[med-svn] [gubbins] branch upstream updated (9662833 -> f64633a)

[Andreas Tille]

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

tille pushed a change to branch upstream
in repository gubbins.

      from  9662833   Imported Upstream version 1.3.4
       new  f64633a   Imported Upstream version 1.4.2

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:
 .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, 842 insertions(+), 541 deletions(-)
 create mode 100644 .travis.yml
 create mode 100644 install_dependencies.sh
 create mode 100644 python/gubbins/Fastml.py
 create mode 100755 python/gubbins/tests/bin/dummy_custom_fastml2
 create mode 100755 python/gubbins/tests/bin/dummy_fastml2
 create mode 100755 python/gubbins/tests/bin/dummy_fastml3
 create mode 100755 python/gubbins/tests/test_fastml.py

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