[med-svn] [python-dendropy] branch master updated (ce947dc -> 16e3163)
Andreas Tille
tille at debian.org
Wed Jul 29 11:20:32 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository python-dendropy.
from ce947dc Delete date file from master branch
new 3288d65 Deactivate tests for the moment
new 666c65d Add Github location
new 9278860 Imported Upstream version 4.0.3
new 5d82733 Merge tag 'upstream/4.0.3'
new 8d9f669 Upstream now provides test data inside download tarball
new 16e3163 Adapt patches to new upstream version
The 6 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 | 15 +-
DendroPy.egg-info/PKG-INFO | 23 +-
DendroPy.egg-info/SOURCES.txt | 463 +
LICENSE.rst | 104 +-
MANIFEST.in | 1 +
PKG-INFO | 23 +-
README.rst | 19 +
applications/sumtrees/sumtrees.py | 25 +-
debian/changelog | 2 +-
debian/copyright | 1 +
debian/get-test-data | 8 -
...where-encoding-for-default-locale-is-None.patch | 11 +-
...PAUP-based-tests-unless-path-to-PAUP-is-p.patch | 252 +-
debian/rules | 3 -
dendropy/__init__.py | 8 +-
dendropy/__main__.py | 4 +-
dendropy/calculate/__init__.py | 4 +-
dendropy/calculate/mathfn.py | 4 +-
dendropy/calculate/popgenstat.py | 4 +-
dendropy/calculate/probability.py | 4 +-
dendropy/calculate/statistics.py | 4 +-
dendropy/calculate/treecompare.py | 4 +-
dendropy/calculate/treemeasure.py | 4 +-
dendropy/calculate/treescore.py | 5 +-
dendropy/calculate/treesum.py | 4 +-
dendropy/dataio/__init__.py | 4 +-
dendropy/dataio/fastareader.py | 4 +-
dendropy/dataio/fastawriter.py | 4 +-
dendropy/dataio/ioservice.py | 4 +-
dendropy/dataio/newick.py | 4 +-
dendropy/dataio/newickreader.py | 4 +-
dendropy/dataio/newickwriter.py | 4 +-
dendropy/dataio/newickyielder.py | 4 +-
dendropy/dataio/nexmlreader.py | 4 +-
dendropy/dataio/nexmlwriter.py | 4 +-
dendropy/dataio/nexmlyielder.py | 4 +-
dendropy/dataio/nexusprocessing.py | 5 +-
dendropy/dataio/nexusreader.py | 5 +-
dendropy/dataio/nexuswriter.py | 10 +-
dendropy/dataio/nexusyielder.py | 4 +-
dendropy/dataio/phylipreader.py | 4 +-
dendropy/dataio/phylipwriter.py | 4 +-
dendropy/dataio/tokenizer.py | 4 +-
dendropy/dataio/xmlprocessing.py | 4 +-
dendropy/datamodel/__init__.py | 4 +-
dendropy/datamodel/basemodel.py | 4 +-
dendropy/datamodel/charmatrixmodel.py | 8 +-
dendropy/datamodel/charstatemodel.py | 4 +-
dendropy/datamodel/datasetmodel.py | 4 +-
dendropy/datamodel/taxonmodel.py | 4 +-
dendropy/datamodel/treecollectionmodel.py | 17 +-
dendropy/datamodel/treemodel.py | 12 +-
dendropy/interop/__init__.py | 4 +-
dendropy/interop/ape.py | 4 +-
dendropy/interop/biopython.py | 4 +-
dendropy/interop/entrez.py | 4 +-
dendropy/interop/ete.py | 4 +-
dendropy/interop/gbif.py | 4 +-
dendropy/interop/genbank.py | 4 +-
dendropy/interop/muscle.py | 4 +-
dendropy/interop/paup.py | 6 +-
dendropy/interop/raxml.py | 4 +-
dendropy/interop/rstats.py | 22 +-
dendropy/interop/seqgen.py | 4 +-
dendropy/legacy/__init__.py | 4 +-
dendropy/legacy/coalescent.py | 4 +-
dendropy/legacy/continuous.py | 4 +-
dendropy/legacy/ncbi.py | 4 +-
dendropy/legacy/popgensim.py | 4 +-
dendropy/legacy/popgenstat.py | 4 +-
dendropy/legacy/reconcile.py | 4 +-
dendropy/legacy/seqmodel.py | 4 +-
dendropy/legacy/seqsim.py | 4 +-
dendropy/legacy/treecalc.py | 4 +-
dendropy/legacy/treemanip.py | 4 +-
dendropy/legacy/treesim.py | 4 +-
dendropy/legacy/treesplit.py | 4 +-
dendropy/legacy/treesum.py | 4 +-
dendropy/mathlib/__init__.py | 4 +-
dendropy/mathlib/mathfn.py | 4 +-
dendropy/mathlib/probability.py | 4 +-
dendropy/mathlib/statistics.py | 4 +-
dendropy/model/__init__.py | 19 +
dendropy/model/birthdeath.py | 288 +-
dendropy/model/coalescent.py | 49 +-
dendropy/model/continuous.py | 4 +-
dendropy/model/discrete.py | 4 +-
dendropy/model/parsimony.py | 120 +-
dendropy/model/protractedspeciation.py | 522 +
dendropy/model/reconcile.py | 4 +-
dendropy/model/treeshape.py | 4 +-
dendropy/simulate/__init__.py | 4 +-
dendropy/simulate/charsim.py | 4 +-
dendropy/simulate/popgensim.py | 4 +-
dendropy/simulate/treesim.py | 4 +-
dendropy/test/__init__.py | 4 +-
dendropy/test/__main__.py | 23 +-
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dendropy/test/data/chars/caenophidia_mos.chars.txt | 114 +
