Merge code reviews fix

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2325 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 1a35ff8f60aee0bd150db7b571b13a50e843851a

28 files changed, 264 insertions, 191 deletions

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 18cd0ca2..aef771d0 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -16,6 +16,8 @@ enable_testing()
 include("${CMAKE_MODULE_PATH}/GUDHI_user_version_target.txt")
 # For "make doxygen"
 include("${CMAKE_MODULE_PATH}/GUDHI_doxygen_target.txt")
+# This variable is used by Cython CMakeLists.txt to know its path
+set(GUDHI_CYTHON_PATH "src/cython")
 # For third parties libraries management - To be done last as CGAL updates CMAKE_MODULE_PATH
 include("${CMAKE_MODULE_PATH}/GUDHI_third_party_libraries.txt")
 
@@ -87,6 +89,5 @@ add_subdirectory(data/points/generator)
 
 add_subdirectory(src/GudhUI)
 
-# This variable is used by Cython CMakeLists.txt to know its path
-set(GUDHI_CYTHON_PATH "src/cython")
+# specific for cython module
 add_subdirectory(${GUDHI_CYTHON_PATH})
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 4fa73662..0c16c9cc 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -13,6 +13,8 @@ list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/modules/")
 set(GUDHI_USER_VERSION_DIR ${CMAKE_SOURCE_DIR})
 include(${CMAKE_MODULE_PATH}/GUDHI_doxygen_target.txt)
 
+# This variable is used by Cython CMakeLists.txt to know its path
+set(GUDHI_CYTHON_PATH "cython")
 # For third parties libraries management - To be done last as CGAL updates CMAKE_MODULE_PATH
 include("${CMAKE_MODULE_PATH}/GUDHI_third_party_libraries.txt")
 
@@ -56,12 +58,9 @@ add_subdirectory(example/Bottleneck_distance)
 # data points generator
 add_subdirectory(data/points/generator)
 
-# Please let GudhUI in last compilation position as QT is known to modify CMAKE_CXX_FLAGS
-# GudhUI
 add_subdirectory(GudhUI)
 
-# This variable is used by Cython CMakeLists.txt to know its path
-set(GUDHI_CYTHON_PATH "cython")
+# specific for cython module
 add_subdirectory(${GUDHI_CYTHON_PATH})
 #---------------------------------------------------------------------------------------
 
diff --git a/src/cmake/modules/GUDHI_third_party_libraries.txt b/src/cmake/modules/GUDHI_third_party_libraries.txt
index 1974f70f..2ddc9f1f 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.txt
+++ b/src/cmake/modules/GUDHI_third_party_libraries.txt
@@ -105,3 +105,49 @@ LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
 
 message(STATUS "boost include dirs:" ${Boost_INCLUDE_DIRS})
 message(STATUS "boost library dirs:" ${Boost_LIBRARY_DIRS})
+
+macro( find_the_lib placeholder THE_LIBS )
+  set (THE_LIB_WE_FOUND "NO")
+  foreach(THE_LIB ${THE_LIBS})
+    if(EXISTS ${THE_LIB})
+      get_filename_component(THE_LIB_WE ${THE_LIB} NAME_WE)
+      if (NOT THE_LIB_WE_FOUND)
+        set (THE_LIB_WE_FOUND "YES")
+        set(returnValue "${THE_LIB_WE}")
+      endif(NOT THE_LIB_WE_FOUND)
+    endif(EXISTS ${THE_LIB})
+  endforeach(THE_LIB ${THE_LIBS})
+endmacro( find_the_lib )
+
+# Find the correct Python interpreter.
+# Can be set with -DPYTHON_EXECUTABLE=/usr/bin/python3 or -DPython_ADDITIONAL_VERSIONS=3 for instance.
+if(PYTHON_EXECUTABLE)
+  if(NOT EXISTS "${PYTHON_EXECUTABLE}")
+    message(FATAL_ERROR "ERROR: ${PYTHON_EXECUTABLE} does not exist.")
+  endif(NOT EXISTS "${PYTHON_EXECUTABLE}")
+endif(PYTHON_EXECUTABLE)
+find_package(PythonInterp)
+
+if(NOT GUDHI_CYTHON_PATH)
+  message(FATAL_ERROR "ERROR: GUDHI_CYTHON_PATH is not valid.")
+endif(NOT GUDHI_CYTHON_PATH)
+
+if(PYTHONINTERP_FOUND)
+  # Default found version 2
+  if(PYTHON_VERSION_MAJOR EQUAL 2)
+    FIND_PROGRAM(CYTHON_PATH cython)
+    # Unitary tests are available through py.test
+    find_program( PYTEST_PATH py.test )
+    # Documentation generation is available through sphinx
+    find_program( SPHINX_PATH sphinx-build )
+  elseif(PYTHON_VERSION_MAJOR EQUAL 3)
+    FIND_PROGRAM(CYTHON_PATH cython3)
+    # Unitary tests are available through py.test
+    find_program( PYTEST_PATH py.test )
+    # Documentation generation is available through sphinx
+    set(SPHINX_PATH "${CMAKE_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build")
+  else()
+    message(FATAL_ERROR "ERROR: Try to compile the Cython interface. Python version ${PYTHON_VERSION_STRING} is not valid.")
+  endif(PYTHON_VERSION_MAJOR EQUAL 2)
+endif(PYTHONINTERP_FOUND)
+
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 9dcb2cf4..51c208aa 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -1,45 +1,6 @@
 cmake_minimum_required(VERSION 2.8)
 project(Cython)
 
