[med-svn] [python-dendropy] 02/03: Merge branch 'master' into debian/jessie-backports
Andreas Tille
tille at debian.org
Thu Jun 8 07:36:17 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 python-dendropy.
commit 7f27e2ecfca12ab29078bd473e25c0d834a84ae1
Merge: 94a63c3 0703a46
Author: Andreas Tille <tille at debian.org>
Date: Thu Jun 8 09:12:29 2017 +0200
Merge branch 'master' into debian/jessie-backports
CHANGES.rst | 47 +
DendroPy.egg-info/PKG-INFO | 6 +-
DendroPy.egg-info/SOURCES.txt | 42 +
DendroPy.egg-info/requires.txt | 2 +-
PKG-INFO | 6 +-
README.rst | 2 +-
applications/sumtrees/sumtrees.py | 310 +-
debian/changelog | 22 +
debian/compat | 2 +-
debian/control | 11 +-
...where-encoding-for-default-locale-is-None.patch | 2 +-
debian/rules | 3 -
debian/sumtrees.1 | 2 +-
debian/watch | 6 +-
dendropy/__init__.py | 26 +-
dendropy/calculate/combinatorics.py | 71 +
dendropy/calculate/phylogeneticdistance.py | 1569 +++++++
dendropy/calculate/popgenstat.py | 57 +-
dendropy/calculate/probability.py | 37 +-
dendropy/calculate/profiledistance.py | 327 ++
dendropy/calculate/statistics.py | 10 +
dendropy/calculate/treecompare.py | 391 +-
dendropy/calculate/treemeasure.py | 126 +-
dendropy/calculate/treesum.py | 6 +-
dendropy/dataio/fastawriter.py | 6 +-
dendropy/dataio/ioservice.py | 25 +-
dendropy/dataio/newickreader.py | 121 +-
dendropy/dataio/newickwriter.py | 103 +-
dendropy/dataio/newickyielder.py | 7 +-
dendropy/dataio/nexmlreader.py | 12 +-
dendropy/dataio/nexmlwriter.py | 24 +-
dendropy/dataio/nexmlyielder.py | 5 +-
dendropy/dataio/nexusprocessing.py | 11 +-
dendropy/dataio/nexusreader.py | 90 +-
dendropy/dataio/nexuswriter.py | 142 +-
dendropy/dataio/nexusyielder.py | 6 +-
dendropy/dataio/phylipreader.py | 30 +-
dendropy/dataio/phylipwriter.py | 37 +-
dendropy/dataio/xmlprocessing.py | 5 +-
dendropy/datamodel/basemodel.py | 32 +-
dendropy/datamodel/charmatrixmodel.py | 256 +-
dendropy/datamodel/charstatemodel.py | 38 +-
dendropy/datamodel/datasetmodel.py | 25 +-
dendropy/datamodel/taxonmodel.py | 173 +-
dendropy/datamodel/treecollectionmodel.py | 277 +-
dendropy/datamodel/treemodel.py | 1384 ++++--
dendropy/interop/entrez.py | 5 +-
dendropy/interop/paup.py | 68 +-
dendropy/interop/rstats.py | 99 +-
dendropy/interop/seqgen.py | 4 -
dendropy/legacy/ncbi.py | 7 +-
dendropy/legacy/treecalc.py | 10 +-
dendropy/model/birthdeath.py | 17 +-
dendropy/model/coalescent.py | 39 +-
dendropy/model/discrete.py | 8 +-
dendropy/model/multispeciescoalescent.py | 275 ++
dendropy/model/parsimony.py | 14 +-
dendropy/model/protractedspeciation.py | 1015 ++++-
dendropy/model/reconcile.py | 12 +-
dendropy/model/treeshape.py | 5 +-
dendropy/simulate/popgensim.py | 4 -
.../benchmark_newick_light_tree_parser.py | 5 +-
.../test/benchmark/benchmark_newick_tree_parser.py | 4 -
dendropy/test/data/chars/community.data.tsv | 6 +
dendropy/test/data/other/community.data.tsv | 6 +
...mmunity.data.weighted.unnormalized.ses.mntd.csv | 6 +
...ommunity.data.weighted.unnormalized.ses.mpd.csv | 6 +
