Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-12-12

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All times shown according to UTC.

Time Nick Message
02:10 towodo joined #opentreeoflife
11:14 josephwb joined #opentreeoflife
12:30 towodo joined #opentreeoflife
13:33 josephwb joined #opentreeoflife
14:15 towodo joined #opentreeoflife
16:16 kcranstn joined #opentreeoflife
16:17 kcranstn hey @jimallman - did that figure capture your concerns about the viz?
16:18 jimallman yes, it definitely communicates the appearance of “cohorts”
16:18 jimallman (which to my eye, read either as ranks or maybe “Cambrian explosion” type events)
17:01 josephwb you there jimallman?
17:03 jimallman yes, hi!
17:03 josephwb hi. i am in the curator, but cannot find out the treeIDs.
17:03 josephwb ot_172
17:03 josephwb nevermind. i see now.
17:03 jimallman easiest place is in the browser’s address bar (when you pop up a tree)
17:03 josephwb click on it, appears in address
17:04 jimallman right.. early on, we decided that our ids were not interesting to people in general, so you have to spot them in the margins. :)
17:04 josephwb maybe this should be listed in the Properties tab?
17:04 jimallman see my last comment.
17:04 josephwb maybe not then.
17:05 josephwb but a number of services use treeIDs. tedious to find them.
17:05 josephwb a little bit tedious.
17:05 josephwb i can deal.
17:05 jimallman it seems to me that the more people use the APIs and devote “brain space” to our tools, the more useful (and justifiable) it would be to show our ids, etc. maybe something to check periodically with the larger group..?
17:06 towodo I think showing ids, but downplayed, is good
17:07 jimallman yeah, i can move them to rollover messages, that kind of thing. you might also try mousing over links (tree name in a list, etc) and looking for the hyperlink to appear in the lower left (or status bar)
17:08 josephwb that would be convenient
17:08 towodo I don’t consider ‘rollover’ or ‘hovering’ to be ‘showing’…
17:09 towodo a rollover might explain that they’re for use with the API, or in bug reports
17:16 towodo_ joined #opentreeoflife
17:20 josephwb jimallman: has the study download issue from the other day been fixed? about to try to download a whack of studies.
17:20 josephwb brb; tea.
17:24 josephwb ok, back.
17:24 josephwb you there jimallman?
17:24 jimallman yes, hi
17:25 jimallman by study download issue, do you mean the missing metadata (bare trees)?
17:25 josephwb the error thingy from the other day: could not find study(?)
17:25 jimallman ah yes.
17:25 josephwb http error
17:25 jimallman yeah, that should be fixed in the latest.
17:25 josephwb great.
17:27 jimallman we believe mtholder has a solid fix for this. it had to with with WIP branches, and thread-safe tracking of what studies “exist” on the master branch. please holler if you see the same types of errors now.
17:29 josephwb i will.
18:02 kcranstn joined #opentreeoflife
18:03 josephwb jimallman: getting same error
18:03 josephwb nevermind.
18:03 josephwb was set to devapi. api works.
18:04 josephwb (should devapi work too?)
18:05 jimallman hm, i probably need to update devapi. i’lll bet these fixes went straight from testing on mtholder’s private setup to production.
18:05 josephwb right
18:34 josephwb hey jimallman.
18:35 josephwb curator is not finding this DOI: 10.1126/science.1251385
18:36 kcranstn did they publish a treefile for that study?
18:36 josephwb tons of them.
18:36 kcranstn w00t
18:36 josephwb too many.
18:36 kcranstn boo
18:36 josephwb was just going to in main Fig. 1
18:36 kcranstn that sounds reasonable
18:37 josephwb doing conflict in birds with stephen
18:37 kcranstn nice
18:37 kcranstn good timing!
18:37 josephwb data are here: http://gigadb.org/dataset/101041
18:38 josephwb jimallman?
18:42 kcranstn the DOI hasn’t proliferated through crossref yet
18:42 kcranstn http://search.crossref.org/?q=10.1126%2Fscience.1251385
18:43 josephwb yeesh.
18:43 josephwb why can't they be bleeding-edge like us?
18:45 josephwb kcranstn: is there a way to submit the DOI to crossref?
18:45 kcranstn no
18:45 kcranstn it just takes time
18:46 josephwb i guess it did strictly come out today...
18:46 kcranstn yup
18:54 josephwb jimallman: you back yet?
18:57 towodo joined #opentreeoflife
18:58 josephwb curator not reading in node annotations
18:58 josephwb e.g. :1.244)[&95%={65.8,72.4}]:19.3779)
