GUDHI 2.0.0 as released by upstream in a tarball.upstream/2.0.0

7 files changed, 251 insertions, 69 deletions

diff --git a/cmake/modules/FindCython.cmake b/cmake/modules/FindCython.cmake
new file mode 100644
index 00000000..04aed1f8
--- /dev/null
+++ b/cmake/modules/FindCython.cmake
@@ -0,0 +1,44 @@
+# Find the Cython compiler.
+#
+# This code sets the following variables:
+#
+#  CYTHON_EXECUTABLE
+#
+# See also UseCython.cmake
+
+#=============================================================================
+# Copyright 2011 Kitware, Inc.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#=============================================================================
+
+# Use the Cython executable that lives next to the Python executable
+# if it is a local installation.
+find_package( PythonInterp )
+if( PYTHONINTERP_FOUND )
+  get_filename_component( _python_path ${PYTHON_EXECUTABLE} PATH )
+  find_program( CYTHON_EXECUTABLE
+    NAMES cython cython.bat cython3
+    HINTS ${_python_path}
+    )
+else()
+  find_program( CYTHON_EXECUTABLE
+    NAMES cython cython.bat cython3
+    )
+endif()
+
+
+include( FindPackageHandleStandardArgs )
+FIND_PACKAGE_HANDLE_STANDARD_ARGS( Cython REQUIRED_VARS CYTHON_EXECUTABLE )
+
+mark_as_advanced( CYTHON_EXECUTABLE )
diff --git a/cmake/modules/FindGMPXX.cmake b/cmake/modules/FindGMPXX.cmake
index 277e4b19..dda302c0 100644
--- a/cmake/modules/FindGMPXX.cmake
+++ b/cmake/modules/FindGMPXX.cmake
@@ -33,6 +33,10 @@ if(GMP_FOUND)
                DOC "Path to the GMPXX library"
                )
 
+  if ( GMPXX_LIBRARIES )
+    get_filename_component(GMPXX_LIBRARIES_DIR ${GMPXX_LIBRARIES} PATH CACHE )
+  endif()
+
   include(FindPackageHandleStandardArgs)
 
   find_package_handle_standard_args(GMPXX "DEFAULT_MSG" GMPXX_LIBRARIES GMPXX_INCLUDE_DIR )
diff --git a/cmake/modules/FindQGLViewer.cmake b/cmake/modules/FindQGLViewer.cmake
index 65723d67..56c1b3cf 100644
--- a/cmake/modules/FindQGLViewer.cmake
+++ b/cmake/modules/FindQGLViewer.cmake
@@ -15,7 +15,7 @@ find_path(QGLVIEWER_INCLUDE_DIR
          )
 
