debian/0000755000000000000000000000000012152161621007163 5ustar debian/control0000644000000000000000000000227012146437726010606 0ustar Source: mgltools-viewerframework Section: non-free/science Priority: optional Maintainer: Debian Med Packaging Team XS-Autobuild: yes Uploaders: Steffen Moeller , Sargis Dallakyan , Thorsten Alteholz , Andreas Tille Build-Depends: debhelper (>= 8), python-all (>= 2.6) Standards-Version: 3.9.4 XS-Python-Version: >= 2.5 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mgltools/viewerframework/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mgltools/viewerframework/trunk/ Homepage: http://mgltools.scripps.edu/ Package: mgltools-viewerframework XB-Python-Version: ${python:Versions} Architecture: all Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, mgltools-bhtree, idle Description: ViewerFramework supports building visualization applications This framework provides support for loading dynamically commands from libraries as they are needed. It has been designed to be specialized and extended in modular way. ViewerFramework is used to build Python Molecular Viewer and AutoDockTools that are distributed with MGLTools. debian/pycompat0000644000000000000000000000000210733046600010734 0ustar 2 debian/copyright0000644000000000000000000001045312152154546011131 0ustar This package was debianized by Steffen Moeller on Thu, 10 Jul 2008 00:03:24 +0200 It was downloaded from http://mgltools.scripps.edu Upstream Authors: The main development is performed by the researchers and developers at the Molecular Graphics Laboratory led by Michael F. Sanner with contributions by Ruth Huey Sophie Coon Kevin Chan Guillaume Vareille Michael F. Sanner Copyright: The respective authors and the Scripps Research Institute Copyright 1989-2013 Michael Sanner License: All files distributed or redistributed in this package are subject to the here presented license, regardless of the information that is explicitly stated or omitted in the respective files themselves. The original copyright holders have made respective agreements regarding this redistribution. 1. Grant Of Limited License; Software Use Restrictions. The programs received by you will be used only for NON COMMERCIAL purposes. This license is issued to you as an individual. For COMMERCIAL use done with the software please contact Michel F. Sanner for details about commercial usage license agreements. For any question regarding license agreements, please contact Michel Sanner: TSRI, Molecular Biology Department, TCP 26, 10550 North Torrey Pines Road, La Jolla, CA 92037 sanner@scripps.edu tel (858) 784-7742 fax (858) 784-2341 2. COMMERCIAL USAGE is defined as revenues generating activities. These include using this software for consulting activities and selling applications built on top of, or using this software. Scientific research in an academic environment and teaching are considered NON COMMERCIAL. 3. Copying Restrictions. You will not sell or otherwise distribute commercially these programs or derivatives to any other party, whether with or without consideration. 4. Ownership of Software. You will not obtain, and will not attempt to obtain copyright coverage thereon without the express purpose written consent of The Scripps Research Institute and Dr. Sanner. 5. IN NO EVENT SHALL THE AUTHORS OR DISTRIBUTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OF THIS SOFTWARE, ITS DOCUMENTATION, OR ANY DERIVATIVES THEREOF, EVEN IF THE AUTHORS HAVE BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 6. THE AUTHORS AND DISTRIBUTORS SPECIFICALLY DISCLAIM ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND NON-INFRINGEMENT. THIS SOFTWARE IS PROVIDED ON AN "AS IS" BASIS, AND THE AUTHORS AND DISTRIBUTORS HAVE NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS. The Debian packaging is Copyright (C) 2007-2008, Steffen Moeller and is licensed under the GPL, see '/usr/share/common-licenses/GPL'. In addition to the license above, the Debian project also got the explicit permission from the copyright owner to distribute the software: Date: Mon, 20 May 2013 10:07:13 -0700 From: Michel Sanner To: Thorsten Alteholz Cc: "annao >> Anna Omelchenko" Subject: Re: mgltools license Hello Thorsten Sorry for not following up this earlier. We are delighted to have Debian include the MGLTools in their distribution. So you need us to amend the License text or will this email suffice ? Thanks -- ----------------------------------------------------------------------- o / Michel F. Sanner Ph.D. The Scripps Research Institute o Associate Professor Department of Molecular Biology \ 10550 North Torrey Pines Road o Tel. (858) 784-7742 La Jolla, CA 92037, TPC 26 / Fax. (858) 784-2341 o sanner@scripps.edu http://www.scripps.edu/~sanner ----------------------------------------------------------------------- debian/changelog0000644000000000000000000000731312152154546011051 0ustar mgltools-viewerframework (1.5.7~rc1~cvs.20130519-1) unstable; urgency=low * New upstream version. * debian/control: bump standard to 3.9.4 (no changes) * debian/control: remove DM-Upload-Allowed * debian/copyright: add permission for debian to distribute mgltools -- Thorsten Alteholz Sun, 19 May 2013 12:00:00 +0200 mgltools-viewerframework (1.5.6~rc3~cvs.20120206-2) unstable; urgency=low * Fixing assignment to self.