GUDHI 2.2.0 as released by upstream in a tarball.upstream/2.2.0

100 files changed, 742 insertions, 449 deletions

diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt
index afca9d60..17d440ee 100644
--- a/cython/CMakeLists.txt
+++ b/cython/CMakeLists.txt
@@ -1,4 +1,3 @@
-cmake_minimum_required(VERSION 2.8)
 project(Cython)
 
 function( add_gudhi_cython_lib THE_LIB )
@@ -32,35 +31,6 @@ if(CYTHON_FOUND)
   set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ")
   set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_SYSTEM_NO_DEPRECATED', ")
 
-  # 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)
     set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'/fp:strict', ")
@@ -99,11 +69,16 @@ if(CYTHON_FOUND)
   endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
 
   if(CGAL_FOUND)
+    can_cgal_use_cxx11_thread_local()
+    if (NOT CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT)
+      add_gudhi_cython_lib(${Boost_THREAD_LIBRARY})
+      set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ")
+    endif()
     # Add CGAL compilation args
     if(CGAL_HEADER_ONLY)
       set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ")
     else(CGAL_HEADER_ONLY)
-      add_gudhi_cython_lib(${CGAL_LIBRARIES})
+      add_gudhi_cython_lib(${CGAL_LIBRARY})
       set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ")
       # If CGAL is not header only, CGAL library may link with boost system,
       add_gudhi_cython_lib(${Boost_SYSTEM_LIBRARY})
@@ -135,7 +110,7 @@ if(CYTHON_FOUND)
   endforeach()
   set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${CMAKE_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/include', ")
 
-  if (TBB_FOUND)
+  if (TBB_FOUND AND WITH_GUDHI_USE_TBB)
     set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DGUDHI_USE_TBB', ")
     add_gudhi_cython_lib(${TBB_RELEASE_LIBRARY})
     add_gudhi_cython_lib(${TBB_MALLOC_RELEASE_LIBRARY})
@@ -181,7 +156,7 @@ if(CYTHON_FOUND)
              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)
+             --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
 
     add_gudhi_py_test(test_tangential_complex)
 
diff --git a/cython/cython/alpha_complex.pyx b/cython/cython/alpha_complex.pyx
index a0e8f9b7..4f772e31 100644
--- a/cython/cython/alpha_complex.pyx
+++ b/cython/cython/alpha_complex.pyx
@@ -11,7 +11,7 @@ import os
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -28,7 +28,7 @@ import os
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 cdef extern from "Alpha_complex_interface.h" namespace "Gudhi":
diff --git a/cython/cython/bottleneck_distance.pyx b/cython/cython/bottleneck_distance.pyx
index 9fb377ff..76ef81f4 100644
--- a/cython/cython/bottleneck_distance.pyx
+++ b/cython/cython/bottleneck_distance.pyx
@@ -9,7 +9,7 @@ import os
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -26,7 +26,7 @@ import os
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 cdef extern from "Bottleneck_distance_interface.h" namespace "Gudhi::persistence_diagram":
diff --git a/cython/cython/cubical_complex.pyx b/cython/cython/cubical_complex.pyx
index ffc85130..e94cd539 100644
--- a/cython/cython/cubical_complex.pyx
+++ b/cython/cython/cubical_complex.pyx
@@ -11,7 +11,7 @@ import os
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -28,7 +28,7 @@ import os
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 cdef extern from "Cubical_complex_interface.h" namespace "Gudhi":
@@ -104,22 +104,21 @@ cdef class CubicalComplex:
         return self.pcohptr != NULL
 
     def num_simplices(self):
-        """This function returns the number of simplices of the simplicial
-        complex.
+        """This function returns the number of all cubes in the complex.
 
-        :returns:  int -- the simplicial complex number of simplices.
+        :returns:  int -- the number of all cubes in the complex.
         """
         return self.thisptr.num_simplices()
 
     def dimension(self):
-        """This function returns the dimension of the simplicial complex.
+        """This function returns the dimension of the complex.
 
-        :returns:  int -- the simplicial complex dimension.
+        :returns:  int -- the complex dimension.
         """
         return self.thisptr.dimension()
 
     def persistence(self, homology_coeff_field=11, min_persistence=0):
-        """This function returns the persistence of the simplicial complex.
+        """This function returns the persistence of the complex.
 
         :param homology_coeff_field: The homology coefficient field. Must be a
             prime number
@@ -130,7 +129,7 @@ cdef class CubicalComplex:
             Sets min_persistence to -1.0 to see all values.
         :type min_persistence: float.
         :returns: list of pairs(dimension, pair(birth, death)) -- the
-            persistence of the simplicial complex.
+            persistence of the complex.
         """
         if self.pcohptr != NULL:
             del self.pcohptr
@@ -142,12 +141,15 @@ cdef class CubicalComplex:
         return persistence_result
 
     def betti_numbers(self):
-        """This function returns the Betti numbers of the simplicial complex.
+        """This function returns the Betti numbers of the complex.
 
         :returns: list of int -- The Betti numbers ([B0, B1, ..., Bn]).
 
         :note: betti_numbers function requires persistence function to be
             launched first.
+
+        :note: betti_numbers function always returns [1, 0, 0, ...] as infinity
+            filtration cubes are not removed from the complex.
         """
         cdef vector[int] bn_result
         if self.pcohptr != NULL:
@@ -155,8 +157,7 @@ cdef class CubicalComplex:
         return bn_result
 
     def persistent_betti_numbers(self, from_value, to_value):
-        """This function returns the persistent Betti numbers of the
-        simplicial complex.
+        """This function returns the persistent Betti numbers of the complex.
 
         :param from_value: The persistence birth limit to be added in the
             numbers (persistent birth <= from_value).
@@ -177,8 +178,8 @@ cdef class CubicalComplex:
         return pbn_result
 
     def persistence_intervals_in_dimension(self, dimension):
-        """This function returns the persistence intervals of the simplicial
-        complex in a specific dimension.
+        """This function returns the persistence intervals of the complex in a
+        specific dimension.
 
         :param dimension: The specific dimension.
         :type from_value: int.
diff --git a/cython/cython/euclidean_strong_witness_complex.pyx b/cython/cython/euclidean_strong_witness_complex.pyx
index c1523892..62b7cf71 100644
--- a/cython/cython/euclidean_strong_witness_complex.pyx
+++ b/cython/cython/euclidean_strong_witness_complex.pyx
@@ -8,7 +8,7 @@ from libcpp.utility cimport pair
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -25,7 +25,7 @@ from libcpp.utility cimport pair
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 cdef extern from "Euclidean_strong_witness_complex_interface.h" namespace "Gudhi":
diff --git a/cython/cython/euclidean_witness_complex.pyx b/cython/cython/euclidean_witness_complex.pyx
index 7c443b6b..c10ca73d 100644
--- a/cython/cython/euclidean_witness_complex.pyx
+++ b/cython/cython/euclidean_witness_complex.pyx
@@ -8,7 +8,7 @@ from libcpp.utility cimport pair
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -25,7 +25,7 @@ from libcpp.utility cimport pair
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 cdef extern from "Euclidean_witness_complex_interface.h" namespace "Gudhi":
diff --git a/cython/cython/off_reader.pyx b/cython/cython/off_reader.pyx
index b6e107ef..b939013f 100644
--- a/cython/cython/off_reader.pyx
+++ b/cython/cython/off_reader.pyx
@@ -9,7 +9,7 @@ import os
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -26,7 +26,7 @@ import os
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 cdef extern from "Off_reader_interface.h" namespace "Gudhi":
@@ -46,4 +46,5 @@ def read_off(off_file=''):
             return read_points_from_OFF_file(str.encode(off_file))
         else:
             print("file " + off_file + " not found.")
+            return []
 
diff --git a/cython/cython/periodic_cubical_complex.pyx b/cython/cython/periodic_cubical_complex.pyx
index 3025f125..e626950b 100644
--- a/cython/cython/periodic_cubical_complex.pyx
+++ b/cython/cython/periodic_cubical_complex.pyx
@@ -11,7 +11,7 @@ import os
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -28,7 +28,7 @@ import os
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 cdef extern from "Cubical_complex_interface.h" namespace "Gudhi":
@@ -106,22 +106,21 @@ cdef class PeriodicCubicalComplex:
         return self.pcohptr != NULL
 
     def num_simplices(self):
-        """This function returns the number of simplices of the simplicial
-        complex.
+        """This function returns the number of all cubes in the complex.
 
-        :returns:  int -- the simplicial complex number of simplices.
+        :returns:  int -- the number of all cubes in the complex.
         """
         return self.thisptr.num_simplices()
 
     def dimension(self):
-        """This function returns the dimension of the simplicial complex.
+        """This function returns the dimension of the complex.
 
-        :returns:  int -- the simplicial complex dimension.
+        :returns:  int -- the complex dimension.
         """
         return self.thisptr.dimension()
 
     def persistence(self, homology_coeff_field=11, min_persistence=0):
-        """This function returns the persistence of the simplicial complex.
+        """This function returns the persistence of the complex.
 
         :param homology_coeff_field: The homology coefficient field. Must be a
             prime number
@@ -132,7 +131,7 @@ cdef class PeriodicCubicalComplex:
             Sets min_persistence to -1.0 to see all values.
         :type min_persistence: float.
         :returns: list of pairs(dimension, pair(birth, death)) -- the
-            persistence of the simplicial complex.
+            persistence of the complex.
         """
         if self.pcohptr != NULL:
             del self.pcohptr
@@ -144,12 +143,15 @@ cdef class PeriodicCubicalComplex:
         return persistence_result
 
     def betti_numbers(self):
-        """This function returns the Betti numbers of the simplicial complex.
+        """This function returns the Betti numbers of the complex.
 
         :returns: list of int -- The Betti numbers ([B0, B1, ..., Bn]).
 
         :note: betti_numbers function requires persistence function to be
             launched first.
+
+        :note: betti_numbers function always returns [1, 0, 0, ...] as infinity
+            filtration cubes are not removed from the complex.
         """
         cdef vector[int] bn_result
         if self.pcohptr != NULL:
@@ -157,8 +159,7 @@ cdef class PeriodicCubicalComplex:
         return bn_result
 
     def persistent_betti_numbers(self, from_value, to_value):
-        """This function returns the persistent Betti numbers of the
-        simplicial complex.
+        """This function returns the persistent Betti numbers of the complex.
 
         :param from_value: The persistence birth limit to be added in the
             numbers (persistent birth <= from_value).
@@ -179,8 +180,8 @@ cdef class PeriodicCubicalComplex:
         return pbn_result
 
     def persistence_intervals_in_dimension(self, dimension):
-        """This function returns the persistence intervals of the simplicial
-        complex in a specific dimension.
+        """This function returns the persistence intervals of the complex in a
+        specific dimension.
 
         :param dimension: The specific dimension.
         :type from_value: int.
diff --git a/cython/cython/persistence_graphical_tools.py b/cython/cython/persistence_graphical_tools.py
index fb837e29..216ab8d6 100755
--- a/cython/cython/persistence_graphical_tools.py
+++ b/cython/cython/persistence_graphical_tools.py
@@ -1,4 +1,5 @@
 import matplotlib.pyplot as plt
+import matplotlib.patches as mpatches
 import numpy as np
 import os
 
@@ -8,7 +9,7 @@ import os
 
    Author(s):       Vincent Rouvreau, Bertrand Michel
 
-   Copyright (C) 2016 INRIA
+   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
@@ -25,16 +26,16 @@ import os
 """
 
 __author__ = "Vincent Rouvreau, Bertrand Michel"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
-def __min_birth_max_death(persistence, band_boot=0.):
+def __min_birth_max_death(persistence, band=0.):
     """This function returns (min_birth, max_death) from the persistence.
 
