[med-svn] r5060 - trunk/packages/python-cogent/trunk/debian

Fri Jul 23 23:00:37 UTC 2010

Author: moeller
Date: 2010-07-23 23:00:33 +0000 (Fri, 23 Jul 2010)
New Revision: 5060

Added:
   trunk/packages/python-cogent/trunk/debian/README.Debian
   trunk/packages/python-cogent/trunk/debian/examples
Modified:
   trunk/packages/python-cogent/trunk/debian/changelog
   trunk/packages/python-cogent/trunk/debian/control
   trunk/packages/python-cogent/trunk/debian/copyright
   trunk/packages/python-cogent/trunk/debian/docs
   trunk/packages/python-cogent/trunk/debian/python-cogent.doc-base
Log:
Uploaded new version after confirmation by upstream that redistribution is ok - it has to go to non-free because of a limit to academia


Added: trunk/packages/python-cogent/trunk/debian/README.Debian
===================================================================

--- trunk/packages/python-cogent/trunk/debian/README.Debian	                        (rev 0)
+++ trunk/packages/python-cogent/trunk/debian/README.Debian	2010-07-23 23:00:33 UTC (rev 5060)
@@ -0,0 +1,3 @@
+The package is in non-free just because some comparatively tiny contribution
+by someone who is limiting his code for free use in acedemia only.
+The user needs to think strongly if he/she can use this package.

Modified: trunk/packages/python-cogent/trunk/debian/changelog
===================================================================
--- trunk/packages/python-cogent/trunk/debian/changelog	2010-07-23 18:07:44 UTC (rev 5059)
+++ trunk/packages/python-cogent/trunk/debian/changelog	2010-07-23 23:00:33 UTC (rev 5060)
@@ -2,5 +2,5 @@
 
   * Initial release (Closes: #587161)
 
- -- Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>  Fri, 25 Jun 2010 17:23:58 +0200
+ -- Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>  Sat, 24 Jul 2010 00:53:31 +0200
 

Modified: trunk/packages/python-cogent/trunk/debian/control
===================================================================
--- trunk/packages/python-cogent/trunk/debian/control	2010-07-23 18:07:44 UTC (rev 5059)
+++ trunk/packages/python-cogent/trunk/debian/control	2010-07-23 23:00:33 UTC (rev 5060)
@@ -1,5 +1,5 @@
 Source: python-cogent
-Section: python
+Section: non-free/python
 Priority: extra
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>, Steffen Moeller <moeller at debian.org>

Modified: trunk/packages/python-cogent/trunk/debian/copyright
===================================================================
--- trunk/packages/python-cogent/trunk/debian/copyright	2010-07-23 18:07:44 UTC (rev 5059)
+++ trunk/packages/python-cogent/trunk/debian/copyright	2010-07-23 23:00:33 UTC (rev 5060)
@@ -6,12 +6,41 @@
 
 It was downloaded from <http://pycogent.sorceforge.net>
 
-Upstream Authors:
+Files: *
 
+Upstream authors:
+
+    Andreas Wilm <andreas.wilm at ucd.ie>
+    Andrew Butterfield
+    Amanda Birmingham <amanda.birmingham at thermofisher.com>
+    Brett Easton
+    Catherine Lozuopone <lozupone at colorado.edu>
+    Daniel McDonald <mcdonadt at colorado.edu>
+    Edward Lang
+    Felix Schill
     Gavin Huttley <gavin.huttley at anu.edu.au>
-    Andrew Butterfield
-    Peter Maxwell
-    Rob Knight
+    Greg Caporaso <gregcaporaso at gmail.com,caporaso at colorado.edu>
+    Helen Lindsay
+    Hua Ying <Hua.Ying at anu.edu.au>
+    Jeremy Widmann <jeremy.widmann at colorado.edu>
+    Jens Reeder <jreeder at colorado.edu>
+    Jesse Zaneveld
+    Julia Goodrich <julia.goodrich at colorado.edu>
+    Justin Kuczynski <justinak at gmail.com>
+    Kyle Bittinger <kylebittinger at gmail.com>
+    Kristian Rother <krother at rubor.de>
+    Matthrew Wakefield <matthew.wakefield at wehi.edu.au>
+    Marcin Cieslik <mpc4p at virginia.edu>
+    Micah Hamady <hamady at colorado.edu>
+    Mike Robeson
+    Peter Maxwell <pm67nz at gmail.com>
+    Rob Knight <rob at spot.colorado.edu>
+    Sandra Smit <sandra.smit at colorado.edu>
+    Shandy Wikman <ens01svn at cs.umu.se>
+    Stephanie Wilson
+    Tianlin Wang
+    Von Bing Yap
+    Zongzhi Liu <zongzhi.liu at gmail.com>
 
