Merge last trunk modification

Fix doc issue
Still doc issue


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@1739 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 0a99345f06e93a3525691699a6fe1505979e8e8e

16 files changed, 337 insertions, 192 deletions

diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 383dd08a..81fbe8fe 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -5,116 +5,128 @@ FIND_PROGRAM( PYTHON_PATH python )
 FIND_PROGRAM( CYTHON_PATH cython )
 
 if(PYTHON_PATH AND CYTHON_PATH)
-  # Gudhi and CGAL compilation option
-  if(MSVC)
-    set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'/fp:strict', ")
-  else(MSVC)
-    set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-std=c++11', ")
-  endif(MSVC)
-  if(CMAKE_COMPILER_IS_GNUCXX)
-    set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-frounding-math', ")
-  endif(CMAKE_COMPILER_IS_GNUCXX)
-  if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
-    set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-fp-model strict', ")
-  endif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
+  find_package(Boost REQUIRED COMPONENTS system REQUIRED)
 
-  find_package(Eigen3 3.1.0)
-  
-  if (EIGEN3_FOUND)
-    # No problem, even if no CGAL found
-    set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ")
-    set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${EIGEN3_INCLUDE_DIR}', ")
-  endif (EIGEN3_FOUND)
-  
-  # Copy recursively include, cython and test repositories before packages finding
-  # Some tests files are removed in case some packages are not found
-  file(COPY include DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
-  file(COPY cython DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
-  file(COPY test DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
-  
-  if (CGAL_FOUND)
-    if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
-      # If CGAL_VERSION >= 4.7.0, include alpha complex
-      set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'CGAL', ")
-      set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ")
-      # GMP and GMPXX are not required, but if present, CGAL will link with them.
-      if(GMP_FOUND)
-        set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMP', ")
-        set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'gmp', ")
-        set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMP_LIBRARIES_DIR}', ")
-        if(GMPXX_FOUND)
-          set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMPXX', ")
-          set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'gmpxx', ")
-          set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMPXX_LIBRARIES_DIR}', ")
-        endif(GMPXX_FOUND)
-      endif(GMP_FOUND)
-  
-      set(GUDHI_CYTHON_ALPHA_COMPLEX "include 'cython/alpha_complex.pyx'")
-    else (NOT CGAL_VERSION VERSION_LESS 4.7.0)
-      # Remove alpha complex unitary tests
-      file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_alpha_complex.py)
-    endif (NOT CGAL_VERSION VERSION_LESS 4.7.0)
-  endif (CGAL_FOUND)
-  
-  # Loop on INCLUDE_DIRECTORIES PROPERTY
-  get_property(GUDHI_INCLUDE_DIRECTORIES DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY INCLUDE_DIRECTORIES)
-  foreach(GUDHI_INCLUDE_DIRECTORY ${GUDHI_INCLUDE_DIRECTORIES})
-    set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${GUDHI_INCLUDE_DIRECTORY}', ")
-  endforeach()
-  set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${CMAKE_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/include', ")
+  if(NOT Boost_FOUND)
+    message(FATAL_ERROR "NOTICE: This demo requires Boost and will not be compiled.")
+  else(NOT Boost_FOUND)
+
+    set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_RESULT_OF_USE_DECLTYPE', ")
+    set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ")
+    set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${Boost_INCLUDE_DIRS}', ")
+    set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'boost_system', ")
+    set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ")
+
+    # Gudhi and CGAL compilation option
+    if(MSVC)
+      set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'/fp:strict', ")
+    else(MSVC)
+      set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-std=c++11', ")
+    endif(MSVC)
+    if(CMAKE_COMPILER_IS_GNUCXX)
+      set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-frounding-math', ")
+    endif(CMAKE_COMPILER_IS_GNUCXX)
+    if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
+      set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-fp-model strict', ")
+    endif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
   