     :param persistence: The persistence to plot.
     :type persistence: list of tuples(dimension, tuple(birth, death)).
-    :param band_boot: bootstrap band
-    :type band_boot: float.
+    :param band: band
+    :type band: float.
     :returns: (float, float) -- (min_birth, max_death).
     """
     # Look for minimum birth date and maximum death date for plot optimisation
@@ -48,8 +49,8 @@ def __min_birth_max_death(persistence, band_boot=0.):
             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
+    if band > 0.:
+        max_death += band
     return (min_birth, max_death)
 
 """
@@ -59,37 +60,27 @@ palette = ['#ff0000', '#00ff00', '#0000ff', '#00ffff', '#ff00ff', '#ffff00',
            '#000000', '#880000', '#008800', '#000088', '#888800', '#880088',
            '#008888']
  
-def show_palette_values(alpha=0.6):
-    """This function shows palette color values in function of the dimension.
+def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6,
+        max_barcodes=1000, inf_delta=0.1, legend=False):
+    """This function plots the persistence bar code from persistence values list
+    or from a :doc:`persistence file <fileformats>`.
 
-    :param alpha: alpha value in [0.0, 1.0] for horizontal bars (default is 0.6).
-    :type alpha: float.
-    :returns: plot the dimension palette values.
-    """
-    colors = []
-    for color in palette:
-        colors.append(color)
-
-    y_pos = np.arange(len(palette))
-
-    plt.barh(y_pos, y_pos + 1, align='center', alpha=alpha, color=colors)
-    plt.ylabel('Dimension')
-    plt.title('Dimension palette values')
-    return plt
-
-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.
+    :param persistence: Persistence values list.
     :type persistence: list of tuples(dimension, tuple(birth, death)).
-    :param persistence_file: A persistence file style name (reset persistence if both are set).
+    :param persistence_file: A :doc:`persistence file <fileformats>` 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).
+    :param alpha: barcode transparency value (0.0 transparent through 1.0 opaque - default is 0.6).
     :type alpha: float.
-    :param max_barcodes: number of maximal barcodes to be displayed
+    :param max_barcodes: number of maximal barcodes to be displayed.
+        Set it to 0 to see all, Default value is 1000.
         (persistence will be sorted by life time if max_barcodes is set)
     :type max_barcodes: int.
-    :returns: plot -- An horizontal bar plot of persistence.
+    :param inf_delta: Infinity is placed at ((max_death - min_birth) x inf_delta).
+        A reasonable value is between 0.05 and 0.5 - default is 0.1.
+    :type inf_delta: float.
+    :returns: A matplotlib object containing horizontal bar plot of persistence
+        (launch `show()` method on it to display it).
     """
     if persistence_file is not '':
         if os.path.isfile(persistence_file):
@@ -107,9 +98,11 @@ def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, max
         # Sort by life time, then takes only the max_plots elements
         persistence = sorted(persistence, key=lambda life_time: life_time[1][1]-life_time[1][0], reverse=True)[:max_barcodes]
 
+    persistence = sorted(persistence, key=lambda birth: birth[1][0])
+
     (min_birth, max_death) = __min_birth_max_death(persistence)
     ind = 0
-    delta = ((max_death - min_birth) / 10.0)
+    delta = ((max_death - min_birth) * inf_delta)
     # Replace infinity values with max_death + delta for bar code to be more
     # readable
     infinity = max_death + delta
@@ -120,33 +113,49 @@ def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, max
             # Finite death case
             plt.barh(ind, (interval[1][1] - interval[1][0]), height=0.8,
                      left = interval[1][0], alpha=alpha,
-                     color = palette[interval[0]])
+                     color = palette[interval[0]],
+                     linewidth=0)
         else:
             # Infinite death case for diagram to be nicer
             plt.barh(ind, (infinity - interval[1][0]), height=0.8,
                      left = interval[1][0], alpha=alpha,
-                     color = palette[interval[0]])
+                     color = palette[interval[0]],
+                     linewidth=0)
         ind = ind + 1
 
+    if legend:
+        dimensions = list(set(item[0] for item in persistence))
+        plt.legend(handles=[mpatches.Patch(color=palette[dim],
+                                           label=str(dim)) for dim in dimensions],
+                   loc='lower right')
     plt.title('Persistence barcode')
     # Ends plot on infinity value and starts a little bit before min_birth
     plt.axis([axis_start, infinity, 0, ind])
     return plt
 
-def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, band_boot=0., max_plots=0):
-    """This function plots the persistence diagram with an optional confidence band.
+def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6,
+        band=0., max_plots=1000, inf_delta=0.1, legend=False):
+    """This function plots the persistence diagram from persistence values list
+    or from a :doc:`persistence file <fileformats>`.
 
-    :param persistence: The persistence to plot.
+    :param persistence: Persistence values list.
     :type persistence: list of tuples(dimension, tuple(birth, death)).
-    :param persistence_file: A persistence file style name (reset persistence if both are set).
+    :param persistence_file: A :doc:`persistence file <fileformats>` 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).
+    :param alpha: plot transparency value (0.0 transparent through 1.0 opaque - default is 0.6).
     :type alpha: float.
-    :param band_boot: bootstrap band (not displayed if :math:`\leq` 0.)
-    :type band_boot: float.
+    :param band: band (not displayed if :math:`\leq` 0. - default is 0.)
+    :type band: float.
     :param max_plots: number of maximal plots to be displayed
+        Set it to 0 to see all, Default value is 1000.
+        (persistence will be sorted by life time if max_plots is set)
     :type max_plots: int.
-    :returns: plot -- A diagram plot of persistence.
+    :param inf_delta: Infinity is placed at ((max_death - min_birth) x inf_delta).
+        A reasonable value is between 0.05 and 0.5 - default is 0.1.
+    :type inf_delta: float.
+    :returns: A matplotlib object containing diagram plot of persistence
+        (launch `show()` method on it to display it).
     """
     if persistence_file is not '':
         if os.path.isfile(persistence_file):
@@ -164,9 +173,9 @@ def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, ban
         # 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)
+    (min_birth, max_death) = __min_birth_max_death(persistence, band)
     ind = 0
-    delta = ((max_death - min_birth) / 10.0)
+    delta = ((max_death - min_birth) * inf_delta)
     # Replace infinity values with max_death + delta for diagram to be more
     # readable
     infinity = max_death + delta
@@ -179,8 +188,8 @@ def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, ban
     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')
+    if band > 0.:
+        plt.fill_between(x, x, x+band, alpha=alpha, facecolor='red')
 
     # Draw points in loop
     for interval in reversed(persistence):
@@ -194,6 +203,10 @@ def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, ban
                         color = palette[interval[0]])
         ind = ind + 1
 
+    if legend:
+        dimensions = list(set(item[0] for item in persistence))
+        plt.legend(handles=[mpatches.Patch(color=palette[dim], label=str(dim)) for dim in dimensions])
+
     plt.title('Persistence diagram')
     plt.xlabel('Birth')
     plt.ylabel('Death')
diff --git a/cython/cython/reader_utils.pyx b/cython/cython/reader_utils.pyx
index 3a17c5a0..e4572db0 100644
--- a/cython/cython/reader_utils.pyx
+++ b/cython/cython/reader_utils.pyx
@@ -11,7 +11,7 @@ import os
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2017 INRIA
+   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
@@ -28,7 +28,7 @@ import os
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2017 INRIA"
+__copyright__ = "Copyright (C) 2017 Inria"
 __license__ = "GPL v3"
 
 cdef extern from "Reader_utils_interface.h" namespace "Gudhi":
diff --git a/cython/cython/rips_complex.pyx b/cython/cython/rips_complex.pyx
index ad9b0a4d..59c16bff 100644
--- a/cython/cython/rips_complex.pyx
+++ b/cython/cython/rips_complex.pyx
@@ -11,7 +11,7 @@ import os
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -28,14 +28,12 @@ import os
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 cdef extern from "Rips_complex_interface.h" namespace "Gudhi":
     cdef cppclass Rips_complex_interface "Gudhi::rips_complex::Rips_complex_interface":
         Rips_complex_interface(vector[vector[double]] values, double threshold, bool euclidean)
-        # bool from_file is a workaround for cython to find the correct signature
-        Rips_complex_interface(string file_name, double threshold, bool euclidean, bool from_file)
         void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, int dim_max)
 
 # RipsComplex python interface
@@ -49,7 +47,7 @@ cdef class RipsComplex:
     cdef Rips_complex_interface * thisptr
 
     # Fake constructor that does nothing but documenting the constructor
-    def __init__(self, points=None, off_file='', distance_matrix=None, csv_file='', max_edge_length=float('inf')):
+    def __init__(self, points=None, distance_matrix=None, max_edge_length=float('inf')):
         """RipsComplex constructor.
 
         :param max_edge_length: Rips value.
@@ -60,41 +58,14 @@ cdef class RipsComplex:
 
         Or
 
-        :param off_file: An OFF file style name.
-        :type off_file: string
-
-        Or
-
         :param distance_matrix: A distance matrix (full square or lower
         triangular).
         :type points: list of list of double
-
-        Or
-
-        :param csv_file: A csv file style name containing a full square or a
-        lower triangular distance matrix.
-        :type csv_file: string
         """
 
     # The real cython constructor
-    def __cinit__(self, points=None, off_file='', distance_matrix=None, csv_file='', max_edge_length=float('inf')):
-        if off_file is not '':
-            if os.path.isfile(off_file):
-                self.thisptr = new Rips_complex_interface(str.encode(off_file),
-                                                          max_edge_length,
-                                                          True,
-                                                          True)
-            else:
-                print("file " + off_file + " not found.")
-        elif csv_file is not '':
-            if os.path.isfile(csv_file):
-                self.thisptr = new Rips_complex_interface(str.encode(csv_file),
-                                                          max_edge_length,
-                                                          False,
-                                                          True)
-            else:
-                print("file " + csv_file + " not found.")
-        elif distance_matrix is not None:
+    def __cinit__(self, points=None, distance_matrix=None, max_edge_length=float('inf')):
+        if distance_matrix is not None:
             self.thisptr = new Rips_complex_interface(distance_matrix, max_edge_length, False)
         else:
             if points is None:
diff --git a/cython/cython/simplex_tree.pyx b/cython/cython/simplex_tree.pyx
index 0cb575d2..e302486b 100644
--- a/cython/cython/simplex_tree.pyx
+++ b/cython/cython/simplex_tree.pyx
@@ -10,7 +10,7 @@ from libcpp.string cimport string
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -27,7 +27,7 @@ from libcpp.string cimport string
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 cdef extern from "Simplex_tree_interface.h" namespace "Gudhi":
@@ -55,6 +55,7 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi":
         void expansion(int max_dim)
         void remove_maximal_simplex(vector[int] simplex)
         bool prune_above_filtration(double filtration)
+        bool make_filtration_non_decreasing()
 
 cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi":
     cdef cppclass Simplex_tree_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>>":
@@ -64,6 +65,7 @@ cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi":
         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)
+        vector[pair[vector[int], vector[int]]] persistence_pairs()
 
 # SimplexTree python interface
 cdef class SimplexTree:
@@ -399,6 +401,26 @@ cdef class SimplexTree:
         """
         self.thisptr.expansion(max_dim)
 
+    def make_filtration_non_decreasing(self):
+        """This function ensures that each simplex has a higher filtration
+        value than its faces by increasing the filtration values.
+
+        :returns: The filtration modification information.
+        :rtype: bint
+
+
+        .. note::
+
+            Some simplex tree functions require the filtration to be valid.
+            make_filtration_non_decreasing function is not launching
+            :func:`initialize_filtration()<gudhi.SimplexTree.initialize_filtration>`
+            but returns the filtration modification
+            information. If the complex has changed , please call
+            :func:`initialize_filtration()<gudhi.SimplexTree.initialize_filtration>`
+            to recompute it.
+        """
+        return self.thisptr.make_filtration_non_decreasing()
+
     def persistence(self, homology_coeff_field=11, min_persistence=0, persistence_dim_max = False):
         """This function returns the persistence of the simplicial complex.
 
