Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2015-04-27

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All times shown according to UTC.

Time Nick Message
00:38 jimallman joined #opentreeoflife
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01:36 travis-ci OpenTreeOfLife/phylesystem-api#780 (support-tree-collections - 4a3b804 : Jim Allman): The build passed.
01:36 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/79305f20ba0d...4a3b8046a917
01:36 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/60158190
01:36 travis-ci left #opentreeoflife
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01:47 Topic for #opentreeoflife is now Open Tree Of Life | opentreeoflife.org | github.com/opentreeoflife | http://irclog.perlgeek.de/opentreeoflife/today
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01:53 travis-ci OpenTreeOfLife/phylesystem-api#782 (support-tree-collections - 1c6cc6f : Jim Allman): The build passed.
01:53 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/cd99a9e2f7e9...1c6cc6fd92b7
01:53 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/60159041
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02:06 travis-ci OpenTreeOfLife/phylesystem-api#783 (support-tree-collections - 27f9ce0 : Jim Allman): The build passed.
02:06 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/1c6cc6fd92b7...27f9ce07331c
02:06 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/60159712
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02:22 travis-ci OpenTreeOfLife/phylesystem-api#784 (support-tree-collections - e2a5004 : Jim Allman): The build passed.
02:22 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/27f9ce07331c...e2a500448369
02:22 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/60160609
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02:36 travis-ci OpenTreeOfLife/phylesystem-api#786 (support-tree-collections - f6b473b : Jim Allman): The build passed.
02:36 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/e3ac864b1f36...f6b473bbbfb8
02:36 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/60161418
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02:40 travis-ci OpenTreeOfLife/phylesystem-api#787 (support-tree-collections - b879e9c : Jim Allman): The build passed.
02:40 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/f6b473bbbfb8...b879e9c5048c
02:40 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/60161649
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02:41 travis-ci OpenTreeOfLife/phylesystem-api#788 (support-tree-collections - 0678d7d : Jim Allman): The build passed.
02:41 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/b879e9c5048c...0678d7d3a4ff
02:41 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/60161780
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02:49 travis-ci OpenTreeOfLife/phylesystem-api#789 (support-tree-collections - 484a663 : Jim Allman): The build passed.
02:49 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/0678d7d3a4ff...484a66329a9d
02:49 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/60162224
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02:57 travis-ci OpenTreeOfLife/phylesystem-api#790 (support-tree-collections - 4570cd1 : Jim Allman): The build passed.
02:57 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/484a66329a9d...4570cd11c60d
02:57 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/60162687
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03:02 josephwb hey kcranstn
03:02 josephwb you there jimalllman?
03:03 josephwb jimallman, that is
03:03 jimallman hi!
03:03 josephwb hey
03:03 jimallman josephwb: ^
03:03 josephwb do you know if kcranstn is around?
03:03 jimallman we haven’t chatted today. i’m guessing she’s afk
03:04 jimallman (away from keyboard)
03:04 josephwb thanks for the spelling out ;)
03:04 * jimallman had a hunch
03:04 josephwb hehe
03:05 josephwb i fixed 99.999% of the tree problems
03:05 jimallman sweet!
03:05 josephwb will have a db tomorrown morning where most webservices work
03:05 josephwb most importantly, source info for the tree browser
03:05 jimallman i was just going to ask :)
03:06 josephwb had that fixed a couple of days ago, but knew i'd be making incremenetal improvements to the db
03:07 josephwb was going to ask karen when revisions were going to be submitted. do you know?
03:07 jimallman no idea, sorry (still buried in peyotl and tree-collection apis)
03:08 josephwb no problem
03:09 josephwb don't know what we are going to do with the treemachine branch we are using. a PR review seems nuts; a different beast altogether.
03:10 josephwb just replace master, work from that
03:11 jimallman maybe a PR with a different set of reviewers?
03:11 josephwb only issue is that some webservices don't work (and should probably be retired, anyway)
03:12 jimallman hmm
03:13 josephwb i mean the PR review would be cray-zee. the code is SO different.
03:14 josephwb webservices is the only relevant issue
03:14 josephwb but, discussion for another day
03:16 josephwb alright, i am taking an early night; slightly blind from scrutinizing trees for a couple of days straight.
03:16 josephwb l8r jimallman
03:16 jimallman a’ight
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04:32 travis-ci OpenTreeOfLife/phylesystem-api#791 (support-tree-collections - 62059b7 : Jim Allman): The build passed.
04:32 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/4570cd11c60d...62059b7f4dcc
04:32 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/60167643
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12:31 kcranstn hey josephwb
12:31 josephwb howdy
12:31 josephwb just a sec; getting tea
12:31 kcranstn :)
12:34 josephwb ok, back
12:34 kcranstn sounds like we should devote some of tomorrow’s meeting to web services and other code updates
12:35 josephwb probably
12:35 kcranstn what web services don’t work?
12:35 josephwb but i was able to remove almost all of the unsupported nodes this weekend
12:35 josephwb getsourcetree
12:35 kcranstn remove how?
