From 1210ddafd2e26e842e66714d92f6dbfc0c3ba003 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 28 Mar 2017 19:15:44 +0000
Subject: 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
---
 src/cython/CMakeLists.txt | 429 +++++++++++++++++++++++++---------------------
 1 file changed, 229 insertions(+), 200 deletions(-)

(limited to 'src/cython/CMakeLists.txt')

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)
-- 
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