-macro( find_the_lib placeholder THE_LIBS )
-  set (THE_LIB_WE_FOUND "NO")
-  foreach(THE_LIB ${THE_LIBS})
-    if(EXISTS ${THE_LIB})
-      get_filename_component(THE_LIB_WE ${THE_LIB} NAME_WE)
-      if (NOT THE_LIB_WE_FOUND)
-        set (THE_LIB_WE_FOUND "YES")
-        set(returnValue "${THE_LIB_WE}")
-      endif(NOT THE_LIB_WE_FOUND)
-    endif(EXISTS ${THE_LIB})
-  endforeach(THE_LIB ${THE_LIBS})
-endmacro( find_the_lib )
-
-# Find the correct Python interpreter. Can be set with -DPYTHON_EXECUTABLE=/usr/bin/python3 for instance.
-if(PYTHON_EXECUTABLE)
-  if(NOT EXISTS "${PYTHON_EXECUTABLE}")
-    message(FATAL_ERROR "ERROR: ${PYTHON_EXECUTABLE} does not exist.")
-  endif(NOT EXISTS "${PYTHON_EXECUTABLE}")
-endif(PYTHON_EXECUTABLE)
-include(FindPythonInterp)
-
-if(PYTHONINTERP_FOUND)
-  if(PYTHON_VERSION_MAJOR EQUAL 2)
-    FIND_PROGRAM(CYTHON_PATH cython)
-    # Unitary tests are available through py.test
-    find_program( PYTEST_PATH py.test )
-    # Documentation generation is available through sphinx
-    find_program( SPHINX_PATH sphinx-build )
-  elseif(PYTHON_VERSION_MAJOR EQUAL 3)
-    FIND_PROGRAM(CYTHON_PATH cython3)
-    # Unitary tests are available through py.test
-    find_program( PYTEST_PATH py.test )
-    # Documentation generation is available through sphinx
-    set(SPHINX_PATH "${CMAKE_CURRENT_BINARY_DIR}/doc/python3-sphinx-build")
-  else()
-    message(FATAL_ERROR "ERROR: Try to compile the Cython interface. Python version ${PYTHON_VERSION_STRING} is not valid.")
-  endif(PYTHON_VERSION_MAJOR EQUAL 2)
-endif(PYTHONINTERP_FOUND)
-
 if(CYTHON_PATH)
   message("${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_PATH} - py.test is ${PYTEST_PATH} - Sphinx is ${SPHINX_PATH}")
 
@@ -179,8 +140,8 @@ if(CYTHON_PATH)
 
   # Specific for Mac
   if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
-      set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-mmacosx-version-min=10.9', ")
-      set(GUDHI_CYTHON_EXTRA_LINK_ARGS "${GUDHI_CYTHON_EXTRA_LINK_ARGS}'-mmacosx-version-min=10.9', ")
+      set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-mmacosx-version-min=10.12', ")
+      set(GUDHI_CYTHON_EXTRA_LINK_ARGS "${GUDHI_CYTHON_EXTRA_LINK_ARGS}'-mmacosx-version-min=10.12', ")
   endif(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
 
   # Loop on INCLUDE_DIRECTORIES PROPERTY
@@ -215,9 +176,89 @@ if(CYTHON_PATH)
                     COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/ to your PYTHONPATH before using examples or tests")
 
   if(UNIX)
-      set( ENV{PYTHONPATH} $ENV{PYTHONPATH}:${CMAKE_CURRENT_BINARY_DIR}/ )
+    set( ENV{PYTHONPATH} $ENV{PYTHONPATH}:${CMAKE_CURRENT_BINARY_DIR}/ )
   endif(UNIX)
 
+  # Test examples
+  add_test(NAME alpha_complex_from_points_example_py_test
+           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_complex_from_points_example.py")
+  set_tests_properties(alpha_complex_from_points_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+  add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
+           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
+           --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6)
+  set_tests_properties(alpha_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+  add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test
+           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
+           -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
+  set_tests_properties(alpha_rips_persistence_bottleneck_distance_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+  add_test(NAME bottleneck_basic_example_py_test
+           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/bottleneck_basic_example.py")
+  set_tests_properties(bottleneck_basic_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+  add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
+           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
+           --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+  set_tests_properties(euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+  add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
+           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
+           --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+  set_tests_properties(euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+  add_test(NAME periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test
+           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py"
+           --no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt)
+  set_tests_properties(periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+  add_test(NAME random_cubical_complex_persistence_example_py_test
+           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/random_cubical_complex_persistence_example.py"
+           10 10 10)
+  set_tests_properties(random_cubical_complex_persistence_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+  add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test
+           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
+           --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3)
+  set_tests_properties(rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+  add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test
+           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+           COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py
+           --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off  -e 0.25 -d 3)
+  set_tests_properties(rips_complex_diagram_persistence_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+  add_test(NAME rips_complex_from_points_example_py_test
+           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+           COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/rips_complex_from_points_example.py)
+  set_tests_properties(rips_complex_from_points_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+  add_test(NAME simplex_tree_example_py_test
+           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+           COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/simplex_tree_example.py)
+  set_tests_properties(simplex_tree_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+  add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
+           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+           COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
+           --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
+  set_tests_properties(tangential_complex_plain_homology_from_off_file_example_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
+  add_test(NAME witness_complex_from_nearest_landmark_table_py_test
+           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+           COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/example/witness_complex_from_nearest_landmark_table.py)
+  set_tests_properties(witness_complex_from_nearest_landmark_table_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+
   # Unitary tests are available through py.test
   if(PYTEST_PATH)
     add_test(
diff --git a/src/cython/cython/bottleneck_distance.pyx b/src/cython/cython/bottleneck_distance.pyx
index ee3e6ef9..9fb377ff 100644
--- a/src/cython/cython/bottleneck_distance.pyx
+++ b/src/cython/cython/bottleneck_distance.pyx
@@ -33,7 +33,7 @@ cdef extern from "Bottleneck_distance_interface.h" namespace "Gudhi::persistence
     double bottleneck(vector[pair[double, double]], vector[pair[double, double]], double)
     double bottleneck(vector[pair[double, double]], vector[pair[double, double]])
 
-def bottleneck_distance(diagram_1, diagram_2, e=0.0):
+def bottleneck_distance(diagram_1, diagram_2, e=None):
     """This function returns the point corresponding to a given vertex.
 
