[med-svn] [python-dendropy] branch upstream updated (9278860 -> 0ad69d7)
Andreas Tille
tille at debian.org
Sat Nov 14 19:51:16 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository python-dendropy.
from 9278860 Imported Upstream version 4.0.3
new 0ad69d7 Imported Upstream version 4.0.3+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:
doc/Makefile | 177 ---
doc/source/_static/Octocat.png | Bin 2131769 -> 0 bytes
doc/source/_static/dendropy3.png | Bin 6067 -> 0 bytes
doc/source/_static/dendropy_icon.png | Bin 80904 -> 0 bytes
doc/source/_static/dendropy_logo.png | Bin 11493 -> 0 bytes
doc/source/_static/google-groups-logo1.png | Bin 13911 -> 0 bytes
doc/source/_static/logo_cipres.gif | Bin 5400 -> 0 bytes
doc/source/_static/nsf.gif | Bin 6975 -> 0 bytes
doc/source/_themes/rtd-fabric/static/rtd.css | 773 -----------
doc/source/_themes/rtd-fabric/theme.conf | 3 -
doc/source/_themes/sphinx_dendropy_theme/logo.html | 3 -
.../sphinx_dendropy_theme/side_supplemental.html | 78 --
.../_themes/sphinx_dendropy_theme/static/rtd.css | 775 -----------
.../_themes/sphinx_dendropy_theme/theme.conf | 3 -
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 -
doc/source/examples/bdtree_multi2.py | 20 -
doc/source/examples/bibtex_annotations1.py | 24 -
doc/source/examples/bibtex_annotations2.py | 23 -
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 -
doc/source/examples/orti1994.nex | 32 -
doc/source/examples/paup_estimate_model.py | 18 -
doc/source/examples/paup_estimate_tree_ml.py | 15 -
doc/source/examples/paup_estimate_tree_nj.py | 11 -
doc/source/examples/pbhg.py | 16 -
doc/source/examples/pdm.py | 12 -
doc/source/examples/pgstats1.py | 33 -
doc/source/examples/pic1.py | 35 -
doc/source/examples/pic2.py | 7 -
doc/source/examples/pic3.py | 10 -
doc/source/examples/pic4.py | 26 -
doc/source/examples/pic_annotated.py | 32 -
.../examples/preorder_filtered_edge_iteration.py | 10 -
.../examples/preorder_filtered_node_iteration.py | 10 -
doc/source/examples/primates.cc.combined.nex | 17 -
doc/source/examples/primates.cc.nex | 12 -
doc/source/examples/primates.cc.tre | 1 -
.../examples/primates.chars.interleaved.nexus | 228 ----
doc/source/examples/primates.chars.nexus | 45 -
.../primates.chars.simple.interleaved.nexus | 202 ---
doc/source/examples/primates.chars.simple.nexus | 27 -
.../examples/primates.chars.subsets-1stpos.nexus | 20 -
.../examples/primates.chars.subsets-2ndpos.nexus | 20 -
.../examples/primates.chars.subsets-3rdpos.nexus | 20 -
.../examples/primates.chars.subsets-all.nexus | 72 --
.../examples/primates.chars.subsets-coding.nexus | 20 -
.../primates.chars.subsets-noncoding.nexus | 20 -
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 ---------------
doc/source/examples/pythonidae.mle.nex | 46 -
doc/source/examples/pythonidae.nex | 97 --
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 -
doc/source/library/treemodel.rst | 33 -
doc/source/library/treescore.rst | 8 -
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 --
doc/source/primer/paup.rst | 17 -
.../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 -
.../fasta_restrictionsitescharactermatrix_get.py | 9 -
.../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 -
.../schemas/interfaces/newick_dataset_get.py | 24 -
.../schemas/interfaces/newick_dataset_read.py | 23 -
doc/source/schemas/interfaces/newick_tree_get.py | 23 -
.../interfaces/newick_tree_get_from_path.py | 22 -
