git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/kernels@3778 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 189ac5572f69842e1d8d1cec68ca6a4f62e39bd4

47 files changed, 3001 insertions, 496 deletions

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 54f56a25..afacede9 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -36,7 +36,6 @@ add_gudhi_module(Subsampling)
 add_gudhi_module(Tangential_complex)
 add_gudhi_module(Witness_complex)
 add_gudhi_module(Nerve_GIC)
-add_gudhi_module(Kernels)
 
 message("++ GUDHI_MODULES list is:\"${GUDHI_MODULES}\"")
 
diff --git a/biblio/bibliography.bib b/biblio/bibliography.bib
index 24c0f718..9dfabdb2 100644
--- a/biblio/bibliography.bib
+++ b/biblio/bibliography.bib
@@ -1079,6 +1079,30 @@ language={English}
   year = {2016}
 }
 
+@inproceedings{cavanna15geometric,
+  author = {Nicholas J. Cavanna and Mahmoodreza Jahanseir and Donald R. Sheehy},
+  booktitle = {Proceedings of the Canadian Conference on Computational Geometry},
+  title = {A Geometric Perspective on Sparse Filtrations},
+  year = {2015}
+}
+
+@inproceedings{cavanna15visualizing,
+  author = {Nicholas J. Cavanna and Mahmoodreza Jahanseir and Donald R. Sheehy},
+  booktitle = {Proceedings of the 31st International Symposium on Computational Geometry},
+  title = {Visualizing Sparse Filtrations},
+  year = {2015},
+  doi = {10.4230/LIPIcs.SOCG.2015.23}
+}
+
+@article{sheehy13linear,
+  title = {Linear-Size Approximations to the {V}ietoris-{R}ips Filtration},
+  author = {Donald R. Sheehy},
+  journal = {Discrete \& Computational Geometry},
+  volume = {49},
+  number = {4},
+  pages = {778--796},
+  year = {2013}
+}
 
 @InProceedings{pmlr-v70-carriere17a,
   title = 	 {Sliced {W}asserstein Kernel for Persistence Diagrams},
@@ -1100,4 +1124,3 @@ language={English}
     booktitle = {In Neural Information Processing Systems},
     year = {2007}
 }
-
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/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/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/CMakeLists.txt b/src/CMakeLists.txt
index 37178492..6c446104 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -34,7 +34,6 @@ add_gudhi_module(Subsampling)
 add_gudhi_module(Tangential_complex)
 add_gudhi_module(Witness_complex)
 add_gudhi_module(Nerve_GIC)
-add_gudhi_module(Kernels)
 
 message("++ GUDHI_MODULES list is:\"${GUDHI_MODULES}\"")
 
