From 866f6ce614e9c09c97fed12c8c0c2c9fb84fad3f Mon Sep 17 00:00:00 2001
From: Gard Spreemann <gspreemann@gmail.com>
Date: Sun, 8 Oct 2017 11:15:17 +0200
Subject: GUDHI 2.0.1 as released by upstream in a tarball.

---
 cython/CMakeLists.txt                              | 376 +++++++++++----------
 cython/cython/persistence_graphical_tools.py       |  76 ++++-
 cython/cython/reader_utils.pyx                     |  95 ++++++
 cython/cython/simplex_tree.pyx                     |  81 +++--
 cython/cythonize_gudhi.py.in                       |  48 ---
 cython/doc/Makefile.in                             |  44 ---
 cython/doc/_templates/layout.html                  |   1 +
 cython/doc/alpha_complex_sum.rst                   |   4 +-
 cython/doc/alpha_complex_user.rst                  |  11 +-
 cython/doc/bottleneck_distance_sum.rst             |   2 +-
 cython/doc/bottleneck_distance_user.rst            |   4 +-
 cython/doc/citation.rst                            |   2 +-
 cython/doc/conf.py                                 |  90 +----
 cython/doc/cubical_complex_sum.rst                 |  22 +-
 cython/doc/cubical_complex_user.rst                |  20 +-
 cython/doc/examples.rst                            |  19 +-
 cython/doc/fileformats.rst                         |  33 ++
 cython/doc/generate_examples.py                    |  43 ---
 cython/doc/index.rst                               |  27 +-
 cython/doc/installation.rst                        |  23 +-
 cython/doc/make.bat.in                             |  67 ----
 cython/doc/persistence_graphical_tools_user.rst    |  31 +-
 cython/doc/persistent_cohomology_sum.rst           |   2 +-
 cython/doc/persistent_cohomology_user.rst          |   2 +-
 cython/doc/pyplots/barcode_persistence.py          |   6 +-
 cython/doc/pyplots/diagram_persistence.py          |   9 +-
 cython/doc/pyplots/show_palette_values.py          |   3 +-
 cython/doc/python3-sphinx-build                    |  11 -
 cython/doc/python3-sphinx-build.py                 |  11 +
 cython/doc/reader_utils_ref.rst                    |  11 +
 cython/doc/rips_complex_sum.rst                    |   2 +-
 cython/doc/rips_complex_user.rst                   |   8 +-
 cython/doc/simplex_tree_sum.rst                    |   2 +-
 cython/doc/tangential_complex_sum.rst              |   4 +-
 cython/doc/tangential_complex_user.rst             |  17 +-
 cython/doc/witness_complex_sum.rst                 |  26 +-
 cython/doc/witness_complex_user.rst                |   4 +-
 ...ex_diagram_persistence_from_off_file_example.py |   4 +-
 ...ex_diagram_persistence_from_off_file_example.py |   5 +-
 ...ex_diagram_persistence_from_off_file_example.py |   5 +-
 cython/example/gudhi_graphical_tools_example.py    |   9 +-
 ...ersistence_from_distance_matrix_file_example.py |  47 ++-
 ...ex_diagram_persistence_from_off_file_example.py |   4 +-
 cython/example/rips_persistence_diagram.py         |   3 +-
 cython/example/simplex_tree_example.py             |   1 -
 ...complex_plain_homology_from_off_file_example.py |   4 +-
 cython/gudhi.pyx.in                                |  20 +-
 cython/include/Reader_utils_interface.h            |  56 +++
 cython/include/Rips_complex_interface.h            |   6 +-
 cython/include/Simplex_tree_interface.h            |   8 +-
 cython/setup.py.in                                 |  49 +++
 cython/test/test_cubical_complex.py                |   4 +-
 cython/test/test_reader_utils.py                   |  88 +++++
 cython/test/test_simplex_tree.py                   |   1 -
 54 files changed, 879 insertions(+), 672 deletions(-)
 create mode 100644 cython/cython/reader_utils.pyx
 delete mode 100644 cython/cythonize_gudhi.py.in
 delete mode 100644 cython/doc/Makefile.in
 create mode 100644 cython/doc/fileformats.rst
 delete mode 100755 cython/doc/generate_examples.py
 delete mode 100644 cython/doc/make.bat.in
 delete mode 100755 cython/doc/python3-sphinx-build
 create mode 100755 cython/doc/python3-sphinx-build.py
 create mode 100644 cython/doc/reader_utils_ref.rst
 create mode 100644 cython/include/Reader_utils_interface.h
 create mode 100644 cython/setup.py.in
 create mode 100755 cython/test/test_reader_utils.py

(limited to 'cython')

diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt
index 96c2acb3..afca9d60 100644
--- a/cython/CMakeLists.txt
+++ b/cython/CMakeLists.txt
@@ -1,20 +1,65 @@
 cmake_minimum_required(VERSION 2.8)
 project(Cython)
 
+function( add_gudhi_cython_lib THE_LIB )
+  if(EXISTS ${THE_LIB})
+    get_filename_component(THE_LIB_FILE_NAME ${THE_LIB} NAME_WE)
+    if(WIN32)
+      message("++ ${THE_LIB} => THE_LIB_FILE_NAME = ${THE_LIB_FILE_NAME}")
+      set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'${THE_LIB_FILE_NAME}', " PARENT_SCOPE)
+    else(WIN32)
+      STRING(REGEX REPLACE "lib" "" UNIX_LIB_FILE_NAME ${THE_LIB_FILE_NAME})
+      message("++ ${THE_LIB} => UNIX_LIB_FILE_NAME = ${UNIX_LIB_FILE_NAME}")
+      set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'${UNIX_LIB_FILE_NAME}', " PARENT_SCOPE)
+    endif(WIN32)
+  endif(EXISTS ${THE_LIB})
+endfunction( add_gudhi_cython_lib )
+
+# THE_TEST is the python test file name (without .py extension) containing tests functions
+function( add_gudhi_py_test THE_TEST )
+  # use ${PYTHON_EXECUTABLE} -B, otherwise a __pycache__ directory is created in sources by python
+  # use py.test no cache provider, otherwise a .cache file is created in sources by py.test
+  add_test(NAME ${THE_TEST}_py_test
+           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+           COMMAND ${PYTHON_EXECUTABLE} -B -m pytest -p no:cacheprovider ${CMAKE_CURRENT_SOURCE_DIR}/test/${THE_TEST}.py)
+endfunction( add_gudhi_py_test )
+
+
 if(CYTHON_FOUND)
-  message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_EXECUTABLE} - py.test is ${PYTEST_PATH} - Sphinx is ${SPHINX_PATH}")
+  message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_EXECUTABLE} - Sphinx is ${SPHINX_PATH}")
 
   set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_RESULT_OF_USE_DECLTYPE', ")
   set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ")
-  set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ")
-  if(WIN32)
-    set( returnValue "" )
-    find_the_lib (${returnValue} ${Boost_SYSTEM_LIBRARY})
-    set(BOOST_SYSTEM_LIB_NAME ${returnValue})
-  else()
-      set(BOOST_SYSTEM_LIB_NAME "boost_system")
-      endif()
-  set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'${BOOST_SYSTEM_LIB_NAME}', ")
+  set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_SYSTEM_NO_DEPRECATED', ")
+
+  # This is because of https://github.com/CGAL/cgal/blob/master/Installation/include/CGAL/tss.h
+  # CGAL is using boost thread if thread_local is not ready (requires XCode 8 for Mac).
+  # The test in https://github.com/CGAL/cgal/blob/master/Installation/include/CGAL/config.h
+  #   #if __has_feature(cxx_thread_local) || \
+  #       ( (__GNUC__ * 100 + __GNUC_MINOR__) >= 408 && __cplusplus >= 201103L ) || \
+  #       ( _MSC_VER >= 1900 )
+  #   #define CGAL_CAN_USE_CXX11_THREAD_LOCAL
+  #   #endif
+  set(CGAL_CAN_USE_CXX11_THREAD_LOCAL "
+      int main() {
+      #ifndef __has_feature
+        #define __has_feature(x) 0  // Compatibility with non-clang compilers.
+      #endif
+      #if __has_feature(cxx_thread_local) || \
+          ( (__GNUC__ * 100 + __GNUC_MINOR__) >= 408 && __cplusplus >= 201103L ) || \
+          ( _MSC_VER >= 1900 )
+        bool has_feature_thread_local = true;
+      #else
+        // Explicit error of compilation for CMake test purpose - has_feature_thread_local is not defined
+      #endif
+        bool result = has_feature_thread_local;
+      }  ")
+  check_cxx_source_compiles("${CGAL_CAN_USE_CXX11_THREAD_LOCAL}" CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT)
+
+  if (NOT CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT)
+    add_gudhi_cython_lib(${Boost_THREAD_LIBRARY})
+    set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ")
+  endif()
 
   # Gudhi and CGAL compilation option
   if(MSVC)
@@ -25,9 +70,9 @@ if(CYTHON_FOUND)
   if(CMAKE_COMPILER_IS_GNUCXX)
     set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-frounding-math', ")
   endif(CMAKE_COMPILER_IS_GNUCXX)
-  if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
+  if (CMAKE_CXX_COMPILER_ID MATCHES Intel)
     set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-fp-model strict', ")
-  endif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
+  endif(CMAKE_CXX_COMPILER_ID MATCHES Intel)
   if (DEBUG_TRACES)
     # For programs to be more verbose
     set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DDEBUG_TRACES', ")
@@ -38,101 +83,40 @@ if(CYTHON_FOUND)
     set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ")
   endif (EIGEN3_FOUND)
 
-  # Copy recursively include, cython, example, doc and test repositories before packages finding
-  # Some tests and doc files are removed in case some packages are not found
-  file(COPY include DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
-  file(COPY cython DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
-  file(COPY example DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
-  file(COPY test DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
-  file(COPY doc DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
-  # Developper version for doc images
-  file(GLOB GUDHI_DEV_DOC_IMAGES "${CMAKE_SOURCE_DIR}/src/*/doc/*.png")
-  file(COPY ${GUDHI_DEV_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img")
-  file(GLOB GUDHI_DEV_DOC_IMAGES "${CMAKE_SOURCE_DIR}/src/*/doc/*.svg")
-  file(COPY ${GUDHI_DEV_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img")
-  # User version for doc images
-  file(GLOB GUDHI_USER_DOC_IMAGES "${CMAKE_SOURCE_DIR}/doc/*/*.png")
-  file(COPY ${GUDHI_USER_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img")
-  file(GLOB GUDHI_USER_DOC_IMAGES "${CMAKE_SOURCE_DIR}/doc/*/*.svg")
-  file(COPY ${GUDHI_USER_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img")
-  # Biblio
-  file(GLOB GUDHI_BIB_FILES "${CMAKE_SOURCE_DIR}/biblio/*.bib")
-  file(COPY ${GUDHI_BIB_FILES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
-  # Cubical complex perseus doc example
-  file(GLOB GUDHI_CUBICAL_PERSEUS_FILES "${CMAKE_SOURCE_DIR}/data/bitmap/*cubicalcomplexdoc.txt")
-  file(COPY ${GUDHI_CUBICAL_PERSEUS_FILES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
-  file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
-  file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
-  # Persistence graphical tools examples
-  file(COPY "${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
-  file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
-
   if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-    # If CGAL_VERSION >= 4.8.1, include subsampling
-    set(GUDHI_CYTHON_SUBSAMPLING "include 'cython/subsampling.pyx'")
-    set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include 'cython/tangential_complex.pyx'")
-    set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include 'cython/bottleneck_distance.pyx'")
-  else (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-    # Remove subsampling unitary tests
-    file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_subsampling.py)
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_ref.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_sum.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_user.rst")
-    # Remove tangential complex and bottleneck unitary tests
-    file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_tangential_complex.py)
-    file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_bottleneck_distance.py)
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/bottleneck_distance_ref.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/bottleneck_distance_sum.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/bottleneck_distance_user.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_ref.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_sum.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_user.rst")
+    set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/bottleneck_distance.pyx'")
   endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-  if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
-    # If CGAL_VERSION >= 4.7.0, include alpha
-    set(GUDHI_CYTHON_ALPHA_COMPLEX "include 'cython/alpha_complex.pyx'")
-  else (NOT CGAL_VERSION VERSION_LESS 4.7.0)
-    # Remove alpha complex unitary tests
-    file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_alpha_complex.py)
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/alpha_complex_ref.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/alpha_complex_sum.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/alpha_complex_user.rst")
-  endif (NOT CGAL_VERSION VERSION_LESS 4.7.0)
-  if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
-    # If CGAL_VERSION >= 4.6.0, include euclidean versions of witness complex
+  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+    set(GUDHI_CYTHON_SUBSAMPLING "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/subsampling.pyx'")
+    set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/tangential_complex.pyx'")
+  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
+    set(GUDHI_CYTHON_ALPHA_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/alpha_complex.pyx'")
+  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
+  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
     set(GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX
-        "include 'cython/euclidean_witness_complex.pyx'\ninclude 'cython/euclidean_strong_witness_complex.pyx'\n")
-  else (NOT CGAL_VERSION VERSION_LESS 4.6.0)
-    # Remove alpha complex unitary tests
-    file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_euclidean_witness_complex.py)
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/euclidean_witness_complex_ref.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/euclidean_strong_witness_complex_ref.rst")
-  endif (NOT CGAL_VERSION VERSION_LESS 4.6.0)
+        "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_witness_complex.pyx'\ninclude '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_strong_witness_complex.pyx'\n")
+  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
 
