1 files changed, 406 insertions, 276 deletions
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index afca9d60..dc2e9278 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -1,4 +1,3 @@
-cmake_minimum_required(VERSION 2.8)
 project(Cython)
 
 function( add_gudhi_cython_lib THE_LIB )
@@ -17,298 +16,429 @@ endfunction( add_gudhi_cython_lib )
 
 # THE_TEST is the python test file name (without .py extension) containing tests functions
 function( add_gudhi_py_test THE_TEST )
-  # use ${PYTHON_EXECUTABLE} -B, otherwise a __pycache__ directory is created in sources by python
-  # use py.test no cache provider, otherwise a .cache file is created in sources by py.test
-  add_test(NAME ${THE_TEST}_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} -B -m pytest -p no:cacheprovider ${CMAKE_CURRENT_SOURCE_DIR}/test/${THE_TEST}.py)
+  if(PYTEST_FOUND)
+    # use ${PYTHON_EXECUTABLE} -B, otherwise a __pycache__ directory is created in sources by python
+    # use py.test no cache provider, otherwise a .cache file is created in sources by py.test
+    add_test(NAME ${THE_TEST}_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${PYTHON_EXECUTABLE} -B -m pytest -p no:cacheprovider ${CMAKE_CURRENT_SOURCE_DIR}/test/${THE_TEST}.py)
+  endif()
 endfunction( add_gudhi_py_test )
 
+# Set gudhi.__debug_info__
+# WARNING : to be done before gudhi.pyx.in configure_file
+function( add_gudhi_debug_info DEBUG_INFO )
+  set(GUDHI_CYTHON_DEBUG_INFO "${GUDHI_CYTHON_DEBUG_INFO}    \"${DEBUG_INFO}\\n\" \\\n" PARENT_SCOPE)
+endfunction( add_gudhi_debug_info )
+
+if(PYTHONINTERP_FOUND)
+  if(CYTHON_FOUND)
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}off_reader;")
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}simplex_tree;")
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}rips_complex;")
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}cubical_complex;")
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}periodic_cubical_complex;")
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}persistence_graphical_tools;")
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}reader_utils;")
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}witness_complex;")
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}strong_witness_complex;")
+
+    add_gudhi_debug_info("Python version ${PYTHON_VERSION_STRING}")
+    add_gudhi_debug_info("Cython version ${CYTHON_VERSION}")
+    if(PYTEST_FOUND)
+      add_gudhi_debug_info("Pytest version ${PYTEST_VERSION}")
+    endif()
+    if(MATPLOTLIB_FOUND)
+      add_gudhi_debug_info("Matplotlib version ${MATPLOTLIB_VERSION}")
+    endif()
+    if(NUMPY_FOUND)
+      add_gudhi_debug_info("Numpy version ${NUMPY_VERSION}")
+    endif()
+    if(SCIPY_FOUND)
+      add_gudhi_debug_info("Scipy version ${SCIPY_VERSION}")
+    endif()
+    if(MATPLOTLIB_FOUND AND NUMPY_FOUND AND SCIPY_FOUND)
+      set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}persistence_graphical_tools;")
+    else()
+        set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MODULES}persistence_graphical_tools;")
+    endif()
 
