10 files changed, 40 insertions, 44 deletions
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index ec8589f0..afca9d60 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -185,6 +185,19 @@ if(CYTHON_FOUND)
 
     add_gudhi_py_test(test_tangential_complex)
 
+    # Witness complex AND Subsampling
+    add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
+             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+
+    add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
+             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+
     # Subsampling
     add_gudhi_py_test(test_subsampling)
 
@@ -218,18 +231,6 @@ if(CYTHON_FOUND)
 
   if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
     # Euclidean witness
-    add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
-             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
-
-    add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
-             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
-
     add_gudhi_py_test(test_euclidean_witness_complex)
 
   endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
diff --git a/src/cython/cython/simplex_tree.pyx b/src/cython/cython/simplex_tree.pyx
index 47aa5311..45487158 100644
--- a/src/cython/cython/simplex_tree.pyx
+++ b/src/cython/cython/simplex_tree.pyx
@@ -36,9 +36,7 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi":
 
     cdef cppclass Simplex_tree_interface_full_featured "Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_full_featured>":
         Simplex_tree()
-        double filtration()
         double simplex_filtration(vector[int] simplex)
-        void set_filtration(double filtration)
         void initialize_filtration()
         int num_vertices()
         int num_simplices()
@@ -115,14 +113,6 @@ cdef class SimplexTree:
         """
         return self.thisptr.simplex_filtration(simplex)
 
-    def set_filtration(self, filtration):
-        """This function sets the main simplicial complex filtration value.
-
-        :param filtration: The filtration value.
-        :type filtration: float.
-        """
-        self.thisptr.set_filtration(<double> filtration)
-
     def initialize_filtration(self):
         """This function initializes and sorts the simplicial complex
         filtration vector.
diff --git a/src/cython/doc/bottleneck_distance_user.rst b/src/cython/doc/bottleneck_distance_user.rst
index 0066992f..7692dce2 100644
--- a/src/cython/doc/bottleneck_distance_user.rst
+++ b/src/cython/doc/bottleneck_distance_user.rst
@@ -25,7 +25,7 @@ This example computes the bottleneck distance from 2 persistence diagrams:
     message = "Bottleneck distance approximation=" + '%.2f' % gudhi.bottleneck_distance(diag1, diag2, 0.1)
     print(message)
 
-    message = "Bottleneck distance exact value=" + '%.2f' % gudhi.bottleneck_distance(diag1, diag2, 0)
+    message = "Bottleneck distance value=" + '%.2f' % gudhi.bottleneck_distance(diag1, diag2)
     print(message)
 
 The output is:
@@ -33,4 +33,4 @@ The output is:
 .. testoutput::
 
     Bottleneck distance approximation=0.81
-    Bottleneck distance exact value=0.75
+    Bottleneck distance value=0.75
diff --git a/src/cython/doc/citation.rst b/src/cython/doc/citation.rst
index 6cdfb7cc..f4fdf83b 100644
--- a/src/cython/doc/citation.rst
+++ b/src/cython/doc/citation.rst
@@ -12,4 +12,4 @@ Manual, as well as for publications directly related to the GUDHI library.
 GUDHI bibtex
 ************
 
-.. literalinclude:: how_to_cite_gudhi.bib
+.. literalinclude:: ../../biblio/how_to_cite_gudhi.bib
diff --git a/src/cython/doc/cubical_complex_user.rst b/src/cython/doc/cubical_complex_user.rst
index 36fa3ba9..2bfac62a 100644
--- a/src/cython/doc/cubical_complex_user.rst
+++ b/src/cython/doc/cubical_complex_user.rst
@@ -59,7 +59,7 @@ directions, allows to determine, dimension, neighborhood, boundary and coboundar
 :math:`C \in \mathcal{K}`.
 
 .. figure::
-    img/Cubical_complex_representation.png
+    ../../doc/Bitmap_cubical_complex/Cubical_complex_representation.png
     :alt: Cubical complex.
     :figclass: align-center
 
@@ -87,7 +87,7 @@ in the example below). Next, in lexicographical order, the filtration of top dim
 20 4 7 6 5 in the example below).
 