-  # Generate cythonize_gudhi.py file to cythonize Gudhi
-  configure_file(cythonize_gudhi.py.in "${CMAKE_CURRENT_BINARY_DIR}/cythonize_gudhi.py" @ONLY)
-  # Generate gudhi.pyx - Gudhi cython file 
-  configure_file(gudhi.pyx.in "${CMAKE_CURRENT_BINARY_DIR}/gudhi.pyx" @ONLY)
+    find_package(Eigen3 3.1.0)
+    
+    if (EIGEN3_FOUND)
+      # No problem, even if no CGAL found
+      set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ")
+      set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${EIGEN3_INCLUDE_DIR}', ")
+    endif (EIGEN3_FOUND)
+    
+    # Copy recursively include, cython and test repositories before packages finding
+    # Some tests files are removed in case some packages are not found
+    file(COPY include DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+    file(COPY cython DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+    file(COPY test DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+    
+    if (CGAL_FOUND)
+      if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+        # If CGAL_VERSION >= 4.7.0, include alpha complex
+        set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'CGAL', ")
+        set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ")
+        # GMP and GMPXX are not required, but if present, CGAL will link with them.
+        if(GMP_FOUND)
+          set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMP', ")
+          set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'gmp', ")
+          set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMP_LIBRARIES_DIR}', ")
+          if(GMPXX_FOUND)
+            set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMPXX', ")
+            set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'gmpxx', ")
+            set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMPXX_LIBRARIES_DIR}', ")
+          endif(GMPXX_FOUND)
+        endif(GMP_FOUND)
+    
+        set(GUDHI_CYTHON_ALPHA_COMPLEX "include 'cython/alpha_complex.pyx'")
+      else (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+        # Remove alpha complex unitary tests
+        file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_alpha_complex.py)
+      endif (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+    endif (CGAL_FOUND)
+    
+    # Loop on INCLUDE_DIRECTORIES PROPERTY
+    get_property(GUDHI_INCLUDE_DIRECTORIES DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY INCLUDE_DIRECTORIES)
+    foreach(GUDHI_INCLUDE_DIRECTORY ${GUDHI_INCLUDE_DIRECTORIES})
+      set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${GUDHI_INCLUDE_DIRECTORY}', ")
+    endforeach()
+    set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${CMAKE_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/include', ")
+    
+    # Generate cythonize_gudhi.py file to cythonize Gudhi
+    configure_file(cythonize_gudhi.py.in "${CMAKE_CURRENT_BINARY_DIR}/cythonize_gudhi.py" @ONLY)
+    # Generate gudhi.pyx - Gudhi cython file 
+    configure_file(gudhi.pyx.in "${CMAKE_CURRENT_BINARY_DIR}/gudhi.pyx" @ONLY)
+    
+    add_custom_command(
+        OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
+        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+        COMMAND python "${CMAKE_CURRENT_BINARY_DIR}/cythonize_gudhi.py" "build_ext" "--inplace")
+    
+    add_custom_target(cythonize_gudhi ALL DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
+                      COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/gudhi.so to your PYTHONPATH before using examples")
   
-  add_custom_command(
-      OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
-      WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-      COMMAND python "${CMAKE_CURRENT_BINARY_DIR}/cythonize_gudhi.py" "build_ext" "--inplace")
+    # Unitary tests are available through py.test
+    find_program( PYTEST_PATH py.test )
+    if(PYTEST_PATH)
+      add_test(
+          NAME gudhi_cython_py_test
+          WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+          COMMAND ${PYTEST_PATH})
+      set_tests_properties(gudhi_cython_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
+    endif(PYTEST_PATH)
   
