[med-svn] [libpll] branch upstream updated (1ae4973 -> 241b1fd)
Andreas Tille
tille at debian.org
Fri May 5 13:05:15 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 1ae4973 New upstream version 0.0.20170317
adds 7a71aa4 New upstream version 0.0+20160909
new 241b1fd New upstream version 0.0+20160909+ds1
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:
configure.ac | 17 +-
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/lg4/lg4.c | 2 +-
examples/load-utree/load-utree.c | 2 +-
examples/newick-fasta-rooted/newick-fasta-rooted.c | 2 +-
.../newick-fasta-unrooted/newick-fasta-unrooted.c | 10 +-
.../newick-phylip-unrooted.c | 2 +-
examples/partial-traversal/partial.c | 16 +-
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/Makefile | 2 +-
examples/unrooted/unrooted.c | 2 +-
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 --
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/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 +-
106 files changed, 3109 insertions(+), 12720 deletions(-)
create mode 100644 debian/changelog
create mode 100644 debian/clean
create mode 100644 debian/compat
create mode 100644 debian/control
create mode 100644 debian/copyright
create mode 100755 debian/get-orig-source
create mode 100755 debian/rules
create mode 100644 debian/source/format
create mode 100644 debian/upstream/metadata
create mode 100644 debian/watch
delete mode 100644 examples/stepwise/Makefile
delete mode 100644 examples/stepwise/stepwise.c
delete mode 100644 examples/stepwise/target.mk
delete mode 100644 m4/ax_check_compile_flag.m4
delete mode 100644 m4/ax_ext.m4
delete mode 100644 m4/ax_gcc_x86_avx_xgetbv.m4
delete mode 100644 m4/ax_gcc_x86_cpuid.m4
delete mode 100644 src/core_derivatives_avx2.c
delete mode 100644 src/core_likelihood_avx2.c
delete mode 100644 src/core_partials_avx2.c
delete mode 100644 src/core_pmatrix_avx2.c
delete mode 100644 src/fast_parsimony.c
delete mode 100644 src/fast_parsimony_avx.c
delete mode 100644 src/fast_parsimony_avx2.c
delete mode 100644 src/fast_parsimony_sse.c
delete mode 100644 src/stepwise.c
delete mode 100644 test/out/00010_NMDU_lkcalc.out
delete mode 100644 test/out/00011_NMAU_lkcalc.out
delete mode 100644 test/out/00012_NMOU_lkcalc.out
delete mode 100644 test/out/00020_NMDR_lkcalc.out
delete mode 100644 test/out/00021_NMAR_lkcalc.out
delete mode 100644 test/out/00022_NMOR_lkcalc.out
delete mode 100644 test/out/00030_NMDU_gamma.out
rename test/out/{00110_NPDN_fasta.exe.out => fasta-dna.exe.out} (100%)
rename test/out/{00110_NPDN_fasta.out => fasta-dna.out} (100%)
rename test/out/{00120_NPAN_fasta.exe.out => fasta-prot.exe.out} (100%)
rename test/out/{00120_NPAN_fasta.out => fasta-prot.out} (100%)
rename test/out/{00032_NMOU_gamma.out => odd-states.out} (100%)
delete mode 100644 test/src/00010_NMDU_lkcalc.c
delete mode 100644 test/src/00011_NMAU_lkcalc.c
delete mode 100644 test/src/00012_NMOU_lkcalc.c
delete mode 100644 test/src/00020_NMDR_lkcalc.c
delete mode 100644 test/src/00021_NMAR_lkcalc.c
delete mode 100644 test/src/00022_NMOR_lkcalc.c
delete mode 100644 test/src/00030_NMDU_gamma.c
rename test/src/{00110_NPDN_fasta.c => fasta-dna.c} (100%)
rename test/src/{00120_NPAN_fasta.c => fasta-prot.c} (100%)
rename test/src/{00032_NMOU_gamma.c => odd-states.c} (100%)
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