[med-svn] [hyphy] 01/02: Merge branch 'master' into debian/jessie-backports

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch debian/jessie-backports
in repository hyphy.

commit 5903c45058a02360426a796affd266c4a49e2f98
Merge: 6d84b97 d728603
Author: Andreas Tille <tille at debian.org>
Date:   Wed Jun 7 13:49:13 2017 +0200

    Merge branch 'master' into debian/jessie-backports

 .gitattributes                                     |    1 +
 .travis.yml                                        |   52 +
 CMakeLists.txt                                     |   13 +-
 README.md                                          |   97 +-
 debian/00todo                                      |   12 +
 debian/README.Debian                               |    8 -
 debian/changelog                                   |   55 +
 debian/control                                     |   71 +-
 debian/hyphy-common.examples                       |    2 +-
 debian/patches/arch_all_files_to_usr_share.patch   |   16 -
 debian/patches/drop_profiling_option.patch         |    4 +-
 debian/patches/msse_option_only_if_available.patch |    2 +-
 debian/patches/remove_arch_specific_flags.patch    |   25 +
 debian/patches/series                              |    2 +-
 debian/patches/spelling.patch                      |   35 +-
 debian/patches/use_debian_sqlite.patch             |   56 +-
 debian/python-hyphy.examples                       |    1 -
 debian/python-hyphy.links                          |    2 -
 debian/python3-hyphy.examples                      |    1 -
 debian/python3-hyphy.links                         |    2 -
 debian/rules                                       |   33 +-
 debian/watch                                       |    2 +-
 package.json                                       |   12 -
 res/SubstitutionModels/Codon/MG94_REV_3x4.mdl copy |    0
 res/TemplateBatchFiles/BUSTED.bf                   |    2 +-
 res/TemplateBatchFiles/BranchSiteREL.bf            |    4 +-
 res/TemplateBatchFiles/PairwiseDNDS.bf             |    0
 .../QuickSelectionDetectionMF.bf                   |    3 +-
 .../dNdSDistributionComparisonMF.bf                |    0
 res/TemplateBatchFiles/files.lst                   |    1 +
 src/gui/HYChartWindow.cpp                          |   24 +-
 src/gui/HYModelWindow.cpp                          |    2 +-
 .../gtk/WindowClasses/HYPlatformModelWindow.cpp    |    2 +-
 src/lib/Examples/HBL/F81.bf                        |    1 -
 src/lib/Examples/HBL/HKY85.bf                      |    1 -
 src/lib/Examples/HBL/data/hiv.nuc                  |    1 -
 src/lib/Examples/Python/BasicHyPhy.py              |  112 -
 src/lib/Examples/R/BasicHyPhy.R                    |  126 -
 src/lib/LibraryModules/Python/HyPhy/__init__.py    |   78 -
 src/lib/LibraryModules/R/HyPhy.R                   | 1338 ----
 src/lib/README                                     |   53 -
 src/lib/SWIGWrappers/THyPhy_R.cpp                  | 3344 ---------
 src/lib/SWIGWrappers/THyPhy_py3.cpp                | 7440 --------------------
 src/lib/SWIGWrappers/THyPhy_python.cpp             | 7440 --------------------
 src/lib/build.sh                                   |  186 -
 src/lib/{Link => link}/THyPhy.cpp                  |    0
 src/lib/{Link => link}/THyPhy.h                    |    0
 src/lib/setup.py                                   |   95 -
 48 files changed, 299 insertions(+), 20458 deletions(-)

diff --cc debian/changelog
index 94de561,4438a39..2c69303
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,9 -1,58 +1,64 @@@
+ hyphy (2.2.7+dfsg-1) unstable; urgency=medium
+ 
+   * New upstream version
+   * Use xz compression in d/watch
+   * python-hyphy is now distributed in separate source archive so
+     removing it from this package
+ 
+  -- Andreas Tille <tille at debian.org>  Fri, 14 Oct 2016 08:01:08 +0200
+ 
+ hyphy (2.2.6+dfsg-5) unstable; urgency=medium
+ 
+   * Fix error: narrowing conversion from 'double' to 'unsigned char'
+   * Fix error: replacing false with nil 
+     Closes: #811866
+ 
+  -- Andreas Tille <tille at debian.org>  Mon, 15 Aug 2016 12:44:58 +0200
+ 
+ hyphy (2.2.6+dfsg-4) unstable; urgency=medium
+ 
+   * Fix gcc-6 build issue by incorporating upstream patch
+     Closes: #811866
+   * cme fix dpkg-control
+   * Fix more spelling errors
+   * hardening=+bindnow
+ 
+  -- Andreas Tille <tille at debian.org>  Fri, 22 Jul 2016 15:05:54 +0200
+ 
+ hyphy (2.2.6+dfsg-3) unstable; urgency=medium
+ 
+   * Change build-dep on python3-dev to python3-all-dev to enable building for
+     all supported python3 versions (thanks to Scott Kitterman
+     <debian at kitterman.com> for the patch)
+     Closes: #809452
+ 
+  -- Andreas Tille <tille at debian.org>  Wed, 30 Dec 2015 21:49:03 +0100
+ 
+ hyphy (2.2.6+dfsg-2) unstable; urgency=medium
+ 
+   [ Matthias Klose ]
+   * Hand-edit swig generated file to build with Python3.5.
+     Closes: #802999
+ 
+   [ Andreas Tille ]
+   * Remove arch specific flags
+     Closes: #802994
+ 
+  -- Andreas Tille <tille at debian.org>  Mon, 26 Oct 2015 11:20:39 +0100
+ 
+ hyphy (2.2.6+dfsg-1) unstable; urgency=medium
+ 
+   * New upstream version
+   * Hack around a mac-ism in setup.py
+ 
+  -- Andreas Tille <tille at debian.org>  Tue, 22 Sep 2015 17:50:33 +0200
+ 
 +hyphy (2.2.5+dfsg-1~bpo8+1) jessie-backports; urgency=medium
 +
 +  * Backport to Jessie
 +
 + -- Andreas Tille <tille at debian.org>  Fri, 31 Jul 2015 16:46:29 +0200
 +
  hyphy (2.2.5+dfsg-2) unstable; urgency=medium
  
    * Versioned Build-Depends: cmake (>= 3.0)

-- 
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