   if(CGAL_FOUND)
     # Add CGAL compilation args
     if(CGAL_HEADER_ONLY)
       set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ")
     else(CGAL_HEADER_ONLY)
-      if(WIN32)
-        set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'CGAL-vc140-mt-4.7', ")
-      else(WIN32)
-        set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'CGAL', ")
-      endif(WIN32)
+      add_gudhi_cython_lib(${CGAL_LIBRARIES})
       set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ")
+      # If CGAL is not header only, CGAL library may link with boost system,
+      add_gudhi_cython_lib(${Boost_SYSTEM_LIBRARY})
+      set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ")
     endif(CGAL_HEADER_ONLY)
     # GMP and GMPXX are not required, but if present, CGAL will link with them.
     if(GMP_FOUND)
       set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMP', ")
-      if(WIN32)
-        set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'libgmp-10', ")
-      else(WIN32)
-        set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'gmp', ")
-      endif(WIN32)
-        set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMP_LIBRARIES_DIR}', ")
+      add_gudhi_cython_lib(${GMP_LIBRARIES})
+      set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMP_LIBRARIES_DIR}', ")
       if(GMPXX_FOUND)
         set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMPXX', ")
-        set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'gmpxx', ")
+        add_gudhi_cython_lib(${GMPXX_LIBRARIES})
         set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMPXX_LIBRARIES_DIR}', ")
       endif(GMPXX_FOUND)
     endif(GMP_FOUND)
@@ -153,132 +137,178 @@ if(CYTHON_FOUND)
 
   if (TBB_FOUND)
     set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DGUDHI_USE_TBB', ")
-    set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'tbb', 'tbbmalloc', ")
+    add_gudhi_cython_lib(${TBB_RELEASE_LIBRARY})
+    add_gudhi_cython_lib(${TBB_MALLOC_RELEASE_LIBRARY})
     set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${TBB_LIBRARY_DIRS}', ")
     set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${TBB_INCLUDE_DIRS}', ")
   endif()
 
-  # set sphinx-build in make files
-  configure_file(doc/Makefile.in "${CMAKE_CURRENT_BINARY_DIR}/doc/Makefile" @ONLY)
-  configure_file(doc/make.bat.in "${CMAKE_CURRENT_BINARY_DIR}/doc/make.bat" @ONLY)
+  if(UNIX)
+    set( GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}")
+  endif(UNIX)
 
-  # Generate cythonize_gudhi.py file to cythonize Gudhi
-  configure_file(cythonize_gudhi.py.in "${CMAKE_CURRENT_BINARY_DIR}/cythonize_gudhi.py" @ONLY)
+  # Generate setup.py file to cythonize Gudhi - This file must be named setup.py by convention
+  configure_file(setup.py.in "${CMAKE_CURRENT_BINARY_DIR}/setup.py" @ONLY)
   # Generate gudhi.pyx - Gudhi cython file
   configure_file(gudhi.pyx.in "${CMAKE_CURRENT_BINARY_DIR}/gudhi.pyx" @ONLY)
 
   add_custom_command(
-      OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
+      OUTPUT gudhi.so
       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-      COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/cythonize_gudhi.py" "build_ext" "--inplace")
+      COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/setup.py" "build_ext" "--inplace")
 
-  add_custom_target(cython ALL DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
+  add_custom_target(cython ALL DEPENDS gudhi.so
                     COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/ to your PYTHONPATH before using examples or tests")
 
-  if(UNIX)
-    set( ENV{PYTHONPATH} $ENV{PYTHONPATH}:${CMAKE_CURRENT_BINARY_DIR}/ )
-  endif(UNIX)
+  # For installation purpose
+  # TODO(VR) : files matching pattern mechanism is copying all cython directory
+  install(DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}" DESTINATION "${PYTHON_SITE_PACKAGES}/" FILES_MATCHING
+      PATTERN "*.so"
+      PATTERN "*.dylib"
+      PATTERN "*.pyd")
 
   # Test examples
-  add_test(NAME alpha_complex_from_points_example_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_complex_from_points_example.py")
-  set_tests_properties(alpha_complex_from_points_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+    # Bottleneck and Alpha
+    add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
+             -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
 
-  add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
-           --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6)
-  set_tests_properties(alpha_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+    # 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 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
 
-  add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
-           -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
-  set_tests_properties(alpha_rips_persistence_bottleneck_distance_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+    add_gudhi_py_test(test_tangential_complex)
 
-  add_test(NAME bottleneck_basic_example_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/bottleneck_basic_example.py")
-  set_tests_properties(bottleneck_basic_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+    # 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_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
-           --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
-  set_tests_properties(euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+    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)
 
-  add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
-           --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
-  set_tests_properties(euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+    # Subsampling
+    add_gudhi_py_test(test_subsampling)
 
+  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+    # Bottleneck
+    add_test(NAME bottleneck_basic_example_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
+
+    add_gudhi_py_test(test_bottleneck_distance)
+  endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+
+  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
+    # Alpha
+    add_test(NAME alpha_complex_from_points_example_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
+
+    add_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)
+
+    add_gudhi_py_test(test_alpha_complex)
+
+  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
+
+  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
+    # Euclidean witness
+    add_gudhi_py_test(test_euclidean_witness_complex)
+
+  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
+
+  # Cubical
   add_test(NAME periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py"
+           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+           ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py"
            --no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt)
-  set_tests_properties(periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
   add_test(NAME random_cubical_complex_persistence_example_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/random_cubical_complex_persistence_example.py"
+           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)
-  set_tests_properties(random_cubical_complex_persistence_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
+  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 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
+           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 ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3)
-  set_tests_properties(rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
   add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py
+           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 ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off  -e 0.25 -d 3)
-  set_tests_properties(rips_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
 
   add_test(NAME rips_complex_from_points_example_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/rips_complex_from_points_example.py)
-  set_tests_properties(rips_complex_from_points_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+           ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py)
+
+  add_gudhi_py_test(test_rips_complex)
 
+  # Simplex tree
   add_test(NAME simplex_tree_example_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/simplex_tree_example.py)
-  set_tests_properties(simplex_tree_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+           ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py)
 
-  add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
-           --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
-  set_tests_properties(tangential_complex_plain_homology_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+  add_gudhi_py_test(test_simplex_tree)
 
+  # Witness
   add_test(NAME witness_complex_from_nearest_landmark_table_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/witness_complex_from_nearest_landmark_table.py)
-  set_tests_properties(witness_complex_from_nearest_landmark_table_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
-
-  # Unitary tests are available through py.test
-  if(PYTEST_PATH)
-    add_test(
-        NAME gudhi_cython_py_test
-        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-        COMMAND ${PYTHON_EXECUTABLE} "${PYTEST_PATH}")
-    set_tests_properties(gudhi_cython_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
-  endif(PYTEST_PATH)
-
-  # Documentation generation is available through sphinx
-  if(SPHINX_PATH)
-    if (UNIX)
-      add_custom_target(sphinx
-          WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc
-          DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
-          COMMAND make html doctest)
-    else (UNIX)
-      add_custom_target(sphinx
-          WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc
-          COMMAND make.bat html doctest)
-    endif (UNIX)
-  endif(SPHINX_PATH)
+           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+           ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py)
+
+  add_gudhi_py_test(test_witness_complex)
+
+  # Reader utils
+  add_gudhi_py_test(test_reader_utils)
+
+  # Documentation generation is available through sphinx - requires all modules
+  if(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+    set (GUDHI_SPHINX_MESSAGE "Generating API documentation with Sphinx in ${CMAKE_CURRENT_BINARY_DIR}/sphinx/")
+    # User warning - Sphinx is a static pages generator, and configured to work fine with user_version
+    # Images and biblio warnings because not found on developper version
+    if (GUDHI_CYTHON_PATH STREQUAL "src/cython")
+      set (GUDHI_SPHINX_MESSAGE "${GUDHI_SPHINX_MESSAGE} \n WARNING : Sphinx is configured for user version, you run it on developper version. Images and biblio will miss")
+    endif()
+    # sphinx target requires gudhi.so, because conf.py reads gudhi version from it
+    add_custom_target(sphinx
+        WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc
+        COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+        ${SPHINX_PATH} -b html ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/sphinx
+        DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
+        COMMENT "${GUDHI_SPHINX_MESSAGE}" VERBATIM)
+
+    add_test(NAME sphinx_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/doctest)
+
+  endif(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
 endif(CYTHON_FOUND)
diff --git a/cython/cython/persistence_graphical_tools.py b/cython/cython/persistence_graphical_tools.py
index a984633e..fb837e29 100755
--- a/cython/cython/persistence_graphical_tools.py
+++ b/cython/cython/persistence_graphical_tools.py
@@ -1,11 +1,12 @@
 import matplotlib.pyplot as plt
 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.
 
-   Author(s):       Vincent Rouvreau
+   Author(s):       Vincent Rouvreau, Bertrand Michel
 
    Copyright (C) 2016 INRIA
 
@@ -23,15 +24,17 @@ import numpy as np
    along with this program.  If not, see <http://www.gnu.org/licenses/>.
 """
 
-__author__ = "Vincent Rouvreau"
+__author__ = "Vincent Rouvreau, Bertrand Michel"
 __copyright__ = "Copyright (C) 2016 INRIA"
 __license__ = "GPL v3"
 
-def __min_birth_max_death(persistence):
+def __min_birth_max_death(persistence, band_boot=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_boot: bootstrap band
+    :type band_boot: float.
     :returns: (float, float) -- (min_birth, max_death).
     """
     # Look for minimum birth date and maximum death date for plot optimisation
@@ -45,6 +48,8 @@ def __min_birth_max_death(persistence):
             max_death = float(interval[1][0])
         if float(interval[1][0]) < min_birth:
             min_birth = float(interval[1][0])
+    if band_boot > 0.:
+        max_death += band_boot
     return (min_birth, max_death)
 
 """
@@ -59,7 +64,7 @@ def show_palette_values(alpha=0.6):
 
     :param alpha: alpha value in [0.0, 1.0] for horizontal bars (default is 0.6).
     :type alpha: float.
-    :returns: plot -- An horizontal bar plot of dimensions color.
+    :returns: plot the dimension palette values.
     """
     colors = []
     for color in palette:
@@ -70,18 +75,38 @@ def show_palette_values(alpha=0.6):
     plt.barh(y_pos, y_pos + 1, align='center', alpha=alpha, color=colors)
     plt.ylabel('Dimension')
     plt.title('Dimension palette values')
+    return plt
 
-    plt.show()
-
-def plot_persistence_barcode(persistence, alpha=0.6):
+def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, max_barcodes=0):
     """This function plots the persistence bar code.
 
     :param persistence: The persistence to plot.
     :type persistence: list of tuples(dimension, tuple(birth, death)).
+    :param persistence_file: A persistence file style name (reset persistence if both are set).
+    :type persistence_file: string
     :param alpha: alpha value in [0.0, 1.0] for horizontal bars (default is 0.6).
     :type alpha: float.
+    :param max_barcodes: number of maximal barcodes to be displayed
+        (persistence will be sorted by life time if max_barcodes is set)
+    :type max_barcodes: int.
     :returns: plot -- An horizontal bar plot of persistence.
     """
+    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]
+
     (min_birth, max_death) = __min_birth_max_death(persistence)
     ind = 0
     delta = ((max_death - min_birth) / 10.0)
@@ -106,18 +131,40 @@ def plot_persistence_barcode(persistence, alpha=0.6):
     plt.title('Persistence barcode')
     # Ends plot on infinity value and starts a little bit before min_birth
     plt.axis([axis_start, infinity, 0, ind])
-    plt.show()
+    return plt
 
-def plot_persistence_diagram(persistence, alpha=0.6):
-    """This function plots the persistence diagram.
+def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, band_boot=0., max_plots=0):
+    """This function plots the persistence diagram with an optional confidence band.
 