__debug__ (Closes: #659273). -- Steffen Moeller Fri, 10 Feb 2012 10:53:15 +0100 mgltools-viewerframework (1.5.6~rc3~cvs.20120206-1) unstable; urgency=low * New upstream version. * debian/control: vcs fields corrected -- Thorsten Alteholz Mon, 06 Feb 2012 18:00:00 +0100 mgltools-viewerframework (1.5.6~rc2+cvs.20111222-1) unstable; urgency=low * New upstream version. * Changed runtime dependency to idle (from idle|python2.6) -- Steffen Moeller Thu, 22 Dec 2011 17:10:12 +0100 mgltools-viewerframework (1.5.6~rc2+cvs.20110926-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Tue, 27 Sep 2011 10:58:16 +0200 mgltools-viewerframework (1.5.6~rc1+cvs.20110617-2) unstable; urgency=low * Correcting dependencies. -- Steffen Moeller Thu, 23 Jun 2011 21:35:29 +0200 mgltools-viewerframework (1.5.6~rc1+cvs.20110617-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Fri, 17 Jun 2011 01:20:31 +0200 mgltools-viewerframework (1.5.4.cvs.20100912-2) unstable; urgency=low [ Thorsten Alteholz ] * Build-Depends: debhelper (>= 8) * debian/source/format: 3.0 (quilt) * debian/control: Build-Depends: python-all (>= 2.6) to enable python-support2 * debian/rules: switch to short dh syntax which makes dh_python2 easy (Closes: #616901) * Suppress lintian warning about duplicate license file [ Andreas Tille ] * Added myself to Uploaders * debian/compat: 8 * debian/rules: No need for overriding dh_clean * Apply patch by Barry Warsaw to fix byte compilation issue with Python 2.7 (Thanks to Barry) (Closes: #590821) (LP: #685476) -- Andreas Tille Fri, 10 Jun 2011 09:58:41 +0200 mgltools-viewerframework (1.5.4.cvs.20100912-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Sun, 12 Sep 2010 00:20:31 +0200 mgltools-viewerframework (1.5.4.cvs.20090603-1.1) unstable; urgency=low * Non-maintainer upload. * Allow byte-compilation for Python >= 2.5 (closes: #586850) -- Piotr Ożarowski Wed, 30 Jun 2010 22:38:16 +0200 mgltools-viewerframework (1.5.4.cvs.20090603-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Wed, 03 Jun 2009 11:48:26 +0200 mgltools-viewerframework (1.5.4.cvs.20090528-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Sat, 16 May 2009 00:51:33 +0200 mgltools-viewerframework (1.5.4.cvs.20090514-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Thu, 14 May 2009 21:46:47 +0200 mgltools-viewerframework (1.5.4.cvs.20081126-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Wed, 26 Nov 2008 14:43:21 +0100 mgltools-viewerframework (1.5.2.cvs.20081109-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Sun, 09 Nov 2008 15:02:42 +0100 mgltools-viewerframework (1.5.2.cvs.20080731-1) unstable; urgency=low * Initial release, contributes to closing ITP #458811. -- Steffen Moeller Thu, 31 Jul 2008 22:00:07 +0200 debian/compat0000644000000000000000000000000211574350230010364 0ustar 8 debian/watch0000644000000000000000000000012511041154622010211 0ustar version=3 http://mgltools.scripps.edu/downloads/.*mgltools_source_([0-9.]+)\.tar\.gz debian/get-orig-source/0000755000000000000000000000000012152161621012176 5ustar debian/get-orig-source/rc-version0000644000000000000000000000000512146202375014210 0ustar ~rc1 debian/get-orig-source/current-branch0000644000000000000000000000001112146202375015033 0ustar rc-1-5-7 debian/get-orig-source/get-orig-source0000755000000000000000000000555712145665571015172 0ustar #!/bin/bash # # usage: get-orig-source # e.g.: get-orig-source VolumeDIST rc-1-5-6 ~rc1 # package=$1 branch=$2 rcversion=$3 REMOTECVSROOT=:pserver:anonymous@mgl1.scripps.edu:2401/opt/cvs CVS=/usr/bin/cvs MGLTOOLSCVS=../../mgltools-cvs # Expected by svn-buildpackage as 'tarballs' TARDIR=../tarballs PREFIX="mgltools-" if [ "$package" == "AutoDockToolsDIST" ]; then PREFIX="" fi DEBPACKAGE=$PREFIX`echo $package|sed "s/DIST//g"| tr 'A'-'Z' 'a'-'z'` # do some stuff echo "I: get $package (-> $DEBPACKAGE) from branch $branch" loginDone=`grep "$REMOTECVSROOT" ~/.cvspass|wc -l` if [ "$loginDone" == "0" ]; then $CVS -d$REMOTECVSROOT login fi if [ -d "$MGLTOOLSCVS" ]; then echo "I: cvs directory already available" else echo "I: create directory '$MGLTOOLSCVS' to store new CVS checkout" mkdir "$MGLTOOLSCVS" fi if [ -d $MGLTOOLSCVS/$package ]; then echo "I: ... checkout already done" if [ -r "$MGLTOOLSCVS/$package/CVS/Tag" ]; then echo "W: check whether this is the correct tag: `cat $MGLTOOLSCVS/$package/CVS/Tag`" else echo "W: no tag file found. You may be working on the trunk, not on the release branch. Is that what you want?" fi sleep 3 (cd $MGLTOOLSCVS/$package && $CVS -z3 update -d) else echo "I: ... now performing checkout" (cd "$MGLTOOLSCVS" && $CVS -z3 -d$REMOTECVSROOT co -r $branch $package) fi version=`echo $branch|sed "s/rc-//g"|tr '-' '.'