Make Python interface compile, test and doc for Python2 and Python3

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2267 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: f7397ecc5aba27ad4ecc794f4fbf5ca857847113

14 files changed, 369 insertions, 642 deletions

diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index ba38fe3d..c51d9a1e 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -14,205 +14,234 @@ macro( find_the_lib placeholder THE_LIBS )
   endforeach(THE_LIB ${THE_LIBS})
 endmacro( find_the_lib )
 
-FIND_PROGRAM( PYTHON_PATH python )
-FIND_PROGRAM( CYTHON_PATH cython )
-
-if(PYTHON_PATH AND CYTHON_PATH)
-  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_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ")
-  if(WIN32)
-    set( returnValue "" )
-    find_the_lib (${returnValue} ${Boost_SYSTEM_LIBRARY})
-    set(BOOST_SYSTEM_LIB_NAME ${returnValue})
+# Find the correct Python interpreter. Can be set with -DPYTHON_EXECUTABLE=/usr/bin/python3 for instance.
+if(PYTHON_EXECUTABLE)
+  if(NOT EXISTS "${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)
+    if(NOT CYTHON_PATH)
+      message(FATAL_ERROR "ERROR: Try to compile the Cython interface. Python is set to 2.X while no cython installed.")
+    endif(NOT CYTHON_PATH)
+    # 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)
+    if(NOT CYTHON_PATH)
+      message(FATAL_ERROR "ERROR: Try to compile the Cython interface. Python is set to 3.X while no cython3 installed.")
+    endif(NOT CYTHON_PATH)
+    # Unitary tests are available through py.test
+    find_program( PYTEST_PATH py.test )
+    # Documentation generation is available through sphinx
+    set(SPHINX_PATH "${CMAKE_CURRENT_BINARY_DIR}/doc/python3-sphinx-build")
   else()
-      set(BOOST_SYSTEM_LIB_NAME "boost_system")
-      endif()
-  set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'${BOOST_SYSTEM_LIB_NAME}', ")
-
-  # Gudhi and CGAL compilation option
-  if(MSVC)
-    set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${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("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
-  if (DEBUG_TRACES)
-    # For programs to be more verbose
-    set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DDEBUG_TRACES', ")
-  endif()
-
-  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', ")
-  endif (EIGEN3_FOUND)
-
-  # Copy recursively include, cython, example, doc and test repositories before packages finding
-  # Some tests and doc 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 example DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
-  file(COPY test DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
-  file(COPY doc DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
-  # Developper version for doc images
-  file(GLOB GUDHI_DEV_DOC_IMAGES "${CMAKE_SOURCE_DIR}/src/*/doc/*.png")
-  file(COPY ${GUDHI_DEV_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img")
-  file(GLOB GUDHI_DEV_DOC_IMAGES "${CMAKE_SOURCE_DIR}/src/*/doc/*.svg")
-  file(COPY ${GUDHI_DEV_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img")
-  # User version for doc images
-  file(GLOB GUDHI_USER_DOC_IMAGES "${CMAKE_SOURCE_DIR}/doc/*/*.png")
-  file(COPY ${GUDHI_USER_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img")
-  file(GLOB GUDHI_USER_DOC_IMAGES "${CMAKE_SOURCE_DIR}/doc/*/*.svg")
-  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/")
-  file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" DESTINATION "${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 (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-    # If CGAL_VERSION >= 4.8.1, include subsampling
-    set(GUDHI_CYTHON_SUBSAMPLING "include 'cython/subsampling.pyx'")
-    set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include 'cython/tangential_complex.pyx'")
-    set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include 'cython/bottleneck_distance.pyx'")
-  else (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-    # Remove subsampling unitary tests
-    file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_subsampling.py)
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_ref.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_sum.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_user.rst")
-    # Remove tangential complex and bottleneck unitary tests
-    file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_tangential_complex.py)
-    file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_bottleneck_distance.py)
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/bottleneck_distance_ref.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/bottleneck_distance_sum.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/bottleneck_distance_user.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_ref.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_sum.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_user.rst")
-  endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-  if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
-    # If CGAL_VERSION >= 4.7.0, include alpha
-    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 ${CMAKE_CURRENT_BINARY_DIR}/test/test_alpha_complex.py)
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/alpha_complex_ref.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/alpha_complex_sum.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/alpha_complex_user.rst")
-  endif (NOT CGAL_VERSION VERSION_LESS 4.7.0)
-  if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
-    # If CGAL_VERSION >= 4.6.0, include euclidean versions of witness complex
-    set(GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX
-        "include 'cython/euclidean_witness_complex.pyx'\ninclude 'cython/euclidean_strong_witness_complex.pyx'\n")
-  else (NOT CGAL_VERSION VERSION_LESS 4.6.0)
-    # Remove alpha complex unitary tests
-    file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_euclidean_witness_complex.py)
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/euclidean_witness_complex_ref.rst")
-    file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/euclidean_strong_witness_complex_ref.rst")
