[med-svn] [python-dendropy] branch upstream updated (0ad69d7 -> 5b9f5b0)
Sascha Steinbiss
satta at debian.org
Sun Jul 31 20:15:29 UTC 2016
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satta pushed a change to branch upstream
in repository python-dendropy.
from 0ad69d7 Imported Upstream version 4.0.3+dfsg
new 5b9f5b0 Imported Upstream version 4.1.0+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 | 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(-)
create mode 100644 dendropy/calculate/combinatorics.py
create mode 100644 dendropy/calculate/phylogeneticdistance.py
create mode 100644 dendropy/test/data/chars/community.data.tsv
create mode 100644 dendropy/test/data/other/community.data.tsv
create mode 100644 dendropy/test/data/other/community.data.weighted.unnormalized.ses.mntd.csv
create mode 100644 dendropy/test/data/other/community.data.weighted.unnormalized.ses.mpd.csv
create mode 100644 dendropy/test/data/other/hiv1.distances.csv
create mode 100644 dendropy/test/data/other/hiv1.node-to-node-dists.csv
create mode 100644 dendropy/test/data/other/hiv1.unweighted.node-to-node-dists.csv
create mode 100644 dendropy/test/data/other/laurasiatherian.distances.ml.csv
create mode 100644 dendropy/test/data/other/pythonidae.mle.node-to-node-dists.csv
create mode 100644 dendropy/test/data/other/pythonidae.mle.unweighted.node-to-node-dists.csv
create mode 100644 dendropy/test/data/other/pythonidae.mle.unweighted.pdm.csv
create mode 100644 dendropy/test/data/other/pythonidae.mle.weighted.pdm.csv
create mode 100644 dendropy/test/data/other/saitou_and_nei_1987_table1.csv
create mode 100644 dendropy/test/data/other/wpnjex.csv
create mode 100644 dendropy/test/data/other/wpupgmaex.csv
create mode 100644 dendropy/test/data/trees/community.tree.newick
create mode 100644 dendropy/test/data/trees/pythonidae.mle.numbered-nodes.newick
create mode 100644 dendropy/test/test_phylogenetic_distance_matrix.py
create mode 100644 dendropy/test/test_protractedspeciation.py
create mode 100644 dendropy/test/test_tree_shape_kernel.py
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