@@ -72,7 +71,7 @@ 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.in b/src/Doxyfile.in
new file mode 100644
index 00000000..858a9299
--- /dev/null
+++ b/src/Doxyfile.in
@@ -0,0 +1,2300 @@
+# Doxyfile 1.8.6
+
+# This file describes the settings to be used by the documentation system
+# doxygen (www.doxygen.org) for a project.
+#
+# All text after a double hash (##) is considered a comment and is placed in
+# front of the TAG it is preceding.
+#
+# All text after a single hash (#) is considered a comment and will be ignored.
+# The format is:
+# TAG = value [value, ...]
+# For lists, items can also be appended using:
+# TAG += value [value, ...]
+# Values that contain spaces should be placed between quotes (\" \").
+
+#---------------------------------------------------------------------------
+# Project related configuration options
+#---------------------------------------------------------------------------
+
+# This tag specifies the encoding used for all characters in the config file
+# that follow. The default is UTF-8 which is also the encoding used for all text
+# before the first occurrence of this tag. Doxygen uses libiconv (or the iconv
+# built into libc) for the transcoding. See http://www.gnu.org/software/libiconv
+# for the list of possible encodings.
+# The default value is: UTF-8.
+
+DOXYFILE_ENCODING      = UTF-8
+
+# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by
+# double-quotes, unless you are using Doxywizard) that should identify the
+# project for which the documentation is generated. This name is used in the
+# title of most generated pages and in a few other places.
+# The default value is: My Project.
+
+PROJECT_NAME           = "GUDHI"
+
+# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
+# could be handy for archiving the generated documentation or if some version
+# control system is used.
+
+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
+# quick idea about the purpose of the project. Keep the description short.
+
+PROJECT_BRIEF          = "C++ library for Topological Data Analysis (TDA) and Higher Dimensional Geometry Understanding."
+
+# With the PROJECT_LOGO tag one can specify an logo or icon that is included in
+# the documentation. The maximum height of the logo should not exceed 55 pixels
+# and the maximum width should not exceed 200 pixels. Doxygen will copy the logo
+# to the output directory.
+
+PROJECT_LOGO           =
+
+# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
+# into which the generated documentation will be written. If a relative path is
+# entered, it will be relative to the location where doxygen was started. If
+# left blank the current directory will be used.
+
+OUTPUT_DIRECTORY       = "doc/"
+
+# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create 4096 sub-
+# directories (in 2 levels) under the output directory of each output format and
+# will distribute the generated files over these directories. Enabling this
+# option can be useful when feeding doxygen a huge amount of source files, where
+# putting all generated files in the same directory would otherwise causes
+# performance problems for the file system.
+# The default value is: NO.
+
+CREATE_SUBDIRS         = NO
+
+# The OUTPUT_LANGUAGE tag is used to specify the language in which all
+# documentation generated by doxygen is written. Doxygen will use this
+# information to generate all constant output in the proper language.
+# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese,
+# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States),
+# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian,
+# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages),
+# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian,
+# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian,
+# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish,
+# Ukrainian and Vietnamese.
+# The default value is: English.
+
+OUTPUT_LANGUAGE        = English
+
+# If the BRIEF_MEMBER_DESC tag is set to YES doxygen will include brief member
+# descriptions after the members that are listed in the file and class
+# documentation (similar to Javadoc). Set to NO to disable this.
+# The default value is: YES.
+
+BRIEF_MEMBER_DESC      = YES
+
+# If the REPEAT_BRIEF tag is set to YES doxygen will prepend the brief
+# description of a member or function before the detailed description
+#
+# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
+# brief descriptions will be completely suppressed.
+# The default value is: YES.
+
+REPEAT_BRIEF           = YES
+
+# This tag implements a quasi-intelligent brief description abbreviator that is
+# used to form the text in various listings. Each string in this list, if found
+# as the leading text of the brief description, will be stripped from the text
+# and the result, after processing the whole list, is used as the annotated
+# text. Otherwise, the brief description is used as-is. If left blank, the
+# following values are used ($name is automatically replaced with the name of
+# the entity):The $name class, The $name widget, The $name file, is, provides,
+# specifies, contains, represents, a, an and the.
+
+ABBREVIATE_BRIEF       =
+
+# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
+# doxygen will generate a detailed section even if there is only a brief
+# description.
+# The default value is: NO.
+
+ALWAYS_DETAILED_SEC    = NO
+
+# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
+# inherited members of a class in the documentation of that class as if those
+# members were ordinary class members. Constructors, destructors and assignment
+# operators of the base classes will not be shown.
+# The default value is: NO.
+
+INLINE_INHERITED_MEMB  = NO
+
+# If the FULL_PATH_NAMES tag is set to YES doxygen will prepend the full path
+# before files name in the file list and in the header files. If set to NO the
+# shortest path that makes the file name unique will be used
+# The default value is: YES.
+
+FULL_PATH_NAMES        = YES
+
+# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path.
+# Stripping is only done if one of the specified strings matches the left-hand
+# part of the path. The tag can be used to show relative paths in the file list.
+# If left blank the directory from which doxygen is run is used as the path to
+# strip.
+#
+# Note that you can specify absolute paths here, but also relative paths, which
+# will be relative from the directory where doxygen is started.
+# This tag requires that the tag FULL_PATH_NAMES is set to YES.
+
+STRIP_FROM_PATH        =
+
+# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the
+# path mentioned in the documentation of a class, which tells the reader which
+# header file to include in order to use a class. If left blank only the name of
+# the header file containing the class definition is used. Otherwise one should
+# specify the list of include paths that are normally passed to the compiler
+# using the -I flag.
+
+STRIP_FROM_INC_PATH    = include concept
+
+# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but
+# less readable) file names. This can be useful is your file systems doesn't
+# support long names like on DOS, Mac, or CD-ROM.
+# The default value is: NO.
+
+SHORT_NAMES            = NO
+
+# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the
+# first line (until the first dot) of a Javadoc-style comment as the brief
+# description. If set to NO, the Javadoc-style will behave just like regular Qt-
+# style comments (thus requiring an explicit @brief command for a brief
+# description.)
+# The default value is: NO.
+
+JAVADOC_AUTOBRIEF      = NO
+
+# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first
+# line (until the first dot) of a Qt-style comment as the brief description. If
+# set to NO, the Qt-style will behave just like regular Qt-style comments (thus
+# requiring an explicit \brief command for a brief description.)
+# The default value is: NO.
+
+QT_AUTOBRIEF           = NO
+
+# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a
+# multi-line C++ special comment block (i.e. a block of //! or /// comments) as
+# a brief description. This used to be the default behavior. The new default is
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+# tag to YES if you prefer the old behavior instead.
+#
+# Note that setting this tag to YES also means that rational rose comments are
+# not recognized any more.
+# The default value is: NO.
+
+MULTILINE_CPP_IS_BRIEF = NO
+
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+# documentation from any documented member that it re-implements.
+# The default value is: YES.
+
+INHERIT_DOCS           = YES
+
+# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce a
+# new page for each member. If set to NO, the documentation of a member will be
+# part of the file/class/namespace that contains it.
+# The default value is: NO.
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+SEPARATE_MEMBER_PAGES  = NO
+
+# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen
+# uses this value to replace tabs by spaces in code fragments.
+# Minimum value: 1, maximum value: 16, default value: 4.
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+TAB_SIZE               = 4
+
+# This tag can be used to specify a number of aliases that act as commands in
+# the documentation. An alias has the form:
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+# For example adding
+# "sideeffect=@par Side Effects:\n"
+# will allow you to put the command \sideeffect (or @sideeffect) in the
+# documentation, which will result in a user-defined paragraph with heading
+# "Side Effects:". You can put \n's in the value part of an alias to insert
+# newlines.
+
+ALIASES                =
+
+# This tag can be used to specify a number of word-keyword mappings (TCL only).
+# A mapping has the form "name=value". For example adding "class=itcl::class"
+# will allow you to use the command class in the itcl::class meaning.
+
+TCL_SUBST              =
+
+# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources
+# only. Doxygen will then generate output that is more tailored for C. For
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+# The default value is: NO.
+
+OPTIMIZE_OUTPUT_FOR_C  = NO
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+# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or
+# Python sources only. Doxygen will then generate output that is more tailored
+# for that language. For instance, namespaces will be presented as packages,
+# qualified scopes will look different, etc.
+# The default value is: NO.
+
+OPTIMIZE_OUTPUT_JAVA   = NO
+
+# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
+# sources. Doxygen will then generate output that is tailored for Fortran.
+# The default value is: NO.
+
+OPTIMIZE_FOR_FORTRAN   = NO
+
+# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
+# sources. Doxygen will then generate output that is tailored for VHDL.
+# The default value is: NO.
+
+OPTIMIZE_OUTPUT_VHDL   = NO
+
+# Doxygen selects the parser to use depending on the extension of the files it
+# parses. With this tag you can assign which parser to use for a given
+# extension. Doxygen has a built-in mapping, but you can override or extend it
+# using this tag. The format is ext=language, where ext is a file extension, and
+# language is one of the parsers supported by doxygen: IDL, Java, Javascript,
+# C#, C, C++, D, PHP, Objective-C, Python, Fortran, VHDL. For instance to make
+# doxygen treat .inc files as Fortran files (default is PHP), and .f files as C
+# (default is Fortran), use: inc=Fortran f=C.
+#
+# Note For files without extension you can use no_extension as a placeholder.
+#
+# Note that for custom extensions you also need to set FILE_PATTERNS otherwise
+# the files are not read by doxygen.
+
+EXTENSION_MAPPING      =
+
+# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments
+# according to the Markdown format, which allows for more readable
+# documentation. See http://daringfireball.net/projects/markdown/ for details.
+# The output of markdown processing is further processed by doxygen, so you can
+# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in
+# case of backward compatibilities issues.
+# The default value is: YES.
+
+MARKDOWN_SUPPORT       = YES
+
+# When enabled doxygen tries to link words that correspond to documented
+# classes, or namespaces to their corresponding documentation. Such a link can
+# be prevented in individual cases by by putting a % sign in front of the word
+# or globally by setting AUTOLINK_SUPPORT to NO.
+# The default value is: YES.
+
+AUTOLINK_SUPPORT       = YES
+
+# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
+# to include (a tag file for) the STL sources as input, then you should set this
+# tag to YES in order to let doxygen match functions declarations and
+# definitions whose arguments contain STL classes (e.g. func(std::string);
+# versus func(std::string) {}). This also make the inheritance and collaboration
+# diagrams that involve STL classes more complete and accurate.
+# The default value is: NO.
+
+BUILTIN_STL_SUPPORT    = NO
+
+# If you use Microsoft's C++/CLI language, you should set this option to YES to
+# enable parsing support.
+# The default value is: NO.
+
+CPP_CLI_SUPPORT        = NO
+
+# Set the SIP_SUPPORT tag to YES if your project consists of sip (see:
+# http://www.riverbankcomputing.co.uk/software/sip/intro) sources only. Doxygen
+# will parse them like normal C++ but will assume all classes use public instead
+# of private inheritance when no explicit protection keyword is present.
+# The default value is: NO.
+
+SIP_SUPPORT            = NO
+
+# For Microsoft's IDL there are propget and propput attributes to indicate
+# getter and setter methods for a property. Setting this option to YES will make
+# doxygen to replace the get and set methods by a property in the documentation.
+# This will only work if the methods are indeed getting or setting a simple
+# type. If this is not the case, or you want to show the methods anyway, you
+# should set this option to NO.
+# The default value is: YES.
+
+IDL_PROPERTY_SUPPORT   = YES
+
+# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
+# tag is set to YES, then doxygen will reuse the documentation of the first
+# member in the group (if any) for the other members of the group. By default
+# all members of a group must be documented explicitly.
+# The default value is: NO.
+
+DISTRIBUTE_GROUP_DOC   = NO
+
+# Set the SUBGROUPING tag to YES to allow class member groups of the same type
+# (for instance a group of public functions) to be put as a subgroup of that
+# type (e.g. under the Public Functions section). Set it to NO to prevent
+# subgrouping. Alternatively, this can be done per class using the
+# \nosubgrouping command.
+# The default value is: YES.
+
+SUBGROUPING            = YES
+
+# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions
+# are shown inside the group in which they are included (e.g. using \ingroup)
+# instead of on a separate page (for HTML and Man pages) or section (for LaTeX
+# and RTF).
+#
+# Note that this feature does not work in combination with
+# SEPARATE_MEMBER_PAGES.
+# The default value is: NO.
+
+INLINE_GROUPED_CLASSES = NO
+
+# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions
+# with only public data fields or simple typedef fields will be shown inline in
+# the documentation of the scope in which they are defined (i.e. file,
+# namespace, or group documentation), provided this scope is documented. If set
+# to NO, structs, classes, and unions are shown on a separate page (for HTML and
+# Man pages) or section (for LaTeX and RTF).
+# The default value is: NO.
+
+INLINE_SIMPLE_STRUCTS  = NO
+
+# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or
+# enum is documented as struct, union, or enum with the name of the typedef. So
+# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
+# with name TypeT. When disabled the typedef will appear as a member of a file,
+# namespace, or class. And the struct will be named TypeS. This can typically be
+# useful for C code in case the coding convention dictates that all compound
+# types are typedef'ed and only the typedef is referenced, never the tag name.
+# The default value is: NO.
+
+TYPEDEF_HIDES_STRUCT   = NO
+
+# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
+# cache is used to resolve symbols given their name and scope. Since this can be
+# an expensive process and often the same symbol appears multiple times in the
+# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small
+# doxygen will become slower. If the cache is too large, memory is wasted. The
+# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range
+# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536
+# symbols. At the end of a run doxygen will report the cache usage and suggest
+# the optimal cache size from a speed point of view.
+# Minimum value: 0, maximum value: 9, default value: 0.
+
+LOOKUP_CACHE_SIZE      = 0
+
+#---------------------------------------------------------------------------
+# Build related configuration options
+#---------------------------------------------------------------------------
+
+# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
+# documentation are documented, even if no documentation was available. Private
+# class members and static file members will be hidden unless the
+# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES.
+# Note: This will also disable the warnings about undocumented members that are
+# normally produced when WARNINGS is set to YES.
+# The default value is: NO.
+
+EXTRACT_ALL            = NO
+
+# If the EXTRACT_PRIVATE tag is set to YES all private members of a class will
+# be included in the documentation.
+# The default value is: NO.
+
+EXTRACT_PRIVATE        = NO
+
+# If the EXTRACT_PACKAGE tag is set to YES all members with package or internal
+# scope will be included in the documentation.
+# The default value is: NO.
+
+EXTRACT_PACKAGE        = NO
+
+# If the EXTRACT_STATIC tag is set to YES all static members of a file will be
+# included in the documentation.
+# The default value is: NO.
+
+EXTRACT_STATIC         = NO
+
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) defined
+# locally in source files will be included in the documentation. If set to NO
+# only classes defined in header files are included. Does not have any effect
+# for Java sources.
+# The default value is: YES.
+
+EXTRACT_LOCAL_CLASSES  = NO
+
+# This flag is only useful for Objective-C code. When set to YES local methods,
+# which are defined in the implementation section but not in the interface are
+# included in the documentation. If set to NO only methods in the interface are
+# included.
+# The default value is: NO.
+
+EXTRACT_LOCAL_METHODS  = NO
+
+# If this flag is set to YES, the members of anonymous namespaces will be
+# extracted and appear in the documentation as a namespace called
+# 'anonymous_namespace{file}', where file will be replaced with the base name of
+# the file that contains the anonymous namespace. By default anonymous namespace
+# are hidden.
+# The default value is: NO.
+
+EXTRACT_ANON_NSPACES   = NO
+
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all
+# undocumented members inside documented classes or files. If set to NO these
+# members will be included in the various overviews, but no documentation
+# section is generated. This option has no effect if EXTRACT_ALL is enabled.
+# The default value is: NO.
+
+HIDE_UNDOC_MEMBERS     = YES
+
+# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all
+# undocumented classes that are normally visible in the class hierarchy. If set
+# to NO these classes will be included in the various overviews. This option has
+# no effect if EXTRACT_ALL is enabled.
+# The default value is: NO.
+
+HIDE_UNDOC_CLASSES     = YES
+
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend
+# (class|struct|union) declarations. If set to NO these declarations will be
+# included in the documentation.
+# The default value is: NO.
+
+HIDE_FRIEND_COMPOUNDS  = NO
+
+# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any
+# documentation blocks found inside the body of a function. If set to NO these
+# blocks will be appended to the function's detailed documentation block.
+# The default value is: NO.
+
+HIDE_IN_BODY_DOCS      = NO
+
+# The INTERNAL_DOCS tag determines if documentation that is typed after a
+# \internal command is included. If the tag is set to NO then the documentation
+# will be excluded. Set it to YES to include the internal documentation.
+# The default value is: NO.
+
+INTERNAL_DOCS          = NO
+
+# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file
+# names in lower-case letters. If set to YES upper-case letters are also
+# allowed. This is useful if you have classes or files whose names only differ
+# in case and if your file system supports case sensitive file names. Windows
+# and Mac users are advised to set this option to NO.
+# The default value is: system dependent.
+
+CASE_SENSE_NAMES       = NO
+
+# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with
+# their full class and namespace scopes in the documentation. If set to YES the
+# scope will be hidden.
+# The default value is: NO.
+
+HIDE_SCOPE_NAMES       = NO
+
+# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
+# the files that are included by a file in the documentation of that file.
+# The default value is: YES.
+
+SHOW_INCLUDE_FILES     = NO
+
+# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
+# grouped member an include statement to the documentation, telling the reader
+# which file to include in order to use the member.
+# The default value is: NO.
+
+SHOW_GROUPED_MEMB_INC  = NO
+
+# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include
+# files with double quotes in the documentation rather than with sharp brackets.
+# The default value is: NO.
+
+FORCE_LOCAL_INCLUDES   = NO
+
+# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the
+# documentation for inline members.
+# The default value is: YES.
+
+INLINE_INFO            = YES
+
+# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the
+# (detailed) documentation of file and class members alphabetically by member
+# name. If set to NO the members will appear in declaration order.
+# The default value is: YES.
+
+SORT_MEMBER_DOCS       = YES
+
+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief
+# descriptions of file, namespace and class members alphabetically by member
+# name. If set to NO the members will appear in declaration order. Note that
+# this will also influence the order of the classes in the class list.
+# The default value is: NO.
+
+SORT_BRIEF_DOCS        = NO
+
+# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
+# (brief and detailed) documentation of class members so that constructors and
+# destructors are listed first. If set to NO the constructors will appear in the
+# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS.
+# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief
+# member documentation.
+# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting
+# detailed member documentation.
+# The default value is: NO.
+
+SORT_MEMBERS_CTORS_1ST = NO
+
+# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
+# of group names into alphabetical order. If set to NO the group names will
+# appear in their defined order.
+# The default value is: NO.
+
+SORT_GROUP_NAMES       = NO
+
+# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by
+# fully-qualified names, including namespaces. If set to NO, the class list will
+# be sorted only by class name, not including the namespace part.
+# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
+# Note: This option applies only to the class list, not to the alphabetical
+# list.
+# The default value is: NO.
+
+SORT_BY_SCOPE_NAME     = NO
+
+# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper
+# type resolution of all parameters of a function it will reject a match between
+# the prototype and the implementation of a member function even if there is
+# only one candidate or it is obvious which candidate to choose by doing a
+# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still
+# accept a match between prototype and implementation in such cases.
+# The default value is: NO.
+
+STRICT_PROTO_MATCHING  = NO
+
+# The GENERATE_TODOLIST tag can be used to enable ( YES) or disable ( NO) the
+# todo list. This list is created by putting \todo commands in the
+# documentation.
+# The default value is: YES.
+
+GENERATE_TODOLIST      = NO
+
+# The GENERATE_TESTLIST tag can be used to enable ( YES) or disable ( NO) the
+# test list. This list is created by putting \test commands in the
+# documentation.
+# The default value is: YES.
+
+GENERATE_TESTLIST      = NO
+
+# The GENERATE_BUGLIST tag can be used to enable ( YES) or disable ( NO) the bug
+# list. This list is created by putting \bug commands in the documentation.
+# The default value is: YES.
+
+GENERATE_BUGLIST       = NO
+
+# The GENERATE_DEPRECATEDLIST tag can be used to enable ( YES) or disable ( NO)
+# the deprecated list. This list is created by putting \deprecated commands in
+# the documentation.
+# The default value is: YES.
+
+GENERATE_DEPRECATEDLIST= NO
+
+# The ENABLED_SECTIONS tag can be used to enable conditional documentation
+# sections, marked by \if <section_label> ... \endif and \cond <section_label>
+# ... \endcond blocks.
+
+ENABLED_SECTIONS       =
+
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the
+# initial value of a variable or macro / define can have for it to appear in the
+# documentation. If the initializer consists of more lines than specified here
+# it will be hidden. Use a value of 0 to hide initializers completely. The
+# appearance of the value of individual variables and macros / defines can be
+# controlled using \showinitializer or \hideinitializer command in the
+# documentation regardless of this setting.
+# Minimum value: 0, maximum value: 10000, default value: 30.
+
+MAX_INITIALIZER_LINES  = 30
+
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at
+# the bottom of the documentation of classes and structs. If set to YES the list
+# will mention the files that were used to generate the documentation.
+# The default value is: YES.
+
+SHOW_USED_FILES        = YES
+
+# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
+# will remove the Files entry from the Quick Index and from the Folder Tree View
+# (if specified).
+# The default value is: YES.
+
+SHOW_FILES             = YES
+
+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces
+# page. This will remove the Namespaces entry from the Quick Index and from the
+# Folder Tree View (if specified).
+# The default value is: YES.
+
+SHOW_NAMESPACES        = YES
+
+# The FILE_VERSION_FILTER tag can be used to specify a program or script that
+# doxygen should invoke to get the current version for each file (typically from
+# the version control system). Doxygen will invoke the program by executing (via
+# popen()) the command command input-file, where command is the value of the
+# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided
+# by doxygen. Whatever the program writes to standard output is used as the file
+# version. For an example see the documentation.
+
+FILE_VERSION_FILTER    =
+
+# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
+# by doxygen. The layout file controls the global structure of the generated
+# output files in an output format independent way. To create the layout file
+# that represents doxygen's defaults, run doxygen with the -l option. You can
+# optionally specify a file name after the option, if omitted DoxygenLayout.xml
+# will be used as the name of the layout file.
+#
+# Note that if you run doxygen from a directory containing a file called
+# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
+# tag is left empty.
+
+LAYOUT_FILE            =
+
+# The CITE_BIB_FILES tag can be used to specify one or more bib files containing
+# the reference definitions. This must be a list of .bib files. The .bib
+# extension is automatically appended if omitted. This requires the bibtex tool
+# to be installed. See also http://en.wikipedia.org/wiki/BibTeX for more info.
+# For LaTeX the style of the bibliography can be controlled using
+# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
+# search path. Do not use file names with spaces, bibtex cannot handle them. See
+# also \cite for info how to create references.
+
+CITE_BIB_FILES         = biblio/bibliography.bib \
+                        biblio/how_to_cite_cgal.bib \
+                        biblio/how_to_cite_gudhi.bib
+
+#---------------------------------------------------------------------------
+# Configuration options related to warning and progress messages
+#---------------------------------------------------------------------------
+
+# The QUIET tag can be used to turn on/off the messages that are generated to
+# standard output by doxygen. If QUIET is set to YES this implies that the
+# messages are off.
+# The default value is: NO.
+
+QUIET                  = NO
+
+# The WARNINGS tag can be used to turn on/off the warning messages that are
+# generated to standard error ( stderr) by doxygen. If WARNINGS is set to YES
+# this implies that the warnings are on.
+#
+# Tip: Turn warnings on while writing the documentation.
+# The default value is: YES.
+
+WARNINGS               = YES
+
+# If the WARN_IF_UNDOCUMENTED tag is set to YES, then doxygen will generate
+# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag
+# will automatically be disabled.
+# The default value is: YES.
+
+WARN_IF_UNDOCUMENTED   = YES
+
+# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
+# potential errors in the documentation, such as not documenting some parameters
+# in a documented function, or documenting parameters that don't exist or using
+# markup commands wrongly.
+# The default value is: YES.
+
+WARN_IF_DOC_ERROR      = YES
+
+# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that
+# are documented, but have no documentation for their parameters or return
+# value. If set to NO doxygen will only warn about wrong or incomplete parameter
+# documentation, but not about the absence of documentation.
+# The default value is: NO.
+
+WARN_NO_PARAMDOC       = NO
+
+# The WARN_FORMAT tag determines the format of the warning messages that doxygen
+# can produce. The string should contain the $file, $line, and $text tags, which
+# will be replaced by the file and line number from which the warning originated
+# and the warning text. Optionally the format may contain $version, which will
+# be replaced by the version of the file (if it could be obtained via
+# FILE_VERSION_FILTER)
+# The default value is: $file:$line: $text.
+
+WARN_FORMAT            = "$file:$line: $text"
+
+# The WARN_LOGFILE tag can be used to specify a file to which warning and error
+# messages should be written. If left blank the output is written to standard
+# error (stderr).
+
+WARN_LOGFILE           =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the input files
+#---------------------------------------------------------------------------
+
+# The INPUT tag is used to specify the files and/or directories that contain
+# documented source files. You may enter file names like myfile.cpp or
+# directories like /usr/src/myproject. Separate the files or directories with
+# spaces.
+# Note: If this tag is empty the current directory is searched.
+
+INPUT                  =
+
+# This tag can be used to specify the character encoding of the source files
+# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
+# libiconv (or the iconv built into libc) for the transcoding. See the libiconv
+# documentation (see: http://www.gnu.org/software/libiconv) for the list of
+# possible encodings.
+# The default value is: UTF-8.
+
+INPUT_ENCODING         = UTF-8
+
+# If the value of the INPUT tag contains directories, you can use the
+# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and
+# *.h) to filter out the source-files in the directories. If left blank the
+# following patterns are tested:*.c, *.cc, *.cxx, *.cpp, *.c++, *.java, *.ii,
+# *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h, *.hh, *.hxx, *.hpp,
+# *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc, *.m, *.markdown,
+# *.md, *.mm, *.dox, *.py, *.f90, *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf,
+# *.qsf, *.as and *.js.
+
+FILE_PATTERNS          =
+
+# The RECURSIVE tag can be used to specify whether or not subdirectories should
+# be searched for input files as well.
+# The default value is: NO.
+
+RECURSIVE              = YES
+
+# The EXCLUDE tag can be used to specify files and/or directories that should be
+# excluded from the INPUT source files. This way you can easily exclude a
+# subdirectory from a directory tree whose root is specified with the INPUT tag.
+#
+# Note that relative paths are relative to the directory from which doxygen is
+# run.
+
+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
+# from the input.
+# The default value is: NO.
+
+EXCLUDE_SYMLINKS       = NO
+
+# If the value of the INPUT tag contains directories, you can use the
+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
+# certain files from those directories.
+#
+# Note that the wildcards are matched against the file with absolute path, so to
+# exclude all test directories for example use the pattern */test/*
+
+EXCLUDE_PATTERNS       = */utilities/*/*.md
+
+# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
+# (namespaces, classes, functions, etc.) that should be excluded from the
+# output. The symbol name can be a fully qualified name, a word, or if the
+# wildcard * is used, a substring. Examples: ANamespace, AClass,
+# AClass::ANamespace, ANamespace::*Test
+#
+# Note that the wildcards are matched against the file with absolute path, so to
+# exclude all test directories use the pattern */test/*
+
+EXCLUDE_SYMBOLS        =
+
+# The EXAMPLE_PATH tag can be used to specify one or more files or directories
+# that contain example code fragments that are included (see the \include
+# command).
+
+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
+# *.h) to filter out the source-files in the directories. If left blank all
+# files are included.
+
+EXAMPLE_PATTERNS       = 
+
+# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
+# searched for input files to be used with the \include or \dontinclude commands
+# irrespective of the value of the RECURSIVE tag.
+# The default value is: NO.
+
+EXAMPLE_RECURSIVE      = NO
+
+# The IMAGE_PATH tag can be used to specify one or more files or directories
+# that contain images that are to be included in the documentation (see the
+# \image command).
+
+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
+# by executing (via popen()) the command:
+#
+# <filter> <input-file>
+#
+# where <filter> is the value of the INPUT_FILTER tag, and <input-file> is the
+# name of an input file. Doxygen will then use the output that the filter
+# program writes to standard output. If FILTER_PATTERNS is specified, this tag
+# will be ignored.
+#
+# Note that the filter must not add or remove lines; it is applied before the
+# code is scanned, but not when the output code is generated. If lines are added
+# or removed, the anchors will not be placed correctly.
+
+INPUT_FILTER           =
+
+# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
+# basis. Doxygen will compare the file name with each pattern and apply the
+# filter if there is a match. The filters are a list of the form: pattern=filter
+# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how
+# filters are used. If the FILTER_PATTERNS tag is empty or if none of the
+# patterns match the file name, INPUT_FILTER is applied.
+
+FILTER_PATTERNS        =
+
+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
+# INPUT_FILTER ) will also be used to filter the input files that are used for
+# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES).
+# The default value is: NO.
+
+FILTER_SOURCE_FILES    = NO
+
+# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
+# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and
+# it is also possible to disable source filtering for a specific pattern using
+# *.ext= (so without naming a filter).
+# This tag requires that the tag FILTER_SOURCE_FILES is set to YES.
+
+FILTER_SOURCE_PATTERNS =
+
+# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that
+# is part of the input, its contents will be placed on the main page
+# (index.html). This can be useful if you have a project on for instance GitHub
+# and want to reuse the introduction page also for the doxygen output.
+
+USE_MDFILE_AS_MAINPAGE =
+
+#---------------------------------------------------------------------------
+# Configuration options related to source browsing
+#---------------------------------------------------------------------------
+
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will be
+# generated. Documented entities will be cross-referenced with these sources.
+#
+# Note: To get rid of all source code in the generated output, make sure that
+# also VERBATIM_HEADERS is set to NO.
+# The default value is: NO.
+
+SOURCE_BROWSER         = NO
+
+# Setting the INLINE_SOURCES tag to YES will include the body of functions,
+# classes and enums directly into the documentation.
+# The default value is: NO.
+
+INLINE_SOURCES         = NO
+
+# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any
+# special comment blocks from generated source code fragments. Normal C, C++ and
+# Fortran comments will always remain visible.
+# The default value is: YES.
+
+STRIP_CODE_COMMENTS    = YES
+
+# If the REFERENCED_BY_RELATION tag is set to YES then for each documented
+# function all documented functions referencing it will be listed.
+# The default value is: NO.
+
+REFERENCED_BY_RELATION = NO
+
+# If the REFERENCES_RELATION tag is set to YES then for each documented function
+# all documented entities called/used by that function will be listed.
+# The default value is: NO.
+
+REFERENCES_RELATION    = NO
+
+# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set
+# to YES, then the hyperlinks from functions in REFERENCES_RELATION and
+# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will
+# link to the documentation.
+# The default value is: YES.
+
+REFERENCES_LINK_SOURCE = YES
+
+# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the
+# source code will show a tooltip with additional information such as prototype,
+# brief description and links to the definition and documentation. Since this
+# will make the HTML file larger and loading of large files a bit slower, you
+# can opt to disable this feature.
+# The default value is: YES.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
+
+SOURCE_TOOLTIPS        = YES
+
+# If the USE_HTAGS tag is set to YES then the references to source code will
+# point to the HTML generated by the htags(1) tool instead of doxygen built-in
+# source browser. The htags tool is part of GNU's global source tagging system
+# (see http://www.gnu.org/software/global/global.html). You will need version
+# 4.8.6 or higher.
+#
+# To use it do the following:
+# - Install the latest version of global
+# - Enable SOURCE_BROWSER and USE_HTAGS in the config file
+# - Make sure the INPUT points to the root of the source tree
+# - Run doxygen as normal
+#
+# Doxygen will invoke htags (and that will in turn invoke gtags), so these
+# tools must be available from the command line (i.e. in the search path).
+#
+# The result: instead of the source browser generated by doxygen, the links to
+# source code will now point to the output of htags.
+# The default value is: NO.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
+
+USE_HTAGS              = NO
+
+# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a
+# verbatim copy of the header file for each class for which an include is
+# specified. Set to NO to disable this.
+# See also: Section \class.
+# The default value is: YES.
+
+VERBATIM_HEADERS       = YES
+
+#---------------------------------------------------------------------------
+# Configuration options related to the alphabetical class index
+#---------------------------------------------------------------------------
+
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all
+# compounds will be generated. Enable this if the project contains a lot of
+# classes, structs, unions or interfaces.
+# The default value is: YES.
+
+ALPHABETICAL_INDEX     = YES
+
+# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in
+# which the alphabetical index list will be split.
+# Minimum value: 1, maximum value: 20, default value: 5.
+# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
+
+COLS_IN_ALPHA_INDEX    = 5
+
+# In case all classes in a project start with a common prefix, all classes will
+# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag
+# can be used to specify a prefix (or a list of prefixes) that should be ignored
+# while generating the index headers.
+# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
+
+IGNORE_PREFIX          =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the HTML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_HTML tag is set to YES doxygen will generate HTML output
+# The default value is: YES.
+
+GENERATE_HTML          = YES
+
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_OUTPUT            = html
+
+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
+# generated HTML page (for example: .htm, .php, .asp).
+# The default value is: .html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_FILE_EXTENSION    = .html
+
+# The HTML_HEADER tag can be used to specify a user-defined HTML header file for
+# each generated HTML page. If the tag is left blank doxygen will generate a
+# standard header.
+#
+# To get valid HTML the header file that includes any scripts and style sheets
+# that doxygen needs, which is dependent on the configuration options used (e.g.
+# the setting GENERATE_TREEVIEW). It is highly recommended to start with a
+# default header using
+# doxygen -w html new_header.html new_footer.html new_stylesheet.css
