[med-svn] [libpll] 02/05: Merge tag 'upstream/0.0.20170317'
Andreas Tille
tille at debian.org
Mon Mar 20 21:22:51 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository libpll.
commit 8d007548c9179fc18ccd17d4f099c2ee611dd99e
Merge: a9a0d57 1ae4973
Author: Andreas Tille <tille at debian.org>
Date: Mon Mar 20 16:03:08 2017 +0100
Merge tag 'upstream/0.0.20170317'
Upstream version 0.0.20170317
.travis.yml | 7 +
AUTHORS | 0
ChangeLog | 24 -
ChangeLog.md | 49 +
INSTALL | 370 -
COPYING => LICENSE.txt | 147 +-
MPI/Makefile.am | 33 -
MPI/Makefile.in | 2354 ---
Makefile.am | 9 +-
Makefile.in | 814 -
NEWS | 0
README | 0
README.md | 297 +
aclocal.m4 | 1158 --
autogen.sh | 2 +
compile | 347 -
config.guess | 1558 --
config.h.in | 248 -
config.sub | 1791 --
configure | 20260 -------------------
configure.ac | 152 +-
depcomp | 791 -
examples/Makefile.am | 17 +-
examples/Makefile.in | 620 -
examples/PLL/Makefile.AVX | 21 -
examples/PLL/Makefile.AVX-MPI | 20 -
examples/PLL/Makefile.AVX-PTHREADS | 21 -
examples/PLL/Makefile.AVX.clang | 21 -
examples/PLL/Makefile.SSE3 | 19 -
examples/PLL/Makefile.SSE3-MPI | 20 -
examples/PLL/Makefile.SSE3-PTHREADS | 21 -
examples/PLL/Makefile.SSE3.clang | 21 -
examples/PLL/Makefile.am | 3 -
examples/PLL/Makefile.in | 495 -
examples/PLL/main.c | 238 -
examples/README | 11 -
examples/README.md | 66 +
examples/heterotachy/Makefile | 42 +
examples/heterotachy/README.md | 129 +
examples/heterotachy/heterotachy.c | 214 +
examples/heterotachy/target.mk | 2 +
examples/lg4/Makefile | 44 +
examples/lg4/data/example.fas | 42 +
examples/lg4/data/example.tree | 9 +
examples/lg4/lg4.c | 422 +
examples/lg4/target.mk | 4 +
examples/load-utree/Makefile | 44 +
examples/load-utree/README.md | 89 +
examples/load-utree/load-utree.c | 82 +
examples/load-utree/target.mk | 2 +
examples/newick-fasta-rooted/Makefile | 44 +
examples/newick-fasta-rooted/newick-fasta-rooted.c | 369 +
examples/newick-fasta-rooted/target.mk | 2 +
examples/newick-fasta-unrooted/Makefile | 44 +
.../newick-fasta-unrooted/newick-fasta-unrooted.c | 385 +
examples/newick-fasta-unrooted/target.mk | 2 +
examples/newick-phylip-unrooted/Makefile | 44 +
.../newick-phylip-unrooted.c | 352 +
examples/newick-phylip-unrooted/target.mk | 2 +
examples/newton/Makefile | 44 +
examples/newton/README.md | 249 +
examples/newton/newton.c | 241 +
examples/newton/target.mk | 2 +
examples/parsimony/Makefile | 44 +
examples/parsimony/npr-pars.c | 274 +
examples/parsimony/target.mk | 2 +
examples/partial-traversal/Makefile | 44 +
examples/partial-traversal/partial.c | 469 +
examples/partial-traversal/target.mk | 2 +
examples/protein-list/Makefile | 44 +
examples/protein-list/protein-list.c | 438 +
examples/protein-list/target.mk | 2 +
examples/rooted-tacg/Makefile | 44 +
examples/rooted-tacg/rooted-tacg.c | 387 +
examples/rooted-tacg/target.mk | 2 +
examples/rooted/Makefile | 44 +
examples/rooted/README.md | 174 +
examples/rooted/rooted.c | 201 +
examples/rooted/target.mk | 2 +
examples/stepwise/Makefile | 44 +
examples/stepwise/stepwise.c | 202 +
examples/stepwise/target.mk | 2 +
examples/unrooted/Makefile | 44 +
examples/unrooted/README.md | 170 +
examples/unrooted/target.mk | 2 +
examples/unrooted/unrooted.c | 215 +
install-sh | 527 -
ltmain.sh | 9661 ---------
m4/ax_check_compile_flag.m4 | 12 +-
m4/ax_ext.m4 | 404 +-
...x_gcc_x86_cpuid.m4 => ax_gcc_x86_avx_xgetbv.m4} | 54 +-
m4/ax_gcc_x86_cpuid.m4 | 23 +-
m4/ax_mpi.m4 | 176 -
m4/libtool.m4 | 8001 --------
m4/ltoptions.m4 | 384 -
m4/ltsugar.m4 | 123 -
m4/ltversion.m4 | 23 -
m4/lt~obsolete.m4 | 98 -
man/Makefile.am | 19 +
man/Makefile.in | 518 -
man/libpll.3 | 666 +-
missing | 215 -
sources.am | 2 -
src/Makefile.am | 131 +-
src/Makefile.in | 3475 ----
src/alignment.c | 832 -
src/avxLikelihood.c | 4106 ----
src/bipartitionList.c | 434 -
src/compress.c | 286 +
src/core_derivatives.c | 589 +
src/core_derivatives_avx.c | 1043 +
src/core_derivatives_avx2.c | 692 +
src/core_derivatives_sse.c | 206 +
src/core_likelihood.c | 844 +
src/core_likelihood_avx.c | 1081 +
src/core_likelihood_avx2.c | 430 +
src/core_likelihood_sse.c | 827 +
src/core_partials.c | 779 +
src/core_partials_avx.c | 1474 ++
src/core_partials_avx2.c | 702 +
src/core_partials_sse.c | 1162 ++
src/core_pmatrix.c | 243 +
src/core_pmatrix_avx.c | 584 +
src/core_pmatrix_avx2.c | 269 +
src/core_pmatrix_sse.c | 235 +
src/cycle.h | 516 -
src/derivatives.c | 312 +
src/errcodes.h | 68 -
src/evaluateGenericSpecial.c | 3322 ---
src/evaluatePartialGenericSpecial.c | 1373 --
src/fastDNAparsimony.c | 1893 --
src/fast_parsimony.c | 774 +
src/fast_parsimony_avx.c | 404 +
src/fast_parsimony_avx2.c | 399 +
src/fast_parsimony_sse.c | 345 +
src/fasta.c | 324 +
src/gamma.c | 271 +
src/genericParallelization.c | 2302 ---
src/genericParallelization.h | 123 -
src/globalVariables.h | 170 -
src/hardware.h | 48 -
src/hash.c | 223 -
src/hash.h | 50 -
src/lex_phylip.l | 96 +
src/lex_rtree.l | 122 +
src/lex_utree.l | 122 +
src/lexer.c | 299 -
src/lexer.h | 88 -
src/likelihood.c | 513 +
src/list.c | 87 +
src/makenewzGenericSpecial.c | 3147 ---
src/maps.c | 1136 ++
src/mem_alloc.h | 17 -
src/mic_native.h | 57 -
src/models.c | 4613 +----
src/newick.c | 594 -
src/newviewGenericSpecial.c | 8985 --------
src/optimizeModel.c | 3155 ---
src/output.c | 96 +
src/parsePartition.c | 394 -
src/parsePartition.h | 52 -
src/parse_phylip.y | 244 +
src/parse_rtree.y | 284 +
src/parse_utree.y | 377 +
src/parsimony.c | 1127 +-
src/partials.c | 214 +
src/pll.c | 1103 +
src/pll.h | 3127 ++-
src/pllInternal.h | 266 -
src/queue.c | 96 -
src/queue.h | 48 -
src/randomTree.c | 177 -
src/recom.c | 688 -
src/restartHashTable.c | 357 -
src/rtree.c | 478 +
src/searchAlgo.c | 3682 ----
src/ssort.c | 121 -
src/stack.c | 85 -
src/stack.h | 48 -
src/stepwise.c | 542 +
src/topologies.c | 778 -
src/trash.c | 129 -
src/treeIO.c | 241 -
src/utils.c | 4087 ----
src/utree.c | 665 +
src/utree_moves.c | 375 +
src/utree_svg.c | 488 +
test/Makefile | 60 +
test/Makefile.w64 | 48 +
test/README.md | 119 +
test/eval_valgrind.sh | 50 +
test/out/00010_NMDU_lkcalc.out | 98 +
test/out/00011_NMAU_lkcalc.out | 354 +
test/out/00012_NMOU_lkcalc.out | 146 +
test/out/00020_NMDR_lkcalc.out | 98 +
test/out/00021_NMAR_lkcalc.out | 354 +
test/out/00022_NMOR_lkcalc.out | 146 +
test/out/00030_NMDU_gamma.out | 98 +
test/out/00032_NMOU_gamma.out | 1228 ++
test/out/00110_NPDN_fasta.exe.out | 50 +
test/out/00110_NPDN_fasta.out | 50 +
test/out/00120_NPAN_fasta.exe.out | 46 +
test/out/00120_NPAN_fasta.out | 46 +
test/out/README.md | 9 +
test/out/alpha-cats.exe.out | 6571 ++++++
test/out/alpha-cats.out | 6346 ++++++
test/out/asc-bias.out | 134 +
test/out/derivatives-oddstates.out | 913 +
test/out/derivatives.out | 913 +
test/out/hky.exe.out | 1011 +
test/out/hky.out | 1011 +
test/out/partial-traversal.out | 124 +
test/out/protein-models.exe.out | 6765 +++++++
test/out/protein-models.out | 6670 ++++++
test/out/rooted-tipinner.out | 733 +
test/out/rooted.out | 733 +
test/out/skip.out | 1 +
test/runtest.py | 440 +
test/src/00010_NMDU_lkcalc.c | 210 +
test/src/00011_NMAU_lkcalc.c | 200 +
test/src/00012_NMOU_lkcalc.c | 221 +
test/src/00020_NMDR_lkcalc.c | 222 +
test/src/00021_NMAR_lkcalc.c | 211 +
test/src/00022_NMOR_lkcalc.c | 246 +
test/src/00030_NMDU_gamma.c | 215 +
test/src/00032_NMOU_gamma.c | 237 +
test/src/00110_NPDN_fasta.c | 212 +
test/src/00120_NPAN_fasta.c | 152 +
test/src/README.md | 104 +
test/src/alpha-cats.c | 187 +
test/src/asc-bias.c | 266 +
test/src/common.c | 209 +
test/src/common.h | 54 +
test/src/derivatives-oddstates.c | 368 +
test/src/derivatives.c | 356 +
test/src/hky.c | 161 +
test/src/partial-traversal.c | 388 +
test/src/pll.h | 1 +
test/src/protein-models.c | 212 +
test/src/rng.h | 172 +
test/src/rooted-tipinner.c | 295 +
test/src/rooted.c | 290 +
test/testwin.sh | 8 +
243 files changed, 71452 insertions(+), 104539 deletions(-)
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