[med-svn] [gubbins] branch debian/jessie-backports updated (0447033 -> c77f95b)
Andreas Tille
tille at debian.org
Tue Jun 6 14:00:48 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch debian/jessie-backports
in repository gubbins.
from 0447033 At lest for Jessie we seem to need libsubunit-dev Build-Depends
adds 65342a4 do not build-dep on python3-all-dev
adds ab4df94 Upload to unstable
adds 16b2e13 Imported Upstream version 1.4.5
adds 3553fe7 Merge tag 'upstream/1.4.5'
adds dbb49c5 New upstream version
adds ea64347 Secure Vcs-Git
adds 6dc5344 Upload to unstable
adds e5b0fa0 Imported Upstream version 1.4.7
adds 597a91d Merge tag 'upstream/1.4.7'
adds cd61fb7 cme fix dpkg-control
adds f29d837 Enhance hardening and upload to unstable
adds 747b52f Imported Upstream version 1.4.9
adds d2f039b Merge tag 'upstream/1.4.9'
adds 98c1f79 New upstream version
adds 8dd366f Upload to unstable
adds acb8f70 Build-Depends: fastml
adds 8cafa0e Imported Upstream version 2.0.0
adds f9a5366 Merge tag 'upstream/2.0.0'
adds 7c4dadc Debian version bump
adds e9130ff fix Vcs-Git
adds 848cd2b remove dependency on FastML
adds 9574346 update patches
adds 713031e update manpage dates
adds 9b0e2b9 bump Standards-Version
adds 5324ed7 add autopkgtests
adds 4ec19bf dch -r
adds 63f5943 Imported Upstream version 2.1.0
adds e7877d3 Merge tag 'upstream/2.1.0'
adds 2861349 New upstream release - but one error in build time test
adds e675cef Test is now OK
adds d341e6c address FTBFS
adds 76e707a dch -r
adds 157c76b add patch headers
adds 99e8d84 New upstream version 2.2.0
adds 6e23c13 Merge tag 'upstream/2.2.0'
adds 7dee080 Debian version bump
new 28d3665 Merge branch 'master' into debian/jessie-backports
new d667413 Rebuild for jessie-backports
new c77f95b Build-Depends: libsubunit-dev needed for Jessie
The 3 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 | 66 +++
Dockerfile | 19 +
INSTALL.md | 25 +-
README.md | 15 +-
VERSION | 2 +-
debian/changelog | 70 +++
debian/control | 12 +-
debian/gubbins_drawer.1 | 2 +-
debian/patches/disable_test.patch | 24 +
debian/patches/gubbins_exe_in_usr_lib.patch | 4 +-
debian/patches/series | 1 +
debian/rules | 5 +
debian/run_gubbins.1 | 2 +-
debian/tests/control | 3 +
debian/tests/run-example | 17 +
depcomp | 487 +++++++++++--------
homebrew/gubbins.rb | 35 --
install-sh | 527 ---------------------
install-userspace.sh | 2 +-
install_dependencies.sh | 20 +-
python/gubbins/Fastml.py | 63 ---
python/gubbins/PreProcessFasta.py | 101 ++++
python/gubbins/RAxMLExecutable.py | 111 +++++
python/gubbins/RAxMLSequenceReconstruction.py | 176 +++++++
python/gubbins/ValidateFastaAlignment.py | 82 ++++
python/gubbins/__init__.py | 1 -
python/gubbins/common.py | 281 +----------
python/gubbins/tests/bin/dummy_custom_fastml2 | 62 ---
python/gubbins/tests/bin/dummy_fastml2 | 60 ---
python/gubbins/tests/bin/dummy_fastml3 | 51 --
.../tests/data/alignment_with_no_variation.aln | 10 -
.../tests/data/all_unique_sequence_names.fa | 2 +
python/gubbins/tests/data/destination_tree.tre | 1 +
.../tests/data/expected_renamed_output_tree | 1 +
python/gubbins/tests/data/non_bi_tree.tre.expected | 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 +
.../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 +
...ance_tree1.tre.reroot_tree_at_midpoint_expected | 2 +-
python/gubbins/tests/data/source_tree.tre | 1 +
python/gubbins/tests/data/valid_alignment.aln | 2 +
.../gubbins/tests/test_alignment_python_methods.py | 5 -
python/gubbins/tests/test_external_dependancies.py | 305 +++---------
python/gubbins/tests/test_fastml.py | 43 --
python/gubbins/tests/test_pre_process_fasta.py | 94 ++++
.../tests/test_raxml_sequence_reconstruction.py | 94 ++++
python/gubbins/tests/test_string_construction.py | 9 -
python/gubbins/tests/test_tree_python_methods.py | 5 -
python/gubbins/tests/test_validate_fasta_input.py | 46 +-
.../gubbins/tests/test_validate_starting_tree.py | 1 -
python/scripts/run_gubbins.py | 5 +-
release/manifests/trustyvm.pp | 8 -
src/branch_sequences.c | 83 +---
src/branch_sequences.h | 1 -
src/snp_sites.c | 2 +-
src/string_cat.c | 9 +-
tests/check_branch_sequences.c | 18 +-
72 files changed, 1486 insertions(+), 1720 deletions(-)
create mode 100644 Dockerfile
create mode 100644 debian/patches/disable_test.patch
create mode 100644 debian/tests/control
create mode 100755 debian/tests/run-example
delete mode 100644 homebrew/gubbins.rb
delete mode 100755 install-sh
mode change 100644 => 100755 install_dependencies.sh
delete mode 100644 python/gubbins/Fastml.py
create mode 100644 python/gubbins/PreProcessFasta.py
create mode 100644 python/gubbins/RAxMLExecutable.py
create mode 100644 python/gubbins/RAxMLSequenceReconstruction.py
create mode 100644 python/gubbins/ValidateFastaAlignment.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
delete mode 100644 python/gubbins/tests/data/alignment_with_no_variation.aln
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/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
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 100755 python/gubbins/tests/test_fastml.py
create mode 100644 python/gubbins/tests/test_pre_process_fasta.py
create mode 100644 python/gubbins/tests/test_raxml_sequence_reconstruction.py
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