go-doxygen

#! /bin/bash

# Making sure that plumed executable is available
echo -n "Searching for plumed ..."
if plumed --no-mpi 2>/dev/null 1>/dev/null ; then
  echo " found"
else
  echo " not found"
  echo -n "Sourcing sourceme.sh and searching again ..."
  if source ../sourceme.sh && plumed --no-mpi 2>/dev/null 1>/dev/null ; then
    echo " found"
  else
    echo "ERROR: you should compile plumed first!"
    exit 1
  fi
fi

LIST="
 IntroPP.txt ../CHANGES InstallationPP.txt SyntaxPP.txt ColvarPP.txt GroupPP.txt FunctionsPP.txt AnalysisPP.txt
  BiasPP.txt ToolsPP.txt MiscPP.txt RegexPP.txt FilesPP.txt ModulesPP.txt TutorialsPP.txt GlossaryPP.txt automatic tutorials"

{
  cat Doxyfile
  echo "PROJECT_NUMBER = \"$(plumed --no-mpi info --long-version)\""
  echo "INPUT+=" $LIST
  # add this to manually control layout:
  # echo "LAYOUT_FILE=PlumedLayout.xml"
} | doxygen -

for file in html/*.html
do
awk -v version=$(plumed --no-mpi info --version) '{
  if(match($0,"<span>Main&#160;Page</span>")){
    sub("Main","Home",$0);
    sub("Page","(v"version")",$0);
    print
  } else if(match($0,"<span>Related&#160;Pages</span>")){
    print "      <li><a href=\"_syntax.html\"><span>Getting&#160;started</span></a></li>"
    print "      <li><a href=\"tutorials.html\"><span>Tutorials</span></a></li>"
    print "      <li><a href=\"glossary.html\"><span>Index&#160;of&#160;Actions</span></a></li>"
  } else print
}' $file > $file.tmp
mv $file.tmp $file
done

cat html/doxygen.css plumed.css > html/doxygen.css.tmp
mv html/doxygen.css.tmp html/doxygen.css

cd latex

# this is a workaround for a problem on the linux workstation
# where I compile the manual - GB
sed -i 's/pdfencoding=unicode/unicode/g' refman.tex
make
cp refman.pdf ../manual.pdf