[med-svn] [gubbins] 02/04: Merge tag 'upstream/1.4.2'

[Andreas Tille]

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tille pushed a commit to branch master
in repository gubbins.

commit ebfbae37134018c78474b28c82d37abccd699517
Merge: c9c687a f64633a
Author: Andreas Tille <tille at debian.org>
Date:   Thu Nov 19 10:44:17 2015 +0100

    Merge tag 'upstream/1.4.2'
    
    Upstream version 1.4.2
    
    Conflicts:
    	debian/changelog

 .travis.yml                                        |  23 +
 INSTALL.md                                         | 252 ++++------
 README.md                                          |   5 +-
 VERSION                                            |   2 +-
 configure.ac                                       |   2 +-
 debian/changelog                                   |   6 +-
 install-userspace.sh                               |   2 +-
 install_dependencies.sh                            | 111 +++++
 python/Makefile.am                                 |   2 +-
 python/gubbins/Fastml.py                           |  63 +++
 python/gubbins/__init__.py                         |   4 +-
 python/gubbins/common.py                           | 514 +++++++++++----------
 python/gubbins/tests/bin/dummy_custom_fastml2      |  62 +++
 python/gubbins/tests/bin/dummy_fastml2             |  60 +++
 python/gubbins/tests/bin/dummy_fastml3             |  51 ++
 python/gubbins/tests/data/non_bi_tree.tre.expected |   2 +-
 ....tre.filter_out_removed_taxa_from_tree_expected |   2 +-
 ...ance_tree1.tre.reroot_tree_at_midpoint_expected |   2 +-
 .../gubbins/tests/test_alignment_python_methods.py |  15 +-
 .../tests/test_converging_recombinations.py        |   2 +-
 python/gubbins/tests/test_external_dependancies.py |  39 +-
 python/gubbins/tests/test_fastml.py                |  43 ++
 python/gubbins/tests/test_string_construction.py   |   2 +-
 python/gubbins/tests/test_tree_python_methods.py   |  43 +-
 python/gubbins/tests/test_validate_fasta_input.py  |   2 +-
 .../gubbins/tests/test_validate_starting_tree.py   |   2 +-
 python/scripts/gubbins_drawer.py                   |  30 +-
 python/scripts/run_gubbins.py                      |   8 +-
 python/setup.py                                    |  10 +-
 release/manifests/trustyvm.pp                      |   7 +-
 src/Newickform.c                                   |   3 +-
 src/alignment_file.c                               |   4 +
 src/parse_vcf.c                                    |   4 +-
 tests/check_branch_sequences.c                     |   4 +-
 34 files changed, 839 insertions(+), 544 deletions(-)

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