Missing a test for cython

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2272 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 223961ca5575e07d0db2c93ee0326864166980d8

1 files changed, 200 insertions, 201 deletions

diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index c51d9a1e..7c650102 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -34,9 +34,6 @@ if(PYTHONINTERP_FOUND)
     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
@@ -46,202 +43,204 @@ if(PYTHONINTERP_FOUND)
   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
+if(CYTHON_PATH)
+  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 ${PYTHON_EXECUTABLE} "${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)
+      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 ${PYTHON_EXECUTABLE} "${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)
+endif(CYTHON_PATH)