This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository python-dendropy.
commit 5d827337bec0fe59d1b35cfcd914be1190bfe9b7 Merge: 666c65d 9278860 Author: Andreas Tille <[email protected]> Date: Wed Jul 29 12:26:42 2015 +0200 Merge tag 'upstream/4.0.3' Upstream version 4.0.3 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 +- 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 +- 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+ .../pythonidae.random.bd0301.midpoint-rooted.tre | 112 + .../pythonidae.random.bd0301.randomly-rooted.tre | 145 + .../test/data/trees/pythonidae.random.bd0301.tre | 143 + .../data/trees/pythonidae.reference-trees.newick | 11 + .../data/trees/pythonidae.reference-trees.nexus | 89 + .../pythonidae.reference-trees.no-taxa-block.nexus | 50 + ...eference-trees.no-taxa-no-translate-block.nexus | 17 + ...nidae.reference-trees.taxon-numbers-only.newick | 11 + dendropy/test/data/trees/rana.trees.nexus | 70 + dendropy/test/data/trees/treebase_s373.xml | 634 + dendropy/test/support/__init__.py | 19 + 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 +- dendropy/test/support/mockreader.py | 18 + dendropy/test/support/pathmap.py | 7 +- dendropy/test/support/paupsplitsreference.py | 4 +- dendropy/test/support/standard_file_test_chars.py | 16 + .../test/support/standard_file_test_datasets.py | 4 +- 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 +- .../test/test_container_frozen_ordered_dict.py | 4 +- .../test/test_container_normalized_bitmask_dict.py | 4 +- dendropy/test/test_container_ordered_set.py | 4 +- dendropy/test/test_continuous.py | 4 +- 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 +- 650 files changed, 605633 insertions(+), 833 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