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dendropy/test/data/trees/APG_Angiosperms.newick | 1 +
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dendropy/test/data/trees/cetaceans.taxa.nex | 29 +
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dendropy/test/data/trees/deepcoal1.nex | 77 +
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.../dendropy-test-trees-n33-unrooted-x100a.json | 132405 ++++++++++++++++++
.../dendropy-test-trees-n33-unrooted-x100a.newick | 100 +
.../dendropy-test-trees-n33-unrooted-x100a.nexml | 13048 ++
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.../dendropy-test-trees-n33-unrooted-x10a.json | 13245 ++
.../dendropy-test-trees-n33-unrooted-x10a.newick | 10 +
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.../dendropy-test-trees-n33-unrooted-x10a.nexus | 68 +
.../dendropy-test-trees-n33-unrooted-x10b.json | 13245 ++
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dendropy/test/data/trees/maj-rule-bug1.trees.nexus | 229 +
dendropy/test/data/trees/maj-rule-bug2.trees.nexus | 233 +
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dendropy/test/data/trees/pythonidae.mb.con | 85 +
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.../test/data/trees/pythonidae.mlboots.newick.tre | 1001 +
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dendropy/test/data/trees/rana.trees.nexus | 70 +
dendropy/test/data/trees/treebase_s373.xml | 634 +
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dendropy/test/support/compare_and_validate.py | 4 +-
dendropy/test/support/coverage_analysis.py | 4 +-
dendropy/test/support/curated_dataset.py | 4 +-
dendropy/test/support/curated_test_tree.py | 4 +-
dendropy/test/support/curated_test_tree_list.py | 4 +-
dendropy/test/support/dendropytest.py | 4 +-
dendropy/test/support/mockrandom.py | 4 +-
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dendropy/test/support/pathmap.py | 7 +-
dendropy/test/support/paupsplitsreference.py | 4 +-
dendropy/test/support/standard_file_test_chars.py | 16 +
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dendropy/test/support/standard_file_test_trees.py | 4 +-
dendropy/test/test_asciitree.py | 4 +-
dendropy/test/test_birthdeath.py | 4 +-
dendropy/test/test_coalescent.py | 4 +-
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dendropy/test/test_dataio_basic_tree.py | 17 +
dendropy/test/test_dataio_fasta_reader.py | 4 +-
dendropy/test/test_dataio_fasta_writer.py | 4 +-
dendropy/test/test_dataio_newick_reader_rooting.py | 4 +-
dendropy/test/test_dataio_newick_reader_tree.py | 4 +-
.../test/test_dataio_newick_reader_tree_iter.py | 4 +-
.../test/test_dataio_newick_reader_tree_list.py | 4 +-
dendropy/test/test_dataio_newick_writer.py | 4 +-
dendropy/test/test_dataio_nexml_reader_chars.py | 4 +-
.../test/test_dataio_nexml_reader_tree_list.py | 4 +-
dendropy/test/test_dataio_nexml_writer_chars.py | 4 +-
dendropy/test/test_dataio_nexml_writer_trees.py | 4 +-
dendropy/test/test_dataio_nexus_reader_chars.py | 4 +-
dendropy/test/test_dataio_nexus_reader_dataset.py | 4 +-
.../test/test_dataio_nexus_reader_tree_list.py | 4 +-
dendropy/test/test_dataio_nexus_taxon_handling.py | 4 +-
dendropy/test/test_dataio_nexus_tree_yielder.py | 4 +-
dendropy/test/test_dataio_nexus_writer_chars.py | 4 +-
dendropy/test/test_dataio_nexus_writer_dataset.py | 4 +-
dendropy/test/test_dataio_nexus_writer_tree.py | 4 +-
.../test/test_dataio_nexus_writer_tree_list.py | 4 +-
dendropy/test/test_dataio_phylip_reader_chars.py | 4 +-
dendropy/test/test_dataio_phylip_writer_chars.py | 4 +-
dendropy/test/test_dataio_tokenizer.py | 4 +-
dendropy/test/test_datamodel_annotations.py | 4 +-
dendropy/test/test_datamodel_bipartitions.py | 4 +-
dendropy/test/test_datamodel_charmatrix.py | 4 +-
dendropy/test/test_datamodel_dataset.py | 4 +-
dendropy/test/test_datamodel_split_bitmasks.py | 225 +-
dendropy/test/test_datamodel_statealphabet.py | 4 +-
dendropy/test/test_datamodel_taxon.py | 4 +-
...model_tree_construction_copying_and_identity.py | 4 +-
.../test/test_datamodel_tree_edge_fundamentals.py | 4 +-
dendropy/test/test_datamodel_tree_list.py | 4 +-
.../test/test_datamodel_tree_node_fundamentals.py | 4 +-
.../test_datamodel_tree_structure_and_iteration.py | 4 +-
.../test/test_datamodel_tree_taxon_management.py | 4 +-
