New upstream version 4.4.0

Release 4.4.0

-------------

-   Calculation of birth-death likelihoods.

-   Bipartitions inherit rooting state of trees.

-   Patristic paths between tips can be tracked in ``PatristicDistanceMatrix``.

-   Character column metadata annotations now actually possible.

-   Standard character matrix defaults to 0-9 alphabet instead of just 01.

-   Reorganization of package directory: from "$HOME/dendropy" and "$HOME/dendropy/test" to more modern "$HOME/src/dendropy" and "$HOME/tests" respectively.

Release 4.3.0

-------------

-   [SumTrees]: Important bugfix in tracking splits on consensus tree from rooted trees: previously it was possible for a split on the consensus tree to be ignored, resulting in a null (0) edge length and no (0.0) support.

-   Added ``sumlabels.py`` application.

-   BD tree (``dendropy.model.birth_death_tree``) now allows for preservation of extinct tips.

-   Birth-death tree (``dendropy.model.birth_death_tree``) now allows for preservation of extinct tips.

-   Improved performance of character subset export

Release 4.2.0

include LICENSE.rst

include doc/Makefile

recursive-include doc/source *

recursive-include dendropy/test/data *

recursive-include tests/data *

global-exclude .DS_Store

global-exclude *.pyc

global-exclude .gitignore

Metadata-Version: 1.1

Name: DendroPy

Version: 4.3.0

Version: 4.4.0

Summary: A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.

Home-page: http://packages.python.org/DendroPy/

Author: Jeet Sukumaran and Mark T. Holder

Author-email: jeetsukumaran@gmail.com and mtholder@ku.edu

Author-email: jeetsukumaran@gmail.com, mtholder@ku.edu

License: BSD

Description: .. image:: https://raw.githubusercontent.com/jeetsukumaran/DendroPy/DendroPy4/doc/source/_static/dendropy_logo.png

           :align: right

        and more.

        Testing

        =======

        .. note::

            Note that some tests rely on PAUP* being available on your system.

            You will need to set the environmental variable ``DENDROPY_PAUP_EXECUTABLE_PATH`` to the path

            of the PAUP* executable for these tests to be run, e.g.::

                DENDROPY_PAUP_EXECUTABLE_PATH=/usr/local/bin/paup python setup.py test

            or::

                DENDROPY_PAUP_EXECUTABLE_PATH=/usr/local/bin/paup python -m dendropy.test

            If this variable is not set or set to "NONE", then any tests that rely on

            PAUP* will NOT be run.

        Tests can be run by typing::

            $ python -m dendropy.test

        By default, all tests are run. You can run specific by providing the

        fully-qualified name of the modules, test cases, or specific test methods to

        run, e.g.::

            $ python -m dendropy.test test_tokenizer

            $ python -m dendropy.test test_tokenizer.TestCase

            $ python -m dendropy.test test_tokenizer.TestCase.test1

            $ python -m dendropy.test test_tokenizer test_datamodel_taxon

        Or special pre-defined sub-groups of tests, e.g.::

            $ python -m dendropy.test @datamodel

            $ python -m dendropy.test @dataio

            $ python -m dendropy.test @datamodel @newick

        A list of all available sub-groups can be seen by::

            $ python -m dendropy.test --help-testgroups

        For any tests run, you can set the level at which the test progress is logged

        by::

            $ python -m dendropy.test -l DEBUG all

        For all options, type::

            $ python -m dendropy.test --help

        License and Warranty

        ====================

        Current Release

        ===============

        The current release of DendroPy is version 4.3.0 (master-e251bcf, 2017-07-06 21:23:19).

        The current release of DendroPy is version 4.4.0.

Keywords: phylogenetics phylogeny phylogenies phylogeography evolution evolutionary biology systematics coalescent population genetics phyloinformatics bioinformatics

and more.

Testing

=======

.. note::

    Note that some tests rely on PAUP* being available on your system.

    You will need to set the environmental variable ``DENDROPY_PAUP_EXECUTABLE_PATH`` to the path

    of the PAUP* executable for these tests to be run, e.g.::

        DENDROPY_PAUP_EXECUTABLE_PATH=/usr/local/bin/paup python setup.py test

    or::

        DENDROPY_PAUP_EXECUTABLE_PATH=/usr/local/bin/paup python -m dendropy.test

    If this variable is not set or set to "NONE", then any tests that rely on

    PAUP* will NOT be run.

Tests can be run by typing::

    $ python -m dendropy.test

By default, all tests are run. You can run specific by providing the

fully-qualified name of the modules, test cases, or specific test methods to

run, e.g.::

    $ python -m dendropy.test test_tokenizer

    $ python -m dendropy.test test_tokenizer.TestCase

    $ python -m dendropy.test test_tokenizer.TestCase.test1

    $ python -m dendropy.test test_tokenizer test_datamodel_taxon

Or special pre-defined sub-groups of tests, e.g.::

    $ python -m dendropy.test @datamodel

    $ python -m dendropy.test @dataio

    $ python -m dendropy.test @datamodel @newick

A list of all available sub-groups can be seen by::

    $ python -m dendropy.test --help-testgroups

For any tests run, you can set the level at which the test progress is logged

by::

    $ python -m dendropy.test -l DEBUG all

For all options, type::

    $ python -m dendropy.test --help

License and Warranty

====================