[med-svn] [libpll] branch upstream updated (0c97daa -> 1ae4973)
Andreas Tille
tille at debian.org
Mon Mar 20 21:22:52 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 0c97daa New upstream version 1.0.11
new 1ae4973 New upstream version 0.0.20170317
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:
.travis.yml | 7 +
AUTHORS | 0
ChangeLog | 24 -
ChangeLog.md | 49 +
INSTALL | 370 -
COPYING => LICENSE.txt | 147 +-
MPI/Makefile.am | 33 -
MPI/Makefile.in | 2354 ---
Makefile.am | 9 +-
Makefile.in | 814 -
NEWS | 0
README | 0
README.md | 297 +
aclocal.m4 | 1158 --
autogen.sh | 2 +
compile | 347 -
config.guess | 1558 --
config.h.in | 248 -
config.sub | 1791 --
configure | 20260 -------------------
configure.ac | 152 +-
depcomp | 791 -
examples/Makefile.am | 17 +-
examples/Makefile.in | 620 -
examples/PLL/Makefile.AVX | 21 -
examples/PLL/Makefile.AVX-MPI | 20 -
examples/PLL/Makefile.AVX-PTHREADS | 21 -
examples/PLL/Makefile.AVX.clang | 21 -
examples/PLL/Makefile.SSE3 | 19 -
examples/PLL/Makefile.SSE3-MPI | 20 -
examples/PLL/Makefile.SSE3-PTHREADS | 21 -
examples/PLL/Makefile.SSE3.clang | 21 -
examples/PLL/Makefile.am | 3 -
examples/PLL/Makefile.in | 495 -
examples/PLL/main.c | 238 -
examples/README | 11 -
examples/README.md | 66 +
examples/heterotachy/Makefile | 42 +
examples/heterotachy/README.md | 129 +
examples/heterotachy/heterotachy.c | 214 +
examples/heterotachy/target.mk | 2 +
examples/lg4/Makefile | 44 +
examples/lg4/data/example.fas | 42 +
examples/lg4/data/example.tree | 9 +
examples/lg4/lg4.c | 422 +
examples/lg4/target.mk | 4 +
examples/load-utree/Makefile | 44 +
examples/load-utree/README.md | 89 +
examples/load-utree/load-utree.c | 82 +
examples/load-utree/target.mk | 2 +
examples/newick-fasta-rooted/Makefile | 44 +
examples/newick-fasta-rooted/newick-fasta-rooted.c | 369 +
examples/newick-fasta-rooted/target.mk | 2 +
examples/newick-fasta-unrooted/Makefile | 44 +
.../newick-fasta-unrooted/newick-fasta-unrooted.c | 385 +
examples/newick-fasta-unrooted/target.mk | 2 +
examples/newick-phylip-unrooted/Makefile | 44 +
.../newick-phylip-unrooted.c | 352 +
examples/newick-phylip-unrooted/target.mk | 2 +
examples/newton/Makefile | 44 +
examples/newton/README.md | 249 +
examples/newton/newton.c | 241 +
examples/newton/target.mk | 2 +
examples/parsimony/Makefile | 44 +
examples/parsimony/npr-pars.c | 274 +
examples/parsimony/target.mk | 2 +
examples/partial-traversal/Makefile | 44 +
examples/partial-traversal/partial.c | 469 +
examples/partial-traversal/target.mk | 2 +
examples/protein-list/Makefile | 44 +
examples/protein-list/protein-list.c | 438 +
examples/protein-list/target.mk | 2 +
examples/rooted-tacg/Makefile | 44 +
examples/rooted-tacg/rooted-tacg.c | 387 +
examples/rooted-tacg/target.mk | 2 +
examples/rooted/Makefile | 44 +
examples/rooted/README.md | 174 +
examples/rooted/rooted.c | 201 +
examples/rooted/target.mk | 2 +
examples/stepwise/Makefile | 44 +
examples/stepwise/stepwise.c | 202 +
examples/stepwise/target.mk | 2 +
examples/unrooted/Makefile | 44 +
examples/unrooted/README.md | 170 +
examples/unrooted/target.mk | 2 +
examples/unrooted/unrooted.c | 215 +
install-sh | 527 -
ltmain.sh | 9661 ---------
m4/ax_check_compile_flag.m4 | 12 +-
m4/ax_ext.m4 | 404 +-