     :param diagram_1: The first diagram.
@@ -53,7 +53,9 @@ def bottleneck_distance(diagram_1, diagram_2, e=0.0):
     :rtype: float
     :returns: the bottleneck distance.
     """
-    if e is 0.0:
+    if e is None:
+        # Default value is the smallest double value (not 0, 0 is for exact version)
         return bottleneck(diagram_1, diagram_2)
     else:
+        # Can be 0 for exact version
         return bottleneck(diagram_1, diagram_2, e)
diff --git a/src/cython/cython/cubical_complex.pyx b/src/cython/cython/cubical_complex.pyx
index 1ed6bc5e..ffc85130 100644
--- a/src/cython/cython/cubical_complex.pyx
+++ b/src/cython/cython/cubical_complex.pyx
@@ -60,16 +60,16 @@ cdef class CubicalComplex:
     def __init__(self, dimensions=None, top_dimensional_cells=None,
                   perseus_file=''):
         """CubicalComplex constructor from dimensions and
-        top_dimensional_cells or from a perseus file style name.
+        top_dimensional_cells or from a Perseus-style file name.
 
         :param dimensions: A list of number of top dimensional cells.
         :type dimensions: list of int
-        :param top_dimensional_cells: A list of top dimensional cells.
+        :param top_dimensional_cells: A list of cells filtration values.
         :type top_dimensional_cells: list of double
 
         Or
 
-        :param perseus_file: A perseus file style name.
+        :param perseus_file: A Perseus-style file name.
         :type perseus_file: string
         """
 
@@ -85,7 +85,7 @@ cdef class CubicalComplex:
                 print("file " + perseus_file + " not found.")
         else:
             print("CubicalComplex can be constructed from dimensions and "
-              "top_dimensional_cells or from a perseus file style name.")
+              "top_dimensional_cells or from a Perseus-style file name.")
 
     def __dealloc__(self):
         if self.thisptr != NULL:
diff --git a/src/cython/cython/periodic_cubical_complex.pyx b/src/cython/cython/periodic_cubical_complex.pyx
index 88cb4395..581c7b69 100644
--- a/src/cython/cython/periodic_cubical_complex.pyx
+++ b/src/cython/cython/periodic_cubical_complex.pyx
@@ -60,16 +60,16 @@ cdef class PeriodicCubicalComplex:
     def __init__(self, dimensions=None, top_dimensional_cells=None,
                   perseus_file=''):
         """PeriodicCubicalComplex constructor from dimensions and
-        top_dimensional_cells or from a perseus file style name.
+        top_dimensional_cells or from a Perseus-style file name.
 
         :param dimensions: A list of number of top dimensional cells.
         :type dimensions: list of int
-        :param top_dimensional_cells: A list of top dimensional cells.
+        :param top_dimensional_cells: A list of cells filtration values.
         :type top_dimensional_cells: list of double
 
         Or
 
-        :param perseus_file: A perseus file style name.
+        :param perseus_file: A Perseus-style file name.
         :type perseus_file: string
         """
 
@@ -85,7 +85,7 @@ cdef class PeriodicCubicalComplex:
                 print("file " + perseus_file + " not found.")
         else:
             print("CubicalComplex can be constructed from dimensions and "
-              "top_dimensional_cells or from a perseus file style name.")
+              "top_dimensional_cells or from a Perseus-style file name.")
 
     def __dealloc__(self):
         if self.thisptr != NULL:
diff --git a/src/cython/cython/simplex_tree.pyx b/src/cython/cython/simplex_tree.pyx
index 148227e1..9d40a8b5 100644
--- a/src/cython/cython/simplex_tree.pyx
+++ b/src/cython/cython/simplex_tree.pyx
@@ -46,9 +46,8 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi":
         bint find_simplex(vector[int] simplex)
         bint insert_simplex_and_subfaces(vector[int] simplex,
                                          double filtration)
-        bint insert_simplex(vector[int] simplex, double filtration)
-        vector[pair[vector[int], double]] get_filtered_tree()
-        vector[pair[vector[int], double]] get_skeleton_tree(int dimension)
+        vector[pair[vector[int], double]] get_filtration()
+        vector[pair[vector[int], double]] get_skeleton(int dimension)
         vector[pair[vector[int], double]] get_star(vector[int] simplex)
         vector[pair[vector[int], double]] get_cofaces(vector[int] simplex,
                                                           int dimension)
@@ -103,14 +102,6 @@ cdef class SimplexTree:
          """
         return self.pcohptr != NULL
 
-    def get_filtration(self):
-        """This function returns the main simplicial complex filtration value.
-
-        :returns:  The simplicial complex filtration value.
-        :rtype:  float
-        """
-        return self.thisptr.filtration()
-
     def filtration(self, simplex):
         """This function returns the simplicial complex filtration value for a
         given N-simplex.
@@ -137,7 +128,7 @@ cdef class SimplexTree:
         .. note::
 
             This function must be launched before persistence, betti_numbers,
-            persistent_betti_numbers or get_filtered_tree after inserting or
+            persistent_betti_numbers or get_filtration after inserting or
             removing simplices.
         """
         self.thisptr.initialize_filtration()
@@ -197,24 +188,7 @@ cdef class SimplexTree:
             complex.push_back(i)
         return self.thisptr.find_simplex(complex)
 
-    def insert_simplex(self, simplex, filtration=0.0):
-        """This function inserts the given N-simplex with the given filtration
-        value (default value is '0.0').
-
-        :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.
-        :rtype:  bool
-        """
-        cdef vector[int] complex
-        for i in simplex:
-            complex.push_back(i)
-        return self.thisptr.insert_simplex(complex, <double>filtration)
-
-    def insert_simplex_and_subfaces(self, simplex, filtration=0.0):
+    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').
 
@@ -232,36 +206,36 @@ cdef class SimplexTree:
         return self.thisptr.insert_simplex_and_subfaces(complex,
                                                         <double>filtration)
 
-    def get_filtered_tree(self):
-        """This function returns the tree sorted by increasing filtration
-        values.
+    def get_filtration(self):
+        """This function returns a list of all simplices with their given
+        filtration values.
 