-  endif (NOT CGAL_VERSION VERSION_LESS 4.6.0)
-
-  if(CGAL_FOUND)
-    # Add CGAL compilation args
-    if(CGAL_HEADER_ONLY)
-      set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ")
-    else(CGAL_HEADER_ONLY)
-      if(WIN32)
-        set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'CGAL-vc140-mt-4.7', ")
-      else(WIN32)
-        set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'CGAL', ")
-      endif(WIN32)
-      set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ")
-    endif(CGAL_HEADER_ONLY)
-    # GMP and GMPXX are not required, but if present, CGAL will link with them.
-    if(GMP_FOUND)
-      set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMP', ")
-      if(WIN32)
-        set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'libgmp-10', ")
-      else(WIN32)
-        set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'gmp', ")
-      endif(WIN32)
-        set(GUDHI_CYTHON_LIBRARY_DIRS "${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}'${GMPXX_LIBRARIES_DIR}', ")
-      endif(GMPXX_FOUND)
-    endif(GMP_FOUND)
-  endif(CGAL_FOUND)
-
-  # Specific for Mac
-  if (${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', ")
-  endif(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
-
-  # 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 (TBB_FOUND)
-    set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DGUDHI_USE_TBB', ")
-    set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'tbb', 'tbbmalloc', ")
-    set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${TBB_LIBRARY_DIRS}', ")
-    set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${TBB_INCLUDE_DIRS}', ")
-  endif()
-
-  # 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"
+    message(FATAL_ERROR "ERROR: Try to compile the Cython interface. Python version ${PYTHON_VERSION_STRING} is not valid.")
+  endif(PYTHON_VERSION_MAJOR EQUAL 2)
+endif(PYTHONINTERP_FOUND)
+
+message("${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_PATH} - py.test is ${PYTEST_PATH} - Sphinx is ${SPHINX_PATH}")
+
+set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_RESULT_OF_USE_DECLTYPE', ")
+set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ")
+set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ")
+if(WIN32)
+  set( returnValue "" )
+  find_the_lib (${returnValue} ${Boost_SYSTEM_LIBRARY})
+  set(BOOST_SYSTEM_LIB_NAME ${returnValue})
+else()
+    set(BOOST_SYSTEM_LIB_NAME "boost_system")
+    endif()
+set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'${BOOST_SYSTEM_LIB_NAME}', ")
+
+# Gudhi and CGAL compilation option
+if(MSVC)
+  set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${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("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
+if (DEBUG_TRACES)
+  # For programs to be more verbose
+  set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DDEBUG_TRACES', ")
+endif()
+
+if (EIGEN3_FOUND)
+  # No problem, even if no CGAL found
+  set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ")
+endif (EIGEN3_FOUND)
+
+# Copy recursively include, cython, example, doc and test repositories before packages finding
+# Some tests and doc 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 example DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+file(COPY test DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+file(COPY doc DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+# Developper version for doc images
+file(GLOB GUDHI_DEV_DOC_IMAGES "${CMAKE_SOURCE_DIR}/src/*/doc/*.png")
+file(COPY ${GUDHI_DEV_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img")
+file(GLOB GUDHI_DEV_DOC_IMAGES "${CMAKE_SOURCE_DIR}/src/*/doc/*.svg")
+file(COPY ${GUDHI_DEV_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img")
+# User version for doc images
+file(GLOB GUDHI_USER_DOC_IMAGES "${CMAKE_SOURCE_DIR}/doc/*/*.png")
+file(COPY ${GUDHI_USER_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/img")
+file(GLOB GUDHI_USER_DOC_IMAGES "${CMAKE_SOURCE_DIR}/doc/*/*.svg")
+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/")
+file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" DESTINATION "${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 (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+  # If CGAL_VERSION >= 4.8.1, include subsampling
+  set(GUDHI_CYTHON_SUBSAMPLING "include 'cython/subsampling.pyx'")
+  set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include 'cython/tangential_complex.pyx'")
+  set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include 'cython/bottleneck_distance.pyx'")
+else (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+  # Remove subsampling unitary tests
+  file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_subsampling.py)
+  file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_ref.rst")
+  file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_sum.rst")
+  file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_user.rst")
+  # Remove tangential complex and bottleneck unitary tests
+  file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_tangential_complex.py)
+  file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_bottleneck_distance.py)
+  file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/bottleneck_distance_ref.rst")
+  file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/bottleneck_distance_sum.rst")
+  file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/bottleneck_distance_user.rst")
+  file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_ref.rst")
+  file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_sum.rst")
+  file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_user.rst")
+endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+  # If CGAL_VERSION >= 4.7.0, include alpha
+  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 ${CMAKE_CURRENT_BINARY_DIR}/test/test_alpha_complex.py)
+  file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/alpha_complex_ref.rst")
+  file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/alpha_complex_sum.rst")
+  file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/alpha_complex_user.rst")
