[med-svn] [iqtree] branch master updated (b5cfc5f -> 2724598)
Kevin Murray
daube-guest at moszumanska.debian.org
Sun Dec 4 01:29:02 UTC 2016
This is an automated email from the git hooks/post-receive script.
daube-guest pushed a change to branch master
in repository iqtree.
from b5cfc5f Update + deactivate patches
new 80d3582 New upstream version 1.5.2+dfsg
new ddcc25e Merge tag 'upstream/1.5.2+dfsg'
new 31c878d Bump changelog, add myself to uploaders
new 631644f Refresh (well, drop) patches
new 2724598 Build a MPI paralellised binary
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:
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 ++
debian/changelog | 7 +
debian/control | 4 +-
debian/patches/series | 2 +-
debian/rules | 8 +-
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 +++++
128 files changed, 14429 insertions(+), 5893 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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