dendropy/test/data/other/hiv1.distances.csv | 194 +
.../test/data/other/hiv1.node-to-node-dists.csv | 386 ++
.../other/hiv1.unweighted.node-to-node-dists.csv | 386 ++
.../data/other/laurasiatherian.distances.ml.csv | 48 +
.../other/multispecies_coalescent_test_data.json | 4680 ++++++++++++++++++++
.../other/pythonidae.mle.node-to-node-dists.csv | 65 +
...ythonidae.mle.unweighted.node-to-node-dists.csv | 65 +
.../data/other/pythonidae.mle.unweighted.pdm.csv | 34 +
.../data/other/pythonidae.mle.weighted.pdm.csv | 34 +
.../test/data/other/saitou_and_nei_1987_table1.csv | 9 +
dendropy/test/data/other/wpnjex.csv | 6 +
dendropy/test/data/other/wpupgmaex.csv | 6 +
dendropy/test/data/trees/community.tree.newick | 1 +
dendropy/test/data/trees/hiv1.newick | 2 +-
dendropy/test/data/trees/hiv1.nexus | 197 +-
.../trees/pythonidae.mle.numbered-nodes.newick | 2 +
dendropy/test/support/compare_and_validate.py | 5 +-
dendropy/test/support/dendropytest.py | 6 +-
dendropy/test/support/pathmap.py | 11 +
dendropy/test/test_dataio_newick_reader_tree.py | 65 +
dendropy/test/test_dataio_tokenizer.py | 5 +-
dendropy/test/test_datamodel_bipartitions.py | 4 -
dendropy/test/test_datamodel_charmatrix.py | 20 +-
dendropy/test/test_datamodel_split_bitmasks.py | 6 +-
dendropy/test/test_fitch.py | 4 -
dendropy/test/test_multispeciescoalescent.py | 307 ++
dendropy/test/test_phylogenetic_distance_matrix.py | 854 ++++
dendropy/test/test_popgenstat.py | 27 +-
dendropy/test/test_protractedspeciation.py | 317 ++
.../test/test_tree_calculations_and_metrics.py | 143 +-
.../test/test_tree_operations_and_manipulations.py | 154 +-
dendropy/test/test_tree_shape_kernel.py | 291 ++
dendropy/utility/bitprocessing.py | 4 +-
dendropy/utility/cli.py | 2 +-
dendropy/utility/container.py | 269 +-
dendropy/utility/error.py | 46 +-
dendropy/utility/processio.py | 13 +-
dendropy/utility/textprocessing.py | 19 +
dendropy/utility/timeprocessing.py | 10 +-
dendropy/utility/vcsinfo.py | 7 +-
setup.py | 6 +
108 files changed, 14212 insertions(+), 2005 deletions(-)
diff --cc debian/changelog
index 18d132a,f668bb1..d0969bd
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,9 -1,25 +1,31 @@@
+ python-dendropy (4.2.0+dfsg-1) unstable; urgency=medium
+
+ * New upstream version
+ * d/watch:
+ - fix pypi URL
+ - xz compression
+ - version=4
+ * cme fix dpkg-control
+ * debhelper 10
+
+ -- Andreas Tille <tille at debian.org> Mon, 09 Jan 2017 17:51:57 +0100
+
+ python-dendropy (4.1.0+dfsg-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream release.
+ * Make watchfile work again.
+ * Use secure Vcs-Git.
+ * Bump Standards-Version.
+
+ -- Sascha Steinbiss <satta at debian.org> Sun, 31 Jul 2016 18:33:39 +0000
+
+python-dendropy (4.0.3+dfsg-1~bpo8+1) jessie-backports; urgency=medium
+
+ * Rebuild for jessie-backports.
+
+ -- Andreas Tille <tille at debian.org> Sat, 05 Dec 2015 18:22:46 +0100
+
python-dendropy (4.0.3+dfsg-1) unstable; urgency=low
* Initial release (Closes: #790408)
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