+endif (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
+  # If CGAL_VERSION >= 4.6.0, include euclidean versions of witness complex
+  set(GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX
+      "include 'cython/euclidean_witness_complex.pyx'\ninclude 'cython/euclidean_strong_witness_complex.pyx'\n")
+else (NOT CGAL_VERSION VERSION_LESS 4.6.0)
+  # Remove alpha complex unitary tests
+  file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_euclidean_witness_complex.py)
+  file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/euclidean_witness_complex_ref.rst")
+  file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/euclidean_strong_witness_complex_ref.rst")
+endif (NOT CGAL_VERSION VERSION_LESS 4.6.0)
+
+if(CGAL_FOUND)
+  # Add CGAL compilation args
+  if(CGAL_HEADER_ONLY)
+    set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ")
+  else(CGAL_HEADER_ONLY)
+    if(WIN32)
+      set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'CGAL-vc140-mt-4.7', ")
+    else(WIN32)
+      set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'CGAL', ")
+    endif(WIN32)
+    set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ")
+  endif(CGAL_HEADER_ONLY)
+  # GMP and GMPXX are not required, but if present, CGAL will link with them.
+  if(GMP_FOUND)
+    set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMP', ")
+    if(WIN32)
+      set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'libgmp-10', ")
+    else(WIN32)
+      set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'gmp', ")
+    endif(WIN32)
+      set(GUDHI_CYTHON_LIBRARY_DIRS "${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}'${GMPXX_LIBRARIES_DIR}', ")
+    endif(GMPXX_FOUND)
+  endif(GMP_FOUND)
+endif(CGAL_FOUND)
+
+# Specific for Mac
+if (${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', ")
+endif(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+
+# 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 (TBB_FOUND)
+  set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DGUDHI_USE_TBB', ")
+  set(GUDHI_CYTHON_LIBRARIES "${GUDHI_CYTHON_LIBRARIES}'tbb', 'tbbmalloc', ")
+  set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${TBB_LIBRARY_DIRS}', ")
+  set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${TBB_INCLUDE_DIRS}', ")
+endif()
+
+# set sphinx-build in make files
+configure_file(doc/Makefile.in "${CMAKE_CURRENT_BINARY_DIR}/doc/Makefile" @ONLY)
+configure_file(doc/make.bat.in "${CMAKE_CURRENT_BINARY_DIR}/doc/make.bat" @ONLY)
+
+# 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 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/cythonize_gudhi.py" "build_ext" "--inplace")
+
+add_custom_target(cython ALL DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
+                  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}/ )
+endif(UNIX)
+
+# Unitary tests are available through py.test
+if(PYTEST_PATH)
+  add_test(
+      NAME gudhi_cython_py_test
       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-      COMMAND python "${CMAKE_CURRENT_BINARY_DIR}/cythonize_gudhi.py" "build_ext" "--inplace")
-
-  add_custom_target(cython ALL DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
-                    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}/ )
-  endif(UNIX)
-
-  # 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)
-    if (UNIX)
-      add_custom_target(sphinx
-          WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc
-          DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
-          COMMAND make html doctest)
-    else (UNIX)
-      add_custom_target(sphinx
-          WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc
-          COMMAND make.bat html)
-    endif (UNIX)
-  endif(SPHINX_PATH)
-endif(PYTHON_PATH AND CYTHON_PATH)
+      COMMAND ${PYTHON_EXECUTABLE} "${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
+if(SPHINX_PATH)
+  if (UNIX)
+    add_custom_target(sphinx
+        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc
+        DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
+        COMMAND make html doctest)
+  else (UNIX)
+    add_custom_target(sphinx
+        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc
+        COMMAND make.bat html doctest)
+  endif (UNIX)
+endif(SPHINX_PATH)
diff --git a/src/cython/cython/alpha_complex.pyx b/src/cython/cython/alpha_complex.pyx
index da537c2e..a0e8f9b7 100644
--- a/src/cython/cython/alpha_complex.pyx
+++ b/src/cython/cython/alpha_complex.pyx
@@ -78,7 +78,7 @@ cdef class AlphaComplex:
     def __cinit__(self, points=None, off_file=''):
         if off_file is not '':
             if os.path.isfile(off_file):
-                self.thisptr = new Alpha_complex_interface(off_file, True)
+                self.thisptr = new Alpha_complex_interface(str.encode(off_file), True)
             else:
                 print("file " + off_file + " not found.")
         else:
diff --git a/src/cython/cython/cubical_complex.pyx b/src/cython/cython/cubical_complex.pyx
index e1344f49..1ed6bc5e 100644
--- a/src/cython/cython/cubical_complex.pyx
+++ b/src/cython/cython/cubical_complex.pyx
@@ -80,7 +80,7 @@ cdef class CubicalComplex:
             self.thisptr = new Bitmap_cubical_complex_base_interface(dimensions, top_dimensional_cells)
         elif (dimensions is None) and (top_dimensional_cells is None) and (perseus_file is not ''):
             if os.path.isfile(perseus_file):
-                self.thisptr = new Bitmap_cubical_complex_base_interface(perseus_file)
+                self.thisptr = new Bitmap_cubical_complex_base_interface(str.encode(perseus_file))
             else:
                 print("file " + perseus_file + " not found.")
         else:
diff --git a/src/cython/cython/off_reader.pyx b/src/cython/cython/off_reader.pyx
index 78c37969..b6e107ef 100644
--- a/src/cython/cython/off_reader.pyx
+++ b/src/cython/cython/off_reader.pyx
@@ -43,7 +43,7 @@ def read_off(off_file=''):
     """
     if off_file is not '':
         if os.path.isfile(off_file):
-            return read_points_from_OFF_file(off_file)
+            return read_points_from_OFF_file(str.encode(off_file))
         else:
             print("file " + off_file + " not found.")
 
