Merge last trunk modifications

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_representation_integration@2479 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: bfadffa81f3cd05c8d4a4c911853ad2f2cd0ac36

3 files changed, 122 insertions, 1 deletions

diff --git a/src/cmake/modules/GUDHI_modules.cmake b/src/cmake/modules/GUDHI_modules.cmake
new file mode 100644
index 00000000..20fc8d17
--- /dev/null
+++ b/src/cmake/modules/GUDHI_modules.cmake
@@ -0,0 +1,26 @@
+# A function to add a new module in GUDHI
+
+set(GUDHI_MODULES "")
+function(add_gudhi_module file_path)
+    set(GUDHI_MODULES ${GUDHI_MODULES} ${file_path} PARENT_SCOPE)
+endfunction(add_gudhi_module)
+
+# message("++ GUDHI_MODULES list is:\"${GUDHI_MODULES}\"")
+
+if (WITH_GUDHI_BENCHMARK)
+  set(GUDHI_SUB_DIRECTORIES "${GUDHI_SUB_DIRECTORIES};benchmark")
+endif()
+if (WITH_GUDHI_EXAMPLE)
+  set(GUDHI_SUB_DIRECTORIES "${GUDHI_SUB_DIRECTORIES};example")
+endif()
+if (NOT WITHOUT_GUDHI_TEST)
+    set(GUDHI_SUB_DIRECTORIES "${GUDHI_SUB_DIRECTORIES};test")
+endif()
+if (NOT WITHOUT_GUDHI_UTILITIES)
+  set(GUDHI_SUB_DIRECTORIES "${GUDHI_SUB_DIRECTORIES};utilities")
+endif()
+
+message("++ GUDHI_SUB_DIRECTORIES list is:\"${GUDHI_SUB_DIRECTORIES}\"")
+
+
+
diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 5f84c602..8cb01d3c 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -135,10 +135,15 @@ if(PYTHONINTERP_FOUND AND CYTHON_FOUND)
     # Documentation generation is available through sphinx
     find_program( SPHINX_PATH sphinx-build )
   elseif(PYTHON_VERSION_MAJOR EQUAL 3)
-    # Documentation generation is available through sphinx
+    # No sphinx-build in Pyton3, just hack it
     set(SPHINX_PATH "${CMAKE_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build")
   else()
     message(FATAL_ERROR "ERROR: Try to compile the Cython interface. Python version ${PYTHON_VERSION_STRING} is not valid.")
   endif(PYTHON_VERSION_MAJOR EQUAL 2)
+  # get PYTHON_SITE_PACKAGES relative path from a python command line
+  execute_process(
+    COMMAND "${PYTHON_EXECUTABLE}" -c "from distutils.sysconfig import get_python_lib; print (get_python_lib(prefix='', plat_specific=True))"
+    OUTPUT_VARIABLE PYTHON_SITE_PACKAGES
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
 endif(PYTHONINTERP_FOUND AND CYTHON_FOUND)
 
diff --git a/src/cmake/modules/GUDHI_user_version_target.cmake b/src/cmake/modules/GUDHI_user_version_target.cmake
new file mode 100644
index 00000000..8642d3bf
--- /dev/null
+++ b/src/cmake/modules/GUDHI_user_version_target.cmake
@@ -0,0 +1,90 @@
+# 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)
+  
+  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
+                     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")
+  set(GUDHI_INCLUDE_DIRECTORIES "include/gudhi;include/gudhi_patches")
+
+  foreach(GUDHI_MODULE ${GUDHI_MODULES})
+    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()