@@ -486,6 +508,25 @@ cdef class SimplexTree:
                   " to be launched first.")
         return intervals_result
 
+    def persistence_pairs(self):
+        """This function returns the persistence pairs of the simplicial
+        complex.
+
+        :returns: The persistence intervals.
+        :rtype:  list of pair of list of int
+
+        :note: intervals_in_dim function requires
+            :func:`persistence()<gudhi.SimplexTree.persistence>`
+            function to be launched first.
+        """
+        cdef vector[pair[vector[int],vector[int]]] persistence_pairs_result
+        if self.pcohptr != NULL:
+            persistence_pairs_result = self.pcohptr.persistence_pairs()
+        else:
+            print("persistence_pairs function requires persistence function"
+                  " to be launched first.")
+        return persistence_pairs_result
+
     def write_persistence_diagram(self, persistence_file=''):
         """This function writes the persistence intervals of the simplicial
         complex in a user given file name.
diff --git a/cython/cython/strong_witness_complex.pyx b/cython/cython/strong_witness_complex.pyx
index 770b46f5..74c5cb05 100644
--- a/cython/cython/strong_witness_complex.pyx
+++ b/cython/cython/strong_witness_complex.pyx
@@ -8,7 +8,7 @@ from libcpp.utility cimport pair
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -25,7 +25,7 @@ from libcpp.utility cimport pair
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 cdef extern from "Strong_witness_complex_interface.h" namespace "Gudhi":
diff --git a/cython/cython/subsampling.pyx b/cython/cython/subsampling.pyx
index 894a4fbe..ac09b7a3 100644
--- a/cython/cython/subsampling.pyx
+++ b/cython/cython/subsampling.pyx
@@ -10,7 +10,7 @@ import os
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -27,7 +27,7 @@ import os
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 cdef extern from "Subsampling_interface.h" namespace "Gudhi::subsampling":
diff --git a/cython/cython/tangential_complex.pyx b/cython/cython/tangential_complex.pyx
index d55bb050..4bb07076 100644
--- a/cython/cython/tangential_complex.pyx
+++ b/cython/cython/tangential_complex.pyx
@@ -11,7 +11,7 @@ import os
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -28,14 +28,14 @@ import os
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 cdef extern from "Tangential_complex_interface.h" namespace "Gudhi":
     cdef cppclass Tangential_complex_interface "Gudhi::tangential_complex::Tangential_complex_interface":
-        Tangential_complex_interface(vector[vector[double]] points)
+        Tangential_complex_interface(int intrisic_dim, vector[vector[double]] points)
         # bool from_file is a workaround for cython to find the correct signature
-        Tangential_complex_interface(string off_file, bool from_file)
+        Tangential_complex_interface(int intrisic_dim, string off_file, bool from_file)
         vector[double] get_point(unsigned vertex)
         unsigned number_of_vertices()
         unsigned number_of_simplices()
@@ -54,9 +54,12 @@ cdef class TangentialComplex:
     cdef Tangential_complex_interface * thisptr
 
     # Fake constructor that does nothing but documenting the constructor
-    def __init__(self, points=None, off_file=''):
+    def __init__(self, intrisic_dim, points=None, off_file=''):
         """TangentialComplex constructor.
 
+        :param intrisic_dim: Intrinsic dimension of the manifold.
+        :type intrisic_dim: integer
+
         :param points: A list of points in d-Dimension.
         :type points: list of list of double
 
@@ -67,17 +70,17 @@ cdef class TangentialComplex:
         """
 
     # The real cython constructor
-    def __cinit__(self, points=None, off_file=''):
+    def __cinit__(self, intrisic_dim, points=None, off_file=''):
         if off_file is not '':
             if os.path.isfile(off_file):
-                self.thisptr = new Tangential_complex_interface(str.encode(off_file), True)
+                self.thisptr = new Tangential_complex_interface(intrisic_dim, str.encode(off_file), True)
             else:
                 print("file " + off_file + " not found.")
         else:
             if points is None:
                 # Empty tangential construction
                 points=[]
-            self.thisptr = new Tangential_complex_interface(points)
+            self.thisptr = new Tangential_complex_interface(intrisic_dim, points)
                 
 
     def __dealloc__(self):
diff --git a/cython/cython/witness_complex.pyx b/cython/cython/witness_complex.pyx
index 96d122bb..8591465a 100644
--- a/cython/cython/witness_complex.pyx
+++ b/cython/cython/witness_complex.pyx
@@ -8,7 +8,7 @@ from libcpp.utility cimport pair
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -25,7 +25,7 @@ from libcpp.utility cimport pair
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 cdef extern from "Witness_complex_interface.h" namespace "Gudhi":
diff --git a/cython/doc/_templates/layout.html b/cython/doc/_templates/layout.html
index 8e4eba40..1161ed8e 100644
--- a/cython/doc/_templates/layout.html
+++ b/cython/doc/_templates/layout.html
@@ -56,6 +56,12 @@
             </a></p>
           {%- endif %}
           {%- endblock %}
+            <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>
+            <h2><a href="examples.html">Examples</a></h2>
           {%- if sidebars != None %}
             {#- new style sidebar: explicitly include/exclude templates #}
             {%- for sidebartemplate in sidebars %}
@@ -64,13 +70,6 @@
           {%- else %}
             {#- 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>
-<h2><a href="examples.html">Examples</a></h2>
-
             {%- include "localtoc.html" %}
             {%- endblock %}
             {%- block sidebarrel %}
@@ -166,60 +165,61 @@
   <body role="document">
   <!-- GUDHI website header BEGIN -->
   <div id="navigation" class="sticky">
-    <nav class="top-bar" role="navigation" data-topbar>
-      <ul class="title-area">
-        <li class="name">
-        <h1 class="show-for-small-only"><a href="http://gudhi.gforge.inria.fr" class="icon-tree"> GUDHI C++ library</a></h1>
-      </li>
-         <!-- Remove the class "menu-icon" to get rid of menu icon. Take out "Menu" to just have icon alone -->
-        <li class="toggle-topbar menu-icon"><a href="#"><span>Navigation</span></a></li>
-      </ul>
-      <section class="top-bar-section">
-        <ul class="right">
-                <li class="divider"></li>
-                <li><a href="http://gudhi.gforge.inria.fr/contact/">Contact</a></li>
-        </ul>
-        <ul class="left">
-                <li><a href="http://gudhi.gforge.inria.fr/"> <img src="http://gudhi.gforge.inria.fr/assets/img/home.png" alt="&nbsp;&nbsp;GUDHI">&nbsp;&nbsp;GUDHI </a></li>
-                <li class="divider"></li>
-                <li class="has-dropdown">
-                  <a href="#">Project</a>
-                    <ul class="dropdown">
-                        <li><a href="http://gudhi.gforge.inria.fr/people/">People</a></li>
-                        <li><a href="http://gudhi.gforge.inria.fr/keepintouch/">Keep in touch</a></li>
-                        <li><a href="http://gudhi.gforge.inria.fr/partners/">Partners and Funding</a></li>
-                        <li><a href="http://gudhi.gforge.inria.fr/relatedprojects/">Related projects</a></li>
-                        <li><a href="http://gudhi.gforge.inria.fr/theyaretalkingaboutus/">They are talking about us</a></li>
-                    </ul>
-                </li>
-                <li class="divider"></li>
-                <li class="has-dropdown">
-                  <a href="#">Download</a>
-                    <ul class="dropdown">
-                        <li><a href="http://gudhi.gforge.inria.fr/licensing/">Licensing</a></li>
-                        <li><a href="https://gforge.inria.fr/frs/?group_id=3865" target="_blank">Get the sources</a></li>
-                        <li><a href="https://gforge.inria.fr/frs/download.php/file/37113/GUDHI_2.0.0_OSX_UTILS.beta.tar.gz" target="_blank">Utils for Mac OSx</a></li>
-                        <li><a href="https://gforge.inria.fr/frs/download.php/file/37112/GUDHI_2.0.0_WIN64_UTILS.beta.zip" target="_blank">Utils for Win x64</a></li>
-                    </ul>
-                </li>
-                <li class="divider"></li>
-                <li class="has-dropdown">
-                  <a href="#">Documentation</a>
-                    <ul class="dropdown">
-                        <li><a href="http://gudhi.gforge.inria.fr/doc/latest/">C++ documentation</a></li>
-                        <li><a href="http://gudhi.gforge.inria.fr/doc/latest/installation.html">C++ installation manual</a></li>
-                        <li><a href="http://gudhi.gforge.inria.fr/python/latest/">Python documentation</a></li>
-                        <li><a href="http://gudhi.gforge.inria.fr/python/latest/installation.html">Python installation manual</a></li>
-                        <li><a href="http://gudhi.gforge.inria.fr/utils/">Utilities</a></li>
-                        <li><a href="http://bertrand.michel.perso.math.cnrs.fr/Enseignements/TDA-Gudhi-Python.html" target="_blank">Tutorial</a></li>
-                    </ul>
-                </li>
-                <li class="divider"></li>
-                <li><a href="http://gudhi.gforge.inria.fr/interfaces/">Interfaces</a></li>
-                <li class="divider"></li>
-        </ul>
-      </section>
-    </nav>
+      <nav class="top-bar" role="navigation" data-topbar>
+          <ul class="title-area">
+              <li class="name">
+                  <h1 class="show-for-small-only"><a href="" class="icon-tree"> GUDHI C++ library</a></h1>
+              </li>
+              <!-- Remove the class "menu-icon" to get rid of menu icon. Take out "Menu" to just have icon alone -->
+              <li class="toggle-topbar menu-icon"><a href="#"><span>Navigation</span></a></li>
+          </ul>
+          <section class="top-bar-section">
+              <ul class="right">
+                  <li class="divider"></li>
+                  <li><a href="/contact/">Contact</a></li>
+              </ul>
+              <ul class="left">
+                  <li><a href="/"> <img src="/assets/img/home.png" alt="&nbsp;&nbsp;GUDHI">&nbsp;&nbsp;GUDHI </a></li>
+                  <li class="divider"></li>
+                  <li class="has-dropdown">
+                      <a href="#">Project</a>
+                      <ul class="dropdown">
+                          <li><a href="/people/">People</a></li>
+                          <li><a href="/keepintouch/">Keep in touch</a></li>
+                          <li><a href="/partners/">Partners and Funding</a></li>
+                          <li><a href="/relatedprojects/">Related projects</a></li>
+                          <li><a href="/theyaretalkingaboutus/">They are talking about us</a></li>
+                      </ul>
+                  </li>
+                  <li class="divider"></li>
+                  <li class="has-dropdown">
+                      <a href="#">Download</a>
+                      <ul class="dropdown">
+                          <li><a href="/licensing/">Licensing</a></li>
+                          <li><a href="https://gforge.inria.fr/frs/download.php/latestzip/5253/library-latest.zip" target="_blank">Get the latest sources</a></li>
+                          <li><a href="https://gforge.inria.fr/frs/download.php/latestzip/5280/utils_osx-latest.zip" target="_blank">Utils for Mac OSx</a></li>
+                          <li><a href="https://gforge.inria.fr/frs/download.php/latestzip/5279/utils_win64-latest.zip" target="_blank">Utils for Win x64</a></li>
+                      </ul>
+                  </li>
+                  <li class="divider"></li>
+                  <li class="has-dropdown">
+                      <a href="#">Documentation</a>
+                      <ul class="dropdown">
+                          <li><a href="/doc/latest/">C++ documentation</a></li>
+                          <li><a href="/doc/latest/installation.html">C++ installation manual</a></li>
+                          <li><a href="/python/latest/">Python documentation</a></li>
+                          <li><a href="/python/latest/installation.html">Python installation manual</a></li>
+                          <li><a href="/utils/">Utilities</a></li>
+                          <li><a href="/tutorials/">Tutorials</a></li>
+                          <li><a href="/dockerfile/">Dockerfile</a></li>
+                      </ul>
+                  </li>
+                  <li class="divider"></li>
+                  <li><a href="/interfaces/">Interfaces</a></li>
+                  <li class="divider"></li>
+              </ul>
+          </section>
+      </nav>
   </div><!-- /#navigation -->
   <!-- GUDHI website header BEGIN -->
 
