[med-svn] [gubbins] branch upstream updated (747b52f -> 8cafa0e)

[Sascha Steinbiss]

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

satta pushed a change to branch upstream
in repository gubbins.

      from  747b52f   Imported Upstream version 1.4.9
       new  8cafa0e   Imported Upstream version 2.0.0

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:
 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(-)
 delete mode 100644 python/gubbins/Fastml.py
 create mode 100644 python/gubbins/RAxMLExecutable.py
 create mode 100644 python/gubbins/RAxMLSequenceReconstruction.py
 delete mode 100755 python/gubbins/tests/bin/dummy_custom_fastml2
 delete mode 100755 python/gubbins/tests/bin/dummy_fastml2
 delete mode 100755 python/gubbins/tests/bin/dummy_fastml3
 create mode 100644 python/gubbins/tests/data/destination_tree.tre
 create mode 100644 python/gubbins/tests/data/expected_renamed_output_tree
 create mode 100644 python/gubbins/tests/data/raxml_sequence_reconstruction/1.fasta
 create mode 100644 python/gubbins/tests/data/raxml_sequence_reconstruction/2.fasta
 create mode 100644 python/gubbins/tests/data/raxml_sequence_reconstruction/expected_ancestor_sequence_from_raxml
 create mode 100644 python/gubbins/tests/data/raxml_sequence_reconstruction/expected_combined_1_2.fasta
 create mode 100644 python/gubbins/tests/data/raxml_sequence_reconstruction/expected_marginalAncestralStates.fasta
 create mode 100644 python/gubbins/tests/data/raxml_sequence_reconstruction/expected_rooted_tree.newick
 create mode 100644 python/gubbins/tests/data/raxml_sequence_reconstruction/input_alignment.fasta
 create mode 100644 python/gubbins/tests/data/raxml_sequence_reconstruction/raw_marginalAncestralStates.phylip
 create mode 100644 python/gubbins/tests/data/raxml_sequence_reconstruction/unrooted_tree.newick
 create mode 100644 python/gubbins/tests/data/source_tree.tre
 delete mode 100644 python/gubbins/tests/test_fastml.py
 create mode 100644 python/gubbins/tests/test_raxml_sequence_reconstruction.py

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