[med-svn] [hyphy] branch upstream updated (04ec654 -> 35f6a34)

[Andreas Tille]

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

tille pushed a change to branch upstream
in repository hyphy.

      from  04ec654   Imported Upstream version 2.2.6+dfsg
       new  35f6a34   Imported Upstream version 2.2.7+dfsg

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 .travis.yml                                        |   52 +
 CMakeLists.txt                                     |   13 +-
 README.md                                          |   97 +-
 package.json                                       |   12 -
 res/TemplateBatchFiles/BUSTED.bf                   |    2 +-
 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                                   |   97 -
 24 files changed, 148 insertions(+), 20274 deletions(-)
 create mode 100644 .travis.yml
 delete mode 100644 package.json
 delete mode 100644 src/lib/Examples/HBL/F81.bf
 delete mode 100644 src/lib/Examples/HBL/HKY85.bf
 delete mode 100644 src/lib/Examples/HBL/data/hiv.nuc
 delete mode 100644 src/lib/Examples/Python/BasicHyPhy.py
 delete mode 100644 src/lib/Examples/R/BasicHyPhy.R
 delete mode 100644 src/lib/LibraryModules/Python/HyPhy/__init__.py
 delete mode 100644 src/lib/LibraryModules/R/HyPhy.R
 delete mode 100644 src/lib/README
 delete mode 100644 src/lib/SWIGWrappers/THyPhy_R.cpp
 delete mode 100644 src/lib/SWIGWrappers/THyPhy_py3.cpp
 delete mode 100644 src/lib/SWIGWrappers/THyPhy_python.cpp
 delete mode 100644 src/lib/build.sh
 rename src/lib/{Link => link}/THyPhy.cpp (100%)
 rename src/lib/{Link => link}/THyPhy.h (100%)
 delete mode 100644 src/lib/setup.py

-- 
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