[med-svn] [gubbins] 01/03: Merge branch 'master' into debian/jessie-backports
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 commit to branch debian/jessie-backports
in repository gubbins.
commit 28d3665bb796ce70bd02a18d6f13a6aaf440adac
Merge: 0447033 7dee080
Author: Andreas Tille <tille at debian.org>
Date: Tue Jun 6 15:52:01 2017 +0200
Merge branch 'master' into debian/jessie-backports
CHANGELOG | 66 +++
Dockerfile | 19 +
INSTALL.md | 25 +-
README.md | 15 +-
VERSION | 2 +-
debian/changelog | 63 +++
debian/control | 15 +-
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, 1480 insertions(+), 1722 deletions(-)
diff --cc debian/changelog
index 9a37389,a80c795..e73f7a9
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,9 -1,66 +1,72 @@@
+ gubbins (2.2.0-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream release.
+
+ -- Sascha Steinbiss <satta at debian.org> Thu, 03 Nov 2016 15:25:15 +0100
+
+ gubbins (2.1.0-2) unstable; urgency=medium
+
+ * Team upload.
+ * Disable tests to address FTBFS caused by failed build time tests
+ relying on external dependencies.
+ Closes: #839320
+
+ -- Sascha Steinbiss <satta at debian.org> Wed, 26 Oct 2016 14:26:18 +0200
+
+ gubbins (2.1.0-1) unstable; urgency=medium
+
+ * New upstream release
+
+ -- Andreas Tille <tille at debian.org> Fri, 09 Sep 2016 10:02:51 +0200
+
+ gubbins (2.0.0-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream release.
+ * Fix Vcs-Git.
+ * Remove dependencies on FastML.
+ * Update manpage dates.
+ * Bump Standards-Version.
+ * Add autopkgtests.
+
+ -- Sascha Steinbiss <satta at debian.org> Wed, 20 Jul 2016 13:08:22 +0000
+
+ gubbins (1.4.9-1) unstable; urgency=medium
+
+ * New upstream version
+ * Build-Depends: fastml
+
+ -- Andreas Tille <tille at debian.org> Wed, 20 Apr 2016 19:55:22 +0200
+
+ gubbins (1.4.7-1) unstable; urgency=medium
+
+ * New upstream version
+ * cme fix dpkg-control
+ * enhance hardening
+
+ -- Andreas Tille <tille at debian.org> Sat, 19 Mar 2016 22:10:44 +0100
+
+ gubbins (1.4.5-1) unstable; urgency=medium
+
+ * New upstream version
+ * Secure Vcs-Git
+
+ -- Andreas Tille <tille at debian.org> Wed, 27 Jan 2016 19:53:33 +0100
+
+ gubbins (1.4.4-2) unstable; urgency=medium
+
+ * do not build-dep on python3-all-dev
+ Closes: #809489
+
+ -- Andreas Tille <tille at debian.org> Thu, 31 Dec 2015 12:49:12 +0100
+
+gubbins (1.4.4-1~bpo8+1) jessie-backports; urgency=medium
+
+ * Rebuild for jessie-backports.
+
+ -- Andreas Tille <tille at debian.org> Wed, 23 Dec 2015 18:21:44 +0100
+
gubbins (1.4.4-1) unstable; urgency=medium
* New upstream version
--
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