[med-svn] [python-dendropy] branch master updated (1e57140 -> 9aa6ad3)
Sascha Steinbiss
satta at debian.org
Sun Jul 31 20:15:26 UTC 2016
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satta pushed a change to branch master
in repository python-dendropy.
from 1e57140 Merge tag 'upstream/4.0.3+dfsg'
new be98825 fix watchfile
new 5b9f5b0 Imported Upstream version 4.1.0+dfsg
new 5267366 Merge tag 'upstream/4.1.0+dfsg'
new 558451b Debian version bump
new a3c6fcf update patches
new d949cb4 use secure Vcs-Git
new 96b7c66 bump Standards-Version
new 9aa6ad3 cme fix dpkg
The 8 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 +++-
debian/changelog | 10 +
debian/control | 4 +-
debian/copyright | 4 +-
...where-encoding-for-default-locale-is-None.patch | 2 +-
...PAUP-based-tests-unless-path-to-PAUP-is-p.patch | 2 +-
debian/watch | 2 +-
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 +-
97 files changed, 8164 insertions(+), 1903 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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