diff --git a/cython/doc/alpha_complex_ref.rst b/cython/doc/alpha_complex_ref.rst
index 6a122b09..7da79543 100644
--- a/cython/doc/alpha_complex_ref.rst
+++ b/cython/doc/alpha_complex_ref.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
 ==============================
 Alpha complex reference manual
 ==============================
diff --git a/cython/doc/alpha_complex_sum.rst b/cython/doc/alpha_complex_sum.inc
index 1680a712..1680a712 100644
--- a/cython/doc/alpha_complex_sum.rst
+++ b/cython/doc/alpha_complex_sum.inc
diff --git a/cython/doc/alpha_complex_user.rst b/cython/doc/alpha_complex_user.rst
index db7edd6f..d1e9c7cd 100644
--- a/cython/doc/alpha_complex_user.rst
+++ b/cython/doc/alpha_complex_user.rst
@@ -1,11 +1,15 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
 Alpha complex user manual
 =========================
 Definition
 ----------
 
-.. include:: alpha_complex_sum.rst
+.. include:: alpha_complex_sum.inc
 
-Alpha_complex is constructing a :doc:`Simplex_tree <simplex_tree_sum>` using
+Alpha_complex is constructing a :doc:`Simplex_tree <simplex_tree_ref>` using
 `Delaunay Triangulation  <http://doc.cgal.org/latest/Triangulation/index.html#Chapter_Triangulations>`_ 
 :cite:`cgal:hdj-t-15b` from `CGAL <http://www.cgal.org/>`_ (the Computational Geometry Algorithms Library
 :cite:`cgal:eb-15b`).
@@ -99,9 +103,9 @@ Filtration value computation algorithm
       **end for**
     **end for**
   **end for**
-  
+
   make_filtration_non_decreasing()
-  
+
   prune_above_filtration()
 
 Dimension 2
diff --git a/cython/doc/bottleneck_distance_sum.rst b/cython/doc/bottleneck_distance_sum.inc
index 030fad9e..030fad9e 100644
--- a/cython/doc/bottleneck_distance_sum.rst
+++ b/cython/doc/bottleneck_distance_sum.inc
diff --git a/cython/doc/bottleneck_distance_user.rst b/cython/doc/bottleneck_distance_user.rst
index 7692dce2..605db022 100644
--- a/cython/doc/bottleneck_distance_user.rst
+++ b/cython/doc/bottleneck_distance_user.rst
@@ -1,9 +1,13 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
 Bottleneck distance user manual
 ===============================
 Definition
 ----------
 
-.. include:: bottleneck_distance_sum.rst
+.. include:: bottleneck_distance_sum.inc
 
 Function
 --------
diff --git a/cython/doc/citation.rst b/cython/doc/citation.rst
index f4fdf83b..117eb9dd 100644
--- a/cython/doc/citation.rst
+++ b/cython/doc/citation.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
 Acknowledging the GUDHI library
 ###############################
 
diff --git a/cython/doc/conf.py b/cython/doc/conf.py
index a13c9751..4a54d4fd 100755
--- a/cython/doc/conf.py
+++ b/cython/doc/conf.py
@@ -85,7 +85,7 @@ version = gudhi.__version__
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = ['_build']
+exclude_patterns = ['_build', '*.inc']
 
 # The reST default role (used for this markup: `text`) to use for all
 # documents.
@@ -125,6 +125,7 @@ html_theme_options = {
      "sidebarbgcolor": "#A1ADCD",
      "sidebartextcolor": "black",
      "sidebarlinkcolor": "#334D5C",
+     "body_max_width": "1200px",
 }
 
 # Add any paths that contain custom themes here, relative to this directory.
diff --git a/cython/doc/cubical_complex_ref.rst b/cython/doc/cubical_complex_ref.rst
index 84aa4223..1fe9d5fb 100644
--- a/cython/doc/cubical_complex_ref.rst
+++ b/cython/doc/cubical_complex_ref.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
 Cubical complex reference manual
 ################################
 
diff --git a/cython/doc/cubical_complex_sum.rst b/cython/doc/cubical_complex_sum.inc
index 280ad0e0..280ad0e0 100644
--- a/cython/doc/cubical_complex_sum.rst
+++ b/cython/doc/cubical_complex_sum.inc
diff --git a/cython/doc/cubical_complex_user.rst b/cython/doc/cubical_complex_user.rst
index 34598f02..320bd79b 100644
--- a/cython/doc/cubical_complex_user.rst
+++ b/cython/doc/cubical_complex_user.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
 Cubical complex user manual
 ===========================
 Definition
@@ -144,6 +148,7 @@ the program output is:
 .. testoutput::
 
     Periodic cubical complex is of dimension 2 - 42 simplices.
+
 Examples.
 ---------
 
@@ -152,6 +157,6 @@ End user programs are available in cython/example/ folder.
 Bibliography
 ============
 
-.. bibliography:: ../../bibliography.bib
+.. bibliography:: ../../biblio/bibliography.bib
    :filter: docnames
    :style: unsrt
diff --git a/cython/doc/euclidean_strong_witness_complex_ref.rst b/cython/doc/euclidean_strong_witness_complex_ref.rst
index bebf0f9a..1a602cd5 100644
--- a/cython/doc/euclidean_strong_witness_complex_ref.rst
+++ b/cython/doc/euclidean_strong_witness_complex_ref.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
 =================================================
 Euclidean strong witness complex reference manual
 =================================================
diff --git a/cython/doc/euclidean_witness_complex_ref.rst b/cython/doc/euclidean_witness_complex_ref.rst
index 29b8806f..28daf965 100644
--- a/cython/doc/euclidean_witness_complex_ref.rst
+++ b/cython/doc/euclidean_witness_complex_ref.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
 ==========================================
 Euclidean witness complex reference manual
 ==========================================
diff --git a/cython/doc/examples.rst b/cython/doc/examples.rst
index 1e596e18..d42f5a92 100644
--- a/cython/doc/examples.rst
+++ b/cython/doc/examples.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
 Examples
 ########
 
diff --git a/cython/doc/fileformats.rst b/cython/doc/fileformats.rst
index 4f0b6f6d..ff20f26e 100644
--- a/cython/doc/fileformats.rst
+++ b/cython/doc/fileformats.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
 File formats
 ############
 
diff --git a/cython/doc/index.rst b/cython/doc/index.rst
index 3945d72a..4e444fb0 100644
--- a/cython/doc/index.rst
+++ b/cython/doc/index.rst
@@ -34,32 +34,32 @@ Data structures
 Alpha complex
 =============
 
-.. include:: alpha_complex_sum.rst
+.. include:: alpha_complex_sum.inc
 
 Cubical complex
 ===============
 
-.. include:: cubical_complex_sum.rst
+.. include:: cubical_complex_sum.inc
 
 Rips complex
 ============
 
-.. include:: rips_complex_sum.rst
+.. include:: rips_complex_sum.inc
 
 Simplex tree
 ============
 
-.. include:: simplex_tree_sum.rst
+.. include:: simplex_tree_sum.inc
 
 Tangential complex
 ==================
 
-.. include:: tangential_complex_sum.rst
+.. include:: tangential_complex_sum.inc
 
 Witness complex
 ===============
 
-.. include:: witness_complex_sum.rst
+.. include:: witness_complex_sum.inc
 
 
 Toolbox
@@ -68,17 +68,17 @@ Toolbox
 Bottleneck distance
 ===================
 
-.. include:: bottleneck_distance_sum.rst
+.. include:: bottleneck_distance_sum.inc
 
 Persistence cohomology
 ======================
 
-.. include:: persistent_cohomology_sum.rst
+.. include:: persistent_cohomology_sum.inc
 
 Persistence graphical tools
 ===========================
 
-.. include:: persistence_graphical_tools_sum.rst
+.. include:: persistence_graphical_tools_sum.inc
 
 Bibliography
 ************
diff --git a/cython/doc/installation.rst b/cython/doc/installation.rst
index c182f176..43ff85c5 100644
--- a/cython/doc/installation.rst
+++ b/cython/doc/installation.rst
@@ -1,12 +1,16 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
 Installation
 ############
 
 Compiling
 *********
-
-The library uses c++11 and requires `Boost <http://www.boost.org/>`_ with
-version 1.48.0 or more recent. It is a multi-platform library and compiles on
-Linux, Mac OSX and Visual Studio 2015.
+The library uses c++11 and requires `Boost <https://www.boost.org/>`_ ≥ 1.48.0
+and `CMake <https://www.cmake.org/>`_   ≥ 3.1.
+It is a multi-platform library and compiles on Linux, Mac OSX and Visual
+Studio 2015.
 It also requires cmake to generate makefiles, and cython to compile the
 library.
 
