances();
   long lower_bound_i = 0;
   long upper_bound_i = sd.size() - 1;
diff --git a/src/Bottleneck_distance/utilities/bottleneckdistance.md b/src/Bottleneck_distance/utilities/bottleneckdistance.md
index 939eb911..a81426cf 100644
--- a/src/Bottleneck_distance/utilities/bottleneckdistance.md
+++ b/src/Bottleneck_distance/utilities/bottleneckdistance.md
@@ -22,5 +22,5 @@ This program computes the Bottleneck distance between two persistence diagram fi
 

 where

 

-* `<file_1.pers>` and `<file_2.pers>` must be in the format described [here](/doc/latest/fileformats.html#FileFormatsPers).

+* `<file_1.pers>` and `<file_2.pers>` must be in the format described [here]({{ site.officialurl }}/doc/latest/fileformats.html#FileFormatsPers).

 * `<tolerance>` is an error bound on the bottleneck distance (set by default to the smallest positive double value).

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index c60346d5..b40d506a 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -6,6 +6,9 @@ include(CMakeGUDHIVersion.txt)
 
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/modules/")
 
+set(GUDHI_MODULES "" CACHE INTERNAL "GUDHI_MODULES")
+set(GUDHI_MISSING_MODULES "" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+
 # This variable is used by Cython CMakeLists.txt and by GUDHI_third_party_libraries to know its path
 set(GUDHI_CYTHON_PATH "cython")
 
@@ -35,8 +38,6 @@ add_gudhi_module(Tangential_complex)
 add_gudhi_module(Witness_complex)
 add_gudhi_module(Nerve_GIC)
 
-message("++ GUDHI_MODULES list is:\"${GUDHI_MODULES}\"")
-
 # For "make doxygen" - Requires GUDHI_USER_VERSION_DIR to be set
 set(GUDHI_USER_VERSION_DIR ${CMAKE_SOURCE_DIR})
 include(GUDHI_doxygen_target)
@@ -60,7 +61,14 @@ add_subdirectory(GudhUI)
 if (WITH_GUDHI_PYTHON)
   # specific for cython module
   add_subdirectory(${GUDHI_CYTHON_PATH})
+else()
+  message("++ Python module will not be compiled because WITH_GUDHI_PYTHON is set to OFF")
+  set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python")
 endif()
+
+message("++ GUDHI_MODULES list is:\"${GUDHI_MODULES}\"")
+message("++ GUDHI_MISSING_MODULES list is:\"${GUDHI_MISSING_MODULES}\"")
+
 #---------------------------------------------------------------------------------------
 
 #---------------------------------------------------------------------------------------
@@ -71,7 +79,7 @@ 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")
+set(CONF_INCLUDE_DIRS "${CMAKE_SOURCE_DIR}/include;${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)
 
diff --git a/src/Cech_complex/example/cech_complex_step_by_step.cpp b/src/Cech_complex/example/cech_complex_step_by_step.cpp
index d2dc8b65..6fbbde5b 100644
--- a/src/Cech_complex/example/cech_complex_step_by_step.cpp
+++ b/src/Cech_complex/example/cech_complex_step_by_step.cpp
@@ -161,6 +161,6 @@ void program_options(int argc, char* argv[], std::string& off_file_points, Filtr
 
     std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
     std::cout << visible << std::endl;
-    std::abort();
+    exit(-1);
   }
 }
diff --git a/src/Cech_complex/utilities/cech_persistence.cpp b/src/Cech_complex/utilities/cech_persistence.cpp
index abd9dbcd..93e92695 100644
--- a/src/Cech_complex/utilities/cech_persistence.cpp
+++ b/src/Cech_complex/utilities/cech_persistence.cpp
@@ -131,6 +131,6 @@ void program_options(int argc, char* argv[], std::string& off_file_points, std::
 
     std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
     std::cout << visible << std::endl;
-    std::abort();
+    exit(-1);
   }
 }
diff --git a/src/Doxyfile b/src/Doxyfile.in
index 020667e9..858a9299 100644
--- a/src/Doxyfile
+++ b/src/Doxyfile.in
@@ -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         = "2.2.0"
+PROJECT_NUMBER         = "@GUDHI_VERSION@"
 
 # 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
@@ -780,12 +780,12 @@ RECURSIVE              = YES
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                = data/ \
-	                     example/    \
-	                     GudhUI/     \
-                             cmake/      \
-                             src/cython/ \
-                             include/gudhi_patches/
+EXCLUDE                = data/                   \
+	                     example/                \
+	                     GudhUI/                 \
+                         cmake/                  \
+                         src/cython/             \
+                         include/gudhi_patches/
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded
@@ -818,9 +818,9 @@ EXCLUDE_SYMBOLS        =
 # that contain example code fragments that are included (see the \include
 # command).
 
-EXAMPLE_PATH           = biblio/ \
-	example/ \
-	utilities/
+EXAMPLE_PATH           = biblio/    \
+	                     example/   \
+	                     utilities/
 
 # If the value of the EXAMPLE_PATH tag contains directories, you can use the
 # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
@@ -840,22 +840,7 @@ EXAMPLE_RECURSIVE      = NO
 # that contain images that are to be included in the documentation (see the
 # \image command).
 
-IMAGE_PATH             = doc/Skeleton_blocker/ \
-	doc/Alpha_complex/ \
-	doc/common/ \
-        doc/Cech_complex/ \
-        doc/Contraction/ \
-	doc/Simplex_tree/ \
-	doc/Persistent_cohomology/ \
-	doc/Witness_complex/ \
-	doc/Bitmap_cubical_complex/ \
-	doc/Rips_complex/ \
-	doc/Subsampling/ \
-	doc/Spatial_searching/ \
-	doc/Tangential_complex/ \
-	doc/Bottleneck_distance/ \
-	doc/Nerve_GIC/ \
-        doc/Persistence_representations/
+IMAGE_PATH             = @GUDHI_DOXYGEN_IMAGE_PATH@
 
 # The INPUT_FILTER tag can be used to specify a program that doxygen should
 # invoke to filter for each input file. Doxygen will invoke the filter program
diff --git a/src/GUDHIConfig.cmake.in b/src/GUDHIConfig.cmake.in
index 02b540dc..8d82f235 100644
--- a/src/GUDHIConfig.cmake.in
+++ b/src/GUDHIConfig.cmake.in
@@ -1,7 +1,12 @@
 # - Config file for the GUDHI package
 # It defines the following variables
 #  GUDHI_INCLUDE_DIRS - include directories for GUDHI
+#
+# Order is :
+# 1. user defined GUDHI_INCLUDE_DIRS
+# 2. ${CMAKE_SOURCE_DIR}/include     => Where the 'cmake' has been done
+# 3. ${CMAKE_INSTALL_PREFIX}/include => Where the 'make install' has been performed
 
 # Compute paths
-set(GUDHI_INCLUDE_DIRS "@CONF_INCLUDE_DIRS@")
+set(GUDHI_INCLUDE_DIRS "${GUDHI_INCLUDE_DIRS};@CONF_INCLUDE_DIRS@")
 
diff --git a/src/GudhUI/CMakeLists.txt b/src/GudhUI/CMakeLists.txt
index b357b8f7..0945e758 100644
--- a/src/GudhUI/CMakeLists.txt
+++ b/src/GudhUI/CMakeLists.txt
@@ -1,40 +1,55 @@
 project(GudhUI)
 
 # Need to find OpenGL first as find_package(Qt5) tries to #include"GL/gl.h" on some platforms
-find_package(OpenGL)
+find_package(OpenGL QUIET)
 
 if (OPENGL_FOUND)
-  find_package(Qt5 COMPONENTS Widgets Xml OpenGL)
-  find_package(QGLViewer)
-  
-  if ( CGAL_FOUND AND Qt5_FOUND AND QGLVIEWER_FOUND AND NOT CGAL_VERSION VERSION_EQUAL 4.8.0)
-  
-    set(CMAKE_AUTOMOC ON)
-    set(CMAKE_AUTOUIC ON)
-    set(CMAKE_INCLUDE_CURRENT_DIR ON)
-  
-    SET(Boost_USE_STATIC_LIBS ON)
-    SET(Boost_USE_MULTITHREAD OFF)
-    include_directories (${QGLVIEWER_INCLUDE_DIR})
-   
-    add_executable  ( GudhUI 
-      gui/gudhui.cpp
-      gui/MainWindow.cpp
-      gui/Menu_k_nearest_neighbors.cpp	
-      gui/Menu_uniform_neighbors.cpp
-      gui/Menu_edge_contraction.cpp  
-      gui/Menu_persistence.cpp
-      view/Viewer_instructor.cpp				
-      view/Viewer.cpp
-    )	
-    target_link_libraries( GudhUI Qt5::Widgets Qt5::Xml Qt5::OpenGL )
-    target_link_libraries( GudhUI ${QGLVIEWER_LIBRARIES} )
-    target_link_libraries( GudhUI ${OPENGL_gl_LIBRARY} ${OPENGL_glu_LIBRARY} )	
-    if (TBB_FOUND)
-      target_link_libraries( GudhUI ${TBB_LIBRARIES})
+  find_package(Qt5 COMPONENTS Widgets Xml OpenGL QUIET)
+  if (Qt5_FOUND)
+    find_package(QGLViewer QUIET)
+    if ( QGLVIEWER_FOUND)
+
+      if ( CGAL_FOUND AND NOT CGAL_VERSION VERSION_EQUAL 4.8.0)
+        set(CMAKE_AUTOMOC ON)
+        set(CMAKE_AUTOUIC ON)
+        set(CMAKE_INCLUDE_CURRENT_DIR ON)
+
+        SET(Boost_USE_STATIC_LIBS ON)
+        SET(Boost_USE_MULTITHREAD OFF)
+        include_directories (${QGLVIEWER_INCLUDE_DIR})
+
+        add_executable  ( GudhUI
+          gui/gudhui.cpp
+          gui/MainWindow.cpp
+          gui/Menu_k_nearest_neighbors.cpp
+          gui/Menu_uniform_neighbors.cpp
+          gui/Menu_edge_contraction.cpp
+          gui/Menu_persistence.cpp
+          view/Viewer_instructor.cpp
+          view/Viewer.cpp
+        )
+        target_link_libraries( GudhUI Qt5::Widgets Qt5::Xml Qt5::OpenGL )
+        target_link_libraries( GudhUI ${QGLVIEWER_LIBRARIES} )
+        target_link_libraries( GudhUI ${OPENGL_gl_LIBRARY} ${OPENGL_glu_LIBRARY} )
+        if (TBB_FOUND)
+          target_link_libraries( GudhUI ${TBB_LIBRARIES})
+        endif()
+
+        install(TARGETS GudhUI DESTINATION bin)
+        set(GUDHI_MODULES ${GUDHI_MODULES} "GudhUI" CACHE INTERNAL "GUDHI_MODULES")
+      else()
+        message("++ GudhUI will not be compiled because CGAL < 4.8.0 or not found")
+        set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "GudhUI" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+      endif()
+    else()
+      message("++ GudhUI will not be compiled because QGLViewer is not found")
+      set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "GudhUI" CACHE INTERNAL "GUDHI_MISSING_MODULES")
     endif()
-  
-    install(TARGETS GudhUI DESTINATION bin)
-  
+  else()
+    message("++ GudhUI will not be compiled because Qt5 COMPONENTS Widgets Xml OpenGL are not found")
+    set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "GudhUI" CACHE INTERNAL "GUDHI_MISSING_MODULES")
   endif()
-endif(OPENGL_FOUND)
+else()
+  message("++ GudhUI will not be compiled because OpenGL is not found")
+  set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "GudhUI" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+endif()
diff --git a/src/Nerve_GIC/include/gudhi/GIC.h b/src/Nerve_GIC/include/gudhi/GIC.h
index fea0b861..30f89d65 100644
--- a/src/Nerve_GIC/include/gudhi/GIC.h
+++ b/src/Nerve_GIC/include/gudhi/GIC.h
@@ -226,7 +226,25 @@ class Cover_complex {
   void set_mask(int nodemask) { mask = nodemask; }
 
  public:
-  /** \brief Reads and stores the input point cloud.
+
+
+  /** \brief Reads and stores the input point cloud from vector stored in memory.
+   *
+   * @param[in] cloud input vector representing the point cloud. Each row is a point and each coordinate is a vector.
+   *
+   */
+  template <class InputRange>
+  void set_point_cloud_from_range(InputRange const & cloud) {
+    n = cloud.size(); data_dimension = cloud[0].size(); point_cloud_name = "matrix";
+    for(int i = 0; i < n; i++){
+      point_cloud.emplace_back(cloud[i].begin(), cloud[i].begin() + data_dimension);
+      boost::add_vertex(one_skeleton_OFF);
+      vertices.push_back(boost::add_vertex(one_skeleton));
+      cover.emplace_back();
+    }
+  }
+
+  /** \brief Reads and stores the input point cloud from .(n)OFF file.
    *
    * @param[in] off_file_name name of the input .OFF or .nOFF file.
    *
@@ -371,6 +389,28 @@ class Cover_complex {
                  distances[index[boost::source(*ei, one_skeleton)]][index[boost::target(*ei, one_skeleton)]]);
   }
 