 Copyright:
 
@@ -21,6 +50,62 @@
 
     GPL-2
 
+
+Files: cogent/maths/matrix_invert.c
+       cogent/maths/eigen.c (partly)
+
+Upstream author: Z. Yang <z.yang at ucl.ac.uk>
+
+Copyright: (C) Z. Yang and the University College London
+
+License:
+
+    Redistribution is ok as long with proper copyright notice.
+    It is free to use/modify/redistribute only for academia. Others
+    need to contact the authors.
+
+    We clarified the situation by the following email exchange:
+
+	> On 07/23/2010 04:33 PM, Ziheng Yang wrote:
+	>>
+	>>
+	>> I have not signed up for any of the open source licenses.  Right now
+	>> paml is free for academics only.  For other users I am dealing with
+	>> the requests on a case-by-case basis.
+	>>
+	>> Yes, it will be fine for you to include paml programs in QIIME, or
+	>> compile executables using the source at the paml web site, as long as
+	>> you include appropriate acknowledgements.
+	>>
+	>> Best wishes,
+	>>
+	>> Ziheng Yang
+	>>
+	>>
+	>>
+	>> At 10:14 28/06/2010 +0200, srigirish wrote:
+	>>> Dear Prof. Yang,
+	>>>
+	>>> I am using the QIIME package
+	>>> <http://qiime.sourceforge.net/>http://qiime.sourceforge.net/ and
+	>>> found the local installation to be non-trivial. Together with my
+	>>> colleague I am now preparing all the build and runtime dependencies
+	>>> to Debian and Ubuntu, in the process of which I got to a note in the
+	>>> PyCogent package, suggesting to get your explicit OK for a
+	>>> redistribution of your code. May I go ahead? Also we'd need a
+	>>> clarification if your code may be modified and still be
+	>>> redistributed. There are plenty of Open Source licenses
+	>>> (<http://en.wikipedia.org/wiki/Open-source_license>http://en.wikipedia.org/wiki/Open-source_license),
+	>>> if you could pick one of these, this would be excellent.
+	>>>
+	>>> I am looking forward to your early reply.
+	>>>
+	>>> Best Regards,
+	>>>
+	>>> S. Sri Girish
+
+Files: debian/*
+
 The Debian packaging is:
 
     Copyright (C) 2010 Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>

Modified: trunk/packages/python-cogent/trunk/debian/docs
===================================================================
--- trunk/packages/python-cogent/trunk/debian/docs	2010-07-23 18:07:44 UTC (rev 5059)
+++ trunk/packages/python-cogent/trunk/debian/docs	2010-07-23 23:00:33 UTC (rev 5060)
@@ -1,4 +1,17 @@
 cogent-requirements.txt
 NumpyPortingNotes.txt
 README
-doc/*
+doc/ChangeLog.rst
+doc/conf.py
+doc/data_file_links.rst
+doc/doctest_rsts.py
+doc/install.rst
+doc/cookbook
+doc/developer_notes.rst
+doc/licenses.rst
+doc/README.rst
+doc/data
+doc/doctest2script.py
+doc/index.rst 
+doc/templates
+

Added: trunk/packages/python-cogent/trunk/debian/examples
===================================================================
--- trunk/packages/python-cogent/trunk/debian/examples	                        (rev 0)
+++ trunk/packages/python-cogent/trunk/debian/examples	2010-07-23 23:00:33 UTC (rev 5060)
@@ -0,0 +1 @@
+doc/examples/*

Modified: trunk/packages/python-cogent/trunk/debian/python-cogent.doc-base
===================================================================
--- trunk/packages/python-cogent/trunk/debian/python-cogent.doc-base	2010-07-23 18:07:44 UTC (rev 5059)
+++ trunk/packages/python-cogent/trunk/debian/python-cogent.doc-base	2010-07-23 23:00:33 UTC (rev 5060)
@@ -3,7 +3,7 @@
 Author: The Cogent Project
 Abstract: This manual introduces to the
  concepts behind PyCogent.
-Section: science
+Section: Science/Biology
 
 Format: text
 Files: /usr/share/doc/python-cogent/cookbook/*


