[med-svn] [iqtree] 01/02: Merge branch 'master' into debian/jessie-backports
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 commit to branch debian/jessie-backports
in repository iqtree.
commit 8f6e7793378518a319d0e05d7c52322f1310f51f
Merge: 9c09c89 e8d6855
Author: Andreas Tille <tille at debian.org>
Date: Wed Feb 22 20:28:26 2017 +0100
Merge branch 'master' into debian/jessie-backports
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 | 66 +
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, 25017 insertions(+), 8812 deletions(-)
diff --cc debian/changelog
index 394943c,de57b1b..179009b
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,9 -1,69 +1,75 @@@
+ iqtree (1.5.3+dfsg-2) unstable; urgency=medium
+
+ [ Roger Shimizu ]
+ * debian/rules:
+ - Run dh_auto_test only if CPUs >= 2 (Closes: #854500).
+
+ [ Andreas Tille ]
+ * Implement remarks given by upstream
+ (https://github.com/Cibiv/IQ-TREE/issues/17)
+
+ -- Andreas Tille <tille at debian.org> Sat, 11 Feb 2017 12:52:45 +0100
+
+ iqtree (1.5.3+dfsg-1) unstable; urgency=medium
+
+ * New upstream version
+ * debhelper 10
+ * d/watch: version=4
+
+ -- Andreas Tille <tille at debian.org> Thu, 19 Jan 2017 08:36:11 +0100
+
+ iqtree (1.5.2+dfsg-1) unstable; urgency=medium
+
+ * New upstream version 1.5.2+dfsg (Closes: #846958)
+ * Enable build of MPI-parallelised executable
+
+ -- Kevin Murray <kdmfoss at gmail.com> Sun, 04 Dec 2016 11:25:38 +1100
+
+ iqtree (1.4.4+dfsg-1) unstable; urgency=medium
+
+ * New upstream version
+ * Disable sse patch
+
+ -- Andreas Tille <tille at debian.org> Fri, 09 Sep 2016 11:07:13 +0200
+
+ iqtree (1.4.3+dfsg-1) unstable; urgency=medium
+
+ * New upstream version
+
+ -- Andreas Tille <tille at debian.org> Mon, 15 Aug 2016 22:24:55 +0200
+
+ iqtree (1.4.2+dfsg-1) unstable; urgency=medium
+
+ [ Andreas Tille ]
+ * New upstream version
+ * Use repack,compression=xz in d/watch instead of adding get-orig-source to
+ d/rules
+ * Do not use -m32 and -msse3 flags
+ Closes: #813436
+ * Do not append 32 to binary name if build on 32bit architecture
+ Closes: #813437
+ * Restrict binary to intel architecture
+ Closes: #813438
+ * cme fix dpkg-control
+ * hardening=+all
+
+ [ Christian Seiler ]
+ * debian/rules:
+ - parallel build
+ - use variants to more elegantly build serial and omp executable
+ - fix build time test
+ * debian/patches/sse.patch
+ - fix PLL_BYTE_ALIGNMENT to work around pll bug
+ - fix SSE patch to properly build on amd64 and i386
+
+ -- Andreas Tille <tille at debian.org> Wed, 29 Jun 2016 13:38:33 +0200
+
+iqtree (1.3.11.1+dfsg-1~bpo8+1) jessie-backports; urgency=medium
+
+ * Rebuild for jessie-backports.
+
+ -- Andreas Tille <tille at debian.org> Fri, 12 Feb 2016 20:03:34 +0100
+
iqtree (1.3.11.1+dfsg-1) unstable; urgency=low
* Initial release (Closes: #798511)
--
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