.../interfaces/newick_tree_get_from_stream.py | 22 -
.../schemas/interfaces/newick_treearray_read.py | 22 -
.../schemas/interfaces/newick_treelist_get.py | 21 -
.../schemas/interfaces/newick_treelist_read.py | 20 -
doc/source/schemas/interfaces/newick_write.py | 23 -
.../schemas/interfaces/nexml_chars_as_string.py | 8 -
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 -
.../schemas/interfaces/nexml_dataset_read.py | 13 -
.../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 -
.../schemas/interfaces/nexml_treearray_get.py | 11 -
.../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(-)
delete mode 100644 doc/Makefile
delete mode 100644 doc/source/_static/Octocat.png
delete mode 100644 doc/source/_static/dendropy3.png
delete mode 100644 doc/source/_static/dendropy_icon.png
delete mode 100644 doc/source/_static/dendropy_logo.png
delete mode 100644 doc/source/_static/google-groups-logo1.png
delete mode 100644 doc/source/_static/logo_cipres.gif
delete mode 100644 doc/source/_static/nsf.gif
delete mode 100644 doc/source/_themes/rtd-fabric/static/rtd.css
delete mode 100644 doc/source/_themes/rtd-fabric/theme.conf
delete mode 100644 doc/source/_themes/sphinx_dendropy_theme/logo.html
delete mode 100644 doc/source/_themes/sphinx_dendropy_theme/side_supplemental.html
delete mode 100644 doc/source/_themes/sphinx_dendropy_theme/static/rtd.css
delete mode 100644 doc/source/_themes/sphinx_dendropy_theme/theme.conf
delete mode 100644 doc/source/acknowledgements.inc
delete mode 100644 doc/source/changes.rst
delete mode 100644 doc/source/citation.inc
delete mode 100644 doc/source/conf.py
delete mode 100644 doc/source/downloading.rst
delete mode 100644 doc/source/examples/bdtree_multi1.py
delete mode 100644 doc/source/examples/bdtree_multi2.py
delete mode 100644 doc/source/examples/bibtex_annotations1.py
delete mode 100644 doc/source/examples/bibtex_annotations2.py
delete mode 100644 doc/source/examples/bibtex_annotations3.py
delete mode 100644 doc/source/examples/build_tree_programmatically.py
delete mode 100644 doc/source/examples/char_mat_concat.py
delete mode 100644 doc/source/examples/char_mat_concat2.py
delete mode 100644 doc/source/examples/chars_access1.py
delete mode 100644 doc/source/examples/chars_access2.py
delete mode 100644 doc/source/examples/chars_access3.py
delete mode 100644 doc/source/examples/chars_access4.py
delete mode 100644 doc/source/examples/contained_coalescent1.py
delete mode 100644 doc/source/examples/contained_coalescent2.py
delete mode 100644 doc/source/examples/ds1.py
delete mode 100644 doc/source/examples/ds2.py
delete mode 100644 doc/source/examples/ds4.py
delete mode 100644 doc/source/examples/ds5.py
delete mode 100644 doc/source/examples/dsrw1.py
delete mode 100644 doc/source/examples/dynamic_annotations1.py
delete mode 100644 doc/source/examples/euctree.py
delete mode 100644 doc/source/examples/find_taxon_node1.py
delete mode 100644 doc/source/examples/find_taxon_node2.py
delete mode 100644 doc/source/examples/hiv1.nexus
delete mode 100644 doc/source/examples/ladderize.py
delete mode 100644 doc/source/examples/ltt.py
delete mode 100644 doc/source/examples/majrule.py
delete mode 100644 doc/source/examples/mcct.py
delete mode 100644 doc/source/examples/mrca.py
delete mode 100644 doc/source/examples/mrca2.py
delete mode 100644 doc/source/examples/node_ages1.py
delete mode 100644 doc/source/examples/orti1994.nex