-  add_custom_target(cythonize_gudhi ALL DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
-                    COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/gudhi.so to your PYTHONPATH before using examples")
-
-  # Unitary tests are available through py.test
-  find_program( PYTEST_PATH py.test )
-  if(PYTEST_PATH)
-    add_test(
-        NAME gudhi_cython_py_test
-        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-        COMMAND ${PYTEST_PATH})
-    set_tests_properties(gudhi_cython_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
-  endif(PYTEST_PATH)
-
-  # Documentation generation is available through sphinx
-  find_program( SPHINX_PATH sphinx-build )
-  if(SPHINX_PATH)
-    file(COPY doc DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
-    # Developper version
-    file(GLOB GUDHI_DEV_DOC_IMAGES "${CMAKE_SOURCE_DIR}/src/*/doc/*.png")
-    file(COPY ${GUDHI_DEV_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img")
-    # User version
-    file(GLOB GUDHI_USER_DOC_IMAGES "${CMAKE_SOURCE_DIR}/doc/*/*.png")
-    file(COPY ${GUDHI_USER_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img")
-    # Biblio
-    file(GLOB GUDHI_BIB_FILES "${CMAKE_SOURCE_DIR}/biblio/*.bib")
-    file(COPY ${GUDHI_BIB_FILES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
-    # Cubical complex perseus doc example
-    file(GLOB GUDHI_CUBICAL_PERSEUS_FILES "${CMAKE_SOURCE_DIR}/data/bitmap/*cubicalcomplexdoc.txt")
-    file(COPY ${GUDHI_CUBICAL_PERSEUS_FILES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
-    file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
-    # Persistence graphical tools examples
-    file(COPY "${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
-    file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
-    if (UNIX)
-      add_custom_target(html 
-          WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc
-          COMMAND make html && make doctest)
-    else (UNIX)
-      add_custom_target(html 
-          WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc
-          COMMAND make.bat html)
-    endif (UNIX)
-  endif(SPHINX_PATH)
-
+    # Documentation generation is available through sphinx
+    find_program( SPHINX_PATH sphinx-build )
+    if(SPHINX_PATH)
+      file(COPY doc DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+      # Developper version
+      file(GLOB GUDHI_DEV_DOC_IMAGES "${CMAKE_SOURCE_DIR}/src/*/doc/*.png")
+      file(COPY ${GUDHI_DEV_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img")
+      # User version
+      file(GLOB GUDHI_USER_DOC_IMAGES "${CMAKE_SOURCE_DIR}/doc/*/*.png")
+      file(COPY ${GUDHI_USER_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img")
+      # Biblio
+      file(GLOB GUDHI_BIB_FILES "${CMAKE_SOURCE_DIR}/biblio/*.bib")
+      file(COPY ${GUDHI_BIB_FILES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
+      # Cubical complex perseus doc example
+      file(GLOB GUDHI_CUBICAL_PERSEUS_FILES "${CMAKE_SOURCE_DIR}/data/bitmap/*cubicalcomplexdoc.txt")
+      file(COPY ${GUDHI_CUBICAL_PERSEUS_FILES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
+      file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
+      # Persistence graphical tools examples
+      file(COPY "${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
+      file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
+      if (UNIX)
+        add_custom_target(html 
+            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc
+            COMMAND make html && make doctest)
+      else (UNIX)
+        add_custom_target(html 
+            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc
+            COMMAND make.bat html)
+      endif (UNIX)
+    endif(SPHINX_PATH)
+  endif(NOT Boost_FOUND)
 endif(PYTHON_PATH AND CYTHON_PATH)
diff --git a/src/cython/cython/alpha_complex.pyx b/src/cython/cython/alpha_complex.pyx
index 44da8c9d..af609863 100644
--- a/src/cython/cython/alpha_complex.pyx
+++ b/src/cython/cython/alpha_complex.pyx
@@ -34,7 +34,7 @@ __license__ = "GPL v3"
 cdef extern from "Alpha_complex_interface.h" namespace "Gudhi":
     cdef cppclass Alpha_complex_interface "Gudhi::alphacomplex::Alpha_complex_interface":
         Alpha_complex_interface(vector[vector[double]] points, double max_alpha_square)
-        # bool from_file is a workaround fro cython to find the correct signature
+        # bool from_file is a workaround for cython to find the correct signature
         Alpha_complex_interface(string off_file, double max_alpha_square, bool from_file)
         double filtration()
         double simplex_filtration(vector[int] simplex)
@@ -54,13 +54,9 @@ cdef extern from "Alpha_complex_interface.h" namespace "Gudhi":
                                                           int dimension)
         void remove_maximal_simplex(vector[int] simplex)
         vector[double] get_point(int vertex)
-
-cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi":
-    cdef cppclass Alpha_complex_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::alphacomplex::Alpha_complex< CGAL::Epick_d< CGAL::Dynamic_dimension_tag > >>":
-        Alpha_complex_persistence_interface(Alpha_complex_interface * st)
         vector[pair[int, pair[double, double]]] get_persistence(int homology_coeff_field, double min_persistence)
-        vector[int] betti_numbers()
-        vector[int] persistent_betti_numbers(double from_value, double to_value)
+        vector[int] get_betti_numbers()
+        vector[int] get_persistent_betti_numbers(double from_value, double to_value)
 
 # AlphaComplex python interface
 cdef class AlphaComplex:
@@ -84,8 +80,6 @@ cdef class AlphaComplex:
 
     cdef Alpha_complex_interface * thisptr
 
-    cdef Alpha_complex_persistence_interface * pcohptr
-
     # Fake constructor that does nothing but documenting the constructor
     def __init__(self, points=None, off_file='', max_alpha_square=float('inf')):
         """AlphaComplex constructor.
@@ -118,19 +112,12 @@ cdef class AlphaComplex:
     def __dealloc__(self):
         if self.thisptr != NULL:
             del self.thisptr
-        if self.pcohptr != NULL:
-            del self.pcohptr
 
     def __is_defined(self):
         """Returns true if AlphaComplex pointer is not NULL.
          """
         return self.thisptr != NULL
 
-    def __is_persistence_defined(self):
-        """Returns true if Persistence pointer is not NULL.
-         """
-        return self.pcohptr != NULL
-
     def get_filtration(self):
         """This function returns the main simplicial complex filtration value.
 
@@ -341,18 +328,10 @@ cdef class AlphaComplex:
             0.0.
             Sets min_persistence to -1.0 to see all values.
         :type min_persistence: float.
-        :returns: list of tuples(dimension, tuple(birth, death)) -- the
+        :note: list of pairs(dimension, pair(birth, death)) -- the
             persistence of the simplicial complex.
         """
-        if self.pcohptr != NULL:
-            del self.pcohptr
-        self.pcohptr = new Alpha_complex_persistence_interface(self.thisptr)
-        cdef vector[pair[int, pair[double, double]]] persistence_result
-        if self.pcohptr != NULL:
-            persistence_result \
-                = self.pcohptr.get_persistence(homology_coeff_field,
-                                               min_persistence)
-        return persistence_result
+        return self.thisptr.get_persistence(homology_coeff_field, min_persistence)
 
