Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-07-24

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All times shown according to UTC.

Time Nick Message
00:13 josephwb joined #opentreeoflife
00:24 towodo joined #opentreeoflife
00:27 jimallman towodo: i’m starting to make Cavia branches, will wait on taxomachine and oti until we talk
00:28 towodo good. that’s the next step.
00:28 towodo are we going current with everything?
00:30 josephwb joined #opentreeoflife
00:33 jimallman i’d say so. i’m looking at active (unmerged) branches, too
00:34 jimallman for opentree, should i review this ‘dochac’ branchof yours from last week?
00:34 jimallman also, should i go ahead and merge my hacky ‘force-neo4j-restart’ from yesterday?
00:35 jimallman dochac looks good but trivial, just a cleanup of the deploy/README
00:41 towodo yes, go ahead. i made a pull request for it
00:41 travis-ci joined #opentreeoflife
00:41 travis-ci [travis-ci] OpenTreeOfLife/phylesystem-api#576 (Cavia - adf5842 : Mark T. Holder): The build passed.
00:41 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/Cavia
00:41 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/30707705
00:41 travis-ci left #opentreeoflife
00:42 towodo force-neo4j-restart - doesn’t matter to me. go ahead.
00:42 jimallman towodo: i’ll go ahead with ‘force-neo4j-restart’ too, unless you object (easy enough to undo if we find a more elegant fix)
00:42 * jimallman nods
00:49 towodo joined #opentreeoflife
00:49 towodo weird, did you see travis’s message?
00:50 towodo does it check every commit to every branch?
00:52 jimallman it looks like it’s triggered (on this repo) on creation of a branch! i don’t know where that’s configured..
00:52 jimallman it’s identical to master, so mtholder shows up there as the author of the most recent commit
00:52 jimallman done with Cavia branches
00:57 * jimallman is chasing a curation error for Dail, then back to this..
01:02 josephwb joined #opentreeoflife
01:05 towodo joined #opentreeoflife
01:26 towodo deploying software now
01:28 towodo SSLCertificateKeyFile: file '/etc/ssl/private/opentreeoflife.org.key' does not exist or is empty
01:38 jimallman ah yes, it’s time for my key-transfer checklist… looking for that gist URL
01:39 jimallman https://gist.github.com/jimallman/2c60be5eb49e7a443133
01:39 jimallman i can do this very quickly. it’s practically a script now, obviously
01:39 * jimallman is copying keys
01:45 jimallman towodo: all keys are now in place on ot18. sorry for the delay, i was chasing a curation bug
01:46 towodo ok, so time to restart apache?
01:52 towodo going to bed now, ttyl
01:54 jimallman ok. i might keep going here for a bit
01:54 jimallman good night!
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12:20 towodo joined #opentreeoflife
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12:23 jimallman towodo: i knocked out most of the Cavia migration checklist last night.
13:00 josephwb joined #opentreeoflife
13:33 josephwb morning ilbot3
13:46 jimallman morning josephwb !
13:46 josephwb howdy
14:09 kcranstn joined #opentreeoflife
14:30 travis-ci joined #opentreeoflife
14:30 travis-ci [travis-ci] OpenTreeOfLife/phylesystem-api#577 (master - 3f4fbdb : Jim Allman): The build passed.
14:30 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/adf5842b770b...3f4fbdb49b52
14:30 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/30755342
14:30 travis-ci left #opentreeoflife
14:32 towodo joined #opentreeoflife
14:55 towodo jimallman, http://mumble.net/~jar/tmp/ot18-status.html
14:56 jimallman towodo: very cool
14:58 kcranstn nice! Thanks!
15:21 josephwb kcranstn: I missed the deadline for getting a reduced rate room for NESCent visit. are there any codes available I could use?
15:21 kcranstn you phoned and they said no?
15:21 josephwb i tried online
15:21 josephwb deadline was yesterday (crap)
15:21 kcranstn try phoning, and let me know what they say
15:22 josephwb erg. i don't have a phone...
15:22 josephwb Do you know of anyone at NESCent (close by) I might crash with?
15:23 kcranstn let me see if we can extend it by a few days - I will need to get the admin folks to phone the hotel
15:23 josephwb sorry for the trouble
15:23 kcranstn you migth be able to share a room with one of the other participants
15:23 josephwb is there a list somewhere?
15:24 kcranstn you should have got a notification about being signed up for the mailing list
15:24 josephwb *looking now*
15:25 kcranstn with your umich address
15:25 kcranstn subject = “Welcome to the "Revbayes2014" mailing list"
15:26 josephwb found it, thanks
15:38 josephwb kranstn are you going to get the admin folks to phone the hotel regardless?
16:46 kcranstn joined #opentreeoflife
16:49 kcranstn I will, but I can’t promise that the hotel will say yes
17:03 josephwb ok, thanks. i will try calling tonight
19:44 josephwb no jimallman?
19:51 towodo he’s in Asheville
19:52 josephwb ok, thanks
20:03 josephwb towodo: looking at your email
20:03 josephwb the Archaea doi goes to a paper on ants
20:03 towodo I know.
20:03 josephwb there are Archaea ants?
20:03 towodo Too lazy to get a proper one, and it doesn’t threaten the explanation of the format.
20:04 josephwb ok
20:04 towodo can you provide a better example?
20:04 towodo that would be best.
20:04 towodo any paper arguing for the monophyly of any group, really
20:04 josephwb FWIW the microbe people (Laura/Dail) do *not* believe in the monophyly of Archaea, and are pushing a tree that purportedly shows that (I don't believe it)
20:05 towodo right.
20:05 towodo they think eukaryotes are degenerate archaea, so we need a new clade+name to include both
20:06 towodo are you looking for a better example or should I?  (welcome distraction)
20:07 josephwb i am busy at the moment
20:07 towodo I will try to find one for mammalia or something
20:08 josephwb but Archaea is good, because there are papers for and (maybe only one) against
20:08 kcranstn let’s pick a non-controversial example to use in the readme
20:08 towodo working on it.
20:08 josephwb Mammalia works
20:08 kcranstn I agree
20:12 towodo refresh now. I picked Chiroptera, which at least I have a DOI for.
20:12 towodo maybe it’s controversial too.
20:12 towodo but if an example weren’t controversial, there wouldn’t be a reference for it
20:13 kcranstn but there should be plenty of papers with trees that contain that clade
20:13 josephwb link doesn't go where you wanted
20:14 kcranstn I asked for suggestions on twitter
20:15 towodo foo.
20:16 kcranstn ^ towodo: was that for your broken link, or my attempts at crowdsourcing?
20:16 josephwb looks like it is Springer's problem
20:17 towodo yes.  they are in violation of the contract with crossref
20:17 towodo s/the/their/
20:17 kcranstn ok, so now we need a non-controversional clade supported by a paper with a resolving DOI
20:17 towodo yes… will try 2nd one on google scholar hit list
20:18 josephwb don't undertand why it doesn't find link.springer.com/article/10.1007/s002390010094
20:18 towodo if I felt like taking the time I’d report the DOI to crossref and hope they get a hefty fine
20:20 towodo http://dx.doi.org/10.1006/mpev.2001.1055  works
20:21 towodo third scholar hit for “mammalia monophyly”
20:21 towodo pushed.
23:31 josephwb joined #opentreeoflife
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