-        :returns:  The tree sorted by increasing filtration values.
+        :returns:  The simplices sorted by increasing filtration values.
         :rtype:  list of tuples(simplex, filtration)
         """
-        cdef vector[pair[vector[int], double]] filtered_tree \
-            = self.thisptr.get_filtered_tree()
+        cdef vector[pair[vector[int], double]] filtration \
+            = self.thisptr.get_filtration()
         ct = []
-        for filtered_complex in filtered_tree:
+        for filtered_complex in filtration:
             v = []
             for vertex in filtered_complex.first:
                 v.append(vertex)
             ct.append((v, filtered_complex.second))
         return ct
 
-    def get_skeleton_tree(self, dimension):
-        """This function returns the tree skeleton of a maximum given
-        dimension.
+    def get_skeleton(self, dimension):
+        """This function returns the (simplices of the) skeleton of a maximum
+        given dimension.
 
         :param dimension: The skeleton dimension value.
         :type dimension: int.
-        :returns:  The skeleton tree of a maximum dimension.
+        :returns:  The (simplices of the) skeleton of a maximum dimension.
         :rtype:  list of tuples(simplex, filtration)
         """
-        cdef vector[pair[vector[int], double]] sk_tree \
-            = self.thisptr.get_skeleton_tree(<int>dimension)
+        cdef vector[pair[vector[int], double]] skeletons \
+            = self.thisptr.get_skeleton(<int>dimension)
         ct = []
-        for filtered_complex in sk_tree:
+        for filtered_complex in skeletons:
             v = []
             for vertex in filtered_complex.first:
                 v.append(vertex)
@@ -273,7 +247,7 @@ cdef class SimplexTree:
 
         :param simplex: The N-simplex, represented by a list of vertex.
         :type simplex: list of int.
-        :returns:  The star tree of a simplex.
+        :returns:  The (simplices of the) star of a simplex.
         :rtype:  list of tuples(simplex, filtration)
         """
         cdef vector[int] complex
@@ -298,7 +272,7 @@ cdef class SimplexTree:
         :param codimension: The codimension. If codimension = 0, all cofaces
             are returned (equivalent of get_star function)
         :type codimension: int.
-        :returns:  The coface tree of a simplex.
+        :returns:  The (simplices of the) cofaces of a simplex
         :rtype:  list of tuples(simplex, filtration)
         """
         cdef vector[int] complex
diff --git a/src/cython/doc/alpha_complex_user.rst b/src/cython/doc/alpha_complex_user.rst
index 68e53a77..2356944d 100644
--- a/src/cython/doc/alpha_complex_user.rst
+++ b/src/cython/doc/alpha_complex_user.rst
@@ -30,7 +30,7 @@ This example builds the Delaunay triangulation from the given points, and initia
         repr(simplex_tree.num_simplices()) + ' simplices - ' + \
         repr(simplex_tree.num_vertices()) + ' vertices.'
     print(result_str)
-    for filtered_value in simplex_tree.get_filtered_tree():
+    for filtered_value in simplex_tree.get_filtration():
         print(filtered_value)
 
 The output is:
@@ -164,7 +164,7 @@ Then, it is asked to display information about the alpha complex:
         repr(simplex_tree.num_simplices()) + ' simplices - ' + \
         repr(simplex_tree.num_vertices()) + ' vertices.'
     print(result_str)
-    for filtered_value in simplex_tree.get_filtered_tree():
+    for filtered_value in simplex_tree.get_filtration():
         print(filtered_value)
 
 the program output is:
diff --git a/src/cython/doc/bottleneck_distance_user.rst b/src/cython/doc/bottleneck_distance_user.rst
index 3bc170f4..8c29d069 100644
--- a/src/cython/doc/bottleneck_distance_user.rst
+++ b/src/cython/doc/bottleneck_distance_user.rst
@@ -26,7 +26,7 @@ This example computes the bottleneck distance from 2 persistence diagrams:
     message = "Bottleneck distance approximation=" + repr(gudhi.bottleneck_distance(diag1, diag2, 0.1))
     print(message)
 
-    message = "Bottleneck distance exact value=" + repr(gudhi.bottleneck_distance(diag1, diag2))
+    message = "Bottleneck distance exact value=" + repr(gudhi.bottleneck_distance(diag1, diag2, 0))
     print(message)
 
 The output is:
diff --git a/src/cython/doc/installation.rst b/src/cython/doc/installation.rst
index e7d8c210..f818366b 100644
--- a/src/cython/doc/installation.rst
+++ b/src/cython/doc/installation.rst
@@ -4,12 +4,19 @@ 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 <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.
 It also requires cmake to generate makefiles, and cython to compile the
 library.
 
+On `Windows <https://wiki.python.org/moin/WindowsCompilers>`_ , only Python
+3.5 and 3.6 are available because of required Visual Studio version.
+
+On other systems, if you have several Python/cython installed, the version 2.X
+will be used by default, but you can force it by adding
+:code:`-DPython_ADDITIONAL_VERSIONS=3` to the cmake command.
+
 GUDHI Cythonization
 ===================
 
@@ -23,8 +30,6 @@ To build the GUDHI cython module, run the following commands in a terminal:
     cmake ..
     make cython
 
-A list of examples is available here.
-
 Test suites
 ===========
 
@@ -33,9 +38,9 @@ following command in a terminal:
 
 .. code-block:: bash
 
-    cd /path-to-gudhi/build/src/cython
+    cd /path-to-gudhi/build/cython
     # For windows, you have to set PYTHONPATH environment variable
-    export PYTHONPATH='$PYTHONPATH:/path-to-gudhi/build/src/cython'
+    export PYTHONPATH='$PYTHONPATH:/path-to-gudhi/build/cython'
     py.test
 
 Documentation
diff --git a/src/cython/doc/rips_complex_user.rst b/src/cython/doc/rips_complex_user.rst
index 027c3bf7..c89409a0 100644
--- a/src/cython/doc/rips_complex_user.rst
+++ b/src/cython/doc/rips_complex_user.rst
@@ -60,7 +60,7 @@ Finally, it is asked to display information about the simplicial complex.
         repr(simplex_tree.num_simplices()) + ' simplices - ' + \
         repr(simplex_tree.num_vertices()) + ' vertices.'
     print(result_str)
-    for filtered_value in simplex_tree.get_filtered_tree():
+    for filtered_value in simplex_tree.get_filtration():
         print(filtered_value)
 