-if(CYTHON_FOUND)
-  message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_EXECUTABLE} - 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 "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ")
-  set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_SYSTEM_NO_DEPRECATED', ")
-
-  # This is because of https://github.com/CGAL/cgal/blob/master/Installation/include/CGAL/tss.h
-  # CGAL is using boost thread if thread_local is not ready (requires XCode 8 for Mac).
-  # The test in https://github.com/CGAL/cgal/blob/master/Installation/include/CGAL/config.h
-  #   #if __has_feature(cxx_thread_local) || \
-  #       ( (__GNUC__ * 100 + __GNUC_MINOR__) >= 408 && __cplusplus >= 201103L ) || \
-  #       ( _MSC_VER >= 1900 )
-  #   #define CGAL_CAN_USE_CXX11_THREAD_LOCAL
-  #   #endif
-  set(CGAL_CAN_USE_CXX11_THREAD_LOCAL "
-      int main() {
-      #ifndef __has_feature
-        #define __has_feature(x) 0  // Compatibility with non-clang compilers.
-      #endif
-      #if __has_feature(cxx_thread_local) || \
-          ( (__GNUC__ * 100 + __GNUC_MINOR__) >= 408 && __cplusplus >= 201103L ) || \
-          ( _MSC_VER >= 1900 )
-        bool has_feature_thread_local = true;
-      #else
-        // Explicit error of compilation for CMake test purpose - has_feature_thread_local is not defined
-      #endif
-        bool result = has_feature_thread_local;
-      }  ")
-  check_cxx_source_compiles("${CGAL_CAN_USE_CXX11_THREAD_LOCAL}" CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT)
-
-  if (NOT CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT)
-    add_gudhi_cython_lib(${Boost_THREAD_LIBRARY})
-    set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ")
-  endif()
-
-  # 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 "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-frounding-math', ")
-  endif(CMAKE_COMPILER_IS_GNUCXX)
-  if (CMAKE_CXX_COMPILER_ID MATCHES Intel)
-    set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-fp-model strict', ")
-  endif(CMAKE_CXX_COMPILER_ID MATCHES Intel)
-  if (DEBUG_TRACES)
-    # For programs to be more verbose
-    set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DDEBUG_TRACES', ")
-  endif()
+    message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_VERSION} - 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 "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ")
+    set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_SYSTEM_NO_DEPRECATED', ")
+
+    # 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 "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-frounding-math', ")
+    endif(CMAKE_COMPILER_IS_GNUCXX)
+    if (CMAKE_CXX_COMPILER_ID MATCHES Intel)
+      set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-fp-model strict', ")
+    endif(CMAKE_CXX_COMPILER_ID MATCHES 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 "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ")
-  endif (EIGEN3_FOUND)
-
-  if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-    set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/bottleneck_distance.pyx'")
-  endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
-    set(GUDHI_CYTHON_SUBSAMPLING "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/subsampling.pyx'")
-    set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/tangential_complex.pyx'")
-  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
-  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
-    set(GUDHI_CYTHON_ALPHA_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/alpha_complex.pyx'")
-  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
-  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
-    set(GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX
-        "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_witness_complex.pyx'\ninclude '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_strong_witness_complex.pyx'\n")
-  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
-
-  if(CGAL_FOUND)
-    # Add CGAL compilation args
-    if(CGAL_HEADER_ONLY)
-      set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ")
-    else(CGAL_HEADER_ONLY)