     :param persistence: The persistence to plot.
     :type persistence: list of tuples(dimension, tuple(birth, death)).
+    :param persistence_file: A persistence file style name (reset persistence if both are set).
+    :type persistence_file: string
     :param alpha: alpha value in [0.0, 1.0] for points and horizontal infinity line (default is 0.6).
     :type alpha: float.
-    :returns: plot -- An diagram plot of persistence.
+    :param band_boot: bootstrap band (not displayed if :math:`\leq` 0.)
+    :type band_boot: float.
+    :param max_plots: number of maximal plots to be displayed
+    :type max_plots: int.
+    :returns: plot -- A diagram plot of persistence.
     """
-    (min_birth, max_death) = __min_birth_max_death(persistence)
+    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_boot)
     ind = 0
     delta = ((max_death - min_birth) / 10.0)
     # Replace infinity values with max_death + delta for diagram to be more
@@ -131,6 +178,9 @@ def plot_persistence_diagram(persistence, alpha=0.6):
     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_boot > 0.:
+        plt.fill_between(x, x, x+band_boot, alpha=alpha, facecolor='red')
 
     # Draw points in loop
     for interval in reversed(persistence):
@@ -149,4 +199,4 @@ def plot_persistence_diagram(persistence, alpha=0.6):
     plt.ylabel('Death')
     # Ends plot on infinity value and starts a little bit before min_birth
     plt.axis([axis_start, infinity, axis_start, infinity + delta])
-    plt.show()
+    return plt
diff --git a/cython/cython/reader_utils.pyx b/cython/cython/reader_utils.pyx
new file mode 100644
index 00000000..3a17c5a0
--- /dev/null
+++ b/cython/cython/reader_utils.pyx
@@ -0,0 +1,95 @@
+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.string cimport string
+from libcpp.map cimport map
+from libcpp.pair cimport pair
+import os
+
+"""This file is part of the Gudhi Library. The Gudhi library
+   (Geometric Understanding in Higher Dimensions) is a generic C++
+   library for computational topology.
+
+   Author(s):       Vincent Rouvreau
+
+   Copyright (C) 2017 INRIA
+
+   This program is free software: you can redistribute it and/or modify
+   it under the terms of the GNU General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   This program is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU General Public License for more details.
+
+   You should have received a copy of the GNU General Public License
+   along with this program.  If not, see <http://www.gnu.org/licenses/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2017 INRIA"
+__license__ = "GPL v3"
+
+cdef extern from "Reader_utils_interface.h" namespace "Gudhi":
+    vector[vector[double]] read_matrix_from_csv_file(string off_file, char separator)
+    map[int, vector[pair[double, double]]] read_pers_intervals_grouped_by_dimension(string filename)
+    vector[pair[double, double]] read_pers_intervals_in_dimension(string filename, int only_this_dim)
+
+def read_lower_triangular_matrix_from_csv_file(csv_file='', separator=';'):
+    """Read lower triangular matrix from a CSV style file.
+
+    :param csv_file: A CSV file style name.
+    :type csv_file: string
+    :param separator: The value separator in the CSV file. Default value is ';'
+    :type separator: char
+
+    :returns:  The lower triangular matrix.
+    :rtype: vector[vector[double]]
+    """
+    if csv_file is not '':
+        if os.path.isfile(csv_file):
+            return read_matrix_from_csv_file(str.encode(csv_file), ord(separator[0]))
+    print("file " + csv_file + " not set or not found.")
+    return []
+
+def read_persistence_intervals_grouped_by_dimension(persistence_file=''):
+    """Reads a file containing persistence intervals.
+    Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
+    The return value is an `map[dim, vector[pair[birth, death]]]`
+    where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
+    Note: the function does not check that birth <= death.
+
+    :param persistence_file: A persistence file style name.
+    :type persistence_file: string
+
+    :returns:  The persistence pairs grouped by dimension.
+    :rtype: map[int, vector[pair[double, double]]]
+    """
+    if persistence_file is not '':
+        if os.path.isfile(persistence_file):
+            return read_pers_intervals_grouped_by_dimension(str.encode(persistence_file))
+    print("file " + persistence_file + " not set or not found.")
+    return []
+
+def read_persistence_intervals_in_dimension(persistence_file='', only_this_dim=-1):
+    """Reads a file containing persistence intervals.
+    Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
+    If `only_this_dim` = -1, dimension is ignored and all lines are returned.
+    If `only_this_dim` is >= 0, only the lines where dimension = `only_this_dim`
+    (or where dimension is not specified) are returned.
+    The return value is an `vector[pair[birth, death]]`
+    where `birth` a `double`, and `death` a `double`.
+    Note: the function does not check that birth <= death.
+
+    :param persistence_file: A persistence file style name.
+    :type persistence_file: string
+
+    :returns:  The persistence pairs grouped by dimension.
+    :rtype: map[int, vector[pair[double, double]]]
+    """
+    if persistence_file is not '':
+        if os.path.isfile(persistence_file):
+            return read_pers_intervals_in_dimension(str.encode(persistence_file), only_this_dim)
+    print("file " + persistence_file + " not set or not found.")
+    return []
diff --git a/cython/cython/simplex_tree.pyx b/cython/cython/simplex_tree.pyx
index 9d40a8b5..45487158 100644
--- a/cython/cython/simplex_tree.pyx
+++ b/cython/cython/simplex_tree.pyx
@@ -2,6 +2,7 @@ from cython cimport numeric
 from libcpp.vector cimport vector
 from libcpp.utility cimport pair
 from libcpp cimport bool
+from libcpp.string cimport string
 
 """This file is part of the Gudhi Library. The Gudhi library
    (Geometric Understanding in Higher Dimensions) is a generic C++
@@ -35,9 +36,7 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi":
 
     cdef cppclass Simplex_tree_interface_full_featured "Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_full_featured>":
         Simplex_tree()
-        double filtration()
         double simplex_filtration(vector[int] simplex)
-        void set_filtration(double filtration)
         void initialize_filtration()
         int num_vertices()
         int num_simplices()
@@ -61,6 +60,7 @@ cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi":
         vector[int] betti_numbers()
         vector[int] persistent_betti_numbers(double from_value, double to_value)
         vector[pair[double,double]] intervals_in_dimension(int dimension)
+        void write_output_diagram(string diagram_file_name)
 
 # SimplexTree python interface
 cdef class SimplexTree:
@@ -113,14 +113,6 @@ cdef class SimplexTree:
         """
         return self.thisptr.simplex_filtration(simplex)
 
-    def set_filtration(self, filtration):
-        """This function sets the main simplicial complex filtration value.
-
-        :param filtration: The filtration value.
-        :type filtration: float.
-        """
-        self.thisptr.set_filtration(<double> filtration)
-
     def initialize_filtration(self):
         """This function initializes and sorts the simplicial complex
         filtration vector.
@@ -183,10 +175,10 @@ cdef class SimplexTree:
         :returns:  true if the simplex was found, false otherwise.
         :rtype:  bool
         """
-        cdef vector[int] complex
+        cdef vector[int] csimplex
         for i in simplex:
-            complex.push_back(i)
-        return self.thisptr.find_simplex(complex)
+            csimplex.push_back(i)
+        return self.thisptr.find_simplex(csimplex)
 
     def insert(self, simplex, filtration=0.0):
         """This function inserts the given N-simplex and its subfaces with the
@@ -200,10 +192,10 @@ cdef class SimplexTree:
         :returns:  true if the simplex was found, false otherwise.
         :rtype:  bool
         """
-        cdef vector[int] complex
+        cdef vector[int] csimplex
         for i in simplex:
-            complex.push_back(i)
-        return self.thisptr.insert_simplex_and_subfaces(complex,
+            csimplex.push_back(i)
+        return self.thisptr.insert_simplex_and_subfaces(csimplex,
                                                         <double>filtration)
 
     def get_filtration(self):
@@ -232,35 +224,35 @@ cdef class SimplexTree:
         :returns:  The (simplices of the) skeleton of a maximum dimension.
         :rtype:  list of tuples(simplex, filtration)
         """
-        cdef vector[pair[vector[int], double]] skeletons \
+        cdef vector[pair[vector[int], double]] skeleton \
             = self.thisptr.get_skeleton(<int>dimension)
         ct = []
-        for filtered_complex in skeletons:
+        for filtered_simplex in skeleton:
             v = []
-            for vertex in filtered_complex.first:
+            for vertex in filtered_simplex.first:
                 v.append(vertex)
-            ct.append((v, filtered_complex.second))
+            ct.append((v, filtered_simplex.second))
         return ct
 
     def get_star(self, simplex):
-        """This function returns the stars of a given N-simplex.
+        """This function returns the star of a given N-simplex.
 
         :param simplex: The N-simplex, represented by a list of vertex.
         :type simplex: list of int.
         :returns:  The (simplices of the) star of a simplex.
         :rtype:  list of tuples(simplex, filtration)
         """
-        cdef vector[int] complex
+        cdef vector[int] csimplex
         for i in simplex:
-            complex.push_back(i)
-        cdef vector[pair[vector[int], double]] stars \
-            = self.thisptr.get_star(complex)
+            csimplex.push_back(i)
+        cdef vector[pair[vector[int], double]] star \
+            = self.thisptr.get_star(csimplex)
         ct = []
-        for filtered_complex in stars:
+        for filtered_simplex in star:
             v = []
-            for vertex in filtered_complex.first:
+            for vertex in filtered_simplex.first:
                 v.append(vertex)
-            ct.append((v, filtered_complex.second))
+            ct.append((v, filtered_simplex.second))
         return ct
 
     def get_cofaces(self, simplex, codimension):
@@ -275,17 +267,17 @@ cdef class SimplexTree:
         :returns:  The (simplices of the) cofaces of a simplex
         :rtype:  list of tuples(simplex, filtration)
         """
-        cdef vector[int] complex
+        cdef vector[int] csimplex
         for i in simplex:
-            complex.push_back(i)
+            csimplex.push_back(i)
         cdef vector[pair[vector[int], double]] cofaces \
-            = self.thisptr.get_cofaces(complex, <int>codimension)
+            = self.thisptr.get_cofaces(csimplex, <int>codimension)
         ct = []
-        for filtered_complex in cofaces:
+        for filtered_simplex in cofaces:
             v = []
-            for vertex in filtered_complex.first:
+            for vertex in filtered_simplex.first:
                 v.append(vertex)
-            ct.append((v, filtered_complex.second))
+            ct.append((v, filtered_simplex.second))
         return ct
 
     def remove_maximal_simplex(self, simplex):
@@ -385,7 +377,7 @@ cdef class SimplexTree:
         complex in a specific dimension.
 
         :param dimension: The specific dimension.
-        :type from_value: int.
+        :type dimension: int.
         :returns: The persistence intervals.
         :rtype:  list of pair of float
 
@@ -399,3 +391,22 @@ cdef class SimplexTree:
             print("intervals_in_dim function requires persistence function"
                   " to be launched first.")
         return intervals_result
+
+    def write_persistence_diagram(self, persistence_file=''):
+        """This function writes the persistence intervals of the simplicial
+        complex in a user given file name.
+
+        :param persistence_file: The specific dimension.
+        :type persistence_file: string.
+
+        :note: intervals_in_dim function requires persistence function to be
+            launched first.
+        """
+        if self.pcohptr != NULL:
+            if persistence_file != '':
+                self.pcohptr.write_output_diagram(str.encode(persistence_file))
+            else:
+                print("persistence_file must be specified")
+        else:
+            print("intervals_in_dim function requires persistence function"
+                  " to be launched first.")
diff --git a/cython/cythonize_gudhi.py.in b/cython/cythonize_gudhi.py.in
deleted file mode 100644
index 5a97e9f3..00000000
--- a/cython/cythonize_gudhi.py.in
+++ /dev/null
@@ -1,48 +0,0 @@
-from distutils.core import setup, Extension
-from Cython.Build import cythonize
-
-"""This file is part of the Gudhi Library. The Gudhi library
-   (Geometric Understanding in Higher Dimensions) is a generic C++
-   library for computational topology.
-
-   Author(s):       Vincent Rouvreau
-
-   Copyright (C) 2016  INRIA
-
-   This program is free software: you can redistribute it and/or modify
-   it under the terms of the GNU General Public License as published by
-   the Free Software Foundation, either version 3 of the License, or
-   (at your option) any later version.
-
-   This program is distributed in the hope that it will be useful,
-   but WITHOUT ANY WARRANTY; without even the implied warranty of
-   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-   GNU General Public License for more details.
-
-   You should have received a copy of the GNU General Public License
-   along with this program.  If not, see <http://www.gnu.org/licenses/>.
-"""
-
-__author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016  INRIA"
-__license__ = "GPL v3"
-
-gudhi = Extension(
-    "gudhi",
-    sources = ['gudhi.pyx',],
-    language = 'c++',
-    extra_compile_args=[@GUDHI_CYTHON_EXTRA_COMPILE_ARGS@],
-    extra_link_args=[@GUDHI_CYTHON_EXTRA_LINK_ARGS@],
-    libraries=[@GUDHI_CYTHON_LIBRARIES@],
-    library_dirs=[@GUDHI_CYTHON_LIBRARY_DIRS@],
-    include_dirs = [@GUDHI_CYTHON_INCLUDE_DIRS@],
-)
-
-setup(
-    name = 'gudhi',
-    author='Vincent Rouvreau',
-    author_email='gudhi-contact@lists.gforge.inria.fr',
-    version='0.1.0',
-    url='http://gudhi.gforge.inria.fr/',
-    ext_modules = cythonize(gudhi),
-)
diff --git a/cython/doc/Makefile.in b/cython/doc/Makefile.in
deleted file mode 100644
index 526350b3..00000000
--- a/cython/doc/Makefile.in
+++ /dev/null
@@ -1,44 +0,0 @@
-# Makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line.
-SPHINXOPTS    =
-SPHINXBUILD   = @SPHINX_PATH@
-PAPER         =
-BUILDDIR      = _build
-
-# User-friendly check for sphinx-build
-ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
-$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
-endif
-
-# Internal variables.
-PAPEROPT_a4     = -D latex_paper_size=a4
-PAPEROPT_letter = -D latex_paper_size=letter
-ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
-# the i18n builder cannot share the environment and doctrees with the others
-I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
-
-.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
-
-help:
-	@echo "Please use \`make <target>' where <target> is one of"
-	@echo "  html       to make standalone HTML files"
-	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
-
-clean:
-	rm -f examples.inc
-	rm -rf $(BUILDDIR)/*
-
-# GUDHI specific : Examples.inc is generated with generate_examples.py (and deleted on clean)
-
-html:
-	./generate_examples.py
-	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
-	@echo
-	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
-
-doctest:
-	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
-	@echo "Testing of doctests in the sources finished, look at the " \
-	      "results in $(BUILDDIR)/doctest/output.txt."
diff --git a/cython/doc/_templates/layout.html b/cython/doc/_templates/layout.html
index b11c1236..243f33c6 100644
--- a/cython/doc/_templates/layout.html
+++ b/cython/doc/_templates/layout.html
@@ -65,6 +65,7 @@
             {#- old style sidebars: using blocks -- should be deprecated #}
             {%- block sidebartoc %}
 <h2><a href="index.html">GUDHI</a></h2>
+<h2><a href="fileformats.html">File formats</a></h2>
 <h2><a href="installation.html">GUDHI installation</a></h2>
 <h2><a href="citation.html">Acknowledging the GUDHI library</a></h2>
 <h2><a href="genindex.html">Index</a></h2>
diff --git a/cython/doc/alpha_complex_sum.rst b/cython/doc/alpha_complex_sum.rst
index 8437e901..1680a712 100644
--- a/cython/doc/alpha_complex_sum.rst
+++ b/cython/doc/alpha_complex_sum.rst
@@ -5,7 +5,7 @@
 
