debian/0000755000000000000000000000000012234712670007172 5ustar debian/patches/0000755000000000000000000000000012234706766010632 5ustar debian/patches/series0000644000000000000000000000006412214165365012037 0ustar ch5m3d.conf.patch Makefile.patch documentation.book debian/patches/Makefile.patch0000644000000000000000000000113612207213201013342 0ustar --- /dev/null +++ b/Makefile @@ -0,0 +1,27 @@ +DESTDIR = +MINIFIED = ch5m3d.js qchem/ch5m3dq.js + +all: $(MINIFIED) + +ch5m3d.js: ch5m3d.full.js + cat ch5m3d.js.license_header > $@ + yui-compressor $< >> $@ + +qchem/ch5m3dq.js: qchem/ch5m3dq.full.js + cat qchem/ch5m3dq.js.license_header > $@ + yui-compressor $< >> $@ + +variations/ch5m3dv.min.js: variations/ch5m3dv.js + yui-compressor -o $@ $< + +documentation.pdf: + htmldoc --batch documentation.book + +clean: + rm -f $(MINIFIED) + find . -name "*~" -exec rm {} \; + +install: + # nothing: debian/install does the work + +.PHONY: all clean install debian/patches/ch5m3d.conf.patch0000644000000000000000000000042712234706766013665 0ustar --- /dev/null +++ b/ch5m3d.conf @@ -0,0 +1,9 @@ +# chemical-structures setup for Apache 2.4 +# with no virtual host + +Alias /ch5m3d /usr/share/javascript/ch5m3d/ + + + AllowOverride None + Require all granted + debian/patches/documentation.book0000644000000000000000000000153312207212767014352 0ustar --- /dev/null +++ b/documentation.book @@ -0,0 +1,3 @@ +#HTMLDOC 1.8.27 +-t pdf14 -f "./documentation.pdf" --book --toclevels 3 --no-numbered --toctitle "Table of Contents" --title --linkstyle underline --size Universal --left 1.00in --right 0.50in --top 0.50in --bottom 0.50in --header .t. --header1 ... --footer h.1 --nup 1 --tocheader .t. --tocfooter ..i --portrait --color --no-pscommands --no-xrxcomments --compression=1 --jpeg=100 --fontsize 11.0 --fontspacing 1.2 --headingfont Helvetica --bodyfont Times --headfootsize 11.0 --headfootfont Helvetica --charset iso-8859-1 --links --embedfonts --pagemode outline --pagelayout single --firstpage c1 --pageeffect none --pageduration 10 --effectduration 1.0 --no-encryption --permissions all --owner-password "" --user-password "" --browserwidth 680 --no-strict --no-overflow +doc/documentation.book.html debian/control0000644000000000000000000000255612234706476010614 0ustar Source: ch5m3d Section: web Priority: extra Maintainer: Georges Khaznadar Build-Depends: debhelper (>= 8.0.0), yui-compressor, dh-apache2 Standards-Version: 3.9.4 Homepage: http://ch5m3d.sourceforge.net/ Package: ch5m3d Architecture: all Recommends: apache2|httpd Depends: ${misc:Depends} Description: create and visualize 3-dimensional drawings of simple molecules This program provides a web interface which has been developed to allow users to create and visualize 3-dimensional drawings of simple molecules without requiring the download of any additional software. In addition to creating structures, users can also load existing XYZ formatted files (such as those generated by Open Babel) containing 3-dimensional coordinates. . Once molecules are created or read from a file, users can examine geometry information (bond lengths, angles, and dihedral angles) and modify these structures. Routines to perform a crude geometry optimization and a simple calculation of atomic charges are also available. . This web interface relies on HTML5 (in particular, the HTML5 Canvas), and as such requires a modern web browser to run. The advantage of this approach is the no additional plugins or Java is required to use this program. Support for mobile devices is currently only partially implemented, but is planned to be included in future versions. debian/get-orig-source.sh0000644000000000000000000000162012207207410012527 0ustar #!