 find_library(QGLVIEWER_LIBRARY_RELEASE 
-             NAMES qglviewer-qt4 qglviewer QGLViewer QGLViewer2
+             NAMES qglviewer-qt5 QGLViewer-qt5 qglviewer QGLViewer QGLViewer2
              PATHS /usr/lib
                    /usr/local/lib
                    ENV QGLVIEWERROOT
diff --git a/cmake/modules/GUDHI_doxygen_target.txt b/cmake/modules/GUDHI_doxygen_target.cmake
index d2cb952d..d2cb952d 100644
--- a/cmake/modules/GUDHI_doxygen_target.txt
+++ b/cmake/modules/GUDHI_doxygen_target.cmake
diff --git a/cmake/modules/GUDHI_test_coverage.cmake b/cmake/modules/GUDHI_test_coverage.cmake
new file mode 100644
index 00000000..ce171a0e
--- /dev/null
+++ b/cmake/modules/GUDHI_test_coverage.cmake
@@ -0,0 +1,14 @@
+
+if (GCOVR_PATH)
+  # for gcovr to make coverage reports - Corbera Jenkins plugin
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
+endif()
+if (GPROF_PATH)
+  # for gprof to make coverage reports - Jenkins
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
+endif()
+
+function(gudhi_add_coverage_test unitary_test)
+  add_test(NAME ${unitary_test} COMMAND $<TARGET_FILE:${unitary_test}>
+      "--log_format=XML" "--log_sink=${CMAKE_BINARY_DIR}/${unitary_test}_UT.xml" "--log_level=test_suite" "--report_level=no")
+endfunction()
diff --git a/cmake/modules/GUDHI_third_party_libraries.cmake b/cmake/modules/GUDHI_third_party_libraries.cmake
new file mode 100644
index 00000000..5f84c602
--- /dev/null
+++ b/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -0,0 +1,144 @@
+# This files manage third party libraries required by GUDHI
+
+find_package(Boost REQUIRED COMPONENTS system filesystem unit_test_framework chrono timer date_time program_options thread)
+
+if(NOT Boost_FOUND)
+  message(FATAL_ERROR "NOTICE: This program requires Boost and will not be compiled.")
+endif(NOT Boost_FOUND)
+
+find_package(GMP)
+if(GMP_FOUND)
+  message(STATUS "GMP_LIBRARIES = ${GMP_LIBRARIES}")
+  INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR})
+  find_package(GMPXX)
+  if(GMPXX_FOUND)
+    message(STATUS "GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}")
+    INCLUDE_DIRECTORIES(${GMPXX_INCLUDE_DIR})
+  endif()
+endif()
+
+# In CMakeLists.txt, when include(${CGAL_USE_FILE}), CMAKE_CXX_FLAGS are overwritten.
+# cf. http://doc.cgal.org/latest/Manual/installation.html#title40
+# A workaround is to include(${CGAL_USE_FILE}) before adding "-std=c++11".
+# A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html
+# or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html
+# but it implies to use cmake version 3.1 at least.
+find_package(CGAL)
+
+# Only CGAL versions > 4.4 supports what Gudhi uses from CGAL
+if (CGAL_VERSION VERSION_LESS 4.4.0)
+  message("CGAL version ${CGAL_VERSION} is considered too old to be used by Gudhi.")
+  unset(CGAL_FOUND)
+endif()
+if(CGAL_FOUND)
+  message(STATUS "CGAL version: ${CGAL_VERSION}.")
+  include( ${CGAL_USE_FILE} )
+
+  if (NOT CGAL_VERSION VERSION_LESS 4.8.0)
+    # HACK to detect CGAL version 4.8.0
+    # CGAL version 4.8, 4.8.1 and 4.8.2 are identified as version 4.8.1000)
+    # cf. https://github.com/CGAL/cgal/issues/1559
+    # Limit the HACK between CGAL versions 4.8 and 4.9 because of file read
+    if (NOT CGAL_VERSION VERSION_GREATER 4.9.0)
+      foreach(CGAL_INCLUDE_DIR ${CGAL_INCLUDE_DIRS})
+        if (EXISTS "${CGAL_INCLUDE_DIR}/CGAL/version.h")
+          FILE(READ "${CGAL_INCLUDE_DIR}/CGAL/version.h" contents)
+          STRING(REGEX REPLACE "\n" ";" contents "${contents}")
+          foreach(Line ${contents})
+            if("${Line}" STREQUAL "#define CGAL_VERSION 4.8")
+              set(CGAL_VERSION 4.8.0)
+              message (">>>>> HACK CGAL version to ${CGAL_VERSION}")