 +----------------------------------------------------------------+------------------------------------------------------------------------+
 | .. figure::                                                    | Alpha_complex is a simplicial complex constructed from the finite      |
-|      img/alpha_complex_representation.png                      | cells of a Delaunay Triangulation.                                     |
+|      ../../doc/Alpha_complex/alpha_complex_representation.png  | cells of a Delaunay Triangulation.                                     |
 |      :alt: Alpha complex representation                        |                                                                        |
 |      :figclass: align-center                                   | The filtration value of each simplex is computed as the square of the  |
 |                                                                | circumradius of the simplex if the circumsphere is empty (the simplex  |
@@ -16,7 +16,7 @@
 |                                                                | complex.                                                               |
 |                                                                |                                                                        |
 |                                                                | This package requires having CGAL version 4.7 or higher (4.8.1 is      |
-|                                                                | advised for better perfomances).                                       |
+|                                                                | advised for better performance).                                       |
 +----------------------------------------------------------------+------------------------------------------------------------------------+
 | :doc:`alpha_complex_user`                                      | :doc:`alpha_complex_ref`                                               |
 +----------------------------------------------------------------+------------------------------------------------------------------------+
diff --git a/cython/doc/alpha_complex_user.rst b/cython/doc/alpha_complex_user.rst
index e8268ef1..db7edd6f 100644
--- a/cython/doc/alpha_complex_user.rst
+++ b/cython/doc/alpha_complex_user.rst
@@ -75,7 +75,7 @@ In order to build the alpha complex, first, a Simplex tree is built from the cel
 (The filtration value is set to NaN, which stands for unknown value):
 
 .. figure::
-    img/alpha_complex_doc.png
+    ../../doc/Alpha_complex/alpha_complex_doc.png
     :figclass: align-center
     :alt: Simplex tree structure construction example
 
@@ -112,7 +112,7 @@ computes the filtration value of the triangle, and then propagates the filtratio
 here:
 
 .. figure::
-    img/alpha_complex_doc_420.png
+    ../../doc/Alpha_complex/alpha_complex_doc_420.png
     :figclass: align-center
     :alt: Filtration value propagation example
 
@@ -142,7 +142,7 @@ Prune above given filtration value
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The simplex tree is pruned from the given maximum alpha squared value (cf. `Simplex_tree::prune_above_filtration()`
-int he `C++ version <http://gudhi.gforge.inria.fr/doc/latest/index.html>`_).
+in the `C++ version <http://gudhi.gforge.inria.fr/doc/latest/index.html>`_).
 In the following example, the value is given by the user as argument of the program.
 
 
@@ -158,7 +158,8 @@ Then, it is asked to display information about the alpha complex:
 .. testcode::
 
     import gudhi
-    alpha_complex = gudhi.AlphaComplex(off_file='alphacomplexdoc.off')
+    alpha_complex = gudhi.AlphaComplex(off_file=gudhi.__root_source_dir__ + \
+        '/data/points/alphacomplexdoc.off')
     simplex_tree = alpha_complex.create_simplex_tree(max_alpha_square=59.0)
     result_str = 'Alpha complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \
         repr(simplex_tree.num_simplices()) + ' simplices - ' + \
@@ -200,6 +201,6 @@ the program output is:
 CGAL citations
 ==============
 
-.. bibliography:: how_to_cite_cgal.bib
+.. bibliography:: ../../biblio/how_to_cite_cgal.bib
    :filter: docnames
    :style: unsrt
diff --git a/cython/doc/bottleneck_distance_sum.rst b/cython/doc/bottleneck_distance_sum.rst
index 5c475d0d..030fad9e 100644
--- a/cython/doc/bottleneck_distance_sum.rst
+++ b/cython/doc/bottleneck_distance_sum.rst
@@ -5,7 +5,7 @@
 
 +-----------------------------------------------------------------+----------------------------------------------------------------------+
 | .. figure::                                                     | Bottleneck distance measures the similarity between two persistence  |
-|      img/perturb_pd.png                                         | diagrams. It's the shortest distance b for which there exists a      |
+|      ../../doc/Bottleneck_distance/perturb_pd.png               | diagrams. It's the shortest distance b for which there exists a      |
 |      :figclass: align-center                                    | perfect matching between the points of the two diagrams (+ all the   |
 |                                                                 | diagonal points) such that any couple of matched points are at       |
 |      Bottleneck distance is the length of                       | distance at most b.                                                  |
diff --git a/cython/doc/bottleneck_distance_user.rst b/cython/doc/bottleneck_distance_user.rst
index 0066992f..7692dce2 100644
--- a/cython/doc/bottleneck_distance_user.rst
+++ b/cython/doc/bottleneck_distance_user.rst
@@ -25,7 +25,7 @@ This example computes the bottleneck distance from 2 persistence diagrams:
     message = "Bottleneck distance approximation=" + '%.2f' % gudhi.bottleneck_distance(diag1, diag2, 0.1)
     print(message)
 
-    message = "Bottleneck distance exact value=" + '%.2f' % gudhi.bottleneck_distance(diag1, diag2, 0)
+    message = "Bottleneck distance value=" + '%.2f' % gudhi.bottleneck_distance(diag1, diag2)
     print(message)
 
 The output is:
@@ -33,4 +33,4 @@ The output is:
 .. testoutput::
 
     Bottleneck distance approximation=0.81
-    Bottleneck distance exact value=0.75
+    Bottleneck distance value=0.75
diff --git a/cython/doc/citation.rst b/cython/doc/citation.rst
index 6cdfb7cc..f4fdf83b 100644
--- a/cython/doc/citation.rst
+++ b/cython/doc/citation.rst
@@ -12,4 +12,4 @@ Manual, as well as for publications directly related to the GUDHI library.
 GUDHI bibtex
 ************
 
-.. literalinclude:: how_to_cite_gudhi.bib
+.. literalinclude:: ../../biblio/how_to_cite_gudhi.bib
diff --git a/cython/doc/conf.py b/cython/doc/conf.py
index 42bfd59c..19a880d4 100755
--- a/cython/doc/conf.py
+++ b/cython/doc/conf.py
@@ -21,7 +21,7 @@ import os
 #sys.path.insert(0, os.path.abspath('.'))
 
 # Path to Gudhi.so from source path
-sys.path.insert(0, os.path.abspath('..'))
+sys.path.insert(0, os.path.abspath('.'))
 
 # -- General configuration ------------------------------------------------
 
@@ -58,18 +58,20 @@ source_suffix = '.rst'
 # The master toctree document.
 master_doc = 'index'
 
+import gudhi
+
 # General information about the project.
-project = u'GUDHI'
-copyright = u'2016, GUDHI Editorial Board'
+project = gudhi.__name__
+copyright = gudhi.__copyright__
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = '2.0'
+version = gudhi.__version__
 # The full version, including alpha/beta/rc tags.
-release = '2.0.0'
+#release = '2.0.1-rc1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -198,81 +200,3 @@ html_static_path = ['_static']
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'GUDHIdoc'
 
-
-# -- Options for LaTeX output ---------------------------------------------
-
-latex_elements = {
-# The paper size ('letterpaper' or 'a4paper').
-#'papersize': 'letterpaper',
-
-# The font size ('10pt', '11pt' or '12pt').
-#'pointsize': '10pt',
-
-# Additional stuff for the LaTeX preamble.
-#'preamble': '',
-}
-
-# Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title,
-#  author, documentclass [howto, manual, or own class]).
-latex_documents = [
-  ('index', 'GUDHI.tex', u'GUDHI Documentation',
-   u'Vincent Rouvreau', 'manual'),
-]
-
-# The name of an image file (relative to this directory) to place at the top of
-# the title page.
-#latex_logo = None
-
-# For "manual" documents, if this is true, then toplevel headings are parts,
-# not chapters.
-#latex_use_parts = False
-
-# If true, show page references after internal links.
-#latex_show_pagerefs = False
-
-# If true, show URL addresses after external links.
-#latex_show_urls = False
-
-# Documents to append as an appendix to all manuals.
-#latex_appendices = []
-
-# If false, no module index is generated.
-#latex_domain_indices = True
-
-
-# -- Options for manual page output ---------------------------------------
-
-# One entry per manual page. List of tuples
-# (source start file, name, description, authors, manual section).
-man_pages = [
-    ('index', 'gudhi', u'GUDHI Documentation',
-     [u'Vincent Rouvreau'], 1)
-]
-
-# If true, show URL addresses after external links.
-#man_show_urls = False
-
-
-# -- Options for Texinfo output -------------------------------------------
-
-# Grouping the document tree into Texinfo files. List of tuples
-# (source start file, target name, title, author,
-#  dir menu entry, description, category)
-texinfo_documents = [
-  ('index', 'GUDHI', u'GUDHI Documentation',
-   u'Vincent Rouvreau', 'GUDHI', 'One line description of project.',
-   'Miscellaneous'),
-]
-
-# Documents to append as an appendix to all manuals.
-#texinfo_appendices = []
-
-# If false, no module index is generated.
-#texinfo_domain_indices = True
-
-# How to display URL addresses: 'footnote', 'no', or 'inline'.
-#texinfo_show_urls = 'footnote'
-
-# If true, do not generate a @detailmenu in the "Top" node's menu.
-#texinfo_no_detailmenu = False
diff --git a/cython/doc/cubical_complex_sum.rst b/cython/doc/cubical_complex_sum.rst
index 3ddf6375..280ad0e0 100644
--- a/cython/doc/cubical_complex_sum.rst
+++ b/cython/doc/cubical_complex_sum.rst
@@ -2,14 +2,14 @@
 :Author: Pawel Dlotko                                              :Introduced in: GUDHI 2.0.0          :Copyright: GPL v3
 =================================================================  ===================================  ===================================
 
-+-----------------------------------------------------------------+----------------------------------------------------------------------+
-| .. figure::                                                     | The cubical complex is an example of a structured complex useful in  |
-|      img/Cubical_complex_representation.png                     | computational mathematics (specially rigorous numerics) and image    |
-|      :alt: Cubical complex representation                       | analysis.                                                            |
-|      :figclass: align-center                                    |                                                                      |
-|                                                                 |                                                                      |
-|      Cubical complex representation                             |                                                                      |
-+-----------------------------------------------------------------+----------------------------------------------------------------------+
-| :doc:`cubical_complex_user`                                     | * :doc:`cubical_complex_ref`                                         |
-|                                                                 | * :doc:`periodic_cubical_complex_ref`                                |
-+-----------------------------------------------------------------+----------------------------------------------------------------------+
++--------------------------------------------------------------------------+----------------------------------------------------------------------+
+| .. figure::                                                              | The cubical complex is an example of a structured complex useful in  |
+|      ../../doc/Bitmap_cubical_complex/Cubical_complex_representation.png | computational mathematics (specially rigorous numerics) and image    |
+|      :alt: Cubical complex representation                                | analysis.                                                            |
+|      :figclass: align-center                                             |                                                                      |
+|                                                                          |                                                                      |
+|      Cubical complex representation                                      |                                                                      |
++--------------------------------------------------------------------------+----------------------------------------------------------------------+
+| :doc:`cubical_complex_user`                                              | * :doc:`cubical_complex_ref`                                         |
+|                                                                          | * :doc:`periodic_cubical_complex_ref`                                |
++--------------------------------------------------------------------------+----------------------------------------------------------------------+
diff --git a/cython/doc/cubical_complex_user.rst b/cython/doc/cubical_complex_user.rst
index 344b9554..2bfac62a 100644
--- a/cython/doc/cubical_complex_user.rst
+++ b/cython/doc/cubical_complex_user.rst
@@ -59,7 +59,7 @@ directions, allows to determine, dimension, neighborhood, boundary and coboundar
 :math:`C \in \mathcal{K}`.
 
 .. figure::
-    img/Cubical_complex_representation.png
+    ../../doc/Bitmap_cubical_complex/Cubical_complex_representation.png
     :alt: Cubical complex.
     :figclass: align-center
 
@@ -87,7 +87,7 @@ in the example below). Next, in lexicographical order, the filtration of top dim
 20 4 7 6 5 in the example below).
 