+# YourConfigFile
+# and then modify the file new_header.html. See also section "Doxygen usage"
+# for information on how to generate the default header that doxygen normally
+# uses.
+# Note: The header is subject to change so you typically have to regenerate the
+# default header when upgrading to a newer version of doxygen. For a description
+# of the possible markers and block names see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_HEADER            = doc/common/header.html
+
+# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
+# generated HTML page. If the tag is left blank doxygen will generate a standard
+# footer. See HTML_HEADER for more information on how to generate a default
+# footer and what special commands can be used inside the footer. See also
+# section "Doxygen usage" for information on how to generate the default footer
+# that doxygen normally uses.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_FOOTER            = doc/common/footer.html
+
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
+# sheet that is used by each HTML page. It can be used to fine-tune the look of
+# the HTML output. If left blank doxygen will generate a default style sheet.
+# See also section "Doxygen usage" for information on how to generate the style
+# sheet that doxygen normally uses.
+# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as
+# it is more robust and this tag (HTML_STYLESHEET) will in the future become
+# obsolete.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_STYLESHEET        = doc/common/stylesheet.css
+
+# The HTML_EXTRA_STYLESHEET tag can be used to specify an additional user-
+# defined cascading style sheet that is included after the standard style sheets
+# created by doxygen. Using this option one can overrule certain style aspects.
+# This is preferred over using HTML_STYLESHEET since it does not replace the
+# standard style sheet and is therefor more robust against future updates.
+# Doxygen will copy the style sheet file to the output directory. For an example
+# see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_EXTRA_STYLESHEET  =
+
+# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the HTML output directory. Note
+# that these files will be copied to the base HTML output directory. Use the
+# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
+# files. In the HTML_STYLESHEET file, use the file name only. Also note that the
+# files will be copied as-is; there are no commands or markers available.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_EXTRA_FILES       =
+
+# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
+# will adjust the colors in the stylesheet and background images according to
+# this color. Hue is specified as an angle on a colorwheel, see
+# http://en.wikipedia.org/wiki/Hue for more information. For instance the value
+# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300
+# purple, and 360 is red again.
+# Minimum value: 0, maximum value: 359, default value: 220.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_HUE    = 220
+
+# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
+# in the HTML output. For a value of 0 the output will use grayscales only. A
+# value of 255 will produce the most vivid colors.
+# Minimum value: 0, maximum value: 255, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_SAT    = 100
+
+# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the
+# luminance component of the colors in the HTML output. Values below 100
+# gradually make the output lighter, whereas values above 100 make the output
+# darker. The value divided by 100 is the actual gamma applied, so 80 represents
+# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not
+# change the gamma.
+# Minimum value: 40, maximum value: 240, default value: 80.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_GAMMA  = 80
+
+# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
+# page will contain the date and time when the page was generated. Setting this
+# to NO can help when comparing the output of multiple runs.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_TIMESTAMP         = YES
+
+# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
+# documentation will contain sections that can be hidden and shown after the
+# page has loaded.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_DYNAMIC_SECTIONS  = NO
+
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
+# shown in the various tree structured indices initially; the user can expand
+# and collapse entries dynamically later on. Doxygen will expand the tree to
+# such a level that at most the specified number of entries are visible (unless
+# a fully collapsed tree already exceeds this amount). So setting the number of
+# entries 1 will produce a full collapsed tree by default. 0 is a special value
+# representing an infinite number of entries and will result in a full expanded
+# tree by default.
+# Minimum value: 0, maximum value: 9999, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
+# If the GENERATE_DOCSET tag is set to YES, additional index files will be
+# generated that can be used as input for Apple's Xcode 3 integrated development
+# environment (see: http://developer.apple.com/tools/xcode/), introduced with
+# OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a
+# Makefile in the HTML output directory. Running make will produce the docset in
+# that directory and running make install will install the docset in
+# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at
+# startup. See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
+# for more information.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_DOCSET        = NO
+
+# This tag determines the name of the docset feed. A documentation feed provides
+# an umbrella under which multiple documentation sets from a single provider
+# (such as a company or product suite) can be grouped.
+# The default value is: Doxygen generated docs.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_FEEDNAME        = "Doxygen generated docs"
+
+# This tag specifies a string that should uniquely identify the documentation
+# set bundle. This should be a reverse domain-name style string, e.g.
+# com.mycompany.MyDocSet. Doxygen will append .docset to the name.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_BUNDLE_ID       = org.doxygen.Project
+
+# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify
+# the documentation publisher. This should be a reverse domain-name style
+# string, e.g. com.mycompany.MyDocSet.documentation.
+# The default value is: org.doxygen.Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_PUBLISHER_ID    = org.doxygen.Publisher
+
+# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher.
+# The default value is: Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_PUBLISHER_NAME  = Publisher
+
+# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three
+# additional HTML index files: index.hhp, index.hhc, and index.hhk. The
+# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop
+# (see: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on
+# Windows.
+#
+# The HTML Help Workshop contains a compiler that can convert all HTML output
+# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML
+# files are now used as the Windows 98 help format, and will replace the old
+# Windows help format (.hlp) on all Windows platforms in the future. Compressed
+# HTML files also contain an index, a table of contents, and you can search for
+# words in the documentation. The HTML workshop also contains a viewer for
+# compressed HTML files.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_HTMLHELP      = NO
+
+# The CHM_FILE tag can be used to specify the file name of the resulting .chm
+# file. You can add a path in front of the file if the result should not be
+# written to the html output directory.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+CHM_FILE               =
+
+# The HHC_LOCATION tag can be used to specify the location (absolute path
+# including file name) of the HTML help compiler ( hhc.exe). If non-empty
+# doxygen will try to run the HTML help compiler on the generated index.hhp.
+# The file has to be specified with full path.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+HHC_LOCATION           =
+
+# The GENERATE_CHI flag controls if a separate .chi index file is generated (
+# YES) or that it should be included in the master .chm file ( NO).
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+GENERATE_CHI           = NO
+
+# The CHM_INDEX_ENCODING is used to encode HtmlHelp index ( hhk), content ( hhc)
+# and project file content.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+CHM_INDEX_ENCODING     =
+
+# The BINARY_TOC flag controls whether a binary table of contents is generated (
+# YES) or a normal table of contents ( NO) in the .chm file.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+BINARY_TOC             = NO
+
+# The TOC_EXPAND flag can be set to YES to add extra items for group members to
+# the table of contents of the HTML help documentation and to the tree view.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+TOC_EXPAND             = NO
+
+# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
+# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that
+# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help
+# (.qch) of the generated HTML documentation.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_QHP           = NO
+
+# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify
+# the file name of the resulting .qch file. The path specified is relative to
+# the HTML output folder.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QCH_FILE               =
+
+# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help
+# Project output. For more information please see Qt Help Project / Namespace
+# (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#namespace).
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_NAMESPACE          = org.doxygen.Project
+
+# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt
+# Help Project output. For more information please see Qt Help Project / Virtual
+# Folders (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#virtual-
+# folders).
+# The default value is: doc.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_VIRTUAL_FOLDER     = doc
+
+# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom
+# filter to add. For more information please see Qt Help Project / Custom
+# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
+# filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_CUST_FILTER_NAME   =
+
+# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the
+# custom filter to add. For more information please see Qt Help Project / Custom
+# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
+# filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_CUST_FILTER_ATTRS  =
+
+# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
+# project's filter section matches. Qt Help Project / Filter Attributes (see:
+# http://qt-project.org/doc/qt-4.8/qthelpproject.html#filter-attributes).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_SECT_FILTER_ATTRS  =
+
+# The QHG_LOCATION tag can be used to specify the location of Qt's
+# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the
+# generated .qhp file.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHG_LOCATION           =
+
+# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be
+# generated, together with the HTML files, they form an Eclipse help plugin. To
+# install this plugin and make it available under the help contents menu in
+# Eclipse, the contents of the directory containing the HTML and XML files needs
+# to be copied into the plugins directory of eclipse. The name of the directory
+# within the plugins directory should be the same as the ECLIPSE_DOC_ID value.
+# After copying Eclipse needs to be restarted before the help appears.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_ECLIPSEHELP   = NO
+
+# A unique identifier for the Eclipse help plugin. When installing the plugin
+# the directory name containing the HTML and XML files should also have this
+# name. Each documentation set should have its own identifier.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES.
+
+ECLIPSE_DOC_ID         = org.doxygen.Project
+
+# If you want full control over the layout of the generated HTML pages it might
+# be necessary to disable the index and replace it with your own. The
+# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top
+# of each HTML page. A value of NO enables the index and the value YES disables
+# it. Since the tabs in the index contain the same information as the navigation
+# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+DISABLE_INDEX          = YES
+
+# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
+# structure should be generated to display hierarchical information. If the tag
+# value is set to YES, a side panel will be generated containing a tree-like
+# index structure (just like the one that is generated for HTML Help). For this
+# to work a browser that supports JavaScript, DHTML, CSS and frames is required
+# (i.e. any modern browser). Windows users are probably better off using the
+# HTML help feature. Via custom stylesheets (see HTML_EXTRA_STYLESHEET) one can
+# further fine-tune the look of the index. As an example, the default style
+# sheet generated by doxygen has an example that shows how to put an image at
+# the root of the tree instead of the PROJECT_NAME. Since the tree basically has
+# the same information as the tab index, you could consider setting
+# DISABLE_INDEX to YES when enabling this option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_TREEVIEW      = YES
+
+# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
+# doxygen will group on one line in the generated HTML documentation.
+#
+# Note that a value of 0 will completely suppress the enum values from appearing
+# in the overview section.
+# Minimum value: 0, maximum value: 20, default value: 4.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+ENUM_VALUES_PER_LINE   = 4
+
+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used
+# to set the initial width (in pixels) of the frame in which the tree is shown.
+# Minimum value: 0, maximum value: 1500, default value: 250.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+TREEVIEW_WIDTH         = 250
+
+# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open links to
+# external symbols imported via tag files in a separate window.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+EXT_LINKS_IN_WINDOW    = NO
+
+# Use this tag to change the font size of LaTeX formulas included as images in
+# the HTML documentation. When you change the font size after a successful
+# doxygen run you need to manually remove any form_*.png images from the HTML
+# output directory to force them to be regenerated.
+# Minimum value: 8, maximum value: 50, default value: 10.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+FORMULA_FONTSIZE       = 10
+
+# Use the FORMULA_TRANPARENT tag to determine whether or not the images
+# generated for formulas are transparent PNGs. Transparent PNGs are not
+# supported properly for IE 6.0, but are supported on all modern browsers.
+#
+# Note that when changing this option you need to delete any form_*.png files in
+# the HTML output directory before the changes have effect.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+FORMULA_TRANSPARENT    = YES
+
+# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see
+# http://www.mathjax.org) which uses client side Javascript for the rendering
+# instead of using prerendered bitmaps. Use this if you do not have LaTeX
+# installed or if you want to formulas look prettier in the HTML output. When
+# enabled you may also need to install MathJax separately and configure the path
+# to it using the MATHJAX_RELPATH option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+USE_MATHJAX            = YES
+
+# When MathJax is enabled you can set the default output format to be used for
+# the MathJax output. See the MathJax site (see:
+# http://docs.mathjax.org/en/latest/output.html) for more details.
+# Possible values are: HTML-CSS (which is slower, but has the best
+# compatibility), NativeMML (i.e. MathML) and SVG.
+# The default value is: HTML-CSS.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_FORMAT         = HTML-CSS
+
+# When MathJax is enabled you need to specify the location relative to the HTML
+# output directory using the MATHJAX_RELPATH option. The destination directory
+# should contain the MathJax.js script. For instance, if the mathjax directory
+# is located at the same level as the HTML output directory, then
+# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax
+# Content Delivery Network so you can quickly see the result without installing
+# MathJax. However, it is strongly recommended to install a local copy of
+# MathJax from http://www.mathjax.org before deployment.
+# The default value is: http://cdn.mathjax.org/mathjax/latest.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_RELPATH        = ../common
+
+# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
+# extension names that should be enabled during MathJax rendering. For example
+# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_EXTENSIONS     = TeX/AMSmath TeX/AMSsymbols
+
+# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
+# of code that will be used on startup of the MathJax code. See the MathJax site
+# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an
+# example see the documentation.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_CODEFILE       =
+
+# When the SEARCHENGINE tag is enabled doxygen will generate a search box for
+# the HTML output. The underlying search engine uses javascript and DHTML and
+# should work on any modern browser. Note that when using HTML help
+# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET)
+# there is already a search function so this one should typically be disabled.
+# For large projects the javascript based search engine can be slow, then
+# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to
+# search using the keyboard; to jump to the search box use <access key> + S
+# (what the <access key> is depends on the OS and browser, but it is typically
+# <CTRL>, <ALT>/<option>, or both). Inside the search box use the <cursor down
+# key> to jump into the search results window, the results can be navigated
+# using the <cursor keys>. Press <Enter> to select an item or <escape> to cancel
+# the search. The filter options can be selected when the cursor is inside the
+# search box by pressing <Shift>+<cursor down>. Also here use the <cursor keys>
+# to select a filter and <Enter> or <escape> to activate or cancel the filter
+# option.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+SEARCHENGINE           = YES
+
+# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
+# implemented using a web server instead of a web client using Javascript. There
+# are two flavours of web server based searching depending on the
+# EXTERNAL_SEARCH setting. When disabled, doxygen will generate a PHP script for
+# searching and an index file used by the script. When EXTERNAL_SEARCH is
+# enabled the indexing and searching needs to be provided by external tools. See
+# the section "External Indexing and Searching" for details.
+# The default value is: NO.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SERVER_BASED_SEARCH    = NO
+
+# When EXTERNAL_SEARCH tag is enabled doxygen will no longer generate the PHP
+# script for searching. Instead the search results are written to an XML file
+# which needs to be processed by an external indexer. Doxygen will invoke an
+# external search engine pointed to by the SEARCHENGINE_URL option to obtain the
+# search results.
+#
+# Doxygen ships with an example indexer ( doxyindexer) and search engine
+# (doxysearch.cgi) which are based on the open source search engine library
+# Xapian (see: http://xapian.org/).
+#
+# See the section "External Indexing and Searching" for details.
+# The default value is: NO.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTERNAL_SEARCH        = NO
+
+# The SEARCHENGINE_URL should point to a search engine hosted by a web server
+# which will return the search results when EXTERNAL_SEARCH is enabled.
+#
+# Doxygen ships with an example indexer ( doxyindexer) and search engine
+# (doxysearch.cgi) which are based on the open source search engine library
+# Xapian (see: http://xapian.org/). See the section "External Indexing and
+# Searching" for details.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SEARCHENGINE_URL       =
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed
+# search data is written to a file for indexing by an external tool. With the
+# SEARCHDATA_FILE tag the name of this file can be specified.
+# The default file is: searchdata.xml.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SEARCHDATA_FILE        = searchdata.xml
