[med-svn] [gubbins] 02/07: Merge tag 'upstream/2.0.0'

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository gubbins.

commit f9a5366c19adad10b2414519db471ce9bff01b6b
Merge: acb8f70 8cafa0e
Author: Sascha Steinbiss <satta at debian.org>
Date:   Wed Jul 20 12:11:49 2016 +0000

    Merge tag 'upstream/2.0.0'
    
    Upstream version 2.0.0

 CHANGELOG                                          |   7 +
 INSTALL.md                                         |  16 +-
 README.md                                          |   2 +-
 VERSION                                            |   2 +-
 depcomp                                            | 487 +++++++++++++--------
 install-userspace.sh                               |   2 +-
 install_dependencies.sh                            |  26 --
 python/gubbins/Fastml.py                           |  63 ---
 python/gubbins/RAxMLExecutable.py                  | 105 +++++
 python/gubbins/RAxMLSequenceReconstruction.py      | 176 ++++++++
 python/gubbins/__init__.py                         |   1 -
 python/gubbins/common.py                           | 133 +-----
 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/destination_tree.tre     |   1 +
 .../tests/data/expected_renamed_output_tree        |   1 +
 .../data/raxml_sequence_reconstruction/1.fasta     |   4 +
 .../data/raxml_sequence_reconstruction/2.fasta     |   8 +
 .../expected_ancestor_sequence_from_raxml          |  22 +
 .../expected_combined_1_2.fasta                    |  12 +
 .../expected_marginalAncestralStates.fasta         |  10 +
 .../expected_rooted_tree.newick                    |   1 +
 .../input_alignment.fasta                          |  12 +
 .../raw_marginalAncestralStates.phylip             |   5 +
 .../unrooted_tree.newick                           |   1 +
 python/gubbins/tests/data/source_tree.tre          |   1 +
 python/gubbins/tests/test_external_dependancies.py |  19 +-
 python/gubbins/tests/test_fastml.py                |  43 --
 python/gubbins/tests/test_pre_process_fasta.py     |   9 +-
 .../tests/test_raxml_sequence_reconstruction.py    |  94 ++++
 python/gubbins/tests/test_string_construction.py   |   9 -
 python/gubbins/tests/test_tree_python_methods.py   |   5 -
 .../gubbins/tests/test_validate_starting_tree.py   |   1 -
 release/manifests/trustyvm.pp                      |   8 -
 35 files changed, 782 insertions(+), 677 deletions(-)

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