-      add_gudhi_cython_lib(${CGAL_LIBRARIES})
-      set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ")
-      # If CGAL is not header only, CGAL library may link with boost system,
-      add_gudhi_cython_lib(${Boost_SYSTEM_LIBRARY})
-      set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ")
-    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 "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMP', ")
-      add_gudhi_cython_lib(${GMP_LIBRARIES})
-      set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMP_LIBRARIES_DIR}', ")
-      if(GMPXX_FOUND)
-        set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMPXX', ")
-        add_gudhi_cython_lib(${GMPXX_LIBRARIES})
-        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=10.12', ")
-      set(GUDHI_CYTHON_EXTRA_LINK_ARGS "${GUDHI_CYTHON_EXTRA_LINK_ARGS}'-mmacosx-version-min=10.12', ")
-  endif(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
-
-  # Loop on INCLUDE_DIRECTORIES PROPERTY
-  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 "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DGUDHI_USE_TBB', ")
-    add_gudhi_cython_lib(${TBB_RELEASE_LIBRARY})
-    add_gudhi_cython_lib(${TBB_MALLOC_RELEASE_LIBRARY})
-    set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${TBB_LIBRARY_DIRS}', ")
-    set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${TBB_INCLUDE_DIRS}', ")
-  endif()
+    if (EIGEN3_FOUND)
+      add_gudhi_debug_info("Eigen3 version ${EIGEN3_VERSION}")
+      # No problem, even if no CGAL found
+      set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ")
+    endif (EIGEN3_FOUND)
+
+    if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+      set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/bottleneck_distance.pyx'")
+      set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}bottleneck_distance;")
+      set(GUDHI_CYTHON_NERVE_GIC "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/nerve_gic.pyx'")
+      set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}nerve_gic;")
+    else()
+      set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}bottleneck_distance;")
+      set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}nerve_gic;")
+    endif ()
+    if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+      set(GUDHI_CYTHON_SUBSAMPLING "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/subsampling.pyx'")
+      set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}subsampling;")
+      set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/tangential_complex.pyx'")
+      set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}tangential_complex;")
+    else()
+      set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}subsampling;")
+      set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}tangential_complex;")
+    endif ()
+    if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
+      set(GUDHI_CYTHON_ALPHA_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/alpha_complex.pyx'")
+      set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}alpha_complex;")
+    else()
+      set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}alpha_complex;")
+    endif ()
+    if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
+      set(GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX
+          "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_witness_complex.pyx'\ninclude '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_strong_witness_complex.pyx'\n")
+      set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}euclidean_witness_complex;")
+      set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}euclidean_strong_witness_complex;")
+    else()
+      set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}euclidean_witness_complex;")
+      set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}euclidean_strong_witness_complex;")
+    endif ()
+
+    add_gudhi_debug_info("Installed modules are: ${GUDHI_CYTHON_MODULES}")
+    if(GUDHI_CYTHON_MISSING_MODULES)
+      add_gudhi_debug_info("Missing modules are: ${GUDHI_CYTHON_MISSING_MODULES}")
+    endif()
 