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the
+# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is
+# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple
+# projects and redirect the results back to the right project.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTERNAL_SEARCH_ID     =
+
+# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen
+# projects other than the one defined by this configuration file, but that are
+# all added to the same external search index. Each project needs to have a
+# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id of
+# to a relative location where the documentation can be found. The format is:
+# EXTRA_SEARCH_MAPPINGS = tagname1=loc1 tagname2=loc2 ...
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTRA_SEARCH_MAPPINGS  =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the LaTeX output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_LATEX tag is set to YES doxygen will generate LaTeX output.
+# The default value is: YES.
+
+GENERATE_LATEX         = NO
+
+# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: latex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_OUTPUT           = latex
+
+# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
+# invoked.
+#
+# Note that when enabling USE_PDFLATEX this option is only used for generating
+# bitmaps for formulas in the HTML output, but not in the Makefile that is
+# written to the output directory.
+# The default file is: latex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_CMD_NAME         = latex
+
+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate
+# index for LaTeX.
+# The default file is: makeindex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+MAKEINDEX_CMD_NAME     = makeindex
+
+# If the COMPACT_LATEX tag is set to YES doxygen generates more compact LaTeX
+# documents. This may be useful for small projects and may help to save some
+# trees in general.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+COMPACT_LATEX          = NO
+
+# The PAPER_TYPE tag can be used to set the paper type that is used by the
+# printer.
+# Possible values are: a4 (210 x 297 mm), letter (8.5 x 11 inches), legal (8.5 x
+# 14 inches) and executive (7.25 x 10.5 inches).
+# The default value is: a4.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+PAPER_TYPE             = a4
+
+# The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names
+# that should be included in the LaTeX output. To get the times font for
+# instance you can specify
+# EXTRA_PACKAGES=times
+# If left blank no extra packages will be included.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+EXTRA_PACKAGES         = amsfonts amsmath amssymb
+
+# The LATEX_HEADER tag can be used to specify a personal LaTeX header for the
+# generated LaTeX document. The header should contain everything until the first
+# chapter. If it is left blank doxygen will generate a standard header. See
+# section "Doxygen usage" for information on how to let doxygen write the
+# default header to a separate file.
+#
+# Note: Only use a user-defined header if you know what you are doing! The
+# following commands have a special meaning inside the header: $title,
+# $datetime, $date, $doxygenversion, $projectname, $projectnumber. Doxygen will
+# replace them by respectively the title of the page, the current date and time,
+# only the current date, the version number of doxygen, the project name (see
+# PROJECT_NAME), or the project number (see PROJECT_NUMBER).
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_HEADER           =
+
+# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for the
+# generated LaTeX document. The footer should contain everything after the last
+# chapter. If it is left blank doxygen will generate a standard footer.
+#
+# Note: Only use a user-defined footer if you know what you are doing!
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_FOOTER           =
+
+# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the LATEX_OUTPUT output
+# directory. Note that the files will be copied as-is; there are no commands or
+# markers available.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_EXTRA_FILES      =
+
+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated is
+# prepared for conversion to PDF (using ps2pdf or pdflatex). The PDF file will
+# contain links (just like the HTML output) instead of page references. This
+# makes the output suitable for online browsing using a PDF viewer.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+PDF_HYPERLINKS         = YES
+
+# If the LATEX_PDFLATEX tag is set to YES, doxygen will use pdflatex to generate
+# the PDF file directly from the LaTeX files. Set this option to YES to get a
+# higher quality PDF documentation.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+USE_PDFLATEX           = YES
+
+# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode
+# command to the generated LaTeX files. This will instruct LaTeX to keep running
+# if errors occur, instead of asking the user for help. This option is also used
+# when generating formulas in HTML.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_BATCHMODE        = NO
+
+# If the LATEX_HIDE_INDICES tag is set to YES then doxygen will not include the
+# index chapters (such as File Index, Compound Index, etc.) in the output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_HIDE_INDICES     = NO
+
+# If the LATEX_SOURCE_CODE tag is set to YES then doxygen will include source
+# code with syntax highlighting in the LaTeX output.
+#
+# Note that which sources are shown also depends on other settings such as
+# SOURCE_BROWSER.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_SOURCE_CODE      = NO
+
+# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
+# bibliography, e.g. plainnat, or ieeetr. See
+# http://en.wikipedia.org/wiki/BibTeX and \cite for more info.
+# The default value is: plain.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_BIB_STYLE        = plain
+
+#---------------------------------------------------------------------------
+# Configuration options related to the RTF output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_RTF tag is set to YES doxygen will generate RTF output. The
+# RTF output is optimized for Word 97 and may not look too pretty with other RTF
+# readers/editors.
+# The default value is: NO.
+
+GENERATE_RTF           = NO
+
+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: rtf.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_OUTPUT             = rtf
+
+# If the COMPACT_RTF tag is set to YES doxygen generates more compact RTF
+# documents. This may be useful for small projects and may help to save some
+# trees in general.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+COMPACT_RTF            = NO
+
+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated will
+# contain hyperlink fields. The RTF file will contain links (just like the HTML
+# output) instead of page references. This makes the output suitable for online
+# browsing using Word or some other Word compatible readers that support those
+# fields.
+#
+# Note: WordPad (write) and others do not support links.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_HYPERLINKS         = NO
+
+# Load stylesheet definitions from file. Syntax is similar to doxygen's config
+# file, i.e. a series of assignments. You only have to provide replacements,
+# missing definitions are set to their default value.
+#
+# See also section "Doxygen usage" for information on how to generate the
+# default style sheet that doxygen normally uses.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_STYLESHEET_FILE    =
+
+# Set optional variables used in the generation of an RTF document. Syntax is
+# similar to doxygen's config file. A template extensions file can be generated
+# using doxygen -e rtf extensionFile.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_EXTENSIONS_FILE    =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the man page output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_MAN tag is set to YES doxygen will generate man pages for
+# classes and files.
+# The default value is: NO.
+
+GENERATE_MAN           = NO
+
+# The MAN_OUTPUT tag is used to specify where the man pages will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it. A directory man3 will be created inside the directory specified by
+# MAN_OUTPUT.
+# The default directory is: man.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_OUTPUT             = man
+
+# The MAN_EXTENSION tag determines the extension that is added to the generated
+# man pages. In case the manual section does not start with a number, the number
+# 3 is prepended. The dot (.) at the beginning of the MAN_EXTENSION tag is
+# optional.
+# The default value is: .3.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_EXTENSION          = .3
+
+# If the MAN_LINKS tag is set to YES and doxygen generates man output, then it
+# will generate one additional man file for each entity documented in the real
+# man page(s). These additional files only source the real man page, but without
+# them the man command would be unable to find the correct page.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_LINKS              = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the XML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_XML tag is set to YES doxygen will generate an XML file that
+# captures the structure of the code including all documentation.
+# The default value is: NO.
+
+GENERATE_XML           = NO
+
+# The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: xml.
+# This tag requires that the tag GENERATE_XML is set to YES.
+
+XML_OUTPUT             = xml
+
+# If the XML_PROGRAMLISTING tag is set to YES doxygen will dump the program
+# listings (including syntax highlighting and cross-referencing information) to
+# the XML output. Note that enabling this will significantly increase the size
+# of the XML output.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_XML is set to YES.
+
+XML_PROGRAMLISTING     = YES
+
+#---------------------------------------------------------------------------
+# Configuration options related to the DOCBOOK output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_DOCBOOK tag is set to YES doxygen will generate Docbook files
+# that can be used to generate PDF.
+# The default value is: NO.
+
+GENERATE_DOCBOOK       = NO
+
+# The DOCBOOK_OUTPUT tag is used to specify where the Docbook pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in
+# front of it.
+# The default directory is: docbook.
+# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
+
+DOCBOOK_OUTPUT         = docbook
+
+#---------------------------------------------------------------------------
+# Configuration options for the AutoGen Definitions output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_AUTOGEN_DEF tag is set to YES doxygen will generate an AutoGen
+# Definitions (see http://autogen.sf.net) file that captures the structure of
+# the code including all documentation. Note that this feature is still
+# experimental and incomplete at the moment.
+# The default value is: NO.
+
+GENERATE_AUTOGEN_DEF   = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the Perl module output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_PERLMOD tag is set to YES doxygen will generate a Perl module
+# file that captures the structure of the code including all documentation.
+#
+# Note that this feature is still experimental and incomplete at the moment.
+# The default value is: NO.
+
+GENERATE_PERLMOD       = NO
+
+# If the PERLMOD_LATEX tag is set to YES doxygen will generate the necessary
+# Makefile rules, Perl scripts and LaTeX code to be able to generate PDF and DVI
+# output from the Perl module output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_LATEX          = NO
+
+# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be nicely
+# formatted so it can be parsed by a human reader. This is useful if you want to
+# understand what is going on. On the other hand, if this tag is set to NO the
+# size of the Perl module output will be much smaller and Perl will parse it
+# just the same.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_PRETTY         = YES
+
+# The names of the make variables in the generated doxyrules.make file are
+# prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. This is useful
+# so different doxyrules.make files included by the same Makefile don't
+# overwrite each other's variables.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_MAKEVAR_PREFIX =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the preprocessor
+#---------------------------------------------------------------------------
+
+# If the ENABLE_PREPROCESSING tag is set to YES doxygen will evaluate all
+# C-preprocessor directives found in the sources and include files.
+# The default value is: YES.
+
+ENABLE_PREPROCESSING   = YES
+
+# If the MACRO_EXPANSION tag is set to YES doxygen will expand all macro names
+# in the source code. If set to NO only conditional compilation will be
+# performed. Macro expansion can be done in a controlled way by setting
+# EXPAND_ONLY_PREDEF to YES.
+# The default value is: NO.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+MACRO_EXPANSION        = YES
+
+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
+# the macro expansion is limited to the macros specified with the PREDEFINED and
+# EXPAND_AS_DEFINED tags.
+# The default value is: NO.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+EXPAND_ONLY_PREDEF     = YES
+
+# If the SEARCH_INCLUDES tag is set to YES the includes files in the
+# INCLUDE_PATH will be searched if a #include is found.
+# The default value is: YES.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+SEARCH_INCLUDES        = YES
+
+# The INCLUDE_PATH tag can be used to specify one or more directories that
+# contain include files that are not input files but should be processed by the
+# preprocessor.
+# This tag requires that the tag SEARCH_INCLUDES is set to YES.
+
+INCLUDE_PATH           =
+
+# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
+# patterns (like *.h and *.hpp) to filter out the header-files in the
+# directories. If left blank, the patterns specified with FILE_PATTERNS will be
+# used.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+INCLUDE_FILE_PATTERNS  =
+
+# The PREDEFINED tag can be used to specify one or more macro names that are
+# defined before the preprocessor is started (similar to the -D option of e.g.
+# gcc). The argument of the tag is a list of macros of the form: name or
+# name=definition (no spaces). If the definition and the "=" are omitted, "=1"
+# is assumed. To prevent a macro definition from being undefined via #undef or
+# recursively expanded use the := operator instead of the = operator.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+PREDEFINED             = protected=private
+
+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
+# tag can be used to specify a list of macro names that should be expanded. The
+# macro definition that is found in the sources will be used. Use the PREDEFINED
+# tag if you want to use a different macro definition that overrules the
+# definition found in the source code.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+EXPAND_AS_DEFINED      =
+
+# If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will
+# remove all refrences to function-like macros that are alone on a line, have an
+# all uppercase name, and do not end with a semicolon. Such function macros are
+# typically used for boiler-plate code, and will confuse the parser if not
+# removed.
+# The default value is: YES.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+SKIP_FUNCTION_MACROS   = YES
+
+#---------------------------------------------------------------------------
+# Configuration options related to external references
+#---------------------------------------------------------------------------
+
+# The TAGFILES tag can be used to specify one or more tag files. For each tag
+# file the location of the external documentation should be added. The format of
+# a tag file without this location is as follows:
+# TAGFILES = file1 file2 ...
+# Adding location for the tag files is done as follows:
+# TAGFILES = file1=loc1 "file2 = loc2" ...
+# where loc1 and loc2 can be relative or absolute paths or URLs. See the
+# section "Linking to external documentation" for more information about the use
+# of tag files.
+# Note: Each tag file must have an unique name (where the name does NOT include
+# the path). If a tag file is not located in the directory in which doxygen is
+# run, you must also specify the path to the tagfile here.
+
+TAGFILES               =
+
+# When a file name is specified after GENERATE_TAGFILE, doxygen will create a
+# tag file that is based on the input files it reads. See section "Linking to
+# external documentation" for more information about the usage of tag files.
+
+GENERATE_TAGFILE       =
+
+# If the ALLEXTERNALS tag is set to YES all external class will be listed in the
+# class index. If set to NO only the inherited external classes will be listed.
+# The default value is: NO.
+
+ALLEXTERNALS           = NO
+
+# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed in
+# the modules index. If set to NO, only the current project's groups will be
+# listed.
+# The default value is: YES.
+
+EXTERNAL_GROUPS        = YES
+
+# If the EXTERNAL_PAGES tag is set to YES all external pages will be listed in
+# the related pages index. If set to NO, only the current project's pages will
+# be listed.
+# The default value is: YES.
+
+EXTERNAL_PAGES         = YES
+
+# The PERL_PATH should be the absolute path and name of the perl script
+# interpreter (i.e. the result of 'which perl').
+# The default file (with absolute path) is: /usr/bin/perl.
+
+PERL_PATH              = /usr/bin/perl
+
+#---------------------------------------------------------------------------
+# Configuration options related to the dot tool
+#---------------------------------------------------------------------------
+
+# If the CLASS_DIAGRAMS tag is set to YES doxygen will generate a class diagram
+# (in HTML and LaTeX) for classes with base or super classes. Setting the tag to
+# NO turns the diagrams off. Note that this option also works with HAVE_DOT
+# disabled, but it is recommended to install and use dot, since it yields more
+# powerful graphs.
+# The default value is: YES.
+
+CLASS_DIAGRAMS         = NO
+
+# You can define message sequence charts within doxygen comments using the \msc
+# command. Doxygen will then run the mscgen tool (see:
+# http://www.mcternan.me.uk/mscgen/)) to produce the chart and insert it in the
+# documentation. The MSCGEN_PATH tag allows you to specify the directory where
+# the mscgen tool resides. If left empty the tool is assumed to be found in the
+# default search path.
+
+MSCGEN_PATH            =
+
+# You can include diagrams made with dia in doxygen documentation. Doxygen will
+# then run dia to produce the diagram and insert it in the documentation. The
+# DIA_PATH tag allows you to specify the directory where the dia binary resides.
+# If left empty dia is assumed to be found in the default search path.
+
+DIA_PATH               =
+
+# If set to YES, the inheritance and collaboration graphs will hide inheritance
+# and usage relations if the target is undocumented or is not a class.
+# The default value is: YES.
+
+HIDE_UNDOC_RELATIONS   = YES
+
+# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
+# available from the path. This tool is part of Graphviz (see:
+# http://www.graphviz.org/), a graph visualization toolkit from AT&T and Lucent
+# Bell Labs. The other options in this section have no effect if this option is
+# set to NO
+# The default value is: NO.
+
+HAVE_DOT               = YES
+
+# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is allowed
+# to run in parallel. When set to 0 doxygen will base this on the number of
+# processors available in the system. You can set it explicitly to a value
+# larger than 0 to get control over the balance between CPU load and processing
+# speed.
+# Minimum value: 0, maximum value: 32, default value: 0.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_NUM_THREADS        = 0
+
+# When you want a differently looking font n the dot files that doxygen
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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/Persistence_representations/doc/Persistence_representations_doc.h b/src/Persistence_representations/doc/Persistence_representations_doc.h
index 73800d0d..3aa99315 100644
--- a/src/Persistence_representations/doc/Persistence_representations_doc.h
+++ b/src/Persistence_representations/doc/Persistence_representations_doc.h
@@ -227,6 +227,9 @@ namespace Persistence_representations {
  to diagonal are given then sometimes the kernel have support that reaches the region
  below the diagonal. If the value of this parameter is true, then the values below diagonal can be erased.
 