@@ -43,6 +47,9 @@ following command in a terminal:
     export PYTHONPATH='$PYTHONPATH:/path-to-gudhi/build/cython'
     ctest -R py_test
 
+If tests fail, please try to :code:`import gudhi` and check the errors.
+The problem can come from a third-party library bad link or installation.
+
 Documentation
 =============
 
diff --git a/cython/doc/periodic_cubical_complex_ref.rst b/cython/doc/periodic_cubical_complex_ref.rst
index c6190a1b..4b831647 100644
--- a/cython/doc/periodic_cubical_complex_ref.rst
+++ b/cython/doc/periodic_cubical_complex_ref.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
 Periodic cubical complex reference manual
 #########################################
 
diff --git a/cython/doc/persistence_graphical_tools_ref.rst b/cython/doc/persistence_graphical_tools_ref.rst
index 27c2f68a..a2c6bcef 100644
--- a/cython/doc/persistence_graphical_tools_ref.rst
+++ b/cython/doc/persistence_graphical_tools_ref.rst
@@ -1,8 +1,11 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
 ============================================
 Persistence graphical tools reference manual
 ============================================
 
 .. autofunction:: gudhi.__min_birth_max_death
-.. autofunction:: gudhi.show_palette_values
 .. autofunction:: gudhi.plot_persistence_barcode
 .. autofunction:: gudhi.plot_persistence_diagram
diff --git a/cython/doc/persistence_graphical_tools_sum.rst b/cython/doc/persistence_graphical_tools_sum.inc
index d602daa7..d602daa7 100644
--- a/cython/doc/persistence_graphical_tools_sum.rst
+++ b/cython/doc/persistence_graphical_tools_sum.inc
diff --git a/cython/doc/persistence_graphical_tools_user.rst b/cython/doc/persistence_graphical_tools_user.rst
index 9033331f..292915eb 100644
--- a/cython/doc/persistence_graphical_tools_user.rst
+++ b/cython/doc/persistence_graphical_tools_user.rst
@@ -1,49 +1,26 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
 Persistence graphical tools user manual
 =======================================
 Definition
 ----------
-.. include:: persistence_graphical_tools_sum.rst
-
-
-Show palette values
--------------------
-
-This function is useful to show the color palette values of dimension:
-
+.. include:: persistence_graphical_tools_sum.inc
 
-.. testcode::
-
-    import gudhi
-    plt = gudhi.show_palette_values(alpha=1.0)
-    plt.show()
-
-.. plot::
-
-    import gudhi
-    plt = gudhi.show_palette_values(alpha=1.0)
-    plt.show()
 
 Show persistence as a barcode
 -----------------------------
 
 This function can display the persistence result as a barcode:
 
-.. testcode::
-
-    import gudhi
-    
-    periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \
-        '/data/bitmap/3d_torus.txt')
-    diag = periodic_cc.persistence()
-    plt = gudhi.plot_persistence_barcode(diag)
-    plt.show()
-
 .. plot::
+   :include-source:
 
     import gudhi
 
-    periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \
-        '/data/bitmap/3d_torus.txt')
+    perseus_file = gudhi.__root_source_dir__ + '/data/bitmap/3d_torus.txt'
+    periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=perseus_file)
     diag = periodic_cc.persistence()
     print("diag = ", diag)
     plt = gudhi.plot_persistence_barcode(diag)
@@ -54,24 +31,32 @@ Show persistence as a diagram
 
 This function can display the persistence result as a diagram:
 
-.. testcode::
+.. plot::
+   :include-source:
 
     import gudhi
-    
-    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)
+
+    # rips_on_tore3D_1307.pers obtained from write_persistence_diagram method
+    persistence_file=gudhi.__root_source_dir__ + \
+        '/data/persistence_diagram/rips_on_tore3D_1307.pers'
+    plt = gudhi.plot_persistence_diagram(persistence_file=persistence_file,
+        legend=True)
     plt.show()
 
+If you want more information on a specific dimension, for instance:
+
 .. plot::
+   :include-source:
 
     import gudhi
 
-    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)
+    persistence_file=gudhi.__root_source_dir__ + \
+        '/data/persistence_diagram/rips_on_tore3D_1307.pers'
+    diag = \
+        gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file=\
+            persistence_file)
+    dim = 1
+    # Display all points with some transparency
+    plt = gudhi.plot_persistence_diagram([(dim,interval) for interval in diag[dim]],
+        max_plots=0, alpha=0.1)
     plt.show()
diff --git a/cython/doc/persistent_cohomology_sum.rst b/cython/doc/persistent_cohomology_sum.inc
index a26df1dc..a26df1dc 100644
--- a/cython/doc/persistent_cohomology_sum.rst
+++ b/cython/doc/persistent_cohomology_sum.inc
diff --git a/cython/doc/persistent_cohomology_user.rst b/cython/doc/persistent_cohomology_user.rst
index bf90c163..ce7fc685 100644
--- a/cython/doc/persistent_cohomology_user.rst
+++ b/cython/doc/persistent_cohomology_user.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
 Persistent cohomology user manual
 =================================
 Definition
diff --git a/cython/doc/pyplots/barcode_persistence.py b/cython/doc/pyplots/barcode_persistence.py
deleted file mode 100755
index de33d506..00000000
--- a/cython/doc/pyplots/barcode_persistence.py
+++ /dev/null
@@ -1,7 +0,0 @@
-import gudhi
-
-periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \
-    '/data/bitmap/3d_torus.txt')
-diag = periodic_cc.persistence()
-plt = gudhi.plot_persistence_barcode(diag)
-plt.show()
diff --git a/cython/doc/pyplots/diagram_persistence.py b/cython/doc/pyplots/diagram_persistence.py
deleted file mode 100755
index c2fbf801..00000000
--- a/cython/doc/pyplots/diagram_persistence.py
+++ /dev/null
@@ -1,8 +0,0 @@
-import gudhi
-
-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
deleted file mode 100755
index fdf9645f..00000000
--- a/cython/doc/pyplots/show_palette_values.py
+++ /dev/null
@@ -1,3 +0,0 @@
-import gudhi
-plt = gudhi.show_palette_values(alpha=1.0)
-plt.show()
diff --git a/cython/doc/reader_utils_ref.rst b/cython/doc/reader_utils_ref.rst
index 9c1ea6fc..f3ecebad 100644
--- a/cython/doc/reader_utils_ref.rst
+++ b/cython/doc/reader_utils_ref.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
 =============================
 Reader utils reference manual
 =============================
diff --git a/cython/doc/rips_complex_ref.rst b/cython/doc/rips_complex_ref.rst
index b17dc4e0..22b5616c 100644
--- a/cython/doc/rips_complex_ref.rst
+++ b/cython/doc/rips_complex_ref.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
 =============================
 Rips complex reference manual
 =============================
diff --git a/cython/doc/rips_complex_sum.rst b/cython/doc/rips_complex_sum.inc
index 5616bfa9..5616bfa9 100644
--- a/cython/doc/rips_complex_sum.rst
+++ b/cython/doc/rips_complex_sum.inc
diff --git a/cython/doc/rips_complex_user.rst b/cython/doc/rips_complex_user.rst
index 96ba9944..a8c06cf9 100644
--- a/cython/doc/rips_complex_user.rst
+++ b/cython/doc/rips_complex_user.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
 Rips complex user manual
 =========================
 Definition
@@ -101,8 +105,8 @@ Finally, it is asked to display information about the Rips complex.
 .. testcode::
 
     import gudhi
-    rips_complex = gudhi.RipsComplex(off_file=gudhi.__root_source_dir__ + \
-        '/data/points/alphacomplexdoc.off', max_edge_length=12.0)
+    point_cloud = gudhi.read_off(off_file=gudhi.__root_source_dir__ + '/data/points/alphacomplexdoc.off')
+    rips_complex = gudhi.RipsComplex(points=point_cloud, 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 - ' + \
@@ -197,7 +201,7 @@ Example from csv file
 ^^^^^^^^^^^^^^^^^^^^^
 
 This example builds the :doc:`Rips_complex <rips_complex_ref>` from the given
-points in an OFF file, and max_edge_length value.
+distance matrix in a csv file, and max_edge_length value.
 Then it creates a :doc:`Simplex_tree <simplex_tree_ref>` with it.
 
 Finally, it is asked to display information about the Rips complex.
@@ -206,8 +210,9 @@ Finally, it is asked to display information about the Rips complex.
 .. testcode::
 
     import gudhi
-    rips_complex = gudhi.RipsComplex(csv_file=gudhi.__root_source_dir__ + \
-        '/data/distance_matrix/full_square_distance_matrix.csv', max_edge_length=12.0)
+    distance_matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file=gudhi.__root_source_dir__ + \
+        '/data/distance_matrix/full_square_distance_matrix.csv')
+    rips_complex = gudhi.RipsComplex(distance_matrix=distance_matrix, 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 - ' + \
@@ -240,3 +245,72 @@ the program output is:
     [0, 3] -> 9.43
     [4, 6] -> 9.49
     [3, 6] -> 11.00
+
+Correlation matrix
+------------------
+
+Example from  a correlation matrix
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Analogously to the case of distance matrix, Rips complexes can be also constructed based on correlation matrix.
+Given a correlation matrix M, comportment-wise 1-M is a distance matrix.
+This example builds the one skeleton graph from the given corelation matrix and threshold value.
+Then it creates a :doc:`Simplex_tree <simplex_tree_ref>` with it.
+
+Finally, it is asked to display information about the simplicial complex.
+
+.. testcode::
+
+    import gudhi
+    import numpy as np
+
+    # User defined correlation matrix is:
+    # |1     0.06    0.23    0.01    0.89|
+    # |0.06  1       0.74    0.01    0.61|
+    # |0.23  0.74    1       0.72    0.03|
+    # |0.01  0.01    0.72    1       0.7 |
+    # |0.89  0.61    0.03    0.7     1   |
+    correlation_matrix=np.array([[1., 0.06, 0.23, 0.01, 0.89],
+                                [0.06, 1., 0.74, 0.01, 0.61],
+                                [0.23, 0.74, 1., 0.72, 0.03],
+                                [0.01, 0.01, 0.72, 1., 0.7],
+                                [0.89, 0.61, 0.03, 0.7, 1.]], float)
+
+    distance_matrix = np.ones((correlation_matrix.shape),float) - correlation_matrix
+    rips_complex = gudhi.RipsComplex(distance_matrix=distance_matrix, max_edge_length=1.0)
+
+    simplex_tree = rips_complex.create_simplex_tree(max_dimension=1)
+    result_str = 'Rips complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \
+        repr(simplex_tree.num_simplices()) + ' simplices - ' + \
+        repr(simplex_tree.num_vertices()) + ' vertices.'
+    print(result_str)
+    fmt = '%s -> %.2f'
+    for filtered_value in simplex_tree.get_filtration():
+        print(fmt % tuple(filtered_value))
+
+When launching (Rips maximal distance between 2 points is 12.0, is expanded
+until dimension 1 - one skeleton graph in other words), the output is:
+
+.. testoutput::
+
+    Rips complex is of dimension 1 - 15 simplices - 5 vertices.
+    [0] -> 0.00
+    [1] -> 0.00
+    [2] -> 0.00
+    [3] -> 0.00
+    [4] -> 0.00
+    [0, 4] -> 0.11
+    [1, 2] -> 0.26
+    [2, 3] -> 0.28
+    [3, 4] -> 0.30
+    [1, 4] -> 0.39
+    [0, 2] -> 0.77
+    [0, 1] -> 0.94
+    [2, 4] -> 0.97
+    [0, 3] -> 0.99
+    [1, 3] -> 0.99
+
+.. note::
+    As persistence diagrams points will be under the diagonal,
+    bottleneck distance and persistence graphical tool will not work properly,
+    this is a known issue.
diff --git a/cython/doc/simplex_tree_ref.rst b/cython/doc/simplex_tree_ref.rst
index 6d196843..9eb8c199 100644
--- a/cython/doc/simplex_tree_ref.rst
+++ b/cython/doc/simplex_tree_ref.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
 =============================
 Simplex tree reference manual
 =============================
diff --git a/cython/doc/simplex_tree_sum.rst b/cython/doc/simplex_tree_sum.inc
index fb0e54c1..fb0e54c1 100644
--- a/cython/doc/simplex_tree_sum.rst
+++ b/cython/doc/simplex_tree_sum.inc
diff --git a/cython/doc/simplex_tree_user.rst b/cython/doc/simplex_tree_user.rst
index 4b1dde19..aebeb29f 100644
--- a/cython/doc/simplex_tree_user.rst
+++ b/cython/doc/simplex_tree_user.rst
@@ -1,9 +1,13 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
 Simplex tree user manual
 ========================
 Definition
 ----------
 