 .. figure::
-    img/exampleBitmap.png
+    ../../doc/Bitmap_cubical_complex/exampleBitmap.png
     :alt: Example of a input data.
     :figclass: align-center
 
@@ -95,14 +95,15 @@ in the example below). Next, in lexicographical order, the filtration of top dim
 
 The input file for the following complex is:
 
-.. literalinclude:: cubicalcomplexdoc.txt
+.. literalinclude:: ../../data/bitmap/cubicalcomplexdoc.txt
 
-.. centered:: cubicalcomplexdoc.txt
+.. centered:: ../../data/bitmap/cubicalcomplexdoc.txt
 
 .. testcode::
 
     import gudhi
-    cubical_complex = gudhi.CubicalComplex(perseus_file='cubicalcomplexdoc.txt')
+    cubical_complex = gudhi.CubicalComplex(perseus_file=gudhi.__root_source_dir__ + \
+        '/data/bitmap/cubicalcomplexdoc.txt')
     result_str = 'Cubical complex is of dimension ' + repr(cubical_complex.dimension()) + ' - ' + \
         repr(cubical_complex.num_simplices()) + ' simplices.'
     print(result_str)
@@ -127,16 +128,17 @@ complex with periodic boundary conditions. One can also use Perseus style input
 conditions in a given direction, then number of top dimensional cells in this direction have to be multiplied by -1.
 For instance:
 
-.. literalinclude:: periodiccubicalcomplexdoc.txt
+.. literalinclude:: ../../data/bitmap/periodiccubicalcomplexdoc.txt
 
-.. centered:: periodiccubicalcomplexdoc.txt
+.. centered:: ../../data/bitmap/periodiccubicalcomplexdoc.txt
 
 Indicate that we have imposed periodic boundary conditions in the direction x, but not in the direction y.
 
 .. testcode::
 
     import gudhi
-    periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='periodiccubicalcomplexdoc.txt')
+    periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \
+        '/data/bitmap/periodiccubicalcomplexdoc.txt')
     result_str = 'Periodic cubical complex is of dimension ' + repr(periodic_cc.dimension()) + ' - ' + \
         repr(periodic_cc.num_simplices()) + ' simplices.'
     print(result_str)
@@ -155,6 +157,6 @@ End user programs are available in cython/example/ folder.
 Bibliography
 ============
 
-.. bibliography:: bibliography.bib
+.. bibliography:: ../../bibliography.bib
    :filter: docnames
    :style: unsrt
diff --git a/cython/doc/examples.rst b/cython/doc/examples.rst
index a89e0596..1e596e18 100644
--- a/cython/doc/examples.rst
+++ b/cython/doc/examples.rst
@@ -1,4 +1,21 @@
 Examples
 ########
 
-.. include:: examples.inc
+.. only:: builder_html
+
+    * :download:`rips_complex_from_points_example.py <../example/rips_complex_from_points_example.py>`
+    * :download:`alpha_complex_from_points_example.py <../example/alpha_complex_from_points_example.py>`
+    * :download:`simplex_tree_example.py <../example/simplex_tree_example.py>`
+    * :download:`alpha_rips_persistence_bottleneck_distance.py <../example/alpha_rips_persistence_bottleneck_distance.py>`
+    * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>`
+    * :download:`alpha_complex_diagram_persistence_from_off_file_example.py <../example/alpha_complex_diagram_persistence_from_off_file_example.py>`
+    * :download:`periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py <../example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py>`
+    * :download:`bottleneck_basic_example.py <../example/bottleneck_basic_example.py>`
+    * :download:`gudhi_graphical_tools_example.py <../example/gudhi_graphical_tools_example.py>`
+    * :download:`witness_complex_from_nearest_landmark_table.py <../example/witness_complex_from_nearest_landmark_table.py>`
+    * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>`
+    * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>`
+    * :download:`rips_complex_diagram_persistence_from_off_file_example.py <../example/rips_complex_diagram_persistence_from_off_file_example.py>`
+    * :download:`rips_complex_diagram_persistence_from_distance_matrix_file_example.py <../example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py>`
+    * :download:`rips_persistence_diagram.py <../example/rips_persistence_diagram.py>`
+    * :download:`random_cubical_complex_persistence_example.py <../example/random_cubical_complex_persistence_example.py>`
diff --git a/cython/doc/fileformats.rst b/cython/doc/fileformats.rst
new file mode 100644
index 00000000..156ef4e4
--- /dev/null
+++ b/cython/doc/fileformats.rst
@@ -0,0 +1,33 @@
+File formats
+############
+
+Persistence Diagram
+*******************
+
+Such a file, whose extension is usually ``.pers``, contains a list of
+persistence intervals.
+
+Lines starting with ``#`` are ignored (comments).
+
+Other lines might contain 2, 3 or 4 values (the number of values on each line
+must be the same for all lines)::
+
+    [[field] dimension] birth death
+
+Here is a simple sample file::
+
+    # Persistence diagram example
+    2 2.7 3.7
+    2 9.6 14.
+    # Some comments
+    3 34.2 34.974
+    4 3. inf
+
+Other sample files can be found in the data/persistence_diagram folder.
+
+Such files can be generated with
+:meth:`gudhi.SimplexTree.write_persistence_diagram`, read with
+:meth:`gudhi.read_persistence_intervals_grouped_by_dimension`, or
+:meth:`gudhi.read_persistence_intervals_in_dimension` and displayed with
+:meth:`gudhi.plot_persistence_barcode` or
+:meth:`gudhi.plot_persistence_diagram`.
diff --git a/cython/doc/generate_examples.py b/cython/doc/generate_examples.py
deleted file mode 100755
index d64d506c..00000000
--- a/cython/doc/generate_examples.py
+++ /dev/null
@@ -1,43 +0,0 @@
-#!/usr/bin/env python
-
-from os import listdir
-
-"""This file is part of the Gudhi Library. The Gudhi library
-   (Geometric Understanding in Higher Dimensions) is a generic C++
-   library for computational topology.
-
-   Author(s):       Vincent Rouvreau
-
-   Copyright (C) 2017 INRIA
-
-   This program is free software: you can redistribute it and/or modify
-   it under the terms of the GNU General Public License as published by
-   the Free Software Foundation, either version 3 of the License, or
-   (at your option) any later version.
-
-   This program is distributed in the hope that it will be useful,
-   but WITHOUT ANY WARRANTY; without even the implied warranty of
-   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-   GNU General Public License for more details.
-
-   You should have received a copy of the GNU General Public License
-   along with this program.  If not, see <http://www.gnu.org/licenses/>.
-"""
-
-__author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2017 INRIA"
-__license__ = "GPL v3"
-
-"""
-generate_examples.py generates examples.inc to be included in examples.rst.
-Refer to Makefile and make.bat to see if it is correctly launched.
-"""
-
-output_file = open('examples.inc','w')
-
-output_file.write('.. only:: builder_html\n\n')
-
-for file in listdir('../example/'):
-    output_file.write("    * :download:`" + file + " <../example/" + file + ">`\n")
-
-output_file.close()
diff --git a/cython/doc/index.rst b/cython/doc/index.rst
index 94dbc65a..3945d72a 100644
--- a/cython/doc/index.rst
+++ b/cython/doc/index.rst
@@ -1,15 +1,17 @@
-GUDHI documentation
-###################
+GUDHI Python module documentation
+#################################
 
-.. image:: img/Gudhi_banner.png
-   :align: center
+.. figure::
+     ../../doc/common/Gudhi_banner.png
+     :alt: Gudhi banner
+     :figclass: align-center
 
 Introduction
 ************
 
-The Gudhi library (Geometry Understanding in Higher Dimensions) is a generic
-open source `C++ library <http://gudhi.gforge.inria.fr/doc/latest/>`_, with a
-`Python interface <http://gudhi.gforge.inria.fr/python/latest/>`_, for
+The Python interface for the Gudhi library (Geometry Understanding in Higher
+Dimensions) is a generic open source
+`Python module <http://gudhi.gforge.inria.fr/python/latest/>`_, for
 Computational Topology and Topological Data Analysis
 (`TDA <https://en.wikipedia.org/wiki/Topological_data_analysis>`_).
 The GUDHI library intends to help the development of new algorithmic solutions
@@ -20,12 +22,11 @@ data structures.
 The current release of the GUDHI library includes:
 
 * Data structures to represent, construct and manipulate simplicial complexes.
-* Algorithms to compute persistent homology and multi-field persistent homology.
-* Simplication of simplicial complexes by edge contraction.
+* Simplification of simplicial complexes by edge contraction.
+* Algorithms to compute persistent homology and bottleneck distance.
 
-All data-structures are generic and several of their aspects can be
-parameterized via template classes. We refer to :cite:`gudhilibrary_ICMS14`
-for a detailed description of the design of the library.
+We refer to :cite:`gudhilibrary_ICMS14` for a detailed description of the
+design of the library.
 
 Data structures
 ***************
@@ -82,6 +83,6 @@ Persistence graphical tools
 Bibliography
 ************
 
-.. bibliography:: bibliography.bib
+.. bibliography:: ../../biblio/bibliography.bib
    :filter: docnames
    :style: unsrt
diff --git a/cython/doc/installation.rst b/cython/doc/installation.rst
index f98a5039..c182f176 100644
--- a/cython/doc/installation.rst
+++ b/cython/doc/installation.rst
@@ -68,31 +68,32 @@ The :doc:`Alpha complex </alpha_complex_user>`,
 C++ library which provides easy access to efficient and reliable geometric
 algorithms.
 
-Having CGAL version 4.6.0 or higher installed is recommended. The procedure to
-install this library according to your operating system is detailed
+Having CGAL,  the Computational Geometry Algorithms Library, version 4.7.0 or
+higher installed is recommended. The procedure to install this library
+according to your operating system is detailed
 `here <http://doc.cgal.org/latest/Manual/installation.html>`_.
 
-The following examples require the Computational Geometry Algorithms Library:
-
-.. only:: builder_html
-
-    * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>`
-    * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>`
-
-The following example requires CGAL version ≥ 4.7.0:
+The following examples requires CGAL version ≥ 4.7.0:
 
 .. only:: builder_html
 
     * :download:`alpha_complex_diagram_persistence_from_off_file_example.py <../example/alpha_complex_diagram_persistence_from_off_file_example.py>`
     * :download:`alpha_complex_from_points_example.py <../example/alpha_complex_from_points_example.py>`
 
-The following example requires CGAL version ≥ 4.8.0:
+The following examples requires CGAL version ≥ 4.8.0:
 
 .. only:: builder_html
 
     * :download:`bottleneck_basic_example.py <../example/bottleneck_basic_example.py>`
     * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>`
 
+The following examples requires CGAL version ≥ 4.8.1:
+
+.. only:: builder_html
+
+    * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>`
+    * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>`
+
 Eigen3
 ======
 
diff --git a/cython/doc/make.bat.in b/cython/doc/make.bat.in
deleted file mode 100644
index ff1a6d56..00000000
--- a/cython/doc/make.bat.in
+++ /dev/null
@@ -1,67 +0,0 @@
-@ECHO OFF
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-        set SPHINXBUILD=@SPHINX_PATH@
-)
-set BUILDDIR=_build
-set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% .
-set I18NSPHINXOPTS=%SPHINXOPTS% .
-if NOT "%PAPER%" == "" (
-	set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
-	set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS%
-)
-
-if "%1" == "" goto help
-
-if "%1" == "help" (
-	:help
-	echo.Please use `make ^<target^>` where ^<target^> is one of
-	echo.  html       to make standalone HTML files
-	echo.  doctest    to run all doctests embedded in the documentation if enabled
-	goto end
-)
-
-if "%1" == "clean" (
-	del examples.inc
-	for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i
-	del /q /s %BUILDDIR%\*
-	goto end
-)
-
-
-%SPHINXBUILD% 2> nul
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.http://sphinx-doc.org/
-	exit /b 1
-)
-
-:: GUDHI specific : Examples.inc is generated with generate_examples.py (and deleted on clean)
-
-if "%1" == "html" (
-	generate_examples.py
-	%SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html
-	if errorlevel 1 exit /b 1
-	echo.
-	echo.Build finished. The HTML pages are in %BUILDDIR%/html.
-	goto end
-)
-
-if "%1" == "doctest" (
-	%SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest
-	if errorlevel 1 exit /b 1
-	echo.
-	echo.Testing of doctests in the sources finished, look at the ^
-results in %BUILDDIR%/doctest/output.txt.
-	goto end
-)
-
-:end
diff --git a/cython/doc/persistence_graphical_tools_user.rst b/cython/doc/persistence_graphical_tools_user.rst
index cae18323..9033331f 100644
--- a/cython/doc/persistence_graphical_tools_user.rst
+++ b/cython/doc/persistence_graphical_tools_user.rst
@@ -14,12 +14,14 @@ This function is useful to show the color palette values of dimension:
 .. testcode::
 
     import gudhi
-    gudhi.show_palette_values(alpha=1.0)
+    plt = gudhi.show_palette_values(alpha=1.0)
+    plt.show()
 
 .. plot::
 
     import gudhi
-    gudhi.show_palette_values(alpha=1.0)
+    plt = gudhi.show_palette_values(alpha=1.0)
+    plt.show()
 
 Show persistence as a barcode
 -----------------------------
@@ -30,17 +32,22 @@ This function can display the persistence result as a barcode:
 
     import gudhi
     
-    periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt')
+    periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \
+        '/data/bitmap/3d_torus.txt')
     diag = periodic_cc.persistence()
-    gudhi.plot_persistence_barcode(diag)
+    plt = gudhi.plot_persistence_barcode(diag)
+    plt.show()
 
