[med-svn] [libpll] branch upstream updated (241b1fd -> d3809d0)
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 change to branch upstream
in repository libpll.
from 241b1fd New upstream version 0.0+20160909+ds1
new d3809d0 New upstream version 0.3.0
The 1 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 | 5 -
debian/clean | 18 -
debian/compat | 1 -
debian/control | 50 -
debian/copyright | 673 --
debian/get-orig-source | 35 -
debian/rules | 21 -
debian/source/format | 1 -
debian/upstream/metadata | 7 -
debian/watch | 7 -
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 +
137 files changed, 26744 insertions(+), 6426 deletions(-)
create mode 100644 .gitignore
delete mode 100644 debian/changelog
delete mode 100644 debian/clean
delete mode 100644 debian/compat
delete mode 100644 debian/control
delete mode 100644 debian/copyright
delete mode 100755 debian/get-orig-source
delete mode 100755 debian/rules
delete mode 100644 debian/source/format
delete mode 100644 debian/upstream/metadata
delete mode 100644 debian/watch
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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