[med-svn] [iqtree] branch debian/jessie-backports updated (9c09c89 -> ff01216)
Andreas Tille
tille at debian.org
Thu Feb 23 06:43:27 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 iqtree.
from 9c09c89 Backport to Jessie
adds b8172a0 Imported Upstream version 1.3.13+dfsg
adds 2d30c01 Merge tag 'upstream/1.3.13+dfsg'
adds 56ad3f0 New upstream version
adds c69d762 Do not use -m32 and -msse flags
adds b0e94c9 Do not append 32 to binary name if build on 32bit architecture
adds c7510ed Drop -mavx option
adds 4038452 Use repack,compression=xz in d/watch instead of adding get-orig-source to d/rules
adds 79edd15 Imported Upstream version 1.3.14+dfsg
adds e8b9f92 Merge tag 'upstream/1.3.14+dfsg'
adds 4c99d87 Imported Upstream version 1.4.0+dfsg
adds 1bc8ee3 Refresh patches
adds b59ce0c New upstream version
adds a074fcb Disable avoid_mavx.patch since it breaks compilation which checks for this option by preprocessor directives
adds 7c679f3 Restrict binary to intel architecture
adds 4e2b777 cme fix dpkg-control
adds 5abbd97 Update sse3 removel patch
adds 35c46f5 Imported Upstream version 1.4.0+dfsg
adds a68a042 Imported Upstream version 1.4.2+dfsg
adds 8f72194 Merge tag 'upstream/1.4.2+dfsg'
adds 27da97f New upstream version
adds c867ed1 Patches provided by Christian Seiler <christian at iwakd.de> to enhance build process and fix test
adds 2cb169d Fix SSE patch provided by Christian Seiler <christian at iwakd.de> to enable portable (and correct) build
adds 8169663 Update changelog
adds 8835bdc Bump policy version (as cme call in changelog would do)
adds 09fba10 Fix location of GPL-3 text
adds c6dded0 hardening=+all
adds 1c93d20 Fix line endings in patch
adds b61c6aa Update spelling patch
adds 4709d4d Upload to unstable
adds d67f0c4 Imported Upstream version 1.4.3+dfsg
adds 45ea220 Merge tag 'upstream/1.4.3+dfsg'
adds 9fc96d9 New upstream version
adds 2190669 Upload to unstable
adds cda5433 New upstream version 1.4.4+dfsg
adds ea8cbe3 Merge tag 'upstream/1.4.4+dfsg'
adds 226aa9a New upstream version
adds b5cfc5f Update + deactivate patches
adds 80d3582 New upstream version 1.5.2+dfsg
adds ddcc25e Merge tag 'upstream/1.5.2+dfsg'
adds 31c878d Bump changelog, add myself to uploaders
adds 631644f Refresh (well, drop) patches
adds 2724598 Build a MPI paralellised binary
adds 3f5df9c Add bug number
adds 5bb8dce Upload to unstable
adds 173db0c New upstream version 1.5.3+dfsg
adds 6a1f154 Merge tag 'upstream/1.5.3+dfsg'
adds ce88f8c New upstream version
adds 0f11609 debhelper 10
adds 61ac236 d/watch: version=4
adds 68ee35d Upload to unstable
adds e02d5f0 debian/rules: Run dh_auto_test only if CPUs >= 2
adds 7b695c7 Implement remarks given by upstream
adds e8d6855 Upload to unstable
new 8f6e779 Merge branch 'master' into debian/jessie-backports
new ff01216 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:
CMakeLists.txt | 418 +++--
MPIHelper.cpp | 560 +++++++
MPIHelper.h | 305 ++++
ObjectStream.cpp | 113 ++
ObjectStream.h | 82 +
README.md | 71 +-
TreeCollection.cpp | 56 +
TreeCollection.h | 63 +
alignment.cpp | 448 ++++--
alignment.h | 53 +-
alignmentpairwise.cpp | 3 +-
