[med-svn] [libpll] 02/04: Merge tag 'upstream/0.0+20160909'
Andreas Tille
tille at debian.org
Wed May 3 13:17:44 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to tag debian/0.0+20160909-1
in repository libpll.
commit 98930e7b3769078c14a712df7296f2410d47d113
Merge: 51a1547 7a71aa4
Author: Andreas Tille <tille at debian.org>
Date: Tue Apr 25 17:54:11 2017 +0200
Merge tag 'upstream/0.0+20160909'
Upstream version 0.0+20160909
.gitignore | 6 +
configure.ac | 17 +-
examples/Makefile.am | 1 -
examples/lg4/lg4.c | 2 +-
examples/load-utree/load-utree.c | 2 +-
examples/newick-fasta-rooted/.gitignore | 1 +
examples/newick-fasta-rooted/newick-fasta-rooted.c | 2 +-
examples/newick-fasta-unrooted/.gitignore | 2 +
.../newick-fasta-unrooted/newick-fasta-unrooted.c | 10 +-
.../newick-phylip-unrooted.c | 2 +-
examples/partial-traversal/.gitignore | 1 +
examples/partial-traversal/partial.c | 16 +-
examples/protein-list/.gitignore | 1 +
examples/protein-list/protein-list.c | 4 +-
examples/rooted-tacg/rooted-tacg.c | 2 +-
examples/rooted/rooted.c | 2 +-
examples/stepwise/Makefile | 44 -
examples/stepwise/stepwise.c | 202 -----
examples/stepwise/target.mk | 2 -
examples/unrooted/.gitignore | 1 +
examples/unrooted/Makefile | 2 +-
examples/unrooted/unrooted.c | 2 +-
src/Makefile.am | 70 +-
src/core_derivatives.c | 124 +--
src/core_derivatives_avx.c | 745 +++++++---------
src/core_derivatives_avx2.c | 692 ---------------
src/core_derivatives_sse.c | 128 +--
src/core_likelihood.c | 219 +----
src/core_likelihood_avx.c | 362 +-------
src/core_likelihood_avx2.c | 430 ---------
src/core_likelihood_sse.c | 25 +-
src/core_partials.c | 160 +---
src/core_partials_avx.c | 596 ++-----------
src/core_partials_avx2.c | 702 ---------------
src/core_partials_sse.c | 3 +-
src/core_pmatrix.c | 78 +-
src/core_pmatrix_avx.c | 517 ++---------
src/core_pmatrix_avx2.c | 269 ------
src/core_pmatrix_sse.c | 102 +--
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/lex_phylip.l | 39 +-
src/lex_rtree.l | 58 +-
src/lex_utree.l | 58 +-
src/likelihood.c | 34 +-
src/maps.c | 41 +-
src/models.c | 94 +-
src/parse_phylip.y | 31 +-
src/parse_rtree.y | 76 +-
src/parse_utree.y | 93 +-
src/parsimony.c | 64 +-
src/partials.c | 1 -
src/pll.c | 23 +-
src/pll.h | 466 ++--------
src/rtree.c | 12 +-
src/stepwise.c | 542 ------------
src/utree.c | 35 +-
src/utree_svg.c | 6 +-
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 | 98 ---
test/out/asc-bias.out | 92 +-
test/out/derivatives-oddstates.out | 972 ++++++++++-----------
test/out/derivatives.out | 972 ++++++++++-----------
...{00110_NPDN_fasta.exe.out => fasta-dna.exe.out} | 0
test/out/{00110_NPDN_fasta.out => fasta-dna.out} | 0
...00120_NPAN_fasta.exe.out => fasta-prot.exe.out} | 0
test/out/{00120_NPAN_fasta.out => fasta-prot.out} | 0
test/out/{00032_NMOU_gamma.out => odd-states.out} | 0
test/runtest.py | 32 +-
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/README.md | 3 -
test/src/asc-bias.c | 130 ++-
test/src/common.c | 44 +-
test/src/common.h | 11 -
test/src/derivatives-oddstates.c | 8 +-
test/src/derivatives.c | 8 +-
test/src/{00110_NPDN_fasta.c => fasta-dna.c} | 0
test/src/{00120_NPAN_fasta.c => fasta-prot.c} | 0
test/src/{00032_NMOU_gamma.c => odd-states.c} | 0
test/src/partial-traversal.c | 51 +-
test/src/rooted-tipinner.c | 13 +-
test/src/rooted.c | 19 +-
99 files changed, 2308 insertions(+), 12174 deletions(-)
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