     def betti_numbers(self):
         """This function returns the Betti numbers of the simplicial complex.
@@ -362,13 +341,7 @@ cdef class AlphaComplex:
         :note: betti_numbers function requires persistence function to be
             launched first.
         """
-        cdef vector[int] bn_result
-        if self.pcohptr != NULL:
-            bn_result = self.pcohptr.betti_numbers()
-        else:
-            print("betti_numbers function requires persistence function"
-                  " to be launched first.")
-        return bn_result
+        return self.thisptr.get_betti_numbers()
 
     def persistent_betti_numbers(self, from_value, to_value):
         """This function returns the persistent Betti numbers of the
@@ -387,12 +360,4 @@ cdef class AlphaComplex:
         :note: persistent_betti_numbers function requires persistence
             function to be launched first.
         """
-        cdef vector[int] pbn_result
-        if self.pcohptr != NULL:
-            pbn_result \
-                = self.pcohptr.persistent_betti_numbers(<double>from_value,
-                                                        <double>to_value)
-        else:
-            print("persistent_betti_numbers function requires persistence "
-                  "function to be launched first.")
-        return pbn_result
+        return self.thisptr.get_persistent_betti_numbers(from_value, to_value)
diff --git a/src/cython/cython/rips_complex.pyx b/src/cython/cython/rips_complex.pyx
index ee4c34b0..08bd2388 100644
--- a/src/cython/cython/rips_complex.pyx
+++ b/src/cython/cython/rips_complex.pyx
@@ -1,6 +1,8 @@
 from cython cimport numeric
 from libcpp.vector cimport vector
 from libcpp.utility cimport pair
+from libcpp.string cimport string
+from libcpp cimport bool
 
 """This file is part of the Gudhi Library. The Gudhi library
    (Geometric Understanding in Higher Dimensions) is a generic C++
@@ -53,6 +55,8 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi":
         void remove_maximal_simplex(vector[int] simplex)
         void graph_expansion(vector[vector[double]] points, int max_dimension,
                              double max_edge_length)
+        void graph_expansion(string off_file, int max_dimension,
+                             double max_edge_length, bool from_file)
 
 cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi":
     cdef cppclass Rips_complex_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>>":
@@ -79,12 +83,18 @@ cdef class RipsComplex:
     cdef Rips_complex_persistence_interface * pcohptr
 
     # Fake constructor that does nothing but documenting the constructor
-    def __init__(self, points=[], max_dimension=3,
-                 max_edge_length=float('inf')):
+    def __init__(self, points=[], off_file='', max_dimension=3,
+                  max_edge_length=float('inf')):
         """RipsComplex constructor.
 
         :param points: A list of points in d-Dimension.
         :type points: list of list of double
+
+        Or
+
+        :param off_file: An OFF file style name.
+        :type off_file: string
+
         :param max_dimension: Maximum dimension of the complex to be expanded.
         :type max_dimension: int
         :param max_edge_length: Maximum edge length value (rips radius).
@@ -92,11 +102,17 @@ cdef class RipsComplex:
         """
 
     # The real cython constructor
-    def __cinit__(self, points=[], max_dimension=3,
+    def __cinit__(self, points=[], off_file='', max_dimension=3,
                   max_edge_length=float('inf')):
         self.thisptr = new Rips_complex_interface()
         # Constructor from graph expansion
-        if points is not None:
+        if off_file is not '':
+            if os.path.isfile(off_file):
+                self.thisptr.graph_expansion(off_file, max_dimension,
+                                         max_edge_length, True)
+            else:
+                print("file " + off_file + " not found.")
+        else:
             self.thisptr.graph_expansion(points, max_dimension,
                                          max_edge_length)
 
diff --git a/src/cython/doc/alpha_complex_sum.rst b/src/cython/doc/alpha_complex_sum.rst
index b608050e..b3689556 100644
--- a/src/cython/doc/alpha_complex_sum.rst
+++ b/src/cython/doc/alpha_complex_sum.rst
@@ -1,5 +1,7 @@
 =====================================  =====================================  =====================================
-:Author: Vincent Rouvreau              :Introduced in: GUDHI PYTHON 1.4.0     :Copyright: GPL v3
+:Author: Vincent Rouvreau              :Introduced in: GUDHI 1.3.0            :Copyright: GPL v3
+=====================================  =====================================  =====================================
+:Requires:                             CGAL &ge 4.7.0                         Eigen3
 =====================================  =====================================  =====================================
 
