extract

#! /bin/bash

source ../sourceme.sh

# initial cleanup
rm -f errors example_errors
rm -rf automatic example-check
mkdir automatic
mkdir example-check


# Check for files that register actions with no documentation
for file in ../src/*/*.cpp
do
  nreg=`grep "PLUMED_REGISTER_ACTION" $file | wc -l | awk '{print $1}'`
  if [ $nreg -gt 0 ] ; then
       ndoc=`grep PLUMEDOC $file | wc -l | awk '{print $1}'`
       if [ $ndoc -eq 0 ] ; then
          echo The following file registered an action but provided no documentation: $file >> errors
       fi
  fi 
done

# Create the list of codes that plumed works with from the set of available patches
for file in ../patches/*.diff
do
   myengine=`echo "$file" | sed -e 's/.diff//' | sed -e 's/..\/patches\///'`
   mytag=`echo "$myengine" | sed -e 's/\./-/g'`
   echo "- $mytag" >> automatic/CODESL.list # list only, for Intro
   echo "- \subpage $mytag " >> automatic/CODES.list
   echo "/**" >> automatic/$myengine.txt
   echo "\page $mytag $myengine" >> automatic/$myengine.txt
   ../src/lib/plumed --no-mpi patch -e $myengine -i -q >> automatic/$myengine.txt
   echo "*/" >> automatic/$myengine.txt 
done

# Generate all the documentation pages from comments
{
cat ../*/*/*cpp
# documentation for scripts:
for file in ../scripts/*.sh
do
  name=$(basename ${file%.sh})
  cat << EOF
//+PLUMEDOC TOOLS $name
/*
EOF
  ../src/lib/plumed $name --description

  cat << EOF

\note This command line tool is implemented as a shell script. Its help message is pasted below:

\verbatim
EOF
  ../src/lib/plumed --no-mpi $name --help
  cat << EOF
\endverbatim
*/
//+ENDPLUMEDOC
EOF

done

} |
awk 'BEGIN{gfile="automatic/GLOSSARY.list"; dfile="automatic/DICTIONARY.list"; }{
  if($1=="//+ENDPLUMEDOC" && inside){
     inside=0;
     module=0
     print "*/" >output
  }
  if(inside>=2 && NF==0){
     print "</td> </tr>" >> lfile
     if(module==1) print "</td> </tr>" >> mfile
     if(inside==2){ printf "</td> </tr>\n" > gfile; }
     if(inside==3){ printf "</td> </tr>\n" > dfile; }
     inside=1
     module=0
  }
  if(inside==1 && $1!="/*" && $1!="*/") print $0 > output
  if(inside>=2 && $1!="/*" && $1!="*/" ){
     print $0 > output
     printf "%s", $0 >> lfile
     if(module==1) printf "%s", $0 >> mfile
     if(inside==2){ printf "%s", $0 > gfile; }
     if(inside==3){ printf "%s", $0 > dfile; }
  }
  if($1=="//+PLUMEDOC"){
    if( $2=="TOPOLOGY" || 
        $2=="COLVAR" || 
        $2=="MCOLVAR" || 
        $2=="DCOLVAR"|| 
        $2=="MFILTERS" || 
        $2=="MTRANSFORMS" || 
        $2=="VOLUMES" || 
        $2=="MCOLVARF" || 
        $2=="MCOLVARB" || 
        $2=="MATRIX" || 
        $2=="MATRIXF" || 
        $2=="CONCOMP" || 
        $2=="FUNCTION" || 
        $2=="GRIDCALC" || 
        $2=="REWEIGHTING"|| 
        $2=="PRINTANALYSIS" || 
        $2=="DIMRED" || 
        $2=="GRIDANALYSIS" || 
        $2=="BIAS" || 
        $2=="GENERIC" || 
        $2=="VATOM" || 
        $2=="TOOLS" || 
        $2=="ANALYSIS" || 
        $2=="LANDMARKS" ){
      if(lfile!="") close(lfile)
      lfile="automatic/"$2".list"
      
      printf "<tr> <td width=%s> \\subpage %s </td> <td>","5%", $3 >> lfile
#       printf "<tr> <td width=5%> \\ref %s </td><td> %s </td><td>",$3, $2 > gfile
      printf "<tr> <td width=%s> \\ref %s </td><td> %s </td><td>","5%",$3, $2 > gfile

