Merge last trunk modifications

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2263 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 9b430e79ecc94bee975d748eb3e2106c7dbab3ce

14 files changed, 261 insertions, 287 deletions

diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 25cf952e..ba38fe3d 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -18,213 +18,201 @@ FIND_PROGRAM( PYTHON_PATH python )
 FIND_PROGRAM( CYTHON_PATH cython )
 
 if(PYTHON_PATH AND CYTHON_PATH)
-  find_package(Boost REQUIRED COMPONENTS system REQUIRED)
-
-  if(NOT Boost_FOUND)
-    message(FATAL_ERROR "NOTICE: This demo requires Boost and will not be compiled.")
-  else(NOT Boost_FOUND)
-
-    set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_RESULT_OF_USE_DECLTYPE', ")
-    set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ")
-    set(GUDHI_CYTHON_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()
-  
-    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
-        # CGAL things are done in CGAL_VERSION >= 4.8.0
-        set(GUDHI_CYTHON_SUBSAMPLING "include 'cython/subsampling.pyx'")
-    else (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-      # Remove alpha complex 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")
-    endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-    if (NOT CGAL_VERSION VERSION_LESS 4.8.0)
-      # If CGAL_VERSION >= 4.8.0, include tangential complex
-      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 4.8.0)
-      # 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 4.8.0)
-    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 "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
+  set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${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()
+
+  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"
+      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 ${CMAKE_CURRENT_BINARY_DIR}
-        COMMAND python "${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(NOT Boost_FOUND)
+        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)
diff --git a/src/cython/include/Alpha_complex_interface.h b/src/cython/include/Alpha_complex_interface.h
index d74ff304..d47db71f 100644
--- a/src/cython/include/Alpha_complex_interface.h
+++ b/src/cython/include/Alpha_complex_interface.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef ALPHA_COMPLEX_INTERFACE_H
-#define	ALPHA_COMPLEX_INTERFACE_H
+#ifndef INCLUDE_ALPHA_COMPLEX_INTERFACE_H_
+#define INCLUDE_ALPHA_COMPLEX_INTERFACE_H_
 
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Alpha_complex.h>
@@ -79,4 +79,4 @@ class Alpha_complex_interface {
 
 }  // namespace Gudhi
 
-#endif  // ALPHA_COMPLEX_INTERFACE_H
+#endif  // INCLUDE_ALPHA_COMPLEX_INTERFACE_H_
diff --git a/src/cython/include/Bottleneck_distance_interface.h b/src/cython/include/Bottleneck_distance_interface.h
index 6819734b..d5fbf6ea 100644
--- a/src/cython/include/Bottleneck_distance_interface.h
+++ b/src/cython/include/Bottleneck_distance_interface.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef BOTTLENECK_DISTANCE_INTERFACE_H
-#define	BOTTLENECK_DISTANCE_INTERFACE_H
+#ifndef INCLUDE_BOTTLENECK_DISTANCE_INTERFACE_H_
+#define INCLUDE_BOTTLENECK_DISTANCE_INTERFACE_H_
 
 #include <gudhi/Bottleneck.h>
 
@@ -45,9 +45,9 @@ namespace persistence_diagram {
     return bottleneck_distance(diag1, diag2);
   }
 
-}  // namespace alpha_complex
+}  // namespace persistence_diagram
 
 }  // namespace Gudhi
 
 
-#endif  // BOTTLENECK_DISTANCE_INTERFACE_H
+#endif  // INCLUDE_BOTTLENECK_DISTANCE_INTERFACE_H_
diff --git a/src/cython/include/Cubical_complex_interface.h b/src/cython/include/Cubical_complex_interface.h
index 4c53523b..7c0148f1 100644
--- a/src/cython/include/Cubical_complex_interface.h
+++ b/src/cython/include/Cubical_complex_interface.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef CUBICAL_COMPLEX_INTERFACE_H
-#define	CUBICAL_COMPLEX_INTERFACE_H
+#ifndef INCLUDE_CUBICAL_COMPLEX_INTERFACE_H_
+#define INCLUDE_CUBICAL_COMPLEX_INTERFACE_H_
 
