[med-svn] r9344 - trunk/packages/libhmsbeagle/trunk/debian

[Andreas Tille]

Author: tille
Date: 2012-01-19 21:44:43 +0000 (Thu, 19 Jan 2012)
New Revision: 9344

Added:
   trunk/packages/libhmsbeagle/trunk/debian/upstream-metadata.yaml
Modified:
   trunk/packages/libhmsbeagle/trunk/debian/README.Debian
   trunk/packages/libhmsbeagle/trunk/debian/changelog
   trunk/packages/libhmsbeagle/trunk/debian/control
   trunk/packages/libhmsbeagle/trunk/debian/libhmsbeagle-dev.lintian-overrides
Log:
upstream-metadata.yaml


Modified: trunk/packages/libhmsbeagle/trunk/debian/README.Debian
===================================================================
--- trunk/packages/libhmsbeagle/trunk/debian/README.Debian	2012-01-19 21:24:57 UTC (rev 9343)
+++ trunk/packages/libhmsbeagle/trunk/debian/README.Debian	2012-01-19 21:44:43 UTC (rev 9344)
@@ -3,7 +3,10 @@
 
 This is compiled from SVN.  Used the internal name 'libhmsbeagle' to
 differentiate from the other 'beagle'.
-In the first instance I've not tested that the Java stuff works, only
-that the package is sufficient to work with MrBayes.
 
+For more information you might like to read
+
+   http://tree.bio.ed.ac.uk/publications/390/
+
+
  -- Tim Booth <tbooth at ceh.ac.uk>  Thu, 08 Dec 2011 17:05:04 +0000

Modified: trunk/packages/libhmsbeagle/trunk/debian/changelog
===================================================================
--- trunk/packages/libhmsbeagle/trunk/debian/changelog	2012-01-19 21:24:57 UTC (rev 9343)
+++ trunk/packages/libhmsbeagle/trunk/debian/changelog	2012-01-19 21:44:43 UTC (rev 9344)
@@ -6,12 +6,15 @@
   * debian/control:
     - Add Java library package
     - Added needed Java (Build-)Depends
+    - Moved citation information to upstream-metadata.yaml and
+      README.Debian
   * debian/rules: Build Java Library
   * debian/copyright: DEP5
   * debian/libhmsbeagle-dev.lintian-overrides: Make less noise about
     broken doxygen manpages
+  * debian/upstream-metadata.yaml: Citation information
 
- -- Andreas Tille <tille at debian.org>  Thu, 19 Jan 2012 16:02:12 +0100
+ -- Andreas Tille <tille at debian.org>  Thu, 19 Jan 2012 22:43:44 +0100
 
 libhmsbeagle (0.1052-2) unstable; urgency=low
 

Modified: trunk/packages/libhmsbeagle/trunk/debian/control
===================================================================
--- trunk/packages/libhmsbeagle/trunk/debian/control	2012-01-19 21:24:57 UTC (rev 9343)
+++ trunk/packages/libhmsbeagle/trunk/debian/control	2012-01-19 21:44:43 UTC (rev 9344)
@@ -51,16 +51,6 @@
  of phylogenetic software, both Bayesian samplers and Maximum Likelihood
  optimizers.  This allows these packages to make use of implementations that
  make use of optimized hardware such as graphics processing units.
- .
- A manuscript is now in press describing the BEAGLE API and library:
- .
- http://sysbio.oxfordjournals.org/content/early/2011/09/29/sysbio.syr100.abstract
- .
- The paper describing the algorithms used for calculating likelihoods of
- sequences on trees using many core devices like graphics processing units
- (GPUs) is available from:
- .
- http://tree.bio.ed.ac.uk/publications/390/ 
 
 Package: libbeagle-java
 Architecture: all

Modified: trunk/packages/libhmsbeagle/trunk/debian/libhmsbeagle-dev.lintian-overrides
===================================================================
--- trunk/packages/libhmsbeagle/trunk/debian/libhmsbeagle-dev.lintian-overrides	2012-01-19 21:24:57 UTC (rev 9343)
+++ trunk/packages/libhmsbeagle/trunk/debian/libhmsbeagle-dev.lintian-overrides	2012-01-19 21:44:43 UTC (rev 9344)
@@ -7,7 +7,9 @@
 libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/VecUnion.3.gz
 libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_Beagle.3.gz
 libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_BeagleException.3.gz
+libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_BeagleErrorCode.3.gz
 libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_BeagleFactory.3.gz
+libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_BeagleFlag.3.gz
 libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_BeagleImpl.3.gz
 libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_BeagleImplFactory.3.gz
 libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_BeagleInfo.3.gz

Added: trunk/packages/libhmsbeagle/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/libhmsbeagle/trunk/debian/upstream-metadata.yaml	                        (rev 0)
+++ trunk/packages/libhmsbeagle/trunk/debian/upstream-metadata.yaml	2012-01-19 21:44:43 UTC (rev 9344)
@@ -0,0 +1,12 @@
+Contact: Andrew Rambaut <rambaut at gmail.com>
+DOI: 10.1093/sysbio/syr100
+Homepage:  http://code.google.com/p/beagle-lib
+Name: beagle-lib
+PMID: 21963610
+Reference:
+  author: Daniel L. Ayres, Aaron Darling, Derrick J. Zwickl, Peter Beerli, Mark T. Holder, Paul O. Lewis, John P. Huelsenbeck, Fredrik Ronquist, David L. Swofford, Michael P. Cummings, Andrew Rambaut and Marc A. Suchard
+  title: BEAGLE: an Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics
+  journal: Systematic Biology
+  year: 2011
+  URL: http://sysbio.oxfordjournals.org/content/early/2011/09/29/sysbio.syr100.abstract
+  eprint: http://sysbio.oxfordjournals.org/content/early/2011/09/29/sysbio.syr100.full.pdf+html