      if(output!="")close(output);
      output="automatic/"$3".tmp";
      print "/**" > output
      print "\\page "$3" "$3 > output
#      print "\\section "$3 >output
      inside=2;
      module=0
    } else if ( $2=="INTERNAL" ){
      if(output!="")close(output);

      printf "<tr> <td width=%s> \\subpage %s </td><td> %s </td><td>","5%",$3, $2 > dfile

      output="automatic/"$3".tmp";
      lfile="automatic/"$3".tmp";
      print "/**" > output
      print "\\page "$3" "$3 > output
#      print "\\section "$3 >output
      inside=3;
      module=0
    } else {
# this is the place where other modules are checked for
      if(mfile!="") close(mfile)
      mfile="automatic/"$2".list"
      printf "<tr> <td width=%s> \\subpage %s </td> <td>","5%", $3 >> mfile
      printf "<tr> <td width=%s> \\ref %s </td><td> %s </td><td>","5%",$3, $2 > gfile
      if(output!="")close(output);
      output="automatic/"$3".tmp";
      print "/**" > output
      print "\\page "$3" "$3 > output
      inside=2
      module=1
      split($2,array,"_");
      if(lfile!="") close(lfile)
      lfile="automatic/"array[2]"_OTHERMODULES.list"
      printf "<tr> <td width=%s> \\ref %s </td><td> (from \\ref %s module) ","5%", $3 ,array[1] >> lfile
      if(afile!="") close(afile)
      afile="automatic/ADDITIONALMODULES.list"
      cmd="grep description: " array[1]".md | sed -e 's/description://'"
      cmd | getline describe
      close(cmd)
      cmd="grep authors: " array[1]".md | sed -e 's/authors://'"
      cmd | getline authors 
      close(cmd)
      cmd="grep reference: " array[1]".md | sed -e 's/reference://'"
      cmd | getline reference 
      close(cmd)
      printf "<tr><td width=%s> \\subpage %s </td><td> %s </td><td> %s </td><td> %s </td></tr>\n", "10%", array[1], describe, authors, reference >> afile
    }
  }
}'

# Now put all list files in alphabetical order
for file in automatic/*.list ; do

# -k 5 is required to mix together refs and subpages
  sort -k 5 $file | uniq > $file-1
  mv $file-1 $file
done

# The following are not proper "list" files so should be generated after sorting

long_version="$(../src/lib/plumed --no-mpi info --long-version)"
git_version="$(../src/lib/plumed --no-mpi info --git-version)"

cat > automatic/VERSION.list << EOF
This manual has been compiled from PLUMED version <b> $long_version </b>
(git version: <b> $git_version </b>).
EOF

if test "$TRAVIS" == true ; then
cat >> automatic/VERSION.list << EOF
Manual built on Travis CI for branch $TRAVIS_BRANCH.
EOF
fi

if test -d regtests ; then
cat >> automatic/VERSION.list << EOF

Regtest results for this version can be found <a href="../regtests/report.html">here</a>.
EOF
fi

for file in ../CHANGES/* ; do
echo "- Changes for \\subpage $(cat $file | grep "@page" | awk '{print $2}')"
done > automatic/CHANGES.list

touch automatic/PDFMANUAL.list
if test "$make_pdfdoc" = yes ; then
cat >> automatic/PDFMANUAL.list << EOF
\htmlonly
An experimental PDF copy of this manual can be found
<a href="../manual.pdf"> here</a>, but the html documentation should 
be considered as the official one.
The PDF version has some known issue (e.g. some
links are not working properly and images are not correctly included).
The goal of the PDF manual is to allow people to download a full copy on the documentation for offline
access and to perform easily full-text searches.
Notice that the manual is updated very frequently (sometime more than once per week),
so keep your local version of the PDF manual up to date. 
Since the PDF manual is 200+ pages and is continuously updated,
<b>
please do not print it!
</b>
\endhtmlonly
EOF
fi