19:05 jimallman josephwb: back now, reading...
19:06 jimallman yes, i just did the same CrossRef search.. still no dice.
19:07 jimallman these node annotations.. i assume that’s Newick?
19:07 jimallman josephwb: ^
19:07 josephwb Nexus
19:07 jimallman in any case, that’s a peyotl question… unless i’m garbling them in transmission
19:08 josephwb i don't think it is standard format
19:11 josephwb the regex is pretty sweet (although I am not used to javascript-flavoured regex).
19:11 josephwb big time saver
19:11 jimallman tell your friends!
19:12 jimallman i can add more examples if that would help
19:13 josephwb maybe?
19:13 josephwb i am used to replacing with \1, rather than $1
19:13 josephwb anyway, your link anabled me to figure it out.
19:19 jimallman wonderful
19:22 josephwb hey jimallman: why is the curator saying my ingroup clade is Unnamed internal node?
19:22 josephwb i named the focal clade, and the MRCAs look good.
19:23 jimallman focal clade =/= ingroup clade, i think
19:23 jimallman you choose the ingroup clade by clicking a node in the tree viz, then pick from the options menu.
19:23 josephwb hmm, i did that too.
19:23 jimallman (i’m hazy on the distinction, myself)
19:24 jimallman if the chosen node (root of ingroup clade) isn’t labeled in the tree data, it’ll still report as an unnamed internal node.
19:26 josephwb ok. i don't think it will ever (or nearly ever) be labelled in the tree itself.
19:28 jimallman c’est la vie. since we can’t know for sure whether a study’s focal clade is the same as the ingroup clade of a particular tree...
19:28 josephwb but i entered in both the focal clade, and specified the ingroup (named by the MRCA function).
19:30 jimallman maybe i’m misremembering the UI, heading there now…
19:30 mtholder joined #opentreeoflife
19:33 jimallman hm, i see where you’re coming from. we use the MRCA tests to very that a tree’s ingroup is what the curator intended, but i don’t think we store this result. it’s more of a sanity check.
19:37 josephwb ok
19:37 mtholder hello all. When  you load https://github.com/orgs/OpenTreeOfLife/dashboard does it say "mtholder pushed to master..." for all the recent phylesystem commits?
19:38 mtholder the author is right on https://github.com/OpenTreeOfLife/phylesystem-1/commits/master
19:38 mtholder so I'm not sure why the dashboard is bogus.
19:38 jimallman yes, “mtholder pushed” for the last five commits
19:39 kcranstn that mtholder guy is busy
19:39 mtholder odd. the server should not have my credentials.
19:39 mtholder does make me look busy
19:39 jimallman committed vs. pushed, not the same in git
19:40 mtholder but the commits are correctly attributed to the curator (JWB in this case) on the commits page.
19:40 jimallman author vs. committer, i mean!
19:40 jimallman (it’s weird, i know)… most of the time GitHub’s UI will show both, with author featured and “committer” as a mini-thumbnail (see Dail’s commits in phylesystem-1 link above)
19:41 jimallman i see your point. it looks like the “dashboard” is tracking push as a distinct act. i take it you merged or pushed between repos?
19:42 mtholder nope.
19:42 jimallman looks like it tracks issue actions (creating, commenting), pushes and merges but not individual commits.
19:43 mtholder the ~/.gitconfig on the server lists:
19:43 mtholder [user]
19:43 mtholder name = OpenTree API
19:43 mtholder email = api@opentreeoflife.org
19:43 mtholder as usual.
19:43 jimallman hmm. if you really had nothing to do with this stuff getting to master, it must be a GH bug.
19:44 jimallman maybe because you’re the owner / creator of the peyotl repo?
19:44 jimallman phylesystem-1, i mean
19:45 mtholder I was poking around on that machine a couple of logs for the bug that JWB reported. but I don't think I did anything that would have left my git info on the machine...
19:45 mtholder I guess we can see if it is resolved by GH. As long as the commits are being correctly attributed, we have the correct info in the history.
19:49 jimallman towodo: looks like there’s a single listing of PRs throughout all OpenTree repos:  https://github.com/pulls?user=OpenTreeOfLife
19:49 jimallman that’s news to me
20:43 mtholder joined #opentreeoflife
20:44 towodo oh wow
21:00 mtholder joined #opentreeoflife
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23:59 towodo joined #opentreeoflife

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