-  if(UNIX)
-    set( GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}")
-  endif(UNIX)
-
-  # Generate setup.py file to cythonize Gudhi - This file must be named setup.py by convention
-  configure_file(setup.py.in "${CMAKE_CURRENT_BINARY_DIR}/setup.py" @ONLY)
-  # Generate gudhi.pyx - Gudhi cython file
-  configure_file(gudhi.pyx.in "${CMAKE_CURRENT_BINARY_DIR}/gudhi.pyx" @ONLY)
-
-  add_custom_command(
-      OUTPUT gudhi.so
-      WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-      COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/setup.py" "build_ext" "--inplace")
-
-  add_custom_target(cython ALL DEPENDS gudhi.so
-                    COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/ to your PYTHONPATH before using examples or tests")
-
-  # For installation purpose
-  # TODO(VR) : files matching pattern mechanism is copying all cython directory
-  install(DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}" DESTINATION "${PYTHON_SITE_PACKAGES}/" FILES_MATCHING
-      PATTERN "*.so"
-      PATTERN "*.dylib"
-      PATTERN "*.pyd")
-
-  # Test examples
-  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
-    # Bottleneck and Alpha
-    add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
-             -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
+    if(CGAL_FOUND)
+      can_cgal_use_cxx11_thread_local()
+      if (NOT CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT)
+        if(CMAKE_BUILD_TYPE MATCHES Debug)
+          add_gudhi_cython_lib("${Boost_THREAD_LIBRARY_DEBUG}")
+        else()
+          add_gudhi_cython_lib("${Boost_THREAD_LIBRARY_RELEASE}")
+        endif()
+        set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ")
+      endif()
+      # Add CGAL compilation args
+      if(CGAL_HEADER_ONLY)
+        add_gudhi_debug_info("CGAL header only version ${CGAL_VERSION}")
+        set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ")
+      else(CGAL_HEADER_ONLY)
+        add_gudhi_debug_info("CGAL version ${CGAL_VERSION}")
+        add_gudhi_cython_lib("${CGAL_LIBRARY}")
+        set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ")
+        # If CGAL is not header only, CGAL library may link with boost system,
+        if(CMAKE_BUILD_TYPE MATCHES Debug)
+          add_gudhi_cython_lib("${Boost_SYSTEM_LIBRARY_DEBUG}")
+        else()
+          add_gudhi_cython_lib("${Boost_SYSTEM_LIBRARY_RELEASE}")
+        endif()
+        set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ")
+      endif(CGAL_HEADER_ONLY)
+      # GMP and GMPXX are not required, but if present, CGAL will link with them.
+      if(GMP_FOUND)
+        add_gudhi_debug_info("GMP_LIBRARIES = ${GMP_LIBRARIES}")
+        set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMP', ")
+        add_gudhi_cython_lib("${GMP_LIBRARIES}")
+        set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMP_LIBRARIES_DIR}', ")
+        if(GMPXX_FOUND)
+          add_gudhi_debug_info("GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}")
+          set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMPXX', ")
+          add_gudhi_cython_lib("${GMPXX_LIBRARIES}")
+          set(GUDHI_CYTHON_LIBRARY_DIRS "${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 "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-mmacosx-version-min=10.12', ")
+        set(GUDHI_CYTHON_EXTRA_LINK_ARGS "${GUDHI_CYTHON_EXTRA_LINK_ARGS}'-mmacosx-version-min=10.12', ")
+    endif(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+
+    # Loop on INCLUDE_DIRECTORIES PROPERTY
+    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 AND WITH_GUDHI_USE_TBB)
+      add_gudhi_debug_info("TBB version ${TBB_INTERFACE_VERSION} found and used")
+      set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DGUDHI_USE_TBB', ")
+      if(CMAKE_BUILD_TYPE MATCHES Debug)
+        add_gudhi_cython_lib("${TBB_DEBUG_LIBRARY}")
+        add_gudhi_cython_lib("${TBB_MALLOC_DEBUG_LIBRARY}")
+      else()
+        add_gudhi_cython_lib("${TBB_RELEASE_LIBRARY}")
+        add_gudhi_cython_lib("${TBB_MALLOC_RELEASE_LIBRARY}")
+      endif()
+      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()
 