...x_gcc_x86_cpuid.m4 => ax_gcc_x86_avx_xgetbv.m4} | 54 +-
m4/ax_gcc_x86_cpuid.m4 | 23 +-
m4/ax_mpi.m4 | 176 -
m4/libtool.m4 | 8001 --------
m4/ltoptions.m4 | 384 -
m4/ltsugar.m4 | 123 -
m4/ltversion.m4 | 23 -
m4/lt~obsolete.m4 | 98 -
man/Makefile.am | 19 +
man/Makefile.in | 518 -
man/libpll.3 | 666 +-
missing | 215 -
sources.am | 2 -
src/Makefile.am | 131 +-
src/Makefile.in | 3475 ----
src/alignment.c | 832 -
src/avxLikelihood.c | 4106 ----
src/bipartitionList.c | 434 -
src/compress.c | 286 +
src/core_derivatives.c | 589 +
src/core_derivatives_avx.c | 1043 +
src/core_derivatives_avx2.c | 692 +
src/core_derivatives_sse.c | 206 +
src/core_likelihood.c | 844 +
src/core_likelihood_avx.c | 1081 +
src/core_likelihood_avx2.c | 430 +
src/core_likelihood_sse.c | 827 +
src/core_partials.c | 779 +
src/core_partials_avx.c | 1474 ++
src/core_partials_avx2.c | 702 +
src/core_partials_sse.c | 1162 ++
src/core_pmatrix.c | 243 +
src/core_pmatrix_avx.c | 584 +
src/core_pmatrix_avx2.c | 269 +
src/core_pmatrix_sse.c | 235 +
src/cycle.h | 516 -
src/derivatives.c | 312 +
src/errcodes.h | 68 -
src/evaluateGenericSpecial.c | 3322 ---
src/evaluatePartialGenericSpecial.c | 1373 --
src/fastDNAparsimony.c | 1893 --
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 | 324 +
src/gamma.c | 271 +
src/genericParallelization.c | 2302 ---
src/genericParallelization.h | 123 -
src/globalVariables.h | 170 -
src/hardware.h | 48 -
src/hash.c | 223 -
src/hash.h | 50 -
src/lex_phylip.l | 96 +
src/lex_rtree.l | 122 +
src/lex_utree.l | 122 +
src/lexer.c | 299 -
src/lexer.h | 88 -
src/likelihood.c | 513 +
src/list.c | 87 +
src/makenewzGenericSpecial.c | 3147 ---
src/maps.c | 1136 ++
src/mem_alloc.h | 17 -
src/mic_native.h | 57 -
src/models.c | 4613 +----
src/newick.c | 594 -
src/newviewGenericSpecial.c | 8985 --------
src/optimizeModel.c | 3155 ---
src/output.c | 96 +
src/parsePartition.c | 394 -
src/parsePartition.h | 52 -
src/parse_phylip.y | 244 +
src/parse_rtree.y | 284 +
src/parse_utree.y | 377 +
src/parsimony.c | 1127 +-
src/partials.c | 214 +
src/pll.c | 1103 +
src/pll.h | 3127 ++-
src/pllInternal.h | 266 -
src/queue.c | 96 -
src/queue.h | 48 -
src/randomTree.c | 177 -
src/recom.c | 688 -
src/restartHashTable.c | 357 -
src/rtree.c | 478 +
src/searchAlgo.c | 3682 ----
src/ssort.c | 121 -
src/stack.c | 85 -
src/stack.h | 48 -
src/stepwise.c | 542 +
src/topologies.c | 778 -
src/trash.c | 129 -
src/treeIO.c | 241 -
src/utils.c | 4087 ----
src/utree.c | 665 +
src/utree_moves.c | 375 +
src/utree_svg.c | 488 +
test/Makefile | 60 +
test/Makefile.w64 | 48 +
test/README.md | 119 +
test/eval_valgrind.sh | 50 +
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/00032_NMOU_gamma.out | 1228 ++
test/out/00110_NPDN_fasta.exe.out | 50 +
test/out/00110_NPDN_fasta.out | 50 +
test/out/00120_NPAN_fasta.exe.out | 46 +
test/out/00120_NPAN_fasta.out | 46 +
test/out/README.md | 9 +
test/out/alpha-cats.exe.out | 6571 ++++++
test/out/alpha-cats.out | 6346 ++++++
test/out/asc-bias.out | 134 +
test/out/derivatives-oddstates.out | 913 +
test/out/derivatives.out | 913 +
test/out/hky.exe.out | 1011 +
test/out/hky.out | 1011 +
test/out/partial-traversal.out | 124 +
test/out/protein-models.exe.out | 6765 +++++++
test/out/protein-models.out | 6670 ++++++