diff --git a/src/cython/cython/periodic_cubical_complex.pyx b/src/cython/cython/periodic_cubical_complex.pyx
index 1445d429..88cb4395 100644
--- a/src/cython/cython/periodic_cubical_complex.pyx
+++ b/src/cython/cython/periodic_cubical_complex.pyx
@@ -80,7 +80,7 @@ cdef class PeriodicCubicalComplex:
             self.thisptr = new Periodic_cubical_complex_base_interface(dimensions, top_dimensional_cells)
         elif (dimensions is None) and (top_dimensional_cells is None) and (perseus_file is not ''):
             if os.path.isfile(perseus_file):
-                self.thisptr = new Periodic_cubical_complex_base_interface(perseus_file)
+                self.thisptr = new Periodic_cubical_complex_base_interface(str.encode(perseus_file))
             else:
                 print("file " + perseus_file + " not found.")
         else:
diff --git a/src/cython/cython/rips_complex.pyx b/src/cython/cython/rips_complex.pyx
index 6bfb4482..ad9b0a4d 100644
--- a/src/cython/cython/rips_complex.pyx
+++ b/src/cython/cython/rips_complex.pyx
@@ -80,7 +80,7 @@ cdef class RipsComplex:
     def __cinit__(self, points=None, off_file='', distance_matrix=None, csv_file='', max_edge_length=float('inf')):
         if off_file is not '':
             if os.path.isfile(off_file):
-                self.thisptr = new Rips_complex_interface(off_file,
+                self.thisptr = new Rips_complex_interface(str.encode(off_file),
                                                           max_edge_length,
                                                           True,
                                                           True)
@@ -88,7 +88,7 @@ cdef class RipsComplex:
                 print("file " + off_file + " not found.")
         elif csv_file is not '':
             if os.path.isfile(csv_file):
-                self.thisptr = new Rips_complex_interface(csv_file,
+                self.thisptr = new Rips_complex_interface(str.encode(csv_file),
                                                           max_edge_length,
                                                           False,
                                                           True)
diff --git a/src/cython/cython/subsampling.pyx b/src/cython/cython/subsampling.pyx
index a25d196d..894a4fbe 100644
--- a/src/cython/cython/subsampling.pyx
+++ b/src/cython/cython/subsampling.pyx
@@ -65,10 +65,10 @@ def choose_n_farthest_points(points=None, off_file='', nb_points=0, starting_poi
     if off_file is not '':
         if os.path.isfile(off_file):
             if starting_point is '':
-                return subsampling_n_farthest_points_from_file(off_file,
+                return subsampling_n_farthest_points_from_file(str.encode(off_file),
                                                                nb_points)
             else:
-                return subsampling_n_farthest_points_from_file(off_file,
+                return subsampling_n_farthest_points_from_file(str.encode(off_file),
                                                                nb_points,
                                                                starting_point)
         else:
@@ -101,7 +101,8 @@ def pick_n_random_points(points=None, off_file='', nb_points=0):
     """
     if off_file is not '':
         if os.path.isfile(off_file):
-            return subsampling_n_random_points_from_file(off_file, nb_points)
+            return subsampling_n_random_points_from_file(str.encode(off_file),
+                nb_points)
         else:
             print("file " + off_file + " not found.")
     else:
@@ -128,7 +129,7 @@ def sparsify_point_set(points=None, off_file='', min_squared_dist=0.0):
     """
     if off_file is not '':
         if os.path.isfile(off_file):
-            return subsampling_sparsify_points_from_file(off_file,
+            return subsampling_sparsify_points_from_file(str.encode(off_file),
                                                          min_squared_dist)
         else:
             print("file " + off_file + " not found.")
diff --git a/src/cython/cython/tangential_complex.pyx b/src/cython/cython/tangential_complex.pyx
index 52bd8111..d55bb050 100644
--- a/src/cython/cython/tangential_complex.pyx
+++ b/src/cython/cython/tangential_complex.pyx
@@ -70,7 +70,7 @@ cdef class TangentialComplex:
     def __cinit__(self, points=None, off_file=''):
         if off_file is not '':
             if os.path.isfile(off_file):
-                self.thisptr = new Tangential_complex_interface(off_file, True)
+                self.thisptr = new Tangential_complex_interface(str.encode(off_file), True)
             else:
                 print("file " + off_file + " not found.")
         else:
diff --git a/src/cython/doc/Makefile b/src/cython/doc/Makefile
deleted file mode 100644
index be3ff7c4..00000000
--- a/src/cython/doc/Makefile
+++ /dev/null
@@ -1,181 +0,0 @@
-# Makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line.
-SPHINXOPTS    =
-SPHINXBUILD   = sphinx-build
-PAPER         =
-BUILDDIR      = _build
-
-# User-friendly check for sphinx-build
-ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
-$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
-endif
-
-# Internal variables.
-PAPEROPT_a4     = -D latex_paper_size=a4
-PAPEROPT_letter = -D latex_paper_size=letter
-ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
-# the i18n builder cannot share the environment and doctrees with the others
-I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
-
-.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
-
-help:
-	@echo "Please use \`make <target>' where <target> is one of"
-	@echo "  html       to make standalone HTML files"
-	@echo "  dirhtml    to make HTML files named index.html in directories"
-	@echo "  singlehtml to make a single large HTML file"
-	@echo "  pickle     to make pickle files"
-	@echo "  json       to make JSON files"
-	@echo "  htmlhelp   to make HTML files and a HTML help project"