+ public:
+  /** \brief Reads and stores the distance matrices from vector stored in memory.
+   *
+   * @param[in] distance_matrix input vector representing the distance matrix.
+   *
+   */
+  template <class InputRange>
+  void set_distances_from_range(InputRange const & distance_matrix) {
+    if(point_cloud.size() == 0){
+      n = distance_matrix.size();
+      point_cloud_name = "matrix";
+      data_dimension = 0;
+      for(int i = 0; i < n; i++){
+        point_cloud.emplace_back();
+        boost::add_vertex(one_skeleton_OFF);
+        vertices.push_back(boost::add_vertex(one_skeleton));
+        cover.emplace_back();
+      }
+    }
+    distances = distance_matrix;
+  }
+
  public:  // Pairwise distances.
           /** \private \brief Computes all pairwise distances.
            */
@@ -500,9 +540,17 @@ class Cover_complex {
            *
            */
   void set_function_from_coordinate(int k) {
-    for (int i = 0; i < n; i++) func.push_back(point_cloud[i][k]);
-    functional_cover = true;
-    cover_name = "coordinate " + std::to_string(k);
+    if(point_cloud[0].size() > 0){
+      for (int i = 0; i < n; i++) func.push_back(point_cloud[i][k]);
+      functional_cover = true;
+      cover_name = "coordinate " + std::to_string(k);
+    }
+    else{
+      std::cout << "Only pairwise distances provided---cannot access " << k << "th coordinate; returning null vector instead" << std::endl;
+      for (int i = 0; i < n; i++) func.push_back(0.0);
+      functional_cover = true;
+      cover_name = "null";
+    }
   }
 
  public:  // Set function from vector.
@@ -953,9 +1001,17 @@ class Cover_complex {
            *
            */
   void set_color_from_coordinate(int k = 0) {
-    for (int i = 0; i < n; i++) func_color.push_back(point_cloud[i][k]);
-    color_name = "coordinate ";
-    color_name.append(std::to_string(k));
+    if(point_cloud[0].size() > 0){
+      for (int i = 0; i < n; i++) func_color.push_back(point_cloud[i][k]);
+      color_name = "coordinate ";
+      color_name.append(std::to_string(k));
+    }
+    else{
+      std::cout << "Only pairwise distances provided---cannot access " << k << "th coordinate; returning null vector instead" << std::endl;
+      for (int i = 0; i < n; i++) func.push_back(0.0);
+      functional_cover = true;
+      cover_name = "null";
+    }
   }
 
  public:  // Set color from vector.
@@ -964,7 +1020,7 @@ class Cover_complex {
    * @param[in] color input vector of values.
    *
    */
-  void set_color_from_vector(std::vector<double> color) {
+  void set_color_from_range(std::vector<double> color) {
     for (unsigned int i = 0; i < color.size(); i++) func_color.push_back(color[i]);
   }
 
@@ -1108,7 +1164,7 @@ class Cover_complex {
   /** \brief Computes the extended persistence diagram of the complex.
    *
    */
-  void compute_PD() {
+  Persistence_diagram compute_PD() {
     Simplex_tree st;
 
     // Compute max and min
@@ -1121,15 +1177,18 @@ class Cover_complex {
 
     // Build filtration
     for (auto const& simplex : simplices) {
-      std::vector<int> splx = simplex; splx.push_back(-2);
+      std::vector<int> splx = simplex;
+      splx.push_back(-2);
       st.insert_simplex_and_subfaces(splx, -3);
     }
 
     for (std::map<int, double>::iterator it = cover_std.begin(); it != cover_std.end(); it++) {
       int vertex = it->first; float val = it->second;
       int vert[] = {vertex}; int edge[] = {vertex, -2};
-      st.assign_filtration(st.find(vert), -2 + (val - minf)/(maxf - minf));
-      st.assign_filtration(st.find(edge),  2 - (val - minf)/(maxf - minf));
+      if(st.find(vert) != st.null_simplex()){
+        st.assign_filtration(st.find(vert), -2 + (val - minf)/(maxf - minf));
+        st.assign_filtration(st.find(edge),  2 - (val - minf)/(maxf - minf));
+      }
     }
     st.make_filtration_non_decreasing();
 
@@ -1159,6 +1218,7 @@ class Cover_complex {
         if (verbose) std::cout << "  [" << birth << ", " << death << "]" << std::endl;
       }
     }
+    return PD;
   }
 
  public:
@@ -1184,7 +1244,7 @@ class Cover_complex {
           Cboot.point_cloud.push_back(this->point_cloud[id]); Cboot.cover.emplace_back(); Cboot.func.push_back(this->func[id]);
           boost::add_vertex(Cboot.one_skeleton_OFF); Cboot.vertices.push_back(boost::add_vertex(Cboot.one_skeleton));
         }
-  Cboot.set_color_from_vector(Cboot.func);
+        Cboot.set_color_from_range(Cboot.func);
 
         for (int j = 0; j < n; j++) {
           std::vector<double> dist(n);
@@ -1230,7 +1290,7 @@ class Cover_complex {
     unsigned int N = distribution.size();
     double level = 1;
     for (unsigned int i = 0; i < N; i++)
-      if (distribution[i] > d){ level = i * 1.0 / N; break; }
+      if (distribution[i] >= d){ level = i * 1.0 / N; break; }
     if (verbose)  std::cout << "Confidence level of distance " << d << " is " << level << std::endl;
     return level;
   }
diff --git a/src/Persistent_cohomology/example/persistence_from_file.cpp b/src/Persistent_cohomology/example/persistence_from_file.cpp
index c40434a4..53456919 100644
--- a/src/Persistent_cohomology/example/persistence_from_file.cpp
+++ b/src/Persistent_cohomology/example/persistence_from_file.cpp
@@ -138,6 +138,6 @@ void program_options(int argc, char * argv[]
 
     std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
     std::cout << visible << std::endl;
-    std::abort();
+    exit(-1);
   }
 }
diff --git a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
index 626ec2ef..d6a5bdad 100644
--- a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
@@ -149,6 +149,6 @@ void program_options(int argc, char * argv[]
 
     std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
     std::cout << visible << std::endl;
-    std::abort();
+    exit(-1);
   }
 }
diff --git a/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp b/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp
index 7c81fcfb..796cfa3a 100644
--- a/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp
+++ b/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp
@@ -161,6 +161,6 @@ void program_options(int argc, char * argv[]
 
     std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
     std::cout << visible << std::endl;
-    std::abort();
+    exit(-1);
   }
 }
diff --git a/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp b/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp
index c7607dce..71fc0802 100644
--- a/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp
+++ b/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp
@@ -167,6 +167,6 @@ void program_options(int argc, char * argv[]
 
     std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
     std::cout << visible << std::endl;
-    std::abort();
+    exit(-1);
   }
 }
diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
index c68b5c0b..c51e47a5 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
@@ -300,7 +300,10 @@ class Persistent_cohomology {
     // with multiplicity. We used to sum the coefficients directly in
     // annotations_in_boundary by using a map, we now do it later.
     typedef std::pair<Column *, int> annotation_t;
-    thread_local std::vector<annotation_t> annotations_in_boundary;
+#ifdef GUDHI_CAN_USE_CXX11_THREAD_LOCAL
+    thread_local
+#endif  // GUDHI_CAN_USE_CXX11_THREAD_LOCAL
+    std::vector<annotation_t> annotations_in_boundary;
     annotations_in_boundary.clear();
     int sign = 1 - 2 * (dim_sigma % 2);  // \in {-1,1} provides the sign in the
                                          // alternate sum in the boundary.
diff --git a/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp b/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp
index c78677d2..287e8915 100644
--- a/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp
+++ b/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp
@@ -166,6 +166,6 @@ void program_options(int argc, char* argv[], std::string& csv_matrix_file, std::
 
     std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
     std::cout << visible << std::endl;
-    std::abort();
+    exit(-1);
   }
 }
diff --git a/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp b/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp
index 53191ca7..c73152cf 100644
--- a/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp
+++ b/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp
@@ -128,6 +128,6 @@ void program_options(int argc, char* argv[], std::string& csv_matrix_file, std::
 
     std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
     std::cout << visible << std::endl;
-    std::abort();
+    exit(-1);
   }
 }
diff --git a/src/Rips_complex/utilities/rips_persistence.cpp b/src/Rips_complex/utilities/rips_persistence.cpp
index 7cee927e..9410b9c2 100644
--- a/src/Rips_complex/utilities/rips_persistence.cpp
+++ b/src/Rips_complex/utilities/rips_persistence.cpp
@@ -130,6 +130,6 @@ void program_options(int argc, char* argv[], std::string& off_file_points, std::
 
     std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
     std::cout << visible << std::endl;
-    std::abort();
+    exit(-1);
   }
 }
diff --git a/src/Rips_complex/utilities/sparse_rips_persistence.cpp b/src/Rips_complex/utilities/sparse_rips_persistence.cpp
index bcd5c2c5..6d4d86fd 100644
--- a/src/Rips_complex/utilities/sparse_rips_persistence.cpp
+++ b/src/Rips_complex/utilities/sparse_rips_persistence.cpp
@@ -128,6 +128,6 @@ void program_options(int argc, char* argv[], std::string& off_file_points, std::
 
     std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
     std::cout << visible << std::endl;
-    std::abort();
+    exit(-1);
   }
 }
diff --git a/src/Simplex_tree/example/cech_complex_cgal_mini_sphere_3d.cpp b/src/Simplex_tree/example/cech_complex_cgal_mini_sphere_3d.cpp
index 08ed74bb..34092ef6 100644
--- a/src/Simplex_tree/example/cech_complex_cgal_mini_sphere_3d.cpp
+++ b/src/Simplex_tree/example/cech_complex_cgal_mini_sphere_3d.cpp
@@ -171,7 +171,7 @@ void program_options(int argc, char* argv[], std::string& off_file_points, Filtr
 
     std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
     std::cout << visible << std::endl;
-    std::abort();
+    exit(-1);
   }
 }
 
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index 2c4c53a3..3339606c 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -1058,7 +1058,10 @@ class Simplex_tree {
     Dictionary_it next = siblings->members().begin();
     ++next;
 
-    thread_local std::vector<std::pair<Vertex_handle, Node> > inter;
+#ifdef GUDHI_CAN_USE_CXX11_THREAD_LOCAL
+    thread_local
+#endif  // GUDHI_CAN_USE_CXX11_THREAD_LOCAL
+    std::vector<std::pair<Vertex_handle, Node> > inter;
     for (Dictionary_it s_h = siblings->members().begin();
          s_h != siblings->members().end(); ++s_h, ++next) {
       Simplex_handle root_sh = find_vertex(s_h->first);
diff --git a/src/Witness_complex/utilities/strong_witness_persistence.cpp b/src/Witness_complex/utilities/strong_witness_persistence.cpp
index 9d23df74..f386e992 100644
--- a/src/Witness_complex/utilities/strong_witness_persistence.cpp
+++ b/src/Witness_complex/utilities/strong_witness_persistence.cpp
@@ -151,6 +151,6 @@ void program_options(int argc, char* argv[], int& nbL, std::string& file_name, s
 
     std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
     std::cout << visible << std::endl;
-    std::abort();
+    exit(-1);
   }
 }
diff --git a/src/Witness_complex/utilities/weak_witness_persistence.cpp b/src/Witness_complex/utilities/weak_witness_persistence.cpp
index 1315d2ba..ea00cfe7 100644
--- a/src/Witness_complex/utilities/weak_witness_persistence.cpp
+++ b/src/Witness_complex/utilities/weak_witness_persistence.cpp
@@ -151,6 +151,6 @@ void program_options(int argc, char* argv[], int& nbL, std::string& file_name, s
 
     std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
     std::cout << visible << std::endl;
-    std::abort();
+    exit(-1);
   }
 }
diff --git a/src/Witness_complex/utilities/witnesscomplex.md b/src/Witness_complex/utilities/witnesscomplex.md
index da453cce..7ea397b9 100644
--- a/src/Witness_complex/utilities/witnesscomplex.md
+++ b/src/Witness_complex/utilities/witnesscomplex.md
@@ -10,7 +10,7 @@ Leave the lines above as it is required by the web site generator 'Jekyll'
 {:/comment}

 

 

-For more details about the witness complex, please read the [user manual of the package](/doc/latest/group__witness__complex.html).