test/out/rooted-tipinner.out | 733 +
test/out/rooted.out | 733 +
test/out/skip.out | 1 +
test/runtest.py | 440 +
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/00032_NMOU_gamma.c | 237 +
test/src/00110_NPDN_fasta.c | 212 +
test/src/00120_NPAN_fasta.c | 152 +
test/src/README.md | 104 +
test/src/alpha-cats.c | 187 +
test/src/asc-bias.c | 266 +
test/src/common.c | 209 +
test/src/common.h | 54 +
test/src/derivatives-oddstates.c | 368 +
test/src/derivatives.c | 356 +
test/src/hky.c | 161 +
test/src/partial-traversal.c | 388 +
test/src/pll.h | 1 +
test/src/protein-models.c | 212 +
test/src/rng.h | 172 +
test/src/rooted-tipinner.c | 295 +
test/src/rooted.c | 290 +
test/testwin.sh | 8 +
243 files changed, 71452 insertions(+), 104539 deletions(-)
create mode 100644 .travis.yml
delete mode 100644 AUTHORS
delete mode 100644 ChangeLog
create mode 100644 ChangeLog.md
delete mode 100644 INSTALL
rename COPYING => LICENSE.txt (86%)
delete mode 100644 MPI/Makefile.am
delete mode 100644 MPI/Makefile.in
delete mode 100644 Makefile.in
delete mode 100644 NEWS
delete mode 100644 README
create mode 100644 README.md
delete mode 100644 aclocal.m4
create mode 100755 autogen.sh
delete mode 100755 compile
delete mode 100755 config.guess
delete mode 100644 config.h.in
delete mode 100755 config.sub
delete mode 100755 configure
delete mode 100755 depcomp
delete mode 100644 examples/Makefile.in
delete mode 100644 examples/PLL/Makefile.AVX
delete mode 100644 examples/PLL/Makefile.AVX-MPI
delete mode 100644 examples/PLL/Makefile.AVX-PTHREADS
delete mode 100644 examples/PLL/Makefile.AVX.clang
delete mode 100644 examples/PLL/Makefile.SSE3
delete mode 100644 examples/PLL/Makefile.SSE3-MPI
delete mode 100644 examples/PLL/Makefile.SSE3-PTHREADS
delete mode 100644 examples/PLL/Makefile.SSE3.clang
delete mode 100644 examples/PLL/Makefile.am
delete mode 100644 examples/PLL/Makefile.in
delete mode 100644 examples/PLL/main.c
delete mode 100644 examples/README
create mode 100644 examples/README.md
create mode 100644 examples/heterotachy/Makefile
create mode 100644 examples/heterotachy/README.md
create mode 100644 examples/heterotachy/heterotachy.c
create mode 100644 examples/heterotachy/target.mk
create mode 100644 examples/lg4/Makefile
create mode 100644 examples/lg4/data/example.fas
create mode 100644 examples/lg4/data/example.tree
create mode 100644 examples/lg4/lg4.c
create mode 100644 examples/lg4/target.mk
create mode 100644 examples/load-utree/Makefile
create mode 100644 examples/load-utree/README.md
create mode 100644 examples/load-utree/load-utree.c
create mode 100644 examples/load-utree/target.mk
create mode 100644 examples/newick-fasta-rooted/Makefile
create mode 100644 examples/newick-fasta-rooted/newick-fasta-rooted.c
create mode 100644 examples/newick-fasta-rooted/target.mk
create mode 100644 examples/newick-fasta-unrooted/Makefile
create mode 100644 examples/newick-fasta-unrooted/newick-fasta-unrooted.c
create mode 100644 examples/newick-fasta-unrooted/target.mk
create mode 100644 examples/newick-phylip-unrooted/Makefile
create mode 100644 examples/newick-phylip-unrooted/newick-phylip-unrooted.c
create mode 100644 examples/newick-phylip-unrooted/target.mk
create mode 100644 examples/newton/Makefile