/bin/sh set -ex UPSTREAM_VERSION=$2 ORIG_ZIP=$3 WORKING_DIR=$(dirname ${ORIG_ZIP}) ORIG_TARBALL=ch5m3d_${UPSTREAM_VERSION}+dfsg.orig.tar.gz PKGDIR=../ch5m3d-${UPSTREAM_VERSION}+dfsg TMPDIR=$(mktemp -d --tmpdir=${WORKING_DIR}) cd ${TMPDIR} unzip -qq ${ORIG_ZIP} mkdir ${PKGDIR} ######################################################## # remove the uglified javascript, but keep its license # ######################################################## sed '/function/,$ d' ch5m3d/ch5m3d.js > ch5m3d/ch5m3d.js.license_header rm ch5m3d/ch5m3d.js sed '/function/,$ d' ch5m3d/qchem/ch5m3dq.js > ch5m3d/qchem/ch5m3dq.js.license_header rm ch5m3d/qchem/ch5m3dq.js ######################################################## mv ch5m3d/* ${PKGDIR} cd .. tar czf ${ORIG_TARBALL} $(basename ${PKGDIR}) rm -rf $(basename ${TMPDIR}) $(basename ${ORIG_ZIP}) $(basename ${PKGDIR}) echo "Created ../${ORIG_TARBALL}" exit 0 debian/compat0000644000000000000000000000000212145467452010376 0ustar 8 debian/Readme.source0000644000000000000000000000076512207214173011614 0ustar Processing the source package for Debian ======================================== The source file is retreived from Sourceforge.net thanks to the files debian/watch and debian/get-orig-source.sh To get a new souce tarball, just run 'uscan'. This gets a ZIP file from sourforge.net... Uglified javascripts are removed from the upstream tree, but the licenses in their headers are fed into files named *.js.license_header, then the tree is compressed back to a dfsg-suffixed debian source package. debian/watch0000644000000000000000000000020312207204650010210 0ustar version=3 opts=dversionmangle=s/\+dfsg$// \ http://sf.net/ch5m3d/ch5m3d\.(.+)\.zip \ debian /bin/sh debian/get-orig-source.sh debian/copyright0000644000000000000000000000214312145526172011126 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: ch5m3d Source: http://sourceforge.net/projects/ch5m3d/files/ch5m3d.1.0.zip/download Files: * Copyright: 2013 Clarke Earley License: GPL-3.0+ Files: debian/* Copyright: 2013 Georges Khaznadar License: GPL-3.0+ License: GPL-3.0+ This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. . This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program. If not, see . . On Debian systems, the complete text of the GNU General Public License version 3 can be found in "/usr/share/common-licenses/GPL-3". debian/source/0000755000000000000000000000000012145467452010500 5ustar debian/source/format0000644000000000000000000000001412145467452011706 0ustar 3.0 (quilt) debian/postrm0000644000000000000000000000247112234712656010451 0ustar #!/bin/sh # postrm script for ch5m3d # # see: dh_installdeb(1) set -e # summary of how this script can be called: # * `remove' # * `purge' # * `upgrade' # * `failed-upgrade' # * `abort-install' # * `abort-install' # * `abort-upgrade' # * `disappear' # # for details, see http://www.debian.org/doc/debian-policy/ or # the debian-policy package case "$1" in purge) if [ -e /usr/share/apache2/apache2-maintscript-helper ] ; then . /usr/share/apache2/apache2-maintscript-helper apache2_invoke disconf ch5m3d.conf fi rm -f /etc/apache2/conf-available/ch5m3d.conf ;; remove|upgrade|failed-upgrade|abort-install|abort-upgrade|disappear) if [ -e /usr/share/apache2/apache2-maintscript-helper ] ; then . /usr/share/apache2/apache2-maintscript-helper apache2_invoke disconf ch5m3d.conf fi ;; *) echo "postrm called with unknown argument \`$1'" >&2 exit 1 ;; esac # dh_installdeb will replace this with shell code automatically # generated by other debhelper scripts. #DEBHELPER# exit 