[med-svn] [python-dendropy] branch upstream updated (5b9f5b0 -> aa688cf)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository python-dendropy.

      from  5b9f5b0   Imported Upstream version 4.1.0+dfsg
       new  aa688cf   New upstream version 4.2.0+dfsg

The 1 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:
 CHANGES.rst                                        |   18 +-
 DendroPy.egg-info/PKG-INFO                         |    4 +-
 DendroPy.egg-info/SOURCES.txt                      |    4 +
 DendroPy.egg-info/requires.txt                     |    2 +-
 PKG-INFO                                           |    4 +-
 applications/sumtrees/sumtrees.py                  |   82 +-
 dendropy/__init__.py                               |    4 +-
 dendropy/calculate/phylogeneticdistance.py         |   49 +-
 dendropy/calculate/popgenstat.py                   |   37 +-
 dendropy/calculate/profiledistance.py              |  327 ++
 dendropy/calculate/treecompare.py                  |  135 +-
 dendropy/dataio/newickreader.py                    |   46 +-
 dendropy/dataio/newickyielder.py                   |    2 +-
 dendropy/dataio/nexusreader.py                     |    4 +-
 dendropy/dataio/nexuswriter.py                     |   15 +-
 dendropy/dataio/nexusyielder.py                    |    5 +-
 dendropy/datamodel/basemodel.py                    |    5 +-
 dendropy/datamodel/taxonmodel.py                   |   14 +-
 dendropy/datamodel/treemodel.py                    |   43 +-
 dendropy/interop/paup.py                           |   37 +-
 dendropy/model/coalescent.py                       |    6 +-
 dendropy/model/multispeciescoalescent.py           |  275 ++
 .../other/multispecies_coalescent_test_data.json   | 4680 ++++++++++++++++++++
 dendropy/test/test_dataio_newick_reader_tree.py    |   65 +
 dendropy/test/test_multispeciescoalescent.py       |  307 ++
 dendropy/test/test_phylogenetic_distance_matrix.py |    2 +-
 dendropy/test/test_popgenstat.py                   |   27 +-
 dendropy/utility/error.py                          |   10 +
 dendropy/utility/processio.py                      |   13 +-
 dendropy/utility/timeprocessing.py                 |   10 +-
 setup.py                                           |    6 +
 31 files changed, 6088 insertions(+), 150 deletions(-)
 create mode 100644 dendropy/calculate/profiledistance.py
 create mode 100644 dendropy/model/multispeciescoalescent.py
 create mode 100644 dendropy/test/data/other/multispecies_coalescent_test_data.json
 create mode 100644 dendropy/test/test_multispeciescoalescent.py

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