+ We also provide two methods to perform exact calculations. In both methods, the kernel is no longer provided as a filter (i.e. a square matrix---see parameters above), but rather as
+ a function assigning a real value to a 2D point. In the first method, calculations are done on a grid, leading to a finite-dimensional representation.
+ On the other hand, in the second method, we do not use grids, meaning that diagrams are represented as functions. Thus, only scalar products are available.
 
  \section sec_persistence_vectors Persistence vectors
  <b>Reference manual:</b> \ref Gudhi::Persistence_representations::Vector_distances_in_diagram <br>
@@ -273,10 +276,8 @@ namespace Persistence_representations {
 
  the program output is:
 
- \code $> Approx SW distance: 5.33648
- $> Exact SW distance: 5.33798
- $> Approx SW kernel: 0.0693743
- $> Exact  SW kernel: 0.0693224
+ \code $> Approx SW kernel: 0.0693743
+ $> Exact  SW kernel: 0.0693218
  $> Distance induced by approx SW kernel: 1.36428
  $> Distance induced by exact  SW kernel: 1.3643
  \endcode
diff --git a/src/Persistence_representations/example/persistence_heat_maps.cpp b/src/Persistence_representations/example/persistence_heat_maps.cpp
index f1791e97..5874336e 100644
--- a/src/Persistence_representations/example/persistence_heat_maps.cpp
+++ b/src/Persistence_representations/example/persistence_heat_maps.cpp
@@ -77,7 +77,7 @@ int main(int argc, char** argv) {
   // to compute scalar product of hm1 and hm2:
   std::cout << "Scalar product is : " << hm1.compute_scalar_product(hm2) << std::endl;
 
-  Gudhi::Persistence_representations::Kernel k = Gudhi::Persistence_representations::Gaussian_kernel(1.0);
+  Gudhi::Persistence_representations::Kernel2D k = Gudhi::Persistence_representations::Gaussian_kernel(1.0);
 
   Persistence_heat_maps hm1k(persistence1, k);
   Persistence_heat_maps hm2k(persistence2, k);
diff --git a/src/Persistence_representations/example/sliced_wasserstein.cpp b/src/Persistence_representations/example/sliced_wasserstein.cpp
index 2104e2b2..089172a0 100644
--- a/src/Persistence_representations/example/sliced_wasserstein.cpp
+++ b/src/Persistence_representations/example/sliced_wasserstein.cpp
@@ -50,8 +50,6 @@ int main(int argc, char** argv) {
   SW swex1(persistence1, 1, -1);
   SW swex2(persistence2, 1, -1);
 
-  std::cout << "Approx SW distance: " << sw1.compute_sliced_wasserstein_distance(sw2) << std::endl;
-  std::cout << "Exact SW distance: " << swex1.compute_sliced_wasserstein_distance(swex2) << std::endl;
   std::cout << "Approx SW kernel: " << sw1.compute_scalar_product(sw2) << std::endl;
   std::cout << "Exact  SW kernel: " << swex1.compute_scalar_product(swex2) << std::endl;
   std::cout << "Distance induced by approx SW kernel: " << sw1.distance(sw2) << std::endl;
diff --git a/src/Persistence_representations/include/gudhi/Persistence_heat_maps.h b/src/Persistence_representations/include/gudhi/Persistence_heat_maps.h
index 63c6e239..12188526 100644
--- a/src/Persistence_representations/include/gudhi/Persistence_heat_maps.h
+++ b/src/Persistence_representations/include/gudhi/Persistence_heat_maps.h
@@ -249,14 +249,14 @@ class Persistence_heat_maps {
    * to turn the diagram into a function.
   **/
   Persistence_heat_maps(const Persistence_diagram & interval, size_t number_of_x_pixels, size_t number_of_y_pixels,
-                        double min_x = 0, double max_x = 1, double min_y = 0, double max_y = 1, const Kernel & kernel = Gaussian_kernel(1.0));
+                        double min_x = 0, double max_x = 1, double min_y = 0, double max_y = 1, const Kernel2D & kernel = Gaussian_kernel(1.0));
 
   /**
    * Construction that takes as inputs (1) the diagram and (2) a universal kernel on the plane used
    * to turn the diagram into a function. Note that this construction is infinite dimensional so
    * only compute_scalar_product() method is valid after calling this constructor.
   **/
-  Persistence_heat_maps(const Persistence_diagram & interval, const Kernel & kernel = Gaussian_kernel(1.0));
+  Persistence_heat_maps(const Persistence_diagram & interval, const Kernel2D & kernel = Gaussian_kernel(1.0));
 
