[med-svn] [python-dendropy] branch master updated (9aa6ad3 -> 0703a46)
Andreas Tille
tille at debian.org
Mon Jan 9 17:29:19 UTC 2017
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tille pushed a change to branch master
in repository python-dendropy.
from 9aa6ad3 cme fix dpkg
new aa688cf New upstream version 4.2.0+dfsg
new 5ca0d65 Merge tag 'upstream/4.2.0+dfsg'
new 0703a46 Mass commit after having messed up Git repository since I again forgot tp git pull first :-(
The 3 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
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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 +-
debian/changelog | 12 +
debian/compat | 2 +-
debian/control | 7 +-
debian/copyright | 4 +-
...where-encoding-for-default-locale-is-None.patch | 2 +-
...PAUP-based-tests-unless-path-to-PAUP-is-p.patch | 2 +-
debian/rules | 3 -
debian/sumtrees.1 | 2 +-
debian/watch | 4 +-
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 +
40 files changed, 6111 insertions(+), 165 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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