create mode 100644 examples/newton/README.md
create mode 100644 examples/newton/newton.c
create mode 100644 examples/newton/target.mk
create mode 100644 examples/parsimony/Makefile
create mode 100644 examples/parsimony/npr-pars.c
create mode 100644 examples/parsimony/target.mk
create mode 100644 examples/partial-traversal/Makefile
create mode 100644 examples/partial-traversal/partial.c
create mode 100644 examples/partial-traversal/target.mk
create mode 100644 examples/protein-list/Makefile
create mode 100644 examples/protein-list/protein-list.c
create mode 100644 examples/protein-list/target.mk
create mode 100644 examples/rooted-tacg/Makefile
create mode 100644 examples/rooted-tacg/rooted-tacg.c
create mode 100644 examples/rooted-tacg/target.mk
create mode 100644 examples/rooted/Makefile
create mode 100644 examples/rooted/README.md
create mode 100644 examples/rooted/rooted.c
create mode 100644 examples/rooted/target.mk
create mode 100644 examples/stepwise/Makefile
create mode 100644 examples/stepwise/stepwise.c
create mode 100644 examples/stepwise/target.mk
create mode 100644 examples/unrooted/Makefile
create mode 100644 examples/unrooted/README.md
create mode 100644 examples/unrooted/target.mk
create mode 100644 examples/unrooted/unrooted.c
delete mode 100755 install-sh
delete mode 100644 ltmain.sh
copy m4/{ax_gcc_x86_cpuid.m4 => ax_gcc_x86_avx_xgetbv.m4} (57%)
delete mode 100644 m4/ax_mpi.m4
delete mode 100644 m4/libtool.m4
delete mode 100644 m4/ltoptions.m4
delete mode 100644 m4/ltsugar.m4
delete mode 100644 m4/ltversion.m4
delete mode 100644 m4/lt~obsolete.m4
delete mode 100644 man/Makefile.in
delete mode 100755 missing
delete mode 100644 sources.am
delete mode 100644 src/Makefile.in
delete mode 100644 src/alignment.c
delete mode 100644 src/avxLikelihood.c
delete mode 100644 src/bipartitionList.c
create mode 100644 src/compress.c
create mode 100644 src/core_derivatives.c
create mode 100644 src/core_derivatives_avx.c
create mode 100644 src/core_derivatives_avx2.c
create mode 100644 src/core_derivatives_sse.c
create mode 100644 src/core_likelihood.c
create mode 100644 src/core_likelihood_avx.c
create mode 100644 src/core_likelihood_avx2.c
create mode 100644 src/core_likelihood_sse.c
create mode 100644 src/core_partials.c
create mode 100644 src/core_partials_avx.c
create mode 100644 src/core_partials_avx2.c
create mode 100644 src/core_partials_sse.c
create mode 100644 src/core_pmatrix.c
create mode 100644 src/core_pmatrix_avx.c
create mode 100644 src/core_pmatrix_avx2.c
create mode 100644 src/core_pmatrix_sse.c
delete mode 100644 src/cycle.h
create mode 100644 src/derivatives.c
delete mode 100644 src/errcodes.h
delete mode 100644 src/evaluateGenericSpecial.c
delete mode 100644 src/evaluatePartialGenericSpecial.c
delete mode 100644 src/fastDNAparsimony.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/fasta.c
create mode 100644 src/gamma.c
delete mode 100644 src/genericParallelization.c
delete mode 100644 src/genericParallelization.h
delete mode 100644 src/globalVariables.h
delete mode 100644 src/hardware.h
delete mode 100644 src/hash.c
delete mode 100644 src/hash.h
create mode 100644 src/lex_phylip.l
create mode 100644 src/lex_rtree.l
create mode 100644 src/lex_utree.l
delete mode 100644 src/lexer.c