delete mode 100644 doc/source/examples/paup_estimate_model.py
delete mode 100644 doc/source/examples/paup_estimate_tree_ml.py
delete mode 100644 doc/source/examples/paup_estimate_tree_nj.py
delete mode 100644 doc/source/examples/pbhg.py
delete mode 100644 doc/source/examples/pdm.py
delete mode 100644 doc/source/examples/pgstats1.py
delete mode 100644 doc/source/examples/pic1.py
delete mode 100644 doc/source/examples/pic2.py
delete mode 100644 doc/source/examples/pic3.py
delete mode 100644 doc/source/examples/pic4.py
delete mode 100644 doc/source/examples/pic_annotated.py
delete mode 100644 doc/source/examples/preorder_filtered_edge_iteration.py
delete mode 100644 doc/source/examples/preorder_filtered_node_iteration.py
delete mode 100644 doc/source/examples/primates.cc.combined.nex
delete mode 100644 doc/source/examples/primates.cc.nex
delete mode 100644 doc/source/examples/primates.cc.tre
delete mode 100644 doc/source/examples/primates.chars.interleaved.nexus
delete mode 100644 doc/source/examples/primates.chars.nexus
delete mode 100644 doc/source/examples/primates.chars.simple.interleaved.nexus
delete mode 100644 doc/source/examples/primates.chars.simple.nexus
delete mode 100644 doc/source/examples/primates.chars.subsets-1stpos.nexus
delete mode 100644 doc/source/examples/primates.chars.subsets-2ndpos.nexus
delete mode 100644 doc/source/examples/primates.chars.subsets-3rdpos.nexus
delete mode 100644 doc/source/examples/primates.chars.subsets-all.nexus
delete mode 100644 doc/source/examples/primates.chars.subsets-coding.nexus
delete mode 100644 doc/source/examples/primates.chars.subsets-noncoding.nexus
delete mode 100644 doc/source/examples/prune_taxa_with_labels.py
delete mode 100644 doc/source/examples/pure_kingman1.py
delete mode 100644 doc/source/examples/pythonidae.beast-mcmc.trees
delete mode 100644 doc/source/examples/pythonidae.chars.nexus
delete mode 100644 doc/source/examples/pythonidae.chars.phylip
delete mode 100644 doc/source/examples/pythonidae.fasta
delete mode 100644 doc/source/examples/pythonidae.mb.run1.t
delete mode 100644 doc/source/examples/pythonidae.mb.run2.t
delete mode 100644 doc/source/examples/pythonidae.mb.run3.t
delete mode 100644 doc/source/examples/pythonidae.mb.run4.t
delete mode 100644 doc/source/examples/pythonidae.mcmc-con.nex
delete mode 100644 doc/source/examples/pythonidae.mcmc.nex
delete mode 100644 doc/source/examples/pythonidae.mle.nex
delete mode 100644 doc/source/examples/pythonidae.nex
delete mode 100644 doc/source/examples/pythonidae.random.bd0301.tre
delete mode 100644 doc/source/examples/pythonidae_combined.nex
delete mode 100644 doc/source/examples/pythonidae_continuous.chars.nexml
delete mode 100644 doc/source/examples/pythonidae_cytb.fasta
delete mode 100644 doc/source/examples/raxml_estimate_tree.py
delete mode 100644 doc/source/examples/readroot.py
delete mode 100644 doc/source/examples/readroot2.py
delete mode 100644 doc/source/examples/remove_branch_lengths.py
delete mode 100644 doc/source/examples/reroot_at_external_edge.py
delete mode 100644 doc/source/examples/reroot_at_internal_edge.py
delete mode 100644 doc/source/examples/reroot_at_midpoint.py
delete mode 100644 doc/source/examples/reroot_at_node.py
delete mode 100644 doc/source/examples/rescale_tree_length.py
delete mode 100644 doc/source/examples/retain_taxa_with_labels.py
delete mode 100644 doc/source/examples/seqgen.py
delete mode 100644 doc/source/examples/setroot1.py