+For more details about the witness complex, please read the [user manual of the package]({{ site.officialurl }}/doc/latest/group__witness__complex.html).

 

 ## weak_witness_persistence ##

 This program computes the persistent homology with coefficient field *Z/pZ* of a Weak witness complex defined on a set of input points.

diff --git a/src/cmake/modules/FindCython.cmake b/src/cmake/modules/FindCython.cmake
deleted file mode 100644
index 04aed1f8..00000000
--- a/src/cmake/modules/FindCython.cmake
+++ /dev/null
@@ -1,44 +0,0 @@
-# Find the Cython compiler.
-#
-# This code sets the following variables:
-#
-#  CYTHON_EXECUTABLE
-#
-# See also UseCython.cmake
-
-#=============================================================================
-# Copyright 2011 Kitware, Inc.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#=============================================================================
-
-# Use the Cython executable that lives next to the Python executable
-# if it is a local installation.
-find_package( PythonInterp )
-if( PYTHONINTERP_FOUND )
-  get_filename_component( _python_path ${PYTHON_EXECUTABLE} PATH )
-  find_program( CYTHON_EXECUTABLE
-    NAMES cython cython.bat cython3
-    HINTS ${_python_path}
-    )
-else()
-  find_program( CYTHON_EXECUTABLE
-    NAMES cython cython.bat cython3
-    )
-endif()
-
-
-include( FindPackageHandleStandardArgs )
-FIND_PACKAGE_HANDLE_STANDARD_ARGS( Cython REQUIRED_VARS CYTHON_EXECUTABLE )
-
-mark_as_advanced( CYTHON_EXECUTABLE )
diff --git a/src/cmake/modules/GUDHI_compilation_flags.cmake b/src/cmake/modules/GUDHI_compilation_flags.cmake
index a01d6e13..86cd531b 100644
--- a/src/cmake/modules/GUDHI_compilation_flags.cmake
+++ b/src/cmake/modules/GUDHI_compilation_flags.cmake
@@ -5,7 +5,7 @@ include(CheckCXXSourceCompiles)
 
 # add a compiler flag only if it is accepted
 macro(add_cxx_compiler_flag _flag)
-  string(REPLACE "-" "_" _flag_var ${_flag})
+  string(REPLACE "-" "_" "/" _flag_var ${_flag})
   check_cxx_accepts_flag("${_flag}" CXX_COMPILER_${_flag_var}_OK)
   if(CXX_COMPILER_${_flag_var}_OK)
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${_flag}")
@@ -43,12 +43,15 @@ set (CMAKE_CXX_STANDARD 11)
 enable_testing()
 
 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")
+  add_cxx_compiler_flag("/W3")
+else()
+  add_cxx_compiler_flag("-Wall")
+  # Only for dev version
+  if(PROJECT_NAME STREQUAL "GUDHIdev")
+    add_cxx_compiler_flag("-pedantic")
+  endif()
 endif()
 
-add_cxx_compiler_flag("-Wall")
-
 if (DEBUG_TRACES)
   # For programs to be more verbose
   message(STATUS "DEBUG_TRACES are activated")
diff --git a/src/cmake/modules/GUDHI_doxygen_target.cmake b/src/cmake/modules/GUDHI_doxygen_target.cmake
index f3e2d9f5..7a84c4e0 100644
--- a/src/cmake/modules/GUDHI_doxygen_target.cmake
+++ b/src/cmake/modules/GUDHI_doxygen_target.cmake
@@ -1,16 +1,21 @@
 # add a target to generate API documentation with Doxygen
-find_package(Doxygen)
+find_package(Doxygen QUIET)
 if(DOXYGEN_FOUND)
-  # configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile @ONLY)
+  set(GUDHI_MODULES ${GUDHI_MODULES} "cpp-documentation" CACHE INTERNAL "GUDHI_MODULES")
 
-  #starting from cmake 3.9 the usage of DOXYGEN_EXECUTABLE is deprecated
+  # starting from cmake 3.9 the usage of DOXYGEN_EXECUTABLE is deprecated
   if(TARGET Doxygen::doxygen)
     get_property(DOXYGEN_EXECUTABLE TARGET Doxygen::doxygen PROPERTY IMPORTED_LOCATION)
   endif()
 
   add_custom_target(doxygen ${DOXYGEN_EXECUTABLE} ${GUDHI_USER_VERSION_DIR}/Doxyfile
                     WORKING_DIRECTORY ${GUDHI_USER_VERSION_DIR}
-                    DEPENDS ${GUDHI_USER_VERSION_DIR}/Doxyfile ${GUDHI_DOXYGEN_DEPENDENCY}
                     COMMENT "Generating API documentation with Doxygen in ${GUDHI_USER_VERSION_DIR}/doc/html/" VERBATIM)
 
-endif(DOXYGEN_FOUND)
+  if(TARGET user_version)
+    # In dev version, doxygen target depends on user_version target. Not existing in user version
+    add_dependencies(doxygen user_version)
+  endif()
+else()
+  set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "cpp-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+endif()
diff --git a/src/cmake/modules/GUDHI_modules.cmake b/src/cmake/modules/GUDHI_modules.cmake
index f95d0c34..aab1dd08 100644
--- a/src/cmake/modules/GUDHI_modules.cmake
+++ b/src/cmake/modules/GUDHI_modules.cmake
@@ -1,11 +1,12 @@
 # A function to add a new module in GUDHI
 
-set(GUDHI_MODULES "")
 set(GUDHI_MODULES_FULL_LIST "")
 function(add_gudhi_module file_path)
   option("WITH_MODULE_GUDHI_${file_path}" "Activate/desactivate ${file_path} compilation and installation" ON)
   if (WITH_MODULE_GUDHI_${file_path})
-    set(GUDHI_MODULES ${GUDHI_MODULES} ${file_path} PARENT_SCOPE)
+    set(GUDHI_MODULES ${GUDHI_MODULES} ${file_path} CACHE INTERNAL "GUDHI_MODULES")
+  else()
+    set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} ${file_path} CACHE INTERNAL "GUDHI_MISSING_MODULES")
   endif()
   # Required by user_version
   set(GUDHI_MODULES_FULL_LIST ${GUDHI_MODULES_FULL_LIST} ${file_path} PARENT_SCOPE)
diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 7433f2f3..b020ebfc 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -8,11 +8,9 @@ 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()
@@ -23,11 +21,11 @@ endif()
 # 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)
+find_package(CGAL QUIET)
 
 # 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.")
+  message("++ CGAL version ${CGAL_VERSION} is considered too old to be used by Gudhi.")
   unset(CGAL_FOUND)
 endif()
 if(CGAL_FOUND)
@@ -79,7 +77,6 @@ endif(WITH_GUDHI_USE_TBB)
 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)
@@ -119,7 +116,39 @@ message(STATUS "boost library dirs:" ${Boost_LIBRARY_DIRS})
 
 # Find the correct Python interpreter.
 # Can be set with -DPYTHON_EXECUTABLE=/usr/bin/python3 or -DPython_ADDITIONAL_VERSIONS=3 for instance.
-find_package(Cython)
+find_package( PythonInterp )
+
+# find_python_module tries to import module in Python interpreter and to retrieve its version number
+# returns ${PYTHON_MODULE_NAME_UP}_VERSION and ${PYTHON_MODULE_NAME_UP}_FOUND
+function( find_python_module PYTHON_MODULE_NAME )
+  string(TOUPPER ${PYTHON_MODULE_NAME} PYTHON_MODULE_NAME_UP)
+  execute_process(
+          COMMAND ${PYTHON_EXECUTABLE}  -c "import ${PYTHON_MODULE_NAME}; print(${PYTHON_MODULE_NAME}.__version__)"
+          RESULT_VARIABLE PYTHON_MODULE_RESULT
+          OUTPUT_VARIABLE PYTHON_MODULE_VERSION
+          ERROR_VARIABLE PYTHON_MODULE_ERROR)
+  message ("PYTHON_MODULE_NAME = ${PYTHON_MODULE_NAME}
+   - PYTHON_MODULE_RESULT = ${PYTHON_MODULE_RESULT}
+   - PYTHON_MODULE_VERSION = ${PYTHON_MODULE_VERSION}
+   - PYTHON_MODULE_ERROR = ${PYTHON_MODULE_ERROR}")
+  if(PYTHON_MODULE_RESULT EQUAL 0)
+    # Remove carriage return
+    string(STRIP ${PYTHON_MODULE_VERSION} PYTHON_MODULE_VERSION)
+    set(${PYTHON_MODULE_NAME_UP}_VERSION ${PYTHON_MODULE_VERSION} PARENT_SCOPE)
+    set(${PYTHON_MODULE_NAME_UP}_FOUND TRUE PARENT_SCOPE)
+  else()
+    unset(${PYTHON_MODULE_NAME_UP}_VERSION PARENT_SCOPE)
+    set(${PYTHON_MODULE_NAME_UP}_FOUND FALSE PARENT_SCOPE)
+  endif()
+endfunction( find_python_module )
+
+if( PYTHONINTERP_FOUND )
+  find_python_module("cython")
+  find_python_module("pytest")
+  find_python_module("matplotlib")
+  find_python_module("numpy")
+  find_python_module("scipy")
+endif()
 
 if(NOT GUDHI_CYTHON_PATH)
   message(FATAL_ERROR "ERROR: GUDHI_CYTHON_PATH is not valid.")
diff --git a/src/cmake/modules/GUDHI_user_version_target.cmake b/src/cmake/modules/GUDHI_user_version_target.cmake
index 1205966a..d43a6fa6 100644
--- a/src/cmake/modules/GUDHI_user_version_target.cmake
+++ b/src/cmake/modules/GUDHI_user_version_target.cmake
@@ -1,94 +1,95 @@
-# Some functionnalities requires CMake 2.8.11 minimum
-if (NOT CMAKE_VERSION VERSION_LESS 2.8.11)
+# Definition of the custom target user_version
+add_custom_target(user_version)
 
-  # Definition of the custom target user_version
-  add_custom_target(user_version)
-  
-  if(DEFINED USER_VERSION_DIR)
-    # set the GUDHI_USER_VERSION_DIR with USER_VERSION_DIR defined by the user
-    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()
+if(DEFINED USER_VERSION_DIR)
+  # set the GUDHI_USER_VERSION_DIR with USER_VERSION_DIR defined by the user
+  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()
 
-  set(GUDHI_DOXYGEN_DEPENDENCY user_version)
+add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                   make_directory ${GUDHI_USER_VERSION_DIR}
+                   COMMENT "user_version creation in ${GUDHI_USER_VERSION_DIR}")
 
