[med-svn] [python-dendropy] 03/08: Merge tag 'upstream/4.1.0+dfsg'

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository python-dendropy.

commit 52673662d37997ebcf7bbf7106b36c7bb3b21b73
Merge: be98825 5b9f5b0
Author: Sascha Steinbiss <satta at debian.org>
Date:   Sun Jul 31 18:36:39 2016 +0000

    Merge tag 'upstream/4.1.0+dfsg'
    
    Upstream version 4.1.0+dfsg

 CHANGES.rst                                        |   33 +
 DendroPy.egg-info/PKG-INFO                         |    6 +-
 DendroPy.egg-info/SOURCES.txt                      |   38 +
 PKG-INFO                                           |    6 +-
 README.rst                                         |    2 +-
 applications/sumtrees/sumtrees.py                  |  246 +++-
 dendropy/__init__.py                               |   24 +-
 dendropy/calculate/combinatorics.py                |   71 +
 dendropy/calculate/phylogeneticdistance.py         | 1526 ++++++++++++++++++++
 dendropy/calculate/popgenstat.py                   |   20 +-
 dendropy/calculate/probability.py                  |   37 +-
 dendropy/calculate/statistics.py                   |   10 +
 dendropy/calculate/treecompare.py                  |  324 ++++-
 dendropy/calculate/treemeasure.py                  |  126 +-
 dendropy/calculate/treesum.py                      |    6 +-
 dendropy/dataio/fastawriter.py                     |    6 +-
 dendropy/dataio/ioservice.py                       |   25 +-
 dendropy/dataio/newickreader.py                    |   79 +-
 dendropy/dataio/newickwriter.py                    |  103 +-
 dendropy/dataio/newickyielder.py                   |    5 +-
 dendropy/dataio/nexmlreader.py                     |   12 +-
 dendropy/dataio/nexmlwriter.py                     |   24 +-
 dendropy/dataio/nexmlyielder.py                    |    5 +-
 dendropy/dataio/nexusprocessing.py                 |   11 +-
 dendropy/dataio/nexusreader.py                     |   86 +-
 dendropy/dataio/nexuswriter.py                     |  127 +-
 dendropy/dataio/nexusyielder.py                    |    1 +
 dendropy/dataio/phylipreader.py                    |   30 +-
 dendropy/dataio/phylipwriter.py                    |   37 +-
 dendropy/dataio/xmlprocessing.py                   |    5 +-
 dendropy/datamodel/basemodel.py                    |   27 +-
 dendropy/datamodel/charmatrixmodel.py              |  256 ++--
 dendropy/datamodel/charstatemodel.py               |   38 +-
 dendropy/datamodel/datasetmodel.py                 |   25 +-
 dendropy/datamodel/taxonmodel.py                   |  159 +-
 dendropy/datamodel/treecollectionmodel.py          |  277 ++--
 dendropy/datamodel/treemodel.py                    | 1341 ++++++++++++-----
 dendropy/interop/entrez.py                         |    5 +-
 dendropy/interop/paup.py                           |   31 +-
 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                       |   33 +-
 dendropy/model/discrete.py                         |    8 +-
 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/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_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_phylogenetic_distance_matrix.py |  854 +++++++++++
 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                          |   36 +-
 dendropy/utility/textprocessing.py                 |   19 +
 dendropy/utility/vcsinfo.py                        |    7 +-
 91 files changed, 8147 insertions(+), 1896 deletions(-)

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