Merge last trunk modifications

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/3billions_simplices_fix@1483 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 1eafe2e93f1fc3a2780d9452aae1981481786f95

4 files changed, 132 insertions, 1 deletions

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index c02f816d..cde949e1 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -15,6 +15,10 @@ if(NOT Boost_FOUND)
   message(FATAL_ERROR "NOTICE: This demo requires Boost and will not be compiled.")
 else()
 
+  # For "make doxygen"
+  set(GUDHI_USER_VERSION_DIR ${CMAKE_SOURCE_DIR})
+  include(${CMAKE_MODULE_PATH}/GUDHI_doxygen_target.txt)
+
   find_package(GMP)
   if(GMP_FOUND)
     message(STATUS "GMP_LIBRARIES = ${GMP_LIBRARIES}")
diff --git a/src/cmake/modules/GUDHI_doxygen_target.txt b/src/cmake/modules/GUDHI_doxygen_target.txt
new file mode 100644
index 00000000..d2cb952d
--- /dev/null
+++ b/src/cmake/modules/GUDHI_doxygen_target.txt
@@ -0,0 +1,11 @@
+# add a target to generate API documentation with Doxygen
+find_package(Doxygen)
+if(DOXYGEN_FOUND)
+  # configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile @ONLY)
+
+  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)
+
+endif(DOXYGEN_FOUND)
diff --git a/src/cmake/modules/GUDHI_user_version_target.txt b/src/cmake/modules/GUDHI_user_version_target.txt
new file mode 100644
index 00000000..805f0a83
--- /dev/null
+++ b/src/cmake/modules/GUDHI_user_version_target.txt
@@ -0,0 +1,115 @@
+# 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)
+  
+  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
+    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}/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 ${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}/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")
+  
+  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()
+
+endif()
diff --git a/src/common/doc/header.html b/src/common/doc/header.html
index c958390c..a6f3ed9c 100644
--- a/src/common/doc/header.html
+++ b/src/common/doc/header.html
@@ -40,6 +40,7 @@ $extrastylesheet
                       <li><a href="http://gudhi.gforge.inria.fr/getinvolved/">Get involved</a></li>
                       <li><a href="http://gudhi.gforge.inria.fr/partners/">Partners and Funding</a></li>
                       <li><a href="http://gudhi.gforge.inria.fr/relatedprojects/">Related projects</a></li>
+                      <li><a href="http://gudhi.gforge.inria.fr/theyaretalkingaboutus/">They are talking about us</a></li>
                   </ul>
               </li>
               <li class="divider"></li>
@@ -52,7 +53,7 @@ $extrastylesheet
                   </ul>
               </li>
               <li class="divider"></li>
-              <li><a href="http://gudhi.gforge.inria.fr/doc/latest/modules.html">Documentation</a></li>
+              <li><a href="http://gudhi.gforge.inria.fr/doc/latest/">Documentation</a></li>
               <li class="divider"></li>
               <li><a href="http://gudhi.gforge.inria.fr/interfaces/">Interfaces</a></li>
               <li class="divider"></li>