-  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                     make_directory ${GUDHI_USER_VERSION_DIR}
-                     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)
-  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                     copy ${CMAKE_SOURCE_DIR}/src/CMakeLists.txt ${GUDHI_USER_VERSION_DIR}/CMakeLists.txt)
-  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                     copy ${CMAKE_SOURCE_DIR}/src/Doxyfile ${GUDHI_USER_VERSION_DIR}/Doxyfile)
-  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                     copy ${CMAKE_SOURCE_DIR}/src/GUDHIConfigVersion.cmake.in ${GUDHI_USER_VERSION_DIR}/GUDHIConfigVersion.cmake.in)
-  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                     copy ${CMAKE_SOURCE_DIR}/src/GUDHIConfig.cmake.in ${GUDHI_USER_VERSION_DIR}/GUDHIConfig.cmake.in)
-  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                     copy ${CMAKE_SOURCE_DIR}/CMakeGUDHIVersion.txt ${GUDHI_USER_VERSION_DIR}/CMakeGUDHIVersion.txt)
-  
-  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/GudhUI ${GUDHI_USER_VERSION_DIR}/GudhUI)
-  
-  set(GUDHI_DIRECTORIES "doc;example;concept;utilities")
-  if (CGAL_VERSION VERSION_LESS 4.11.0)
-    set(GUDHI_INCLUDE_DIRECTORIES "include/gudhi;include/Miniball;include/gudhi_patches")
-  else ()
-      set(GUDHI_INCLUDE_DIRECTORIES "include/gudhi;include/Miniball")
-  endif ()
+foreach(GUDHI_MODULE ${GUDHI_MODULES_FULL_LIST})
+  set(GUDHI_DOXYGEN_IMAGE_PATH "${GUDHI_DOXYGEN_IMAGE_PATH}    doc/${GUDHI_MODULE}/ \\  \n")
+endforeach(GUDHI_MODULE ${GUDHI_MODULES_FULL_LIST})
 
-  foreach(GUDHI_MODULE ${GUDHI_MODULES_FULL_LIST})
-    foreach(GUDHI_DIRECTORY ${GUDHI_DIRECTORIES})
-      # Find files
-      file(GLOB GUDHI_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/${GUDHI_DIRECTORY}/*)
+# Generate setup.py file to cythonize Gudhi - This file must be named setup.py by convention
+configure_file(${CMAKE_SOURCE_DIR}/src/Doxyfile.in "${CMAKE_CURRENT_BINARY_DIR}/src/Doxyfile" @ONLY)
 
-      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})
+add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+        copy ${CMAKE_CURRENT_BINARY_DIR}/src/Doxyfile ${GUDHI_USER_VERSION_DIR}/Doxyfile)
 
-    foreach(GUDHI_INCLUDE_DIRECTORY ${GUDHI_INCLUDE_DIRECTORIES})
-      # include files
-      file(GLOB GUDHI_INCLUDE_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/${GUDHI_INCLUDE_DIRECTORY}/*)
+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)
+add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                   copy ${CMAKE_SOURCE_DIR}/src/CMakeLists.txt ${GUDHI_USER_VERSION_DIR}/CMakeLists.txt)
+add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                   copy ${CMAKE_SOURCE_DIR}/src/GUDHIConfigVersion.cmake.in ${GUDHI_USER_VERSION_DIR}/GUDHIConfigVersion.cmake.in)
+add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                   copy ${CMAKE_SOURCE_DIR}/src/GUDHIConfig.cmake.in ${GUDHI_USER_VERSION_DIR}/GUDHIConfig.cmake.in)
+add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                   copy ${CMAKE_SOURCE_DIR}/CMakeGUDHIVersion.txt ${GUDHI_USER_VERSION_DIR}/CMakeGUDHIVersion.txt)
 
-      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})
+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/GudhUI ${GUDHI_USER_VERSION_DIR}/GudhUI)
 
-  endforeach(GUDHI_MODULE ${GUDHI_MODULES_FULL_LIST})
+set(GUDHI_DIRECTORIES "doc;example;concept;utilities")
+if (CGAL_VERSION VERSION_LESS 4.11.0)
+  set(GUDHI_INCLUDE_DIRECTORIES "include/gudhi;include/gudhi_patches")
+else ()
+    set(GUDHI_INCLUDE_DIRECTORIES "include/gudhi")
+endif ()
 
-endif()
+foreach(GUDHI_MODULE ${GUDHI_MODULES_FULL_LIST})
+  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_FULL_LIST})
\ No newline at end of file
diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h
index 12407c18..df7eed37 100644
--- a/src/common/doc/installation.h
+++ b/src/common/doc/installation.h
@@ -2,22 +2,34 @@
  *  \tableofcontents
  * 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 utilities.
  * 
  * \section compiling Compiling
  * The library uses c++11 and requires <a target="_blank" href="http://www.boost.org/">Boost</a>  &ge; 1.48.0
  * and <a target="_blank" href="https://www.cmake.org/">CMake</a> &ge; 3.1.
  * It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2015.
  * 
- * \subsection demos Demos and examples
- * To build the demos and examples, run the following commands in a terminal:
+ * \subsection utilities Utilities and examples
+ * To build the utilities, run the following commands in a terminal:
 \verbatim  cd /path-to-gudhi/
 mkdir build
 cd build/
 cmake ..
 make \endverbatim
- * A list of examples is available <a href="examples.html">here</a>.
+ * By default, examples are disabled. You can activate their compilation with
+ * <a href="https://cmake.org/cmake/help/v3.0/manual/ccmake.1.html">ccmake</a> (on Linux and Mac OSX),
+ * <a href="https://cmake.org/cmake/help/v3.0/manual/cmake-gui.1.html">cmake-gui</a> (on Windows) or by modifying the
+ * cmake command as follows :
+\verbatim  cmake -DWITH_GUDHI_EXAMPLE=ON ..
+make \endverbatim
+ * A list of utilities and examples is available <a href="examples.html">here</a>.
  * 
+ * \subsection libraryinstallation Installation
+ * To install the library (headers and activated utilities), run the following command in a terminal:
+ * \verbatim  make install \endverbatim
+ * This action may require to be in the sudoer or administrator of the machine in function of the operating system and
+ * of <a href="https://cmake.org/cmake/help/v3.0/variable/CMAKE_INSTALL_PREFIX.html">CMAKE_INSTALL_PREFIX</a>.
+ *
  * \subsection testsuites Test suites
  * To test your build, run the following command in a terminal:
  * \verbatim  make test \endverbatim
@@ -31,6 +43,10 @@ make doxygen
 # You can customize the directory name by calling `cmake -DUSER_VERSION_DIR=/my/custom/folder`
 \endverbatim
  *
+ * \subsection helloworld Hello world !
+ * The <a target="_blank" href="https://gitlab.inria.fr/GUDHI/hello-gudhi-world">Hello world for GUDHI</a>
+ * project is an example to help developers to make their own C++ project on top of the GUDHI library.
+ *
  * \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
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 8f1dec76..dc2e9278 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -16,306 +16,429 @@ endfunction( add_gudhi_cython_lib )
 
 # THE_TEST is the python test file name (without .py extension) containing tests functions
 function( add_gudhi_py_test THE_TEST )
-  # use ${PYTHON_EXECUTABLE} -B, otherwise a __pycache__ directory is created in sources by python
-  # use py.test no cache provider, otherwise a .cache file is created in sources by py.test
-  add_test(NAME ${THE_TEST}_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} -B -m pytest -p no:cacheprovider ${CMAKE_CURRENT_SOURCE_DIR}/test/${THE_TEST}.py)
-endfunction( add_gudhi_py_test )
-
-
-if(CYTHON_FOUND)
-  message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_EXECUTABLE} - Sphinx is ${SPHINX_PATH}")
-
-  set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_RESULT_OF_USE_DECLTYPE', ")
-  set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ")
-  set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_SYSTEM_NO_DEPRECATED', ")
-
-  # 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 "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-frounding-math', ")
-  endif(CMAKE_COMPILER_IS_GNUCXX)
-  if (CMAKE_CXX_COMPILER_ID MATCHES Intel)
-    set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-fp-model strict', ")
-  endif(CMAKE_CXX_COMPILER_ID MATCHES Intel)
-  if (DEBUG_TRACES)
-    # For programs to be more verbose
-    set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DDEBUG_TRACES', ")
+  if(PYTEST_FOUND)
+    # use ${PYTHON_EXECUTABLE} -B, otherwise a __pycache__ directory is created in sources by python
+    # use py.test no cache provider, otherwise a .cache file is created in sources by py.test
+    add_test(NAME ${THE_TEST}_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${PYTHON_EXECUTABLE} -B -m pytest -p no:cacheprovider ${CMAKE_CURRENT_SOURCE_DIR}/test/${THE_TEST}.py)
   endif()
+endfunction( add_gudhi_py_test )
 
-  if (EIGEN3_FOUND)
-    # No problem, even if no CGAL found
-    set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ")
-  endif (EIGEN3_FOUND)
-
-  if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-    set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/bottleneck_distance.pyx'")
-    set(GUDHI_CYTHON_NERVE_GIC "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/nerve_gic.pyx'")
-  endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
-    set(GUDHI_CYTHON_SUBSAMPLING "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/subsampling.pyx'")
-    set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/tangential_complex.pyx'")
-  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
-  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
-    set(GUDHI_CYTHON_ALPHA_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/alpha_complex.pyx'")
-  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
-  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
-    set(GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX
-        "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_witness_complex.pyx'\ninclude '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_strong_witness_complex.pyx'\n")
-  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
-
-  if(CGAL_FOUND)
-    can_cgal_use_cxx11_thread_local()
-    if (NOT CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT)
-      add_gudhi_cython_lib(${Boost_THREAD_LIBRARY})
-      set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ")
+# Set gudhi.__debug_info__
+# WARNING : to be done before gudhi.pyx.in configure_file
+function( add_gudhi_debug_info DEBUG_INFO )
+  set(GUDHI_CYTHON_DEBUG_INFO "${GUDHI_CYTHON_DEBUG_INFO}    \"${DEBUG_INFO}\\n\" \\\n" PARENT_SCOPE)
+endfunction( add_gudhi_debug_info )
+
+if(PYTHONINTERP_FOUND)
+  if(CYTHON_FOUND)
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}off_reader;")
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}simplex_tree;")
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}rips_complex;")
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}cubical_complex;")
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}periodic_cubical_complex;")
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}persistence_graphical_tools;")
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}reader_utils;")
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}witness_complex;")
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}strong_witness_complex;")
+
+    add_gudhi_debug_info("Python version ${PYTHON_VERSION_STRING}")
+    add_gudhi_debug_info("Cython version ${CYTHON_VERSION}")
+    if(PYTEST_FOUND)
+      add_gudhi_debug_info("Pytest version ${PYTEST_VERSION}")
+    endif()
+    if(MATPLOTLIB_FOUND)
+      add_gudhi_debug_info("Matplotlib version ${MATPLOTLIB_VERSION}")
+    endif()
+    if(NUMPY_FOUND)
+      add_gudhi_debug_info("Numpy version ${NUMPY_VERSION}")
+    endif()
+    if(SCIPY_FOUND)
+      add_gudhi_debug_info("Scipy version ${SCIPY_VERSION}")
+    endif()
+    if(MATPLOTLIB_FOUND AND NUMPY_FOUND AND SCIPY_FOUND)
+      set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}persistence_graphical_tools;")
+    else()
+        set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MODULES}persistence_graphical_tools;")
     endif()
-    # Add CGAL compilation args
-    if(CGAL_HEADER_ONLY)
-      set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ")
-    else(CGAL_HEADER_ONLY)
-      add_gudhi_cython_lib(${CGAL_LIBRARY})
-      set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ")
-      # If CGAL is not header only, CGAL library may link with boost system,
-      add_gudhi_cython_lib(${Boost_SYSTEM_LIBRARY})
-      set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ")
-    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 "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMP', ")
-      add_gudhi_cython_lib(${GMP_LIBRARIES})
-      set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMP_LIBRARIES_DIR}', ")
-      if(GMPXX_FOUND)
-        set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMPXX', ")
-        add_gudhi_cython_lib(${GMPXX_LIBRARIES})
-        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=10.12', ")
-      set(GUDHI_CYTHON_EXTRA_LINK_ARGS "${GUDHI_CYTHON_EXTRA_LINK_ARGS}'-mmacosx-version-min=10.12', ")
-  endif(${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 AND WITH_GUDHI_USE_TBB)
-    set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DGUDHI_USE_TBB', ")
-    add_gudhi_cython_lib(${TBB_RELEASE_LIBRARY})
-    add_gudhi_cython_lib(${TBB_MALLOC_RELEASE_LIBRARY})
-    set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${TBB_LIBRARY_DIRS}', ")
-    set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${TBB_INCLUDE_DIRS}', ")
-  endif()
-
-  if(UNIX)
-    set( GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}")
-  endif(UNIX)
-
-  # Generate setup.py file to cythonize Gudhi - This file must be named setup.py by convention
-  configure_file(setup.py.in "${CMAKE_CURRENT_BINARY_DIR}/setup.py" @ONLY)
-  # Generate gudhi.pyx - Gudhi cython file
-  configure_file(gudhi.pyx.in "${CMAKE_CURRENT_BINARY_DIR}/gudhi.pyx" @ONLY)
-
-  add_custom_command(
-      OUTPUT gudhi.so
-      WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-      COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/setup.py" "build_ext" "--inplace")
-
-  add_custom_target(cython ALL DEPENDS gudhi.so
-                    COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/ to your PYTHONPATH before using examples or tests")
-
-  # For installation purpose
-  # TODO(VR) : files matching pattern mechanism is copying all cython directory
-  install(DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}" DESTINATION "${PYTHON_SITE_PACKAGES}/" FILES_MATCHING
-      PATTERN "*.so"
-      PATTERN "*.dylib"
-      PATTERN "*.pyd")
-
-  # Test examples
-  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
-    # Bottleneck and Alpha
-    add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
-             -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
-
-    # Tangential
-    add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
-             --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
-
-    add_gudhi_py_test(test_tangential_complex)
 