   /**
    * Compute a mean value of a collection of heat maps and store it in the current object. Note that all the persistence
@@ -531,8 +531,8 @@ class Persistence_heat_maps {
 
   void construct_image_from_exact_universal_kernel(const Persistence_diagram & interval,
                                                    size_t number_of_x_pixels = 10, size_t number_of_y_pixels = 10,
-                                                   double min_x = 0, double max_x = 1, double min_y = 0, double max_y = 1, const Kernel & kernel = Gaussian_kernel(1.0));
-  void construct_kernel_from_exact_universal_kernel(const Persistence_diagram & interval, const Kernel & kernel = Gaussian_kernel(1.0));
+                                                   double min_x = 0, double max_x = 1, double min_y = 0, double max_y = 1, const Kernel2D & kernel = Gaussian_kernel(1.0));
+  void construct_kernel_from_exact_universal_kernel(const Persistence_diagram & interval, const Kernel2D & kernel = Gaussian_kernel(1.0));
 
   void set_up_parameters_for_basic_classes() {
     this->number_of_functions_for_vectorization = 1;
@@ -543,7 +543,7 @@ class Persistence_heat_maps {
   bool discrete = true;
 
   // PWGK
-  Kernel k;
+  Kernel2D k;
   Persistence_diagram d;
   std::vector<double> weights;
 
@@ -559,23 +559,22 @@ template <typename Scalling_of_kernels>
 void Persistence_heat_maps<Scalling_of_kernels>::construct_image_from_exact_universal_kernel(const Persistence_diagram & diagram,
                                                                                              size_t number_of_x_pixels, size_t number_of_y_pixels,
                                                                                              double min_x, double max_x,
-                                                                                             double min_y, double max_y, const Kernel & kernel) {
+                                                                                             double min_y, double max_y, const Kernel2D & kernel) {
 
   this->discrete = true; Scalling_of_kernels f; this->f = f; this->min_ = min_x; this->max_ = max_x;
-  for(size_t i = 0; i < number_of_y_pixels; i++)  this->heat_map.emplace_back();
+  this->heat_map.resize(number_of_y_pixels);
   double step_x = (max_x - min_x)/(number_of_x_pixels - 1); double step_y = (max_y - min_y)/(number_of_y_pixels - 1);
 
   int num_pts = diagram.size();
 
   for(size_t i = 0; i < number_of_y_pixels; i++){
-    double y = min_y + i*step_y;
+    double y = min_y + i*step_y; this->heat_map[i].reserve(number_of_x_pixels);
     for(size_t j = 0; j < number_of_x_pixels; j++){
       double x = min_x + j*step_x;
 
       std::pair<double, double> grid_point(x,y); double pixel_value = 0;
       for(int k = 0; k < num_pts; k++){
-        double px = diagram[k].first; double py = diagram[k].second; std::pair<double, double> diagram_point(px,py);
-        pixel_value += this->f(diagram_point) * kernel(diagram_point, grid_point);
+        pixel_value += this->f(diagram[k]) * kernel(diagram[k], grid_point);
       }
       this->heat_map[i].push_back(pixel_value);
 
@@ -589,13 +588,13 @@ template <typename Scalling_of_kernels>
 Persistence_heat_maps<Scalling_of_kernels>::Persistence_heat_maps(const Persistence_diagram & diagram,
                                                                   size_t number_of_x_pixels, size_t number_of_y_pixels,
                                                                   double min_x, double max_x,
-                                                                  double min_y, double max_y, const Kernel & kernel) {
+                                                                  double min_y, double max_y, const Kernel2D & kernel) {
   this->construct_image_from_exact_universal_kernel(diagram, number_of_x_pixels, number_of_y_pixels, min_x, max_x, min_y, max_y, kernel);
   this->set_up_parameters_for_basic_classes();
 }
 
 template <typename Scalling_of_kernels>
-void Persistence_heat_maps<Scalling_of_kernels>::construct_kernel_from_exact_universal_kernel(const Persistence_diagram & diagram, const Kernel & kernel){
+void Persistence_heat_maps<Scalling_of_kernels>::construct_kernel_from_exact_universal_kernel(const Persistence_diagram & diagram, const Kernel2D & kernel){
   this->discrete = false; Scalling_of_kernels f; this->f = f; this->k = kernel; this->d = diagram;
   int num_pts = this->d.size();
   for (int i = 0; i < num_pts; i++)  this->weights.push_back(this->f(this->d[i]));
@@ -603,7 +602,7 @@ void Persistence_heat_maps<Scalling_of_kernels>::construct_kernel_from_exact_uni
 
 
 template <typename Scalling_of_kernels>
-Persistence_heat_maps<Scalling_of_kernels>::Persistence_heat_maps(const Persistence_diagram& diagram, const Kernel & kernel) {
+Persistence_heat_maps<Scalling_of_kernels>::Persistence_heat_maps(const Persistence_diagram& diagram, const Kernel2D & kernel) {
   this->construct_kernel_from_exact_universal_kernel(diagram, kernel);
   this->set_up_parameters_for_basic_classes();
 }
diff --git a/src/Persistence_representations/include/gudhi/Sliced_Wasserstein.h b/src/Persistence_representations/include/gudhi/Sliced_Wasserstein.h
index 8c92ab54..a3c0dc2f 100644
--- a/src/Persistence_representations/include/gudhi/Sliced_Wasserstein.h
+++ b/src/Persistence_representations/include/gudhi/Sliced_Wasserstein.h
@@ -28,18 +28,6 @@
 #include <gudhi/common_persistence_representations.h>
 #include <gudhi/Debug_utils.h>
 
-// standard include
-#include <cmath>
-#include <iostream>
-#include <vector>
-#include <limits>
-#include <fstream>
-#include <sstream>
-#include <algorithm>
-#include <string>
-#include <utility>
-#include <functional>
-
 namespace Gudhi {
 namespace Persistence_representations {
 
@@ -70,12 +58,15 @@ namespace Persistence_representations {
 class Sliced_Wasserstein {
 
  protected:
-    Persistence_diagram diagram;
-    int approx;
-    double sigma;
-    std::vector<std::vector<double> > projections, projections_diagonal;
 
- public:
+  Persistence_diagram diagram;
+  int approx;
+  double sigma;
+  std::vector<std::vector<double> > projections, projections_diagonal;
+
+  // **********************************
+  // Utils.
+  // **********************************
 
   void build_rep(){
 
@@ -96,28 +87,14 @@ class Sliced_Wasserstein {
         }
 
         std::sort(l.begin(), l.end()); std::sort(l_diag.begin(), l_diag.end());
-        projections.push_back(l); projections_diagonal.push_back(l_diag);
+        projections.push_back(std::move(l)); projections_diagonal.push_back(std::move(l_diag));
 
       }
 
+      diagram.clear();
     }
-
   }
 
-  /** \brief Sliced Wasserstein kernel constructor.
-   * \ingroup Sliced_Wasserstein
-   *
-   * @param[in] _diagram  persistence diagram.
-   * @param[in] _sigma  bandwidth parameter.
-   * @param[in] _approx number of directions used to approximate the integral in the Sliced Wasserstein distance, set to -1 for exact computation.
-   *
-   */
-  Sliced_Wasserstein(const Persistence_diagram & _diagram, double _sigma = 1.0, int _approx = 100){diagram = _diagram; approx = _approx; sigma = _sigma; build_rep();}
-
-  // **********************************
-  // Utils.
-  // **********************************
-
   // Compute the angle formed by two points of a PD
   double compute_angle(const Persistence_diagram & diag, int i, int j) const {
     std::pair<double,double> vect; double x1,y1, x2,y2;
@@ -177,21 +154,7 @@ class Sliced_Wasserstein {
     return norm*integral;
   }
 
-
-
-
-  // **********************************
-  // Scalar product + distance.
-  // **********************************
-
-  /** \brief Evaluation of the Sliced Wasserstein Distance between a pair of diagrams.
-   * \ingroup Sliced_Wasserstein
-   *
-   * @pre       approx attribute needs to be the same for both instances.
-   * @param[in] second other instance of class Sliced_Wasserstein.
-   *
-   *
-   */
+  // Evaluation of the Sliced Wasserstein Distance between a pair of diagrams.
   double compute_sliced_wasserstein_distance(const Sliced_Wasserstein & second) const {
 
     GUDHI_CHECK(this->approx != second.approx, std::invalid_argument("Error: different approx values for representations"));
@@ -232,8 +195,8 @@ class Sliced_Wasserstein {
       }
 
       // Sort angles.
-      std::sort(angles1.begin(), angles1.end(), [=](const std::pair<double, std::pair<int,int> >& p1, const std::pair<double, std::pair<int,int> >& p2){return (p1.first < p2.first);});
-      std::sort(angles2.begin(), angles2.end(), [=](const std::pair<double, std::pair<int,int> >& p1, const std::pair<double, std::pair<int,int> >& p2){return (p1.first < p2.first);});
+      std::sort(angles1.begin(), angles1.end(), [](const std::pair<double, std::pair<int,int> >& p1, const std::pair<double, std::pair<int,int> >& p2){return (p1.first < p2.first);});
+      std::sort(angles2.begin(), angles2.end(), [](const std::pair<double, std::pair<int,int> >& p1, const std::pair<double, std::pair<int,int> >& p2){return (p1.first < p2.first);});
 
       // Initialize orders of the points of both PDs (given by ordinates when theta = -pi/2).
       std::vector<int> orderp1, orderp2;
@@ -291,11 +254,13 @@ class Sliced_Wasserstein {
 
     else{
 
-      double step = pi/this->approx;
+      double step = pi/this->approx; std::vector<double> v1, v2;
       for (int i = 0; i < this->approx; i++){
 
-        std::vector<double> v1; std::vector<double> l1 = this->projections[i]; std::vector<double> l1bis = second.projections_diagonal[i]; std::merge(l1.begin(), l1.end(), l1bis.begin(), l1bis.end(), std::back_inserter(v1));
-        std::vector<double> v2; std::vector<double> l2 = second.projections[i]; std::vector<double> l2bis = this->projections_diagonal[i]; std::merge(l2.begin(), l2.end(), l2bis.begin(), l2bis.end(), std::back_inserter(v2));
+        v1.clear(); v2.clear();
+        std::merge(this->projections[i].begin(), this->projections[i].end(), second.projections_diagonal[i].begin(), second.projections_diagonal[i].end(), std::back_inserter(v1));
+        std::merge(second.projections[i].begin(), second.projections[i].end(), this->projections_diagonal[i].begin(), this->projections_diagonal[i].end(), std::back_inserter(v2));
+
         int n = v1.size(); double f = 0;
         for (int j = 0; j < n; j++)  f += std::abs(v1[j] - v2[j]);
         sw += f*step;
@@ -306,6 +271,20 @@ class Sliced_Wasserstein {
     return sw/pi;
   }
 
+ public:
+
+  /** \brief Sliced Wasserstein kernel constructor.
+   * \ingroup Sliced_Wasserstein
+   *
+   * @param[in] _diagram  persistence diagram.
+   * @param[in] _sigma    bandwidth parameter.
+   * @param[in] _approx   number of directions used to approximate the integral in the Sliced Wasserstein distance, set to -1 for exact computation. If positive, then projections of the diagram
+   *                      points on all directions are stored in memory to reduce computation time.
+   *
+   */
+  // This class implements the following concepts: Topological_data_with_distances, Real_valued_topological_data, Topological_data_with_scalar_product
+  Sliced_Wasserstein(const Persistence_diagram & _diagram, double _sigma = 1.0, int _approx = 10):diagram(_diagram), approx(_approx), sigma(_sigma) {build_rep();}
+
   /** \brief Evaluation of the kernel on a pair of diagrams.
    * \ingroup Sliced_Wasserstein
    *
@@ -331,8 +310,6 @@ class Sliced_Wasserstein {
   }
 
