[med-svn] [python-dendropy] 03/03: Merge tag 'upstream/4.0.3+dfsg'
Andreas Tille
tille at debian.org
Sat Nov 14 19:51:15 UTC 2015
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tille pushed a commit to branch master
in repository python-dendropy.
commit 1e5714073f269c0d67157e5dbb7b4bf114439b21
Merge: 5018a67 0ad69d7
Author: Andreas Tille <tille at debian.org>
Date: Sat Nov 14 20:16:46 2015 +0100
Merge tag 'upstream/4.0.3+dfsg'
Upstream version 4.0.3+dfsg
doc/Makefile | 177 ---
doc/source/_static/Octocat.png | Bin 2131769 -> 0 bytes
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doc/source/_static/google-groups-logo1.png | Bin 13911 -> 0 bytes
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.../_themes/sphinx_dendropy_theme/static/rtd.css | 775 -----------
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doc/source/acknowledgements.inc | 5 -
doc/source/changes.rst | 3 -
doc/source/citation.inc | 15 -
doc/source/conf.py | 559 --------
doc/source/downloading.rst | 51 -
doc/source/examples/bdtree_multi1.py | 22 -
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doc/source/examples/bibtex_annotations1.py | 24 -
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doc/source/examples/bibtex_annotations3.py | 29 -
doc/source/examples/build_tree_programmatically.py | 51 -
doc/source/examples/char_mat_concat.py | 20 -
doc/source/examples/char_mat_concat2.py | 12 -
doc/source/examples/chars_access1.py | 18 -
doc/source/examples/chars_access2.py | 18 -
doc/source/examples/chars_access3.py | 32 -
doc/source/examples/chars_access4.py | 32 -
doc/source/examples/contained_coalescent1.py | 19 -
doc/source/examples/contained_coalescent2.py | 19 -
doc/source/examples/ds1.py | 43 -
doc/source/examples/ds2.py | 16 -
doc/source/examples/ds4.py | 10 -
doc/source/examples/ds5.py | 11 -
doc/source/examples/dsrw1.py | 13 -
doc/source/examples/dynamic_annotations1.py | 34 -
doc/source/examples/euctree.py | 19 -
doc/source/examples/find_taxon_node1.py | 8 -
doc/source/examples/find_taxon_node2.py | 7 -
doc/source/examples/hiv1.nexus | 399 ------
doc/source/examples/ladderize.py | 22 -
doc/source/examples/ltt.py | 36 -
doc/source/examples/majrule.py | 15 -
doc/source/examples/mcct.py | 19 -
doc/source/examples/mrca.py | 9 -
doc/source/examples/mrca2.py | 11 -
doc/source/examples/node_ages1.py | 19 -
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doc/source/examples/paup_estimate_tree_nj.py | 11 -
doc/source/examples/pbhg.py | 16 -
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doc/source/examples/pgstats1.py | 33 -
doc/source/examples/pic1.py | 35 -
doc/source/examples/pic2.py | 7 -
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doc/source/examples/pic_annotated.py | 32 -
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doc/source/examples/primates.cc.combined.nex | 17 -
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.../examples/primates.chars.interleaved.nexus | 228 ----
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doc/source/examples/prune_taxa_with_labels.py | 17 -
doc/source/examples/pure_kingman1.py | 11 -
doc/source/examples/pythonidae.beast-mcmc.trees | 1079 ----------------
doc/source/examples/pythonidae.chars.nexus | 99 --
doc/source/examples/pythonidae.chars.phylip | 34 -
doc/source/examples/pythonidae.fasta | 99 --
doc/source/examples/pythonidae.mb.run1.t | 108 --
doc/source/examples/pythonidae.mb.run2.t | 108 --
doc/source/examples/pythonidae.mb.run3.t | 108 --
doc/source/examples/pythonidae.mb.run4.t | 108 --
doc/source/examples/pythonidae.mcmc-con.nex | 13 -
doc/source/examples/pythonidae.mcmc.nex | 1035 ---------------
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doc/source/examples/pythonidae.random.bd0301.tre | 143 ---
doc/source/examples/pythonidae_combined.nex | 494 --------
.../examples/pythonidae_continuous.chars.nexml | 1339 --------------------
doc/source/examples/pythonidae_cytb.fasta | 99 --