-.. include:: simplex_tree_sum.rst
+.. include:: simplex_tree_sum.inc
 
 A simplicial complex :math:`\mathbf{K}` on a set of vertices :math:`V = \{1, \cdots ,|V|\}` is a collection of
 simplices :math:`\{\sigma\}`, :math:`\sigma \subseteq V` such that
diff --git a/cython/doc/strong_witness_complex_ref.rst b/cython/doc/strong_witness_complex_ref.rst
index 4ed4fe46..d624d711 100644
--- a/cython/doc/strong_witness_complex_ref.rst
+++ b/cython/doc/strong_witness_complex_ref.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
 =======================================
 Strong witness complex reference manual
 =======================================
diff --git a/cython/doc/tangential_complex_ref.rst b/cython/doc/tangential_complex_ref.rst
index 35589475..cdfda082 100644
--- a/cython/doc/tangential_complex_ref.rst
+++ b/cython/doc/tangential_complex_ref.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
 ===================================
 Tangential complex reference manual
 ===================================
diff --git a/cython/doc/tangential_complex_sum.rst b/cython/doc/tangential_complex_sum.inc
index 72b4d7ba..72b4d7ba 100644
--- a/cython/doc/tangential_complex_sum.rst
+++ b/cython/doc/tangential_complex_sum.inc
diff --git a/cython/doc/tangential_complex_user.rst b/cython/doc/tangential_complex_user.rst
index efa6d7ce..5ce69e86 100644
--- a/cython/doc/tangential_complex_user.rst
+++ b/cython/doc/tangential_complex_user.rst
@@ -1,6 +1,10 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
 Tangential complex user manual
 ==============================
-.. include:: tangential_complex_sum.rst
+.. include:: tangential_complex_sum.inc
 
 Definition
 ----------
@@ -122,8 +126,8 @@ This example builds the Tangential complex of point set read in an OFF file.
 .. testcode::
 
     import gudhi
-    tc = gudhi.TangentialComplex(off_file=gudhi.__root_source_dir__ + \
-        '/data/points/alphacomplexdoc.off')
+    tc = gudhi.TangentialComplex(intrisic_dim = 1,
+        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)
@@ -169,7 +173,8 @@ simplices.
 .. testcode::
 
    import gudhi
-   tc = gudhi.TangentialComplex(points=[[0.0, 0.0], [1.0, 0.0], [0.0, 1.0], [1.0, 1.0]])
+   tc = gudhi.TangentialComplex(intrisic_dim = 1,
+       points=[[0.0, 0.0], [1.0, 0.0], [0.0, 1.0], [1.0, 1.0]])
    result_str = 'Tangential contains ' + repr(tc.num_vertices()) + ' vertices.'
    print(result_str)
 
diff --git a/cython/doc/todos.rst b/cython/doc/todos.rst
index 78972a4c..ca274ced 100644
--- a/cython/doc/todos.rst
+++ b/cython/doc/todos.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
 ==========
 To be done
 ==========
diff --git a/cython/doc/witness_complex_ref.rst b/cython/doc/witness_complex_ref.rst
index c78760cb..9987d3fd 100644
--- a/cython/doc/witness_complex_ref.rst
+++ b/cython/doc/witness_complex_ref.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
 ================================
 Witness complex reference manual
 ================================
diff --git a/cython/doc/witness_complex_sum.rst b/cython/doc/witness_complex_sum.inc
index a8a126a0..a8a126a0 100644
--- a/cython/doc/witness_complex_sum.rst
+++ b/cython/doc/witness_complex_sum.inc
diff --git a/cython/doc/witness_complex_user.rst b/cython/doc/witness_complex_user.rst
index 99be5185..40e94134 100644
--- a/cython/doc/witness_complex_user.rst
+++ b/cython/doc/witness_complex_user.rst
@@ -1,7 +1,11 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
 Witness complex user manual
 ===========================
 
-.. include:: witness_complex_sum.rst
+.. include:: witness_complex_sum.inc
 
 Definitions
 -----------
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 b4487be4..4abe22d4 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
@@ -9,7 +9,7 @@ import argparse
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -26,7 +26,7 @@ import argparse
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 parser = argparse.ArgumentParser(description='AlphaComplex creation from '
@@ -38,7 +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("-b", "--band", 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 +64,7 @@ with open(args.file, 'r') as f:
         print(simplex_tree.betti_numbers())
     
         if args.no_diagram == False:
-            pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+            pplot = gudhi.plot_persistence_diagram(diag, band=args.band)
             pplot.show()
     else:
         print(args.file, "is not a valid OFF file")
diff --git a/cython/example/alpha_complex_from_points_example.py b/cython/example/alpha_complex_from_points_example.py
index 7d6278ce..ad73c744 100755
--- a/cython/example/alpha_complex_from_points_example.py
+++ b/cython/example/alpha_complex_from_points_example.py
@@ -8,7 +8,7 @@ from gudhi import AlphaComplex, SimplexTree
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -25,7 +25,7 @@ from gudhi import AlphaComplex, SimplexTree
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 print("#####################################################################")
diff --git a/cython/example/alpha_rips_persistence_bottleneck_distance.py b/cython/example/alpha_rips_persistence_bottleneck_distance.py
index ab5fc1e9..b51fa7a8 100755
--- a/cython/example/alpha_rips_persistence_bottleneck_distance.py
+++ b/cython/example/alpha_rips_persistence_bottleneck_distance.py
@@ -10,7 +10,7 @@ import math
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -27,7 +27,7 @@ import math
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 parser = argparse.ArgumentParser(description='AlphaComplex and RipsComplex '
@@ -45,13 +45,14 @@ 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'):
+        point_cloud = gudhi.read_off(off_file=args.file)
         print("#####################################################################")
         print("RipsComplex creation from points read in a OFF file")
 
         message = "RipsComplex with max_edge_length=" + repr(args.threshold)
         print(message)
 
-        rips_complex = gudhi.RipsComplex(off_file=args.file,
+        rips_complex = gudhi.RipsComplex(points=point_cloud,
                                          max_edge_length=args.threshold)
 
         rips_stree = rips_complex.create_simplex_tree(max_dimension=args.max_dimension)
@@ -67,7 +68,7 @@ with open(args.file, 'r') as f:
         message = "AlphaComplex with max_edge_length=" + repr(args.threshold)
         print(message)
 
-        alpha_complex = gudhi.AlphaComplex(off_file=args.file)
+        alpha_complex = gudhi.AlphaComplex(points=point_cloud)
         alpha_stree = alpha_complex.create_simplex_tree(max_alpha_square=(args.threshold * args.threshold))
 
         message = "Number of simplices=" + repr(alpha_stree.num_simplices())
diff --git a/cython/example/bottleneck_basic_example.py b/cython/example/bottleneck_basic_example.py
index 31cecb29..287956e7 100755
--- a/cython/example/bottleneck_basic_example.py
+++ b/cython/example/bottleneck_basic_example.py
@@ -8,7 +8,7 @@ import gudhi
 
    Author(s):       Francois Godi, Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -25,11 +25,9 @@ import gudhi
 """
 
 __author__ = "Francois Godi, Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
-import gudhi
-
 diag1 = [[2.7, 3.7],[9.6, 14.],[34.2, 34.974], [3.,float('Inf')]]
 
 diag2 = [[2.8, 4.45],[9.5, 14.1],[3.2,float('Inf')]]
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 e3f362dc..3b29781f 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
@@ -9,7 +9,7 @@ import argparse
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -26,7 +26,7 @@ import argparse
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 parser = argparse.ArgumentParser(description='EuclideanStrongWitnessComplex creation from '
@@ -40,7 +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("-b", "--band", 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()
@@ -71,7 +71,7 @@ with open(args.file, 'r') as f:
         print(simplex_tree.betti_numbers())
 
         if args.no_diagram == False:
-            pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+            pplot = gudhi.plot_persistence_diagram(diag, band=args.band)
             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 c236d992..db34962d 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
@@ -9,7 +9,7 @@ import argparse
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -26,7 +26,7 @@ import argparse
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 parser = argparse.ArgumentParser(description='EuclideanWitnessComplex creation from '
@@ -40,7 +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("-b", "--band", 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()
@@ -71,7 +71,7 @@ with open(args.file, 'r') as f:
         print(simplex_tree.betti_numbers())
 
         if args.no_diagram == False:
-            pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+            pplot = gudhi.plot_persistence_diagram(diag, band=args.band)
             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 ed87806b..ac3d146c 100755
--- a/cython/example/gudhi_graphical_tools_example.py
+++ b/cython/example/gudhi_graphical_tools_example.py
@@ -8,7 +8,7 @@ import gudhi
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -25,15 +25,10 @@ import gudhi
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 print("#####################################################################")
-print("Show palette colors values for dimension")
-
-gudhi.show_palette_values()
-
-print("#####################################################################")
 print("Show barcode persistence example")
 
 persistence = [(2, (1.0, float('inf'))), (1, (1.4142135623730951, float('inf'))),
@@ -50,5 +45,5 @@ pplot.show()
 print("#####################################################################")
 print("Show diagram persistence example with a confidence band")
 