 #include <gudhi/Bitmap_cubical_complex.h>
 #include <gudhi/Bitmap_cubical_complex_base.h>
@@ -38,7 +38,6 @@ namespace cubical_complex {
 template<typename CubicalComplexOptions = Bitmap_cubical_complex_base<double>>
 class Cubical_complex_interface : public Bitmap_cubical_complex<CubicalComplexOptions> {
  public:
-
   Cubical_complex_interface(const std::vector<unsigned>& dimensions,
                             const std::vector<double>& top_dimensional_cells)
   : Bitmap_cubical_complex<CubicalComplexOptions>(dimensions, top_dimensional_cells) {
@@ -47,12 +46,11 @@ class Cubical_complex_interface : public Bitmap_cubical_complex<CubicalComplexOp
   Cubical_complex_interface(const std::string& perseus_file)
   : Bitmap_cubical_complex<CubicalComplexOptions>(perseus_file.c_str()) {
   }
-
 };
 
 }  // namespace cubical_complex
 
 }  // namespace Gudhi
 
-#endif  // CUBICAL_COMPLEX_INTERFACE_H
+#endif  // INCLUDE_CUBICAL_COMPLEX_INTERFACE_H_
 
diff --git a/src/cython/include/Euclidean_strong_witness_complex_interface.h b/src/cython/include/Euclidean_strong_witness_complex_interface.h
index 67d85e18..b9dd8177 100644
--- a/src/cython/include/Euclidean_strong_witness_complex_interface.h
+++ b/src/cython/include/Euclidean_strong_witness_complex_interface.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef EUCLIDEAN_STRONG_WITNESS_COMPLEX_INTERFACE_H
-#define	EUCLIDEAN_STRONG_WITNESS_COMPLEX_INTERFACE_H
+#ifndef INCLUDE_EUCLIDEAN_STRONG_WITNESS_COMPLEX_INTERFACE_H_
+#define INCLUDE_EUCLIDEAN_STRONG_WITNESS_COMPLEX_INTERFACE_H_
 
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Euclidean_strong_witness_complex.h>
@@ -50,7 +50,7 @@ class Euclidean_strong_witness_complex_interface {
   Euclidean_strong_witness_complex_interface(const std::vector<std::vector<double>>& landmarks,
                                              const std::vector<std::vector<double>>& witnesses) {
     landmarks_.reserve(landmarks.size());
-    for(auto& landmark : landmarks)
+    for (auto& landmark : landmarks)
       landmarks_.emplace_back(landmark.begin(), landmark.end());
     witness_complex_ = new Euclidean_strong_witness_complex<Dynamic_kernel>(landmarks_, witnesses);
   }
@@ -87,7 +87,7 @@ class Euclidean_strong_witness_complex_interface {
 
 }  // namespace witness_complex
 
-} // namespace Gudhi
+}  // namespace Gudhi
 
-#endif  // EUCLIDEAN_STRONG_WITNESS_COMPLEX_INTERFACE_H
+#endif  // INCLUDE_EUCLIDEAN_STRONG_WITNESS_COMPLEX_INTERFACE_H_
 
diff --git a/src/cython/include/Euclidean_witness_complex_interface.h b/src/cython/include/Euclidean_witness_complex_interface.h
index a2db6a2d..2a09b3b5 100644
--- a/src/cython/include/Euclidean_witness_complex_interface.h
+++ b/src/cython/include/Euclidean_witness_complex_interface.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef EUCLIDEAN_WITNESS_COMPLEX_INTERFACE_H
-#define	EUCLIDEAN_WITNESS_COMPLEX_INTERFACE_H
+#ifndef INCLUDE_EUCLIDEAN_WITNESS_COMPLEX_INTERFACE_H_
+#define INCLUDE_EUCLIDEAN_WITNESS_COMPLEX_INTERFACE_H_
 
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Euclidean_witness_complex.h>
@@ -50,7 +50,7 @@ class Euclidean_witness_complex_interface {
   Euclidean_witness_complex_interface(const std::vector<std::vector<double>>& landmarks,
                                       const std::vector<std::vector<double>>& witnesses) {
     landmarks_.reserve(landmarks.size());
-    for(auto& landmark : landmarks)
+    for (auto& landmark : landmarks)
       landmarks_.emplace_back(landmark.begin(), landmark.end());
     witness_complex_ = new Euclidean_witness_complex<Dynamic_kernel>(landmarks_, witnesses);
   }
@@ -86,7 +86,7 @@ class Euclidean_witness_complex_interface {
 