-	@echo "  qthelp     to make HTML files and a qthelp project"
-	@echo "  devhelp    to make HTML files and a Devhelp project"
-	@echo "  epub       to make an epub"
-	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
-	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
-	@echo "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
-	@echo "  text       to make text files"
-	@echo "  man        to make manual pages"
-	@echo "  texinfo    to make Texinfo files"
-	@echo "  info       to make Texinfo files and run them through makeinfo"
-	@echo "  gettext    to make PO message catalogs"
-	@echo "  changes    to make an overview of all changed/added/deprecated items"
-	@echo "  xml        to make Docutils-native XML files"
-	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
-	@echo "  linkcheck  to check all external links for integrity"
-	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
-
-clean:
-	rm -f examples.inc
-	rm -rf $(BUILDDIR)/*
-
-# GUDHI specific : Examples.inc is generated with generate_examples.py (and deleted on clean)
-
-html:
-	./generate_examples.py
-	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
-	@echo
-	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
-
-dirhtml:
-	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
-	@echo
-	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
-
-singlehtml:
-	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
-	@echo
-	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
-
-pickle:
-	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
-	@echo
-	@echo "Build finished; now you can process the pickle files."
-
-json:
-	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
-	@echo
-	@echo "Build finished; now you can process the JSON files."
-
-htmlhelp:
-	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
-	@echo
-	@echo "Build finished; now you can run HTML Help Workshop with the" \
-	      ".hhp project file in $(BUILDDIR)/htmlhelp."
-
-qthelp:
-	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
-	@echo
-	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
-	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
-	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/pouet.qhcp"
-	@echo "To view the help file:"
-	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/pouet.qhc"
-
-devhelp:
-	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
-	@echo
-	@echo "Build finished."
-	@echo "To view the help file:"
-	@echo "# mkdir -p $$HOME/.local/share/devhelp/pouet"
-	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/pouet"
-	@echo "# devhelp"
-
-epub:
-	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
-	@echo
-	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
-
-latex:
-	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
-	@echo
-	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
-	@echo "Run \`make' in that directory to run these through (pdf)latex" \
-	      "(use \`make latexpdf' here to do that automatically)."
-
-latexpdf:
-	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
-	@echo "Running LaTeX files through pdflatex..."
-	$(MAKE) -C $(BUILDDIR)/latex all-pdf
-	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
-
-latexpdfja:
-	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
-	@echo "Running LaTeX files through platex and dvipdfmx..."
-	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
-	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
-
-text:
-	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
-	@echo
-	@echo "Build finished. The text files are in $(BUILDDIR)/text."
-
-man:
-	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
-	@echo
-	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
-
-texinfo:
-	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
-	@echo
-	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
-	@echo "Run \`make' in that directory to run these through makeinfo" \
-	      "(use \`make info' here to do that automatically)."
-
-info:
-	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
-	@echo "Running Texinfo files through makeinfo..."
-	make -C $(BUILDDIR)/texinfo info
-	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
-
-gettext:
-	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
-	@echo
-	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
-
-changes:
-	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
-	@echo
-	@echo "The overview file is in $(BUILDDIR)/changes."
-
-linkcheck:
-	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
-	@echo
-	@echo "Link check complete; look for any errors in the above output " \
-	      "or in $(BUILDDIR)/linkcheck/output.txt."
-
-doctest:
-	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
-	@echo "Testing of doctests in the sources finished, look at the " \
-	      "results in $(BUILDDIR)/doctest/output.txt."
-
-xml:
-	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
-	@echo
-	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
-
-pseudoxml:
-	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
-	@echo
-	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
diff --git a/src/cython/doc/Makefile.in b/src/cython/doc/Makefile.in
new file mode 100644
index 00000000..526350b3
--- /dev/null
+++ b/src/cython/doc/Makefile.in
@@ -0,0 +1,44 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = @SPHINX_PATH@
+PAPER         =
+BUILDDIR      = _build
+
+# User-friendly check for sphinx-build
+ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
+$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
+endif
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	rm -f examples.inc
+	rm -rf $(BUILDDIR)/*
+
+# GUDHI specific : Examples.inc is generated with generate_examples.py (and deleted on clean)
+
+html:
+	./generate_examples.py
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
diff --git a/src/cython/doc/make.bat b/src/cython/doc/make.bat
deleted file mode 100644
index ba009a90..00000000
--- a/src/cython/doc/make.bat
+++ /dev/null
@@ -1,246 +0,0 @@
-@ECHO OFF