+            endif("${Line}" STREQUAL "#define CGAL_VERSION 4.8")
+          endforeach(Line ${contents})
+        endif (EXISTS "${CGAL_INCLUDE_DIR}/CGAL/version.h")
+      endforeach(CGAL_INCLUDE_DIR ${CGAL_INCLUDE_DIRS})
+    endif(NOT CGAL_VERSION VERSION_GREATER 4.9.0)
+
+    # For dev version
+    include_directories(BEFORE "src/common/include/gudhi_patches")
+    # For user version
+    include_directories(BEFORE "include/gudhi_patches")
+  endif()
+endif()
+
+# Find TBB package for parallel sort - not mandatory, just optional.
+set(TBB_FIND_QUIETLY ON)
+find_package(TBB)
+if (TBB_FOUND)
+  include(${TBB_USE_FILE})
+  message("TBB found in ${TBB_LIBRARY_DIRS}")
+  add_definitions(-DGUDHI_USE_TBB)
+endif()
+
+set(CGAL_WITH_EIGEN3_VERSION 0.0.0)
+find_package(Eigen3 3.1.0)
+if (EIGEN3_FOUND)
+  message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
+  include( ${EIGEN3_USE_FILE} )
+  set(CGAL_WITH_EIGEN3_VERSION ${CGAL_VERSION})
+endif (EIGEN3_FOUND)
+
+# Required programs for unitary tests purpose
+FIND_PROGRAM( GCOVR_PATH gcovr )
+if (GCOVR_PATH)
+  message("gcovr found in ${GCOVR_PATH}")
+endif()
+# Required programs for unitary tests purpose
+FIND_PROGRAM( GPROF_PATH gprof )
+if (GPROF_PATH)
+  message("gprof found in ${GPROF_PATH}")
+endif()
+FIND_PROGRAM( DIFF_PATH diff )
+if (DIFF_PATH)
+  message("diff found in ${DIFF_PATH}")
+endif()
+
+# BOOST ISSUE result_of vs C++11
+add_definitions(-DBOOST_RESULT_OF_USE_DECLTYPE)
+# BOOST ISSUE with Libraries name resolution under Windows
+add_definitions(-DBOOST_ALL_NO_LIB)
+# problem with Visual Studio link on Boost program_options
+add_definitions( -DBOOST_ALL_DYN_LINK )
+
+INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
+LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
+
+message(STATUS "boost include dirs:" ${Boost_INCLUDE_DIRS})
+message(STATUS "boost library dirs:" ${Boost_LIBRARY_DIRS})
+
+macro( find_the_lib placeholder THE_LIBS )
+  set (THE_LIB_WE_FOUND "NO")
+  foreach(THE_LIB ${THE_LIBS})
+    if(EXISTS ${THE_LIB})
+      get_filename_component(THE_LIB_WE ${THE_LIB} NAME_WE)
+      if (NOT THE_LIB_WE_FOUND)
+        set (THE_LIB_WE_FOUND "YES")
+        set(returnValue "${THE_LIB_WE}")
+      endif(NOT THE_LIB_WE_FOUND)
+    endif(EXISTS ${THE_LIB})
+  endforeach(THE_LIB ${THE_LIBS})
+endmacro( find_the_lib )
+
+# Find the correct Python interpreter.
+# Can be set with -DPYTHON_EXECUTABLE=/usr/bin/python3 or -DPython_ADDITIONAL_VERSIONS=3 for instance.
+find_package(Cython)
+
+if(NOT GUDHI_CYTHON_PATH)
+  message(FATAL_ERROR "ERROR: GUDHI_CYTHON_PATH is not valid.")
+endif(NOT GUDHI_CYTHON_PATH)
+
+if(PYTHONINTERP_FOUND AND CYTHON_FOUND)
+  # Unitary tests are available through py.test
+  find_program( PYTEST_PATH py.test )
+  # Default found version 2
+  if(PYTHON_VERSION_MAJOR EQUAL 2)
+    # Documentation generation is available through sphinx
+    find_program( SPHINX_PATH sphinx-build )
+  elseif(PYTHON_VERSION_MAJOR EQUAL 3)
+    # Documentation generation is available through sphinx
+    set(SPHINX_PATH "${CMAKE_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build")
+  else()
+    message(FATAL_ERROR "ERROR: Try to compile the Cython interface. Python version ${PYTHON_VERSION_STRING} is not valid.")
+  endif(PYTHON_VERSION_MAJOR EQUAL 2)
+endif(PYTHONINTERP_FOUND AND CYTHON_FOUND)
+
diff --git a/cmake/modules/GUDHI_user_version_target.txt b/cmake/modules/GUDHI_user_version_target.txt
index 805f0a83..ca6bcd34 100644
--- a/cmake/modules/GUDHI_user_version_target.txt
+++ b/cmake/modules/GUDHI_user_version_target.txt
@@ -1,8 +1,6 @@
 # Some functionnalities requires CMake 2.8.11 minimum
 if (NOT CMAKE_VERSION VERSION_LESS 2.8.11)
 