12:35 josephwb it was a problem with otcetera
12:35 josephwb when it pruned contested taxa
12:35 kcranstn is the tree still changing? I thought that it was final
12:36 josephwb contested taxa are missing from the subproblem newicks, but present in the originals, so they did not correspond
12:36 kcranstn or, that’s what stephen told ruchi
12:36 josephwb i was working on this on my own
12:37 josephwb i had to rebuild the db to get webservices to work anyway, so i fixed those
12:37 kcranstn so what’s in the db does not match what we gave to ruchi?
12:38 josephwb ruchi is redoing it for me
12:38 kcranstn can we please keep these conversations on the mailing list? It is too hard to keep track, otherwise
12:38 josephwb this was just an experiment
12:39 josephwb didn't want to delay revisions; fine if it doesn't go through
12:39 kcranstn will you revert the db, then?
12:39 josephwb i can
12:39 kcranstn ok, probably need to decide this tomorrow
12:40 kcranstn not probably, definitely
12:40 josephwb whatever you want is fine by me
12:42 josephwb unsupported nodes are almost all missing resolution. new tree almost identical, but with those ~40 nodes fixed
12:42 josephwb gotta take kid to school. back later.
12:42 jar286 the code has to be reviewed, the question is when.
12:43 kcranstn josephwb just left
12:46 jar286 yes I know… speaking to the wind
12:47 jar286 am I the only one made berserk by statements like “Each v ∈ V is a clade hypothesis (or clade)” ?
12:48 jar286 it’s like saying “Fred wore a shoe, also known as a rock (or a cloud)”
12:49 kcranstn yeah… the doc needs massive revision
12:52 jar286 it’s daunting… 22 pages. I don’t know how I’m going to read it, much less review or rewrite
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14:00 travis-ci OpenTreeOfLife/phylesystem-api#792 (support-tree-collections - 537bcf7 : Jim Allman): The build passed.
14:00 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/62059b7f4dcc...537bcf77fdd0
14:00 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/60221401
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14:22 travis-ci OpenTreeOfLife/phylesystem-api#793 (support-tree-collections - 94879aa : Jim Allman): The build passed.
14:22 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/537bcf77fdd0...94879aabc56b
14:22 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/60224372
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14:25 travis-ci OpenTreeOfLife/phylesystem-api#794 (support-tree-collections - 520b07e : Jim Allman): The build passed.
14:25 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/94879aabc56b...520b07e2b1a6
14:25 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/60224663
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16:17 josephwb hey jimallmna
16:17 josephwb jimallman
16:17 josephwb getting ready to push treemachine db to dev.
16:18 jimallman okie-doke
16:18 josephwb 99.99% sure i need to push to devapi (and not devtree). confirm?
16:18 jimallman correct.
16:18 josephwb sweet. thanks.
16:18 jimallman i’m testing other stuff at the moment, just let me know if you need to restart or freeze things.
16:19 jimallman (other stuff on devtree + devapi, i mean)
16:19 josephwb i don't know what devtree does
16:19 josephwb i am just pushing the db. neo4j will restart (i believe)
16:19 jimallman devtree = web apps (tree viewer and curation app)
16:20 josephwb i guess the treeviewer should restart when the new db is in place, right?
16:20 josephwb or will it "just work"?
16:21 josephwb either way, i do not have access to devtree, so cannot do anything there
16:22 josephwb there may still be a treemachine db in the Downloads of devtree. can you check/delete jimallman?
16:22 jimallman sorry, i was busy elsewhere.. catching up now
16:23 jimallman after db update, devtree should Just Work (picks up the new goods from devapi)
16:23 jimallman checking devtree now…
16:23 josephwb thanks
16:23 josephwb jonathan may have deleted it
16:24 jimallman do you have a path? not sure what “Downloads” means here
16:24 josephwb is there not a downloads directory? there is on devapi
16:25 jimallman ah, i see it
16:25 josephwb i thought that was where dbs enter
16:25 josephwb capitalization may have been off
16:25 josephwb is it still there?
16:25 jimallman yes, there’s an old treemachine.db.tgz (from Apr 10)
16:26 josephwb sounds right
16:26 jimallman clobber this? i assume this should have gone to devapi
16:26 josephwb yes, please incinerate
16:26 jimallman *POOF*
16:26 josephwb that should free up some space
16:26 jimallman oh, i guess incinerate should be *FWOOOSH!*
16:27 jimallman 10GB or so, yes
16:27 josephwb thanks
16:27 jimallman np
16:27 jimallman back to my knitting...
16:28 josephwb *FWOOOSH!* ("ah, it burns! why me? why?!?....")
16:30 josephwb shitshitshitshitshit
16:30 kcranstn what’s going on?
16:30 josephwb used the wrong version of treemachine to build the db
16:31 josephwb tree is correct, but doesn't have the webservice stuff
16:31 kcranstn boo
16:31 josephwb setting up right one now
16:43 * jimallman is setting up an IRC alert for “shitshitshit”…
16:43 kcranstn there are probably a few synonyms that you want to include
16:46 jimallman this might take awhile...
16:47 jimallman i’ll need a German dictionary and thesaurus, too
16:49 josephwb hehe
16:50 josephwb maybe some Québécois, too
16:50 josephwb eh?
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19:33 kcranstn jar286?
19:42 jar286 kcranst, here, stepped out to get a snack in lieu of lunch
19:43 jar286 kcranstn that is
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