[med-svn] r2258 - trunk/packages/mgltools/geomutils/trunk/debian

Fri Jul 18 20:27:39 UTC 2008

Author: smoe-guest
Date: 2008-07-18 20:27:38 +0000 (Fri, 18 Jul 2008)
New Revision: 2258

Modified:
   trunk/packages/mgltools/geomutils/trunk/debian/README.Debian
   trunk/packages/mgltools/geomutils/trunk/debian/README.source
   trunk/packages/mgltools/geomutils/trunk/debian/changelog
   trunk/packages/mgltools/geomutils/trunk/debian/copyright
Log:
Revision of copyright file, inspection of all files for their copyright.


Modified: trunk/packages/mgltools/geomutils/trunk/debian/README.Debian
===================================================================

--- trunk/packages/mgltools/geomutils/trunk/debian/README.Debian	2008-07-18 16:30:27 UTC (rev 2257)
+++ trunk/packages/mgltools/geomutils/trunk/debian/README.Debian	2008-07-18 20:27:38 UTC (rev 2258)
@@ -1,23 +1,27 @@
-mgltools-pybabel
-================
+mgltools-geomutils for Debian
+=============================
 
-This package 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.  Lintian warns about the
-copyright-without-copyright-notice, which is an artifact of the source tar
-file being extracted from a larger tar file that represents the MGLtools.
+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 constraint to non-commercial research clearly renders the MGLtools
-to be non-free and one could argue for it being acceptable for Debian at
-all. SM was in contact with Sargis from the upstream developers and it
-was confirmed that upstream is eager to see Debian packages to become
-a reality. Actually, this may be a good opportunity to thank Sargis
-Dallakyan <sargis at scripps.edu> for his help in easing the compatibility
-with Debian by accepting our patches and providing more himself.
+The Debian community shall thank Sargis Dallakyan <sargis at scripps.edu>
+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 <moeller at debian.org>
+ -- Steffen Moeller <moeller at debian.org>  Thu, 10 Jul 2008 00:06:50 +0200

Modified: trunk/packages/mgltools/geomutils/trunk/debian/README.source
===================================================================
--- trunk/packages/mgltools/geomutils/trunk/debian/README.source	2008-07-18 16:30:27 UTC (rev 2257)
+++ trunk/packages/mgltools/geomutils/trunk/debian/README.source	2008-07-18 20:27:38 UTC (rev 2258)
@@ -1,5 +1,5 @@
-PyBabel
-=======
+mgltools-geomutils
+==================
 
 The URL presented in debian/watch guides to a tar file 
 as the source distribution of the MGLtools set. That tar file
@@ -10,4 +10,13 @@
 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 <moeller at debian.org>

Modified: trunk/packages/mgltools/geomutils/trunk/debian/changelog
===================================================================
--- trunk/packages/mgltools/geomutils/trunk/debian/changelog	2008-07-18 16:30:27 UTC (rev 2257)
+++ trunk/packages/mgltools/geomutils/trunk/debian/changelog	2008-07-18 20:27:38 UTC (rev 2258)
@@ -1,3 +1,21 @@
+mgltools-geomutils (5.2.cvs.20080713-1) experimental; urgency=low
+
+  * New upstream version.
+
+ -- Steffen Moeller <moeller at debian.org>  Sun, 13 Jul 2008 01:48:46 +0200
+
+mgltools-geomutils (5.2.cvs.20080713) experimental; urgency=low
+
+  * New upstream version.
+
+ -- Steffen Moeller <moeller at debian.org>  Sun, 13 Jul 2008 01:47:41 +0200
+
+mgltools-geomutils (5.2.cvs.20080713) experimental; urgency=low
+
+  * New upstream version.
+
+ -- Steffen Moeller <moeller at debian.org>  Sun, 13 Jul 2008 01:46:39 +0200
+
 mgltools-geomutils (1.5.1-1) experimental; urgency=low
 
   * Initial release.

