[med-svn] r2987 - trunk/packages/python-biopython/trunk/debian

plessy at alioth.debian.org plessy at alioth.debian.org
Thu Jan 15 04:50:21 UTC 2009 

Author: plessy
Date: 2009-01-15 04:50:20 +0000 (Thu, 15 Jan 2009)
New Revision: 2987

Modified:
   trunk/packages/python-biopython/trunk/debian/changelog
   trunk/packages/python-biopython/trunk/debian/control
   trunk/packages/python-biopython/trunk/debian/copyright
   trunk/packages/python-biopython/trunk/debian/watch
Log:
New upstream release; some issues remain to be fixed before upload.

  * New upstream release.
    - uses NumPy rather than its precursor Numeric (Closes: #478457)
    - Martel, Bio.Mindy, Bio.MetaTool, Bio.EUtils, Bio.Saf, Bio.NBRF, and
      Bio.IntelliGenetics are deprecated.
    - Bio.PubMed and the online code in Bio.GenBank are now considered obsolete
      and will be deprecated in a future release.
    - Bio.Fasta is also considered to be obsolete and will eventually be
      deprecated.
  * debian/control:
    - added myself as Uploader.
    - depends on python-numpy instead of python-numeric-ext.
    - moved python-martel to oldlibs section, priority extra as it is
      deprecated, and indicate this in the description.
  * debian/copyright: added myself to the Hall of Fame and updated to latest
    draft of the machine-readable format.
  * debian/watch: makes beta versions lower by prepending a tiled between
    numbers and letters (1.49b -> 1.49~b).


Modified: trunk/packages/python-biopython/trunk/debian/changelog
===================================================================
--- trunk/packages/python-biopython/trunk/debian/changelog	2009-01-14 22:15:10 UTC (rev 2986)
+++ trunk/packages/python-biopython/trunk/debian/changelog	2009-01-15 04:50:20 UTC (rev 2987)
@@ -1,3 +1,25 @@
+python-biopython (1.49-1) UNRELEASED; urgency=low
+
+  * New upstream release.
+    - uses NumPy rather than its precursor Numeric (Closes: #478457)
+    - Martel, Bio.Mindy, Bio.MetaTool, Bio.EUtils, Bio.Saf, Bio.NBRF, and
+      Bio.IntelliGenetics are deprecated.
+    - Bio.PubMed and the online code in Bio.GenBank are now considered obsolete
+      and will be deprecated in a future release.
+    - Bio.Fasta is also considered to be obsolete and will eventually be
+      deprecated.
+  * debian/control:
+    - added myself as Uploader.
+    - depends on python-numpy instead of python-numeric-ext.
+    - moved python-martel to oldlibs section, priority extra as it is
+      deprecated, and indicate this in the description.
+  * debian/copyright: added myself to the Hall of Fame and updated to latest
+    draft of the machine-readable format.
+  * debian/watch: makes beta versions lower by prepending a tiled between
+    numbers and letters (1.49b -> 1.49~b).
+
+ -- Charles Plessy <plessy at debian.org>  Thu, 15 Jan 2009 13:15:44 +0900
+
 python-biopython (1.47-1) unstable; urgency=low
 
   * New upstream release

Modified: trunk/packages/python-biopython/trunk/debian/control
===================================================================
--- trunk/packages/python-biopython/trunk/debian/control	2009-01-14 22:15:10 UTC (rev 2986)
+++ trunk/packages/python-biopython/trunk/debian/control	2009-01-15 04:50:20 UTC (rev 2987)
@@ -3,9 +3,12 @@
 Section: python
 Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Philipp Benner <pbenner at uni-osnabrueck.de>
+           Charles Plessy <plessy at debian.org>
 DM-Upload-Allowed: yes
 Build-Depends: debhelper (>= 5.0.37.2), python-all-dev, flex, python-support,
- python-egenix-mxtexttools, python-reportlab, python-numeric
+ python-reportlab, python-numpy,
+# Should be removed when the deprecated Martel and Bio.Mindy are removed from upstream source.:
+ python-egenix-mxtexttools
 XS-Python-Version: >= 2.3
 Standards-Version: 3.8.0
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/python-biopython/trunk/?rev=0&sc=0
@@ -14,14 +17,15 @@
 