-

-REM Command file for Sphinx documentation

-

-if "%SPHINXBUILD%" == "" (

-	set SPHINXBUILD=sphinx-build

-)

-set BUILDDIR=_build

-set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% .

-set I18NSPHINXOPTS=%SPHINXOPTS% .

-if NOT "%PAPER%" == "" (

-	set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%

-	set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS%

-)

-

-if "%1" == "" goto help

-

-if "%1" == "help" (

-	:help

-	echo.Please use `make ^<target^>` where ^<target^> is one of

-	echo.  html       to make standalone HTML files

-	echo.  dirhtml    to make HTML files named index.html in directories

-	echo.  singlehtml to make a single large HTML file

-	echo.  pickle     to make pickle files

-	echo.  json       to make JSON files

-	echo.  htmlhelp   to make HTML files and a HTML help project

-	echo.  qthelp     to make HTML files and a qthelp project

-	echo.  devhelp    to make HTML files and a Devhelp project

-	echo.  epub       to make an epub

-	echo.  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter

-	echo.  text       to make text files

-	echo.  man        to make manual pages

-	echo.  texinfo    to make Texinfo files

-	echo.  gettext    to make PO message catalogs

-	echo.  changes    to make an overview over all changed/added/deprecated items

-	echo.  xml        to make Docutils-native XML files

-	echo.  pseudoxml  to make pseudoxml-XML files for display purposes

-	echo.  linkcheck  to check all external links for integrity

-	echo.  doctest    to run all doctests embedded in the documentation if enabled

-	goto end

-)

-

-if "%1" == "clean" (

-	del examples.inc

-	for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i

-	del /q /s %BUILDDIR%\*

-	goto end

-)

-

-

-%SPHINXBUILD% 2> nul

-if errorlevel 9009 (

-	echo.