 When launching (Rips maximal distance between 2 points is 12.0, is expanded
@@ -107,7 +107,7 @@ Finally, it is asked to display information about the Rips complex.
         repr(simplex_tree.num_simplices()) + ' simplices - ' + \
         repr(simplex_tree.num_vertices()) + ' vertices.'
     print(result_str)
-    for filtered_value in simplex_tree.get_filtered_tree():
+    for filtered_value in simplex_tree.get_filtration():
         print(filtered_value)
 
 the program output is:
@@ -162,7 +162,7 @@ Finally, it is asked to display information about the simplicial complex.
         repr(simplex_tree.num_simplices()) + ' simplices - ' + \
         repr(simplex_tree.num_vertices()) + ' vertices.'
     print(result_str)
-    for filtered_value in simplex_tree.get_filtered_tree():
+    for filtered_value in simplex_tree.get_filtration():
         print(filtered_value)
 
 When launching (Rips maximal distance between 2 points is 12.0, is expanded
@@ -209,7 +209,7 @@ Finally, it is asked to display information about the Rips complex.
         repr(simplex_tree.num_simplices()) + ' simplices - ' + \
         repr(simplex_tree.num_vertices()) + ' vertices.'
     print(result_str)
-    for filtered_value in simplex_tree.get_filtered_tree():
+    for filtered_value in simplex_tree.get_filtration():
         print(filtered_value)
 
 the program output is:
diff --git a/src/cython/doc/simplex_tree_user.rst b/src/cython/doc/simplex_tree_user.rst
index cbfd34a7..b2efca8b 100644
--- a/src/cython/doc/simplex_tree_user.rst
+++ b/src/cython/doc/simplex_tree_user.rst
@@ -35,9 +35,9 @@ Example
 
    import gudhi
    st = gudhi.SimplexTree()
-   if st.insert_simplex([0, 1]):
+   if st.insert([0, 1]):
        print("[0, 1] inserted")
-   if st.insert_simplex_and_subfaces([0, 1, 2], filtration=4.0):
+   if st.insert([0, 1, 2], filtration=4.0):
        print("[0, 1, 2] inserted")
    if st.find([0, 1]):
        print("[0, 1] found")
@@ -45,8 +45,8 @@ Example
    print(result_str)
    result_str = 'num_simplices=' + repr(st.num_simplices())
    print(result_str)
-   print("skeleton_tree(2) =")
-   for sk_value in st.get_skeleton_tree(2):
+   print("skeleton(2) =")
+   for sk_value in st.get_skeleton(2):
        print(sk_value)
 
 
@@ -54,16 +54,16 @@ The output is:
 
 .. testoutput::
 
-   [0, 1] inserted
-   [0, 1, 2] inserted
-   [0, 1] found
-   num_vertices=3
-   num_simplices=7
-   skeleton_tree(2) =
-   ([0, 1, 2], 4.0)
-   ([0, 1], 0.0)
-   ([0, 2], 4.0)
-   ([0], 0.0)
-   ([1, 2], 4.0)
-   ([1], 4.0)
-   ([2], 4.0)
+    [0, 1] inserted
+    [0, 1, 2] inserted
+    [0, 1] found
+    num_vertices=3
+    num_simplices=7
+    skeleton(2) =
+    ([0, 1, 2], 4.0)
+    ([0, 1], 0.0)
+    ([0, 2], 4.0)
+    ([0], 0.0)
+    ([1, 2], 4.0)
+    ([1], 0.0)
+    ([2], 4.0)
diff --git a/src/cython/doc/tangential_complex_user.rst b/src/cython/doc/tangential_complex_user.rst
index 6a7e6e41..24f68f85 100644
--- a/src/cython/doc/tangential_complex_user.rst
+++ b/src/cython/doc/tangential_complex_user.rst
@@ -133,7 +133,7 @@ This example builds the Tangential complex of point set read in an OFF file.
         ' - ' + repr(st.num_simplices()) + ' simplices - ' + \
         repr(st.num_vertices()) + ' vertices.'
     print(result_str)
-    for filtered_value in st.get_filtered_tree():
+    for filtered_value in st.get_filtration():
         print(filtered_value)
 
 The output is:
diff --git a/src/cython/example/alpha_complex_from_points_example.py b/src/cython/example/alpha_complex_from_points_example.py
index 688edb65..7d6278ce 100755
--- a/src/cython/example/alpha_complex_from_points_example.py
+++ b/src/cython/example/alpha_complex_from_points_example.py
@@ -59,7 +59,7 @@ else:
     print("[4] Not found...")
 
 print("dimension=", simplex_tree.dimension())
-print("filtered_tree=", simplex_tree.get_filtered_tree())
+print("filtrations=", simplex_tree.get_filtration())
 print("star([0])=", simplex_tree.get_star([0]))
 print("coface([0], 1)=", simplex_tree.get_cofaces([0], 1))
 
diff --git a/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
index 2474fc87..2371c36c 100755
--- a/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
+++ b/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
@@ -32,7 +32,7 @@ __license__ = "GPL v3"
 parser = argparse.ArgumentParser(description='EuclideanStrongWitnessComplex creation from '
                                  'points read in a OFF file.',
                                  epilog='Example: '
-                                 'example/witness_complex_diagram_persistence_from_off_file_example.py '
+                                 'example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py '
                                  '-f ../data/points/tore3D_300.off -a 1.0 -n 20 -d 2'
                                  '- Constructs a strong witness complex with the '
                                  'points from the given OFF file.')
diff --git a/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
index 5a75417b..5748aa8a 100755
--- a/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
+++ b/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
@@ -32,7 +32,7 @@ __license__ = "GPL v3"
 parser = argparse.ArgumentParser(description='EuclideanWitnessComplex creation from '
                                  'points read in a OFF file.',
                                  epilog='Example: '
-                                 'example/witness_complex_diagram_persistence_from_off_file_example.py '
+                                 'example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py '
                                  '-f ../data/points/tore3D_300.off -a 1.0 -n 20 -d 2'
                                  '- Constructs a weak witness complex with the '
                                  'points from the given OFF file.')
diff --git a/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py b/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py
index db530161..00334121 100755
--- a/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py
+++ b/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py
@@ -49,7 +49,7 @@ def is_file_perseus(file):
         return False
 
 parser = argparse.ArgumentParser(description='Periodic cubical complex from a '
-                                 'perseus file style name.',
+                                 'Perseus-style file name.',
                                  epilog='Example: '
                                  './periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py'
                                  ' -f ../data/bitmap/CubicalTwoSphere.txt')
diff --git a/src/cython/example/random_cubical_complex_persistence_example.py b/src/cython/example/random_cubical_complex_persistence_example.py
index 1c55f777..c832d6bf 100755
--- a/src/cython/example/random_cubical_complex_persistence_example.py
+++ b/src/cython/example/random_cubical_complex_persistence_example.py
@@ -2,6 +2,7 @@
 
 import gudhi
 import numpy
+from functools import reduce
 import argparse
 import operator
 