# Generate links to standard tutorial pages
for file in ./tutorials/*.txt ; do

    link=`grep link: $file | sed -e 's/link://' | sed -e 's/\@/\\\/'`
    describe=`grep description: $file | sed -e 's/description://'`

    echo "<tr> <td> $link </td> <td> $describe </td> </tr>" >> automatic/TUTORIALS.list  
    # This tests the examples in the tutorials
    splits=`echo $file | sed -e 's/\// /g'`
    nf=`echo $splits | awk '{print NF}'`
    fname=`echo $splits | awk -v n=$nf '{print $n}'`
    cp $file automatic/$fname
    ./test_examples automatic/$fname

done

# Generate links to old tutorial pages
for file in ./tutorials/old_tutorials/*.txt ; do

    link=`grep link: $file | sed -e 's/link://' | sed -e 's/\@/\\\/'`
    describe=`grep description: $file | sed -e 's/description://'`

    echo "<tr> <td> $link </td> <td> $describe </td> </tr>" >> automatic/OLDTUTORIALS.list  
    # This tests the examples in the tutorials
    splits=`echo $file | sed -e 's/\// /g'`
    nf=`echo $splits | awk '{print NF}'`
    fname=`echo $splits | awk -v n=$nf '{print $n}'`
    cp $file automatic/$fname 
    ./test_examples automatic/$fname

done

# Generate links to websites
for file in ./tutorials/*.site; do

   link=`grep link: $file | sed -e 's/link://'  | sed -e 's/\@/\\\/'`
   describe=`grep description: $file | sed -e 's/description://'`

   echo "<tr> <td> $link </td> <td> $describe </td> </tr>" >> automatic/WEBSITES.list
   # This tests the examples in the tutorials
   splits=`echo $file | sed -e 's/\// /g'`
   nf=`echo $splits | awk '{print NF}'`
   fname=`echo $splits | awk -v n=$nf '{print $n}'`
   cp $file automatic/$fname 
   ./test_examples automatic/$fname

done

# Generate links for module specific tutorials
for file in ./tutorials/others/*.txt ; do

    arrIN=(${file//.\/tutorials\/others\// }); 
    temp=$(echo $arrIN | tr "-" "\n"); 
    modtut=$(echo $temp | awk '{print toupper($1)}')

    link=`grep link: $file | sed -e 's/link://'`
    describe=`grep description: $file | sed -e 's/description://'`

    echo "<tr> <td> $link </td> <td> $describe </td> </tr>" >> automatic/"$modtut"_TUTORIALS.list  

done


# Find what modules the user has installed
# Find the list of modules
# if [ -d ../mymodules ] ;  then
#  sed -i '' -e 's/type="user" visible="no" url="mymodules.html"/type="user" visible="yes" url="mymodules.html"/' PlumedLayout.xml
echo "<table align=center frame=void width=65%% cellpadding=5%%>" > automatic/MODULES.list
echo "<tr> <td> <b> Module name </b> </td> <td> <b> Default behavior </b> </td> </tr>" >> automatic/MODULES.list
for file in `ls ../src/*/module.type | sed -e 's/..\/src\///' | sed -e 's/\/module.type//'`
do
   defoff=0
   dstr=`head ../src/$file/module.type`
   if [ "$dstr" != "always" ] ; then
         echo "<tr> <td> $file </td>" >> automatic/MODULES.list
         if [ "$dstr" == "default-on" ] ; then
            echo "<td> on </td> </tr>" >> automatic/MODULES.list
         else 
            echo "<td> off </td> </tr>" >> automatic/MODULES.list
            defoff=1
         fi
#        # Generate documentation and accreditation on modules page
#        echo "\section $file" >> automatic/mymodules.list
#        echo >> automatic/mymodules.list
#        echo "<table  align=center frame=void width=95%% celpadding=5%%>" >> automatic/mymodules.list
#        echo "<tr> <td width=70%%> </td> </tr> <td>" >> automatic/mymodules.list
#        author=`grep AUTHOR: ../mymodules/available-modules/"$file" | sed -e 's/AUTHOR://'` 
#        echo "<b> author: $author </b>" >> automatic/mymodules.list
#        echo "</td> </tr>" >> automatic/mymodules.list
#        echo "<tr> <td colspan="2">" >> automatic/mymodules.list
#        dline=`grep -n DESCRIPTION: ../mymodules/available-modules/"$file" | sed -n 's/^\([0-9]*\)[:].*/\1/p'` >> automatic/mymodules.list
#        tail -n +$(($dline+1)) ../mymodules/available-modules/"$file" >> automatic/mymodules.list
#        echo "</td> </tr> </table>" >> automatic/mymodules.list
#        echo >> automatic/mymodules.list
#        echo >> automatic/mymodules.list
        