doc/source/examples/raxml_estimate_tree.py | 14 -
doc/source/examples/readroot.py | 20 -
doc/source/examples/readroot2.py | 14 -
doc/source/examples/remove_branch_lengths.py | 11 -
doc/source/examples/reroot_at_external_edge.py | 19 -
doc/source/examples/reroot_at_internal_edge.py | 19 -
doc/source/examples/reroot_at_midpoint.py | 18 -
doc/source/examples/reroot_at_node.py | 18 -
doc/source/examples/rescale_tree_length.py | 12 -
doc/source/examples/retain_taxa_with_labels.py | 18 -
doc/source/examples/seqgen.py | 28 -
doc/source/examples/setroot1.py | 26 -
doc/source/examples/sim_and_count_deepcoal1.py | 71 --
doc/source/examples/sim_and_count_deepcoal2.py | 65 -
doc/source/examples/splitfreq.py | 16 -
doc/source/examples/splits_on_trees.py | 16 -
doc/source/examples/symdiff1.py | 21 -
doc/source/examples/symdiff2.py | 37 -
doc/source/examples/taxa_mgmt1.py | 12 -
doc/source/examples/taxa_mgmt1a.py | 10 -
doc/source/examples/taxa_mgmt1b.py | 13 -
doc/source/examples/taxa_mgmt2.py | 18 -
doc/source/examples/taxa_mgmt3.py | 42 -
doc/source/examples/taxa_mgmt4.py | 18 -
doc/source/examples/taxa_mgmt5.py | 12 -
doc/source/examples/taxon_labels1.py | 35 -
doc/source/examples/taxon_labels2.py | 35 -
doc/source/examples/taxon_labels2b.py | 35 -
doc/source/examples/taxon_labels3.py | 35 -
doc/source/examples/taxon_labels4.py | 36 -
doc/source/examples/to_outgroup_position.py | 18 -
doc/source/examples/tree_copy1.py | 26 -
doc/source/examples/tree_copy2.py | 23 -
doc/source/examples/tree_evolve_char1.py | 20 -
doc/source/examples/tree_evolve_char2.py | 19 -
doc/source/examples/tree_iter1.py | 30 -
doc/source/examples/tree_iter2.py | 22 -
doc/source/examples/tree_length_crit.py | 14 -
doc/source/examples/tree_list_add1.py | 6 -
doc/source/examples/tree_list_copy1.py | 24 -
doc/source/examples/tree_list_copy2.py | 26 -
doc/source/examples/tree_list_copy3.py | 23 -
doc/source/examples/tree_list_ops1.py | 38 -
doc/source/examples/tree_list_ops2.py | 28 -
doc/source/examples/tree_rootings1.py | 36 -
doc/source/examples/treemeasures1.py | 30 -
doc/source/examples/weightedrf1.py | 22 -
doc/source/glossary.rst | 310 -----
doc/source/index.rst | 118 --
doc/source/library/basemodel.rst | 38 -
doc/source/library/birthdeath.rst | 8 -
doc/source/library/charmatrixmodel.rst | 88 --
doc/source/library/charstatemodel.rst | 19 -
doc/source/library/coalescent.rst | 9 -
doc/source/library/continuous.rst | 8 -
doc/source/library/datasetmodel.rst | 7 -
doc/source/library/discrete.rst | 9 -
doc/source/library/index.rst | 59 -
doc/source/library/parsimony.rst | 9 -
doc/source/library/popgensim.rst | 10 -
doc/source/library/popgenstat.rst | 8 -
doc/source/library/probability.rst | 8 -
doc/source/library/reconcile.rst | 9 -
doc/source/library/statistics.rst | 8 -
doc/source/library/taxonmodel.rst | 23 -
doc/source/library/treecollectionmodel.rst | 54 -
doc/source/library/treecompare.rst | 8 -
doc/source/library/treemeasure.rst | 7 -
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doc/source/library/treeshape.rst | 8 -
doc/source/library/treesim.rst | 10 -
doc/source/license.inc | 79 --
doc/source/migration.rst | 269 ----
doc/source/primer/bipartitions.rst | 404 ------
doc/source/primer/chars.rst | 181 ---
doc/source/primer/converting.rst | 86 --
doc/source/primer/dataobjects.rst | 89 --
doc/source/primer/datasets.rst | 178 ---
doc/source/primer/genbank.rst | 565 ---------
doc/source/primer/index.rst | 78 --
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.../primer/phylogenetic_character_analyses.rst | 139 --
doc/source/primer/popgenstats.rst | 46 -
doc/source/primer/raxml.rst | 20 -
doc/source/primer/reading_and_writing.rst | 250 ----
doc/source/primer/seqgen.rst | 13 -
doc/source/primer/taxa.rst | 277 ----
doc/source/primer/taxa_partitions.rst | 142 ---
doc/source/primer/treecollections.rst | 108 --
doc/source/primer/treemanips.rst | 452 -------
doc/source/primer/trees.rst | 220 ----