-    # Witness complex AND Subsampling
-    add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
-             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+    message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_VERSION} - Sphinx is ${SPHINX_PATH}")
+    set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_RESULT_OF_USE_DECLTYPE', ")
+    set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ")
+    set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_SYSTEM_NO_DEPRECATED', ")
+
+    # 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 "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-frounding-math', ")
+    endif(CMAKE_COMPILER_IS_GNUCXX)
+    if (CMAKE_CXX_COMPILER_ID MATCHES Intel)
+      set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-fp-model strict', ")
+    endif(CMAKE_CXX_COMPILER_ID MATCHES Intel)
+    if (DEBUG_TRACES)
+      # For programs to be more verbose
+      set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DDEBUG_TRACES', ")
+    endif()
 
-    add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
-             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+    if (EIGEN3_FOUND)
+      add_gudhi_debug_info("Eigen3 version ${EIGEN3_VERSION}")
+      # No problem, even if no CGAL found
+      set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ")
+    endif (EIGEN3_FOUND)
+
+    if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+      set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/bottleneck_distance.pyx'")
+      set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}bottleneck_distance;")
+      set(GUDHI_CYTHON_NERVE_GIC "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/nerve_gic.pyx'")
+      set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}nerve_gic;")
+    else()
+      set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}bottleneck_distance;")
+      set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}nerve_gic;")
+    endif ()
+    if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+      set(GUDHI_CYTHON_SUBSAMPLING "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/subsampling.pyx'")
+      set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}subsampling;")
+      set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/tangential_complex.pyx'")
+      set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}tangential_complex;")
+    else()
+      set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}subsampling;")
+      set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}tangential_complex;")
+    endif ()
+    if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
+      set(GUDHI_CYTHON_ALPHA_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/alpha_complex.pyx'")
+      set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}alpha_complex;")
+    else()
+      set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}alpha_complex;")
+    endif ()
+    if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
+      set(GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX
+          "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_witness_complex.pyx'\ninclude '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_strong_witness_complex.pyx'\n")
+      set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}euclidean_witness_complex;")
+      set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}euclidean_strong_witness_complex;")
+    else()
+      set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}euclidean_witness_complex;")
+      set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}euclidean_strong_witness_complex;")
+    endif ()
+
+    add_gudhi_debug_info("Installed modules are: ${GUDHI_CYTHON_MODULES}")
+    if(GUDHI_CYTHON_MISSING_MODULES)
+      add_gudhi_debug_info("Missing modules are: ${GUDHI_CYTHON_MISSING_MODULES}")
+    endif()
 
-    # Subsampling
-    add_gudhi_py_test(test_subsampling)
+    if(CGAL_FOUND)
+      can_cgal_use_cxx11_thread_local()
+      if (NOT CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT)
+        if(CMAKE_BUILD_TYPE MATCHES Debug)
+          add_gudhi_cython_lib("${Boost_THREAD_LIBRARY_DEBUG}")
+        else()
+          add_gudhi_cython_lib("${Boost_THREAD_LIBRARY_RELEASE}")
+        endif()
+        set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ")
+      endif()
+      # Add CGAL compilation args
+      if(CGAL_HEADER_ONLY)
+        add_gudhi_debug_info("CGAL header only version ${CGAL_VERSION}")
+        set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ")
+      else(CGAL_HEADER_ONLY)
+        add_gudhi_debug_info("CGAL version ${CGAL_VERSION}")
+        add_gudhi_cython_lib("${CGAL_LIBRARY}")
+        set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ")
+        # If CGAL is not header only, CGAL library may link with boost system,
+        if(CMAKE_BUILD_TYPE MATCHES Debug)
+          add_gudhi_cython_lib("${Boost_SYSTEM_LIBRARY_DEBUG}")
+        else()
+          add_gudhi_cython_lib("${Boost_SYSTEM_LIBRARY_RELEASE}")
+        endif()
+        set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ")
+      endif(CGAL_HEADER_ONLY)
+      # GMP and GMPXX are not required, but if present, CGAL will link with them.
+      if(GMP_FOUND)
+        add_gudhi_debug_info("GMP_LIBRARIES = ${GMP_LIBRARIES}")
+        set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMP', ")
+        add_gudhi_cython_lib("${GMP_LIBRARIES}")
+        set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMP_LIBRARIES_DIR}', ")
+        if(GMPXX_FOUND)
+          add_gudhi_debug_info("GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}")
+          set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMPXX', ")
+          add_gudhi_cython_lib("${GMPXX_LIBRARIES}")
+          set(GUDHI_CYTHON_LIBRARY_DIRS "${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 "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-mmacosx-version-min=10.12', ")
+        set(GUDHI_CYTHON_EXTRA_LINK_ARGS "${GUDHI_CYTHON_EXTRA_LINK_ARGS}'-mmacosx-version-min=10.12', ")
+    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 AND WITH_GUDHI_USE_TBB)
+      add_gudhi_debug_info("TBB version ${TBB_INTERFACE_VERSION} found and used")
+      set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DGUDHI_USE_TBB', ")
+      if(CMAKE_BUILD_TYPE MATCHES Debug)
+        add_gudhi_cython_lib("${TBB_DEBUG_LIBRARY}")
+        add_gudhi_cython_lib("${TBB_MALLOC_DEBUG_LIBRARY}")
+      else()
+        add_gudhi_cython_lib("${TBB_RELEASE_LIBRARY}")
+        add_gudhi_cython_lib("${TBB_MALLOC_RELEASE_LIBRARY}")
+      endif()
+      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()
 
-  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
-  if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-    # Bottleneck
-    add_test(NAME bottleneck_basic_example_py_test
+    if(UNIX)
+      set( GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}")
+    endif(UNIX)
+
+    # Generate setup.py file to cythonize Gudhi - This file must be named setup.py by convention
+    configure_file(setup.py.in "${CMAKE_CURRENT_BINARY_DIR}/setup.py" @ONLY)
+    # Generate gudhi.pyx - Gudhi cython file
+    configure_file(gudhi.pyx.in "${CMAKE_CURRENT_BINARY_DIR}/gudhi.pyx" @ONLY)
+
+    add_custom_command(
+        OUTPUT gudhi.so
+        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+        COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/setup.py" "build_ext" "--inplace")
+
+    add_custom_target(cython ALL DEPENDS gudhi.so
+                      COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/ to your PYTHONPATH before using examples or tests")
+
+    # For installation purpose
+    # TODO(VR) : files matching pattern mechanism is copying all cython directory
+    install(DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}" DESTINATION "${PYTHON_SITE_PACKAGES}/" FILES_MATCHING
+        PATTERN "*.so"
+        PATTERN "*.dylib"
+        PATTERN "*.pyd")
+
+    # Test examples
+    if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+      # Bottleneck and Alpha
+      add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
+               -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
+
+      if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
+        # Tangential
+        add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
+                 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+                 COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+                 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
+                 --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
+
+        add_gudhi_py_test(test_tangential_complex)
+
+        # Witness complex AND Subsampling
+        add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
+                 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+                 COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+                 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
+                 --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+
+        add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
+                 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+                 COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+                 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
+                 --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+      endif()
+
+      # Subsampling
+      add_gudhi_py_test(test_subsampling)
+
+    endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+    if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+      # Bottleneck
+      add_test(NAME bottleneck_basic_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
+
+      add_gudhi_py_test(test_bottleneck_distance)
+
+      # Cover complex
+      file(COPY ${CMAKE_SOURCE_DIR}/data/points/human.off DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+      file(COPY ${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat.off DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+      file(COPY ${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1 DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+      add_test(NAME cover_complex_nerve_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/nerve_of_a_covering.py"
+               -f human.off -c 2 -r 10 -g 0.3)
+
+      add_test(NAME cover_complex_coordinate_gic_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/coordinate_graph_induced_complex.py"
+               -f human.off -c 0 -v)
+
+      add_test(NAME cover_complex_functional_gic_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/functional_graph_induced_complex.py"
+               -o lucky_cat.off
+               -f lucky_cat_PCA1 -v)
+
+      add_test(NAME cover_complex_voronoi_gic_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/voronoi_graph_induced_complex.py"
+               -f human.off -n 700 -v)
+
+      add_gudhi_py_test(test_cover_complex)
+    endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+
+    if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
+      # Alpha
+      add_test(NAME alpha_complex_from_points_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
+
+      if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
+        add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
+               --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6)
+      endif()
+
+      add_gudhi_py_test(test_alpha_complex)
+
+    endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
+
+    if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
+      # Euclidean witness
+      add_gudhi_py_test(test_euclidean_witness_complex)
+
+    endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
+
+    # Cubical
+    add_test(NAME periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
              COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py"
+             --no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt)
+
+    if(NUMPY_FOUND)
+      add_test(NAME random_cubical_complex_persistence_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py"
+               10 10 10)
+    endif()
 
-    add_gudhi_py_test(test_bottleneck_distance)
+    add_gudhi_py_test(test_cubical_complex)
+
+    # Rips
+    if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
+      add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
+               --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3)
+
+      add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py
+               --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off  -e 0.25 -d 3)
+    endif()
 
-    # Cover complex
-    file(COPY ${CMAKE_SOURCE_DIR}/data/points/human.off DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
-    file(COPY ${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat.off DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
-    file(COPY ${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1 DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
-    add_test(NAME cover_complex_nerve_example_py_test
+    add_test(NAME rips_complex_from_points_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
              COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/nerve_of_a_covering.py"
-             -f human.off -c 2 -r 10 -g 0.3)
+             ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py)
 
-    add_test(NAME cover_complex_coordinate_gic_example_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/coordinate_graph_induced_complex.py"
-             -f human.off -c 0 -v)
+    add_gudhi_py_test(test_rips_complex)
 
-    add_test(NAME cover_complex_functional_gic_example_py_test
+    # Simplex tree
+    add_test(NAME simplex_tree_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
              COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/functional_graph_induced_complex.py"
-             -o lucky_cat.off
-             -f lucky_cat_PCA1 -v)
+             ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py)
 
-    add_test(NAME cover_complex_voronoi_gic_example_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/voronoi_graph_induced_complex.py"
-             -f human.off -n 700 -v)
-
-    add_gudhi_py_test(test_cover_complex)
-  endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-
-  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
-    # Alpha
-    add_test(NAME alpha_complex_from_points_example_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
+    add_gudhi_py_test(test_simplex_tree)
 