 +-------------------------------------------+----------------------------------------------------------------------+
diff --git a/src/cython/doc/conf.py b/src/cython/doc/conf.py
index 8d6483af..8b42ce37 100755
--- a/src/cython/doc/conf.py
+++ b/src/cython/doc/conf.py
@@ -67,9 +67,9 @@ copyright = u'2016, Vincent Rouvreau'
 # built documents.
 #
 # The short X.Y version.
-version = '1.3.1'
+version = '1.4.beta'
 # The full version, including alpha/beta/rc tags.
-release = '1.3.1'
+release = '1.4.beta'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/src/cython/doc/cubical_complex_sum.rst b/src/cython/doc/cubical_complex_sum.rst
index 4008a1fd..98e23849 100644
--- a/src/cython/doc/cubical_complex_sum.rst
+++ b/src/cython/doc/cubical_complex_sum.rst
@@ -1,5 +1,5 @@
 =====================================  =====================================  =====================================
-:Author: Pawel Dlotko                  :Introduced in: GUDHI PYTHON 1.4.0     :Copyright: GPL v3
+:Author: Pawel Dlotko                  :Introduced in: GUDHI 1.3.0            :Copyright: GPL v3
 =====================================  =====================================  =====================================
 
 +---------------------------------------------+----------------------------------------------------------------------+
diff --git a/src/cython/doc/persistence_graphical_tools_ref.rst b/src/cython/doc/persistence_graphical_tools_ref.rst
new file mode 100644
index 00000000..aa214edf
--- /dev/null
+++ b/src/cython/doc/persistence_graphical_tools_ref.rst
@@ -0,0 +1,8 @@
+============================================
+Persistence graphical tools reference manual
+============================================
+
+.. automethod:: gudhi.__min_birth_max_death
+.. automethod:: gudhi.show_palette_values
+.. automethod:: gudhi.barcode_persistence
+.. automethod:: gudhi.diagram_persistence
\ No newline at end of file
diff --git a/src/cython/doc/persistence_graphical_tools_sum.rst b/src/cython/doc/persistence_graphical_tools_sum.rst
new file mode 100644
index 00000000..a6260032
--- /dev/null
+++ b/src/cython/doc/persistence_graphical_tools_sum.rst
@@ -0,0 +1,13 @@
+=====================================  =====================================  =====================================
+:Author: Vincent Rouvreau              :Introduced in: GUDHI 1.4.0            :Copyright: GPL v3
+=====================================  =====================================  =====================================
+:Requires:                             Matplotlib                             Numpy
+=====================================  =====================================  =====================================
+
++---------------------------------------------+----------------------------------------------------------------------+
+| .. image::                                  | These graphical tools comes on top of persistence results and allows |
+|      img/graphical_tools_representation.png |  the user to build easily barcode and persistence diagram.           |
+|                                             |                                                                      |
++---------------------------------------------+----------------------------------------------------------------------+
+|  :doc:`persistence_graphical_tools_user`    | * :doc:`persistence_graphical_tools_ref`                             |
++---------------------------------------------+----------------------------------------------------------------------+
diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst
new file mode 100644
index 00000000..0cb61cf1
--- /dev/null
+++ b/src/cython/doc/persistence_graphical_tools_user.rst
@@ -0,0 +1,46 @@
+=======================================
+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:
+
+
+.. testcode::
+
+    import gudhi
+    gudhi.show_palette_values(alpha=1.0)
+
+Show persistence as a barcode
+-----------------------------
+
+This function can display the persistence result as a barcode:
+
+.. testcode::
+
+    import gudhi
+    
+    periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt')
+    diag = periodic_cc.persistence()
+    gudhi.barcode_persistence(diag)
+
+
+Show persistence as a diagram
+-----------------------------
+
+This function can display the persistence result as a diagram:
+
+.. testcode::
+
+    import gudhi
+    
+    alpha_complex = gudhi.AlphaComplex(off_file='tore3D_300.off')
+    alpha_complex.initialize_filtration()
+    diag = alpha_complex.persistence()
+    gudhi.diagram_persistence(diag)
diff --git a/src/cython/doc/persistent_cohomology_sum.rst b/src/cython/doc/persistent_cohomology_sum.rst
index 081399a5..b306b3d4 100644
--- a/src/cython/doc/persistent_cohomology_sum.rst
+++ b/src/cython/doc/persistent_cohomology_sum.rst
@@ -1,5 +1,5 @@
 =====================================  =====================================  =====================================
-:Author: Clément Maria                 :Introduced in: GUDHI PYTHON 1.4.0     :Copyright: GPL v3
+:Author: Clément Maria                 :Introduced in: GUDHI 1.0.0            :Copyright: GPL v3
 =====================================  =====================================  =====================================
 