@@ -54,4 +55,4 @@ if dimension_multiplication > 1:
     print(cubical_complex.persistence(homology_coeff_field=2, min_persistence=0))
 
     print("betti_numbers()=")
-    print(cubical_complex.betti_numbers())
\ No newline at end of file
+    print(cubical_complex.betti_numbers())
diff --git a/src/cython/example/rips_complex_from_points_example.py b/src/cython/example/rips_complex_from_points_example.py
index 9b7fc79d..5d411b1a 100755
--- a/src/cython/example/rips_complex_from_points_example.py
+++ b/src/cython/example/rips_complex_from_points_example.py
@@ -35,6 +35,6 @@ rips = gudhi.RipsComplex(points=[[0, 0], [1, 0], [0, 1], [1, 1]],
 
 simplex_tree = rips.create_simplex_tree(max_dimension=1)
 
-print("filtered_tree=", simplex_tree.get_filtered_tree())
+print("filtrations=", simplex_tree.get_filtration())
 print("star([0])=", simplex_tree.get_star([0]))
 print("coface([0], 1)=", simplex_tree.get_cofaces([0], 1))
diff --git a/src/cython/example/simplex_tree_example.py b/src/cython/example/simplex_tree_example.py
index bf5f17a2..3af20fcf 100755
--- a/src/cython/example/simplex_tree_example.py
+++ b/src/cython/example/simplex_tree_example.py
@@ -61,6 +61,6 @@ print("filtration[4, 2]=", st.filtration([4, 2]))
 print("num_simplices=", st.num_simplices())
 print("num_vertices=", st.num_vertices())
 
-print("skeleton_tree[2]=", st.get_skeleton_tree(2))
-print("skeleton_tree[1]=", st.get_skeleton_tree(1))
-print("skeleton_tree[0]=", st.get_skeleton_tree(0))
+print("skeleton[2]=", st.get_skeleton(2))
+print("skeleton[1]=", st.get_skeleton(1))
+print("skeleton[0]=", st.get_skeleton(0))
diff --git a/src/cython/include/Simplex_tree_interface.h b/src/cython/include/Simplex_tree_interface.h
index 4266b3ef..45ce1916 100644
--- a/src/cython/include/Simplex_tree_interface.h
+++ b/src/cython/include/Simplex_tree_interface.h
@@ -52,29 +52,32 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
     return (Base::find(vh) != Base::null_simplex());
   }
 
+  bool insert(const Simplex& simplex, Filtration_value filtration = 0) {
+    Insertion_result result = Base::insert_simplex_and_subfaces(simplex, filtration);
+    return (result.second);
+  }
+
+  // Do not interface this function, only used in alpha complex interface for complex creation
   bool insert_simplex(const Simplex& simplex, Filtration_value filtration = 0) {
     Insertion_result result = Base::insert_simplex(simplex, filtration);
-    Base::initialize_filtration();
     return (result.second);
   }
 
+  // Do not interface this function, only used in interface for complex creation
   bool insert_simplex_and_subfaces(const Simplex& simplex, Filtration_value filtration = 0) {
     Insertion_result result = Base::insert_simplex_and_subfaces(simplex, filtration);
-    Base::initialize_filtration();
     return (result.second);
   }
 
   // Do not interface this function, only used in strong witness interface for complex creation
   bool insert_simplex(const std::vector<std::size_t>& complex, Filtration_value filtration = 0) {
     Insertion_result result = Base::insert_simplex(complex, filtration);
-    Base::initialize_filtration();
     return (result.second);
   }
 
   // Do not interface this function, only used in strong witness interface for complex creation
   bool insert_simplex_and_subfaces(const std::vector<std::size_t>& complex, Filtration_value filtration = 0) {
     Insertion_result result = Base::insert_simplex_and_subfaces(complex, filtration);
-    Base::initialize_filtration();
     return (result.second);
   }
 
@@ -87,28 +90,29 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
     Base::initialize_filtration();
   }
 
-  Complex get_filtered_tree() {
-    Complex filtered_tree;
+  Complex get_filtration() {
+    Base::initialize_filtration();
+    Complex filtrations;
     for (auto f_simplex : Base::filtration_simplex_range()) {
       Simplex simplex;
       for (auto vertex : Base::simplex_vertex_range(f_simplex)) {
         simplex.insert(simplex.begin(), vertex);
       }
-      filtered_tree.push_back(std::make_pair(simplex, Base::filtration(f_simplex)));
+      filtrations.push_back(std::make_pair(simplex, Base::filtration(f_simplex)));
     }
-    return filtered_tree;
+    return filtrations;
   }
 
-  Complex get_skeleton_tree(int dimension) {
-    Complex skeleton_tree;
+  Complex get_skeleton(int dimension) {
+    Complex skeletons;
     for (auto f_simplex : Base::skeleton_simplex_range(dimension)) {
       Simplex simplex;
       for (auto vertex : Base::simplex_vertex_range(f_simplex)) {
         simplex.insert(simplex.begin(), vertex);
       }
-      skeleton_tree.push_back(std::make_pair(simplex, Base::filtration(f_simplex)));
+      skeletons.push_back(std::make_pair(simplex, Base::filtration(f_simplex)));
     }
-    return skeleton_tree;
+    return skeletons;
   }
 