-    add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
+    # Witness
+    add_test(NAME witness_complex_from_nearest_landmark_table_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
              COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
-             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6)
-
-    add_gudhi_py_test(test_alpha_complex)
-
-  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
-
-  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
-    # Euclidean witness
-    add_gudhi_py_test(test_euclidean_witness_complex)
-
-  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
-
-  # Cubical
-  add_test(NAME periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-           ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py"
-           --no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt)
-
-  add_test(NAME random_cubical_complex_persistence_example_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-           ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py"
-           10 10 10)
-
-  add_gudhi_py_test(test_cubical_complex)
-
-  # Rips
-  add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-           ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
-           --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3)
-
-  add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-           ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py
-           --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off  -e 0.25 -d 3)
-
-  add_test(NAME rips_complex_from_points_example_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-           ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py)
-
-  add_gudhi_py_test(test_rips_complex)
-
-  # Simplex tree
-  add_test(NAME simplex_tree_example_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-           ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py)
-
-  add_gudhi_py_test(test_simplex_tree)
-
-  # Witness
-  add_test(NAME witness_complex_from_nearest_landmark_table_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-           ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py)
-
-  add_gudhi_py_test(test_witness_complex)
-
-  # Reader utils
-  add_gudhi_py_test(test_reader_utils)
-
-  # Documentation generation is available through sphinx - requires all modules
-  if(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
-    set (GUDHI_SPHINX_MESSAGE "Generating API documentation with Sphinx in ${CMAKE_CURRENT_BINARY_DIR}/sphinx/")
-    # User warning - Sphinx is a static pages generator, and configured to work fine with user_version
-    # Images and biblio warnings because not found on developper version
-    if (GUDHI_CYTHON_PATH STREQUAL "src/cython")
-      set (GUDHI_SPHINX_MESSAGE "${GUDHI_SPHINX_MESSAGE} \n WARNING : Sphinx is configured for user version, you run it on developper version. Images and biblio will miss")
-    endif()
-    # sphinx target requires gudhi.so, because conf.py reads gudhi version from it
-    add_custom_target(sphinx
-        WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc
-        COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-        ${SPHINX_PATH} -b html ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/sphinx
-        DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
-        COMMENT "${GUDHI_SPHINX_MESSAGE}" VERBATIM)
-
-    add_test(NAME sphinx_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/doctest)
-
-  endif(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
-endif(CYTHON_FOUND)
+             ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py)
+
+    add_gudhi_py_test(test_witness_complex)
+
+    # Reader utils
+    add_gudhi_py_test(test_reader_utils)
+
+    # Documentation generation is available through sphinx - requires all modules
+    if(SPHINX_PATH)
+      if(MATPLOTLIB_FOUND)
+        if(NUMPY_FOUND)
+          if(SCIPY_FOUND)
+            if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+              set (GUDHI_SPHINX_MESSAGE "Generating API documentation with Sphinx in ${CMAKE_CURRENT_BINARY_DIR}/sphinx/")
+              # User warning - Sphinx is a static pages generator, and configured to work fine with user_version
+              # Images and biblio warnings because not found on developper version
+              if (GUDHI_CYTHON_PATH STREQUAL "src/cython")
+                set (GUDHI_SPHINX_MESSAGE "${GUDHI_SPHINX_MESSAGE} \n WARNING : Sphinx is configured for user version, you run it on developper version. Images and biblio will miss")
+              endif()
+              # sphinx target requires gudhi.so, because conf.py reads gudhi version from it
+              add_custom_target(sphinx
+                  WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc
+                  COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+                  ${SPHINX_PATH} -b html ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/sphinx
+                  DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
+                  COMMENT "${GUDHI_SPHINX_MESSAGE}" VERBATIM)
+
+              add_test(NAME sphinx_py_test
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+                       COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+                       ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/doctest)
+
+              # Set missing or not modules
+              set(GUDHI_MODULES ${GUDHI_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MODULES")
+            else(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+              message("++ Python documentation module will not be compiled because it requires a CGAL with Eigen3 version greater or equal than 4.8.1")
+              set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+            endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+          else(SCIPY_FOUND)
+            message("++ Python documentation module will not be compiled because scipy was not found")
+            set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+          endif(SCIPY_FOUND)
+        else(NUMPY_FOUND)
+          message("++ Python documentation module will not be compiled because numpy was not found")
+          set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+        endif(NUMPY_FOUND)
+      else(MATPLOTLIB_FOUND)
+        message("++ Python documentation module will not be compiled because matplotlib was not found")
+        set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+      endif(MATPLOTLIB_FOUND)
+    else(SPHINX_PATH)
+      message("++ Python documentation module will not be compiled because sphinx and sphinxcontrib-bibtex were not found")
+      set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+    endif(SPHINX_PATH)
+
+
+    # Set missing or not modules
+    set(GUDHI_MODULES ${GUDHI_MODULES} "python" CACHE INTERNAL "GUDHI_MODULES")
+  else(CYTHON_FOUND)
+    message("++ Python module will not be compiled because cython was not found")
+    set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+  endif(CYTHON_FOUND)
+else(PYTHONINTERP_FOUND)
+  message("++ Python module will not be compiled because no Python interpreter was found")
+  set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+endif(PYTHONINTERP_FOUND)
diff --git a/src/cython/cython/nerve_gic.pyx b/src/cython/cython/nerve_gic.pyx
index 30a14d3b..5f01b379 100644
--- a/src/cython/cython/nerve_gic.pyx
+++ b/src/cython/cython/nerve_gic.pyx
@@ -38,14 +38,14 @@ cdef extern from "Nerve_gic_interface.h" namespace "Gudhi":
         double compute_distance_from_confidence_level(double alpha)
         void compute_distribution(int N)
         double compute_p_value()
-        void compute_PD()
+        vector[pair[double, double]] compute_PD()
         void find_simplices()
         void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree)
         bool read_point_cloud(string off_file_name)
         double set_automatic_resolution()
         void set_color_from_coordinate(int k)
         void set_color_from_file(string color_file_name)
-        void set_color_from_vector(vector[double] color)
+        void set_color_from_range(vector[double] color)
         void set_cover_from_file(string cover_file_name)
         void set_cover_from_function()
         void set_cover_from_Euclidean_Voronoi(int m)
@@ -67,6 +67,8 @@ cdef extern from "Nerve_gic_interface.h" namespace "Gudhi":
         void write_info()
         void plot_DOT()
         void plot_OFF()
+        void set_point_cloud_from_range(vector[vector[double]] cloud)
+        void set_distances_from_range(vector[vector[double]] distance_matrix)
 
 # CoverComplex python interface
 cdef class CoverComplex:
@@ -102,6 +104,22 @@ cdef class CoverComplex:
          """
         return self.thisptr != NULL
 
+    def set_point_cloud_from_range(self, cloud):
+        """ Reads and stores the input point cloud from a vector stored in memory.
+
+        :param cloud: Input vector containing the point cloud.
+        :type cloud: vector[vector[double]]
+        """
+        return self.thisptr.set_point_cloud_from_range(cloud)
+
+    def set_distances_from_range(self, distance_matrix):
+        """ Reads and stores the input distance matrix from a vector stored in memory.
+
+        :param distance_matrix: Input vector containing the distance matrix.
+        :type distance_matrix: vector[vector[double]]
+        """
+        return self.thisptr.set_distances_from_range(distance_matrix)
+
     def compute_confidence_level_from_distance(self, distance):
         """Computes the confidence level of a specific bottleneck distance
         threshold.
@@ -145,7 +163,7 @@ cdef class CoverComplex:
     def compute_PD(self):
         """Computes the extended persistence diagram of the complex.
         """
-        self.thisptr.compute_PD()
+        return self.thisptr.compute_PD()
 
     def create_simplex_tree(self):
         """
@@ -162,7 +180,7 @@ cdef class CoverComplex:
         self.thisptr.find_simplices()
 
     def read_point_cloud(self, off_file):
-        """Reads and stores the input point cloud.
+        """Reads and stores the input point cloud from .(n)OFF file.
 
         :param off_file: Name of the input .OFF or .nOFF file.
         :type off_file: string
@@ -206,14 +224,14 @@ cdef class CoverComplex:
         else:
             print("file " + color_file_name + " not found.")
 
-    def set_color_from_vector(self, color):
+    def set_color_from_range(self, color):
         """Computes the function used to color the nodes of the simplicial
         complex from a vector stored in memory.
 
         :param color: Input vector of values.
         :type color: vector[double]
         """
-        self.thisptr.set_color_from_vector(color)
+        self.thisptr.set_color_from_range(color)
 
     def set_cover_from_file(self, cover_file_name):
         """Creates the cover C from a file containing the cover elements of
diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py
index 216ab8d6..d7be936f 100755..100644
--- a/src/cython/cython/persistence_graphical_tools.py
+++ b/src/cython/cython/persistence_graphical_tools.py
@@ -1,8 +1,3 @@
-import matplotlib.pyplot as plt
-import matplotlib.patches as mpatches
-import numpy as np
-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.
@@ -59,157 +54,295 @@ Only 13 colors for the palette
 palette = ['#ff0000', '#00ff00', '#0000ff', '#00ffff', '#ff00ff', '#ffff00',
            '#000000', '#880000', '#008800', '#000088', '#888800', '#880088',
            '#008888']
- 
+
 def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6,
-        max_barcodes=1000, inf_delta=0.1, legend=False):
+                             max_intervals=1000, max_barcodes=1000,
+                             inf_delta=0.1, legend=False):
     """This function plots the persistence bar code from persistence values list
     or from a :doc:`persistence file <fileformats>`.
 
-    :param persistence: Persistence values list.
+    :param persistence: Persistence intervals values list grouped by dimension.
     :type persistence: list of tuples(dimension, tuple(birth, death)).
     :param persistence_file: A :doc:`persistence file <fileformats>` style name
         (reset persistence if both are set).
     :type persistence_file: string
-    :param alpha: barcode transparency value (0.0 transparent through 1.0 opaque - default is 0.6).
+    :param alpha: barcode transparency value (0.0 transparent through 1.0
+        opaque - default is 0.6).
     :type alpha: float.
-    :param max_barcodes: number of maximal barcodes to be displayed.
-        Set it to 0 to see all, Default value is 1000.
-        (persistence will be sorted by life time if max_barcodes is set)
-    :type max_barcodes: int.
-    :param inf_delta: Infinity is placed at ((max_death - min_birth) x inf_delta).
-        A reasonable value is between 0.05 and 0.5 - default is 0.1.
+    :param max_intervals: maximal number of intervals to display.
+        Selected intervals are those with the longest life time. Set it
+        to 0 to see all. Default value is 1000.
+    :type max_intervals: int.
+    :param inf_delta: Infinity is placed at :code:`((max_death - min_birth) x
+        inf_delta)` above :code:`max_death` value. A reasonable value is
+        between 0.05 and 0.5 - default is 0.1.
     :type inf_delta: float.
+    :param legend: Display the dimension color legend (default is False).
+    :type legend: boolean.
     :returns: A matplotlib object containing horizontal bar plot of persistence
         (launch `show()` method on it to display it).
     """
-    if persistence_file is not '':
-        if os.path.isfile(persistence_file):
-            # Reset persistence
-            persistence = []
-            diag = read_persistence_intervals_grouped_by_dimension(persistence_file=persistence_file)
-            for key in diag.keys():
-                for persistence_interval in diag[key]:
-                    persistence.append((key, persistence_interval))
-        else:
-            print("file " + persistence_file + " not found.")
-            return None
-
-    if max_barcodes > 0 and max_barcodes < len(persistence):
-        # Sort by life time, then takes only the max_plots elements
-        persistence = sorted(persistence, key=lambda life_time: life_time[1][1]-life_time[1][0], reverse=True)[:max_barcodes]
-
-    persistence = sorted(persistence, key=lambda birth: birth[1][0])
-
-    (min_birth, max_death) = __min_birth_max_death(persistence)
-    ind = 0
-    delta = ((max_death - min_birth) * inf_delta)
-    # 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]],
-                     linewidth=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]],
-                     linewidth=0)
-        ind = ind + 1
-
-    if legend:
-        dimensions = list(set(item[0] for item in persistence))
-        plt.legend(handles=[mpatches.Patch(color=palette[dim],
-                                           label=str(dim)) for dim in dimensions],
-                   loc='lower right')
-    plt.title('Persistence barcode')
-    # Ends plot on infinity value and starts a little bit before min_birth
-    plt.axis([axis_start, infinity, 0, ind])
-    return plt
+    try:
+        import matplotlib.pyplot as plt
+        import matplotlib.patches as mpatches
+        import numpy as np
+        import os
+
+        if persistence_file is not '':
+            if os.path.isfile(persistence_file):
+                # Reset persistence
+                persistence = []
+                diag = read_persistence_intervals_grouped_by_dimension(persistence_file=persistence_file)
+                for key in diag.keys():
+                    for persistence_interval in diag[key]:
+                        persistence.append((key, persistence_interval))
+            else:
+                print("file " + persistence_file + " not found.")
+                return None
+
+        if max_barcodes is not 1000:
+            print('Deprecated parameter. It has been replaced by max_intervals')
+            max_intervals = max_barcodes
+
+        if max_intervals > 0 and max_intervals < len(persistence):
+            # Sort by life time, then takes only the max_intervals elements
+            persistence = sorted(persistence, key=lambda life_time: life_time[1][1]-life_time[1][0], reverse=True)[:max_intervals]
+
+        persistence = sorted(persistence, key=lambda birth: birth[1][0])
+
+        (min_birth, max_death) = __min_birth_max_death(persistence)
+        ind = 0
+        delta = ((max_death - min_birth) * inf_delta)
+        # 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]],
+                         linewidth=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]],
+                         linewidth=0)
+            ind = ind + 1
+
+        if legend:
+            dimensions = list(set(item[0] for item in persistence))
+            plt.legend(handles=[mpatches.Patch(color=palette[dim],
+                                               label=str(dim)) for dim in dimensions],
+                       loc='lower right')
+        plt.title('Persistence barcode')
+        # Ends plot on infinity value and starts a little bit before min_birth
+        plt.axis([axis_start, infinity, 0, ind])
+        return plt
+
+    except ImportError:
+        print("This function is not available, you may be missing numpy and/or matplotlib.")
 
