From be083160166c5a371a884609cd5231a6412609a6 Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Tue, 3 Jun 2014 11:56:14 +0100
Subject: [PATCH] Improved manual built
"extract" is way faster. Additionally, spaces are better preserved
in the manual (especially in indented input files)
---
user-doc/extract | 225 +++++++++++++++-----------------------------
user-doc/go-doxygen | 15 +++
2 files changed, 91 insertions(+), 149 deletions(-)
diff --git a/user-doc/extract b/user-doc/extract
index 570d9bab8..538665eca 100755
--- a/user-doc/extract
+++ b/user-doc/extract
@@ -1,19 +1,26 @@
#! /bin/bash
-if ! plumed ; then
- echo "plumed executable not found, I try to source ../sourceme.sh"
- source ../sourceme.sh
- if ! plumed ; then
- echo "Compile plumed first!"
+# Making sure that plumed executable is available
+echo -n "Searching for plumed ..."
+if plumed 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 2>/dev/null 1>/dev/null ; then
+ echo " found"
+ else
+ echo "ERROR: you should compile plumed first!"
exit 1
fi
fi
+# initial cleanup
+rm -f errors
rm -rf automatic
mkdir automatic
# Check for files that register actions with no documentation
-rm errors
for file in ../src/*/*.cpp
do
nreg=`grep "PLUMED_REGISTER_ACTION" $file | wc -l | awk '{print $1}'`
@@ -37,18 +44,9 @@ do
echo "*/" >> automatic/$myengine.txt
done
-## Check for utilities that register actions with no documentation
-#for file in ../utilities/*.cpp
-#do
-# ndoc=`grep PLUMEDOC $file | grep TOOL | wc -l | awk '{print $1}'`
-# if [ $ndoc -eq 0 ] ; then
-# echo The following utility has been provided without documentation: $file >> errors
-# fi
-#done
-
# Generate all the documentation pages from comments
cat ../*/*/*cpp |
-awk 'BEGIN{gfile="automatic/GLOSSARY1.list"; dfile="automatic/DICTIONARY1.list"; }{
+awk 'BEGIN{gfile="automatic/GLOSSARY.list"; dfile="automatic/DICTIONARY.list"; }{
if($1=="//+ENDPLUMEDOC"){
inside=0;
print "*/" >output
@@ -96,8 +94,11 @@ awk 'BEGIN{gfile="automatic/GLOSSARY1.list"; dfile="automatic/DICTIONARY1.list";
}'
# Now put the glossary in alphabetical order
-sort automatic/GLOSSARY1.list > automatic/GLOSSARY.list
-sort automatic/DICTIONARY1.list > automatic/DICTIONARY.list
+sort automatic/GLOSSARY.list > automatic/GLOSSARY1.list
+mv automatic/GLOSSARY1.list automatic/GLOSSARY.list
+
+sort automatic/DICTIONARY.list > automatic/DICTIONARY1.list
+mv automatic/DICTIONARY1.list automatic/DICTIONARY.list
# Generate links to tutorial pages
for file in ./tutorials/*.txt ; do
@@ -151,156 +152,82 @@ do
# echo >> automatic/mymodules.list
# Find src files in module and add a link to the module description
- for srcfile in `ls ../src/"$file"/*cpp` ; do
- ndocs=`grep PLUMEDOC "$srcfile" | grep -v END | wc -l | awk '{print $1}'`
- for ((line=1;line<=$ndocs;++line)) ; do
- docfile=`grep PLUMEDOC "$srcfile" | grep -v END | head -n $line | tail -n 1 | awk '{print $3}'`
- cat automatic/"$docfile".tmp |
- {
- while read -r LINE ; do
- if `echo $LINE | grep "\\page $docfile" 1>/dev/null 2>&1`
- then
- echo $LINE
- echo "<table align=center frame=void width=95%% celpadding=5%%>"