   Complex get_star(const Simplex& simplex) {
@@ -140,6 +144,7 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
   }
 
   void create_persistence(Gudhi::Persistent_cohomology_interface<Base>* pcoh) {
+    Base::initialize_filtration();
     pcoh = new Gudhi::Persistent_cohomology_interface<Base>(*this);
   }
 };
diff --git a/src/cython/test/test_alpha_complex.py b/src/cython/test/test_alpha_complex.py
index 2625d529..2c76d9d7 100755
--- a/src/cython/test/test_alpha_complex.py
+++ b/src/cython/test/test_alpha_complex.py
@@ -42,7 +42,7 @@ def test_infinite_alpha():
     assert simplex_tree.num_simplices() == 11
     assert simplex_tree.num_vertices() == 4
  
-    assert simplex_tree.get_filtered_tree() == \
+    assert simplex_tree.get_filtration() == \
            [([0], 0.0), ([1], 0.0), ([2], 0.0), ([3], 0.0),
             ([0, 1], 0.25), ([0, 2], 0.25), ([1, 3], 0.25),
             ([2, 3], 0.25), ([1, 2], 0.5), ([0, 1, 2], 0.5),
@@ -76,7 +76,7 @@ def test_filtered_alpha():
     assert filtered_alpha.get_point(4) == []
     assert filtered_alpha.get_point(125) == []
 
-    assert simplex_tree.get_filtered_tree() == \
+    assert simplex_tree.get_filtration() == \
            [([0], 0.0), ([1], 0.0), ([2], 0.0), ([3], 0.0),
             ([0, 1], 0.25), ([0, 2], 0.25), ([1, 3], 0.25),
             ([2, 3], 0.25)]
diff --git a/src/cython/test/test_cubical_complex.py b/src/cython/test/test_cubical_complex.py
index c8df8089..2e281ee4 100755
--- a/src/cython/test/test_cubical_complex.py
+++ b/src/cython/test/test_cubical_complex.py
@@ -45,7 +45,7 @@ def test_dimension_or_perseus_file_constructor():
     test_file.write('2\n3\n3\n0\n0\n0\n0\n100\n0\n0\n0\n0\n')
     test_file.close()
     # CubicalComplex can be constructed from dimensions and
-    # top_dimensional_cells OR from a perseus file style name.
+    # top_dimensional_cells OR from a Perseus-style file name.
     cub = CubicalComplex(dimensions=[3, 3],
                          top_dimensional_cells = [1,2,3,4,5,6,7,8,9],
                          perseus_file='CubicalOneSphere.txt')
diff --git a/src/cython/test/test_euclidean_witness_complex.py b/src/cython/test/test_euclidean_witness_complex.py
index 0947cc09..737f1ef4 100755
--- a/src/cython/test/test_euclidean_witness_complex.py
+++ b/src/cython/test/test_euclidean_witness_complex.py
@@ -42,7 +42,7 @@ def test_witness_complex():
     assert landmarks[1] == euclidean_witness_complex.get_point(1)
     assert landmarks[2] == euclidean_witness_complex.get_point(2)
 
-    assert simplex_tree.get_filtered_tree() == [([0], 0.0), ([1], 0.0),
+    assert simplex_tree.get_filtration() == [([0], 0.0), ([1], 0.0),
         ([0, 1], 0.0), ([2], 0.0), ([0, 2], 0.0), ([1, 2], 0.0),
         ([0, 1, 2], 0.0)]
 
@@ -61,11 +61,11 @@ def test_strong_witness_complex():
     assert landmarks[1] == euclidean_strong_witness_complex.get_point(1)
     assert landmarks[2] == euclidean_strong_witness_complex.get_point(2)
 
-    assert simplex_tree.get_filtered_tree() == [([0], 0.0), ([1], 0.0), ([2], 0.0)]
+    assert simplex_tree.get_filtration() == [([0], 0.0), ([1], 0.0), ([2], 0.0)]
 
     simplex_tree = euclidean_strong_witness_complex.create_simplex_tree(max_alpha_square=100.0)
 
-    assert simplex_tree.get_filtered_tree() == [([0], 0.0), ([1], 0.0),
+    assert simplex_tree.get_filtration() == [([0], 0.0), ([1], 0.0),
     ([2], 0.0), ([1, 2], 15.0), ([0, 2], 34.0), ([0, 1], 37.0),
     ([0, 1, 2], 37.0)]
 
diff --git a/src/cython/test/test_rips_complex.py b/src/cython/test/test_rips_complex.py
index 286a645b..c7d2ead4 100755
--- a/src/cython/test/test_rips_complex.py
+++ b/src/cython/test/test_rips_complex.py
@@ -44,7 +44,7 @@ def test_rips_from_points():
     assert simplex_tree.num_simplices() == 10
     assert simplex_tree.num_vertices() == 4
 
-    assert simplex_tree.get_filtered_tree() == \
+    assert simplex_tree.get_filtration() == \
            [([0], 0.0), ([1], 0.0), ([2], 0.0), ([3], 0.0),
             ([0, 1], 1.0), ([0, 2], 1.0), ([1, 3], 1.0),
             ([2, 3], 1.0), ([1, 2], 1.4142135623730951),
@@ -83,7 +83,7 @@ def test_rips_from_distance_matrix():
     assert simplex_tree.num_simplices() == 10
     assert simplex_tree.num_vertices() == 4
 
-    assert simplex_tree.get_filtered_tree() == \
+    assert simplex_tree.get_filtration() == \
            [([0], 0.0), ([1], 0.0), ([2], 0.0), ([3], 0.0),
             ([0, 1], 1.0), ([0, 2], 1.0), ([1, 3], 1.0),
             ([2, 3], 1.0), ([1, 2], 1.4142135623730951),
diff --git a/src/cython/test/test_simplex_tree.py b/src/cython/test/test_simplex_tree.py
index af5b639a..3ae537e3 100755
--- a/src/cython/test/test_simplex_tree.py
+++ b/src/cython/test/test_simplex_tree.py
@@ -33,8 +33,8 @@ def test_insertion():
     assert st.__is_persistence_defined() == False
 