 .. figure::
-    img/exampleBitmap.png
+    ../../doc/Bitmap_cubical_complex/exampleBitmap.png
     :alt: Example of a input data.
     :figclass: align-center
 
@@ -95,9 +95,9 @@ in the example below). Next, in lexicographical order, the filtration of top dim
 
 The input file for the following complex is:
 
-.. literalinclude:: cubicalcomplexdoc.txt
+.. literalinclude:: ../../data/bitmap/cubicalcomplexdoc.txt
 
-.. centered:: data/bitmap/cubicalcomplexdoc.txt
+.. centered:: ../../data/bitmap/cubicalcomplexdoc.txt
 
 .. testcode::
 
@@ -128,9 +128,9 @@ complex with periodic boundary conditions. One can also use Perseus style input
 conditions in a given direction, then number of top dimensional cells in this direction have to be multiplied by -1.
 For instance:
 
-.. literalinclude:: periodiccubicalcomplexdoc.txt
+.. literalinclude:: ../../data/bitmap/periodiccubicalcomplexdoc.txt
 
-.. centered:: 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.
 
diff --git a/src/cython/doc/installation.rst b/src/cython/doc/installation.rst
index f98a5039..c182f176 100644
--- a/src/cython/doc/installation.rst
+++ b/src/cython/doc/installation.rst
@@ -68,31 +68,32 @@ The :doc:`Alpha complex </alpha_complex_user>`,
 C++ library which provides easy access to efficient and reliable geometric
 algorithms.
 
-Having CGAL version 4.6.0 or higher installed is recommended. The procedure to
-install this library according to your operating system is detailed
+Having CGAL,  the Computational Geometry Algorithms Library, version 4.7.0 or
+higher installed is recommended. The procedure to install this library
+according to your operating system is detailed
 `here <http://doc.cgal.org/latest/Manual/installation.html>`_.
 
-The following examples require the Computational Geometry Algorithms Library:
-
-.. only:: builder_html
-
-    * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>`
-    * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>`
-
-The following example requires CGAL version ≥ 4.7.0:
+The following examples requires CGAL version ≥ 4.7.0:
 
 .. only:: builder_html
 
     * :download:`alpha_complex_diagram_persistence_from_off_file_example.py <../example/alpha_complex_diagram_persistence_from_off_file_example.py>`
     * :download:`alpha_complex_from_points_example.py <../example/alpha_complex_from_points_example.py>`
 
-The following example requires CGAL version ≥ 4.8.0:
+The following examples requires CGAL version ≥ 4.8.0:
 
 .. only:: builder_html
 
     * :download:`bottleneck_basic_example.py <../example/bottleneck_basic_example.py>`
     * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>`
 
+The following examples requires CGAL version ≥ 4.8.1:
+
+.. only:: builder_html
+
+    * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>`
+    * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>`
+
 Eigen3
 ======
 
diff --git a/src/cython/example/simplex_tree_example.py b/src/cython/example/simplex_tree_example.py
index 7e4b0b6c..51a60e73 100755
--- a/src/cython/example/simplex_tree_example.py
+++ b/src/cython/example/simplex_tree_example.py
@@ -50,7 +50,6 @@ else:
 
 print("dimension=", st.dimension())
 
-st.set_filtration(4.0)
 st.initialize_filtration()
 print("filtration=", st.get_filtration())
 print("filtration[1, 2]=", st.filtration([1, 2]))
diff --git a/src/cython/include/Reader_utils_interface.h b/src/cython/include/Reader_utils_interface.h
index b87b6cca..8ec34f61 100644
--- a/src/cython/include/Reader_utils_interface.h
+++ b/src/cython/include/Reader_utils_interface.h
@@ -28,6 +28,8 @@
 #include <iostream>
 #include <vector>
 #include <string>
+#include <map>
+#include <utility>  // for pair<>
 
 namespace Gudhi {
 
diff --git a/src/cython/include/Rips_complex_interface.h b/src/cython/include/Rips_complex_interface.h
index d06ee4bd..02985727 100644
--- a/src/cython/include/Rips_complex_interface.h
+++ b/src/cython/include/Rips_complex_interface.h
@@ -71,6 +71,10 @@ class Rips_complex_interface {
     }
   }
 
+  ~Rips_complex_interface() {
+    delete rips_complex_;
+  }
+
   void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, int dim_max) {
     rips_complex_->create_complex(*simplex_tree, dim_max);
     simplex_tree->initialize_filtration();
diff --git a/src/cython/test/test_simplex_tree.py b/src/cython/test/test_simplex_tree.py
index a6d6a9f3..801d52b7 100755
--- a/src/cython/test/test_simplex_tree.py
+++ b/src/cython/test/test_simplex_tree.py
@@ -57,7 +57,6 @@ def test_insertion():
     assert st.find([2, 3]) == False
 
     # filtration test
-    st.set_filtration(5.0)
     st.initialize_filtration()
     assert st.filtration([0, 1, 2]) == 4.0
     assert st.filtration([0, 2]) == 4.0