-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx

-	echo.installed, then set the SPHINXBUILD environment variable to point

-	echo.to the full path of the 'sphinx-build' executable. Alternatively you

-	echo.may add the Sphinx directory to PATH.

-	echo.

-	echo.If you don't have Sphinx installed, grab it from

-	echo.http://sphinx-doc.org/

-	exit /b 1

-)

-

-:: GUDHI specific : Examples.inc is generated with generate_examples.py (and deleted on clean)

-

-if "%1" == "html" (

-	generate_examples.py

-	%SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html

-	if errorlevel 1 exit /b 1

-	echo.

-	echo.Build finished. The HTML pages are in %BUILDDIR%/html.

-	goto end

-)

-

-if "%1" == "dirhtml" (

-	%SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml

-	if errorlevel 1 exit /b 1

-	echo.

-	echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml.

-	goto end

-)

-

-if "%1" == "singlehtml" (

-	%SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml

-	if errorlevel 1 exit /b 1

-	echo.

-	echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml.

-	goto end

-)

-

-if "%1" == "pickle" (

-	%SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle

-	if errorlevel 1 exit /b 1

-	echo.

-	echo.Build finished; now you can process the pickle files.

-	goto end

-)

-

-if "%1" == "json" (

-	%SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json

-	if errorlevel 1 exit /b 1

-	echo.

-	echo.Build finished; now you can process the JSON files.

-	goto end

-)

-

-if "%1" == "htmlhelp" (

-	%SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp

-	if errorlevel 1 exit /b 1

-	echo.

-	echo.Build finished; now you can run HTML Help Workshop with the ^

-.hhp project file in %BUILDDIR%/htmlhelp.

-	goto end

-)

-

-if "%1" == "qthelp" (

-	%SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp

-	if errorlevel 1 exit /b 1

-	echo.

-	echo.Build finished; now you can run "qcollectiongenerator" with the ^

-.qhcp project file in %BUILDDIR%/qthelp, like this:

-	echo.^> qcollectiongenerator %BUILDDIR%\qthelp\pouet.qhcp

-	echo.To view the help file:

-	echo.^> assistant -collectionFile %BUILDDIR%\qthelp\pouet.ghc

-	goto end

-)

-

-if "%1" == "devhelp" (

-	%SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp

-	if errorlevel 1 exit /b 1

-	echo.

-	echo.Build finished.

-	goto end

-)

-

-if "%1" == "epub" (

-	%SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub

-	if errorlevel 1 exit /b 1

-	echo.

-	echo.Build finished. The epub file is in %BUILDDIR%/epub.

-	goto end

-)

-

-if "%1" == "latex" (

-	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex

-	if errorlevel 1 exit /b 1

-	echo.

-	echo.Build finished; the LaTeX files are in %BUILDDIR%/latex.

-	goto end

-)

-

-if "%1" == "latexpdf" (

-	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex

-	cd %BUILDDIR%/latex

-	make all-pdf

-	cd %BUILDDIR%/..

-	echo.

-	echo.Build finished; the PDF files are in %BUILDDIR%/latex.

-	goto end

-)

-

-if "%1" == "latexpdfja" (

-	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex

-	cd %BUILDDIR%/latex

-	make all-pdf-ja

-	cd %BUILDDIR%/..

-	echo.

-	echo.Build finished; the PDF files are in %BUILDDIR%/latex.

-	goto end

-)

-

-if "%1" == "text" (

-	%SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text

-	if errorlevel 1 exit /b 1

-	echo.

-	echo.Build finished. The text files are in %BUILDDIR%/text.

-	goto end

-)

-

-if "%1" == "man" (

-	%SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man

-	if errorlevel 1 exit /b 1

-	echo.

-	echo.Build finished. The manual pages are in %BUILDDIR%/man.

-	goto end

-)

-

-if "%1" == "texinfo" (

-	%SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo

-	if errorlevel 1 exit /b 1

-	echo.

-	echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo.

-	goto end

-)

-

-if "%1" == "gettext" (

-	%SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale

-	if errorlevel 1 exit /b 1

-	echo.

-	echo.Build finished. The message catalogs are in %BUILDDIR%/locale.

-	goto end

-)

-

-if "%1" == "changes" (

-	%SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes

-	if errorlevel 1 exit /b 1

-	echo.

-	echo.The overview file is in %BUILDDIR%/changes.