     # insert test
-    assert st.insert_simplex([0, 1]) == True
-    assert st.insert_simplex_and_subfaces([0, 1, 2], filtration=4.0) == True
+    assert st.insert([0, 1]) == True
+    assert st.insert([0, 1, 2], filtration=4.0) == True
     # FIXME: Remove this line
     st.set_dimension(2)
     assert st.num_simplices() == 7
@@ -55,31 +55,30 @@ def test_insertion():
     # filtration test
     st.set_filtration(5.0)
     st.initialize_filtration()
-    assert st.get_filtration() == 5.0
     assert st.filtration([0, 1, 2]) == 4.0
     assert st.filtration([0, 2]) == 4.0
     assert st.filtration([1, 2]) == 4.0
     assert st.filtration([2]) == 4.0
     assert st.filtration([0, 1]) == 0.0
     assert st.filtration([0]) == 0.0
-    assert st.filtration([1]) == 4.0
+    assert st.filtration([1]) == 0.0
 
-    # skeleton_tree test
-    assert st.get_skeleton_tree(2) == \
+    # skeleton test
+    assert st.get_skeleton(2) == \
         [([0, 1, 2], 4.0), ([0, 1], 0.0), ([0, 2], 4.0),
-        ([0], 0.0), ([1, 2], 4.0), ([1], 4.0), ([2], 4.0)]
-    assert st.get_skeleton_tree(1) == \
+        ([0], 0.0), ([1, 2], 4.0), ([1], 0.0), ([2], 4.0)]
+    assert st.get_skeleton(1) == \
         [([0, 1], 0.0), ([0, 2], 4.0), ([0], 0.0),
-        ([1, 2], 4.0), ([1], 4.0), ([2], 4.0)]
-    assert st.get_skeleton_tree(0) == \
-        [([0], 0.0), ([1], 4.0), ([2], 4.0)]
+        ([1, 2], 4.0), ([1], 0.0), ([2], 4.0)]
+    assert st.get_skeleton(0) == \
+        [([0], 0.0), ([1], 0.0), ([2], 4.0)]
 
     # remove_maximal_simplex test
     assert st.get_cofaces([0, 1, 2], 1) == []
     st.remove_maximal_simplex([0, 1, 2])
-    assert st.get_skeleton_tree(2) == \
+    assert st.get_skeleton(2) == \
         [([0, 1], 0.0), ([0, 2], 4.0), ([0], 0.0),
-        ([1, 2], 4.0), ([1], 4.0), ([2], 4.0)]
+        ([1, 2], 4.0), ([1], 0.0), ([2], 4.0)]
     assert st.find([0, 1, 2]) == False
     assert st.find([0, 1]) == True
     assert st.find([0, 2]) == True
@@ -103,20 +102,20 @@ def test_expansion():
     assert st.__is_persistence_defined() == False
 
     # insert test
-    assert st.insert_simplex_and_subfaces([3, 2], 0.1) == True
-    assert st.insert_simplex_and_subfaces([2, 0], 0.2) == True
-    assert st.insert_simplex_and_subfaces([1, 0], 0.3) == True
-    assert st.insert_simplex_and_subfaces([3, 1], 0.4) == True
-    assert st.insert_simplex_and_subfaces([2, 1], 0.5) == True
-    assert st.insert_simplex_and_subfaces([6, 5], 0.6) == True
-    assert st.insert_simplex_and_subfaces([4, 2], 0.7) == True
-    assert st.insert_simplex_and_subfaces([3, 0], 0.8) == True
-    assert st.insert_simplex_and_subfaces([6, 4], 0.9) == True
-    assert st.insert_simplex_and_subfaces([6, 3], 1.0) == True
+    assert st.insert([3, 2], 0.1) == True
+    assert st.insert([2, 0], 0.2) == True
+    assert st.insert([1, 0], 0.3) == True
+    assert st.insert([3, 1], 0.4) == True
+    assert st.insert([2, 1], 0.5) == True
+    assert st.insert([6, 5], 0.6) == True
+    assert st.insert([4, 2], 0.7) == True
+    assert st.insert([3, 0], 0.8) == True
+    assert st.insert([6, 4], 0.9) == True
+    assert st.insert([6, 3], 1.0) == True
 
     assert st.num_vertices() == 7
     assert st.num_simplices() == 17
-    assert st.get_filtered_tree() == [([2], 0.1), ([3], 0.1), ([2, 3], 0.1),
+    assert st.get_filtration() == [([2], 0.1), ([3], 0.1), ([2, 3], 0.1),
     ([0], 0.2), ([0, 2], 0.2), ([1], 0.3), ([0, 1], 0.3), ([1, 3], 0.4),
     ([1, 2], 0.5), ([5], 0.6), ([6], 0.6), ([5, 6], 0.6), ([4], 0.7),
     ([2, 4], 0.7), ([0, 3], 0.8), ([4, 6], 0.9), ([3, 6], 1.0)]
@@ -126,7 +125,7 @@ def test_expansion():
     assert st.num_simplices() == 22
     st.initialize_filtration()
 
-    assert st.get_filtered_tree() == [([2], 0.1), ([3], 0.1), ([2, 3], 0.1),
+    assert st.get_filtration() == [([2], 0.1), ([3], 0.1), ([2, 3], 0.1),
     ([0], 0.2), ([0, 2], 0.2), ([1], 0.3), ([0, 1], 0.3), ([1, 3], 0.4),
     ([1, 2], 0.5), ([0, 1, 2], 0.5), ([1, 2, 3], 0.5), ([5], 0.6), ([6], 0.6),
     ([5, 6], 0.6), ([4], 0.7), ([2, 4], 0.7), ([0, 3], 0.8), ([0, 1, 3], 0.8),
diff --git a/src/cython/test/test_tangential_complex.py b/src/cython/test/test_tangential_complex.py
index c191baa4..8aa4023c 100755
--- a/src/cython/test/test_tangential_complex.py
+++ b/src/cython/test/test_tangential_complex.py
@@ -40,7 +40,7 @@ def test_tangential():
     assert st.num_simplices() == 6
     assert st.num_vertices() == 4
  
-    assert st.get_filtered_tree() == \
+    assert st.get_filtration() == \
         [([0], 0.0), ([1], 0.0), ([2], 0.0), ([0, 2], 0.0), ([3], 0.0), ([1, 3], 0.0)]
     assert st.get_cofaces([0], 1) == [([0, 2], 0.0)]