 }  // namespace witness_complex
 
-} // namespace Gudhi
+}  // namespace Gudhi
 
-#endif  // EUCLIDEAN_WITNESS_COMPLEX_INTERFACE_H
+#endif  // INCLUDE_EUCLIDEAN_WITNESS_COMPLEX_INTERFACE_H_
 
diff --git a/src/cython/include/Off_reader_interface.h b/src/cython/include/Off_reader_interface.h
index 97d64d3e..0ca55500 100644
--- a/src/cython/include/Off_reader_interface.h
+++ b/src/cython/include/Off_reader_interface.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef OFF_READER_INTERFACE_H
-#define	OFF_READER_INTERFACE_H
+#ifndef INCLUDE_OFF_READER_INTERFACE_H_
+#define INCLUDE_OFF_READER_INTERFACE_H_
 
 #include <gudhi/Points_off_io.h>
 
@@ -38,5 +38,5 @@ std::vector<std::vector<double>> read_points_from_OFF_file(const std::string& of
 
 }  // namespace Gudhi
 
-#endif  // OFF_READER_INTERFACE_H
+#endif  // INCLUDE_OFF_READER_INTERFACE_H_
 
diff --git a/src/cython/include/Persistent_cohomology_interface.h b/src/cython/include/Persistent_cohomology_interface.h
index 1ff0e09b..55028fd0 100644
--- a/src/cython/include/Persistent_cohomology_interface.h
+++ b/src/cython/include/Persistent_cohomology_interface.h
@@ -20,13 +20,14 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef PERSISTENT_COHOMOLOGY_INTERFACE_H
-#define	PERSISTENT_COHOMOLOGY_INTERFACE_H
+#ifndef INCLUDE_PERSISTENT_COHOMOLOGY_INTERFACE_H_
+#define INCLUDE_PERSISTENT_COHOMOLOGY_INTERFACE_H_
 
 #include <gudhi/Persistent_cohomology.h>
 
 #include <vector>
 #include <utility>  // for std::pair
+#include <algorithm>  // for sort
 
 namespace Gudhi {
 
@@ -34,12 +35,10 @@ template<class FilteredComplex>
 class Persistent_cohomology_interface : public
 persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomology::Field_Zp> {
  private:
-
   /*
    * Compare two intervals by dimension, then by length.
    */
   struct cmp_intervals_by_dim_then_length {
-
     explicit cmp_intervals_by_dim_then_length(FilteredComplex * sc)
         : sc_(sc) { }
 
@@ -55,23 +54,26 @@ persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomol
   };
 
  public:
-
   Persistent_cohomology_interface(FilteredComplex* stptr)
       : persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomology::Field_Zp>(*stptr),
       stptr_(stptr) { }
 
   Persistent_cohomology_interface(FilteredComplex* stptr, bool persistence_dim_max)
-      : persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomology::Field_Zp>(*stptr,
-                                                                                                       persistence_dim_max),
-      stptr_(stptr) { }
+      : persistent_cohomology::Persistent_cohomology<FilteredComplex,
+          persistent_cohomology::Field_Zp>(*stptr, persistence_dim_max),
+        stptr_(stptr) { }
 
-  std::vector<std::pair<int, std::pair<double, double>>> get_persistence(int homology_coeff_field, double min_persistence) {
-    persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomology::Field_Zp>::init_coefficients(homology_coeff_field);
-    persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomology::Field_Zp>::compute_persistent_cohomology(min_persistence);
+  std::vector<std::pair<int, std::pair<double, double>>> get_persistence(int homology_coeff_field,
+                                                                         double min_persistence) {
+    persistent_cohomology::Persistent_cohomology<FilteredComplex,
+      persistent_cohomology::Field_Zp>::init_coefficients(homology_coeff_field);
+    persistent_cohomology::Persistent_cohomology<FilteredComplex,
+      persistent_cohomology::Field_Zp>::compute_persistent_cohomology(min_persistence);
 
     // Custom sort and output persistence
     cmp_intervals_by_dim_then_length cmp(stptr_);
-    auto persistent_pairs = persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomology::Field_Zp>::get_persistent_pairs();
+    auto persistent_pairs = persistent_cohomology::Persistent_cohomology<FilteredComplex,
+      persistent_cohomology::Field_Zp>::get_persistent_pairs();
     std::sort(std::begin(persistent_pairs), std::end(persistent_pairs), cmp);
 
     std::vector<std::pair<int, std::pair<double, double>>> persistence;
@@ -81,16 +83,13 @@ persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomol
                                                           stptr_->filtration(get<1>(pair)))));
     }
     return persistence;
-
   }
 
  private:
   // A copy
   FilteredComplex* stptr_;
-
 };
 
