[med-svn] [hyphy] branch master updated (d4a66a8 -> 8e0069e)

[Andreas Tille]

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

tille pushed a change to branch master
in repository hyphy.

      from  d4a66a8   Update changelog
       new  8dc877e   Use xz compression in d/watch
       new  35f6a34   Imported Upstream version 2.2.7+dfsg
       new  6d8af81   Merge tag 'upstream/2.2.7+dfsg'
       new  5c0441b   New upstream with adapted patches
       new  8e0069e   Seem the Python module is discontinued

The 5 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 +-
 debian/changelog                                   |    7 +
 debian/hyphy-common.examples                       |    2 +-
 debian/patches/arch_all_files_to_usr_share.patch   |   16 -
 debian/patches/drop_profiling_option.patch         |    4 +-
 debian/patches/gcc-6.1_false_is_not_nil.patch      |   50 -
 debian/patches/gcc-6.1_narrowing_conversion.patch  |   34 -
 debian/patches/gcc-6.patch                         |   22 -
 debian/patches/msse_option_only_if_available.patch |    2 +-
 debian/patches/python3.5.patch                     |   78 -
 debian/patches/remove_arch_specific_flags.patch    |    4 +-
 debian/patches/series                              |    6 -
 debian/patches/setup_fix_clean_target.patch        |   18 -
 debian/patches/spelling.patch                      |   11 -
 debian/patches/use_debian_sqlite.patch             |   56 +-
 debian/python-hyphy.examples                       |    1 -
 debian/rules                                       |   28 -
 debian/watch                                       |    2 +-
 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 -
 41 files changed, 170 insertions(+), 20593 deletions(-)
 create mode 100644 .travis.yml
 delete mode 100644 debian/patches/arch_all_files_to_usr_share.patch
 delete mode 100644 debian/patches/gcc-6.1_false_is_not_nil.patch
 delete mode 100644 debian/patches/gcc-6.1_narrowing_conversion.patch
 delete mode 100644 debian/patches/gcc-6.patch
 delete mode 100644 debian/patches/python3.5.patch
 delete mode 100644 debian/patches/setup_fix_clean_target.patch
 delete mode 100644 debian/python-hyphy.examples
 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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