[med-svn] [libpll] branch master updated (d6ae178 -> 0bdba7c)
Andreas Tille
tille at debian.org
Mon May 15 07:52:52 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository libpll.
from d6ae178 Deal with +ds1 in Debian version name
new 1f0a55e Upstream starts using release tags
new d3809d0 New upstream version 0.3.0
new 6b7da28 Updated version 0.3.0 from 'upstream/0.3.0'
new f33ad7e Update patch
new 0bdba7c New upstream version uses runtime detection and thus does not use AVX and SSE on i386 and other architectures
The 5 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.gitignore | 6 +
.travis.yml | 98 +-
ChangeLog.md | 34 +
configure.ac | 75 +-
debian/changelog | 7 +-
debian/patches/have_x86intrin_h.patch | 4 +-
debian/watch | 6 +-
examples/Makefile.am | 1 +
examples/heterotachy/heterotachy.c | 2 +-
examples/lg4/lg4.c | 146 +-
examples/load-utree/load-utree.c | 27 +-
examples/{load-utree => 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/{parsimony => stepwise}/Makefile | 2 +-
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 +
130 files changed, 26751 insertions(+), 5618 deletions(-)
create mode 100644 .gitignore
copy examples/{load-utree => newick-export}/Makefile (93%)
create mode 100644 examples/newick-export/newick-export.c
create mode 100644 examples/newick-export/target.mk
create mode 100644 examples/newick-fasta-rooted/.gitignore
create mode 100644 examples/newick-fasta-unrooted/.gitignore
create mode 100644 examples/partial-traversal/.gitignore
create mode 100644 examples/protein-list/.gitignore
copy examples/{parsimony => stepwise}/Makefile (98%)
create mode 100644 examples/stepwise/stepwise.c
create mode 100644 examples/stepwise/target.mk
create mode 100644 examples/unrooted/.gitignore
create mode 100644 m4/ax_check_compile_flag.m4
create mode 100644 m4/ax_ext.m4
create mode 100644 m4/ax_gcc_x86_avx_xgetbv.m4
create mode 100644 m4/ax_gcc_x86_cpuid.m4
create mode 100644 src/core_derivatives_avx2.c
create mode 100644 src/core_likelihood_avx2.c
create mode 100644 src/core_partials_avx2.c
create mode 100644 src/core_pmatrix_avx2.c
create mode 100644 src/fast_parsimony.c
create mode 100644 src/fast_parsimony_avx.c
create mode 100644 src/fast_parsimony_avx2.c
create mode 100644 src/fast_parsimony_sse.c
create mode 100644 src/hardware.c
copy test/src/common.h => src/init.c (53%)
delete mode 100644 src/lex_phylip.l
delete mode 100644 src/parse_phylip.y
create mode 100644 src/phylip.c
create mode 100644 src/random.c
create mode 100644 src/stepwise.c
create mode 100644 test/.gitignore
create mode 100644 test/out/00010_NMDU_lkcalc.out
create mode 100644 test/out/00011_NMAU_lkcalc.out
create mode 100644 test/out/00012_NMOU_lkcalc.out
create mode 100644 test/out/00020_NMDR_lkcalc.out
create mode 100644 test/out/00021_NMAR_lkcalc.out
create mode 100644 test/out/00022_NMOR_lkcalc.out
create mode 100644 test/out/00030_NMDU_gamma.out
create mode 100644 test/out/00032_NMOU_gamma.out
rename test/out/{fasta-dna.exe.out => 00110_NPDN_fasta.exe.out} (100%)
rename test/out/{fasta-dna.out => 00110_NPDN_fasta.out} (100%)
rename test/out/{fasta-prot.exe.out => 00120_NPAN_fasta.exe.out} (100%)
rename test/out/{fasta-prot.out => 00120_NPAN_fasta.out} (100%)
delete mode 100644 test/out/odd-states.out
create mode 100644 test/out/scaling.out
create mode 100644 test/src/00010_NMDU_lkcalc.c
create mode 100644 test/src/00011_NMAU_lkcalc.c
create mode 100644 test/src/00012_NMOU_lkcalc.c
create mode 100644 test/src/00020_NMDR_lkcalc.c
create mode 100644 test/src/00021_NMAR_lkcalc.c
create mode 100644 test/src/00022_NMOR_lkcalc.c
create mode 100644 test/src/00030_NMDU_gamma.c
rename test/src/{odd-states.c => 00032_NMOU_gamma.c} (68%)
rename test/src/{fasta-dna.c => 00110_NPDN_fasta.c} (98%)
rename test/src/{fasta-prot.c => 00120_NPAN_fasta.c} (100%)
create mode 100644 test/src/scaling.c
--
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