 def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6,
-        band=0., max_plots=1000, inf_delta=0.1, legend=False):
-    """This function plots the persistence diagram from persistence values list
-    or from a :doc:`persistence file <fileformats>`.
+        band=0., max_intervals=1000, max_plots=1000, inf_delta=0.1, legend=False):
+    """This function plots the persistence diagram from persistence values
+    list or from a :doc:`persistence file <fileformats>`.
 
-    :param persistence: Persistence values list.
+    :param persistence: Persistence intervals values list grouped by dimension.
     :type persistence: list of tuples(dimension, tuple(birth, death)).
     :param persistence_file: A :doc:`persistence file <fileformats>` style name
         (reset persistence if both are set).
     :type persistence_file: string
-    :param alpha: plot transparency value (0.0 transparent through 1.0 opaque - default is 0.6).
+    :param alpha: plot transparency value (0.0 transparent through 1.0
+        opaque - default is 0.6).
     :type alpha: float.
     :param band: band (not displayed if :math:`\leq` 0. - default is 0.)
     :type band: float.
-    :param max_plots: number of maximal plots to be displayed
-        Set it to 0 to see all, Default value is 1000.
-        (persistence will be sorted by life time if max_plots is set)
-    :type max_plots: int.
-    :param inf_delta: Infinity is placed at ((max_death - min_birth) x inf_delta).
-        A reasonable value is between 0.05 and 0.5 - default is 0.1.
+    :param max_intervals: maximal number of intervals to display.
+        Selected intervals are those with the longest life time. Set it
+        to 0 to see all. Default value is 1000.
+    :type max_intervals: int.
+    :param inf_delta: Infinity is placed at :code:`((max_death - min_birth) x
+        inf_delta)` above :code:`max_death` value. A reasonable value is
+        between 0.05 and 0.5 - default is 0.1.
     :type inf_delta: float.
+    :param legend: Display the dimension color legend (default is False).
+    :type legend: boolean.
     :returns: A matplotlib object containing diagram plot of persistence
         (launch `show()` method on it to display it).
     """
-    if persistence_file is not '':
-        if os.path.isfile(persistence_file):
-            # Reset persistence
-            persistence = []
-            diag = read_persistence_intervals_grouped_by_dimension(persistence_file=persistence_file)
-            for key in diag.keys():
-                for persistence_interval in diag[key]:
-                    persistence.append((key, persistence_interval))
-        else:
-            print("file " + persistence_file + " not found.")
-            return None
-
-    if max_plots > 0 and max_plots < len(persistence):
-        # Sort by life time, then takes only the max_plots elements
-        persistence = sorted(persistence, key=lambda life_time: life_time[1][1]-life_time[1][0], reverse=True)[:max_plots]
-
-    (min_birth, max_death) = __min_birth_max_death(persistence, band)
-    ind = 0
-    delta = ((max_death - min_birth) * inf_delta)
-    # 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)
-    # bootstrap band
-    if band > 0.:
-        plt.fill_between(x, x, x+band, alpha=alpha, facecolor='red')
+    try:
+        import matplotlib.pyplot as plt
+        import matplotlib.patches as mpatches
+        import numpy as np
+        import os
 
-    # 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]])
+        if persistence_file is not '':
+            if os.path.isfile(persistence_file):
+                # Reset persistence
+                persistence = []
+                diag = read_persistence_intervals_grouped_by_dimension(persistence_file=persistence_file)
+                for key in diag.keys():
+                    for persistence_interval in diag[key]:
+                        persistence.append((key, persistence_interval))
+            else:
+                print("file " + persistence_file + " not found.")
+                return None
+
+        if max_plots is not 1000:
+            print('Deprecated parameter. It has been replaced by max_intervals')
+            max_intervals = max_plots
+
+        if max_intervals > 0 and max_intervals < len(persistence):
+            # Sort by life time, then takes only the max_intervals elements
+            persistence = sorted(persistence, key=lambda life_time: life_time[1][1]-life_time[1][0], reverse=True)[:max_intervals]
+
+        (min_birth, max_death) = __min_birth_max_death(persistence, band)
+        delta = ((max_death - min_birth) * inf_delta)
+        # 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)
+        # bootstrap band
+        if band > 0.:
+            plt.fill_between(x, x, x+band, alpha=alpha, facecolor='red')
+
+        # 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]])
+
+        if legend:
+            dimensions = list(set(item[0] for item in persistence))
+            plt.legend(handles=[mpatches.Patch(color=palette[dim], label=str(dim)) for dim in dimensions])
+
+        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])
+        return plt
+
+    except ImportError:
+        print("This function is not available, you may be missing numpy and/or matplotlib.")
+
+def plot_persistence_density(persistence=[], persistence_file='',
+                             nbins=300, bw_method=None,
+                             max_intervals=1000, dimension=None,
+                             cmap=None, legend=False):
+    """This function plots the persistence density from persistence
+    values list or from a :doc:`persistence file <fileformats>`. Be
+    aware that this function does not distinguish the dimension, it is
+    up to you to select the required one. This function also does not handle
+    degenerate data set (scipy correlation matrix inversion can fail).
+
+    :param persistence: Persistence intervals values list grouped by dimension.
+    :type persistence: list of tuples(dimension, tuple(birth, death)).
+    :param persistence_file: A :doc:`persistence file <fileformats>`
+        style name (reset persistence if both are set).
+    :type persistence_file: string
+    :param nbins: Evaluate a gaussian kde on a regular grid of nbins x
+        nbins over data extents (default is 300)
+    :type nbins: int.
+    :param bw_method: The method used to calculate the estimator
+        bandwidth. This can be 'scott', 'silverman', a scalar constant
+        or a callable. If a scalar, this will be used directly as
+        kde.factor. If a callable, it should take a gaussian_kde
+        instance as only parameter and return a scalar. If None
+        (default), 'scott' is used. See
+        `scipy.stats.gaussian_kde documentation
+        <http://scipy.github.io/devdocs/generated/scipy.stats.gaussian_kde.html>`_
+        for more details.
+    :type bw_method: str, scalar or callable, optional.
+    :param max_intervals: maximal number of points used in the density
+        estimation.
+        Selected intervals are those with the longest life time. Set it
+        to 0 to see all. Default value is 1000.
+    :type max_intervals: int.
+    :param dimension: the dimension to be selected in the intervals
+        (default is None to mix all dimensions).
+    :type dimension: int.
+    :param cmap: A matplotlib colormap (default is
+        matplotlib.pyplot.cm.hot_r).
+    :type cmap: cf. matplotlib colormap.
+    :param legend: Display the color bar values (default is False).
+    :type legend: boolean.
+    :returns: A matplotlib object containing diagram plot of persistence
+        (launch `show()` method on it to display it).
+    """
+    try:
+        import matplotlib.pyplot as plt
+        import numpy as np
+        from scipy.stats import kde
+        import os
+        import math
+
+        if persistence_file is not '':
+            if os.path.isfile(persistence_file):
+                # Reset persistence
+                persistence = []
+                diag = read_persistence_intervals_grouped_by_dimension(persistence_file=persistence_file)
+                for key in diag.keys():
+                    for persistence_interval in diag[key]:
+                        persistence.append((key, persistence_interval))
+            else:
+                print("file " + persistence_file + " not found.")
+                return None
+
+        persistence_dim = []
+        if dimension is not None:
+            persistence_dim = [(dim_interval) for dim_interval in persistence if (dim_interval[0] == dimension)]
         else:
-            # Infinite death case for diagram to be nicer
-            plt.scatter(interval[1][0], infinity, alpha=alpha,
-                        color = palette[interval[0]])
-        ind = ind + 1
-
-    if legend:
-        dimensions = list(set(item[0] for item in persistence))
-        plt.legend(handles=[mpatches.Patch(color=palette[dim], label=str(dim)) for dim in dimensions])
-
-    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])
-    return plt
+            persistence_dim = persistence
+
+        if max_intervals > 0 and max_intervals < len(persistence_dim):
+            # Sort by life time, then takes only the max_intervals elements
+            persistence_dim = sorted(persistence_dim,
+                                 key=lambda life_time: life_time[1][1]-life_time[1][0],
+                                 reverse=True)[:max_intervals]
+
+        # Set as numpy array birth and death (remove undefined values - inf and NaN)
+        birth = np.asarray([(interval[1][0]) for interval in persistence_dim if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))])
+        death = np.asarray([(interval[1][1]) for interval in persistence_dim if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))])
+
+        # line display of equation : birth = death
+        x = np.linspace(death.min(), birth.max(), 1000)
+        plt.plot(x, x, color='k', linewidth=1.0)
+
+        # Evaluate a gaussian kde on a regular grid of nbins x nbins over data extents
+        k = kde.gaussian_kde([birth,death], bw_method=bw_method)
+        xi, yi = np.mgrid[birth.min():birth.max():nbins*1j, death.min():death.max():nbins*1j]
+        zi = k(np.vstack([xi.flatten(), yi.flatten()]))
+
+        # default cmap value cannot be done at argument definition level as matplotlib is not yet defined.
+        if cmap is None:
+            cmap = plt.cm.hot_r
+        # Make the plot
+        plt.pcolormesh(xi, yi, zi.reshape(xi.shape), cmap=cmap)
+
+        if legend:
+            plt.colorbar()
+
+        plt.title('Persistence density')
+        plt.xlabel('Birth')
+        plt.ylabel('Death')
+        return plt
+
+    except ImportError:
+        print("This function is not available, you may be missing numpy, matplotlib and/or scipy.")
diff --git a/src/cython/cython/simplex_tree.pyx b/src/cython/cython/simplex_tree.pyx
index e302486b..8397d9d9 100644
--- a/src/cython/cython/simplex_tree.pyx
+++ b/src/cython/cython/simplex_tree.pyx
@@ -515,7 +515,7 @@ cdef class SimplexTree:
         :returns: The persistence intervals.
         :rtype:  list of pair of list of int
 
-        :note: intervals_in_dim function requires
+        :note: persistence_pairs function requires
             :func:`persistence()<gudhi.SimplexTree.persistence>`
             function to be launched first.
         """
diff --git a/src/cython/cython/subsampling.pyx b/src/cython/cython/subsampling.pyx
index ac09b7a3..e9d61a37 100644
--- a/src/cython/cython/subsampling.pyx
+++ b/src/cython/cython/subsampling.pyx
@@ -112,7 +112,8 @@ def pick_n_random_points(points=None, off_file='', nb_points=0):
         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.
+    """Outputs a subset of the input points so that the squared distance
+    between any two points is greater than or equal to min_squared_dist.
 