 
-
-
 }; // class Sliced_Wasserstein
 }  // namespace Persistence_representations
 }  // namespace Gudhi
diff --git a/src/Persistence_representations/include/gudhi/common_persistence_representations.h b/src/Persistence_representations/include/gudhi/common_persistence_representations.h
index 66ed3bf8..f0cd8146 100644
--- a/src/Persistence_representations/include/gudhi/common_persistence_representations.h
+++ b/src/Persistence_representations/include/gudhi/common_persistence_representations.h
@@ -43,16 +43,15 @@ static constexpr double pi = boost::math::constants::pi<double>();
 using Persistence_diagram = std::vector<std::pair<double, double> >;
 
 /**
- * In this module, we use the name Weight for the representation of a function taking a pair of two double and returning a double.
+ * In this module, we use the name Kernel for the representation of a function taking a pair of two points in the plane and returning a double.
  */
-using Weight = std::function<double (std::pair<double, double>) >;
-using Kernel = std::function<double (std::pair<double, double>, std::pair<double, double> )>;
+using Kernel2D = std::function<double (std::pair<double, double>, std::pair<double, double> )>;
 
-Kernel Gaussian_kernel(double sigma){
+inline Kernel2D Gaussian_kernel(double sigma){
   return [=](std::pair<double, double> p, std::pair<double, double> q){return (1.0 / (std::sqrt(2*pi)*sigma)) * std::exp(  -((p.first-q.first)*(p.first-q.first) + (p.second-q.second)*(p.second-q.second)) / (2*sigma*sigma)   );};
 }
 
-Kernel polynomial_kernel(double c, double d){
+inline Kernel2D polynomial_kernel(double c, double d){
   return [=](std::pair<double, double> p, std::pair<double, double> q){return std::pow( p.first*q.first + p.second*q.second + c, d);};
 }
 
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/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/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 ${_python_path}
-    )
-else()
-  find_program( CYTHON_EXECUTABLE
-    NAMES cython cython.bat cython3
-    )
-endif()
-
-
-include( FindPackageHandleStandardArgs )
-FIND_PACKAGE_HANDLE_STANDARD_ARGS( Cython REQUIRED_VARS CYTHON_EXECUTABLE )
-
-mark_as_advanced( CYTHON_EXECUTABLE )
diff --git a/src/cmake/modules/GUDHI_doxygen_target.cmake b/src/cmake/modules/GUDHI_doxygen_target.cmake
index f3e2d9f5..9e10e566 100644
--- a/src/cmake/modules/GUDHI_doxygen_target.cmake
+++ b/src/cmake/modules/GUDHI_doxygen_target.cmake
@@ -3,14 +3,17 @@ find_package(Doxygen)
 if(DOXYGEN_FOUND)
   # configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile @ONLY)
 
-  #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)
 
+  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()
 endif(DOXYGEN_FOUND)
diff --git a/src/cmake/modules/GUDHI_modules.cmake b/src/cmake/modules/GUDHI_modules.cmake
index 205ee8a1..276fb2cc 100644
--- a/src/cmake/modules/GUDHI_modules.cmake
+++ b/src/cmake/modules/GUDHI_modules.cmake
@@ -16,7 +16,7 @@ function(add_gudhi_module file_path)
 
 endfunction(add_gudhi_module)
 
-option(WITH_GUDHI_BENCHMARK "Activate/desactivate benchmark compilation" ON)
+option(WITH_GUDHI_BENCHMARK "Activate/desactivate benchmark compilation" OFF)
 option(WITH_GUDHI_EXAMPLE "Activate/desactivate examples compilation and installation" ON)
 option(WITH_GUDHI_PYTHON "Activate/desactivate python module compilation and installation" ON)
 option(WITH_GUDHI_TEST "Activate/desactivate examples compilation and installation" ON)
diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 7433f2f3..f03c2177 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()
@@ -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 +116,34 @@ 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)
+  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")
+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..c27e4f56 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 y mofifying 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..1849a6ec 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -16,17 +16,51 @@ 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)
+  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 )
 
+# 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(CYTHON_FOUND)
-  message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_EXECUTABLE} - Sphinx is ${SPHINX_PATH}")
+  set(GUDHI_CYTHON_MODULES "${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 ${NUMPY_VERSION}")
+  endif()
+  if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}persistence_graphical_tools;")
+  else()
+      set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MODULES}persistence_graphical_tools;")
+  endif()
 
+  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', ")
@@ -49,25 +83,49 @@ if(CYTHON_FOUND)
   endif()
 
   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 '${CMAKE_CURRENT_SOURCE_DIR}/cython/nerve_gic.pyx'")
-  endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+    set(GUDHI_CYTHON_MODULES "${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 '${CMAKE_CURRENT_SOURCE_DIR}/cython/tangential_complex.pyx'")
-  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+    set(GUDHI_CYTHON_MODULES "${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 '${CMAKE_CURRENT_SOURCE_DIR}/cython/alpha_complex.pyx'")
-  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
+    set(GUDHI_CYTHON_MODULES "${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 '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_strong_witness_complex.pyx'\n")
-  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
+    set(GUDHI_CYTHON_MODULES "${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()
 
   if(CGAL_FOUND)
     can_cgal_use_cxx11_thread_local()
@@ -77,8 +135,10 @@ if(CYTHON_FOUND)
     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,
@@ -87,10 +147,12 @@ if(CYTHON_FOUND)
     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}'${GMPXX_LIBRARIES_DIR}', ")
@@ -112,6 +174,7 @@ if(CYTHON_FOUND)
   set(GUDHI_CYTHON_INCLUDE_DIRS "${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', ")
     add_gudhi_cython_lib(${TBB_RELEASE_LIBRARY})
     add_gudhi_cython_lib(${TBB_MALLOC_RELEASE_LIBRARY})
@@ -152,27 +215,29 @@ if(CYTHON_FOUND)
              ${PYTHON_EXECUTABLE} "${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)
-
-    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(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)
@@ -226,11 +291,13 @@ if(CYTHON_FOUND)
              COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
              ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
 
-    add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
+    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)
 
@@ -249,26 +316,30 @@ if(CYTHON_FOUND)
            ${PYTHON_EXECUTABLE} "${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)
+  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_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)
+  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()
 
   add_test(NAME rips_complex_from_points_example_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
@@ -297,7 +368,7 @@ if(CYTHON_FOUND)
   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)
+  if(SPHINX_PATH AND MATPLOTLIB_FOUND AND NUMPY_FOUND 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
@@ -317,5 +388,5 @@ if(CYTHON_FOUND)
              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()
 endif(CYTHON_FOUND)
diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py
index 216ab8d6..314bd6db 100755
--- 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.
@@ -29,187 +24,197 @@ __author__ = "Vincent Rouvreau, Bertrand Michel"
 __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
-def __min_birth_max_death(persistence, band=0.):
-    """This function returns (min_birth, max_death) from the persistence.
-
-    :param persistence: The persistence to plot.
-    :type persistence: list of tuples(dimension, tuple(birth, death)).
-    :param band: band
-    :type band: float.
-    :returns: (float, float) -- (min_birth, max_death).
-    """
-    # Look for minimum birth date and maximum death date for plot optimisation
-    max_death = 0
-    min_birth = persistence[0][1][0]
-    for interval in reversed(persistence):
-        if float(interval[1][1]) != float('inf'):
-            if float(interval[1][1]) > max_death:
-                max_death = float(interval[1][1])
-        if float(interval[1][0]) > max_death:
-            max_death = float(interval[1][0])
-        if float(interval[1][0]) < min_birth:
-            min_birth = float(interval[1][0])
-    if band > 0.:
-        max_death += band
-    return (min_birth, max_death)
+try:
+    import matplotlib.pyplot as plt
+    import matplotlib.patches as mpatches
+    import numpy as np
+    import os
+
+    def __min_birth_max_death(persistence, band=0.):
+        """This function returns (min_birth, max_death) from the persistence.
+
+        :param persistence: The persistence to plot.
+        :type persistence: list of tuples(dimension, tuple(birth, death)).
+        :param band: band
+        :type band: float.
+        :returns: (float, float) -- (min_birth, max_death).
+        """
+        # Look for minimum birth date and maximum death date for plot optimisation
+        max_death = 0
+        min_birth = persistence[0][1][0]
+        for interval in reversed(persistence):
+            if float(interval[1][1]) != float('inf'):
+                if float(interval[1][1]) > max_death:
+                    max_death = float(interval[1][1])
+            if float(interval[1][0]) > max_death:
+                max_death = float(interval[1][0])
+            if float(interval[1][0]) < min_birth:
+                min_birth = float(interval[1][0])
+        if band > 0.:
+            max_death += band
+        return (min_birth, max_death)
 
-"""
-Only 13 colors for the palette
-"""
-palette = ['#ff0000', '#00ff00', '#0000ff', '#00ffff', '#ff00ff', '#ffff00',
-           '#000000', '#880000', '#008800', '#000088', '#888800', '#880088',
-           '#008888']
- 
-def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6,
-        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.
-    :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).
-    :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.
-    :type inf_delta: float.
-    :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
-
-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>`.
-
-    :param persistence: Persistence values list.
-    :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).
-    :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.
-    :type inf_delta: float.
-    :returns: A matplotlib object containing diagram plot of persistence
-        (launch `show()` method on it to display it).
+    Only 13 colors for the palette
     """
-    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')
-
-    # Draw points in loop
-    for interval in reversed(persistence):
-        if float(interval[1][1]) != float('inf'):
-            # Finite death case
-            plt.scatter(interval[1][0], interval[1][1], alpha=alpha,
-                        color = palette[interval[0]])
-        else:
-            # Infinite death case for diagram to be nicer
-            plt.scatter(interval[1][0], infinity, alpha=alpha,
-                        color = palette[interval[0]])
-        ind = ind + 1
-
-    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
+    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):
+        """This function plots the persistence bar code from persistence values list
+        or from a :doc:`persistence file <fileformats>`.
+
+        :param persistence: Persistence values list.
+        :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).
+        :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.
+        :type inf_delta: float.
+        :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
+
+    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>`.
+
+        :param persistence: Persistence values list.
+        :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).
+        :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.
+        :type inf_delta: float.
+        :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')
+
+        # Draw points in loop
+        for interval in reversed(persistence):
+            if float(interval[1][1]) != float('inf'):
+                # Finite death case
+                plt.scatter(interval[1][0], interval[1][1], alpha=alpha,
+                            color = palette[interval[0]])
+            else:
+                # Infinite death case for diagram to be nicer
+                plt.scatter(interval[1][0], infinity, alpha=alpha,
+                            color = palette[interval[0]])
+            ind = ind + 1
+
+        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:
+    # Continue in case of import error, functions won't be available
+    pass
diff --git a/src/cython/cython/rips_complex.pyx b/src/cython/cython/rips_complex.pyx
index 59c16bff..30ca4443 100644
--- a/src/cython/cython/rips_complex.pyx
+++ b/src/cython/cython/rips_complex.pyx
@@ -51,7 +51,7 @@ cdef class RipsComplex:
         """RipsComplex constructor.
 
         :param max_edge_length: Rips value.
-        :type max_edge_length: int
+        :type max_edge_length: float
 
         :param points: A list of points in d-Dimension.
         :type points: list of list of double
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..43576ec9 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
 =============
 
diff --git a/src/cython/gudhi.pyx.in b/src/cython/gudhi.pyx.in
index 20add9b6..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'
@@ -36,8 +37,6 @@ include '@CMAKE_CURRENT_SOURCE_DIR@/cython/persistence_graphical_tools.py'
 include '@CMAKE_CURRENT_SOURCE_DIR@/cython/reader_utils.pyx'
 include '@CMAKE_CURRENT_SOURCE_DIR@/cython/witness_complex.pyx'
 include '@CMAKE_CURRENT_SOURCE_DIR@/cython/strong_witness_complex.pyx'
-include '@CMAKE_CURRENT_SOURCE_DIR@/cython/kernels.pyx'
-include '@CMAKE_CURRENT_SOURCE_DIR@/cython/vectors.pyx'
 @GUDHI_CYTHON_ALPHA_COMPLEX@
 @GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX@
 @GUDHI_CYTHON_SUBSAMPLING@
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",],
 )