 Package: python-biopython
 Architecture: any
-Depends: ${python:Depends}, ${shlibs:Depends}, python-numeric,
+Depends: ${python:Depends}, ${shlibs:Depends}, python-numpy,
  python-biopython-martel (= ${source:Version}), python-reportlab,
+# Should be removed when the deprecated Martel and Bio.Mindy are removed from upstream source.:
  python-egenix-mxtexttools
 Provides: ${python:Provides}
 Replaces: python2.3-biopython (<< 1.42-1), python2.4-biopython (<< 1.42-1)
 Conflicts: python2.3-biopython (<< 1.42-1), python2.4-biopython (<< 1.42-1)
 XB-Python-Version: ${python:Versions}
-Recommends: python-biopython-doc (= ${source:Version}), python-numeric-ext
+Recommends: python-biopython-doc (= ${source:Version})
 Suggests: python-tk, wise
 Description: Python library for bioinformatics
  The Biopython Project is an international association
@@ -58,6 +62,8 @@
 
 Package: python-biopython-martel
 Architecture: all
+Priority: extra
+Section: oldlibs
 Depends: ${python:Depends}, python-biopython
 Provides: ${python:Provides}
 Replaces: python2.3-biopython-martel (<< 1.42-1), python2.4-biopython-martel (<< 1.42-1)
@@ -69,3 +75,6 @@
  The parse tree information is passed back to the caller using
  XML SAX events. In other words, Martel lets you parse flat
  files as if they are in XML.
+ .
+ Biopython's old parsing infrastructure, Martel (this package) and Bio.Mindy,
+ were deprecated in release 1.49.

Modified: trunk/packages/python-biopython/trunk/debian/copyright
===================================================================
--- trunk/packages/python-biopython/trunk/debian/copyright	2009-01-14 22:15:10 UTC (rev 2986)
+++ trunk/packages/python-biopython/trunk/debian/copyright	2009-01-15 04:50:20 UTC (rev 2987)
@@ -1,7 +1,9 @@
-This package was downloaded from http://biopython.org/DIST/
+Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=424
+Upstream-Name: Biopython
+Upstream-Source: http://biopython.org/DIST/biopython-1.49.tar.gz
 
 Files: *
-Copyright: © 2002-2007 Biopython contributors
+Copyright: © 2002-2009 Biopython contributors
 License: other
  Permission to use, copy, modify, and distribute this software and its
  documentation with or without modifications and for any purpose and
@@ -22,7 +24,8 @@
  OR PERFORMANCE OF THIS SOFTWARE.
 
 Files: debian/*
-Copyright: © 2004-2007 Philipp Benner <pbenner at uni-osnabrueck.de>
+Copyright: © 2009      Charles Plessy <plessy at debian.org>
+             2004-2008 Philipp Benner <pbenner at uni-osnabrueck.de>
 License: GPL-2+
  The Debian packaging information is under the GPL, version 2 or later.
 

Modified: trunk/packages/python-biopython/trunk/debian/watch
===================================================================
--- trunk/packages/python-biopython/trunk/debian/watch	2009-01-14 22:15:10 UTC (rev 2986)
+++ trunk/packages/python-biopython/trunk/debian/watch	2009-01-15 04:50:20 UTC (rev 2987)
@@ -1,5 +1,6 @@
 # Compulsory line, this is a version 3 file
 version=3
 
+opts="uversionmangle=s/b/~b/" \
 http://biopython.org/DIST/biopython-(.\.\w+)\.tar\.gz \
 	debian uupdate

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