[med-svn] r8703 - trunk/packages/python-pynast/trunk/debian

[Andreas Tille]

Author: tille
Date: 2011-11-29 13:01:08 +0000 (Tue, 29 Nov 2011)
New Revision: 8703

Added:
   trunk/packages/python-pynast/trunk/debian/upstream-metadata.yaml
Modified:
   trunk/packages/python-pynast/trunk/debian/README.Debian
   trunk/packages/python-pynast/trunk/debian/changelog
   trunk/packages/python-pynast/trunk/debian/control
Log:
Move some information from long description to upstream-metadata.yaml (citations) and README.Debian (user information about previos versions); Replaces/Provides/Conflicts python-pynast to enable proper upgrades from previous packages; upload to unstable


Modified: trunk/packages/python-pynast/trunk/debian/README.Debian
===================================================================
--- trunk/packages/python-pynast/trunk/debian/README.Debian	2011-11-29 11:04:33 UTC (rev 8702)
+++ trunk/packages/python-pynast/trunk/debian/README.Debian	2011-11-29 13:01:08 UTC (rev 8703)
@@ -1,21 +1,9 @@
 PyNAST for Debian
 =================
 
-Many many thanks got to Jonas from the CDBS team for indicating
-that I indeed need to set the XB and XS flags for python packages.
-A recent update move this all to dh_python2, which does not seem
-to need those any more.
+Since version 1.1, PyNAST no longer exactly matches the output
+of the origianl NAST program. Instead it focuses on getting better
+alignments. Users who wish to exactly match the results of NAST should
+download PyNAST 1.0.
 
-The package is named -pynast, not -nast, since that is the name
-of the python module.
-
-A man page for /usr/bin/pynast is still missing. The package
-was build as a dependency to qiime, so some external help as 
-a contribtion to upstream and this Debian package by a rudimentary
-man page would be appreciated.
-
-The package is in need of someone truly loving it. You will be
-helped, just raise your hand.
-
- -- 
-   Steffen Moeller <moeller at debian.org>  Thu, 25 Aug 2011 23:31:25 +0200
+ -- Andreas Tille <tille at debian.org>  Tue, 29 Nov 2011 11:22:19 +0100

Modified: trunk/packages/python-pynast/trunk/debian/changelog
===================================================================
--- trunk/packages/python-pynast/trunk/debian/changelog	2011-11-29 11:04:33 UTC (rev 8702)
+++ trunk/packages/python-pynast/trunk/debian/changelog	2011-11-29 13:01:08 UTC (rev 8703)
@@ -1,4 +1,4 @@
-python-pynast (1.1-3) UNRELEASED; urgency=low
+python-pynast (1.1-3) unstable; urgency=low
 
   [ Steffen Moeller ]
   * Rendering Tim's fixes available for Debian
@@ -13,12 +13,22 @@
     - Removed duplicated ${misc:Depends}
     - Removed unneeded ${shlibs:Depends}
     - Depends: libjs-jquery, libjs-underscore
+    - Moved citation information from long description to
+      upstream-metadata.yaml
+    - Moved information about previous versions from long description
+      to README.Debian
+    - Provides/Replaces/Conflicts: python-pynast to enable smooth
+      upgrades after renaming the package
   * debian/copyright: DEP5
   * Dephelper 8 (control+compat)
   * debian/links: Link packages JavaScript libraries
   * debian/rules: remove incomplete links to JavaScript libraries
   * debian/doc-base: created docbase file
   * debian/pynast.1: escape hyphen character
+  * debian/upstream-metadata.yaml: Citation information
+  * debian/README.Debian: Replaced outdated and useless content by
+    some information about previous upstream versions (previosely
+    mentioned in long description)
 
  -- Andreas Tille <tille at debian.org>  Tue, 29 Nov 2011 11:22:19 +0100
 

Modified: trunk/packages/python-pynast/trunk/debian/control
===================================================================
--- trunk/packages/python-pynast/trunk/debian/control	2011-11-29 11:04:33 UTC (rev 8702)
+++ trunk/packages/python-pynast/trunk/debian/control	2011-11-29 13:01:08 UTC (rev 8703)
@@ -16,6 +16,9 @@
 Package: pynast
 Architecture: all
 Depends: ${misc:Depends}, ${python:Depends}, libjs-jquery, libjs-underscore
+Provides: python-pynast
+Replaces: python-pynast
+Conflicts: python-pynast
 Description: alignment of short DNA sequences
  The package provices a reimplementation of the Nearest Alignment 
  Space Termination tool in Python. It was prepared for next generation
@@ -29,13 +32,3 @@
  derived from existing alignments such as phylogenetic trees. Because
  any protein or nucleic acid sequences and template alignments can be
  provided, PyNAST is not limited to the analysis of 16s rDNA sequences.
- .
- Since version 1.1, PyNAST no longer exactly matches the output
- of the origianl NAST program. Instead it focuses on getting better
- alignments. Users who wish to exactly match the results of NAST should
- download PyNAST 1.0.
- .
- PyNAST: a flexible tool for aligning sequences to a template
- alignment. J. Gregory Caporaso, Kyle Bittinger, Frederic D. Bushman,
- Todd Z. DeSantis, Gary L. Andersen, and Rob Knight. January 15, 2010,
- DOI 10.1093/bioinformatics/btp636. Bioinformatics 26: 266-267.

Added: trunk/packages/python-pynast/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/python-pynast/trunk/debian/upstream-metadata.yaml	                        (rev 0)
+++ trunk/packages/python-pynast/trunk/debian/upstream-metadata.yaml	2011-11-29 13:01:08 UTC (rev 8703)
@@ -0,0 +1,12 @@
+Name: PyNAST
+Homepage: http://pynast.sourceforge.net/
+DOI: 10.1093/bioinformatics/btp636
+PMID: 19914921
+Reference:
+  Author: J. Gregory Caporaso, Kyle Bittinger, Frederic D. Bushman, Todd Z. DeSantis, Gary L. Andersen, and Rob Knight
+  Title: PyNAST: a flexible tool for aligning sequences to a template alignment
+  Journal: Bioinformatics
+  Volume: 26
+  Pages: 266-267.
+  Year: 2010
+  URL: http://bioinformatics.oxfordjournals.org/content/26/2/266.long