candidateset.cpp | 633 +++++---
candidateset.h | 273 +++-
checkpoint.cpp | 328 ++--
checkpoint.h | 384 ++++-
constrainttree.cpp | 211 +++
constrainttree.h | 81 +
debian/Documents_source/example.sh | 20 +-
debian/changelog | 72 +
debian/compat | 2 +-
debian/control | 12 +-
debian/copyright | 2 +-
debian/patches/series | 1 -
debian/patches/spelling.patch | 15 -
debian/rules | 49 +-
debian/watch | 4 +-
example/example.nex | 6 +-
example/example.phy | 64 +-
gsl/CMakeLists.txt | 8 +
gsl/binomial_tpe.cpp | 381 +++++
gsl/gauss.cpp | 364 +++++
gsl/gaussinv.cpp | 205 +++
gsl/gausspdf.cpp | 40 +
gsl/gsl_nan.h | 45 +
gsl/multinomial.cpp | 82 +
gsl/mygsl.h | 57 +
gsl/pow_int.cpp | 56 +
gsl/rat_eval.h | 25 +
gzstream.cpp | 5 +-
gzstream.h | 2 +
hashsplitset.cpp | 8 +-
hashsplitset.h | 19 +-
iqtree.cpp | 2685 +++++++++++++++++++------------
iqtree.h | 414 +++--
iqtree_config.h.in | 3 +
lpwrapper.c | 2 +-
memslot.cpp | 254 +++
memslot.h | 111 ++
mexttree.cpp | 73 +-
mexttree.h | 10 +
model/modelcodon.cpp | 154 ++
model/modelcodon.h | 20 +
model/modeldna.cpp | 27 +-
model/modeldna.h | 10 +
model/modelfactory.cpp | 636 ++++----
model/modelfactory.h | 50 +-
model/modelgtr.cpp | 110 +-
model/modelgtr.h | 26 +-
model/modelmixture.cpp | 175 +-
model/modelmixture.h | 38 +
model/modelnonrev.cpp | 6 +-
model/modelpomo.cpp | 3 +-
model/modelprotein.cpp | 38 +-
model/modelprotein.h | 10 +
model/modelset.cpp | 144 +-
model/modelset.h | 20 +-
model/modelsubst.cpp | 34 +-
model/modelsubst.h | 31 +-
model/partitionmodel.cpp | 77 +-
model/partitionmodel.h | 35 +-
model/ratefree.cpp | 104 +-
model/ratefree.h | 12 +-
model/ratefreeinvar.cpp | 17 +-
model/ratefreeinvar.h | 12 +-
model/rategamma.cpp | 60 +-
model/rategamma.h | 20 +-
model/rategammainvar.cpp | 229 ++-
model/rategammainvar.h | 64 +-
model/rateheterogeneity.cpp | 35 +-
model/rateheterogeneity.h | 50 +-
model/rateinvar.cpp | 35 +-
model/rateinvar.h | 12 +-
model/ratekategory.cpp | 1 +
model/ratemeyerhaeseler.cpp | 6 +-
modelsblock.h | 11 +-
mpdablock.cpp | 2 +-
msetsblock.cpp | 1 +
msplitsblock.cpp | 2 +-
mtree.cpp | 391 +++--
mtree.h | 123 +-
mtreeset.cpp | 5 +-
ncl/nxscharactersblock.cpp | 10 +-
ncl/nxsdistancesblock.cpp | 1 +
ncl/nxstaxablock.cpp | 1 +
ngs.cpp | 4 +-
ngs.h | 2 +-
node.cpp | 6 +-
node.h | 20 +-
optimization.cpp | 31 +-
optimization.h | 3 +-
pattern.cpp | 10 +-
pattern.h | 22 +-
pda.cpp | 369 ++++-
pdtree.cpp | 5 +-
phyloanalysis.cpp | 1001 ++++++++----
phyloanalysis.h | 8 +-
phylokernel.h | 942 +++++++----
phylokernelavx512.cpp | 120 ++
phylokernelfma.cpp | 164 ++
phylokernelmixrate.h | 32 +
phylokernelmixture.h | 34 +
phylokernelnew.h | 2807 ++++++++++++++++++++++++++++++++
phylokernel.h => phylokernelsafe.h | 1157 +++++++------
phylokernelsitemodel.cpp | 729 +++++++++
phylokernelsitemodel.h | 807 ++++++++++
phylokernelsse.cpp | 169 ++
phylonode.cpp | 49 +-
phylonode.h | 22 +-
phylosupertree.cpp | 159 +-
phylosupertree.h | 35 +-
phylosupertreeplen.cpp | 274 +++-
phylosupertreeplen.h | 54 +-
phylotesting.cpp | 1132 ++++++++++++-
phylotesting.h | 36 +-
phylotree.cpp | 2230 +++++++++-----------------
