added function to read point cloud from array in memory + changed a little bit the API

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/Nerve_GIC@3841 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: f31a3a60b2438d7b767a1ee310d859477330a743

5 files changed, 193 insertions, 137 deletions

diff --git a/src/cmake/modules/FindCython.cmake b/src/cmake/modules/FindCython.cmake
deleted file mode 100644
index 04aed1f8..00000000
--- a/src/cmake/modules/FindCython.cmake
+++ /dev/null
@@ -1,44 +0,0 @@
-# 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/src/cmake/modules/GUDHI_compilation_flags.cmake b/src/cmake/modules/GUDHI_compilation_flags.cmake
new file mode 100644
index 00000000..a01d6e13
--- /dev/null
+++ b/src/cmake/modules/GUDHI_compilation_flags.cmake
@@ -0,0 +1,72 @@
+# This files manage compilation flags required by GUDHI
+
+include(TestCXXAcceptsFlag)
+include(CheckCXXSourceCompiles)
+
+# add a compiler flag only if it is accepted
+macro(add_cxx_compiler_flag _flag)
+  string(REPLACE "-" "_" _flag_var ${_flag})
+  check_cxx_accepts_flag("${_flag}" CXX_COMPILER_${_flag_var}_OK)
+  if(CXX_COMPILER_${_flag_var}_OK)
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${_flag}")
+  endif()
+endmacro()
+
+function(can_cgal_use_cxx11_thread_local)
+  # This is because of https://github.com/CGAL/cgal/blob/master/Installation/include/CGAL/tss.h
+  # CGAL is using boost thread if thread_local is not ready (requires XCode 8 for Mac).
+  # The test in https://github.com/CGAL/cgal/blob/master/Installation/include/CGAL/config.h
+  #   #if __has_feature(cxx_thread_local) || \
+  #       ( (__GNUC__ * 100 + __GNUC_MINOR__) >= 408 && __cplusplus >= 201103L ) || \
+  #       ( _MSC_VER >= 1900 )
+  #   #define CGAL_CAN_USE_CXX11_THREAD_LOCAL
+  #   #endif
+  set(CGAL_CAN_USE_CXX11_THREAD_LOCAL "
+      int main() {
+      #ifndef __has_feature
+        #define __has_feature(x) 0  // Compatibility with non-clang compilers.
+      #endif
+      #if __has_feature(cxx_thread_local) || \
+          ( (__GNUC__ * 100 + __GNUC_MINOR__) >= 408 && __cplusplus >= 201103L ) || \
+          ( _MSC_VER >= 1900 )
+        bool has_feature_thread_local = true;
+      #else
+        // Explicit error of compilation for CMake test purpose - has_feature_thread_local is not defined
+      #endif
+        bool result = has_feature_thread_local;
+      }  ")
+  check_cxx_source_compiles("${CGAL_CAN_USE_CXX11_THREAD_LOCAL}" CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT)
+endfunction()
+
+set (CMAKE_CXX_STANDARD 11)
+
+enable_testing()
+
+if(MSVC)
+  # Turn off some VC++ warnings
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4267 /wd4668 /wd4311 /wd4800 /wd4820 /wd4503 /wd4244 /wd4345 /wd4996 /wd4396 /wd4018")
+endif()
+
+add_cxx_compiler_flag("-Wall")
+
+if (DEBUG_TRACES)
+  # For programs to be more verbose
+  message(STATUS "DEBUG_TRACES are activated")
+  add_definitions(-DDEBUG_TRACES)
+endif()
+
+set(GUDHI_CAN_USE_CXX11_THREAD_LOCAL "
+    int main() {
+      thread_local int result = 0;
+      return result;
+    }  ")
+check_cxx_source_compiles("${GUDHI_CAN_USE_CXX11_THREAD_LOCAL}" GUDHI_CAN_USE_CXX11_THREAD_LOCAL_RESULT)
+if (GUDHI_CAN_USE_CXX11_THREAD_LOCAL_RESULT)
+  add_definitions(-DGUDHI_CAN_USE_CXX11_THREAD_LOCAL)
+endif()
+
+if(CMAKE_BUILD_TYPE MATCHES Debug)
+  message("++ Debug compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_DEBUG}")
+else()
+  message("++ Release compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_RELEASE}")
+endif()
diff --git a/src/cmake/modules/GUDHI_doxygen_target.cmake b/src/cmake/modules/GUDHI_doxygen_target.cmake
index f3e2d9f5..9e10e566 100644
--- a/src/cmake/modules/GUDHI_doxygen_target.cmake
+++ b/src/cmake/modules/GUDHI_doxygen_target.cmake
@@ -3,14 +3,17 @@ find_package(Doxygen)
 if(DOXYGEN_FOUND)
   # configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile @ONLY)
 