-} // namespace Gudhi
-
-#endif  // PERSISTENT_COHOMOLOGY_INTERFACE_H
+}  // namespace Gudhi
 
+#endif  // INCLUDE_PERSISTENT_COHOMOLOGY_INTERFACE_H_
diff --git a/src/cython/include/Rips_complex_interface.h b/src/cython/include/Rips_complex_interface.h
index 01df5366..1879bd74 100644
--- a/src/cython/include/Rips_complex_interface.h
+++ b/src/cython/include/Rips_complex_interface.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef RIPS_COMPLEX_INTERFACE_H
-#define	RIPS_COMPLEX_INTERFACE_H
+#ifndef INCLUDE_RIPS_COMPLEX_INTERFACE_H_
+#define INCLUDE_RIPS_COMPLEX_INTERFACE_H_
 
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Rips_complex.h>
@@ -53,7 +53,6 @@ class Rips_complex_interface {
     } else {
       // Rips construction where values is a distance matrix
       rips_complex_ = new Rips_complex<Simplex_tree_interface<>::Filtration_value>(values, threshold);
-
     }
   }
 
@@ -65,11 +64,10 @@ class Rips_complex_interface {
                                                                                    threshold, Euclidean_distance());
     } else {
       // Rips construction where values is a distance matrix
-      Distance_matrix distances = read_lower_triangular_matrix_from_csv_file<Simplex_tree_interface<>::Filtration_value>(file_name);
+      Distance_matrix distances =
+          read_lower_triangular_matrix_from_csv_file<Simplex_tree_interface<>::Filtration_value>(file_name);
       rips_complex_ = new Rips_complex<Simplex_tree_interface<>::Filtration_value>(distances, threshold);
-
     }
-
   }
 
   void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, int dim_max) {
@@ -85,4 +83,4 @@ class Rips_complex_interface {
 
 }  // namespace Gudhi
 
-#endif  // RIPS_COMPLEX_INTERFACE_H
+#endif  // INCLUDE_RIPS_COMPLEX_INTERFACE_H_
diff --git a/src/cython/include/Simplex_tree_interface.h b/src/cython/include/Simplex_tree_interface.h
index c2783e22..4266b3ef 100644
--- a/src/cython/include/Simplex_tree_interface.h
+++ b/src/cython/include/Simplex_tree_interface.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef SIMPLEX_TREE_INTERFACE_H
-#define	SIMPLEX_TREE_INTERFACE_H
+#ifndef INCLUDE_SIMPLEX_TREE_INTERFACE_H_
+#define INCLUDE_SIMPLEX_TREE_INTERFACE_H_
 
 #include <gudhi/graph_simplicial_complex.h>
 #include <gudhi/distance_functions.h>
@@ -48,7 +48,6 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
   using Complex = std::vector<std::pair<Simplex, Filtration_value>>;
 
  public:
-
   bool find_simplex(const Simplex& vh) {
     return (Base::find(vh) != Base::null_simplex());
   }
@@ -98,7 +97,6 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
       filtered_tree.push_back(std::make_pair(simplex, Base::filtration(f_simplex)));
     }
     return filtered_tree;
-
   }
 
   Complex get_skeleton_tree(int dimension) {
@@ -144,10 +142,8 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
   void create_persistence(Gudhi::Persistent_cohomology_interface<Base>* pcoh) {
     pcoh = new Gudhi::Persistent_cohomology_interface<Base>(*this);
   }
-
 };
 
-} // namespace Gudhi
-
-#endif  // SIMPLEX_TREE_INTERFACE_H
+}  // namespace Gudhi
 
+#endif  // INCLUDE_SIMPLEX_TREE_INTERFACE_H_
diff --git a/src/cython/include/Strong_witness_complex_interface.h b/src/cython/include/Strong_witness_complex_interface.h
index 83bf0f3c..d05eaac5 100644
--- a/src/cython/include/Strong_witness_complex_interface.h
+++ b/src/cython/include/Strong_witness_complex_interface.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef STRONG_WITNESS_COMPLEX_INTERFACE_H
-#define	STRONG_WITNESS_COMPLEX_INTERFACE_H
+#ifndef INCLUDE_STRONG_WITNESS_COMPLEX_INTERFACE_H_
+#define INCLUDE_STRONG_WITNESS_COMPLEX_INTERFACE_H_
 