     :param points: The input point set.
     :type points: vector[vector[double]].
@@ -122,8 +123,9 @@ def sparsify_point_set(points=None, off_file='', min_squared_dist=0.0):
     :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.
+    :param min_squared_dist: Minimum squared distance separating the output \
+    points.
+    :type min_squared_dist: float.
     :returns:  The subsample point set.
     :rtype: vector[vector[double]]
     """
diff --git a/src/cython/doc/installation.rst b/src/cython/doc/installation.rst
index 43ff85c5..ef2f7af2 100644
--- a/src/cython/doc/installation.rst
+++ b/src/cython/doc/installation.rst
@@ -47,9 +47,61 @@ following command in a terminal:
     export PYTHONPATH='$PYTHONPATH:/path-to-gudhi/build/cython'
     ctest -R py_test
 
-If tests fail, please try to :code:`import gudhi` and check the errors.
+Debugging issues
+================
+
+If tests fail, please check your PYTHONPATH and try to :code:`import gudhi`
+and check the errors.
 The problem can come from a third-party library bad link or installation.
 
+If :code:`import gudhi` succeeds, please have a look to debug informations:
+
+.. code-block:: python
+
+    import gudhi
+    print(gudhi.__debug_info__)
+
+You shall have something like:
+
+.. code-block:: none
+
+    Python version 2.7.15
+    Cython version 0.26.1
+    Eigen3 version 3.1.1
+    Installed modules are: off_reader;simplex_tree;rips_complex;cubical_complex;periodic_cubical_complex;
+        persistence_graphical_tools;reader_utils;witness_complex;strong_witness_complex;alpha_complex;
+        euclidean_witness_complex;euclidean_strong_witness_complex;
+    Missing modules are: bottleneck_distance;nerve_gic;subsampling;tangential_complex;persistence_graphical_tools;
+    CGAL version 4.7.1000
+    GMP_LIBRARIES = /usr/lib/x86_64-linux-gnu/libgmp.so
+    GMPXX_LIBRARIES = /usr/lib/x86_64-linux-gnu/libgmpxx.so
+    TBB version 9107 found and used
+
+Here, you can see that bottleneck_distance, nerve_gic, subsampling and
+tangential_complex are missing because of the CGAL version.
+persistence_graphical_tools is not available as numpy and matplotlib are not
+available.
+Unitary tests cannot be run as pytest is missing.
+
+A complete configuration would be :
+
+.. code-block:: none
+
+    Python version 3.6.5
+    Cython version 0.28.2
+    Pytest version 3.3.2
+    Matplotlib version 2.2.2
+    Numpy version 1.14.5
+    Eigen3 version 3.3.4
+    Installed modules are: off_reader;simplex_tree;rips_complex;cubical_complex;periodic_cubical_complex;
+        persistence_graphical_tools;reader_utils;witness_complex;strong_witness_complex;persistence_graphical_tools;
+        bottleneck_distance;nerve_gic;subsampling;tangential_complex;alpha_complex;euclidean_witness_complex;
+        euclidean_strong_witness_complex;
+    CGAL header only version 4.11.0
+    GMP_LIBRARIES = /usr/lib/x86_64-linux-gnu/libgmp.so
+    GMPXX_LIBRARIES = /usr/lib/x86_64-linux-gnu/libgmpxx.so
+    TBB version 9107 found and used
+
 Documentation
 =============
 
@@ -143,7 +195,7 @@ The following examples require the `Matplotlib <http://matplotlib.org>`_:
     * :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
+NumPy
 =====
 
 The :doc:`persistence graphical tools </persistence_graphical_tools_user>`
@@ -164,6 +216,13 @@ The following examples require the `NumPy <http://numpy.org>`_:
     * :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>`
 
+SciPy
+=====
+
+The :doc:`persistence graphical tools </persistence_graphical_tools_user>`
+module requires `SciPy <http://scipy.org>`_, a Python-based ecosystem of
+open-source software for mathematics, science, and engineering.
+
 Threading Building Blocks
 =========================
 
diff --git a/src/cython/doc/nerve_gic_complex_sum.rst b/src/cython/doc/nerve_gic_complex_sum.rst
index 72782c7a..523c119f 100644
--- a/src/cython/doc/nerve_gic_complex_sum.rst
+++ b/src/cython/doc/nerve_gic_complex_sum.rst
@@ -1,5 +1,5 @@
 =================================================================  ===================================  ===================================
-:Author: Mathieu Carrière                                          :Introduced in: GUDHI 2.1.0          :Copyright: GPL v3
+:Author: Mathieu Carrière                                          :Introduced in: GUDHI 2.3.0          :Copyright: GPL v3
 :Requires: CGAL :math:`\geq` 4.8.1
 =================================================================  ===================================  ===================================
 
diff --git a/src/cython/doc/persistence_graphical_tools_ref.rst b/src/cython/doc/persistence_graphical_tools_ref.rst
index a2c6bcef..54aff4bc 100644
--- a/src/cython/doc/persistence_graphical_tools_ref.rst
+++ b/src/cython/doc/persistence_graphical_tools_ref.rst
@@ -9,3 +9,4 @@ Persistence graphical tools reference manual
 .. autofunction:: gudhi.__min_birth_max_death
 .. autofunction:: gudhi.plot_persistence_barcode
 .. autofunction:: gudhi.plot_persistence_diagram
+.. autofunction:: gudhi.plot_persistence_density
diff --git a/src/cython/doc/persistence_graphical_tools_sum.inc b/src/cython/doc/persistence_graphical_tools_sum.inc
index d602daa7..5577cf99 100644
--- a/src/cython/doc/persistence_graphical_tools_sum.inc
+++ b/src/cython/doc/persistence_graphical_tools_sum.inc
@@ -1,11 +1,11 @@
 =================================================================  ===================================  ===================================
 :Author: Vincent Rouvreau                                          :Introduced in: GUDHI 2.0.0          :Copyright: GPL v3
-:Requires: Matplotlib                                              Numpy
+:Requires: matplotlib                                              numpy                                scipy
 =================================================================  ===================================  ===================================
 
 +-----------------------------------------------------------------+-----------------------------------------------------------------------+
 | .. 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.             |
+|      img/graphical_tools_representation.png                     | the user to build easily persistence barcode, diagram or density.     |
 |                                                                 |                                                                       |
 +-----------------------------------------------------------------+-----------------------------------------------------------------------+
 |  :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
index 292915eb..b2124fdd 100644
--- a/src/cython/doc/persistence_graphical_tools_user.rst
+++ b/src/cython/doc/persistence_graphical_tools_user.rst
@@ -12,6 +12,9 @@ Definition
 Show persistence as a barcode
 -----------------------------
 
+.. note::
+    this function requires matplotlib and numpy to be available
+
 This function can display the persistence result as a barcode:
 
 .. plot::
@@ -19,16 +22,22 @@ This function can display the persistence result as a barcode:
 
     import gudhi
 
-    perseus_file = gudhi.__root_source_dir__ + '/data/bitmap/3d_torus.txt'
-    periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=perseus_file)
-    diag = periodic_cc.persistence()
-    print("diag = ", diag)
-    plt = gudhi.plot_persistence_barcode(diag)
-    plt.show()
+    off_file = gudhi.__root_source_dir__ + '/data/points/tore3D_300.off'
+    point_cloud = gudhi.read_off(off_file=off_file)
+
+    rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.7)
+    simplex_tree = rips_complex.create_simplex_tree(max_dimension=3)
+    diag = simplex_tree.persistence(min_persistence=0.4)
+
+    plot = gudhi.plot_persistence_barcode(diag)
+    plot.show()
 
 Show persistence as a diagram
 -----------------------------
 
+.. note::
+    this function requires matplotlib and numpy to be available
+
 This function can display the persistence result as a diagram:
 
 .. plot::
@@ -43,6 +52,12 @@ This function can display the persistence result as a diagram:
         legend=True)
     plt.show()
 
+Persistence density
+-------------------
+
+.. note::
+    this function requires matplotlib, numpy and scipy to be available
+
 If you want more information on a specific dimension, for instance:
 
 .. plot::
@@ -50,13 +65,9 @@ If you want more information on a specific dimension, for instance:
 
     import gudhi
 
+    # rips_on_tore3D_1307.pers obtained from write_persistence_diagram method
     persistence_file=gudhi.__root_source_dir__ + \
         '/data/persistence_diagram/rips_on_tore3D_1307.pers'
-    diag = \
-        gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file=\
-            persistence_file)
-    dim = 1
-    # Display all points with some transparency
-    plt = gudhi.plot_persistence_diagram([(dim,interval) for interval in diag[dim]],
-        max_plots=0, alpha=0.1)
+    plt = gudhi.plot_persistence_density(persistence_file=persistence_file,
+        max_intervals=0, dimension=1, legend=True)
     plt.show()
diff --git a/src/cython/gudhi.pyx.in b/src/cython/gudhi.pyx.in
index 56a72b04..0d4b966b 100644
--- a/src/cython/gudhi.pyx.in
+++ b/src/cython/gudhi.pyx.in
@@ -26,6 +26,7 @@ __license__ = "GPL v3"
 __version__ = "@GUDHI_VERSION@"
 # This variable is used by doctest to find files
 __root_source_dir__ = "@CMAKE_SOURCE_DIR@"
+__debug_info__ = @GUDHI_CYTHON_DEBUG_INFO@
 
 include '@CMAKE_CURRENT_SOURCE_DIR@/cython/off_reader.pyx'
 include '@CMAKE_CURRENT_SOURCE_DIR@/cython/simplex_tree.pyx'
diff --git a/src/cython/include/Alpha_complex_interface.h b/src/cython/include/Alpha_complex_interface.h
index 8cf527fc..faa059d1 100644
--- a/src/cython/include/Alpha_complex_interface.h
+++ b/src/cython/include/Alpha_complex_interface.h
@@ -60,7 +60,7 @@ class Alpha_complex_interface {
       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) {
+    } catch (std::out_of_range const&) {
       // std::out_of_range is thrown in case not found. Other exceptions must be re-thrown
     }
     return vd;
diff --git a/src/cython/include/Nerve_gic_interface.h b/src/cython/include/Nerve_gic_interface.h
index 90edd544..aa71e2a6 100644
--- a/src/cython/include/Nerve_gic_interface.h
+++ b/src/cython/include/Nerve_gic_interface.h
@@ -47,7 +47,7 @@ class Nerve_gic_interface : public Cover_complex<std::vector<double>> {
     set_cover_from_Voronoi(Gudhi::Euclidean_distance(), m);
   }
   double set_graph_from_automatic_euclidean_rips(int N) {
-    set_graph_from_automatic_rips(Gudhi::Euclidean_distance(), N);
+    return set_graph_from_automatic_rips(Gudhi::Euclidean_distance(), N);
   }
   void set_graph_from_euclidean_rips(double threshold) {
     set_graph_from_rips(threshold, Gudhi::Euclidean_distance());
diff --git a/src/cython/setup.py.in b/src/cython/setup.py.in
index ee381a1b..4037aab6 100644
--- a/src/cython/setup.py.in
+++ b/src/cython/setup.py.in
@@ -46,9 +46,5 @@ setup(
     version='@GUDHI_VERSION@',
     url='http://gudhi.gforge.inria.fr/',
     ext_modules = cythonize(gudhi),
-    install_requires = [
-        "matplotlib",
-        "numpy",
-        "cython",
-        ],
+    install_requires = ["cython",],
 )