-    # Tangential
-    add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
+    if(UNIX)
+      set( GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}")
+    endif(UNIX)
+
+    # Generate setup.py file to cythonize Gudhi - This file must be named setup.py by convention
+    configure_file(setup.py.in "${CMAKE_CURRENT_BINARY_DIR}/setup.py" @ONLY)
+    # Generate gudhi.pyx - Gudhi cython file
+    configure_file(gudhi.pyx.in "${CMAKE_CURRENT_BINARY_DIR}/gudhi.pyx" @ONLY)
+
+    add_custom_command(
+        OUTPUT gudhi.so
+        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+        COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/setup.py" "build_ext" "--inplace")
+
+    add_custom_target(cython ALL DEPENDS gudhi.so
+                      COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/ to your PYTHONPATH before using examples or tests")
+
+    # For installation purpose
+    # TODO(VR) : files matching pattern mechanism is copying all cython directory
+    install(DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}" DESTINATION "${PYTHON_SITE_PACKAGES}/" FILES_MATCHING
+        PATTERN "*.so"
+        PATTERN "*.dylib"
+        PATTERN "*.pyd")
+
+    # Test examples
+    if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+      # Bottleneck and Alpha
+      add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
+               -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
+
+      if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
+        # Tangential
+        add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
+                 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+                 COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+                 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
+                 --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
+
+        add_gudhi_py_test(test_tangential_complex)
+
+        # Witness complex AND Subsampling
+        add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
+                 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+                 COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+                 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
+                 --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+
+        add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
+                 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+                 COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+                 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
+                 --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+      endif()
+
+      # Subsampling
+      add_gudhi_py_test(test_subsampling)
+
+    endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+    if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+      # Bottleneck
+      add_test(NAME bottleneck_basic_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
+
+      add_gudhi_py_test(test_bottleneck_distance)
+
+      # Cover complex
+      file(COPY ${CMAKE_SOURCE_DIR}/data/points/human.off DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+      file(COPY ${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat.off DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+      file(COPY ${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1 DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+      add_test(NAME cover_complex_nerve_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/nerve_of_a_covering.py"
+               -f human.off -c 2 -r 10 -g 0.3)
+
+      add_test(NAME cover_complex_coordinate_gic_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/coordinate_graph_induced_complex.py"
+               -f human.off -c 0 -v)
+
+      add_test(NAME cover_complex_functional_gic_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/functional_graph_induced_complex.py"
+               -o lucky_cat.off
+               -f lucky_cat_PCA1 -v)
+
+      add_test(NAME cover_complex_voronoi_gic_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/voronoi_graph_induced_complex.py"
+               -f human.off -n 700 -v)
+
+      add_gudhi_py_test(test_cover_complex)
+    endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+
+    if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
+      # Alpha
+      add_test(NAME alpha_complex_from_points_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
+
+      if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
+        add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
+               --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6)
+      endif()
+
+      add_gudhi_py_test(test_alpha_complex)
+
+    endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
+
+    if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
+      # Euclidean witness
+      add_gudhi_py_test(test_euclidean_witness_complex)
+
+    endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
+
+    # Cubical
+    add_test(NAME periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
              COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
-             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
-
-    add_gudhi_py_test(test_tangential_complex)
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py"
+             --no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt)
+
+    if(NUMPY_FOUND)
+      add_test(NAME random_cubical_complex_persistence_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py"
+               10 10 10)
+    endif()
 
