6 files changed, 84 insertions, 33 deletions
diff --git a/src/cython/cython/simplex_tree.pyx b/src/cython/cython/simplex_tree.pyx
index 8a436619..0cb575d2 100644
--- a/src/cython/cython/simplex_tree.pyx
+++ b/src/cython/cython/simplex_tree.pyx
@@ -106,8 +106,8 @@ cdef class SimplexTree:
         return self.pcohptr != NULL
 
     def filtration(self, simplex):
-        """This function returns the simplicial complex filtration value for a
-        given N-simplex.
+        """This function returns the filtration value for a given N-simplex in
+        this simplicial complex, or +infinity if it is not in the complex.
 
         :param simplex: The N-simplex, represented by a list of vertex.
         :type simplex: list of int.
@@ -222,14 +222,17 @@ cdef class SimplexTree:
 
     def insert(self, simplex, filtration=0.0):
         """This function inserts the given N-simplex and its subfaces with the
-        given filtration value (default value is '0.0').
+        given filtration value (default value is '0.0'). If some of those
+        simplices are already present with a higher filtration value, their
+        filtration value is lowered.
 
         :param simplex: The N-simplex to insert, represented by a list of
             vertex.
         :type simplex: list of int.
         :param filtration: The filtration value of the simplex.
         :type filtration: float.
-        :returns:  true if the simplex was found, false otherwise.
+        :returns:  true if the simplex was not yet in the complex, false
+            otherwise (whatever its original filtration value).
         :rtype:  bool
         """
         cdef vector[int] csimplex
diff --git a/src/cython/doc/cubical_complex_user.rst b/src/cython/doc/cubical_complex_user.rst
index 2bfac62a..34598f02 100644
--- a/src/cython/doc/cubical_complex_user.rst
+++ b/src/cython/doc/cubical_complex_user.rst
@@ -81,23 +81,7 @@ filtration to all cubes. There are a number of constructors that can be used to
 who want to use the code directly. They can be found in the :doc:`cubical_complex_ref`.
 Currently one input from a text file is used. It uses a format used already in
 `Perseus software <http://www.sas.upenn.edu/~vnanda/perseus/>`_ by Vidit Nanda.
-Below we are providing a description of the format. The first line contains a number d begin the dimension of the
-bitmap (2 in the example below). Next d lines are the numbers of top dimensional cubes in each dimensions (3 and 3
-in the example below). Next, in lexicographical order, the filtration of top dimensional cubes is given (1 4 6 8
-20 4 7 6 5 in the example below).
-
-.. figure::
-    ../../doc/Bitmap_cubical_complex/exampleBitmap.png
-    :alt: Example of a input data.
-    :figclass: align-center
-
-    Example of a input data.
-
-The input file for the following complex is:
-
-.. literalinclude:: ../../data/bitmap/cubicalcomplexdoc.txt
-
-.. centered:: ../../data/bitmap/cubicalcomplexdoc.txt
+The file format is described here: :doc:`Perseus <fileformats>`.
 
 .. testcode::
 
@@ -124,15 +108,9 @@ Imposing periodic boundary conditions in the direction i, means that the left an
 :math:`\mathcal{K}` are considered the same. In particular, if for a bitmap :math:`\mathcal{K}` periodic boundary
 conditions are imposed in all directions, then complex :math:`\mathcal{K}` became n-dimensional torus. One can use
 various constructors from the file Bitmap_cubical_complex_periodic_boundary_conditions_base.h to construct cubical
-complex with periodic boundary conditions. One can also use Perseus style input files. To indicate periodic boundary
-conditions in a given direction, then number of top dimensional cells in this direction have to be multiplied by -1.
-For instance:
-
-.. literalinclude:: ../../data/bitmap/periodiccubicalcomplexdoc.txt
-
-.. centered:: ../../data/bitmap/periodiccubicalcomplexdoc.txt
+complex with periodic boundary conditions.
 
-Indicate that we have imposed periodic boundary conditions in the direction x, but not in the direction y.
+One can also use Perseus style input files (see :doc:`Perseus <fileformats>`) for the specific periodic case:
 
 .. testcode::
 
@@ -149,6 +127,23 @@ the program output is:
     
     Periodic cubical complex is of dimension 2 - 42 simplices.
 