 +---------------------------------------------+----------------------------------------------------------------------+
diff --git a/src/cython/doc/pyplots/diagram_persistence.py b/src/cython/doc/pyplots/diagram_persistence.py
index ceeeceb3..b006b0bf 100755
--- a/src/cython/doc/pyplots/diagram_persistence.py
+++ b/src/cython/doc/pyplots/diagram_persistence.py
@@ -1,6 +1,5 @@
 import gudhi
 
 alpha_complex = gudhi.AlphaComplex(off_file='../tore3D_300.off')
-alpha_complex.initialize_filtration()
 diag = alpha_complex.persistence()
 gudhi.diagram_persistence(diag)
diff --git a/src/cython/doc/simplex_tree_sum.rst b/src/cython/doc/simplex_tree_sum.rst
index ffdb2cf4..0f34888a 100644
--- a/src/cython/doc/simplex_tree_sum.rst
+++ b/src/cython/doc/simplex_tree_sum.rst
@@ -1,5 +1,5 @@
 =====================================  =====================================  =====================================
-:Author: Clément Maria                 :Introduced in: GUDHI PYTHON 1.4.0     :Copyright: GPL v3
+:Author: Clément Maria                 :Introduced in: GUDHI 1.0.0            :Copyright: GPL v3
 =====================================  =====================================  =====================================
 
 +-------------------------------------------+----------------------------------------------------------------------+
diff --git a/src/cython/doc/witness_complex_sum.rst b/src/cython/doc/witness_complex_sum.rst
index 0d65d420..005a5a41 100644
--- a/src/cython/doc/witness_complex_sum.rst
+++ b/src/cython/doc/witness_complex_sum.rst
@@ -1,5 +1,5 @@
 =====================================  =====================================  =====================================
-:Author: Siargey Kachanovich           :Introduced in: GUDHI PYTHON 1.4.0     :Copyright: GPL v3
+:Author: Siargey Kachanovich           :Introduced in: GUDHI 1.3.0            :Copyright: GPL v3
 =====================================  =====================================  =====================================
 
 +---------------------------------------------+----------------------------------------------------------------------+
diff --git a/src/cython/include/Alpha_complex_interface.h b/src/cython/include/Alpha_complex_interface.h
index e2e6d100..13412994 100644
--- a/src/cython/include/Alpha_complex_interface.h
+++ b/src/cython/include/Alpha_complex_interface.h
@@ -23,9 +23,12 @@
 #ifndef ALPHA_COMPLEX_INTERFACE_H
 #define	ALPHA_COMPLEX_INTERFACE_H
 
+#include <gudhi/Simplex_tree.h>
 #include <gudhi/Alpha_complex.h>
 #include <CGAL/Epick_d.h>
 
+#include "Persistent_cohomology_interface.h"
+
 #include <vector>
 #include <utility>  // std::pair
 #include <iostream>
@@ -34,51 +37,57 @@ namespace Gudhi {
 
 namespace alpha_complex {
 
-class Alpha_complex_interface : public Alpha_complex< CGAL::Epick_d< CGAL::Dynamic_dimension_tag > > {
-  using Alpha_complex = Alpha_complex< CGAL::Epick_d< CGAL::Dynamic_dimension_tag > > ;
-  typedef typename Alpha_complex::Simplex_handle Simplex_handle;
+class Alpha_complex_interface {
+  using Dynamic_kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >;
+  using Point_d = Dynamic_kernel::Point_d;
+  typedef typename Simplex_tree<>::Simplex_handle Simplex_handle;
   typedef typename std::pair<Simplex_handle, bool> Insertion_result;
   using Simplex = std::vector<Vertex_handle>;
   using Filtered_complex = std::pair<Simplex, Filtration_value>;
   using Complex_tree = std::vector<Filtered_complex>;
-  using Point_d = Alpha_complex::Point_d;
 
- public:
+  typedef typename Simplex_tree<>::Simplex_key Simplex_key;
 
+ public:
   Alpha_complex_interface(std::vector<std::vector<double>>&points, double max_alpha_square)
-  : Alpha_complex(points, max_alpha_square) {
+  : pcoh_(nullptr) {
+    alpha_complex_ = new Alpha_complex<Dynamic_kernel>(points);
+    alpha_complex_->create_complex(simplex_tree_, max_alpha_square);
+    simplex_tree_.initialize_filtration();
   }
 
-  // bool from_file is a workaround fro cython to find the correct signature
-  Alpha_complex_interface(const std::string& off_file, double max_alpha_square, bool from_file)
-  : Alpha_complex(off_file, max_alpha_square) {
+  Alpha_complex_interface(std::string off_file_name, double max_alpha_square, bool from_file = true)
+  : pcoh_(nullptr) {
+    alpha_complex_ = new Alpha_complex<Dynamic_kernel>(off_file_name);
+    alpha_complex_->create_complex(simplex_tree_, max_alpha_square);
+    simplex_tree_.initialize_filtration();
   }
 
   bool find_simplex(const Simplex& vh) {
-    return (Alpha_complex::find(vh) != Alpha_complex::null_simplex());
+    return (simplex_tree_.find(vh) != simplex_tree_.null_simplex());
   }
 
   bool insert_simplex_and_subfaces(const Simplex& complex, Filtration_value filtration = 0) {
-    Insertion_result result = Alpha_complex::insert_simplex_and_subfaces(complex, filtration);
+    Insertion_result result = simplex_tree_.insert_simplex_and_subfaces(complex, filtration);
     return (result.second);
   }
 
