[med-svn] [libpll] branch master updated (028901c -> 8b3d2c6)
Andreas Tille
tille at debian.org
Fri May 5 13:05:12 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 028901c Adapt build to current upstream development branch
adds 51a1547 Use Github code rather than download
adds 7a71aa4 New upstream version 0.0+20160909
adds 98930e7 Merge tag 'upstream/0.0+20160909'
adds 216dd4e Set version to date of latest commit
adds 36d19ed Add ITP
new 1afa054 No need to create same source twice
new ef30fb0 Remove m4/ files which can be found in package autoconf-archive
new 241b1fd New upstream version 0.0+20160909+ds1
new 081318f Updated version 0.0+20160909+ds1 from 'upstream/0.0+20160909+ds1'
new 8b3d2c6 Check for HAVE_X86INTRIN_H
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:
configure.ac | 17 +-
debian/changelog | 19 +-
debian/control | 3 +-
debian/get-orig-source | 35 +
debian/patches/have_x86intrin_h.patch | 17 +
debian/patches/series | 1 +
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 +-
101 files changed, 2362 insertions(+), 12724 deletions(-)
create mode 100755 debian/get-orig-source
create mode 100644 debian/patches/have_x86intrin_h.patch
create mode 100644 debian/patches/series
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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