+Or it can be defined as follows:
+
+.. testcode::
+
+    from gudhi import PeriodicCubicalComplex as pcc
+    periodic_cc = pcc(dimensions=[3,3],
+         top_dimensional_cells= [0, 0, 0, 0, 1, 0, 0, 0, 0],
+         periodic_dimensions=[True, False])
+    result_str = 'Periodic cubical complex is of dimension ' + repr(periodic_cc.dimension()) + ' - ' + \
+        repr(periodic_cc.num_simplices()) + ' simplices.'
+    print(result_str)
+
+the program output is:
+
+.. testoutput::
+
+    Periodic cubical complex is of dimension 2 - 42 simplices.
 Examples.
 ---------
 
diff --git a/src/cython/doc/fileformats.rst b/src/cython/doc/fileformats.rst
index 156ef4e4..4f0b6f6d 100644
--- a/src/cython/doc/fileformats.rst
+++ b/src/cython/doc/fileformats.rst
@@ -23,7 +23,7 @@ Here is a simple sample file::
     3 34.2 34.974
     4 3. inf
 
-Other sample files can be found in the data/persistence_diagram folder.
+Other sample files can be found in the `data/persistence_diagram` folder.
 
 Such files can be generated with
 :meth:`gudhi.SimplexTree.write_persistence_diagram`, read with
@@ -31,3 +31,56 @@ Such files can be generated with
 :meth:`gudhi.read_persistence_intervals_in_dimension` and displayed with
 :meth:`gudhi.plot_persistence_barcode` or
 :meth:`gudhi.plot_persistence_diagram`.
+
+Iso-cuboid
+**********
+
+Such a file describes an iso-oriented cuboid with diagonal opposite vertices
+(min_x, min_y, min_z,...) and (max_x, max_y, max_z, ...). The format is::
+
+    min_x min_y [min_z ...]
+    max_x max_y [max_z ...]
+
+Here is a simple sample file in the 3D case::
+
+    -1. -1. -1.
+    1. 1. 1.
+
+
+Perseus
+*******
+
+This file format is the format used by the
+`Perseus software <http://www.sas.upenn.edu/~vnanda/perseus/>`_ by Vidit Nanda.
+The first line contains a number d begin the dimension of the bitmap (2 in the
+example below). Next d lines are the numbers of top dimensional cubes in each
+dimensions (3 and 3 in the example below). Next, in lexicographical order, the
+filtration of top dimensional cubes is given (1 4 6 8 20 4 7 6 5 in the example
+below).
+
+.. figure::
+    ../../doc/Bitmap_cubical_complex/exampleBitmap.png
+    :alt: Example of a input data.
+    :figclass: align-center
+
+    Example of a input data.
+
+The input file for the following complex is:
+
+.. literalinclude:: ../../data/bitmap/cubicalcomplexdoc.txt
+
+.. centered:: ../../data/bitmap/cubicalcomplexdoc.txt
+
+To indicate periodic boundary conditions in a given direction, then number of
+top dimensional cells in this direction have to be multiplied by -1. For
+instance:
+
+.. literalinclude:: ../../data/bitmap/periodiccubicalcomplexdoc.txt
+
+.. centered:: ../../data/bitmap/periodiccubicalcomplexdoc.txt
+
+
+Indicate that we have imposed periodic boundary conditions in the direction x,
+but not in the direction y.
+
+Other sample files can be found in the `data/bitmap` folder.
diff --git a/src/cython/doc/installation.rst b/src/cython/doc/installation.rst
index c182f176..2f689497 100644
--- a/src/cython/doc/installation.rst
+++ b/src/cython/doc/installation.rst
@@ -5,7 +5,7 @@ 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
+version 1.56.0 or more recent. It is a multi-platform library and compiles on
 Linux, Mac OSX and Visual Studio 2015.
 It also requires cmake to generate makefiles, and cython to compile the
 library.
diff --git a/src/cython/doc/witness_complex_user.rst b/src/cython/doc/witness_complex_user.rst
index 29413269..99be5185 100644
--- a/src/cython/doc/witness_complex_user.rst
+++ b/src/cython/doc/witness_complex_user.rst
@@ -121,7 +121,7 @@ Example2: Computing persistence using strong relaxed witness complex
 
 Here is an example of constructing a strong witness complex filtration and computing persistence on it:
 
-* :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py>`
+* :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>`
 
 Bibliography
 ============
diff --git a/src/cython/include/Tangential_complex_interface.h b/src/cython/include/Tangential_complex_interface.h
index ecf014b3..0c3a510e 100644
--- a/src/cython/include/Tangential_complex_interface.h
+++ b/src/cython/include/Tangential_complex_interface.h
@@ -105,7 +105,7 @@ class Tangential_complex_interface {
   }
 
   void create_simplex_tree(Simplex_tree<>* simplex_tree) {
-    int max_dim = tangential_complex_->create_complex<Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>>(*simplex_tree);
+    tangential_complex_->create_complex<Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>>(*simplex_tree);
     simplex_tree->initialize_filtration();
   }