   Filtration_value simplex_filtration(const Simplex& complex) {
-    return Alpha_complex::filtration(Alpha_complex::find(complex));
+    return simplex_tree_.filtration(simplex_tree_.find(complex));
   }
 
   void remove_maximal_simplex(const Simplex& complex) {
-    return Alpha_complex::remove_maximal_simplex(Alpha_complex::find(complex));
+    return simplex_tree_.remove_maximal_simplex(simplex_tree_.find(complex));
   }
 
   Complex_tree get_filtered_tree() {
     Complex_tree filtered_tree;
-    for (auto f_simplex : Alpha_complex::filtration_simplex_range()) {
+    for (auto f_simplex : simplex_tree_.filtration_simplex_range()) {
       Simplex simplex;
-      for (auto vertex : Alpha_complex::simplex_vertex_range(f_simplex)) {
+      for (auto vertex : simplex_tree_.simplex_vertex_range(f_simplex)) {
         simplex.insert(simplex.begin(), vertex);
       }
-      filtered_tree.push_back(std::make_pair(simplex, Alpha_complex::filtration(f_simplex)));
+      filtered_tree.push_back(std::make_pair(simplex, simplex_tree_.filtration(f_simplex)));
     }
     return filtered_tree;
 
@@ -86,44 +95,73 @@ class Alpha_complex_interface : public Alpha_complex< CGAL::Epick_d< CGAL::Dynam
 
   Complex_tree get_skeleton_tree(int dimension) {
     Complex_tree skeleton_tree;
-    for (auto f_simplex : Alpha_complex::skeleton_simplex_range(dimension)) {
+    for (auto f_simplex : simplex_tree_.skeleton_simplex_range(dimension)) {
       Simplex simplex;
-      for (auto vertex : Alpha_complex::simplex_vertex_range(f_simplex)) {
+      for (auto vertex : simplex_tree_.simplex_vertex_range(f_simplex)) {
         simplex.insert(simplex.begin(), vertex);
       }
-      skeleton_tree.push_back(std::make_pair(simplex, Alpha_complex::filtration(f_simplex)));
+      skeleton_tree.push_back(std::make_pair(simplex, simplex_tree_.filtration(f_simplex)));
     }
     return skeleton_tree;
   }
 
   Complex_tree get_star_tree(const Simplex& complex) {
     Complex_tree star_tree;
-    for (auto f_simplex : Alpha_complex::star_simplex_range(Alpha_complex::find(complex))) {
+    for (auto f_simplex : simplex_tree_.star_simplex_range(simplex_tree_.find(complex))) {
       Simplex simplex;
-      for (auto vertex : Alpha_complex::simplex_vertex_range(f_simplex)) {
+      for (auto vertex : simplex_tree_.simplex_vertex_range(f_simplex)) {
         simplex.insert(simplex.begin(), vertex);
       }
-      star_tree.push_back(std::make_pair(simplex, Alpha_complex::filtration(f_simplex)));
+      star_tree.push_back(std::make_pair(simplex, simplex_tree_.filtration(f_simplex)));
     }
     return star_tree;
   }
 
   Complex_tree get_coface_tree(const Simplex& complex, int dimension) {
     Complex_tree coface_tree;
-    for (auto f_simplex : Alpha_complex::cofaces_simplex_range(Alpha_complex::find(complex), dimension)) {
+    for (auto f_simplex : simplex_tree_.cofaces_simplex_range(simplex_tree_.find(complex), dimension)) {
       Simplex simplex;
-      for (auto vertex : Alpha_complex::simplex_vertex_range(f_simplex)) {
+      for (auto vertex : simplex_tree_.simplex_vertex_range(f_simplex)) {
         simplex.insert(simplex.begin(), vertex);
       }
-      coface_tree.push_back(std::make_pair(simplex, Alpha_complex::filtration(f_simplex)));
+      coface_tree.push_back(std::make_pair(simplex, simplex_tree_.filtration(f_simplex)));
     }
     return coface_tree;
   }
-  
+
+  // Specific to Witness complex because no inheritance
+  Filtration_value filtration() const {
+    return simplex_tree_.filtration();
+  }
+
+  void set_filtration(Filtration_value fil) {
+    simplex_tree_.set_filtration(fil);
+  }
+
+  void initialize_filtration() {
+    simplex_tree_.initialize_filtration();
+  }
+
+  size_t num_vertices() const {
+    return simplex_tree_.num_vertices();
+  }
+
+  size_t num_simplices() {
+    return simplex_tree_.num_simplices();
+  }
+
+  int dimension() const {
+    return simplex_tree_.dimension();
+  }
+
+  void set_dimension(int dimension) {
+    simplex_tree_.set_dimension(dimension);
+  }
+
   std::vector<double> get_point(int vh) {
     std::vector<double> vd;
     try {
-      Point_d ph = Alpha_complex::get_point(vh);
+      Point_d ph = alpha_complex_->get_point(vh);
       for (auto coord = ph.cartesian_begin(); coord < ph.cartesian_end(); coord++)
         vd.push_back(*coord);
     } catch (std::out_of_range outofrange) {
@@ -132,6 +170,34 @@ class Alpha_complex_interface : public Alpha_complex< CGAL::Epick_d< CGAL::Dynam
     return vd;
   }
 
