extract

#!/bin/bash

cat ../src/*/*cpp |
awk '
  /PLUMED_REGISTER_ACTION/{print}
  /namespace/{print}
' |
  sed '
   s/PLUMED_REGISTER_ACTION(/ /
   s/,"/ /
   s/")//
' |
awk '
/namespace/{
 if($1=="namespace"){
   namespace=$2;
   gsub("{","",namespace);
   namespace=namespace"::";
 }
 if(namespace=="PLMD::") namespace="";
 next;
 }
{
  printf("%s","/// \\class PLMD::"namespace""$1"\n");
  printf("%s","/// \\ingroup INPUTDIRECTIVES\n");
  action=tolower($2);
  firstchar=substr($2,1,1);
  n=split(action,actionarray,"");
  lowercase=0;
  if(firstchar==actionarray[1]) lowercase=1;
  printf("%s","/// Provides the keyword <a href=\"../../user-doc/html/");
  for(i=1;i<=n;i++){
    if(actionarray[i]!="_") printf("_");
    printf("%s",actionarray[i]);
  };
  printf("%s",".html\"> "$2" </a>\n");
}' >  links-to-user-manual.txt


# Create a directory to put all the files in
#rm -rf automatic
#mkdir automatic
#
#cp ../src/*{.h,.cpp} automatic

#for file in ../src/*.cpp ; do
#    stripf=`echo $file | sed -e 's/..\/src\///g'`
#    ofile=`echo automatic/$stripf`
#    echo $ofile
#    cat $file | 
#       awk -v output=$ofile -v inside=0 '{
#           if(inside==2 && NF==0){
#              inside=1
#              if(lowercase==0){
#                 printf("%s","///To view the user manual <a href=\"../../user-doc/html/") >> output
#                       for(i=1;i<=n;i++){ printf("_%s", actionarray[i]) >> output }
#                       print ".html\"> click here </a>." >> output
#              } else {
#                 printf("%s","///To view the user manual <a href=\"../../user-doc/html/") >> output 
#                       printf("%s",action) >> output
#                       print ".html\"> click here </a>." >> output
#              }
#          }
#           if(inside==2 && $1!="/**" && $1!="*/" && $1!="//+ENDPLUMEDOC"){
#              print "///" $0 >> output
#           }
#           if($1=="//+PLUMEDOC"){
#              inside=2
#              action=tolower($3)
#              firstchar=substr($3, 1, 1 )
#              n=split(action,actionarray,"");
#              lowercase=0
#              if( firstchar==actionarray[1] ) lowercase=1 
#           }
#           if(inside==0){
#              print $0 >> output 
#           }
#           if($1=="//+ENDPLUMEDOC" && inside==1){
#              inside=0
#           }
#           if($1=="//+ENDPLUMEDOC" && inside==2){
#              inside=0
#              if(lowercase==0){
#                 printf("%s","///To view the more detailed manual <a href=\"../../user-doc/html/") >> output
#                       for(i=1;i<=n;i++){ printf("_%s", actionarray[i]) >> output }
#                       print ".html\"> click here </a>." >> output
#              } else {
#                 printf("%s","///To view the more detailed manual <a href=\"../../user-doc/html/") >> output 
#                       printf("%s",action) >> output
#                       print ".html\"> click here </a>." >> output
#              }
#           }
#       }'
# done