--- mgltools-mglutil-1.5.4.cvs.20090603.orig/mglutil/TestUtil/publishPack.csh +++ mgltools-mglutil-1.5.4.cvs.20090603/mglutil/TestUtil/publishPack.csh @@ -1,4 +1,4 @@ -#!/bin/tcsh +#!/usr/bin/tcsh # 1) go to the mgl version of the packages # cd /mgl/python/share/lib/python2.5/site-packages/ --- mgltools-mglutil-1.5.4.cvs.20090603.orig/debian/control +++ mgltools-mglutil-1.5.4.cvs.20090603/debian/control @@ -0,0 +1,27 @@ +Source: mgltools-mglutil +Section: non-free/science +Priority: optional +Maintainer: Debian-Med Packaging Team +DM-Upload-Allowed: yes +XS-Autobuild: yes +Uploaders: Steffen Moeller , Sargis Dallakyan +Build-Depends: debhelper (>= 5.0.38), python-central (>= 0.5.6), cdbs (>= 0.4), python2.5-dev +Standards-Version: 3.8.1 +XS-Python-Version: 2.5 +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mgltools/pybabel/trunk/?rev=0&sc=0 +Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mgltools/pybabel/trunk/ +Homepage: http://mgltools.scripps.edu/ + +Package: mgltools-mglutil +XB-Python-Version: ${python:Versions} +Architecture: all +Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, mgltools-sff, python-pmw, python-zsi (>= 2.0) +Recommends: qhull-bin +Suggests: tcsh +Description: Molecular Graphics Laboratory utility collection + This package is part of the mgltools set of Python libraries which + provide an infrastructure for the analysis of protein structures and + their docking of chemical compounds. + . + It is needed by mgltools-autodocktools at runtime, providing a series + of utility functions on from parallel programming to statistics. --- mgltools-mglutil-1.5.4.cvs.20090603.orig/debian/rules +++ mgltools-mglutil-1.5.4.cvs.20090603/debian/rules @@ -0,0 +1,23 @@ +#!/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 + +export DEB_PYTHON_SYSTEM=pycentral + +include /usr/share/cdbs/1/rules/debhelper.mk +include /usr/share/cdbs/1/class/python-distutils.mk +#include /usr/share/cdbs/1/rules/simple-patchsys.mk + +clean:: + find . -name CVS -a -type d| xargs -r rm -r + find . -name "*.gif" | xargs -r chmod -x + find . -name "*.csh" | xargs -r sed -i -e 's%#!/bin/tcsh%#!/usr/bin/tcsh%' + find . -name "*.csh" -o -name "getlatest" | xargs -r chmod +x + rm -rf build build-stamp debian/Pmv --- mgltools-mglutil-1.5.4.cvs.20090603.orig/debian/watch +++ mgltools-mglutil-1.5.4.cvs.20090603/debian/watch @@ -0,0 +1,2 @@ +version=3 +http://mgltools.scripps.edu/downloads/.*mgltools_source_([0-9.]+)\.tar\.gz --- mgltools-mglutil-1.5.4.cvs.20090603.orig/debian/README.source +++ mgltools-mglutil-1.5.4.cvs.20090603/debian/README.source @@ -0,0 +1,22 @@ +Any package of the MGLtools suite +================================= + +The URL presented in debian/watch guides to a tar file +as the source distribution of the MGLtools set. That tar file +has a subdirectory MGLPACKS that comprises many tar files +itself, each representing a distinguished Python module. + +For the packaging of the AutoDockTool kit, the maintainers +have decided to package each module individually, to foster +the collaboration between similar applications. + +The maintainers of the Debian package may decide to release +interim version from the upstream CVS source repository, +instead of waiting for an official release by the upstream +developers. + +For further details on how to prepare the source for the +packaging, please refer to +http://svn.debian.org/wsvn/debian-med/trunk/packages/mgltools/BUILD?op=file&rev=0&sc=0 + + -- Steffen Moeller --- mgltools-mglutil-1.5.4.cvs.20090603.orig/debian/changelog +++ mgltools-mglutil-1.5.4.cvs.20090603/debian/changelog @@ -0,0 +1,35 @@ +mgltools-mglutil (1.5.4.cvs.20090603-1) unstable; urgency=low + + * New upstream version. + + -- Steffen Moeller Wed, 03 Jun 2009 11:48:21 +0200 + +mgltools-mglutil (1.5.4.cvs.20090528-1) unstable; urgency=low + + * New upstream version. + + -- Steffen Moeller Sat, 16 May 2009 00:51:24 +0200 + +mgltools-mglutil (1.5.4.cvs.20090514-1) unstable; urgency=low + + * New upstream version. + + -- Steffen Moeller Thu, 14 May 2009 21:46:35 +0200 + +mgltools-mglutil (1.5.4.cvs.20081126-1) unstable; urgency=low + + * New upstream version. + + -- Steffen Moeller Wed, 26 Nov 2008 14:43:12 +0100 + +mgltools-mglutil (1.5.2.cvs.20081109-1) unstable; urgency=low + + * New upstream version. + + -- Steffen Moeller Sun, 09 Nov 2008 15:02:32 +0100 + +mgltools-mglutil (1.5.2.cvs.20080731-1) unstable; urgency=low + + * Initial release, contributes to closing ITP #458811. + + -- Steffen Moeller Thu, 31 Jul 2008 21:59:58 +0200 --- mgltools-mglutil-1.5.4.cvs.20090603.orig/debian/compat +++ mgltools-mglutil-1.5.4.cvs.20090603/debian/compat @@ -0,0 +1 @@ +5 --- mgltools-mglutil-1.5.4.cvs.20090603.orig/debian/README.Debian +++ mgltools-mglutil-1.5.4.cvs.20090603/debian/README.Debian @@ -0,0 +1,27 @@ +autodocktools and other modules of MGLtools for Debian +====================================================== + +This package aims at providing the complete infrastructure for ligand +screening with Debian Linux. It is part of the MGL (Molecular Graphics +Labs at Scripps) Python tools set for the computational