[med-svn] [gubbins] branch upstream updated (e5b0fa0 -> 747b52f)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository gubbins.

      from  e5b0fa0   Imported Upstream version 1.4.7
       new  747b52f   Imported Upstream version 1.4.9

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
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Summary of changes:
 CHANGELOG                                          |  50 ++++
 README.md                                          |   5 +
 VERSION                                            |   2 +-
 homebrew/gubbins.rb                                |  35 ---
 install_dependencies.sh                            |  16 +-
 python/gubbins/PreProcessFasta.py                  |  96 +++++++
 python/gubbins/ValidateFastaAlignment.py           |  82 ++++++
 python/gubbins/common.py                           | 149 +----------
 .../tests/data/alignment_with_no_variation.aln     |  10 -
 .../tests/data/all_unique_sequence_names.fa        |   2 +
 .../tests/data/pairwise.aln.snp_sites.aln_expected |   2 +-
 .../data/preprocessfasta/all_same_sequence.aln     |   8 +
 .../data/preprocessfasta/expected_missing_data.aln |   4 +
 .../expected_multiple_duplicates.aln               |   4 +
 .../preprocessfasta/expected_one_duplicate.aln     |   6 +
 .../tests/data/preprocessfasta/missing_data.aln    |   8 +
 .../data/preprocessfasta/multiple_duplicates.aln   |   8 +
 .../tests/data/preprocessfasta/no_duplicates.aln   |   8 +
 .../tests/data/preprocessfasta/one_duplicate.aln   |   8 +
 python/gubbins/tests/data/valid_alignment.aln      |   2 +
 .../gubbins/tests/test_alignment_python_methods.py |   5 -
 python/gubbins/tests/test_external_dependancies.py | 286 ++++-----------------
 python/gubbins/tests/test_fastml.py                |   0
 python/gubbins/tests/test_pre_process_fasta.py     |  85 ++++++
 python/gubbins/tests/test_validate_fasta_input.py  |  46 ++--
 python/scripts/run_gubbins.py                      |   2 +-
 26 files changed, 485 insertions(+), 444 deletions(-)
 delete mode 100644 homebrew/gubbins.rb
 mode change 100644 => 100755 install_dependencies.sh
 create mode 100644 python/gubbins/PreProcessFasta.py
 create mode 100644 python/gubbins/ValidateFastaAlignment.py
 delete mode 100644 python/gubbins/tests/data/alignment_with_no_variation.aln
 create mode 100644 python/gubbins/tests/data/preprocessfasta/all_same_sequence.aln
 create mode 100644 python/gubbins/tests/data/preprocessfasta/expected_missing_data.aln
 create mode 100644 python/gubbins/tests/data/preprocessfasta/expected_multiple_duplicates.aln
 create mode 100644 python/gubbins/tests/data/preprocessfasta/expected_one_duplicate.aln
 create mode 100644 python/gubbins/tests/data/preprocessfasta/missing_data.aln
 create mode 100644 python/gubbins/tests/data/preprocessfasta/multiple_duplicates.aln
 create mode 100644 python/gubbins/tests/data/preprocessfasta/no_duplicates.aln
 create mode 100644 python/gubbins/tests/data/preprocessfasta/one_duplicate.aln
 mode change 100755 => 100644 python/gubbins/tests/test_external_dependancies.py
 mode change 100755 => 100644 python/gubbins/tests/test_fastml.py
 create mode 100644 python/gubbins/tests/test_pre_process_fasta.py

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