- echo "<tr> <td width=70%%> </td> <td>"
- echo "<b> This is part of the $file \\ref mymodules </b>"
- echo "</td> </tr> </table>"
- else
- echo "$LINE"
- fi
- done
- } > automatic/"$docfile"1.tmp
- mv automatic/"$docfile"1.tmp automatic/"$docfile".tmp
- done
- done
+ docfiles=$(cat ../src/"$file"/*cpp | grep PLUMEDOC | grep -v END | awk '{print $3;}')
+ for docfile in $docfiles ; do
+ cat automatic/"$docfile".tmp |
+ awk '{ print }
+ /\\page '$docfile'/{
+ print "<table align=center frame=void width=95%% celpadding=5%%>"
+ print "<tr> <td width=70%%> </td> <td>"
+ print "<b> This is part of the '$file' \\ref mymodules </b>"
+ print "</td> </tr> </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
-source ../sourceme.sh
for file in automatic/*.tmp
do
- foundinternal=`grep '//+PLUMEDOC INTERNAL' $file | wc -l | awk '{print $1}'`
- flag=`echo $file | sed -e 's/.tmp//g' | sed -e 's/automatic\///g'`
- if [ $foundinternal -eq 0 ] ; then
- foundexample=`grep "\par Examples" $file | wc -l | awk '{print $1}'`
- ../src/lib/plumed manual --action=$flag > automatic/$flag.man 2> shit
- rm shit
- check=`wc -l automatic/$flag.man | awk '{print $1}'`
- if [ $check -eq 0 ] ; then
+ flag=${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 ! plumed 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 [ $foundexample -eq 0 ]
+ elif ! grep -q "\par Examples" $file 1>/dev/null 2>/dev/null
then
echo There are no examples inside documentation for action: $flag >> errors
fi
- cat automatic/$flag.tmp |
{
- while read -r LINE ;
- do
- if [ "$LINE" = "\par Examples" ]
- then
- cat automatic/$flag.man
- echo -E "$LINE"
- else
- echo -E "$LINE"
- fi
- done
+ awk '/\\par Examples/{xx=1}{if(xx==0) printf("%s\n",$0)}' automatic/$flag.tmp
+ cat automatic/$flag.man
+ awk '/\\par Examples/{xx=1}{if(xx==1) printf("%s\n",$0)}' automatic/$flag.tmp
} > automatic/$flag.txt
- else
- cp $file automatic/$flag.txt
fi
done
+for file in COLVAR MCOLVAR DCOLVAR MCOLVARF ANALYSIS BIAS GLOSSARY \
+ DICTIONARY TUTORIALS WEBSITES FUNCTION TOPOLOGY VATOM \
+ 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 Bias Syntax Colvar Functions Group Installation Intro Analysis Glossary Tutorials Modules Regex Misc Tools
do
+# first replace with the content of the files
+# then grep out the special strings
+
cat $file.txt |
-{
- while read -r LINE ;
- do
- if [ "$LINE" = "@COLVAR@" ]
- then
- echo "<table align=center frame=void width=95%% cellpadding=5%%>"
- cat automatic/COLVAR.list
- echo "</table>"
- elif [ "$LINE" = "@MCOLVAR@" ]
- then
- echo "<table align=center frame=void width=95%% cellpadding=5%%>"
- cat automatic/MCOLVAR.list
- echo "</table>"
- elif [ "$LINE" = "@DCOLVAR@" ]
- then
- echo "<table align=center frame=void width=95%% cellpadding=5%%>"
- cat automatic/DCOLVAR.list
- echo "</table>"
- elif [ "$LINE" = "@MCOLVARF@" ]
- then
- echo "<table align=center frame=void width=95%% cellpadding=5%%>"
- cat automatic/MCOLVARF.list
- echo "</table>"
- elif [ "$LINE" = "@ANALYSIS@" ]
- then
- echo "<table align=center frame=void width=95%% cellpadding=5%%>"
- cat automatic/ANALYSIS.list
- echo "</table>"