doc/source/primer/treesims.rst | 285 -----
doc/source/primer/treestats.rst | 189 ---
.../primer/working_with_metadata_annotations.rst | 898 -------------
doc/source/programs/index.rst | 8 -
doc/source/programs/sumtrees.rst | 567 ---------
doc/source/schemas/fasta.rst | 182 ---
doc/source/schemas/index.rst | 36 -
doc/source/schemas/interfaces/fasta_as_string.py | 6 -
doc/source/schemas/interfaces/fasta_dataset_get.py | 36 -
.../schemas/interfaces/fasta_dataset_read.py | 40 -
.../interfaces/fasta_dnacharactermatrix_get.py | 9 -
.../fasta_infinitesitescharactermatrix_get.py | 9 -
.../interfaces/fasta_proteincharactermatrix_get.py | 9 -
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.../interfaces/fasta_rnacharactermatrix_get.py | 8 -
.../fasta_standardcharactermatrix_get.py | 19 -
doc/source/schemas/interfaces/fasta_write.py | 7 -
doc/source/schemas/interfaces/newick_as_string.py | 22 -
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doc/source/schemas/interfaces/newick_tree_get.py | 23 -
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doc/source/schemas/interfaces/nexml_chars_write.py | 9 -
.../schemas/interfaces/nexml_dataset_as_string.py | 8 -
doc/source/schemas/interfaces/nexml_dataset_get.py | 14 -
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.../schemas/interfaces/nexml_dataset_write.py | 9 -
.../interfaces/nexml_dnacharactermatrix_get.py | 10 -
.../nexml_infinitesitescharactermatrix_get.py | 10 -
.../interfaces/nexml_proteincharactermatrix_get.py | 10 -
.../nexml_restrictionsitescharactermatrix_get.py | 10 -
.../interfaces/nexml_rnacharactermatrix_get.py | 10 -
.../nexml_standardcharactermatrix_get.py | 10 -
doc/source/schemas/interfaces/nexml_tree_get.py | 11 -
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.../schemas/interfaces/nexml_treearray_read.py | 10 -
.../schemas/interfaces/nexml_treelist_get.py | 11 -
.../schemas/interfaces/nexml_treelist_read.py | 10 -
.../schemas/interfaces/nexml_trees_as_string.py | 6 -
doc/source/schemas/interfaces/nexml_trees_write.py | 7 -
.../schemas/interfaces/nexus_chars_as_string.py | 20 -
doc/source/schemas/interfaces/nexus_chars_write.py | 21 -
.../schemas/interfaces/nexus_dataset_as_string.py | 32 -
doc/source/schemas/interfaces/nexus_dataset_get.py | 24 -
.../schemas/interfaces/nexus_dataset_read.py | 23 -
.../schemas/interfaces/nexus_dataset_write.py | 33 -
.../interfaces/nexus_dnacharactermatrix_get.py | 9 -
.../nexus_infinitesitescharactermatrix_get.py | 9 -
.../interfaces/nexus_proteincharactermatrix_get.py | 9 -
.../nexus_restrictionsitescharactermatrix_get.py | 9 -
.../interfaces/nexus_rnacharactermatrix_get.py | 8 -
.../nexus_standardcharactermatrix_get.py | 19 -
doc/source/schemas/interfaces/nexus_tree_get.py | 23 -
.../schemas/interfaces/nexus_tree_get_from_path.py | 22 -
.../interfaces/nexus_tree_get_from_stream.py | 22 -
.../schemas/interfaces/nexus_treearray_read.py | 22 -
.../schemas/interfaces/nexus_treelist_get.py | 21 -
.../schemas/interfaces/nexus_treelist_read.py | 20 -
.../schemas/interfaces/nexus_trees_as_string.py | 28 -
doc/source/schemas/interfaces/nexus_trees_write.py | 29 -
doc/source/schemas/interfaces/phylip_as_string.py | 8 -
.../schemas/interfaces/phylip_dataset_get.py | 56 -
.../schemas/interfaces/phylip_dataset_read.py | 60 -
.../interfaces/phylip_dnacharactermatrix_get.py | 13 -
.../phylip_infinitesitescharactermatrix_get.py | 13 -
.../phylip_proteincharactermatrix_get.py | 13 -
.../phylip_restrictionsitescharactermatrix_get.py | 13 -
.../interfaces/phylip_rnacharactermatrix_get.py | 14 -
.../phylip_standardcharactermatrix_get.py | 29 -
doc/source/schemas/interfaces/phylip_write.py | 9 -
doc/source/schemas/newick.rst | 114 --
doc/source/schemas/nexml.rst | 224 ----
doc/source/schemas/nexus.rst | 225 ----
doc/source/schemas/phylip.rst | 180 ---
267 files changed, 19221 deletions(-)
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