[med-svn] [scrm] branch master updated (844e399 -> 1ee113e)

[Kevin Murray]

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

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

      from  844e399   Add d/upstream/metadata
       new  41e78d9   Imported Upstream version 1.7.0
       new  2fad065   Merge tag 'upstream/1.7.0'
       new  2f341c5   Bump version in d/ch
       new  1ee113e   Use secure vcs git url

The 4 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 +-
 debian/changelog                                 |   6 +-
 debian/control                                   |   2 +-
 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 +-
 44 files changed, 985 insertions(+), 812 deletions(-)
 create mode 100755 .travis/setup.sh

-- 
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