-  #starting from cmake 3.9 the usage of DOXYGEN_EXECUTABLE is deprecated
+  # starting from cmake 3.9 the usage of DOXYGEN_EXECUTABLE is deprecated
   if(TARGET Doxygen::doxygen)
     get_property(DOXYGEN_EXECUTABLE TARGET Doxygen::doxygen PROPERTY IMPORTED_LOCATION)
   endif()
 
   add_custom_target(doxygen ${DOXYGEN_EXECUTABLE} ${GUDHI_USER_VERSION_DIR}/Doxyfile
                     WORKING_DIRECTORY ${GUDHI_USER_VERSION_DIR}
-                    DEPENDS ${GUDHI_USER_VERSION_DIR}/Doxyfile ${GUDHI_DOXYGEN_DEPENDENCY}
                     COMMENT "Generating API documentation with Doxygen in ${GUDHI_USER_VERSION_DIR}/doc/html/" VERBATIM)
 
+  if(TARGET user_version)
+    # In dev version, doxygen target depends on user_version target. Not existing in user version
+    add_dependencies(doxygen user_version)
+  endif()
 endif(DOXYGEN_FOUND)
diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index a008dd0a..f03c2177 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -8,11 +8,9 @@ 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()
@@ -54,12 +52,12 @@ if(CGAL_FOUND)
       endforeach(CGAL_INCLUDE_DIR ${CGAL_INCLUDE_DIRS})
     endif(NOT CGAL_VERSION VERSION_GREATER 4.9.0)
 
-    if (NOT CGAL_VERSION VERSION_GREATER 4.11.0)
+    if (CGAL_VERSION VERSION_LESS 4.11.0)
       # For dev version
       include_directories(BEFORE "src/common/include/gudhi_patches")
       # For user version
       include_directories(BEFORE "include/gudhi_patches")
-    endif (NOT CGAL_VERSION VERSION_GREATER 4.11.0)
+    endif ()
   endif()
 endif()
 
@@ -79,7 +77,6 @@ endif(WITH_GUDHI_USE_TBB)
 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)
@@ -119,7 +116,34 @@ message(STATUS "boost library dirs:" ${Boost_LIBRARY_DIRS})
 
 # Find the correct Python interpreter.
 # Can be set with -DPYTHON_EXECUTABLE=/usr/bin/python3 or -DPython_ADDITIONAL_VERSIONS=3 for instance.
-find_package(Cython)
+find_package( PythonInterp )
+
+# find_python_module tries to import module in Python interpreter and to retrieve its version number
+# returns ${PYTHON_MODULE_NAME_UP}_VERSION and ${PYTHON_MODULE_NAME_UP}_FOUND
+function( find_python_module PYTHON_MODULE_NAME )
+  string(TOUPPER ${PYTHON_MODULE_NAME} PYTHON_MODULE_NAME_UP)
+  execute_process(
+          COMMAND ${PYTHON_EXECUTABLE}  -c "import ${PYTHON_MODULE_NAME}; print(${PYTHON_MODULE_NAME}.__version__)"
+          RESULT_VARIABLE PYTHON_MODULE_RESULT
+          OUTPUT_VARIABLE PYTHON_MODULE_VERSION
+          ERROR_VARIABLE PYTHON_MODULE_ERROR)
+  if(PYTHON_MODULE_RESULT EQUAL 0)
+    # Remove carriage return
+    string(STRIP ${PYTHON_MODULE_VERSION} PYTHON_MODULE_VERSION)
+    set(${PYTHON_MODULE_NAME_UP}_VERSION ${PYTHON_MODULE_VERSION} PARENT_SCOPE)
+    set(${PYTHON_MODULE_NAME_UP}_FOUND TRUE PARENT_SCOPE)
+  else()
+    unset(${PYTHON_MODULE_NAME_UP}_VERSION PARENT_SCOPE)
+    set(${PYTHON_MODULE_NAME_UP}_FOUND FALSE PARENT_SCOPE)
+  endif()
+endfunction( find_python_module )
+
+if( PYTHONINTERP_FOUND )
+  find_python_module("cython")
+  find_python_module("pytest")
+  find_python_module("matplotlib")
+  find_python_module("numpy")
+endif()
 
 if(NOT GUDHI_CYTHON_PATH)
   message(FATAL_ERROR "ERROR: GUDHI_CYTHON_PATH is not valid.")
diff --git a/src/cmake/modules/GUDHI_user_version_target.cmake b/src/cmake/modules/GUDHI_user_version_target.cmake
index 4abc2574..d43a6fa6 100644
--- a/src/cmake/modules/GUDHI_user_version_target.cmake
+++ b/src/cmake/modules/GUDHI_user_version_target.cmake
@@ -1,94 +1,95 @@
-# Some functionnalities requires CMake 2.8.11 minimum
-if (NOT CMAKE_VERSION VERSION_LESS 2.8.11)
+# Definition of the custom target user_version
+add_custom_target(user_version)
 
