[med-svn] [phyml] branch master updated (fd0ac4b -> 37c0958)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository phyml.

      from  fd0ac4b   autopkgtest added
       new  253de9c   Wrapper script to call mpi version with same name if the machine has more than one processor
       new  99a0179   Fix changelog entry
       new  2df3d93   Add missing Depends: openmpi-bin
       new  4088c36   Use compression options in d/watch
       new  cf20f11   Imported Upstream version 3.2.20160530+dfsg
       new  6d16643   Merge tag 'upstream/3.2.20160530+dfsg'
       new  37c0958   New upstream version

The 7 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:
 NEWS                                       |    0
 README                                     |   30 +-
 autogen.sh                                 |    0
 config.h.in                                |    3 +
 configure.ac                               |   24 +-
 debian/changelog                           |   19 +-
 debian/control                             |    3 +-
 debian/patches/no-configure-ac-date        |    4 +-
 debian/patches/no-stdc++.patch             |    2 +-
 debian/patches/sse_only_if_supported.patch |    4 +-
 debian/rules                               |    5 +-
 debian/watch                               |    2 +-
 debian/wrapper/phyml                       |   15 +
 doc/fig/phyrexlog.pdf                      |  Bin 0 -> 463638 bytes
 doc/phyml-manual.pdf                       |  Bin 407931 -> 885797 bytes
 doc/phyml-manual.tex                       |  135 +-
 doc/ref.bib                                |   74 +
 examples/phyrex_input_files/h1n1.nxs       |  613 ++++++
 examples/phyrex_input_files/usa_coord.txt  |   53 +
 src/Makefile.am                            |   90 +-
 src/alrt.c                                 |  262 +--
 src/cl.c                                   |  109 +-
 src/cl.h                                   |    1 +
 src/date.c                                 |  789 ++++++++
 src/date.h                                 |   41 +
 src/free.c                                 |  230 ++-
 src/free.h                                 |   12 +-
 src/init.c                                 |  300 ++-
 src/init.h                                 |   10 +-
 src/interface.c                            |   27 +-
 src/invitee.c                              |   60 +-
 src/invitee.h                              |    2 +-
 src/io.c                                   | 1666 ++++------------
 src/io.h                                   |    7 +
 src/lk.c                                   |  958 +++++-----
 src/m4.c                                   |    6 +-
 src/main.c                                 |   29 +-
 src/make.c                                 |  143 +-
 src/make.h                                 |   12 +-
 src/mcmc.c                                 |  370 +++-
 src/mcmc.h                                 |    5 +-
 src/mg.c                                   | 2820 ----------------------------
 src/mg.h                                   |   51 -
 src/mixt.c                                 |  829 ++++++--
 src/mixt.h                                 |   16 +-
 src/models.c                               |   16 +-
 src/mpi_boot.c                             |    2 +-
 src/optimiz.c                              |  221 ++-
 src/pars.c                                 |  182 +-
 src/phyrex.c                               |  375 ++--
 src/phyrex.h                               |    4 +-
 src/rates.c                                |    8 +-
 src/simu.c                                 |  715 +++----
 src/spr.c                                  | 1237 ++++++------
 src/spr.h                                  |   14 +-
 src/stats.c                                |   13 +-
 src/stats.h                                |    2 +-
 src/times.c                                |  507 ++++-
 src/times.h                                |    3 +
 src/utilities.c                            | 2358 ++++++++++++++---------
 src/utilities.h                            |  193 +-
 src/xml.c                                  | 1146 ++++++++++-
 src/xml.h                                  |    3 +
 63 files changed, 9266 insertions(+), 7564 deletions(-)
 delete mode 100644 NEWS
 mode change 100644 => 100755 autogen.sh
 create mode 100755 debian/wrapper/phyml
 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/date.c
 create mode 100644 src/date.h

-- 
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