phylotree.h | 702 +++++---
phylotreeavx.cpp | 199 ++-
phylotreepars.cpp | 354 ++--
phylotreesse.cpp | 3119 ++++++++++++------------------------
pll/pll.h | 2 +-
pllnni.cpp | 53 +-
pllnni.h | 22 +-
pruning.h | 2 +-
quartet.cpp | 1817 +++++++++++++++++++++
split.cpp | 6 +-
split.h | 7 +-
splitgraph.cpp | 67 +-
splitgraph.h | 21 +-
splitset.cpp | 6 +-
splitset.h | 6 +-
stoprule.cpp | 66 +-
stoprule.h | 33 +-
superalignment.cpp | 147 +-
superalignment.h | 34 +-
test_scripts/README | 22 +-
test_scripts/compile.sh | 113 +-
test_scripts/gen_test_standard.py | 34 +-
test_scripts/generate_test_cmds.py | 97 --
test_scripts/run_tests.sh | 50 +
test_scripts/submit_jobs.sh | 8 +-
test_scripts/submitjob.sh | 2 -
test_scripts/test_configs.txt | 18 +-
test_scripts/test_data/d59_8.nex | 2 -
tinatree.cpp | 2 +-
tools.cpp | 754 +++++++--
tools.h | 313 +++-
vectorclass/changelog.txt | 32 +-
vectorclass/dispatch_example.cpp | 12 +-
vectorclass/instrset.h | 60 +-
vectorclass/instrset_detect.cpp | 18 +-
vectorclass/special.zip | Bin 34477 -> 34897 bytes
vectorclass/vectorclass.h | 10 +-
vectorclass/vectorclass.pdf | Bin 476370 -> 431608 bytes
vectorclass/vectorf128.h | 46 +-
vectorclass/vectorf256.h | 14 +-
vectorclass/vectorf256e.h | 13 +-
vectorclass/vectorf512.h | 22 +-
vectorclass/vectorf512e.h | 13 +-
vectorclass/vectori128.h | 140 +-
vectorclass/vectori256.h | 28 +-
vectorclass/vectori256e.h | 21 +-
vectorclass/vectori512.h | 31 +-
vectorclass/vectori512e.h | 25 +-
vectorclass/vectormath_common.h | 93 +-
vectorclass/vectormath_exp.h | 27 +-
vectorclass/vectormath_hyp.h | 9 +-
vectorclass/vectormath_lib.h | 103 +-
vectorclass/vectormath_trig.h | 204 +--
vectorf64.h | 377 +++++
179 files changed, 25023 insertions(+), 8812 deletions(-)
create mode 100644 MPIHelper.cpp
create mode 100644 MPIHelper.h
create mode 100644 ObjectStream.cpp
create mode 100644 ObjectStream.h
create mode 100644 TreeCollection.cpp
create mode 100644 TreeCollection.h
create mode 100644 constrainttree.cpp
create mode 100644 constrainttree.h
delete mode 100644 debian/patches/series
delete mode 100644 debian/patches/spelling.patch
create mode 100644 gsl/CMakeLists.txt
create mode 100644 gsl/binomial_tpe.cpp
create mode 100644 gsl/gauss.cpp
create mode 100644 gsl/gaussinv.cpp
create mode 100644 gsl/gausspdf.cpp
create mode 100644 gsl/gsl_nan.h
create mode 100644 gsl/multinomial.cpp
create mode 100644 gsl/mygsl.h
create mode 100644 gsl/pow_int.cpp
create mode 100644 gsl/rat_eval.h
create mode 100644 memslot.cpp
create mode 100644 memslot.h
create mode 100644 phylokernelavx512.cpp
create mode 100644 phylokernelfma.cpp
create mode 100644 phylokernelnew.h
copy phylokernel.h => phylokernelsafe.h (51%)
create mode 100644 phylokernelsitemodel.cpp
create mode 100644 phylokernelsitemodel.h
create mode 100644 phylokernelsse.cpp
mode change 100755 => 100644 pllnni.cpp
create mode 100644 quartet.cpp
delete mode 100755 test_scripts/generate_test_cmds.py
create mode 100755 test_scripts/run_tests.sh
delete mode 100755 test_scripts/submitjob.sh
create mode 100644 vectorf64.h
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