Modified: trunk/packages/mgltools/geomutils/trunk/debian/copyright
===================================================================
--- trunk/packages/mgltools/geomutils/trunk/debian/copyright	2008-07-18 16:30:27 UTC (rev 2257)
+++ trunk/packages/mgltools/geomutils/trunk/debian/copyright	2008-07-18 20:27:38 UTC (rev 2258)
@@ -1,46 +1,98 @@
 This package was debianized by Steffen Moeller <moeller at debian.org> on
-Thu, 20 Dec 2007 16:27:31 +0100.
+Fri, 18 Jul 2008 21:57:59 +0200
 
 It was downloaded from http://mgltools.scripps.edu
 
 Upstream Authors: 
 
-    Molecular Graphics Laboratory <mgltools at scripps.edu>
+    The main development is performed by the researchers
+    and developers at the
 
+	    Molecular Graphics Laboratory <mgltools at scripps.edu>
+
+    led by
+
+	    Michael F. Sanner <sanner at scripps.edu>
+
+    with contributions by 
+
+	    Anna Omelchenko <annao at scripps.edu>
+	    Guillaume Vareille <vareille at scripps.edu>
+	    Sophie Cohn
+	    qzhang
+	    Michael F. Sanner
+	    Sowjanya Karnati
+            Alex T. Gillet
+
+    Major contributions in src/geomAlgorithms/*.{h,cpp} are 
+    authored by Dan Sunday of softSurfer (www.softsurfer.com.
+
 Copyright: 
 
-    THE SCRIPPS RESEARCH INSTITUTE, <sanner at scripps.edu>
+    The respective authors and the Scripps Research Institute
+    1989-2008 Michael Sanner <sanner at scripps.edu>
 
+    Major contributions in src/geomAlgorithms/*.{h,cpp} are 
+    Copyright (C) 2001-2002 softSurfer (www.softsurfer.com)
+
 License:
 
-    PLEASE READ THIS DOCUMENT CAREFULLY. IF YOU AGREE WITH THE TERMS
-    AND CONDITIONS OF THIS LICENSE AGREEMENT, AND WISH TO RECEIVE AND
-    USE THIS SOFTWARE.
+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 SCIENTIFIC
-       RESEARCH. This license is issued to you as an individual. For
-       institution wide use or commercial use of the software you will
-       have to follow the official registration procedure. To do so you can
-       contact us by e-mail (sanner at scripps.edu), by mail (Michel Sanner,
-       TSRI, Molecular Biology Department, MB5, 10666 North Torrey Pines
-       Road, 92037 La Jolla) or by fax (858) 784-2860.
 
-       Some of the components have their own licensing specificities
-       that are described in the README file that is generated when you
-       download the software. We request that you read the content of
-       this file and comply to the requirements.
-    2. Copying Restrictions. You will not sell or otherwise transfer these
-       programs or derivatives to any other party, whether with or
-       without consideration, for any purpose.
-    3. 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.
-    4. Limitation Of Liability. You will hold harmless from all or any expenses
-       you may incur as a result of or arising from your use, direct or indirect,
-       of these materials. You understand that no other right or license
-       to this program or its derivatives is granted or implied as a
-       result of our transmission of same to you.
+  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.
 
-The Debian packaging is (C) 2007, Steffen Moeller <moeller at debian.org> and
-is licensed under the GPL, see `/usr/share/common-licenses/GPL'.
+     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 at 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 contributions by softSurfer are put under the following license:
+
+    This code may be freely used and modified for any purpose
+    providing that this copyright notice is included with it.
+    SoftSurfer makes no warranty for this code, and cannot be held
+    liable for any real or imagined damage resulting from it's use.
+    Users of this code must verify correctness for their application.
+
+The Debian packaging is (C) 2007-2008, Steffen Moeller <moeller at debian.org> and
+is licensed under the GPL, see '/usr/share/common-licenses/GPL'.


