[med-svn] [bppsuite] 09/10: Import Debian changes 2.2.0-0.1

[Andreas Tille]

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tille pushed a commit to branch master
in repository bppsuite.

commit bfe7fac40b24b7bf9c7df747df4cd4a4032700e7
Merge: d4aec37 1268477
Author: Andreas Beckmann <anbe at debian.org>
Date:   Sat Sep 10 13:35:04 2016 +0200

    Import Debian changes 2.2.0-0.1
    
    bppsuite (2.2.0-0.1) unstable; urgency=low
    
      [ Andreas Beckmann ]
      * Non-maintainer upload.
      * New upstream release 2.2.0 (git commit 7890d12).
        (Closes: #776111, #825443, #708457)
      * Remove hardcoded library dependencies.  (Closes: #811271)
    
      [ Julien Dutheil ]
      * Compatibility update. Bio++ Program Suite version number is now indexed
        on Bio++'s version.
      * Programs support the --seed argument for setting the random seed.
      * bppSeqGen support generic characters as input.
      * bppPhySamp outputs sampled trees.

 CMakeLists.txt                                     |   6 +-
 ChangeLog                                          |  15 +
 .../MaximumLikelihood/Codons/BranchModel/ML.bpp    |   4 +-
 .../Codons/{BranchModel => CladeModel}/ML.bpp      |  17 +-
 Examples/MaximumLikelihood/Codons/M0/ML.bpp        |   3 +-
 .../MaximumLikelihood/Proteins/Homogeneous/ML.bpp  |   2 +-
 Examples/PhylogeneticSampling/PhySamp.bpp          |   6 +
 .../WithSiteSpecificSettings/SeqGen.bpp            |  45 +++
 .../WithSiteSpecificSettings/infos.csv             |  31 ++
 bppSuite/bppAlnScore.cpp                           |   6 +-
 bppSuite/bppAncestor.cpp                           |  24 +-
 bppSuite/bppConsense.cpp                           |  14 +-
 bppSuite/bppDist.cpp                               |  49 ++-
 bppSuite/bppML.cpp                                 |  96 ++---
 bppSuite/bppMixedLikelihoods.cpp                   | 100 +++--
 bppSuite/bppPars.cpp                               |   4 +-
 bppSuite/bppPhyloSampler.cpp                       |  31 +-
 bppSuite/bppReRoot.cpp                             |  16 +-
 bppSuite/bppSeqGen.cpp                             | 275 ++++++++++++--
 bppSuite/bppSeqMan.cpp                             |  82 +++--
 bppSuite/bppTreeDraw.cpp                           |   8 +-
 bppsuite.spec                                      |  26 +-
 buildBin.sh                                        |  18 +
 buildExample.sh                                    |   4 +
 debian/changelog                                   |  17 +
 debian/control                                     |   6 +-
 debian/copyright                                   |   8 +-
 debian/patches/debian-changes-0.8.0-1              |  49 ---
 debian/patches/series                              |   1 -
 doc/bppsuite.texi                                  | 406 +++++++++++++--------
 30 files changed, 940 insertions(+), 429 deletions(-)

diff --cc debian/changelog
index 98112a9,9ac4650..73d9922
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,4 -1,14 +1,21 @@@
 -bppsuite (2.2.0-1) unstable; urgency=low
++bppsuite (2.2.0-0.1) unstable; urgency=low
+ 
++  [ Andreas Beckmann ]
++  * Non-maintainer upload.
++  * New upstream release 2.2.0 (git commit 7890d12).
++    (Closes: #776111, #825443, #708457)
++  * Remove hardcoded library dependencies.  (Closes: #811271)
++
++  [ Julien Dutheil ]
+   * Compatibility update. Bio++ Program Suite version number is now indexed
+     on Bio++'s version.
+   * Programs support the --seed argument for setting the random seed.
 -  * bppSeqGen suport generic characters as input.
++  * bppSeqGen support generic characters as input.
+   * bppPhySamp outputs sampled trees.
+ 
 - -- Julien Dutheil <julien.dutheil at univ-montp2.fr>  Mon, 28 Sep 2014 14:00:00 +0100
++ -- Andreas Beckmann <anbe at debian.org>  Sat, 10 Sep 2016 13:35:04 +0200
+ 
 -bppsuite (0.8.0-1) unstable; urgency=low
 +bppsuite (0.8.0-1+build1) unstable; urgency=low
  
    * New models for proteins (COaLA)
    * New program bppMixedLikelihoods
diff --cc debian/control
index a26ceba,52236d8..78b8d54
--- a/debian/control
+++ b/debian/control
@@@ -9,7 -9,7 +9,7 @@@ Standards-Version: 3.9.
  
  Package: bppsuite
  Architecture: any
- Depends: ${shlibs:Depends}, ${misc:Depends}, libbpp-phyl9 (>= 2.0.3)
 -Depends: ${shlibs:Depends}, ${misc:Depends}, libbpp-phyl9 (>= 2.2.0)
++Depends: ${shlibs:Depends}, ${misc:Depends}
  Description: Bio++ program suite
   Includes programs:
    - BppML for maximum likelihood analysis,

-- 
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