- elif [ "$LINE" = "@BIAS@" ]
- then
- echo "<table align=center frame=void width=95%% cellpadding=5%%>"
- cat automatic/BIAS.list
- echo "</table>"
- elif [ "$LINE" = "@GLOSSARY@" ]
- then
- echo "<table align=center frame=void width=95%% cellpadding=5%%>"
- cat automatic/GLOSSARY.list
- echo "</table>"
- elif [ "$LINE" = "@DICTIONARY@" ]
- then
- echo "<table align=center frame=void width=95%% cellpadding=5%%>"
- cat automatic/DICTIONARY.list
- echo "</table>"
- elif [ "$LINE" = "@TUTORIALS@" ]
- then
- echo "<table align=center frame=void width=95%% cellpadding=5%%>"
- cat automatic/TUTORIALS.list
- echo "</table>"
- elif [ "$LINE" = "@WEBSITES@" ]
- then
- echo "<table align=center frame=void width=95%% cellpadding=5%%>"
- cat automatic/WEBSITES.list
- echo "</table>"
- elif [ "$LINE" = "@MODULES@" ]
- then
- cat automatic/modules.list
- elif [ "$LINE" = "@FUNCTION@" ]
- then
- echo "<table align=center frame=void width=95%% cellpadding=5%%>"
- cat automatic/FUNCTION.list
- echo "</table>"
- elif [ "$LINE" = "@TOPOLOGY@" ]
- then
- echo "<table align=center frame=void width=95%% cellpadding=5%%>"
- cat automatic/TOPOLOGY.list
- echo "</table>"
- elif [ "$LINE" = "@VATOM@" ]
- then
- echo "<table align=center frame=void width=95%% cellpadding=5%%>"
- cat automatic/VATOM.list
- echo "</table>"
- elif [ "$LINE" = "@TOOLS@" ]
- then
- echo "<table align=center frame=void width=95%% cellpadding=5%%>"
- cat automatic/TOOLS.list
- echo "</table>"
- elif [ "$LINE" = "@CODES@" ]
- then
-# echo "<table align=center frame=void width=95%% cellpadding=5%%>"
- cat automatic/codes.list
-# echo "</table>"
- else
- echo -E "$LINE"
- fi
- done
-} > ${file}PP.txt
+ sed "
+ /^ *@COLVAR@ *$/r automatic/COLVAR.list
+ /^ *@MCOLVAR@ *$/r automatic/MCOLVAR.list
+ /^ *@DCOLVAR@ *$/r automatic/DCOLVAR.list
+ /^ *@MCOLVARF@ *$/r automatic/MCOLVARF.list
+ /^ *@ANALYSIS@ *$/r automatic/ANALYSIS.list
+ /^ *@BIAS@ *$/r automatic/BIAS.list
+ /^ *@GLOSSARY@ *$/r automatic/GLOSSARY.list
+ /^ *@DICTIONARY@ *$/r automatic/DICTIONARY.list
+ /^ *@TUTORIALS@ *$/r automatic/TUTORIALS.list
+ /^ *@WEBSITES@ *$/r automatic/WEBSITES.list
+ /^ *@FUNCTION@ *$/r automatic/FUNCTION.list
+ /^ *@TOPOLOGY@ *$/r automatic/TOPOLOGY.list
+ /^ *@VATOM@ *$/r automatic/VATOM.list
+ /^ *@TOOLS@ *$/r automatic/TOOLS.list
+ /^ *@MODULES@ *$/r automatic/modules.list
+ /^ *@CODES@ *$/r automatic/codes.list
+" | grep -Ev '^ *"@[A-Z]*@" *$' > ${file}PP.txt
done
diff --git a/user-doc/go-doxygen b/user-doc/go-doxygen
index 4f8bc67a0..1e6d2b881 100755
--- a/user-doc/go-doxygen
+++ b/user-doc/go-doxygen
@@ -1,5 +1,20 @@
#! /bin/bash
+# Making sure that plumed executable is available
+echo -n "Searching for plumed ..."
+if plumed 2>/dev/null 1>/dev/null ; then
+ echo " found"
+else
+ echo " not found"
+ echo -n "Sourcing sourceme.sh and searching again ..."
+ if source ../sourceme.sh && plumed 2>/dev/null 1>/dev/null ; then
+ echo " found"
+ else
+ echo "ERROR: you should compile plumed first!"
+ exit 1
+ fi
+fi
+
{
cat Doxyfile
echo "PROJECT_NUMBER = \"$(plumed info --version)\""
--
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