Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2015-04-21

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Time Nick Message
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02:08 travis-ci OpenTreeOfLife/phylesystem-api#734 (support-tree-collections - 73a9c89 : Jim Allman): The build passed.
02:08 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/eb55e30eff9c...73a9c89d5ca4
02:08 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/59335839
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13:46 josephwb hey mtholder
13:47 mtholder yes
13:47 mtholder josephwb ^
13:47 josephwb have you looked at otc handling the (many, many) raw subproblem newicks for the unsupported test?
13:47 mtholder no
13:47 josephwb instead of the full newicks
13:47 josephwb ok
13:47 mtholder sorry
13:48 josephwb i get slightly different answers
13:48 josephwb e.g. build with subprobs, test with full newicks
13:49 josephwb is there something i can look at?
13:50 mtholder the root statement in an input subtree is not viewed as providing any support. So, I'm not sure if chopping the trees into pieces preserves all of the support statements.
13:50 josephwb in the older way, when contested tips were pruned, the subprobs did not correspond exactly with the full newicks
13:50 mtholder right- and they still don't wrt tip labels
13:50 mtholder (an internal can be a tip in a subproblem)
13:51 mtholder but they should be closer than before because the new method does not prune tips
13:51 josephwb yes, closer
13:51 mtholder Can you isolate a small case on which they differ?
13:51 josephwb for smaller clades, i can test using the subprobs, and get 0 unsupported
13:51 josephwb ok, i will look
13:52 josephwb have meetings now, but will get you something
13:52 josephwb for those same smaller clades, i can get >0 unsupported when testing with the full newicks
13:53 josephwb ok, will be back later. thanks.
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13:54 josephwb one last thing: removing all subprobs with no phylo structure is fine for the test, right?
13:54 josephwb e.g.
13:54 josephwb (12345);
13:54 josephwb (6789,38735);
13:54 josephwb (32763,3478923879,238792387);
13:54 josephwb etc.
13:56 mtholder yes
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18:55 travis-ci OpenTreeOfLife/phylesystem-api#735 (support-tree-collections - 44813af : Jim Allman): The build passed.
18:55 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/73a9c89d5ca4...44813afc5316
18:55 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/59418483
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21:57 travis-ci OpenTreeOfLife/phylesystem-api#737 (support-tree-collections - e318e47 : Jim Allman): The build passed.
21:57 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/6e53f1561df9...e318e47ea329
21:57 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/59434873
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