dendropy/test/test_datamodel_treearray.py | 4 +-
dendropy/test/test_fitch.py | 7 +-
dendropy/test/test_parsimony_scoring.py | 494 +
dendropy/test/test_paup.py | 4 +-
dendropy/test/test_popgenstat.py | 26 +-
dendropy/test/test_statistics.py | 4 +-
.../test/test_tree_calculations_and_metrics.py | 4 +-
dendropy/test/test_tree_from_splits.py | 4 +-
.../test/test_tree_operations_and_manipulations.py | 5 +-
.../test_tree_reconciliation_and_discordance.py | 24 +-
dendropy/test/test_tree_split_compatibility.py | 4 +-
.../test/test_tree_summarization_and_consensus.py | 4 +-
dendropy/utility/__init__.py | 4 +-
dendropy/utility/bibtex.py | 4 +-
dendropy/utility/bitprocessing.py | 4 +-
dendropy/utility/cli.py | 4 +-
dendropy/utility/constants.py | 4 +-
dendropy/utility/container.py | 4 +-
dendropy/utility/debug.py | 4 +-
dendropy/utility/deprecate.py | 4 +-
dendropy/utility/error.py | 4 +-
dendropy/utility/filesys.py | 4 +-
dendropy/utility/libexec/__init__.py | 5 +-
dendropy/utility/messaging.py | 4 +-
dendropy/utility/metavar.py | 4 +-
dendropy/utility/processio.py | 4 +-
dendropy/utility/terminal.py | 18 +
dendropy/utility/textprocessing.py | 7 +-
dendropy/utility/timeprocessing.py | 4 +-
dendropy/utility/urlio.py | 4 +-
dendropy/utility/vcsinfo.py | 4 +-
doc/source/license.inc | 20 +-
doc/source/programs/sumtrees.rst | 2 +-
setup.py | 4 +-
656 files changed, 601297 insertions(+), 1102 deletions(-)
delete mode 100755 debian/get-test-data
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create mode 100644 dendropy/test/data/chars/GEBA.chars.nexus
create mode 100644 dendropy/test/data/chars/actinopterygii.chars.nexus
create mode 100644 dendropy/test/data/chars/angiosperms.chars.nexus
create mode 100644 dendropy/test/data/chars/angiosperms.chars.txt
create mode 100644 dendropy/test/data/chars/apternodus.chars.hacked-for-tests.txt
create mode 100644 dendropy/test/data/chars/apternodus.chars.interleaved.nexus
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create mode 100644 dendropy/test/data/chars/apternodus.chars.nexus
create mode 100644 dendropy/test/data/chars/avian-ovomucoids.chars.nexus
create mode 100644 dendropy/test/data/chars/avian-ovomucoids.chars.txt
create mode 100644 dendropy/test/data/chars/bad_names.fasta
create mode 100644 dendropy/test/data/chars/caenophidia_mos.chars.fasta
create mode 100644 dendropy/test/data/chars/caenophidia_mos.chars.nexus
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create mode 100644 dendropy/test/data/chars/cetaceans.nex
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create mode 100644 dendropy/test/data/chars/crotaphytus_bicinctores.cytb.aligned.nexml
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create mode 100644 dendropy/test/data/chars/interleaved-charsets-all.nex
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copy {doc/source/examples => dendropy/test/data/chars}/primates.chars.simple.interleaved.nexus (100%)
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copy {doc/source/examples => dendropy/test/data/chars}/primates.chars.subsets-coding.nexus (100%)
copy {doc/source/examples => dendropy/test/data/chars}/primates.chars.subsets-noncoding.nexus (100%)
create mode 100644 dendropy/test/data/chars/pythonidae.chars.beast.calibrated.xml
create mode 100644 dendropy/test/data/chars/pythonidae.chars.beast.uncalibrated.xml
copy doc/source/examples/pythonidae.fasta => dendropy/test/data/chars/pythonidae.chars.fasta (100%)
create mode 100644 dendropy/test/data/chars/pythonidae.chars.interleaved.nexus
copy {doc/source/examples => dendropy/test/data/chars}/pythonidae.chars.nexus (100%)
copy {doc/source/examples => dendropy/test/data/chars}/pythonidae.chars.phylip (100%)
create mode 100644 dendropy/test/data/chars/pythonidae.chars.txt
copy {doc/source/examples => dendropy/test/data/chars}/pythonidae_continuous.chars.nexml (100%)
create mode 100644 dendropy/test/data/chars/pythonidae_continuous.chars.nexus
create mode 100644 dendropy/test/data/chars/pythonidae_continuous.chars.txt
create mode 100644 dendropy/test/data/chars/standard-test-chars-continuous.as_cells.nexml
create mode 100644 dendropy/test/data/chars/standard-test-chars-continuous.as_seqs.nexml
