[med-svn] [iqtree] branch upstream updated (cda5433 -> 80d3582)
Kevin Murray
daube-guest at moszumanska.debian.org
Sun Dec 4 22:43:59 UTC 2016
This is an automated email from the git hooks/post-receive script.
daube-guest pushed a change to branch upstream
in repository iqtree.
from cda5433 New upstream version 1.4.4+dfsg
adds 80d3582 New upstream version 1.5.2+dfsg
No new revisions were added by this update.
Summary of changes:
CMakeLists.txt | 416 ++++--
MPIHelper.cpp | 560 +++++++
MPIHelper.h | 305 ++++
ObjectStream.cpp | 113 ++
ObjectStream.h | 82 ++
README.md | 71 +-
TreeCollection.cpp | 56 +
TreeCollection.h | 63 +
alignment.cpp | 21 +-
alignment.h | 7 +-
candidateset.cpp | 584 +++++---
candidateset.h | 260 ++--
checkpoint.cpp | 120 +-
checkpoint.h | 20 +-
constrainttree.cpp | 211 +++
constrainttree.h | 81 ++
example/example.nex | 6 +-
example/example.phy | 64 +-
gsl/gauss.cpp | 12 +
hashsplitset.h | 19 +-
iqtree.cpp | 2064 +++++++++++++++++---------
iqtree.h | 378 +++--
iqtree_config.h.in | 3 +
lpwrapper.c | 2 +-
memslot.cpp | 254 ++++
memslot.h | 111 ++
mexttree.cpp | 73 +-
mexttree.h | 10 +
model/modelcodon.cpp | 8 +
model/modelfactory.cpp | 34 +-
model/modelmixture.cpp | 26 +-
model/modelmixture.h | 11 +
model/modelpomo.cpp | 3 +-
model/modelset.cpp | 136 +-
model/modelset.h | 7 +-
model/modelsubst.h | 6 +
model/partitionmodel.cpp | 6 +-
model/ratefree.cpp | 23 +-
model/rategamma.cpp | 8 +-
model/rategamma.h | 8 +-
model/rategammainvar.cpp | 3 +-
model/rateheterogeneity.h | 12 +-
model/rateinvar.cpp | 11 +-
model/rateinvar.h | 2 +-
mtree.cpp | 391 +++--
mtree.h | 123 +-
mtreeset.cpp | 1 +
ngs.cpp | 2 +-
node.cpp | 6 +-
node.h | 20 +-
optimization.cpp | 29 +-
pda.cpp | 196 ++-
pdtree.cpp | 5 +-
phyloanalysis.cpp | 369 +++--
phyloanalysis.h | 6 +-
phylokernel.h | 904 +++++++-----
phylokernelavx512.cpp | 120 ++
phylokernelfma.cpp | 164 +++
phylokernelmixrate.h | 2 +-
phylokernelmixture.h | 2 +-
phylokernelnew.h | 2802 ++++++++++++++++++++++++++++++++++++
phylokernel.h => phylokernelsafe.h | 1155 +++++++++------
phylokernelsitemodel.cpp | 6 +-
phylokernelsse.cpp | 169 +++
phylonode.cpp | 49 +-
phylonode.h | 22 +-
phylosupertree.cpp | 76 +-
phylosupertree.h | 7 +-
phylosupertreeplen.cpp | 164 ++-
phylosupertreeplen.h | 9 +-
phylotesting.cpp | 316 +++-
phylotesting.h | 21 +-
phylotree.cpp | 874 ++++++-----
phylotree.h | 400 +++--
phylotreeavx.cpp | 203 +--
phylotreepars.cpp | 354 +++--
phylotreesse.cpp | 2647 ++++++++++------------------------
pllnni.cpp | 53 +-
pllnni.h | 22 +-
quartet.cpp | 2 +-
split.cpp | 6 +-
split.h | 7 +-
splitgraph.cpp | 2 +-
splitgraph.h | 2 +-
splitset.cpp | 6 +-
splitset.h | 6 +-
stoprule.cpp | 44 +-
stoprule.h | 19 +-
superalignment.cpp | 66 +-
superalignment.h | 19 +
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 -
tools.cpp | 339 ++++-
tools.h | 180 ++-
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 +++++
124 files changed, 14411 insertions(+), 5890 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
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 (52%)
create mode 100644 phylokernelsse.cpp
mode change 100755 => 100644 pllnni.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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