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 <[email protected]> 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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libpll.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