-    # Witness complex AND Subsampling
-    add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
-             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+    add_gudhi_py_test(test_cubical_complex)
+
+    # Rips
+    if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
+      add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
+               --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3)
+
+      add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py
+               --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off  -e 0.25 -d 3)
+    endif()
 
-    add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
+    add_test(NAME rips_complex_from_points_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
              COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
-             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+             ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py)
 
-    # Subsampling
-    add_gudhi_py_test(test_subsampling)
+    add_gudhi_py_test(test_rips_complex)
 
-  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
-  if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-    # Bottleneck
-    add_test(NAME bottleneck_basic_example_py_test
+    # Simplex tree
+    add_test(NAME simplex_tree_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
              COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
+             ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py)
 
-    add_gudhi_py_test(test_bottleneck_distance)
-  endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+    add_gudhi_py_test(test_simplex_tree)
 
-  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
-    # Alpha
-    add_test(NAME alpha_complex_from_points_example_py_test
+    # Witness
+    add_test(NAME witness_complex_from_nearest_landmark_table_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
              COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
-
-    add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
-             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6)
-
-    add_gudhi_py_test(test_alpha_complex)
-
-  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
-
-  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
-    # Euclidean witness
-    add_gudhi_py_test(test_euclidean_witness_complex)
-
-  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
-
-  # Cubical
-  add_test(NAME periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-           ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py"
-           --no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt)
-
-  add_test(NAME random_cubical_complex_persistence_example_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-           ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py"
-           10 10 10)
-
-  add_gudhi_py_test(test_cubical_complex)
-
-  # Rips
-  add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-           ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
-           --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3)
-
-  add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-           ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py
-           --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off  -e 0.25 -d 3)
-
-  add_test(NAME rips_complex_from_points_example_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-           ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py)
-
-  add_gudhi_py_test(test_rips_complex)
-
-  # Simplex tree
-  add_test(NAME simplex_tree_example_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-           ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py)
-
-  add_gudhi_py_test(test_simplex_tree)
-
-  # Witness
-  add_test(NAME witness_complex_from_nearest_landmark_table_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-           ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py)
-
-  add_gudhi_py_test(test_witness_complex)
-
-  # Reader utils
-  add_gudhi_py_test(test_reader_utils)
-
-  # Documentation generation is available through sphinx - requires all modules
-  if(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
-    set (GUDHI_SPHINX_MESSAGE "Generating API documentation with Sphinx in ${CMAKE_CURRENT_BINARY_DIR}/sphinx/")
-    # User warning - Sphinx is a static pages generator, and configured to work fine with user_version
-    # Images and biblio warnings because not found on developper version
-    if (GUDHI_CYTHON_PATH STREQUAL "src/cython")
-      set (GUDHI_SPHINX_MESSAGE "${GUDHI_SPHINX_MESSAGE} \n WARNING : Sphinx is configured for user version, you run it on developper version. Images and biblio will miss")
-    endif()
-    # sphinx target requires gudhi.so, because conf.py reads gudhi version from it
-    add_custom_target(sphinx
-        WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc
-        COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-        ${SPHINX_PATH} -b html ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/sphinx
-        DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
-        COMMENT "${GUDHI_SPHINX_MESSAGE}" VERBATIM)
-
-    add_test(NAME sphinx_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/doctest)
-
-  endif(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
-endif(CYTHON_FOUND)
+             ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py)
+
+    add_gudhi_py_test(test_witness_complex)
+
+    # Reader utils
+    add_gudhi_py_test(test_reader_utils)
+
+    # Documentation generation is available through sphinx - requires all modules
+    if(SPHINX_PATH)
+      if(MATPLOTLIB_FOUND)
+        if(NUMPY_FOUND)
+          if(SCIPY_FOUND)
+            if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+              set (GUDHI_SPHINX_MESSAGE "Generating API documentation with Sphinx in ${CMAKE_CURRENT_BINARY_DIR}/sphinx/")
+              # User warning - Sphinx is a static pages generator, and configured to work fine with user_version
+              # Images and biblio warnings because not found on developper version
+              if (GUDHI_CYTHON_PATH STREQUAL "src/cython")
+                set (GUDHI_SPHINX_MESSAGE "${GUDHI_SPHINX_MESSAGE} \n WARNING : Sphinx is configured for user version, you run it on developper version. Images and biblio will miss")
+              endif()
+              # sphinx target requires gudhi.so, because conf.py reads gudhi version from it
+              add_custom_target(sphinx
+                  WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc
+                  COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+                  ${SPHINX_PATH} -b html ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/sphinx
+                  DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
+                  COMMENT "${GUDHI_SPHINX_MESSAGE}" VERBATIM)
+
+              add_test(NAME sphinx_py_test
+                       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+                       COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+                       ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/doctest)
+
+              # Set missing or not modules
+              set(GUDHI_MODULES ${GUDHI_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MODULES")
+            else(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+              message("++ Python documentation module will not be compiled because it requires a CGAL with Eigen3 version greater or equal than 4.8.1")
+              set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+            endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+          else(SCIPY_FOUND)
+            message("++ Python documentation module will not be compiled because scipy was not found")
+            set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+          endif(SCIPY_FOUND)
+        else(NUMPY_FOUND)
+          message("++ Python documentation module will not be compiled because numpy was not found")
+          set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+        endif(NUMPY_FOUND)
+      else(MATPLOTLIB_FOUND)
+        message("++ Python documentation module will not be compiled because matplotlib was not found")
+        set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+      endif(MATPLOTLIB_FOUND)
+    else(SPHINX_PATH)
+      message("++ Python documentation module will not be compiled because sphinx and sphinxcontrib-bibtex were not found")
+      set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+    endif(SPHINX_PATH)
+
+
+    # Set missing or not modules
+    set(GUDHI_MODULES ${GUDHI_MODULES} "python" CACHE INTERNAL "GUDHI_MODULES")
+  else(CYTHON_FOUND)
+    message("++ Python module will not be compiled because cython was not found")
+    set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+  endif(CYTHON_FOUND)
+else(PYTHONINTERP_FOUND)
+  message("++ Python module will not be compiled because no Python interpreter was found")
+  set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+endif(PYTHONINTERP_FOUND)