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commit f9a5366c19adad10b2414519db471ce9bff01b6b Merge: acb8f70 8cafa0e Author: Sascha Steinbiss <[email protected]> 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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/gubbins.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
