This is an automated email from the git hooks/post-receive script. tille pushed a commit to tag debian/4.2.0+dfsg-1 in repository python-dendropy.
commit d63f92527408c23f7f29411fbbe35d2e947430b9 Merge: 1ae84cc 07c2548 Author: Andreas Tille <[email protected]> Date: Mon Jan 9 17:46:35 2017 +0100 Merge tag 'upstream/4.2.0+dfsg' Upstream version 4.2.0+dfsg 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 +- 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 + 101 files changed, 14179 insertions(+), 1990 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-dendropy.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
