Skip to content
Snippets Groups Projects
Commit 86393c8f authored by carlocamilloni's avatar carlocamilloni
Browse files

user-doc: new extract script ready for modules #253 

[makedoc]
parent f7b7f2fb
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
Showing
with 126 additions and 89 deletions
user-doc/extract
+ 126
− 89
View file @ 86393c8f
......@@ -7,52 +7,6 @@ rm -f errors
rm -rf automatic
mkdir automatic
long_version="$(../src/lib/plumed --no-mpi info --long-version)"
git_version="$(../src/lib/plumed --no-mpi info --git-version)"
cat > automatic/version.tmp << 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.tmp << EOF
Manual built on Travis CI for branch $TRAVIS_BRANCH.
EOF
fi
if test -d regtests ; then
cat >> automatic/version.tmp << 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 $2}')"
done > automatic/changes.tmp
if test "$make_pdfdoc" = yes ; then
cat > automatic/pdfmanual.tmp << \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
else
touch automatic/pdfmanual.tmp
fi
# Check for files that register actions with no documentation
for file in ../src/*/*.cpp
......@@ -71,8 +25,8 @@ 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 "- $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
......@@ -84,23 +38,48 @@ cat ../*/*/*cpp |
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" ){
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" ){
if(lfile!="") close(lfile)
lfile="automatic/"$2".list"
......@@ -114,6 +93,7 @@ awk 'BEGIN{gfile="automatic/GLOSSARY.list"; dfile="automatic/DICTIONARY.list"; }
print "\\page "$3" "$3 > output
# print "\\section "$3 >output
inside=2;
module=0
} else if ( $2=="INTERNAL" ){
if(output!="")close(output);
......@@ -125,6 +105,23 @@ awk 'BEGIN{gfile="automatic/GLOSSARY.list"; dfile="automatic/DICTIONARY.list"; }
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]".list"
printf "<tr> <td width=%s> \\subpage %s </td> <td>","5%", $3 >> lfile
}
}
}'
......@@ -136,6 +133,53 @@ for file in automatic/*.list ; do
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 tutorial pages
for file in ./tutorials/*.txt ; do
......@@ -161,18 +205,18 @@ done
# 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
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
echo "<tr> <td> $file </td>" >> automatic/MODULES.list
if [ "$dstr" == "default-on" ] ; then
echo "<td> on </td> </tr>" >> automatic/modules.list
echo "<td> on </td> </tr>" >> automatic/MODULES.list
else
echo "<td> off </td> </tr>" >> automatic/modules.list
echo "<td> off </td> </tr>" >> automatic/MODULES.list
defoff=1
fi
# # Generate documentation and accreditation on modules page
......@@ -217,7 +261,7 @@ do
done
fi
done
echo "</table>" >> automatic/modules.list
echo "</table>" >> automatic/MODULES.list
# fi
# Generate all the documentation from keywords
......@@ -258,11 +302,25 @@ do
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
# 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 $2}' | uniq`
for f in *.txt *.md
do
......@@ -275,38 +333,17 @@ file=${f%.$extension}
# first replace with the content of the files
# then grep out the special strings
cat $f |
sed "
/^ *@COLVAR@ *$/r automatic/COLVAR.list
/^ *@MCOLVAR@ *$/r automatic/MCOLVAR.list
/^ *@DCOLVAR@ *$/r automatic/DCOLVAR.list
/^ *@MFILTERS@ *$/r automatic/MFILTERS.list
/^ *@MTRANSFORMS@ *$/r automatic/MTRANSFORMS.list
/^ *@VOLUMES@ *$/r automatic/VOLUMES.list
/^ *@MCOLVARF@ *$/r automatic/MCOLVARF.list
/^ *@MCOLVARB@ *$/r automatic/MCOLVARB.list
/^ *@REWEIGHTING@ *$/r automatic/REWEIGHTING.list
/^ *@PRINTANALYSIS@ *$/r automatic/PRINTANALYSIS.list
/^ *@GRIDCALC@ *$/r automatic/GRIDCALC.list
/^ *@GRIDANALYSIS@ *$/r automatic/GRIDANALYSIS.list
/^ *@DIMRED@ *$/r automatic/DIMRED.list
/^ *@MATRIX@ *$/r automatic/MATRIX.list
/^ *@MATRIXF@ *$/r automatic/MATRIXF.list
/^ *@CONCOMP@ *$/r automatic/CONCOMP.list
/^ *@BIAS@ *$/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
/^ *@CODESL@ *$/r automatic/codesl.list
/^ *@VERSION@ *$/r automatic/version.tmp
/^ *@CHANGES@ *$/r automatic/changes.tmp
/^ *@PDFMANUAL@ *$/r automatic/pdfmanual.tmp
" | grep -Ev '^ *@[A-Z]*@ *$' > ${file}PP.$extension
cp $f ${file}PP.$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
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment