[med-svn] [libpll] 03/05: Updated version 0.3.0 from 'upstream/0.3.0'
Andreas Tille
tille at debian.org
Mon May 15 07:52:53 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 6b7da28bdb3147581edc61b6d78d03eedf8fa0bc
Merge: 1f0a55e d3809d0
Author: Andreas Tille <tille at debian.org>
Date: Mon May 15 08:46:12 2017 +0200
Updated version 0.3.0 from 'upstream/0.3.0'
with Debian dir 14e71022628b87f46cd17089c5b6312eaa2d6516
.gitignore | 6 +
.travis.yml | 98 +-
ChangeLog.md | 34 +
configure.ac | 75 +-
examples/Makefile.am | 1 +
examples/heterotachy/heterotachy.c | 2 +-
examples/lg4/lg4.c | 146 +-
examples/load-utree/load-utree.c | 27 +-
examples/{unrooted => newick-export}/Makefile | 6 +-
examples/newick-export/newick-export.c | 191 +
examples/newick-export/target.mk | 2 +
examples/newick-fasta-rooted/.gitignore | 1 +
examples/newick-fasta-rooted/newick-fasta-rooted.c | 94 +-
examples/newick-fasta-unrooted/.gitignore | 2 +
.../newick-fasta-unrooted/newick-fasta-unrooted.c | 123 +-
.../newick-phylip-unrooted.c | 124 +-
examples/newton/newton.c | 4 +-
examples/parsimony/npr-pars.c | 79 +-
examples/partial-traversal/.gitignore | 1 +
examples/partial-traversal/partial.c | 125 +-
examples/protein-list/.gitignore | 1 +
examples/protein-list/protein-list.c | 117 +-
examples/rooted-tacg/rooted-tacg.c | 2 +-
examples/rooted/rooted.c | 2 +-
examples/{unrooted => stepwise}/Makefile | 4 +-
examples/stepwise/stepwise.c | 243 +
examples/stepwise/target.mk | 2 +
examples/unrooted/.gitignore | 1 +
examples/unrooted/Makefile | 2 +-
examples/unrooted/unrooted.c | 4 +-
m4/ax_check_compile_flag.m4 | 74 +
m4/ax_ext.m4 | 303 +
m4/ax_gcc_x86_avx_xgetbv.m4 | 79 +
m4/ax_gcc_x86_cpuid.m4 | 90 +
man/libpll.3 | 10 +
src/Makefile.am | 72 +-
src/core_derivatives.c | 267 +-
src/core_derivatives_avx.c | 775 ++-
src/core_derivatives_avx2.c | 692 ++
src/core_derivatives_sse.c | 231 +-
src/core_likelihood.c | 396 +-
src/core_likelihood_avx.c | 403 +-
src/core_likelihood_avx2.c | 430 ++
src/core_likelihood_sse.c | 209 +-
src/core_partials.c | 326 +-
src/core_partials_avx.c | 598 +-
src/core_partials_avx2.c | 702 ++
src/core_partials_sse.c | 197 +-
src/core_pmatrix.c | 92 +-
src/core_pmatrix_avx.c | 527 +-
src/core_pmatrix_avx2.c | 269 +
src/core_pmatrix_sse.c | 112 +-
src/derivatives.c | 115 +-
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 | 2 +-
src/gamma.c | 25 +-
src/hardware.c | 121 +
test/src/common.h => src/init.c | 35 +-
src/lex_phylip.l | 93 -
src/lex_rtree.l | 58 +-
src/lex_utree.l | 58 +-
src/likelihood.c | 34 +-
src/maps.c | 72 +-
src/models.c | 94 +-
src/output.c | 4 +-
src/parse_phylip.y | 229 -
src/parse_rtree.y | 224 +-
src/parse_utree.y | 286 +-
src/parsimony.c | 70 +-
src/partials.c | 1 +
src/phylip.c | 736 ++
src/pll.c | 42 +-
src/pll.h | 927 ++-
src/random.c | 393 ++
src/rtree.c | 206 +-
src/stepwise.c | 546 ++
src/utree.c | 353 +-
src/utree_moves.c | 28 +-
src/utree_svg.c | 138 +-
test/.gitignore | 5 +
test/Makefile | 21 +-
test/README.md | 26 +
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 | 205 +
test/out/00032_NMOU_gamma.out | 2443 +++++++
...{fasta-dna.exe.out => 00110_NPDN_fasta.exe.out} | 0
test/out/{fasta-dna.out => 00110_NPDN_fasta.out} | 0
...fasta-prot.exe.out => 00120_NPAN_fasta.exe.out} | 0
test/out/{fasta-prot.out => 00120_NPAN_fasta.out} | 0
test/out/alpha-cats.out | 7135 ++++++++++++++++++--
test/out/asc-bias.out | 92 +-
test/out/derivatives-oddstates.out | 972 +--
test/out/derivatives.out | 972 +--
test/out/odd-states.out | 1228 ----
test/out/scaling.out | 64 +
test/runtest.py | 39 +-
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 | 251 +
test/src/{odd-states.c => 00032_NMOU_gamma.c} | 154 +-
test/src/{fasta-dna.c => 00110_NPDN_fasta.c} | 2 +-
test/src/{fasta-prot.c => 00120_NPAN_fasta.c} | 0
test/src/README.md | 7 +
test/src/alpha-cats.c | 154 +-
test/src/asc-bias.c | 180 +-
test/src/common.c | 77 +-
test/src/common.h | 17 +-
test/src/derivatives-oddstates.c | 10 +-
test/src/derivatives.c | 10 +-
test/src/hky.c | 2 +-
test/src/partial-traversal.c | 129 +-
test/src/protein-models.c | 2 +-
test/src/rooted-tipinner.c | 61 +-
test/src/rooted.c | 67 +-
test/src/scaling.c | 338 +
127 files changed, 26745 insertions(+), 5609 deletions(-)
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