[med-svn] [phyml] branch master updated (5acfe97 -> 410decc)
Andreas Tille
tille at debian.org
Sat Jun 24 09:44:18 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository phyml.
from 5acfe97 Add todo for past-Stretch release
new cf185c6 New upstream version
new 593167e Introduce phyml-beagle package
adds a845584 Imported Upstream version 3.2.0+dfsg
new 1915459 New upstream version 3.3.20170530+dfsg
new 8d1f2b9 Updated version 3.3.20170530+dfsg from 'upstream/3.3.20170530+dfsg'
new 410decc Refresh patches
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:
ChangeLog | 347 --
NEWS | 0
README | 31 +-
autogen.sh | 0
config.h.in | 10 +-
configure.ac | 74 +-
debian/changelog | 6 +-
debian/control | 30 +-
debian/patches/fix_declaration_of_temp.patch | 4 +-
debian/patches/no-configure-ac-date.patch | 6 +-
debian/patches/no-stdc++.patch | 6 +-
debian/patches/sse_only_if_supported.patch | 11 +-
debian/{links => phyml-beagle.links} | 0
debian/rules | 18 +-
doc/fig/phyrexlog.pdf | Bin 0 -> 463638 bytes
doc/phyml-manual.pdf | Bin 407931 -> 870332 bytes
doc/phyml-manual.tex | 567 +--
doc/ref.bib | 190 +-
examples/phyrex_input_files/h1n1.nxs | 613 +++
examples/phyrex_input_files/usa_coord.txt | 53 +
src/Makefile.am | 171 +-
src/alrt.c | 401 +-
src/avx.c | 424 +++
src/avx.h | 39 +
src/beagle_utils.c | 8 +-
src/bionj.c | 26 +-
src/cl.c | 171 +-
src/cl.h | 1 +
src/date.c | 1249 +++++++
src/date.h | 44 +
src/draw.c | 14 +-
src/eigen.c | 70 +-
src/free.c | 382 +-
src/free.h | 14 +-
src/geo.c | 139 +-
src/help.c | 2 +-
src/init.c | 526 ++-
src/init.h | 11 +-
src/interface.c | 92 +-
src/invitee.c | 191 +-
src/invitee.h | 2 +-
src/io.c | 2708 +++++---------
src/io.h | 12 +-
src/lk.c | 3630 +++++++++---------
src/lk.h | 75 +-
src/m4.c | 230 +-
src/m4.h | 4 +-
src/main.c | 104 +-
src/make.c | 325 +-
src/make.h | 13 +-
src/mcmc.c | 4294 ++++++++++++++-------
src/mcmc.h | 15 +-
src/mg.c | 2820 --------------
src/mg.h | 51 -
src/mixt.c | 1986 ++++++++--
src/mixt.h | 39 +-
src/models.c | 569 ++-
src/models.h | 5 +-
src/mpi_boot.c | 138 +-
src/nexus.c | 12 +-
src/optimiz.c | 1735 ++++-----
src/optimiz.h | 10 +-
src/pars.c | 497 ++-
src/pars.h | 7 +-
src/phyrex.c | 1598 +++++---
src/phyrex.h | 5 +-
src/rates.c | 635 ++--
src/rates.h | 2 +
src/rwrapper.c | 6 +-
src/simu.c | 1118 +++---
src/simu.h | 1 +
src/spr.c | 5201 +++++++-------------------
src/spr.h | 19 +-
src/sse.c | 406 ++
src/sse.h | 36 +
src/stats.c | 606 +--
src/stats.h | 2 +-
src/times.c | 1001 +++--
src/times.h | 8 +-
src/tiporder.c | 122 +-
src/utilities.c | 4849 +++++++++++++-----------
src/utilities.h | 429 ++-
src/xml.c | 1169 +++++-
src/xml.h | 3 +
84 files changed, 23024 insertions(+), 19414 deletions(-)
delete mode 100644 NEWS
mode change 100644 => 100755 autogen.sh
rename debian/{links => phyml-beagle.links} (100%)
create mode 100644 doc/fig/phyrexlog.pdf
create mode 100644 examples/phyrex_input_files/h1n1.nxs
create mode 100644 examples/phyrex_input_files/usa_coord.txt
create mode 100644 src/avx.c
create mode 100644 src/avx.h
create mode 100644 src/date.c
create mode 100644 src/date.h
create mode 100644 src/sse.c
create mode 100644 src/sse.h
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