delete mode 100644 doc/source/examples/sim_and_count_deepcoal1.py
delete mode 100644 doc/source/examples/sim_and_count_deepcoal2.py
delete mode 100644 doc/source/examples/splitfreq.py
delete mode 100644 doc/source/examples/splits_on_trees.py
delete mode 100644 doc/source/examples/symdiff1.py
delete mode 100644 doc/source/examples/symdiff2.py
delete mode 100644 doc/source/examples/taxa_mgmt1.py
delete mode 100644 doc/source/examples/taxa_mgmt1a.py
delete mode 100644 doc/source/examples/taxa_mgmt1b.py
delete mode 100644 doc/source/examples/taxa_mgmt2.py
delete mode 100644 doc/source/examples/taxa_mgmt3.py
delete mode 100644 doc/source/examples/taxa_mgmt4.py
delete mode 100644 doc/source/examples/taxa_mgmt5.py
delete mode 100644 doc/source/examples/taxon_labels1.py
delete mode 100644 doc/source/examples/taxon_labels2.py
delete mode 100644 doc/source/examples/taxon_labels2b.py
delete mode 100644 doc/source/examples/taxon_labels3.py
delete mode 100644 doc/source/examples/taxon_labels4.py
delete mode 100644 doc/source/examples/to_outgroup_position.py
delete mode 100644 doc/source/examples/tree_copy1.py
delete mode 100644 doc/source/examples/tree_copy2.py
delete mode 100644 doc/source/examples/tree_evolve_char1.py
delete mode 100644 doc/source/examples/tree_evolve_char2.py
delete mode 100644 doc/source/examples/tree_iter1.py
delete mode 100644 doc/source/examples/tree_iter2.py
delete mode 100644 doc/source/examples/tree_length_crit.py
delete mode 100644 doc/source/examples/tree_list_add1.py
delete mode 100644 doc/source/examples/tree_list_copy1.py
delete mode 100644 doc/source/examples/tree_list_copy2.py
delete mode 100644 doc/source/examples/tree_list_copy3.py
delete mode 100644 doc/source/examples/tree_list_ops1.py
delete mode 100644 doc/source/examples/tree_list_ops2.py
delete mode 100644 doc/source/examples/tree_rootings1.py
delete mode 100644 doc/source/examples/treemeasures1.py
delete mode 100644 doc/source/examples/weightedrf1.py
delete mode 100644 doc/source/glossary.rst
delete mode 100644 doc/source/index.rst
delete mode 100644 doc/source/library/basemodel.rst
delete mode 100644 doc/source/library/birthdeath.rst
delete mode 100644 doc/source/library/charmatrixmodel.rst
delete mode 100644 doc/source/library/charstatemodel.rst
delete mode 100644 doc/source/library/coalescent.rst
delete mode 100644 doc/source/library/continuous.rst
delete mode 100644 doc/source/library/datasetmodel.rst
delete mode 100644 doc/source/library/discrete.rst
delete mode 100644 doc/source/library/index.rst
delete mode 100644 doc/source/library/parsimony.rst
delete mode 100644 doc/source/library/popgensim.rst
delete mode 100644 doc/source/library/popgenstat.rst
delete mode 100644 doc/source/library/probability.rst
delete mode 100644 doc/source/library/reconcile.rst
delete mode 100644 doc/source/library/statistics.rst
delete mode 100644 doc/source/library/taxonmodel.rst
delete mode 100644 doc/source/library/treecollectionmodel.rst
delete mode 100644 doc/source/library/treecompare.rst
delete mode 100644 doc/source/library/treemeasure.rst
delete mode 100644 doc/source/library/treemodel.rst
delete mode 100644 doc/source/library/treescore.rst
delete mode 100644 doc/source/library/treeshape.rst
delete mode 100644 doc/source/library/treesim.rst
delete mode 100644 doc/source/license.inc
delete mode 100644 doc/source/migration.rst
delete mode 100644 doc/source/primer/bipartitions.rst