-pplot = gudhi.plot_persistence_diagram(persistence, band_boot=0.2)
+pplot = gudhi.plot_persistence_diagram(persistence, band=0.2)
 pplot.show()
diff --git a/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py b/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py
index 00334121..5f968bf1 100755
--- a/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py
+++ b/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py
@@ -9,7 +9,7 @@ import argparse
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -26,7 +26,7 @@ import argparse
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 def is_file_perseus(file):
diff --git a/cython/example/random_cubical_complex_persistence_example.py b/cython/example/random_cubical_complex_persistence_example.py
index c832d6bf..80ff2452 100755
--- a/cython/example/random_cubical_complex_persistence_example.py
+++ b/cython/example/random_cubical_complex_persistence_example.py
@@ -13,7 +13,7 @@ import operator
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -30,7 +30,7 @@ import operator
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 parser = argparse.ArgumentParser(description='Random cubical complex.',
diff --git a/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py b/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py
new file mode 100755
index 00000000..0c9dfc43
--- /dev/null
+++ b/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py
@@ -0,0 +1,84 @@
+#!/usr/bin/env python
+
+import gudhi
+import sys
+import argparse
+
+"""This file is part of the Gudhi Library. The Gudhi library
+   (Geometric Understanding in Higher Dimensions) is a generic C++
+   library for computational topology.
+
+   Author(s):       Vincent Rouvreau
+
+   Copyright (C) 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"
+
+parser = argparse.ArgumentParser(description='RipsComplex creation from '
+                                 'a correlation matrix read in a csv file.',
+                                 epilog='Example: '
+                                 'example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py '
+                                 '-f ../data/correlation_matrix/lower_triangular_correlation_matrix.csv -e 12.0 -d 3'
+                                 '- Constructs a Rips complex with the '
+                                 'correlation matrix from the given csv file.')
+parser.add_argument("-f", "--file", type=str, required=True)
+parser.add_argument("-c", "--min_edge_correlation", type=float, default=0.5)
+parser.add_argument("-d", "--max_dimension", type=int, default=1)
+parser.add_argument("-b", "--band", 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()
+
+if not (-1. < args.min_edge_correlation < 1.):
+    print("Wrong value of the treshold corelation (should be between -1 and 1).")
+    sys.exit(1)
+
+print("#####################################################################")
+print("Caution: as persistence diagrams points will be under the diagonal,")
+print("bottleneck distance and persistence graphical tool will not work")
+print("properly, this is a known issue.")
+
+print("#####################################################################")
+print("RipsComplex creation from correlation matrix read in a csv file")
+
+message = "RipsComplex with min_edge_correlation=" + repr(args.min_edge_correlation)
+print(message)
+
+correlation_matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file=args.file)
+# Given a correlation matrix M, we compute component-wise M'[i,j] = 1-M[i,j] to get a distance matrix:
+distance_matrix = [[1.-correlation_matrix[i][j] for j in range(len(correlation_matrix[i]))] for i in range(len(correlation_matrix))]
+
+rips_complex = gudhi.RipsComplex(distance_matrix=distance_matrix,
+                                 max_edge_length=1.-args.min_edge_correlation)
+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())
+
+# invert the persistence diagram
+invert_diag = [(diag[pers][0],(1.-diag[pers][1][0], 1.-diag[pers][1][1])) for pers in range(len(diag))]
+
+if args.no_diagram == False:
+    pplot = gudhi.plot_persistence_diagram(invert_diag, band=args.band)
+    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 3baebd17..4d2ed577 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
@@ -9,7 +9,7 @@ import argparse
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -26,20 +26,20 @@ import argparse
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 parser = argparse.ArgumentParser(description='RipsComplex creation from '
-                                 'a distance matrix read in a OFF file.',
+                                 'a distance matrix read in a csv file.',
                                  epilog='Example: '
                                  'example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py '
                                  '-f ../data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3'
                                  '- Constructs a Rips complex with the '
-                                 'points from the given OFF file.')
+                                 'distance matrix from the given csv file.')
 parser.add_argument("-f", "--file", type=str, required=True)
 parser.add_argument("-e", "--max_edge_length", type=float, default=0.5)
 parser.add_argument("-d", "--max_dimension", type=int, default=1)
-parser.add_argument("-b", "--band_boot", type=float, default=0.)
+parser.add_argument("-b", "--band", 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()
@@ -50,7 +50,8 @@ 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)
+distance_matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file=args.file)
+rips_complex = gudhi.RipsComplex(distance_matrix=distance_matrix, 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())
@@ -62,5 +63,5 @@ 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 = gudhi.plot_persistence_diagram(diag, band=args.band)
     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 5951eedf..d15d5eb0 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
@@ -9,7 +9,7 @@ import argparse
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -26,7 +26,7 @@ import argparse
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 parser = argparse.ArgumentParser(description='RipsComplex creation from '
@@ -39,7 +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("-b", "--band", 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()
@@ -53,7 +53,8 @@ with open(args.file, 'r') as f:
         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)
+        point_cloud = gudhi.read_off(off_file=args.file)
+        rips_complex = gudhi.RipsComplex(points=point_cloud, 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())
@@ -65,7 +66,7 @@ with open(args.file, 'r') as f:
         print(simplex_tree.betti_numbers())
     
         if args.no_diagram == False:
-            pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+            pplot = gudhi.plot_persistence_diagram(diag, band=args.band)
             pplot.show()
     else:
         print(args.file, "is not a valid OFF file")
diff --git a/cython/example/rips_complex_from_points_example.py b/cython/example/rips_complex_from_points_example.py
index 5d411b1a..ffa9d91f 100755
--- a/cython/example/rips_complex_from_points_example.py
+++ b/cython/example/rips_complex_from_points_example.py
@@ -8,7 +8,7 @@ import gudhi
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -25,7 +25,7 @@ import gudhi
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 print("#####################################################################")
diff --git a/cython/example/rips_persistence_diagram.py b/cython/example/rips_persistence_diagram.py
index 9bfea41c..7a6a9f46 100755
--- a/cython/example/rips_persistence_diagram.py
+++ b/cython/example/rips_persistence_diagram.py
@@ -8,7 +8,7 @@ import gudhi
 
    Author(s):       Marc Glisse
 
-   Copyright (C) 2016 INRIA
+   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
@@ -25,7 +25,7 @@ import gudhi
 """
 
 __author__ = "Marc Glisse"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 print("#####################################################################")
diff --git a/cython/example/simplex_tree_example.py b/cython/example/simplex_tree_example.py
index 51a60e73..28679015 100755
--- a/cython/example/simplex_tree_example.py
+++ b/cython/example/simplex_tree_example.py
@@ -8,7 +8,7 @@ import gudhi
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -25,7 +25,7 @@ import gudhi
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 print("#####################################################################")
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 6145e7f2..0f8f5e80 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
@@ -9,7 +9,7 @@ import argparse
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -26,18 +26,19 @@ import argparse
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 parser = argparse.ArgumentParser(description='TangentialComplex creation from '
                                  'points read in a OFF file.',
                                  epilog='Example: '
                                  'example/tangential_complex_plain_homology_from_off_file_example.py '
-                                 '-f ../data/points/tore3D_300.off'
+                                 '-f ../data/points/tore3D_300.off -i 3'
                                  '- 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("-i", "--intrisic_dim", type=int, required=True)
+parser.add_argument("-b", "--band", 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()
@@ -48,7 +49,7 @@ with open(args.file, 'r') as f:
         print("#####################################################################")
         print("TangentialComplex creation from points read in a OFF file")
         
-        tc = gudhi.TangentialComplex(off_file=args.file)
+        tc = gudhi.TangentialComplex(intrisic_dim = args.intrisic_dim, off_file=args.file)
         st = tc.create_simplex_tree()
     
         message = "Number of simplices=" + repr(st.num_simplices())
@@ -60,7 +61,7 @@ with open(args.file, 'r') as f:
         print(st.betti_numbers())
     
         if args.no_diagram == False:
-            pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+            pplot = gudhi.plot_persistence_diagram(diag, band=args.band)
             pplot.show()
     else:
         print(args.file, "is not a valid OFF file")
diff --git a/cython/example/witness_complex_from_nearest_landmark_table.py b/cython/example/witness_complex_from_nearest_landmark_table.py
index 92ed970b..e6b295ee 100755
--- a/cython/example/witness_complex_from_nearest_landmark_table.py
+++ b/cython/example/witness_complex_from_nearest_landmark_table.py
@@ -8,7 +8,7 @@ from gudhi import StrongWitnessComplex, SimplexTree
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -25,7 +25,7 @@ from gudhi import StrongWitnessComplex, SimplexTree
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 print("#####################################################################")
diff --git a/cython/gudhi.pyx.in b/cython/gudhi.pyx.in
index a8dd9f80..b94f2251 100644
--- a/cython/gudhi.pyx.in
+++ b/cython/gudhi.pyx.in
@@ -4,7 +4,7 @@
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016  INRIA
+   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
@@ -21,7 +21,7 @@
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016  INRIA"
+__copyright__ = "Copyright (C) 2016  Inria"
 __license__ = "GPL v3"
 __version__ = "@GUDHI_VERSION@"
 # This variable is used by doctest to find files
diff --git a/cython/include/Alpha_complex_interface.h b/cython/include/Alpha_complex_interface.h
index d47db71f..8cf527fc 100644
--- a/cython/include/Alpha_complex_interface.h
+++ b/cython/include/Alpha_complex_interface.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2016 INRIA
+ *    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
diff --git a/cython/include/Bottleneck_distance_interface.h b/cython/include/Bottleneck_distance_interface.h
index d5fbf6ea..5ad9d77d 100644
--- a/cython/include/Bottleneck_distance_interface.h
+++ b/cython/include/Bottleneck_distance_interface.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2016 INRIA
+ *    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
diff --git a/cython/include/Cubical_complex_interface.h b/cython/include/Cubical_complex_interface.h
index fad92c2c..85b717b3 100644
--- a/cython/include/Cubical_complex_interface.h
+++ b/cython/include/Cubical_complex_interface.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2016 INRIA
+ *    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
diff --git a/cython/include/Euclidean_strong_witness_complex_interface.h b/cython/include/Euclidean_strong_witness_complex_interface.h
index b9dd8177..d86355d6 100644
--- a/cython/include/Euclidean_strong_witness_complex_interface.h
+++ b/cython/include/Euclidean_strong_witness_complex_interface.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2016 INRIA
+ *    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
diff --git a/cython/include/Euclidean_witness_complex_interface.h b/cython/include/Euclidean_witness_complex_interface.h
index 2a09b3b5..dc303533 100644
--- a/cython/include/Euclidean_witness_complex_interface.h
+++ b/cython/include/Euclidean_witness_complex_interface.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2016 INRIA
+ *    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
diff --git a/cython/include/Off_reader_interface.h b/cython/include/Off_reader_interface.h
index 0ca55500..f6b14f38 100644
--- a/cython/include/Off_reader_interface.h
+++ b/cython/include/Off_reader_interface.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2016 INRIA
+ *    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
diff --git a/cython/include/Persistent_cohomology_interface.h b/cython/include/Persistent_cohomology_interface.h
index 55028fd0..8cf71a4e 100644
--- a/cython/include/Persistent_cohomology_interface.h
+++ b/cython/include/Persistent_cohomology_interface.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2016 INRIA
+ *    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
@@ -85,6 +85,32 @@ persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomol
     return persistence;
   }
 
+  std::vector<std::pair<std::vector<int>, std::vector<int>>> persistence_pairs() {
+    auto pairs = persistent_cohomology::Persistent_cohomology<FilteredComplex,
+      persistent_cohomology::Field_Zp>::get_persistent_pairs();
+
+    std::vector<std::pair<std::vector<int>, std::vector<int>>> persistence_pairs;
+    persistence_pairs.reserve(pairs.size());
+    for (auto pair : pairs) {
+      std::vector<int> birth;
+      if (get<0>(pair) != stptr_->null_simplex()) {
+        for (auto vertex : stptr_->simplex_vertex_range(get<0>(pair))) {
+          birth.push_back(vertex);
+        }
+      }
+
+      std::vector<int> death;
+      if (get<1>(pair) != stptr_->null_simplex()) {
+        for (auto vertex : stptr_->simplex_vertex_range(get<1>(pair))) {
+          death.push_back(vertex);
+        }
+      }
+
+      persistence_pairs.push_back(std::make_pair(birth, death));
+    }
+    return persistence_pairs;
+  }
+
  private:
   // A copy
   FilteredComplex* stptr_;
diff --git a/cython/include/Reader_utils_interface.h b/cython/include/Reader_utils_interface.h
index 8ec34f61..5f7527d9 100644
--- a/cython/include/Reader_utils_interface.h
+++ b/cython/include/Reader_utils_interface.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2017 INRIA
+ *    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
diff --git a/cython/include/Rips_complex_interface.h b/cython/include/Rips_complex_interface.h
index 02985727..8b6c9c35 100644
--- a/cython/include/Rips_complex_interface.h
+++ b/cython/include/Rips_complex_interface.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2016 INRIA
+ *    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
@@ -25,9 +25,7 @@
 
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Rips_complex.h>
-#include <gudhi/Points_off_io.h>
 #include <gudhi/distance_functions.h>
-#include <gudhi/reader_utils.h>
 
 #include "Simplex_tree_interface.h"
 