delete mode 100644 src/lexer.h
create mode 100644 src/likelihood.c
create mode 100644 src/list.c
delete mode 100644 src/makenewzGenericSpecial.c
create mode 100644 src/maps.c
delete mode 100644 src/mem_alloc.h
delete mode 100644 src/mic_native.h
delete mode 100644 src/newick.c
delete mode 100644 src/newviewGenericSpecial.c
delete mode 100644 src/optimizeModel.c
create mode 100644 src/output.c
delete mode 100644 src/parsePartition.c
delete mode 100644 src/parsePartition.h
create mode 100644 src/parse_phylip.y
create mode 100644 src/parse_rtree.y
create mode 100644 src/parse_utree.y
create mode 100644 src/partials.c
create mode 100644 src/pll.c
delete mode 100644 src/pllInternal.h
delete mode 100644 src/queue.c
delete mode 100644 src/queue.h
delete mode 100644 src/randomTree.c
delete mode 100644 src/recom.c
delete mode 100644 src/restartHashTable.c
create mode 100644 src/rtree.c
delete mode 100644 src/searchAlgo.c
delete mode 100644 src/ssort.c
delete mode 100644 src/stack.c
delete mode 100644 src/stack.h
create mode 100644 src/stepwise.c
delete mode 100644 src/topologies.c
delete mode 100644 src/trash.c
delete mode 100644 src/treeIO.c
delete mode 100644 src/utils.c
create mode 100644 src/utree.c
create mode 100644 src/utree_moves.c
create mode 100644 src/utree_svg.c
create mode 100644 test/Makefile
create mode 100644 test/Makefile.w64
create mode 100644 test/README.md
create mode 100755 test/eval_valgrind.sh
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
create mode 100644 test/out/00110_NPDN_fasta.exe.out
create mode 100644 test/out/00110_NPDN_fasta.out
create mode 100644 test/out/00120_NPAN_fasta.exe.out
create mode 100644 test/out/00120_NPAN_fasta.out
create mode 100644 test/out/README.md
create mode 100644 test/out/alpha-cats.exe.out
create mode 100644 test/out/alpha-cats.out
create mode 100644 test/out/asc-bias.out
create mode 100644 test/out/derivatives-oddstates.out
create mode 100644 test/out/derivatives.out
create mode 100644 test/out/hky.exe.out
create mode 100644 test/out/hky.out
create mode 100644 test/out/partial-traversal.out
create mode 100644 test/out/protein-models.exe.out
create mode 100644 test/out/protein-models.out
create mode 100644 test/out/rooted-tipinner.out
create mode 100644 test/out/rooted.out
create mode 100644 test/out/skip.out
create mode 100755 test/runtest.py
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
create mode 100644 test/src/00032_NMOU_gamma.c
create mode 100644 test/src/00110_NPDN_fasta.c
create mode 100644 test/src/00120_NPAN_fasta.c
create mode 100644 test/src/README.md
create mode 100644 test/src/alpha-cats.c
create mode 100644 test/src/asc-bias.c
create mode 100644 test/src/common.c
create mode 100644 test/src/common.h
create mode 100644 test/src/derivatives-oddstates.c
create mode 100644 test/src/derivatives.c
create mode 100644 test/src/hky.c
create mode 100644 test/src/partial-traversal.c
create mode 120000 test/src/pll.h
create mode 100644 test/src/protein-models.c
create mode 100644 test/src/rng.h
create mode 100644 test/src/rooted-tipinner.c
create mode 100644 test/src/rooted.c
create mode 100755 test/testwin.sh
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libpll.git
More information about the debian-med-commit
mailing list