-	goto end

-)

-

-if "%1" == "linkcheck" (

-	%SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck

-	if errorlevel 1 exit /b 1

-	echo.

-	echo.Link check complete; look for any errors in the above output ^

-or in %BUILDDIR%/linkcheck/output.txt.

-	goto end

-)

-

-if "%1" == "doctest" (

-	%SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest

-	if errorlevel 1 exit /b 1

-	echo.

-	echo.Testing of doctests in the sources finished, look at the ^

-results in %BUILDDIR%/doctest/output.txt.

-	goto end

-)

-

-if "%1" == "xml" (

-	%SPHINXBUILD% -b xml %ALLSPHINXOPTS% %BUILDDIR%/xml

-	if errorlevel 1 exit /b 1

-	echo.

-	echo.Build finished. The XML files are in %BUILDDIR%/xml.

-	goto end

-)

-

-if "%1" == "pseudoxml" (

-	%SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml

-	if errorlevel 1 exit /b 1

-	echo.

-	echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml.

-	goto end

-)

-

-:end

diff --git a/src/cython/doc/make.bat.in b/src/cython/doc/make.bat.in
new file mode 100644
index 00000000..ff1a6d56
--- /dev/null
+++ b/src/cython/doc/make.bat.in
@@ -0,0 +1,67 @@
+@ECHO OFF

+

+REM Command file for Sphinx documentation

+

+if "%SPHINXBUILD%" == "" (

+        set SPHINXBUILD=@SPHINX_PATH@

+)

+set BUILDDIR=_build

+set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% .

+set I18NSPHINXOPTS=%SPHINXOPTS% .

+if NOT "%PAPER%" == "" (

+	set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%

+	set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS%

+)

+

+if "%1" == "" goto help

+

+if "%1" == "help" (

+	:help

+	echo.Please use `make ^<target^>` where ^<target^> is one of

+	echo.  html       to make standalone HTML files

+	echo.  doctest    to run all doctests embedded in the documentation if enabled

+	goto end

+)

+

+if "%1" == "clean" (

+	del examples.inc

+	for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i

+	del /q /s %BUILDDIR%\*

+	goto end

+)

+

+

+%SPHINXBUILD% 2> nul

+if errorlevel 9009 (

+	echo.

+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx

+	echo.installed, then set the SPHINXBUILD environment variable to point

+	echo.to the full path of the 'sphinx-build' executable. Alternatively you

+	echo.may add the Sphinx directory to PATH.

+	echo.

+	echo.If you don't have Sphinx installed, grab it from

+	echo.http://sphinx-doc.org/

+	exit /b 1

+)

+

+:: GUDHI specific : Examples.inc is generated with generate_examples.py (and deleted on clean)

+

+if "%1" == "html" (

+	generate_examples.py

+	%SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished. The HTML pages are in %BUILDDIR%/html.

+	goto end

+)

+

+if "%1" == "doctest" (

+	%SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Testing of doctests in the sources finished, look at the ^

+results in %BUILDDIR%/doctest/output.txt.

+	goto end

+)

+

+:end

diff --git a/src/cython/doc/python3-sphinx-build b/src/cython/doc/python3-sphinx-build
new file mode 100755
index 00000000..44b94169
--- /dev/null
+++ b/src/cython/doc/python3-sphinx-build
@@ -0,0 +1,11 @@
+#!/usr/bin/python3
+
+"""
+Emulate sphinx-build for python3
+"""
+
+from sys import exit, argv
+from sphinx import main
+
+if __name__ == '__main__':
+    exit(main(argv))
diff --git a/src/cython/doc/simplex_tree_user.rst b/src/cython/doc/simplex_tree_user.rst
index 6b55c4e7..cbfd34a7 100644
--- a/src/cython/doc/simplex_tree_user.rst
+++ b/src/cython/doc/simplex_tree_user.rst
@@ -41,8 +41,10 @@ Example
        print("[0, 1, 2] inserted")
    if st.find([0, 1]):
        print("[0, 1] found")
-   print("num_vertices=", st.num_vertices())
-   print("num_simplices=", st.num_simplices())
+   result_str = 'num_vertices=' + repr(st.num_vertices())
+   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(sk_value)
@@ -55,8 +57,8 @@ The output is:
    [0, 1] inserted
    [0, 1, 2] inserted
    [0, 1] found
-   ('num_vertices=', 3)
-   ('num_simplices=', 7)
+   num_vertices=3
+   num_simplices=7
    skeleton_tree(2) =
    ([0, 1, 2], 4.0)
    ([0, 1], 0.0)