-  string(TIMESTAMP DATE_AND_TIME "%Y-%m-%d-%H-%M-%S")
-  
   # Definition of the custom target user_version
   add_custom_target(user_version)
   
@@ -11,6 +9,7 @@ if (NOT CMAKE_VERSION VERSION_LESS 2.8.11)
     set(GUDHI_USER_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/${USER_VERSION_DIR})
   else()
     # set the GUDHI_USER_VERSION_DIR with timestamp and Gudhi version number
+    string(TIMESTAMP DATE_AND_TIME "%Y-%m-%d-%H-%M-%S")
     set(GUDHI_USER_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/${DATE_AND_TIME}_GUDHI_${GUDHI_VERSION})
   endif()
 
@@ -21,6 +20,8 @@ if (NOT CMAKE_VERSION VERSION_LESS 2.8.11)
                      COMMENT "user_version creation in ${GUDHI_USER_VERSION_DIR}")
   
   add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                     copy ${CMAKE_SOURCE_DIR}/Conventions.txt ${GUDHI_USER_VERSION_DIR}/Conventions.txt)
+  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
                      copy ${CMAKE_SOURCE_DIR}/README ${GUDHI_USER_VERSION_DIR}/README)
   add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
                      copy ${CMAKE_SOURCE_DIR}/COPYING ${GUDHI_USER_VERSION_DIR}/COPYING)
@@ -34,82 +35,57 @@ if (NOT CMAKE_VERSION VERSION_LESS 2.8.11)
                      copy ${CMAKE_SOURCE_DIR}/src/GUDHIConfig.cmake.in ${GUDHI_USER_VERSION_DIR}/GUDHIConfig.cmake.in)
   add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
                      copy ${CMAKE_SOURCE_DIR}/CMakeGUDHIVersion.txt ${GUDHI_USER_VERSION_DIR}/CMakeGUDHIVersion.txt)
-  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                     copy ${CMAKE_SOURCE_DIR}/GUDHIVersion.cmake.in ${GUDHI_USER_VERSION_DIR}/GUDHIVersion.cmake.in)
   
   add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
                      copy_directory ${CMAKE_SOURCE_DIR}/biblio ${GUDHI_USER_VERSION_DIR}/biblio)
   add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                     copy_directory ${CMAKE_SOURCE_DIR}/src/cython ${GUDHI_USER_VERSION_DIR}/cython)
+  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
                      copy_directory ${CMAKE_SOURCE_DIR}/data ${GUDHI_USER_VERSION_DIR}/data)
   add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
                      copy_directory ${CMAKE_SOURCE_DIR}/src/cmake ${GUDHI_USER_VERSION_DIR}/cmake)
   add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                     copy_directory ${CMAKE_SOURCE_DIR}/src/debian ${GUDHI_USER_VERSION_DIR}/debian)
-  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
                      copy_directory ${CMAKE_SOURCE_DIR}/src/GudhUI ${GUDHI_USER_VERSION_DIR}/GudhUI)
   