        # Find src files in module and add a link to the module description
        docfiles=$(cat ../src/"$file"/*cpp | grep PLUMEDOC | grep -v END | awk '{print $3;}')
        for docfile in $docfiles ; do
          cat automatic/"$docfile".tmp |
          awk -v o=$defoff '{ print }
          /\\page '$docfile'/{
            if( o==0 ){
                print "<table  align=center frame=void width=95%% celpadding=5%%>"
                print "<tr> <td width=70%%> </td> <td>"
                print "<b> This is part of the '$file' \\link mymodules module \\endlink</b>"
                print "</td> </tr> </table>"
            } else {
                print "<table  align=center frame=void width=95%% celpadding=5%%>"
                print "<tr> <td width=60%%> </td> <td>"
                print "<b> This is part of the '$file' \\link mymodules module \\endlink</b>"
                print "</td> </tr>"
                print "<tr> <td width=60%%> </td> <td>"
                print "<b> It is only available if you configure PLUMED with ./configure --enable-modules='$file' . "
                print "Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list.</b>"
                print "</td> </tr>"
                print "</table>"
            }
          }' > automatic/"$docfile"1.tmp
          mv automatic/"$docfile"1.tmp automatic/"$docfile".tmp
        done
   fi 
done
echo "</table>" >> automatic/MODULES.list
# fi

# Generate all the documentation from keywords
for file in automatic/*.tmp
do
  # Test the example input files
  ./test_examples $file
  flag=${file#automatic/}
  flag=${flag/.tmp}
  if grep -q '//+PLUMEDOC INTERNAL' $file 1>/dev/null 2>/dev/null ; then
       cp $file automatic/$flag.txt
  else
     if ! ../src/lib/plumed --no-mpi manual --action=$flag > automatic/$flag.man 2> /dev/null ; then 
        echo Full manual for action $flag will not be generated as you are building the manual from a code where this action was not compiled >> errors
     elif ! grep -q "\par Examples" $file 1>/dev/null 2>/dev/null
     then
       echo There are no examples inside documentation for action: $flag >> errors
     fi
       { 
        awk '{if($1!="*/"){print $0}}END{print "\\par Glossary of keywords and components"}' automatic/$flag.tmp
        awk '{print $0}END{print "*/"}' automatic/$flag.man
       } > automatic/$flag.txt
   fi
done

sed -ie 's/<b> --/<b> \\c \\-\\-/g' automatic/*.txt
rm automatic/*.txte

for file in COLVAR MCOLVAR MFILTERS MTRANSFORMS VOLUMES DCOLVAR MCOLVARF MCOLVARB ANALYSIS LANDMARKS MATRIX MATRIXF CONCOMP REWEIGHTING PRINTANALYSIS BIAS GLOSSARY \
            DICTIONARY TUTORIALS OLDTUTORIALS WEBSITES FUNCTION TOPOLOGY VATOM GRIDCALC GRIDANALYSIS DIMRED \
            TOOLS
do
  mv automatic/$file.list automatic/$file.1.list
  {
    echo "<table align=center frame=void width=95%% cellpadding=5%%>"
    cat automatic/$file.1.list
    echo "</table>"
  } > automatic/$file.list
  rm automatic/$file.1.list
done

for file in automatic/*_*.list
do
  mv $file $file.1
  {
    echo "<table align=center frame=void width=95%% cellpadding=5%%>"
    cat $file.1
    echo "</table>"
  } > $file
  rm $file.1
done

for file in automatic/*_OTHERMODULES.list
do

ff=${file%_OTHERMODULES.list}.list

if test -f "$ff" ; then

mv $ff $ff.1
  {
    cat $ff.1
    echo "In addition to the keywords above, by enabling optional modules you can access to the following keywords:"
    cat $file
  } > $ff
fi
done

# Make all double hyphens appear as double hypens
sed -ie 's/<b> --/<b> \\c \\-\\-/g' automatic/*.txt
rm automatic/*.txte

rm -f *PP.txt *PP.md

keywords=`grep "@[A-Z_]*@" *.md | awk -F"@" '{print $2}' | sort | uniq`

for f in *.txt *.md
do

test -f $f || continue

extension=${f##*.}

file=${f%.$extension}

# first replace with the content of the files
# then grep out the special strings

cp $f ${file}PP.$extension
./test_examples ${file}PP.$extension

for kk in $keywords
do
  sed -ie "
    /^ *@"$kk"@ *$/r     automatic/$kk.list
" ${file}PP.$extension
done
rm -f *."$extension"e

grep -Ev '^ *@[A-Z:_]*@ *$' ${file}PP.$extension > tmp;
mv tmp ${file}PP.$extension

done