Merge last trunk modifications

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_from_correlation_matrix@2725 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 78f35b92214c207f00b26ea87ca88d20abeea53d

5 files changed, 4 insertions, 14 deletions

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/example/simplex_tree_example.py b/src/cython/example/simplex_tree_example.py
index 3af20fcf..831d9da8 100755
--- a/src/cython/example/simplex_tree_example.py
+++ b/src/cython/example/simplex_tree_example.py
@@ -52,7 +52,6 @@ else:
 st.set_dimension(3)
 print("dimension=", st.dimension())
 
-st.set_filtration(4.0)
 st.initialize_filtration()
 print("filtration=", st.get_filtration())
 print("filtration[1, 2]=", st.filtration([1, 2]))
diff --git a/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/test/test_simplex_tree.py b/src/cython/test/test_simplex_tree.py
index 3ae537e3..4d452d7d 100755
--- a/src/cython/test/test_simplex_tree.py
+++ b/src/cython/test/test_simplex_tree.py
@@ -53,7 +53,6 @@ def test_insertion():
     assert st.find([2, 3]) == False
 
     # filtration test
-    st.set_filtration(5.0)
     st.initialize_filtration()
     assert st.filtration([0, 1, 2]) == 4.0
     assert st.filtration([0, 2]) == 4.0