0 debian/dirs0000644000000000000000000000006712145524043010055 0ustar etc/apache2/conf-available usr/share/javascript/ch5m3d debian/install0000644000000000000000000000060212214165542010557 0ustar ch5m3d.css usr/share/javascript/ch5m3d ch5m3d.js usr/share/javascript/ch5m3d ch5m3d.full.js usr/share/javascript/ch5m3d doc usr/share/javascript/ch5m3d documentation.pdf usr/share/javascript/ch5m3d index.html usr/share/javascript/ch5m3d qchem usr/share/javascript/ch5m3d variations usr/share/javascript/ch5m3d molecules usr/share/javascript/ch5m3d ch5m3d.conf etc/apache2/conf-availabledebian/postinst0000644000000000000000000000215012234712365010777 0ustar #!/bin/sh # postinst script for ch5m3d # # see: dh_installdeb(1) set -e # summary of how this script can be called: # * `configure' # * `abort-upgrade' # * `abort-remove' `in-favour' # # * `abort-remove' # * `abort-deconfigure' `in-favour' # `removing' # # for details, see http://www.debian.org/doc/debian-policy/ or # the debian-policy package case "$1" in configure) if [ -e /usr/share/apache2/apache2-maintscript-helper ] ; then . /usr/share/apache2/apache2-maintscript-helper apache2_invoke enconf ch5m3d.conf fi ;; abort-upgrade|abort-remove|abort-deconfigure) ;; *) echo "postinst called with unknown argument \`$1'" >&2 exit 1 ;; esac # dh_installdeb will replace this with shell code automatically # generated by other debhelper scripts. #DEBHELPER# exit 0 debian/changelog0000644000000000000000000000317612234706355011056 0ustar ch5m3d (1.2.5+dfsg-1) unstable; urgency=low * upgraded to the newest upstream version * made changes to comply with apache2 policy (version 2.4) -- Georges Khaznadar Fri, 01 Nov 2013 12:06:34 +0100 ch5m3d (1.2.4+dfsg-2) unstable; urgency=low * modified the place of the configuration file for Apache. Closes: #722462 * added a build-dependency on dh-apache2, and a --with-apache2 switch in debian/rules -- Georges Khaznadar Thu, 12 Sep 2013 00:17:29 +0200 ch5m3d (1.2.4+dfsg-1) unstable; urgency=low * created a debian/watch file and a debian/get-orig-src.sh script * documented that script's usage in debian/Readme.source * modified Makefile and debian/rules to fit with the new upstream filenames * added the file documentation.book to generate documentation.pdf by a batch command using 'htmldoc'. I did not add htmldoc to the set of build-dependencies, since the original pdf file is kept. It can be generated by calling 'make documentation.pdf'. -- Georges Khaznadar Tue, 27 Aug 2013 22:49:29 +0200 ch5m3d (1.2.1-1) unstable; urgency=low * Initial release (Closes: #716873) * Created a watch file and a script debian/myuupdate to refresh the package when necessary * Created a file apache.conf to let users access the library at an absolute path (typically http://localhost/javascript/ch5m3d/) * prettified the javascript source * added a Makefile to create smaller minified javascript code * introduced a build-dependency on yui-compressor -- Georges Khaznadar Sat, 13 Jul 2013 18:37:38 +0200 debian/rules0000755000000000000000000000111112214165760010244 0ustar #!/usr/bin/make -f # -*- makefile -*- # Sample debian/rules that uses debhelper. # This file was originally written by Joey Hess and Craig Small. # As a special exception, when this file is copied by dh-make into a # dh-make output file, you may use that output file without restriction. # This special exception was added by Craig Small in version 0.37 of dh-make. # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 %: dh $@ --with apache2 override_dh_install: dh_install find $(DESTDIR) -name COPYING.txt -exec rm {} \; find $(DESTDIR) -type f -exec chmod -x {} \;