` DATE=`date +"%Y%m%d"` if [ -f $MGLTOOLSCVS/build-for-date ]; then DATE=`cat $MGLTOOLSCVS/build-for-date` fi if [ -z ${rcversion} ]; then echo "I: no rc but real release" origFilename=${DEBPACKAGE}_${version}${rcversion}.orig.tar.gz origDirname=${DEBPACKAGE}-${version}${rcversion} else origFilename=${DEBPACKAGE}_${version}${rcversion}~cvs.${DATE}.orig.tar.gz origDirname=${DEBPACKAGE}-${version}${rcversion}~cvs.${DATE} fi echo "I: Filename of origFile: $origFilename" cd "$MGLTOOLSCVS" if [ -d "$TARDIR" ]; then echo "I: directory for orig tarballs already available" else echo "I: creating directory for irog tarballs: '$TARDIR'" mkdir "$TARDIR" fi if [ -f "$TARDIR"/"$origFilename" ]; then echo "I: delete old file '$origFilename' " rm "$TARDIR"/"$origFilename" fi if [ -n "$origDirname" -a -d "$origDirname" ]; then echo "W: Amazingly, temporary directory name '$origDirname' is already existing. Stop this script if this shall not be removed -- within 3 seconds." sleep 3 rm -r "$origDirname" fi echo "I: remove some files in '$package' " cd $package echo "I: ... *.dll " find . -name *.dll -a -type f| xargs -r rm -rf cd .. echo "I: Temporarily renaming and taring $package " echo " --> $MGLTOOLSCVS/$TARDIR/$origFilename" mv "$package" "$origDirname" echo -n "I: Number of files in package: " GZIP=-9 tar --exclude CVS -czvf "$TARDIR/$origFilename" "$origDirname" | wc -l mv "$origDirname" "$package" echo "I: done" debian/get-orig-source/README0000644000000000000000000000066611600144512013063 0ustar This directory contains all scripts/data/whatsoever to automatically build mgltools-packages. Using svn externals, this directory appears in the debian directory of each package. So in case you need to change anything (like the branch to be used), there is only one place to make the modifications. Command in trunk/debian: svn propset svn:externals \ '^/trunk/packages/mgltools/mgltools-external-get-orig-source get-orig-source' . debian/get-orig-source/rc-version.ok0000644000000000000000000000000512145647165014631 0ustar ~rc3 debian/docs0000644000000000000000000000003110733046600010032 0ustar ViewerFramework/RELNOTES debian/patches/0000755000000000000000000000000012152161621010612 5ustar debian/patches/series0000644000000000000000000000007512146437726012050 0ustar #20.05.2013, ta, applied upstream: do_not_assign_debug.patch debian/patches/do_not_assign_debug.patch0000644000000000000000000000136412146437726015652 0ustar Descritpion: s/__debug__/debug/ was presumably intended by upstream in the first place. Author: Steffen Moeller Index: ViewerFramework-1.5.6~rc3~cvs.20120206/ViewerFramework/VF.py =================================================================== --- ViewerFramework-1.5.6~rc3~cvs.20120206.orig/ViewerFramework/VF.py 2011-10-13 19:28:43.000000000 +0200 +++ ViewerFramework-1.5.6~rc3~cvs.20120206/ViewerFramework/VF.py 2012-02-10 10:51:58.896208928 +0100 @@ -285,7 +285,7 @@ global __debug__ self.withShell = withShell self.trapExceptions = trapExceptions - self.__debug__ = 0 + self.debug = 0 # create a socket communication object try: self.socketComm = Comm() debian/README.source0000644000000000000000000000024011640327245011345 0ustar mgltools-viewerframework ======================== A patch for Python 2.7 compatibility was apparently adopted by upstream, albeit in a slightly different way. debian/rules0000755000000000000000000000075511600425310010245 0ustar #!/usr/bin/make -f # -*- makefile -*- # debian/rules for mgltools-viewerframework # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 BRANCH=`cat debian/get-orig-source/current-branch` RCVERSION=`cat debian/get-orig-source/rc-version` SRC=ViewerFrameworkDIST %: dh $@ --with python2 override_dh_clean: dh_clean find . -name *.png -o -name *.pdb -o -name *.gif -exec chmod 644 '{}' \; get-orig-source: ./debian/get-orig-source/get-orig-source $(SRC) $(BRANCH) $(RCVERSION) debian/mgltools-viewerframework.lintian-overrides0000644000000000000000000000017611573211757017640 0ustar # the license is in debian/copyright but upstream wants to have it there as well mgltools-viewerframework: extra-license-file debian/source/0000755000000000000000000000000012152161621010463 5ustar debian/source/format0000644000000000000000000000001411572471434011704 0ustar 3.0 (quilt)