[doxygen,cmake] Sanitize links for doxygen, a cmake macros is necessary for this

Add preprocessor deprecations to deprecation list in doxygen

cmake/modules/CMakeLists.txt

@@ -2,6 +2,7 @@ set(modules
   AddInputFileLinks.cmake
   CheckConstexpr.cmake
   CopyOfDuneSymlinkOrCopy.cmake
+  DumuxDoxygen.cmake
   DumuxMacros.cmake
   DumuxTestMacros.cmake)
 include(GNUInstallDirs)

cmake/modules/DumuxDoxygen.cmake

+# add_dumux_doxgen_target
+#
+# make sure, that the doxygen links to todo list, bibliography, etc. are correct
+MACRO (add_dumux_doxygen_target)
+  add_doxygen_target()
+  add_custom_command(TARGET doxygen_${ProjectName}
+                     POST_BUILD
+                     COMMAND ${CMAKE_SOURCE_DIR}/doc/doxygen/sanitizelinks.sh)
+ENDMACRO (add_dumux_doxygen_target)

cmake/modules/DumuxMacros.cmake

@@ -2,6 +2,7 @@
 include(CheckConstexpr)
 # additional macros
 include(AddInputFileLinks)
+include(DumuxDoxygen)
 include(DumuxTestMacros)
 
 find_package(Gnuplot)

doc/doxygen/CMakeLists.txt

 # shortcut for creating the Doxyfile.in and Doxyfile
-add_doxygen_target()
+add_dumux_doxygen_target()

doc/doxygen/Doxylocal

@@ -24,8 +24,11 @@ EXTRA_PACKAGES        += amsmath,amssymb,units
 SEARCHENGINE           = YES
 SERVER_BASED_SEARCH    = NO
 
-# disable macro expansion (Otherwise, certain properties will not appear
-# in the documentation properly. This should be fixed at some time.)
-MACRO_EXPANSION = NO
-
-CITE_BIB_FILES = @top_srcdir@/doc/handbook/dumux-handbook
+# the bibliography file used for the doxygen documentation
+CITE_BIB_FILES = @top_srcdir@/doc/handbook/dumux-handbook.bib
+
+# enable macro expansion only for specified macros
+MACRO_EXPANSION        = YES
+EXPAND_ONLY_PREDEF     = YES
+PREDEFINED             = "DUNE_DEPRECATED:=/** \deprecated */" \
+                         "DUNE_DEPRECATED_MSG(A):=/** \deprecated A */"

doc/doxygen/sanitizelinks.sh

+# sanitizes the links to the given lists, because doxygen somehow links
+# to a page with a wrong index
+function sanitizelinks {
+  NEW_FILE=`grep -l "\"title\">$1" html/*html | egrep -o [0-9]+`
+  OLD_FILE=`awk -v a=$NEW_FILE 'BEGIN {printf("%05d", a-1)}'`
+  sed -i "s/$OLD_FILE/$NEW_FILE/g" html/*html
+}
+
+sanitizelinks "Todo List"
+sanitizelinks "Bug List"
+sanitizelinks "Deprecated List"
+sanitizelinks "Bibliography"