lp:~jon-hill/supertree-toolkit/tree_names

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Merged into lp:supertree-toolkit at revision 254

Jon Hill: Approve on 2014-10-13

Diff: 2151 lines (+404/-208)

35 files modified

doc/gui.rst (+18/-8)
schema/phylo_storage.rnc (+2/-2)
schema/phylo_storage.rng (+6/-9)
stk/stk_import_export.py (+1/-0)
stk/supertree_toolkit.py (+69/-23)
stk/test/_import_export.py (+2/-0)
stk/test/_schema_validation.py (+11/-1)
stk/test/_supertree_toolkit.py (+15/-3)
stk/test/data/input/awkward_subs.phyml (+5/-5)
stk/test/data/input/check_data_ind.phyml (+10/-10)
stk/test/data/input/check_data_summary.phyml (+6/-6)
stk/test/data/input/check_fossils.phyml (+6/-6)
stk/test/data/input/check_overlap_ok.phyml (+6/-6)
stk/test/data/input/check_taxa.phyml (+6/-6)
stk/test/data/input/clean_data.phyml (+12/-12)
stk/test/data/input/create_matrix.phyml (+6/-6)
stk/test/data/input/full_tree.phyml (+6/-6)
stk/test/data/input/lots.xml (+1/-1)
stk/test/data/input/non_unique_names.phyml (+8/-8)
stk/test/data/input/old_stk_input.phyml (+40/-40)
stk/test/data/input/old_stk_input_data_summary_test.phyml (+21/-21)
stk/test/data/input/permute_trees.phyml (+9/-9)
stk/test/data/input/single_name.xml (+1/-1)
stk/test/data/input/single_source.phyml (+2/-2)
stk/test/data/input/single_source_no_names.phyml (+67/-0)
stk/test/data/input/sub_taxa.phyml (+3/-3)
stk/test/data/input/two_names.xml (+2/-2)
stk/test/data/input/weighted_trees.phyml (+3/-3)
stk/test/data/output/full_tree.phyml (+3/-3)
stk/test/data/output/lots.xml (+1/-1)
stk/test/data/output/single_name.xml (+1/-1)
stk/test/data/output/two_names.xml (+2/-2)
stk_gui/gui/gui.glade (+11/-0)
stk_gui/plugins/phyml/import_tree.py (+1/-0)
stk_gui/stk_gui/interface.py (+41/-2)

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Bug #1378075: Trees in a dataset should be named

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259. By Jon Hill on 2014-10-13

Adding name trees to standardise names

258. By Jon Hill on 2014-10-13

correct spelling

257. By Jon Hill on 2014-10-10

Mods to manual to say trees names exist

256. By Jon Hill on 2014-10-10

Fixing clean data test which was failing swapping trees in xml

255. By Jon Hill on 2014-10-09

Edited most of the files now to pass tests. Found a function (_swap_tree_in_xml) that'll take more thingking about though

254. By Jon Hill on 2014-10-07

Adding names to the trees. Tests all broken, but need to hook in the function to the gui to name all the trees before I can even attempt to fix these. The two new functions are tested and seem to be working though

253. By Jon Hill on 2014-10-06

Fix for lack of error message when subing taxa

252. By Jon Hill on 2014-07-04

Might help if you test first

251. By Jon Hill on 2014-07-04

Adding colours by genus to itol script

250. By Jon Hill on 2014-06-18

Update to changelog for release 12