[med-svn] [gubbins] branch master updated (f29d837 -> acb8f70)

[Andreas Tille]

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tille pushed a change to branch master
in repository gubbins.

      from  f29d837   Enhance hardening and upload to unstable
       new  747b52f   Imported Upstream version 1.4.9
       new  d2f039b   Merge tag 'upstream/1.4.9'
       new  98c1f79   New upstream version
       new  8dd366f   Upload to unstable
       new  acb8f70   Build-Depends: fastml

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Summary of changes:
 CHANGELOG                                          |  50 ++++
 README.md                                          |   5 +
 VERSION                                            |   2 +-
 debian/changelog                                   |   7 +
 debian/control                                     |   1 +
 debian/patches/gubbins_exe_in_usr_lib.patch        |   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 +-
 29 files changed, 494 insertions(+), 445 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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