+  std::vector<std::pair<int, std::pair<double, double>>> get_persistence(int homology_coeff_field, double min_persistence) {
+    if (pcoh_ != nullptr) {
+      delete pcoh_;
+    }
+    pcoh_ = new Persistent_cohomology_interface<Simplex_tree<>>(&simplex_tree_);
+    return pcoh_->get_persistence(homology_coeff_field, min_persistence);
+  }
+  
+  std::vector<int> get_betti_numbers() const {
+    if (pcoh_ != nullptr) {
+      return pcoh_->betti_numbers();
+    }
+    std::vector<int> betti_numbers;
+    return betti_numbers;
+  }
+
+  std::vector<int> get_persistent_betti_numbers(Filtration_value from, Filtration_value to) const {
+    if (pcoh_ != nullptr) {
+      return pcoh_->persistent_betti_numbers(from, to);
+    }
+    std::vector<int> persistent_betti_numbers;
+    return persistent_betti_numbers;
+  }
+  
+ private:
+  Simplex_tree<> simplex_tree_;
+  Persistent_cohomology_interface<Simplex_tree<>>* pcoh_;
+  Alpha_complex<Dynamic_kernel>* alpha_complex_;
 };
 
 }  // namespace alpha_complex
diff --git a/src/cython/include/Simplex_tree_interface.h b/src/cython/include/Simplex_tree_interface.h
index 9aee630b..ad7be1a8 100644
--- a/src/cython/include/Simplex_tree_interface.h
+++ b/src/cython/include/Simplex_tree_interface.h
@@ -26,6 +26,7 @@
 #include <gudhi/graph_simplicial_complex.h>
 #include <gudhi/distance_functions.h>
 #include <gudhi/Simplex_tree.h>
+#include <gudhi/Points_off_io.h>
 
 #include <vector>
 #include <utility>  // std::pair
@@ -116,6 +117,21 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
     Simplex_tree<SimplexTreeOptions>::initialize_filtration();
   }
 
+  void graph_expansion(std::string& off_file_name, int max_dimension, double max_edge_length, bool from_file=true) {
+    Gudhi::Points_off_reader<std::vector <double>> off_reader(off_file_name);
+    // Check the read operation was correct
+    if (!off_reader.is_valid()) {
+      std::cerr << "Unable to read file " << off_file_name << std::endl;
+    } else {
+      std::vector<std::vector <double>> points = off_reader.get_point_cloud();
+      Graph_t prox_graph = compute_proximity_graph(points, max_edge_length,
+                                                   euclidean_distance<std::vector<double>>);
+      Simplex_tree<SimplexTreeOptions>::insert_graph(prox_graph);
+      Simplex_tree<SimplexTreeOptions>::expansion(max_dimension);
+      Simplex_tree<SimplexTreeOptions>::initialize_filtration();
+    }
+  }
+
 };
 
 struct Simplex_tree_options_mini : Simplex_tree_options_full_featured {
diff --git a/src/cython/include/Witness_complex_interface.h b/src/cython/include/Witness_complex_interface.h
index bdfea91f..ab99adf5 100644
--- a/src/cython/include/Witness_complex_interface.h
+++ b/src/cython/include/Witness_complex_interface.h
@@ -25,7 +25,8 @@
 
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Witness_complex.h>
-#include <gudhi/Landmark_choice_by_furthest_point.h>
+#include <gudhi/Construct_closest_landmark_table.h>
+#include <gudhi/pick_n_random_points.h>
 
 #include "Persistent_cohomology_interface.h"
 
@@ -48,10 +49,11 @@ class Witness_complex_interface {
   Witness_complex_interface(std::vector<std::vector<double>>&points, int number_of_landmarks)
   : pcoh_(nullptr) {
     std::vector<std::vector< int > > knn;
+    std::vector<std::vector<double>> landmarks;
+    Gudhi::subsampling::pick_n_random_points(points, number_of_landmarks, std::back_inserter(landmarks));
+    Gudhi::witness_complex::construct_closest_landmark_table(points, landmarks, knn);
 
-    Gudhi::witness_complex::landmark_choice_by_furthest_point(points, number_of_landmarks, knn);
     Gudhi::witness_complex::witness_complex(knn, number_of_landmarks, points[0].size(), simplex_tree_);
-
   }
 
   bool find_simplex(const Simplex& vh) {