 .. plot::
 
     import gudhi
 
-    periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt')
+    periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \
+        '/data/bitmap/3d_torus.txt')
     diag = periodic_cc.persistence()
-    gudhi.plot_persistence_barcode(diag)
+    print("diag = ", diag)
+    plt = gudhi.plot_persistence_barcode(diag)
+    plt.show()
 
 Show persistence as a diagram
 -----------------------------
@@ -51,16 +58,20 @@ This function can display the persistence result as a diagram:
 
     import gudhi
     
-    rips_complex = gudhi.RipsComplex(off_file='tore3D_300.off', max_edge_length=2.0)
+    rips_complex = gudhi.RipsComplex(off_file=gudhi.__root_source_dir__ + \
+        '/data/points/tore3D_1307.off', max_edge_length=0.2)
     simplex_tree = rips_complex.create_simplex_tree(max_dimension=3)
     diag = simplex_tree.persistence()
-    gudhi.plot_persistence_diagram(diag)
+    plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13)
+    plt.show()
 
 .. plot::
 
     import gudhi
 
-    rips_complex = gudhi.RipsComplex(off_file='tore3D_300.off', max_edge_length=2.0)
+    rips_complex = gudhi.RipsComplex(off_file=gudhi.__root_source_dir__ + \
+        '/data/points/tore3D_1307.off', max_edge_length=0.2)
     simplex_tree = rips_complex.create_simplex_tree(max_dimension=3)
     diag = simplex_tree.persistence()
-    gudhi.plot_persistence_diagram(diag)
+    plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13)
+    plt.show()
diff --git a/cython/doc/persistent_cohomology_sum.rst b/cython/doc/persistent_cohomology_sum.rst
index d1f79cb4..a26df1dc 100644
--- a/cython/doc/persistent_cohomology_sum.rst
+++ b/cython/doc/persistent_cohomology_sum.rst
@@ -4,7 +4,7 @@
 
 +-----------------------------------------------------------------+-----------------------------------------------------------------------+
 | .. figure::                                                     | The theory of homology consists in attaching to a topological space   |
-|      img/3DTorus_poch.png                                       | a sequence of (homology) groups, capturing global topological         |
+|      ../../doc/Persistent_cohomology/3DTorus_poch.png           | a sequence of (homology) groups, capturing global topological         |
 |      :figclass: align-center                                    | features like connected components, holes, cavities, etc. Persistent  |
 |                                                                 | homology studies the evolution -- birth, life and death -- of these   |
 |      Rips Persistent Cohomology on a 3D                         | features when the topological space is changing. Consequently, the    |
diff --git a/cython/doc/persistent_cohomology_user.rst b/cython/doc/persistent_cohomology_user.rst
index 72f1a7f7..bf90c163 100644
--- a/cython/doc/persistent_cohomology_user.rst
+++ b/cython/doc/persistent_cohomology_user.rst
@@ -109,6 +109,6 @@ We provide several example files: run these examples with -h for details on thei
 Bibliography
 ============
 
-.. bibliography:: bibliography.bib
+.. bibliography:: ../../biblio/bibliography.bib
    :filter: docnames
    :style: unsrt
diff --git a/cython/doc/pyplots/barcode_persistence.py b/cython/doc/pyplots/barcode_persistence.py
index c06ac5a7..de33d506 100755
--- a/cython/doc/pyplots/barcode_persistence.py
+++ b/cython/doc/pyplots/barcode_persistence.py
@@ -1,5 +1,7 @@
 import gudhi
 
-periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='../3d_torus.txt')
+periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \
+    '/data/bitmap/3d_torus.txt')
 diag = periodic_cc.persistence()
-gudhi.plot_persistence_barcode(diag)
+plt = gudhi.plot_persistence_barcode(diag)
+plt.show()
diff --git a/cython/doc/pyplots/diagram_persistence.py b/cython/doc/pyplots/diagram_persistence.py
index b4714fe3..c2fbf801 100755
--- a/cython/doc/pyplots/diagram_persistence.py
+++ b/cython/doc/pyplots/diagram_persistence.py
@@ -1,5 +1,8 @@
 import gudhi
 
-alpha_complex = gudhi.AlphaComplex(off_file='../tore3D_300.off')
-diag = alpha_complex.persistence()
-gudhi.plot_persistence_diagram(diag)
+rips_complex = gudhi.RipsComplex(off_file=gudhi.__root_source_dir__ + \
+    '/data/points/tore3D_1307.off', max_edge_length=0.2)
+simplex_tree = rips_complex.create_simplex_tree(max_dimension=3)
+diag = simplex_tree.persistence()
+plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13)
+plt.show()
diff --git a/cython/doc/pyplots/show_palette_values.py b/cython/doc/pyplots/show_palette_values.py
index e72a55fd..fdf9645f 100755
--- a/cython/doc/pyplots/show_palette_values.py
+++ b/cython/doc/pyplots/show_palette_values.py
@@ -1,2 +1,3 @@
 import gudhi
-gudhi.show_palette_values(alpha=1.0)
+plt = gudhi.show_palette_values(alpha=1.0)
+plt.show()
diff --git a/cython/doc/python3-sphinx-build b/cython/doc/python3-sphinx-build
deleted file mode 100755
index 44b94169..00000000
--- a/cython/doc/python3-sphinx-build
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/usr/bin/python3
-
-"""
-Emulate sphinx-build for python3
-"""
-
-from sys import exit, argv
-from sphinx import main
-
-if __name__ == '__main__':
-    exit(main(argv))
diff --git a/cython/doc/python3-sphinx-build.py b/cython/doc/python3-sphinx-build.py
new file mode 100755
index 00000000..44b94169
--- /dev/null
+++ b/cython/doc/python3-sphinx-build.py
@@ -0,0 +1,11 @@
+#!/usr/bin/python3
+
+"""
+Emulate sphinx-build for python3
+"""
+
+from sys import exit, argv
+from sphinx import main
+
+if __name__ == '__main__':
+    exit(main(argv))
diff --git a/cython/doc/reader_utils_ref.rst b/cython/doc/reader_utils_ref.rst
new file mode 100644
index 00000000..9c1ea6fc
--- /dev/null
+++ b/cython/doc/reader_utils_ref.rst
@@ -0,0 +1,11 @@
+=============================
+Reader utils reference manual
+=============================
+
+.. autofunction:: gudhi.read_off
+
+.. autofunction:: gudhi.read_lower_triangular_matrix_from_csv_file
+
+.. autofunction:: gudhi.read_persistence_intervals_grouped_by_dimension
+
+.. autofunction:: gudhi.read_persistence_intervals_in_dimension
diff --git a/cython/doc/rips_complex_sum.rst b/cython/doc/rips_complex_sum.rst
index 2b65fc19..5616bfa9 100644
--- a/cython/doc/rips_complex_sum.rst
+++ b/cython/doc/rips_complex_sum.rst
@@ -4,7 +4,7 @@
 
 +----------------------------------------------------------------+------------------------------------------------------------------------+
 | .. figure::                                                    | Rips complex is a simplicial complex constructed from a one skeleton   |
-|      img/rips_complex_representation.png                       | graph.                                                                 |
+|      ../../doc/Rips_complex/rips_complex_representation.png    | graph.                                                                 |
 |      :figclass: align-center                                   |                                                                        |
 |                                                                | The filtration value of each edge is computed from a user-given        |
 |      Rips complex representation                               | distance function and is inserted until a user-given threshold         |
diff --git a/cython/doc/rips_complex_user.rst b/cython/doc/rips_complex_user.rst
index f9760976..96ba9944 100644
--- a/cython/doc/rips_complex_user.rst
+++ b/cython/doc/rips_complex_user.rst
@@ -26,7 +26,7 @@ structure, and then expands the simplicial complex when required.
 Vertex name correspond to the index of the point in the given range (aka. the point cloud).
 
 .. figure::
-    img/rips_complex_representation.png
+    ../../doc/Rips_complex/rips_complex_representation.png
     :align: center
 
     Rips-complex one skeleton graph representation
@@ -101,7 +101,8 @@ Finally, it is asked to display information about the Rips complex.
 .. testcode::
 
     import gudhi
-    rips_complex = gudhi.RipsComplex(off_file='alphacomplexdoc.off', max_edge_length=12.0)
+    rips_complex = gudhi.RipsComplex(off_file=gudhi.__root_source_dir__ + \
+        '/data/points/alphacomplexdoc.off', max_edge_length=12.0)
     simplex_tree = rips_complex.create_simplex_tree(max_dimension=1)
     result_str = 'Rips complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \
         repr(simplex_tree.num_simplices()) + ' simplices - ' + \
@@ -205,7 +206,8 @@ Finally, it is asked to display information about the Rips complex.
 .. testcode::
 
     import gudhi
-    rips_complex = gudhi.RipsComplex(csv_file='full_square_distance_matrix.csv', max_edge_length=12.0)
+    rips_complex = gudhi.RipsComplex(csv_file=gudhi.__root_source_dir__ + \
+        '/data/distance_matrix/full_square_distance_matrix.csv', max_edge_length=12.0)
     simplex_tree = rips_complex.create_simplex_tree(max_dimension=1)
     result_str = 'Rips complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \
         repr(simplex_tree.num_simplices()) + ' simplices - ' + \
diff --git a/cython/doc/simplex_tree_sum.rst b/cython/doc/simplex_tree_sum.rst
index 3174fb62..fb0e54c1 100644
--- a/cython/doc/simplex_tree_sum.rst
+++ b/cython/doc/simplex_tree_sum.rst
@@ -4,7 +4,7 @@
 
 +----------------------------------------------------------------+------------------------------------------------------------------------+
 | .. figure::                                                    | The simplex tree is an efficient and flexible data structure for       |
-|      img/Simplex_tree_representation.png                       | representing general (filtered) simplicial complexes.                  |
+|      ../../doc/Simplex_tree/Simplex_tree_representation.png    | representing general (filtered) simplicial complexes.                  |
 |      :alt: Simplex tree representation                         |                                                                        |
 |      :figclass: align-center                                   | The data structure is described in                                     |
 |                                                                | :cite:`boissonnatmariasimplextreealgorithmica`                         |
diff --git a/cython/doc/tangential_complex_sum.rst b/cython/doc/tangential_complex_sum.rst
index 2b05bc10..72b4d7ba 100644
--- a/cython/doc/tangential_complex_sum.rst
+++ b/cython/doc/tangential_complex_sum.rst
@@ -5,10 +5,10 @@
 
 +----------------------------------------------------------------+------------------------------------------------------------------------+
 | .. figure::                                                    | A Tangential Delaunay complex is a simplicial complex designed to      |
-|      img/tc_examples.png                                       | reconstruct a :math:`k`-dimensional manifold embedded in :math:`d`-    |
+|      ../../doc/Tangential_complex/tc_examples.png              | reconstruct a :math:`k`-dimensional manifold embedded in :math:`d`-    |
 |      :figclass: align-center                                   | dimensional Euclidean space. The input is a point sample coming from   |
 |                                                                | an unknown manifold. The running time depends only linearly on the     |
-|      **Tangential complex representation**                     | extrinsic dimension :math:`d` and exponentially on the intrinsic       |
+|      Tangential complex representation                         | extrinsic dimension :math:`d` and exponentially on the intrinsic       |
 |                                                                | dimension :math:`k`.                                                   |
 +----------------------------------------------------------------+------------------------------------------------------------------------+
 | :doc:`tangential_complex_user`                                 | :doc:`tangential_complex_ref`                                          |
diff --git a/cython/doc/tangential_complex_user.rst b/cython/doc/tangential_complex_user.rst
index 03f9fea6..efa6d7ce 100644
--- a/cython/doc/tangential_complex_user.rst
+++ b/cython/doc/tangential_complex_user.rst
@@ -22,7 +22,7 @@ Let us start with the description of the Tangential complex of a simple
 example, with :math:`k = 1` and :math:`d = 2`. The input data is 4 points
 :math:`P` located on a curve embedded in 2D.
 
-.. figure:: img/tc_example_01.png
+.. figure:: ../../doc/Tangential_complex/tc_example_01.png
     :alt: The input
     :figclass: align-center
 
@@ -31,7 +31,7 @@ example, with :math:`k = 1` and :math:`d = 2`. The input data is 4 points
 For each point :math:`p`, estimate its tangent subspace :math:`T_p` (e.g.
 using PCA). 
 
-.. figure:: img/tc_example_02.png
+.. figure:: ../../doc/Tangential_complex/tc_example_02.png
     :alt: The estimated normals
     :figclass: align-center
 
@@ -42,7 +42,7 @@ Let us add the Voronoi diagram of the points in orange. For each point
 :math:`p`, construct its star in the Delaunay triangulation of :math:`P`
 restricted to :math:`T_p`.
 
-.. figure:: img/tc_example_03.png
+.. figure:: ../../doc/Tangential_complex/tc_example_03.png
     :alt: The Voronoi diagram
     :figclass: align-center
 
@@ -62,7 +62,7 @@ simplex is not in the star of all its vertices.
 
 Let us take the same example.
 
-.. figure:: img/tc_example_07_before.png
+.. figure:: ../../doc/Tangential_complex/tc_example_07_before.png
     :alt: Before
     :figclass: align-center
 
@@ -70,7 +70,7 @@ Let us take the same example.
 
