From c9dfd0a59bedc3a50c4d648d839e07512bb70dd8 Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gt@eider.asg>
Date: Fri, 6 Dec 2013 18:50:52 +0000
Subject: [PATCH] Added functionality to tell users what module a piece of code
is part of in user documentation
---
user-doc/Modules.txt | 52 ++++++---------------
user-doc/extract | 105 +++++++++++++++++++++++--------------------
2 files changed, 71 insertions(+), 86 deletions(-)
diff --git a/user-doc/Modules.txt b/user-doc/Modules.txt
index 0b6d9c560..f4996b6cb 100644
--- a/user-doc/Modules.txt
+++ b/user-doc/Modules.txt
@@ -1,47 +1,23 @@
/**
-@page mymodules Modules
+@page mymodules module
-PLUMED 2 is written and maintained by five core developers none of whom work full
-time on the maintanence and upkeep of the code. From our point of view it is thus
-desirable to keep the core of the code small. In addition, we are very keen that
-users who contribute functionality to PLUMED get the plaudits that they deserve.
-For these reasons many of PLUMED's more advanced functionalities are provided in
-modules that users can download. To download a module you simply change to the
-<c> plumed2/mymodules </c> directory and issue the following command:
+The functionality in PLUMED 2 is divided into a small number of modules. Some
+users may only wish to use a subset of the functionality available within the
+code while others may wish to use some of PLUMED's more complicated features.
+For this reason the plumed source code is divided into modules, which users can
+activate or deactivate to their hearts content.
-\verbatim
-./plumed-get-module.sh <name of module>
-\endverbatim
+- To activate a module add a file called modulename.on to the plumed2/src directory
+- To deactivate a module add a file called modulename.off to the plumed2/src directory
-The following optional modules can be added to PLUMED 2:
+Obviously, in the above instructions modulename should be replaced by the name of the
+module that you would like to activate or deactivate.
-@MODULES@
-
-\section addmodule Adding a module
-
-If you have a PLUMED module that you would like us to advertise on the website
-you should copy the directory structure from <c> plumed2/template-module </c>
-as well as all the files inside that directory and place your source and regtest
-files in appropriate directories. You are responsible for finding a suitable
-web repository to host the code that you have developed (we use http://www.assembla.com
-for PLUMED). You do not need to give us write access to your repository as ensuring that
-your code keeps working with any new release of PLUMED is YOUR responsibility.
-
-Once you are ready to release your code simply send any email to one of the developers
-with a txt file that contains the following information in the following format:
-
-\verbatim
-NAME: <the name of your module>
+Some modules are active by default in the version of PLUMED 2 that you download from
+the website while others are inactive. The following lists all of the modules that
+are available in plumed and tells you whether or not they are active by default.
-AUTHOR: <the list of people involved in the development of the module>
-
-REPOSITORY: <the command that retreives the code e.g. git clone git@git.assembla.com:plumed2.git>
-
-DESCRIPTION:
-
-<a short description of what it is your module calculates>
-<citations and equations can be included using the usual doxygen commands>
-\endverbatim
+@MODULES@
*/
diff --git a/user-doc/extract b/user-doc/extract
index 6443e5d4d..a8944b12d 100755
--- a/user-doc/extract
+++ b/user-doc/extract
@@ -105,53 +105,62 @@ 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
- for file in `ls ../mymodules/available-modules/`
- do
- #Â Check if module has been installed
- if [ -d "../mymodules/$file" ] ; then
- # 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/"$file" >> automatic/mymodules.list
- echo "</td> </tr> </table>" >> automatic/mymodules.list
- echo >> automatic/mymodules.list
- echo >> automatic/mymodules.list
-
- # Find src files in module and add a link to the module description
- for srcfile in `ls ../mymodules/"$file"/src/*cpp` ; do
- ndocs=`grep PLUMEDOC "$srcfile" | 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 "\section $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 \ref $file module </b>"
- echo "</td> </tr> </table>"
- else
- echo "$LINE"
- fi
- done
- } > automatic/"$docfile"1.tmp
- mv automatic/"$docfile"1.tmp automatic/"$docfile".tmp
- done
- done
- fi
- done
-fi
+# if [ -d ../mymodules ] ; then
+# sed -i '' -e 's/type="user" visible="no" url="mymodules.html"/type="user" visible="yes" url="mymodules.html"/' PlumedLayout.xml
+echo "<table align=center frame=void width=65%% cellpadding=5%%>" > automatic/modules.list
+echo "<tr> <td> <b> Module name </b> </td> <td> <b> Default behavior </b> </td> </tr>" >> automatic/modules.list
+for file in `ls ../src/*/module.type | sed -e 's/..\/src\///' | sed -e 's/\/module.type//'`
+do
+ dstr=`head ../src/$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
+ 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/"$file" >> automatic/mymodules.list
+# echo "</td> </tr> </table>" >> automatic/mymodules.list
+# echo >> automatic/mymodules.list
+# echo >> automatic/mymodules.list
+
+ # Find src files in module and add a link to the module description
+ for srcfile in `ls ../src/"$file"/*cpp` ; do
+ ndocs=`grep PLUMEDOC "$srcfile" | 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 "section $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
+ fi
+done
+echo "</table>" >> automatic/modules.list
+# fi
# Generate all the documentation from keywords
source ../sourceme.sh
@@ -237,7 +246,7 @@ cat $file.txt |
echo "</table>"
elif [ "$LINE" = "@MODULES@" ]
then
- cat automatic/mymodules.list
+ cat automatic/modules.list
elif [ "$LINE" = "@FUNCTION@" ]
then
echo "<table align=center frame=void width=95%% cellpadding=5%%>"
--
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