[med-svn] [hyphy] branch debian/jessie-backports updated (6d84b97 -> 3af42bf)
Andreas Tille
tille at debian.org
Wed Jun 7 12:06:02 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch debian/jessie-backports
in repository hyphy.
from 6d84b97 This should go to master branch
adds cc4e7ee Example for usage of gtest
adds 104a51d More hints about gtest
adds 04ec654 Imported Upstream version 2.2.6+dfsg
adds 4273c8c Merge tag 'upstream/2.2.6+dfsg'
adds c9c225c New upstream version
adds 67ca810 Hack around a mac-ism in setup.py
adds 5b219f2 make generated swig file ready for Python 3.5
adds 5493163 Remove arch specific flags
adds f974bb9 Upload to unstable
adds 4972dd3 Change build-dep on python3-dev to python3-all-dev to enable building for all supported python3 versions
adds 8287388 Upload to unstable
adds 0c8e1a8 Fix gcc-6 build issue by incorporating upstream patch
adds 4b8b73d cme fix dpkg-control
adds 4bd21c2 Refresh quilt patch
adds d1071cf Fix more spelling errors
adds c689175 hardening=+bindnow (+pie fails) + upload to unstable
adds faa1d76 Fix error: narrowing conversion from 'double' to 'unsigned char'
adds 20172b0 Fix all gcc-6.1 build issues.
adds d4a66a8 Update changelog
adds 8dc877e Use xz compression in d/watch
adds 35f6a34 Imported Upstream version 2.2.7+dfsg
adds 6d8af81 Merge tag 'upstream/2.2.7+dfsg'
adds 5c0441b New upstream with adapted patches
adds 8e0069e Seem the Python module is discontinued
adds f8273ac python-hyphy is now distributed in separate source archive so removing it from this package
adds d728603 Upload to unstable
new 5903c45 Merge branch 'master' into debian/jessie-backports
new 3af42bf Rebuild for Jessie backports
The 2 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:
.gitattributes | 1 +
.travis.yml | 52 +
CMakeLists.txt | 13 +-
README.md | 97 +-
debian/00todo | 12 +
debian/README.Debian | 8 -
debian/changelog | 61 +
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, 305 insertions(+), 20458 deletions(-)
create mode 100644 .gitattributes
create mode 100644 .travis.yml
create mode 100644 debian/00todo
delete mode 100644 debian/patches/arch_all_files_to_usr_share.patch
create mode 100644 debian/patches/remove_arch_specific_flags.patch
delete mode 100644 debian/python-hyphy.examples
delete mode 100644 debian/python-hyphy.links
delete mode 100644 debian/python3-hyphy.examples
delete mode 100644 debian/python3-hyphy.links
delete mode 100644 package.json
delete mode 100644 res/SubstitutionModels/Codon/MG94_REV_3x4.mdl copy
delete mode 100644 res/TemplateBatchFiles/PairwiseDNDS.bf
delete mode 100644 res/TemplateBatchFiles/dNdSDistributionComparisonMF.bf
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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