delete mode 100644 doc/source/primer/chars.rst
delete mode 100644 doc/source/primer/converting.rst
delete mode 100644 doc/source/primer/dataobjects.rst
delete mode 100644 doc/source/primer/datasets.rst
delete mode 100644 doc/source/primer/genbank.rst
delete mode 100644 doc/source/primer/index.rst
delete mode 100644 doc/source/primer/paup.rst
delete mode 100644 doc/source/primer/phylogenetic_character_analyses.rst
delete mode 100644 doc/source/primer/popgenstats.rst
delete mode 100644 doc/source/primer/raxml.rst
delete mode 100644 doc/source/primer/reading_and_writing.rst
delete mode 100644 doc/source/primer/seqgen.rst
delete mode 100644 doc/source/primer/taxa.rst
delete mode 100644 doc/source/primer/taxa_partitions.rst
delete mode 100644 doc/source/primer/treecollections.rst
delete mode 100644 doc/source/primer/treemanips.rst
delete mode 100644 doc/source/primer/trees.rst
delete mode 100644 doc/source/primer/treesims.rst
delete mode 100644 doc/source/primer/treestats.rst
delete mode 100644 doc/source/primer/working_with_metadata_annotations.rst
delete mode 100644 doc/source/programs/index.rst
delete mode 100644 doc/source/programs/sumtrees.rst
delete mode 100644 doc/source/schemas/fasta.rst
delete mode 100644 doc/source/schemas/index.rst
delete mode 100644 doc/source/schemas/interfaces/fasta_as_string.py
delete mode 100644 doc/source/schemas/interfaces/fasta_dataset_get.py
delete mode 100644 doc/source/schemas/interfaces/fasta_dataset_read.py
delete mode 100644 doc/source/schemas/interfaces/fasta_dnacharactermatrix_get.py
delete mode 100644 doc/source/schemas/interfaces/fasta_infinitesitescharactermatrix_get.py
delete mode 100644 doc/source/schemas/interfaces/fasta_proteincharactermatrix_get.py
delete mode 100644 doc/source/schemas/interfaces/fasta_restrictionsitescharactermatrix_get.py
delete mode 100644 doc/source/schemas/interfaces/fasta_rnacharactermatrix_get.py
delete mode 100644 doc/source/schemas/interfaces/fasta_standardcharactermatrix_get.py
delete mode 100644 doc/source/schemas/interfaces/fasta_write.py
delete mode 100644 doc/source/schemas/interfaces/newick_as_string.py
delete mode 100644 doc/source/schemas/interfaces/newick_dataset_get.py
delete mode 100644 doc/source/schemas/interfaces/newick_dataset_read.py
delete mode 100644 doc/source/schemas/interfaces/newick_tree_get.py
delete mode 100644 doc/source/schemas/interfaces/newick_tree_get_from_path.py
delete mode 100644 doc/source/schemas/interfaces/newick_tree_get_from_stream.py
delete mode 100644 doc/source/schemas/interfaces/newick_treearray_read.py
delete mode 100644 doc/source/schemas/interfaces/newick_treelist_get.py
delete mode 100644 doc/source/schemas/interfaces/newick_treelist_read.py
delete mode 100644 doc/source/schemas/interfaces/newick_write.py
delete mode 100644 doc/source/schemas/interfaces/nexml_chars_as_string.py
delete mode 100644 doc/source/schemas/interfaces/nexml_chars_write.py
delete mode 100644 doc/source/schemas/interfaces/nexml_dataset_as_string.py
delete mode 100644 doc/source/schemas/interfaces/nexml_dataset_get.py
delete mode 100644 doc/source/schemas/interfaces/nexml_dataset_read.py
delete mode 100644 doc/source/schemas/interfaces/nexml_dataset_write.py
delete mode 100644 doc/source/schemas/interfaces/nexml_dnacharactermatrix_get.py
delete mode 100644 doc/source/schemas/interfaces/nexml_infinitesitescharactermatrix_get.py
delete mode 100644 doc/source/schemas/interfaces/nexml_proteincharactermatrix_get.py
