[med-svn] [gubbins] 02/05: Merge tag 'upstream/1.4.9'

[Andreas Tille]

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

tille pushed a commit to branch master
in repository gubbins.

commit d2f039b7d6abb88ab772c00b4560ea0c81a82fdd
Merge: f29d837 747b52f
Author: Andreas Tille <tille at debian.org>
Date:   Wed Apr 20 19:53:47 2016 +0200

    Merge tag 'upstream/1.4.9'
    
    Upstream version 1.4.9

 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(-)

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/gubbins.git