create mode 100644 dendropy/test/data/chars/standard-test-chars-continuous.interleaved.phylip
create mode 100644 dendropy/test/data/chars/standard-test-chars-continuous.mesquite.interleaved.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-continuous.mesquite.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-continuous.relaxed.phylip
create mode 100644 dendropy/test/data/chars/standard-test-chars-dna.as_cells.nexml
create mode 100644 dendropy/test/data/chars/standard-test-chars-dna.as_seqs.nexml
create mode 100644 dendropy/test/data/chars/standard-test-chars-dna.basic.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-dna.fasta
create mode 100644 dendropy/test/data/chars/standard-test-chars-dna.interleaved.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-dna.matchchar.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-dna.multi.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-dna.relaxed.phylip
create mode 100644 dendropy/test/data/chars/standard-test-chars-dna.simple.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-generic.as_cells.nexml
create mode 100644 dendropy/test/data/chars/standard-test-chars-generic.as_seqs.nexml
create mode 100644 dendropy/test/data/chars/standard-test-chars-generic.basic.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-generic.dotted.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-generic.interleaved.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-generic.relaxed.phylip
create mode 100644 dendropy/test/data/chars/standard-test-chars-generic.simple.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-multiple-char-blocks.1.basic.nexus
copy dendropy/{model/__init__.py => test/data/chars/standard-test-chars-multiple.as_cells.nexml} (100%)
copy dendropy/{model/__init__.py => test/data/chars/standard-test-chars-multiple.as_seqs.nexml} (100%)
create mode 100644 dendropy/test/data/chars/standard-test-chars-protein.as_cells.nexml
create mode 100644 dendropy/test/data/chars/standard-test-chars-protein.as_seqs.nexml
create mode 100644 dendropy/test/data/chars/standard-test-chars-protein.basic.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-protein.fasta
create mode 100644 dendropy/test/data/chars/standard-test-chars-protein.interleaved.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-protein.matchchar.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-protein.multi.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-protein.relaxed.phylip
create mode 100644 dendropy/test/data/chars/standard-test-chars-protein.simple.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-rna.as_cells.nexml
create mode 100644 dendropy/test/data/chars/standard-test-chars-rna.as_seqs.nexml
create mode 100644 dendropy/test/data/chars/standard-test-chars-rna.basic.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-rna.fasta
create mode 100644 dendropy/test/data/chars/standard-test-chars-rna.interleaved.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-rna.matchchar.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-rna.multi.nexus
create mode 100644 dendropy/test/data/chars/standard-test-chars-rna.relaxed.phylip
create mode 100644 dendropy/test/data/chars/standard-test-chars-rna.simple.nexus
create mode 100644 dendropy/test/data/mixed/GEBA.mixed.nexus
create mode 100644 dendropy/test/data/mixed/geospiza.nex
create mode 100644 dendropy/test/data/mixed/multitaxa_mesquite.nex
create mode 100644 dendropy/test/data/mixed/reference_single_taxonset_dataset.nex
create mode 100644 dendropy/test/data/mixed/standard-test-mixed.1.basic.nexus
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create mode 100644 dendropy/test/data/splits/cetaceans.mb.no-clock.mcmc.weighted-01.trees.is-rooted-False.use-tree-weights-None.burnin-150.splits.txt
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create mode 100644 dendropy/test/data/splits/cetaceans.mb.no-clock.mcmc.weighted-01.trees.is-rooted-True.use-tree-weights-True.burnin-150.splits.txt
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create mode 100644 dendropy/test/data/splits/cetaceans.mb.no-clock.mcmc.weighted-02.trees.is-rooted-None.use-tree-weights-None.burnin-150.splits.txt
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