and visual +interaction of protein structures and their ligands. + +The Debian community shall thank Sargis Dallakyan +for his help in easing the compatibility with Debian by accepting our +patches and providing more himself. Also, the leader of the Molecular +Graphics Labs, Prof. Michael Sanner, is thanked for his support. + +Please be continously reminded that that closer a software gets towards +identifying or further describing functional compounds in medicine, +the harder it is to get access to free (as in beer) solutions. And it +certainly does not get much closer than with the AutoDockToolkit. To +have the AutoDockToolkit with Debian is special and good for the world +as it spawns the development of new drugs. We will need to wait a bit +longer for a DFSG compatible license, though. + +If you are a regular user of this package, your feedback to us +packagers would much appreciated. The packaging is organised +via the Debian-Med alioth project that has its own portal on +http://debian-med.alioth.debian.org. + + -- Steffen Moeller Sun, 20 Jul 2008 00:33:11 +0200 --- mgltools-mglutil-1.5.4.cvs.20090603.orig/debian/pycompat +++ mgltools-mglutil-1.5.4.cvs.20090603/debian/pycompat @@ -0,0 +1 @@ +2 --- mgltools-mglutil-1.5.4.cvs.20090603.orig/debian/copyright +++ mgltools-mglutil-1.5.4.cvs.20090603/debian/copyright @@ -0,0 +1,175 @@ +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 + + Guillaume Vareille + Michel Sanner + Sophie I. Coon + William Lindstrom + Daniel Stoffler + Sowjanya Karnati + Yong Zhao + + mglutil/process.py + + Peter Astrand + + mglutil/math/TensorModule.py and + mglutil/math/VectorModule.py + + Konrad Hinsen + + + /mglutil/regression/testplus*.py + + Frederic Giacometti + +Copyright: + + The respective authors and the Scripps Research Institute + Copyright 2000-2008 Michael Sanner + + mglutil/process.py is Copyright (c) 2003-2004 by + + Peter Astrand + + mglutil/math/TensorModule.py and + mglutil/math/VectorModule.py are Copyright 1997-1999 by + + Konrad Hinsen + + /mglutil/regression/testplus*.py + + Copyright (C) 2002 Frederic Bruno Giacometti . All Rights Reserved. + + + +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. + + An exceptional license was given for mglutil/process.py: + + By obtaining, using, and/or copying this software and/or its + associated documentation, you agree that you have read, understood, + and will comply with the following terms and conditions: + + Permission to use, copy, modify, and distribute this software and + its associated documentation for any purpose and without fee is + hereby granted, provided that the above copyright notice appears in + all copies, and that both that copyright notice and this permission + notice appear in supporting documentation, and that the name of the + author not be used in advertising or publicity pertaining to + distribution of the software without specific, written prior + permission. + + THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, + INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. + IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, INDIRECT OR + CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS + OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, + NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION + WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. + + mglutil/math/{Tensor,Vector}Module.py have a special license + + Permission to use, copy, modify, and distribute this software and its + documentation for any purpose and without fee is hereby granted, + provided that the above copyright notice appear in all copies and that + both that copyright notice and this permission notice appear in + supporting documentation. + + THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, + INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO + EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, INDIRECT OR + CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF + USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR + OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR + PERFORMANCE OF THIS SOFTWARE. + + and for + + mglutil/regression/testplus.py + mglutil/regression/testplus_before_2_1.py + + the license is + + The contents of this file are subject to the Mozilla Publics + License Version 1.1 (the "License"); you may not use this file + except in compliance with the License. You may obtain a copy of + the License at http://www.mozilla.org/MPL/ + + Software distributed under the License is distributed on an "AS + IS" basis, WITHOUT WARRANTY OF ANY KIND, either express or + implied. See the License for the specific language governing + rights and limitations under the License. + + The Initial Developer of the Original Code is Frederic Bruno Giacometti. + Portions created by Frederic Bruno Giacometti are + Copyright (C) 2002 Frederic Bruno Giacometti. All Rights Reserved. + Contributor: Frederic Giacometti, frederic.giacometti@arakne.com + + +The Debian packaging is (C) 2007-2008, Steffen Moeller and +is licensed under the GPL, see '/usr/share/common-licenses/GPL'.