 Let us slightly move the tangent subspace :math:`T_q`
 
-.. figure:: img/tc_example_07_after.png
+.. figure:: ../../doc/Tangential_complex/tc_example_07_after.png
     :alt: After
     :figclass: align-center
 
@@ -79,7 +79,7 @@ Let us slightly move the tangent subspace :math:`T_q`
 Now, the star of :math:`Q` contains :math:`QP`, but the star of :math:`P` does
 not contain :math:`QP`. We have an inconsistency.
 
-.. figure:: img/tc_example_08.png
+.. figure:: ../../doc/Tangential_complex/tc_example_08.png
     :alt: After
     :figclass: align-center
 
@@ -122,7 +122,8 @@ This example builds the Tangential complex of point set read in an OFF file.
 .. testcode::
 
     import gudhi
-    tc = gudhi.TangentialComplex(off_file='alphacomplexdoc.off')
+    tc = gudhi.TangentialComplex(off_file=gudhi.__root_source_dir__ + \
+        '/data/points/alphacomplexdoc.off')
     result_str = 'Tangential contains ' + repr(tc.num_simplices()) + \
         ' simplices - ' + repr(tc.num_vertices()) + ' vertices.'
     print(result_str)
@@ -190,6 +191,6 @@ The output is:
 Bibliography
 ============
 
-.. bibliography:: bibliography.bib
+.. bibliography:: ../../biblio/bibliography.bib
    :filter: docnames
    :style: unsrt
diff --git a/cython/doc/witness_complex_sum.rst b/cython/doc/witness_complex_sum.rst
index b65522ba..a8a126a0 100644
--- a/cython/doc/witness_complex_sum.rst
+++ b/cython/doc/witness_complex_sum.rst
@@ -3,15 +3,17 @@
 :Euclidean version requires: CGAL :math:`\geq` 4.6.0               Eigen3
 =================================================================  ===================================  ===================================
 
-+-----------------------------------------------------------------+----------------------------------------------------------------------+
-| .. image::                                                      | Witness complex :math:`Wit(W,L)` is a simplicial complex defined on  |
-|      img/Witness_complex_representation.png                     | two sets of points in :math:`\mathbb{R}^D`.                          |
-|                                                                 |                                                                      |
-|                                                                 | The data structure is described in                                   |
-|                                                                 | :cite:`boissonnatmariasimplextreealgorithmica`.                      |
-+-----------------------------------------------------------------+----------------------------------------------------------------------+
-| :doc:`witness_complex_user`                                     | * :doc:`witness_complex_ref`                                         |
-|                                                                 | * :doc:`strong_witness_complex_ref`                                  |
-|                                                                 | * :doc:`euclidean_witness_complex_ref`                               |
-|                                                                 | * :doc:`euclidean_strong_witness_complex_ref`                        |
-+-----------------------------------------------------------------+----------------------------------------------------------------------+
++-------------------------------------------------------------------+----------------------------------------------------------------------+
+| .. figure::                                                       | Witness complex :math:`Wit(W,L)` is a simplicial complex defined on  |
+|      ../../doc/Witness_complex/Witness_complex_representation.png | two sets of points in :math:`\mathbb{R}^D`.                          |
+|      :alt: Witness complex representation                         |                                                                      |
+|      :figclass: align-center                                      | The data structure is described in                                   |
+|                                                                   | :cite:`boissonnatmariasimplextreealgorithmica`.                      |
+|                                                                   |                                                                      |
+|      Witness complex representation                               |                                                                      |
++-------------------------------------------------------------------+----------------------------------------------------------------------+
+| :doc:`witness_complex_user`                                       | * :doc:`witness_complex_ref`                                         |
+|                                                                   | * :doc:`strong_witness_complex_ref`                                  |
+|                                                                   | * :doc:`euclidean_witness_complex_ref`                               |
+|                                                                   | * :doc:`euclidean_strong_witness_complex_ref`                        |
++-------------------------------------------------------------------+----------------------------------------------------------------------+
diff --git a/cython/doc/witness_complex_user.rst b/cython/doc/witness_complex_user.rst
index aa9cbb2c..29413269 100644
--- a/cython/doc/witness_complex_user.rst
+++ b/cython/doc/witness_complex_user.rst
@@ -33,7 +33,7 @@ Both definitions can be relaxed by a real value :math:`\alpha`:
 which leads to definitions of **weak relaxed witness complex** (or just relaxed witness complex for short) and
 **strong relaxed witness complex** respectively.
 
-.. figure:: img/swit.svg
+.. figure:: ../../doc/Witness_complex/swit.svg
     :alt: Strongly witnessed simplex
     :figclass: align-center
 
@@ -126,6 +126,6 @@ Here is an example of constructing a strong witness complex filtration and compu
 Bibliography
 ============
 
-.. bibliography:: bibliography.bib
+.. bibliography:: ../../biblio/bibliography.bib
    :filter: docnames
    :style: unsrt
diff --git a/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py b/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py
index adedc7d2..b4487be4 100755
--- a/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py
+++ b/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py
@@ -38,6 +38,7 @@ parser = argparse.ArgumentParser(description='AlphaComplex creation from '
                                  'points from the given OFF file.')
 parser.add_argument("-f", "--file", type=str, required=True)
 parser.add_argument("-a", "--max_alpha_square", type=float, default=0.5)
+parser.add_argument("-b", "--band_boot", type=float, default=0.)
 parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -63,7 +64,8 @@ with open(args.file, 'r') as f:
         print(simplex_tree.betti_numbers())
     
         if args.no_diagram == False:
-            gudhi.plot_persistence_diagram(diag)
+            pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+            pplot.show()
     else:
         print(args.file, "is not a valid OFF file")
 
diff --git a/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py b/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
index 2371c36c..e3f362dc 100755
--- a/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
+++ b/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
@@ -40,6 +40,7 @@ parser.add_argument("-f", "--file", type=str, required=True)
 parser.add_argument("-a", "--max_alpha_square", type=float, required=True)
 parser.add_argument("-n", "--number_of_landmarks", type=int, required=True)
 parser.add_argument("-d", "--limit_dimension", type=int, required=True)
+parser.add_argument("-b", "--band_boot", type=float, default=0.)
 parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -70,8 +71,8 @@ with open(args.file, 'r') as f:
         print(simplex_tree.betti_numbers())
 
         if args.no_diagram == False:
-            gudhi.plot_persistence_diagram(diag)
-
+            pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+            pplot.show()
     else:
         print(args.file, "is not a valid OFF file")
 
diff --git a/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py b/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
index 5748aa8a..c236d992 100755
--- a/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
+++ b/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
@@ -40,6 +40,7 @@ parser.add_argument("-f", "--file", type=str, required=True)
 parser.add_argument("-a", "--max_alpha_square", type=float, required=True)
 parser.add_argument("-n", "--number_of_landmarks", type=int, required=True)
 parser.add_argument("-d", "--limit_dimension", type=int, required=True)
+parser.add_argument("-b", "--band_boot", type=float, default=0.)
 parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -70,8 +71,8 @@ with open(args.file, 'r') as f:
         print(simplex_tree.betti_numbers())
 
         if args.no_diagram == False:
-            gudhi.plot_persistence_diagram(diag)
-
+            pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+            pplot.show()
     else:
         print(args.file, "is not a valid OFF file")
 
diff --git a/cython/example/gudhi_graphical_tools_example.py b/cython/example/gudhi_graphical_tools_example.py
index bc3b16ec..ed87806b 100755
--- a/cython/example/gudhi_graphical_tools_example.py
+++ b/cython/example/gudhi_graphical_tools_example.py
@@ -44,4 +44,11 @@ gudhi.plot_persistence_barcode(persistence)
 print("#####################################################################")
 print("Show diagram persistence example")
 
-gudhi.plot_persistence_diagram(persistence)
+pplot = gudhi.plot_persistence_diagram(persistence)
+pplot.show()
+
+print("#####################################################################")
+print("Show diagram persistence example with a confidence band")
+
+pplot = gudhi.plot_persistence_diagram(persistence, band_boot=0.2)
+pplot.show()
diff --git a/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py b/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
index 664eb5c4..3baebd17 100755
--- a/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
+++ b/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
@@ -39,33 +39,28 @@ parser = argparse.ArgumentParser(description='RipsComplex creation from '
 parser.add_argument("-f", "--file", type=str, required=True)
 parser.add_argument("-e", "--max_edge_length", type=float, default=0.5)
 parser.add_argument("-d", "--max_dimension", type=int, default=1)
+parser.add_argument("-b", "--band_boot", type=float, default=0.)
 parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
 
-with open(args.file, 'r') as f:
-    first_line = f.readline()
-    if (first_line == 'OFF\n') or (first_line == 'nOFF\n'):
-        print("#####################################################################")
-        print("RipsComplex creation from distance matrix read in a csv file")
-        
-        message = "RipsComplex with max_edge_length=" + repr(args.max_edge_length)
-        print(message)
-        
-        rips_complex = gudhi.RipsComplex(off_file=args.file, max_edge_length=args.max_edge_length)
-        simplex_tree = rips_complex.create_simplex_tree(max_dimension=args.max_dimension)
-    
-        message = "Number of simplices=" + repr(simplex_tree.num_simplices())
-        print(message)
-        
-        diag = simplex_tree.persistence()
-    
-        print("betti_numbers()=")
-        print(simplex_tree.betti_numbers())
-    
-        if args.no_diagram == False:
-            gudhi.plot_persistence_diagram(diag)
-    else:
-        print(args.file, "is not a valid OFF file")
-
-    f.close()
+print("#####################################################################")
+print("RipsComplex creation from distance matrix read in a csv file")
+
+message = "RipsComplex with max_edge_length=" + repr(args.max_edge_length)
+print(message)
+
+rips_complex = gudhi.RipsComplex(csv_file=args.file, max_edge_length=args.max_edge_length)
+simplex_tree = rips_complex.create_simplex_tree(max_dimension=args.max_dimension)
+
+message = "Number of simplices=" + repr(simplex_tree.num_simplices())
+print(message)
+
+diag = simplex_tree.persistence()
+
+print("betti_numbers()=")
+print(simplex_tree.betti_numbers())
+
+if args.no_diagram == False:
+    pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+    pplot.show()
diff --git a/cython/example/rips_complex_diagram_persistence_from_off_file_example.py b/cython/example/rips_complex_diagram_persistence_from_off_file_example.py
index 4c21b98e..5951eedf 100755
--- a/cython/example/rips_complex_diagram_persistence_from_off_file_example.py
+++ b/cython/example/rips_complex_diagram_persistence_from_off_file_example.py
@@ -39,6 +39,7 @@ parser = argparse.ArgumentParser(description='RipsComplex creation from '
 parser.add_argument("-f", "--file", type=str, required=True)
 parser.add_argument("-e", "--max_edge_length", type=float, default=0.5)
 parser.add_argument("-d", "--max_dimension", type=int, default=1)
+parser.add_argument("-b", "--band_boot", type=float, default=0.)
 parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -64,7 +65,8 @@ with open(args.file, 'r') as f:
         print(simplex_tree.betti_numbers())
     
         if args.no_diagram == False:
-            gudhi.plot_persistence_diagram(diag)
+            pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+            pplot.show()
     else:
         print(args.file, "is not a valid OFF file")
 
diff --git a/cython/example/rips_persistence_diagram.py b/cython/example/rips_persistence_diagram.py
index 4e5cd2c8..9bfea41c 100755
--- a/cython/example/rips_persistence_diagram.py
+++ b/cython/example/rips_persistence_diagram.py
@@ -39,4 +39,5 @@ simplex_tree = rips.create_simplex_tree(max_dimension=1)
 diag = simplex_tree.persistence(homology_coeff_field=2, min_persistence=0)
 print("diag=", diag)
 
-gudhi.plot_persistence_diagram(diag)
+pplot = gudhi.plot_persistence_diagram(diag)
+pplot.show()
diff --git a/cython/example/simplex_tree_example.py b/cython/example/simplex_tree_example.py
index 3af20fcf..831d9da8 100755
--- a/cython/example/simplex_tree_example.py
+++ b/cython/example/simplex_tree_example.py
@@ -52,7 +52,6 @@ else:
 st.set_dimension(3)
 print("dimension=", st.dimension())
 
-st.set_filtration(4.0)
 st.initialize_filtration()
 print("filtration=", st.get_filtration())
 print("filtration[1, 2]=", st.filtration([1, 2]))
diff --git a/cython/example/tangential_complex_plain_homology_from_off_file_example.py b/cython/example/tangential_complex_plain_homology_from_off_file_example.py
index 4845eb47..6145e7f2 100755
--- a/cython/example/tangential_complex_plain_homology_from_off_file_example.py
+++ b/cython/example/tangential_complex_plain_homology_from_off_file_example.py
@@ -37,6 +37,7 @@ parser = argparse.ArgumentParser(description='TangentialComplex creation from '
                                  '- Constructs a tangential complex with the '
                                  'points from the given OFF file')
 parser.add_argument("-f", "--file", type=str, required=True)
+parser.add_argument("-b", "--band_boot", type=float, default=0.)
 parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -59,7 +60,8 @@ with open(args.file, 'r') as f:
         print(st.betti_numbers())
     
         if args.no_diagram == False:
-            gudhi.plot_persistence_diagram(diag)
+            pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+            pplot.show()
     else:
         print(args.file, "is not a valid OFF file")
 
diff --git a/cython/gudhi.pyx.in b/cython/gudhi.pyx.in
index 34d7c3b5..a8dd9f80 100644
--- a/cython/gudhi.pyx.in
+++ b/cython/gudhi.pyx.in
@@ -23,15 +23,19 @@
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016  INRIA"
 __license__ = "GPL v3"
+__version__ = "@GUDHI_VERSION@"
+# This variable is used by doctest to find files
+__root_source_dir__ = "@CMAKE_SOURCE_DIR@"
 