delete mode 100644 doc/source/schemas/interfaces/nexml_restrictionsitescharactermatrix_get.py
delete mode 100644 doc/source/schemas/interfaces/nexml_rnacharactermatrix_get.py
delete mode 100644 doc/source/schemas/interfaces/nexml_standardcharactermatrix_get.py
delete mode 100644 doc/source/schemas/interfaces/nexml_tree_get.py
delete mode 100644 doc/source/schemas/interfaces/nexml_treearray_get.py
delete mode 100644 doc/source/schemas/interfaces/nexml_treearray_read.py
delete mode 100644 doc/source/schemas/interfaces/nexml_treelist_get.py
delete mode 100644 doc/source/schemas/interfaces/nexml_treelist_read.py
delete mode 100644 doc/source/schemas/interfaces/nexml_trees_as_string.py
delete mode 100644 doc/source/schemas/interfaces/nexml_trees_write.py
delete mode 100644 doc/source/schemas/interfaces/nexus_chars_as_string.py
delete mode 100644 doc/source/schemas/interfaces/nexus_chars_write.py
delete mode 100644 doc/source/schemas/interfaces/nexus_dataset_as_string.py
delete mode 100644 doc/source/schemas/interfaces/nexus_dataset_get.py
delete mode 100644 doc/source/schemas/interfaces/nexus_dataset_read.py
delete mode 100644 doc/source/schemas/interfaces/nexus_dataset_write.py
delete mode 100644 doc/source/schemas/interfaces/nexus_dnacharactermatrix_get.py
delete mode 100644 doc/source/schemas/interfaces/nexus_infinitesitescharactermatrix_get.py
delete mode 100644 doc/source/schemas/interfaces/nexus_proteincharactermatrix_get.py
delete mode 100644 doc/source/schemas/interfaces/nexus_restrictionsitescharactermatrix_get.py
delete mode 100644 doc/source/schemas/interfaces/nexus_rnacharactermatrix_get.py
delete mode 100644 doc/source/schemas/interfaces/nexus_standardcharactermatrix_get.py
delete mode 100644 doc/source/schemas/interfaces/nexus_tree_get.py
delete mode 100644 doc/source/schemas/interfaces/nexus_tree_get_from_path.py
delete mode 100644 doc/source/schemas/interfaces/nexus_tree_get_from_stream.py
delete mode 100644 doc/source/schemas/interfaces/nexus_treearray_read.py
delete mode 100644 doc/source/schemas/interfaces/nexus_treelist_get.py
delete mode 100644 doc/source/schemas/interfaces/nexus_treelist_read.py
delete mode 100644 doc/source/schemas/interfaces/nexus_trees_as_string.py
delete mode 100644 doc/source/schemas/interfaces/nexus_trees_write.py
delete mode 100644 doc/source/schemas/interfaces/phylip_as_string.py
delete mode 100644 doc/source/schemas/interfaces/phylip_dataset_get.py
delete mode 100644 doc/source/schemas/interfaces/phylip_dataset_read.py
delete mode 100644 doc/source/schemas/interfaces/phylip_dnacharactermatrix_get.py
delete mode 100644 doc/source/schemas/interfaces/phylip_infinitesitescharactermatrix_get.py
delete mode 100644 doc/source/schemas/interfaces/phylip_proteincharactermatrix_get.py
delete mode 100644 doc/source/schemas/interfaces/phylip_restrictionsitescharactermatrix_get.py
delete mode 100644 doc/source/schemas/interfaces/phylip_rnacharactermatrix_get.py
delete mode 100644 doc/source/schemas/interfaces/phylip_standardcharactermatrix_get.py
delete mode 100644 doc/source/schemas/interfaces/phylip_write.py
delete mode 100644 doc/source/schemas/newick.rst
delete mode 100644 doc/source/schemas/nexml.rst
delete mode 100644 doc/source/schemas/nexus.rst
delete mode 100644 doc/source/schemas/phylip.rst
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-dendropy.git
More information about the debian-med-commit
mailing list