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 <[email protected]> Fri, 25 Jun 2010
17:23:58 +0200
+ -- Sri Girish Srinivasa Murthy <[email protected]> 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
<[email protected]>
Uploaders: Sri Girish Srinivasa Murthy <[email protected]>, Steffen
Moeller <[email protected]>
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 <[email protected]>
+ Andrew Butterfield
+ Amanda Birmingham <[email protected]>
+ Brett Easton
+ Catherine Lozuopone <[email protected]>
+ Daniel McDonald <[email protected]>
+ Edward Lang
+ Felix Schill
Gavin Huttley <[email protected]>
- Andrew Butterfield
- Peter Maxwell
- Rob Knight
+ Greg Caporaso <[email protected],[email protected]>
+ Helen Lindsay
+ Hua Ying <[email protected]>
+ Jeremy Widmann <[email protected]>
+ Jens Reeder <[email protected]>
+ Jesse Zaneveld
+ Julia Goodrich <[email protected]>
+ Justin Kuczynski <[email protected]>
+ Kyle Bittinger <[email protected]>
+ Kristian Rother <[email protected]>
+ Matthrew Wakefield <[email protected]>
+ Marcin Cieslik <[email protected]>
+ Micah Hamady <[email protected]>
+ Mike Robeson
+ Peter Maxwell <[email protected]>
+ Rob Knight <[email protected]>
+ Sandra Smit <[email protected]>
+ Shandy Wikman <[email protected]>
+ Stephanie Wilson
+ Tianlin Wang
+ Von Bing Yap
+ Zongzhi Liu <[email protected]>
Copyright:
@@ -21,6 +50,62 @@
GPL-2
+
+Files: cogent/maths/matrix_invert.c
+ cogent/maths/eigen.c (partly)
+
+Upstream author: Z. Yang <[email protected]>
+
+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 <[email protected]>
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/*
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