-include "cython/off_reader.pyx"
-include "cython/simplex_tree.pyx"
-include "cython/rips_complex.pyx"
-include "cython/cubical_complex.pyx"
-include "cython/periodic_cubical_complex.pyx"
-include "cython/persistence_graphical_tools.py"
-include "cython/witness_complex.pyx"
-include "cython/strong_witness_complex.pyx"
+include '@CMAKE_CURRENT_SOURCE_DIR@/cython/off_reader.pyx'
+include '@CMAKE_CURRENT_SOURCE_DIR@/cython/simplex_tree.pyx'
+include '@CMAKE_CURRENT_SOURCE_DIR@/cython/rips_complex.pyx'
+include '@CMAKE_CURRENT_SOURCE_DIR@/cython/cubical_complex.pyx'
+include '@CMAKE_CURRENT_SOURCE_DIR@/cython/periodic_cubical_complex.pyx'
+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'
 @GUDHI_CYTHON_ALPHA_COMPLEX@
 @GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX@
 @GUDHI_CYTHON_SUBSAMPLING@
diff --git a/cython/include/Reader_utils_interface.h b/cython/include/Reader_utils_interface.h
new file mode 100644
index 00000000..8ec34f61
--- /dev/null
+++ b/cython/include/Reader_utils_interface.h
@@ -0,0 +1,56 @@
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       Vincent Rouvreau
+ *
+ *    Copyright (C) 2017 INRIA
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef INCLUDE_READER_UTILS_INTERFACE_H_
+#define INCLUDE_READER_UTILS_INTERFACE_H_
+
+#include <gudhi/reader_utils.h>
+
+#include <iostream>
+#include <vector>
+#include <string>
+#include <map>
+#include <utility>  // for pair<>
+
+namespace Gudhi {
+
+// Redefine functions with a different name in order the original name can be used in the Python version.
+std::vector<std::vector<double>> read_matrix_from_csv_file(const std::string& filename,
+                                                                const char separator = ';') {
+  return read_lower_triangular_matrix_from_csv_file<double>(filename, separator);
+}
+
+inline std::map<int, std::vector<std::pair<double, double>>>
+    read_pers_intervals_grouped_by_dimension(std::string const& filename) {
+  return read_persistence_intervals_grouped_by_dimension(filename);
+}
+
+inline std::vector<std::pair<double, double>>
+    read_pers_intervals_in_dimension(std::string const& filename, int only_this_dim = -1) {
+  return read_persistence_intervals_in_dimension(filename, only_this_dim);
+}
+
+
+}  // namespace Gudhi
+
+
+#endif  // INCLUDE_READER_UTILS_INTERFACE_H_
diff --git a/cython/include/Rips_complex_interface.h b/cython/include/Rips_complex_interface.h
index 6d813f4a..02985727 100644
--- a/cython/include/Rips_complex_interface.h
+++ b/cython/include/Rips_complex_interface.h
@@ -66,11 +66,15 @@ class Rips_complex_interface {
     } else {
       // Rips construction where values is a distance matrix
       Distance_matrix distances =
-          read_lower_triangular_matrix_from_csv_file<Simplex_tree_interface<>::Filtration_value>(file_name);
+          Gudhi::read_lower_triangular_matrix_from_csv_file<Simplex_tree_interface<>::Filtration_value>(file_name);
       rips_complex_ = new Rips_complex<Simplex_tree_interface<>::Filtration_value>(distances, threshold);
     }
   }
 
+  ~Rips_complex_interface() {
+    delete rips_complex_;
+  }
+
   void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, int dim_max) {
     rips_complex_->create_complex(*simplex_tree, dim_max);
     simplex_tree->initialize_filtration();
diff --git a/cython/include/Simplex_tree_interface.h b/cython/include/Simplex_tree_interface.h
index 45ce1916..09e7e992 100644
--- a/cython/include/Simplex_tree_interface.h
+++ b/cython/include/Simplex_tree_interface.h
@@ -70,14 +70,14 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
   }
 
   // Do not interface this function, only used in strong witness interface for complex creation
-  bool insert_simplex(const std::vector<std::size_t>& complex, Filtration_value filtration = 0) {
-    Insertion_result result = Base::insert_simplex(complex, filtration);
+  bool insert_simplex(const std::vector<std::size_t>& simplex, Filtration_value filtration = 0) {
+    Insertion_result result = Base::insert_simplex(simplex, filtration);
     return (result.second);
   }
 
   // Do not interface this function, only used in strong witness interface for complex creation
-  bool insert_simplex_and_subfaces(const std::vector<std::size_t>& complex, Filtration_value filtration = 0) {
-    Insertion_result result = Base::insert_simplex_and_subfaces(complex, filtration);
+  bool insert_simplex_and_subfaces(const std::vector<std::size_t>& simplex, Filtration_value filtration = 0) {
+    Insertion_result result = Base::insert_simplex_and_subfaces(simplex, filtration);
     return (result.second);
   }
 
diff --git a/cython/setup.py.in b/cython/setup.py.in
new file mode 100644
index 00000000..fefa36bb
--- /dev/null
+++ b/cython/setup.py.in
@@ -0,0 +1,49 @@
+from distutils.core import setup, Extension
+from Cython.Build import cythonize
+
+"""This file is part of the Gudhi Library. The Gudhi library
+   (Geometric Understanding in Higher Dimensions) is a generic C++
+   library for computational topology.
+
+   Author(s):       Vincent Rouvreau
+
+   Copyright (C) 2016  INRIA
+
+   This program is free software: you can redistribute it and/or modify
+   it under the terms of the GNU General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   This program is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU General Public License for more details.
+
+   You should have received a copy of the GNU General Public License
+   along with this program.  If not, see <http://www.gnu.org/licenses/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016  INRIA"
+__license__ = "GPL v3"
+
+gudhi = Extension(
+    "gudhi",
+    sources = ['@CMAKE_CURRENT_BINARY_DIR@/gudhi.pyx',],
+    language = 'c++',
+    extra_compile_args=[@GUDHI_CYTHON_EXTRA_COMPILE_ARGS@],
+    extra_link_args=[@GUDHI_CYTHON_EXTRA_LINK_ARGS@],
+    libraries=[@GUDHI_CYTHON_LIBRARIES@],
+    library_dirs=[@GUDHI_CYTHON_LIBRARY_DIRS@],
+    include_dirs = [@GUDHI_CYTHON_INCLUDE_DIRS@],
+    runtime_library_dirs=[@GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS@],
+)
+
+setup(
+    name = 'gudhi',
+    author='Vincent Rouvreau',
+    author_email='gudhi-contact@lists.gforge.inria.fr',
+    version='@GUDHI_VERSION@',
+    url='http://gudhi.gforge.inria.fr/',
+    ext_modules = cythonize(gudhi),
+)
diff --git a/cython/test/test_cubical_complex.py b/cython/test/test_cubical_complex.py
index 2e281ee4..9a365823 100755
--- a/cython/test/test_cubical_complex.py
+++ b/cython/test/test_cubical_complex.py
@@ -67,7 +67,7 @@ def test_dimension_constructor():
                          top_dimensional_cells = [1,2,3,4,5,6,7,8,9])
     assert cub.__is_defined() == True
     assert cub.__is_persistence_defined() == False
-    assert cub.persistence() == [(1, (0.0, 100.0)), (0, (0.0, 1.8446744073709552e+19))]
+    assert cub.persistence() == [(1, (0.0, 100.0)), (0, (0.0, float('inf')))]
     assert cub.__is_persistence_defined() == True
     assert cub.betti_numbers() == [1, 0]
     assert cub.persistent_betti_numbers(0, 1000) == [0, 0]
@@ -80,7 +80,7 @@ def test_dimension_constructor():
     cub = CubicalComplex(perseus_file='CubicalOneSphere.txt')
     assert cub.__is_defined() == True
     assert cub.__is_persistence_defined() == False
-    assert cub.persistence() == [(1, (0.0, 100.0)), (0, (0.0, 1.8446744073709552e+19))]
+    assert cub.persistence() == [(1, (0.0, 100.0)), (0, (0.0, float('inf')))]
     assert cub.__is_persistence_defined() == True
     assert cub.betti_numbers() == [1, 0, 0]
     assert cub.persistent_betti_numbers(0, 1000) == [1, 0, 0]
diff --git a/cython/test/test_reader_utils.py b/cython/test/test_reader_utils.py
new file mode 100755
index 00000000..25591fb3
--- /dev/null
+++ b/cython/test/test_reader_utils.py
@@ -0,0 +1,88 @@
+import gudhi
+
+"""This file is part of the Gudhi Library. The Gudhi library
+   (Geometric Understanding in Higher Dimensions) is a generic C++
+   library for computational topology.
+
+   Author(s):       Vincent Rouvreau
+
+   Copyright (C) 2017 INRIA
+
+   This program is free software: you can redistribute it and/or modify
+   it under the terms of the GNU General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   This program is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU General Public License for more details.
+
+   You should have received a copy of the GNU General Public License
+   along with this program.  If not, see <http://www.gnu.org/licenses/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2017 INRIA"
+__license__ = "GPL v3"
+
+
+def test_non_existing_csv_file():
+    # Try to open a non existing file
+    matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file='pouetpouettralala.toubiloubabdou')
+    assert matrix == []
+
+def test_full_square_distance_matrix_csv_file():
+    # Create test file
+    test_file = open('full_square_distance_matrix.csv', 'w')
+    test_file.write('0;1;2;3;\n1;0;4;5;\n2;4;0;6;\n3;5;6;0;')
+    test_file.close()
+    matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file="full_square_distance_matrix.csv")
+    assert matrix == [[], [1.0], [2.0, 4.0], [3.0, 5.0, 6.0]]
+
+def test_lower_triangular_distance_matrix_csv_file():
+    # Create test file
+    test_file = open('lower_triangular_distance_matrix.csv', 'w')
+    test_file.write('\n1,\n2,3,\n4,5,6,\n7,8,9,10,')
+    test_file.close()
+    matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file="lower_triangular_distance_matrix.csv", separator=",")
+    assert matrix == [[], [1.0], [2.0, 3.0], [4.0, 5.0, 6.0], [7.0, 8.0, 9.0, 10.0]]
+
+def test_non_existing_persistence_file():
+    # Try to open a non existing file
+    persistence = gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file='pouetpouettralala.toubiloubabdou')
+    assert persistence == []
+    persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='pouetpouettralala.toubiloubabdou', only_this_dim=1)
+    assert persistence == []
+
+def test_read_persistence_intervals_without_dimension():
+    # Create test file
+    test_file = open('persistence_intervals_without_dimension.pers', 'w')
+    test_file.write('# Simple persistence diagram without dimension\n2.7 3.7\n9.6 14.\n34.2 34.974\n3. inf')
+    test_file.close()
+    persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_without_dimension.pers')
+    assert persistence == [(2.7, 3.7), (9.6, 14.), (34.2, 34.974), (3., float('Inf'))]
+    persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_without_dimension.pers', only_this_dim=0)
+    assert persistence == []
+    persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_without_dimension.pers', only_this_dim=1)
+    assert persistence == []
+    persistence = gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file='persistence_intervals_without_dimension.pers')
+    assert persistence == {-1: [(2.7, 3.7), (9.6, 14.0), (34.2, 34.974), (3.0, float('Inf'))]}
+
+def test_read_persistence_intervals_with_dimension():
+    # Create test file
+    test_file = open('persistence_intervals_with_dimension.pers', 'w')
+    test_file.write('# Simple persistence diagram with dimension\n0 2.7 3.7\n1 9.6 14.\n3 34.2 34.974\n1 3. inf')
+    test_file.close()
+    persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers')
+    assert persistence == [(2.7, 3.7), (9.6, 14.), (34.2, 34.974), (3., float('Inf'))]
+    persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers', only_this_dim=0)
+    assert persistence == [(2.7, 3.7)]
+    persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers', only_this_dim=1)
+    assert persistence == [(9.6, 14.), (3., float('Inf'))]
+    persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers', only_this_dim=2)
+    assert persistence == []
+    persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers', only_this_dim=3)
+    assert persistence == [(34.2, 34.974)]
+    persistence = gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file='persistence_intervals_with_dimension.pers')
+    assert persistence == {0: [(2.7, 3.7)], 1: [(9.6, 14.0), (3.0, float('Inf'))], 3: [(34.2, 34.974)]}
diff --git a/cython/test/test_simplex_tree.py b/cython/test/test_simplex_tree.py
index 3ae537e3..4d452d7d 100755
--- a/cython/test/test_simplex_tree.py
+++ b/cython/test/test_simplex_tree.py
@@ -53,7 +53,6 @@ def test_insertion():
     assert st.find([2, 3]) == False
 
     # filtration test
-    st.set_filtration(5.0)
     st.initialize_filtration()
     assert st.filtration([0, 1, 2]) == 4.0
     assert st.filtration([0, 2]) == 4.0
-- 
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