-  set(GUDHI_MODULES "common;Alpha_complex;Bitmap_cubical_complex;Contraction;Hasse_complex;Persistent_cohomology;Simplex_tree;Skeleton_blocker;Witness_complex")
-  
+  set(GUDHI_MODULES "common;Alpha_complex;Bitmap_cubical_complex;Bottleneck_distance;Contraction;Hasse_complex;Persistent_cohomology;Rips_complex;Simplex_tree;Skeleton_blocker;Spatial_searching;Subsampling;Tangential_complex;Witness_complex")
+  set(GUDHI_DIRECTORIES "doc;example;concept")
+  set(GUDHI_INCLUDE_DIRECTORIES "include/gudhi;include/gudhi_patches")
+
   foreach(GUDHI_MODULE ${GUDHI_MODULES})
-    # doc files
-    file(GLOB GUDHI_DOC_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/doc/*)
-  
-    foreach(GUDHI_DOC_FILE ${GUDHI_DOC_FILES})
-      get_filename_component(GUDHI_DOC_FILE_NAME ${GUDHI_DOC_FILE} NAME)
-      # GUDHI_DOC_FILE can be a file or a directory
-      if(IS_DIRECTORY ${GUDHI_DOC_FILE})
-        add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                           copy_directory ${GUDHI_DOC_FILE} ${GUDHI_USER_VERSION_DIR}/doc/${GUDHI_MODULE}/${GUDHI_DOC_FILE_NAME})
-      else()
-        add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                           copy ${GUDHI_DOC_FILE} ${GUDHI_USER_VERSION_DIR}/doc/${GUDHI_MODULE}/${GUDHI_DOC_FILE_NAME})
-      endif()
-    endforeach()
-  
-    # example files
-    file(GLOB GUDHI_EXAMPLE_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/example/*)
-  
-    foreach(GUDHI_EXAMPLE_FILE ${GUDHI_EXAMPLE_FILES})
-      get_filename_component(GUDHI_EXAMPLE_FILE_NAME ${GUDHI_EXAMPLE_FILE} NAME)
-      # GUDHI_EXAMPLE_FILE can be a file or a directory
-      if(IS_DIRECTORY ${GUDHI_EXAMPLE_FILE})
-        add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                           copy_directory ${GUDHI_EXAMPLE_FILE} ${GUDHI_USER_VERSION_DIR}/example/${GUDHI_MODULE}/${GUDHI_EXAMPLE_FILE_NAME})
-      else()
-        add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                           copy ${GUDHI_EXAMPLE_FILE} ${GUDHI_USER_VERSION_DIR}/example/${GUDHI_MODULE}/${GUDHI_EXAMPLE_FILE_NAME})
-      endif()
-    endforeach()
-  
-    # include files
-    file(GLOB GUDHI_INCLUDE_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/include/gudhi/*)
-  
-    foreach(GUDHI_INCLUDE_FILE ${GUDHI_INCLUDE_FILES})
-      get_filename_component(GUDHI_INCLUDE_FILE_NAME ${GUDHI_INCLUDE_FILE} NAME)
-      # GUDHI_INCLUDE_FILE can be a file or a directory
-      if(IS_DIRECTORY ${GUDHI_INCLUDE_FILE})
-        add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                           copy_directory ${GUDHI_INCLUDE_FILE} ${GUDHI_USER_VERSION_DIR}/include/gudhi/${GUDHI_INCLUDE_FILE_NAME})
-      else()
-        add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                           copy ${GUDHI_INCLUDE_FILE} ${GUDHI_USER_VERSION_DIR}/include/gudhi/${GUDHI_INCLUDE_FILE_NAME})
-      endif()
-    endforeach()
-  
-    # concept files
-    file(GLOB GUDHI_CONCEPT_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/concept/*.h)
-  
-    foreach(GUDHI_CONCEPT_FILE ${GUDHI_CONCEPT_FILES})
-      get_filename_component(GUDHI_CONCEPT_FILE_NAME ${GUDHI_CONCEPT_FILE} NAME)
-      # GUDHI_CONCEPT_FILE can be a file or a directory
-      if(IS_DIRECTORY ${GUDHI_CONCEPT_FILE})
-        add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                           copy_directory ${GUDHI_CONCEPT_FILE} ${GUDHI_USER_VERSION_DIR}/concept/${GUDHI_MODULE}/${GUDHI_CONCEPT_FILE_NAME})
-      else()
-        add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                           copy ${GUDHI_CONCEPT_FILE} ${GUDHI_USER_VERSION_DIR}/concept/${GUDHI_MODULE}/${GUDHI_CONCEPT_FILE_NAME})
-      endif()
-    endforeach()
-  endforeach()
+    foreach(GUDHI_DIRECTORY ${GUDHI_DIRECTORIES})
+      # Find files
+      file(GLOB GUDHI_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/${GUDHI_DIRECTORY}/*)
+
+      foreach(GUDHI_FILE ${GUDHI_FILES})
+        get_filename_component(GUDHI_FILE_NAME ${GUDHI_FILE} NAME)
+        # GUDHI_FILE can be a file or a directory
+        if(IS_DIRECTORY ${GUDHI_FILE})
+          add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                             copy_directory ${GUDHI_FILE} ${GUDHI_USER_VERSION_DIR}/${GUDHI_DIRECTORY}/${GUDHI_MODULE}/${GUDHI_FILE_NAME})
+        else()
+          add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                             copy ${GUDHI_FILE} ${GUDHI_USER_VERSION_DIR}/${GUDHI_DIRECTORY}/${GUDHI_MODULE}/${GUDHI_FILE_NAME})
+        endif()
+      endforeach()
+    endforeach(GUDHI_DIRECTORY ${GUDHI_DIRECTORIES})
+
+    foreach(GUDHI_INCLUDE_DIRECTORY ${GUDHI_INCLUDE_DIRECTORIES})
+      # include files
+      file(GLOB GUDHI_INCLUDE_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/${GUDHI_INCLUDE_DIRECTORY}/*)
+
+      foreach(GUDHI_INCLUDE_FILE ${GUDHI_INCLUDE_FILES})
+        get_filename_component(GUDHI_INCLUDE_FILE_NAME ${GUDHI_INCLUDE_FILE} NAME)
+        # GUDHI_INCLUDE_FILE can be a file or a directory
+        if(IS_DIRECTORY ${GUDHI_INCLUDE_FILE})
+          add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                             copy_directory ${GUDHI_INCLUDE_FILE} ${GUDHI_USER_VERSION_DIR}/${GUDHI_INCLUDE_DIRECTORY}/${GUDHI_INCLUDE_FILE_NAME})
+        else()
+          add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                             copy ${GUDHI_INCLUDE_FILE} ${GUDHI_USER_VERSION_DIR}/${GUDHI_INCLUDE_DIRECTORY}/${GUDHI_INCLUDE_FILE_NAME})
+        endif()
+      endforeach()
+    endforeach(GUDHI_INCLUDE_DIRECTORY ${GUDHI_INCLUDE_DIRECTORIES})
+
+  endforeach(GUDHI_MODULE ${GUDHI_MODULES})
 
 endif()