[med-svn] [scrm] branch upstream updated (5b13f3f -> 41e78d9)

[Kevin Murray]

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

daube-guest pushed a change to branch upstream
in repository scrm.

      from  5b13f3f   Imported Upstream version 1.6.1
       new  41e78d9   Imported Upstream version 1.7.0

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:
 .gitignore                                       |   1 +
 .travis.yml                                      |  36 ++--
 .travis/build_win_binaries.sh                    |   2 +
 .travis/setup.sh                                 |  24 +++
 Makefile.am                                      |  32 +--
 NEWS.md                                          |  26 +++
 README.md                                        |   9 +-
 configure.ac                                     |  12 +-
 src/contemporaries_container.h                   | 116 +++++------
 src/forest-debug.cc                              |   1 -
 src/forest.cc                                    | 241 +++++++++++++----------
 src/forest.h                                     |  52 ++---
 src/model.cc                                     | 212 ++++++++++----------
 src/model.h                                      |   9 +-
 src/node_container.cc                            |  46 +++--
 src/node_container.h                             | 130 +++++++-----
 src/param.cc                                     |  10 +-
 src/random/mersenne_twister.cc                   |   7 -
 src/random/mersenne_twister.h                    |  15 +-
 src/random/random_generator.cc                   |   2 +-
 src/random/random_generator.h                    |  27 +--
 src/scrm.cc                                      |  12 +-
 src/summary_statistics/newick_tree.cc            |   6 +-
 src/summary_statistics/newick_tree.h             |   1 -
 src/summary_statistics/oriented_forest.h         |   1 -
 src/summary_statistics/seg_sites.cc              |  36 +++-
 src/summary_statistics/seg_sites.h               |   7 +-
 src/summary_statistics/summary_statistic.h       |   4 +-
 src/summary_statistics/tmrca.cc                  |  11 +-
 src/time_interval.h                              |   9 +-
 tests/algorithmtest/test_algorithm.cc            |  35 +---
 tests/test_binaries.sh                           |  46 ++---
 tests/unittests/test_contemporaries_container.cc |  21 +-
 tests/unittests/test_forest.cc                   | 171 ++++++++--------
 tests/unittests/test_model.cc                    | 168 ++++++++--------
 tests/unittests/test_node.cc                     |   8 +-
 tests/unittests/test_node_container.cc           |  24 +--
 tests/unittests/test_param.cc                    |  89 +++++----
 tests/unittests/test_random_generator.cc         |  16 +-
 tests/unittests/test_summary_statistics.cc       |  45 ++++-
 tests/unittests/test_time_interval.cc            |  63 +++---
 tools/compare_versions.sh                        |   6 +-
 42 files changed, 980 insertions(+), 809 deletions(-)
 create mode 100755 .travis/setup.sh

-- 
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