-  # Definition of the custom target user_version
-  add_custom_target(user_version)
-  
-  if(DEFINED USER_VERSION_DIR)
-    # set the GUDHI_USER_VERSION_DIR with USER_VERSION_DIR defined by the user
-    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()
+if(DEFINED USER_VERSION_DIR)
+  # set the GUDHI_USER_VERSION_DIR with USER_VERSION_DIR defined by the user
+  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()
 
-  set(GUDHI_DOXYGEN_DEPENDENCY user_version)
+add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                   make_directory ${GUDHI_USER_VERSION_DIR}
+                   COMMENT "user_version creation in ${GUDHI_USER_VERSION_DIR}")
 
-  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                     make_directory ${GUDHI_USER_VERSION_DIR}
-                     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)
-  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                     copy ${CMAKE_SOURCE_DIR}/src/CMakeLists.txt ${GUDHI_USER_VERSION_DIR}/CMakeLists.txt)
-  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                     copy ${CMAKE_SOURCE_DIR}/src/Doxyfile ${GUDHI_USER_VERSION_DIR}/Doxyfile)
-  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                     copy ${CMAKE_SOURCE_DIR}/src/GUDHIConfigVersion.cmake.in ${GUDHI_USER_VERSION_DIR}/GUDHIConfigVersion.cmake.in)
-  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                     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_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/GudhUI ${GUDHI_USER_VERSION_DIR}/GudhUI)
-  
-  set(GUDHI_DIRECTORIES "doc;example;concept;utilities")
-  if (NOT CGAL_VERSION VERSION_GREATER 4.11.0)
-    set(GUDHI_INCLUDE_DIRECTORIES "include/gudhi;include/gudhi_patches")
-  else ()
-      set(GUDHI_INCLUDE_DIRECTORIES "include/gudhi")
-  endif ()
+foreach(GUDHI_MODULE ${GUDHI_MODULES_FULL_LIST})
+  set(GUDHI_DOXYGEN_IMAGE_PATH "${GUDHI_DOXYGEN_IMAGE_PATH}    doc/${GUDHI_MODULE}/ \\  \n")
+endforeach(GUDHI_MODULE ${GUDHI_MODULES_FULL_LIST})
 
-  foreach(GUDHI_MODULE ${GUDHI_MODULES_FULL_LIST})
-    foreach(GUDHI_DIRECTORY ${GUDHI_DIRECTORIES})
-      # Find files
-      file(GLOB GUDHI_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/${GUDHI_DIRECTORY}/*)
+# Generate setup.py file to cythonize Gudhi - This file must be named setup.py by convention
+configure_file(${CMAKE_SOURCE_DIR}/src/Doxyfile.in "${CMAKE_CURRENT_BINARY_DIR}/src/Doxyfile" @ONLY)
 
-      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})
+add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+        copy ${CMAKE_CURRENT_BINARY_DIR}/src/Doxyfile ${GUDHI_USER_VERSION_DIR}/Doxyfile)
 
-    foreach(GUDHI_INCLUDE_DIRECTORY ${GUDHI_INCLUDE_DIRECTORIES})
-      # include files
-      file(GLOB GUDHI_INCLUDE_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/${GUDHI_INCLUDE_DIRECTORY}/*)
+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)
+add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                   copy ${CMAKE_SOURCE_DIR}/src/CMakeLists.txt ${GUDHI_USER_VERSION_DIR}/CMakeLists.txt)
+add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                   copy ${CMAKE_SOURCE_DIR}/src/GUDHIConfigVersion.cmake.in ${GUDHI_USER_VERSION_DIR}/GUDHIConfigVersion.cmake.in)
+add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                   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)
 
-      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})
+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/GudhUI ${GUDHI_USER_VERSION_DIR}/GudhUI)
 
-  endforeach(GUDHI_MODULE ${GUDHI_MODULES_FULL_LIST})
+set(GUDHI_DIRECTORIES "doc;example;concept;utilities")
+if (CGAL_VERSION VERSION_LESS 4.11.0)
+  set(GUDHI_INCLUDE_DIRECTORIES "include/gudhi;include/gudhi_patches")
+else ()
+    set(GUDHI_INCLUDE_DIRECTORIES "include/gudhi")
+endif ()
 
-endif()
+foreach(GUDHI_MODULE ${GUDHI_MODULES_FULL_LIST})
+  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_FULL_LIST})
\ No newline at end of file