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Strong_witness_complex.h>
@@ -64,12 +64,10 @@ class Strong_witness_complex_interface {
 
  private:
   Strong_witness_complex<Nearest_landmark_table>* witness_complex_;
-
 };
 
 }  // namespace witness_complex
 
-} // namespace Gudhi
-
-#endif  // STRONG_WITNESS_COMPLEX_INTERFACE_H
+}  // namespace Gudhi
 
+#endif  // INCLUDE_STRONG_WITNESS_COMPLEX_INTERFACE_H_
diff --git a/src/cython/include/Subsampling_interface.h b/src/cython/include/Subsampling_interface.h
index 5fc16767..1c6032c0 100644
--- a/src/cython/include/Subsampling_interface.h
+++ b/src/cython/include/Subsampling_interface.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef SUBSAMPLING_INTERFACE_H
-#define	SUBSAMPLING_INTERFACE_H
+#ifndef INCLUDE_SUBSAMPLING_INTERFACE_H_
+#define INCLUDE_SUBSAMPLING_INTERFACE_H_
 
 #include <gudhi/choose_n_farthest_points.h>
 #include <gudhi/pick_n_random_points.h>
@@ -112,10 +112,8 @@ std::vector<std::vector<double>> subsampling_sparsify_points_from_file(const std
   return subsampling_sparsify_points(points, min_squared_dist);
 }
 
-
 }  // namespace subsampling
 
 }  // namespace Gudhi
 
-#endif  // SUBSAMPLING_INTERFACE_H
-
+#endif  // INCLUDE_SUBSAMPLING_INTERFACE_H_
diff --git a/src/cython/include/Tangential_complex_interface.h b/src/cython/include/Tangential_complex_interface.h
index 2ca4c393..5e9dc0e4 100644
--- a/src/cython/include/Tangential_complex_interface.h
+++ b/src/cython/include/Tangential_complex_interface.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef TANGENTIAL_COMPLEX_INTERFACE_H
-#define	TANGENTIAL_COMPLEX_INTERFACE_H
+#ifndef INCLUDE_TANGENTIAL_COMPLEX_INTERFACE_H_
+#define INCLUDE_TANGENTIAL_COMPLEX_INTERFACE_H_
 
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Tangential_complex.h>
@@ -33,6 +33,7 @@
 #include <vector>
 #include <utility>  // std::pair
 #include <iostream>
+#include <string>
 
 namespace Gudhi {
 
@@ -49,7 +50,7 @@ class Tangential_complex_interface {
     unsigned intrisic_dim = 0;
     if (points.size() > 0)
       intrisic_dim = points[0].size() - 1;
-    
+
     tangential_complex_ = new TC(points, intrisic_dim, k);
     tangential_complex_->compute_tangential_complex();
     num_inconsistencies_ = tangential_complex_->number_of_inconsistent_simplices();
@@ -117,7 +118,6 @@ class Tangential_complex_interface {
 
 }  // namespace tangential_complex
 
-} // namespace Gudhi
-
-#endif  // TANGENTIAL_COMPLEX_INTERFACE_H
+}  // namespace Gudhi
 
+#endif  // INCLUDE_TANGENTIAL_COMPLEX_INTERFACE_H_
diff --git a/src/cython/include/Witness_complex_interface.h b/src/cython/include/Witness_complex_interface.h
index 4f2a903b..6501cc35 100644
--- a/src/cython/include/Witness_complex_interface.h
+++ b/src/cython/include/Witness_complex_interface.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef WITNESS_COMPLEX_INTERFACE_H
-#define	WITNESS_COMPLEX_INTERFACE_H
+#ifndef INCLUDE_WITNESS_COMPLEX_INTERFACE_H_
+#define INCLUDE_WITNESS_COMPLEX_INTERFACE_H_
 
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Witness_complex.h>
@@ -64,12 +64,11 @@ class Witness_complex_interface {
 
  private:
   Witness_complex<Nearest_landmark_table>* witness_complex_;
-
 };
 
 }  // namespace witness_complex
 
-} // namespace Gudhi
+}  // namespace Gudhi
 
-#endif  // WITNESS_COMPLEX_INTERFACE_H
+#endif  // INCLUDE_WITNESS_COMPLEX_INTERFACE_H_