@@ -56,21 +54,6 @@ class Rips_complex_interface {
     }
   }
 
-  Rips_complex_interface(const std::string& file_name, double threshold, bool euclidean, bool from_file = true) {
-    if (euclidean) {
-      // Rips construction where file_name is an OFF file
-      Gudhi::Points_off_reader<Point_d> off_reader(file_name);
-      rips_complex_ = new Rips_complex<Simplex_tree_interface<>::Filtration_value>(off_reader.get_point_cloud(),
-                                                                                   threshold,
-                                                                                   Gudhi::Euclidean_distance());
-    } else {
-      // Rips construction where values is a distance matrix
-      Distance_matrix distances =
-          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_;
   }
diff --git a/cython/include/Simplex_tree_interface.h b/cython/include/Simplex_tree_interface.h
index 54a4f824..3481eeff 100644
--- a/cython/include/Simplex_tree_interface.h
+++ b/cython/include/Simplex_tree_interface.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2016 INRIA
+ *    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
diff --git a/cython/include/Strong_witness_complex_interface.h b/cython/include/Strong_witness_complex_interface.h
index d05eaac5..3c72c916 100644
--- a/cython/include/Strong_witness_complex_interface.h
+++ b/cython/include/Strong_witness_complex_interface.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2016 INRIA
+ *    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
diff --git a/cython/include/Subsampling_interface.h b/cython/include/Subsampling_interface.h
index b0f4a50a..f990da0c 100644
--- a/cython/include/Subsampling_interface.h
+++ b/cython/include/Subsampling_interface.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2016 INRIA
+ *    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
diff --git a/cython/include/Tangential_complex_interface.h b/cython/include/Tangential_complex_interface.h
index 0c3a510e..71418886 100644
--- a/cython/include/Tangential_complex_interface.h
+++ b/cython/include/Tangential_complex_interface.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2016 INRIA
+ *    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
@@ -45,24 +45,19 @@ class Tangential_complex_interface {
   using TC = Tangential_complex<Dynamic_kernel, CGAL::Dynamic_dimension_tag, CGAL::Parallel_tag>;
 
  public:
-  Tangential_complex_interface(const std::vector<std::vector<double>>& points) {
+  Tangential_complex_interface(int intrisic_dim, const std::vector<std::vector<double>>& points) {
     Dynamic_kernel k;
-    unsigned intrisic_dim = 0;
-    if (points.size() > 0)
-      intrisic_dim = points[0].size() - 1;
 
     tangential_complex_ = new TC(points, intrisic_dim, k);
     tangential_complex_->compute_tangential_complex();
     num_inconsistencies_ = tangential_complex_->number_of_inconsistent_simplices();
   }
 
-  Tangential_complex_interface(const std::string& off_file_name, bool from_file = true) {
-    Gudhi::Points_off_reader<Point_d> off_reader(off_file_name);
+  Tangential_complex_interface(int intrisic_dim, const std::string& off_file_name, bool from_file = true) {
     Dynamic_kernel k;
-    unsigned intrisic_dim = 0;
+
+    Gudhi::Points_off_reader<Point_d> off_reader(off_file_name);
     std::vector<Point_d> points = off_reader.get_point_cloud();
-    if (points.size() > 0)
-      intrisic_dim = points[0].size() - 1;
 
     tangential_complex_ = new TC(points, intrisic_dim, k);
     tangential_complex_->compute_tangential_complex();
diff --git a/cython/include/Witness_complex_interface.h b/cython/include/Witness_complex_interface.h
index 6501cc35..01b372e7 100644
--- a/cython/include/Witness_complex_interface.h
+++ b/cython/include/Witness_complex_interface.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2016 INRIA
+ *    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
diff --git a/cython/setup.py.in b/cython/setup.py.in
index c767e93d..ee381a1b 100644
--- a/cython/setup.py.in
+++ b/cython/setup.py.in
@@ -7,7 +7,7 @@ from Cython.Build import cythonize
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016  INRIA
+   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
@@ -24,7 +24,7 @@ from Cython.Build import cythonize
 """
 
 __author__ = "GUDHI Editorial Board"
-__copyright__ = "Copyright (C) 2016  INRIA"
+__copyright__ = "Copyright (C) 2016  Inria"
 __license__ = "GPL v3"
 
 gudhi = Extension(
@@ -46,4 +46,9 @@ setup(
     version='@GUDHI_VERSION@',
     url='http://gudhi.gforge.inria.fr/',
     ext_modules = cythonize(gudhi),
+    install_requires = [
+        "matplotlib",
+        "numpy",
+        "cython",
+        ],
 )
diff --git a/cython/test/test_alpha_complex.py b/cython/test/test_alpha_complex.py
index 2c76d9d7..e97f2530 100755
--- a/cython/test/test_alpha_complex.py
+++ b/cython/test/test_alpha_complex.py
@@ -6,7 +6,7 @@ from gudhi import AlphaComplex, SimplexTree
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -23,7 +23,7 @@ from gudhi import AlphaComplex, SimplexTree
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 
diff --git a/cython/test/test_bottleneck_distance.py b/cython/test/test_bottleneck_distance.py
index 3d982d34..4eb5848f 100755
--- a/cython/test/test_bottleneck_distance.py
+++ b/cython/test/test_bottleneck_distance.py
@@ -6,7 +6,7 @@ import gudhi
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -23,7 +23,7 @@ import gudhi
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 
diff --git a/cython/test/test_cubical_complex.py b/cython/test/test_cubical_complex.py
index 0e81554d..92e591e9 100755
--- a/cython/test/test_cubical_complex.py
+++ b/cython/test/test_cubical_complex.py
@@ -6,7 +6,7 @@ from gudhi import CubicalComplex
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -23,7 +23,7 @@ from gudhi import CubicalComplex
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 
@@ -72,6 +72,17 @@ def test_dimension_simple_constructor():
     assert cub.betti_numbers() == [1, 0, 0]
     assert cub.persistent_betti_numbers(0, 1000) == [0, 0, 0]
 
+def test_user_case_simple_constructor():
+    cub = CubicalComplex(dimensions=[3, 3],
+                         top_dimensional_cells = [float('inf'), 0.,0.,0.,1.,0.,0.,0.,0.])
+    assert cub.__is_defined() == True
+    assert cub.__is_persistence_defined() == False
+    assert cub.persistence() == [(1, (0.0, 1.0)), (0, (0.0, float('inf')))]
+    assert cub.__is_persistence_defined() == True
+    other_cub = CubicalComplex(dimensions=[3, 3],
+                               top_dimensional_cells = [1000., 0.,0.,0.,1.,0.,0.,0.,0.])
+    assert other_cub.persistence() == [(1, (0.0, 1.0)), (0, (0.0, float('inf')))]
+
 def test_dimension_file_constructor():
     # Create test file
     test_file = open('CubicalOneSphere.txt', 'w')
diff --git a/cython/test/test_euclidean_witness_complex.py b/cython/test/test_euclidean_witness_complex.py
index 737f1ef4..2f77210a 100755
--- a/cython/test/test_euclidean_witness_complex.py
+++ b/cython/test/test_euclidean_witness_complex.py
@@ -6,7 +6,7 @@ import gudhi
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -23,7 +23,7 @@ import gudhi
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 
diff --git a/cython/test/test_reader_utils.py b/cython/test/test_reader_utils.py
index 25591fb3..b240c84f 100755
--- a/cython/test/test_reader_utils.py
+++ b/cython/test/test_reader_utils.py
@@ -6,7 +6,7 @@ import gudhi
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2017 INRIA
+   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
@@ -23,7 +23,7 @@ import gudhi
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2017 INRIA"
+__copyright__ = "Copyright (C) 2017 Inria"
 __license__ = "GPL v3"
 
 
diff --git a/cython/test/test_rips_complex.py b/cython/test/test_rips_complex.py
index c7d2ead4..c37b5400 100755
--- a/cython/test/test_rips_complex.py
+++ b/cython/test/test_rips_complex.py
@@ -7,7 +7,7 @@ from math import sqrt
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -24,7 +24,7 @@ from math import sqrt
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 
diff --git a/cython/test/test_simplex_tree.py b/cython/test/test_simplex_tree.py
index 6dec5d94..cb701c9a 100755
--- a/cython/test/test_simplex_tree.py
+++ b/cython/test/test_simplex_tree.py
@@ -6,7 +6,7 @@ from gudhi import SimplexTree
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -23,7 +23,7 @@ from gudhi import SimplexTree
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 
@@ -161,3 +161,47 @@ def test_automatic_dimension():
     assert st.upper_bound_dimension() == 2
     assert st.dimension() == 1
     assert st.upper_bound_dimension() == 1
+
+def test_make_filtration_non_decreasing():
+    st = SimplexTree()
+    assert st.__is_defined() == True
+    assert st.__is_persistence_defined() == False
+
+    # Inserted simplex:
+    #    1
+    #    o
+    #   /X\
+    #  o---o---o---o
+    #  2   0   3\X/4
+    #            o
+    #            5
+    assert st.insert([2, 1, 0], filtration=2.0) == True
+    assert st.insert([3, 0], filtration=2.0) == True
+    assert st.insert([3, 4, 5], filtration=2.0) == True
+
+    assert st.make_filtration_non_decreasing() == False
+
+    # Because of non decreasing property of simplex tree, { 0 } , { 1 } and
+    # { 0, 1 } are going to be set from value 2.0 to 1.0
+    st.insert([0, 1, 6, 7], filtration=1.0);
+
+    assert st.make_filtration_non_decreasing() == False
+
+    # Modify specific values to test make_filtration_non_decreasing
+    st.assign_filtration([0,1,6,7], 0.8);
+    st.assign_filtration([0,1,6], 0.9);
+    st.assign_filtration([0,6], 0.6);
+    st.assign_filtration([3,4,5], 1.2);
+    st.assign_filtration([3,4], 1.1);
+    st.assign_filtration([4,5], 1.99);
+
+    assert st.make_filtration_non_decreasing() == True
+
+    assert st.filtration([0,1,6,7]) == 1.
+    assert st.filtration([0,1,6]) == 1.
+    assert st.filtration([0,1]) == 1.
+    assert st.filtration([0]) == 1.
+    assert st.filtration([1]) == 1.
+    assert st.filtration([3,4,5]) == 2.
+    assert st.filtration([3,4]) == 2.
+    assert st.filtration([4,5]) == 2.
diff --git a/cython/test/test_subsampling.py b/cython/test/test_subsampling.py
index 2caf4ddb..96906a6f 100755
--- a/cython/test/test_subsampling.py
+++ b/cython/test/test_subsampling.py
@@ -6,7 +6,7 @@ import gudhi
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -23,7 +23,7 @@ import gudhi
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 
diff --git a/cython/test/test_tangential_complex.py b/cython/test/test_tangential_complex.py
index 8aa4023c..5385a0d3 100755
--- a/cython/test/test_tangential_complex.py
+++ b/cython/test/test_tangential_complex.py
@@ -6,7 +6,7 @@ from gudhi import TangentialComplex, SimplexTree
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -23,13 +23,13 @@ from gudhi import TangentialComplex, SimplexTree
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
 
 def test_tangential():
     point_list = [[0.0, 0.0], [1.0, 0.0], [0.0, 1.0], [1.0, 1.0]]
-    tc = TangentialComplex(points=point_list)
+    tc = TangentialComplex(intrisic_dim = 1, points=point_list)
     assert tc.__is_defined() == True
     assert tc.num_vertices() == 4
 
diff --git a/cython/test/test_witness_complex.py b/cython/test/test_witness_complex.py
index 7d1fb6be..bcbc521b 100755
--- a/cython/test/test_witness_complex.py
+++ b/cython/test/test_witness_complex.py
@@ -6,7 +6,7 @@ from gudhi import WitnessComplex, StrongWitnessComplex, SimplexTree
 
    Author(s):       Vincent Rouvreau
 
-   Copyright (C) 2016 INRIA
+   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
@@ -23,7 +23,7 @@ from gudhi import WitnessComplex, StrongWitnessComplex, SimplexTree
 """
 
 __author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 INRIA"
+__copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"