Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-09-15

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All times shown according to UTC.

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06:14 karolisr test
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11:22 josephwb hey jimallman
11:22 josephwb you there?
11:24 josephwb i guess stephen pushed our latest synthetic tree to dev.
11:24 josephwb oh, i guess there was a lag. didn't work, but now it does
11:24 josephwb although the autocomplete context just has "ERROR"
11:25 josephwb oh, cannot search in the autocomplete box
11:25 josephwb does oti need to be re-run?
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11:31 kcranstn mornin!
11:31 josephwb hiya
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12:34 jcavner Is anyone there getting anything (audio) from the webex meeting?
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12:49 josephwb hey jimallman
12:50 jimallman good morning! thought i had the webex plugin, fetching it now…
12:56 jimallman josephwb: i see the “ERROR” in autocomplete, chasing this now...
12:57 josephwb thanks
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12:57 josephwb stephen did a straight-up treemachine db psuh
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12:57 josephwb push
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13:01 josephwb ack, on my way over to the hackathon
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13:21 * jimallman is pushing latest taxomachine to devapi
13:21 josephwb hey jimallman.
13:21 jimallman howdy
13:22 josephwb did you look at the autocomplete stuff?
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13:25 jimallman josephwb: yes, this fixed the search menu
13:25 jimallman on devtree
13:25 josephwb yes, just checked. thanks!
13:26 kcranstn need to update the API docs so that the examples are api, not devapi
13:28 josephwb kcranstn: the dev api has a better treemachine DB to query against
13:28 josephwb brand-spankin' new
13:28 kcranstn w00t!
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13:58 josephwb hey mtholder
13:58 josephwb don't know if you are listening in
13:59 josephwb use case: want an older evrsion of a study
13:59 josephwb how to do?
13:59 josephwb don't see a service that takes a GITSHA
14:04 mtholder the GET to study/study_id takes an undocumented arg called "starting_commit_SHA" (bit cryptic). If you pass it a commit SHA you, get the study at that point in the history.
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14:10 josephwb ah, thanks mtholder
14:12 mtholder josephwb, jar286, blackrim, or jimallman do you happen why the tnrs services aren't working on devapi ? (email bug report to list by Yan Wong)
14:12 jimallman i just updated the (old) taxomachine on devtree… will retry his call now
14:14 jimallman mtholder: it’s working now, will respond there
14:14 jimallman (to email, i mean)
14:15 mtholder cool, thanks
14:24 blackrim jimallman: do you know where the d3 version of the tree that I have posted is? just can't find the link
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14:24 jimallman blackrim: sorry, which tree?
14:25 blackrim the one that is on devtree
14:25 jimallman ah.. do the viz links in devtree > About work?
14:25 * jimallman is checking now...
14:26 jimallman blackrim: is this your card?   http://files.opentreeoflife.org/other/synth_viz_dyn.html?ottolID=304358
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14:26 blackrim that is what I was looking for. thanks
14:26 jimallman cool. that’s just a viz link from http://devtree.opentreeoflife.org/about/developer-resources
14:26 blackrim aha. yes, that is what i was looking for
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14:43 kcranstn wow, this is a record for number of opentree irc participants!
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14:46 jimallman 18 and counting
14:47 kcranstn_ we all just got access to the UM non-guest wireless, so things should be speedier
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14:50 blackrim now that we have all these folks on our IRC channel, let's start the flame wars! one VIM to rule them all
14:50 kcranstn_ behave yourself, blackrim. We have guests.
14:51 blackrim :-) on the internet, there are no guests. ok behaving starting now...
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14:55 towodo I keep thinking the piano tuner is almost done
14:56 mjy they can go on for hours ...
14:57 codiferous just can't wait for the choral recital?
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15:36 towodo josephwb1, did the regression tests get run on the new tree?
15:37 josephwb1 towodo: no, not yet. it is only a few hours old at this point. i will get these going at lunch or soon thereafter.
15:38 towodo ok.  i’m thinking about how soon we can move this tree to production
15:39 josephwb1 right
15:39 josephwb1 i will make this a priority
15:39 josephwb1 should be pretty fats. just need a breather to set it up
15:41 josephwb1 fast
15:41 josephwb1 pretty fast
15:41 mtholder I was wondering about that.
15:41 mtholder thought it was slang
15:43 josephwb1 fats = future actual tree statistics
15:45 towodo not sure what other review is planned - blackrim?
15:46 blackrim towodo: yeah, I sent the link. i think most of those folks are not superresponsive so I will poke them individually tomorrow (give them a day). that is it. other ideas?
15:46 towodo I think that’s the best we can do
15:47 josephwb1 ok, so regression tests not super urgent?
15:47 blackrim I look at the base of things and looks pretty darn good. but better to get more on it
15:47 towodo no, i said “other review”, “other” than regression tests
15:47 towodo so both are important
15:47 josephwb1 right
15:48 josephwb1 i will do it over lunch then
15:49 towodo if there are any missing taxa or relationships check the previous tree version - the problems may be old ones, or there could be a mistake in the test set
15:50 josephwb1 ok.
15:50 josephwb1 previous is currently on production?
15:50 towodo yes
15:50 josephwb1 gotcha
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16:47 mwestneat I'll be back at 2P Ann Arbor time
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17:06 josephwb ack. API documentation for graph/source tree is wrong.
17:06 josephwb duplicate of graph/node_status service
17:07 josephwb i will fix this
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17:43 towodo Metadata and PNG: http://dpanswers.com/roztr/content_show.php?id=261
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17:45 ShanKothari testing
17:45 kcranstn_ hello!
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17:45 ShanKothari Hi!
17:46 katielyons hi
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17:48 arlin_stoltzfus we're still chattering here in Michigan, waiting for stragglers
17:48 thackerBob OK, trying to test this thing out
17:49 kcranstn_ thackerBob, not spongeBob?
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17:50 thackerBob it said "spongeBob" was already a registered user (imagine!) and so I changed it
17:50 kcranstn_ ha!
18:00 josephwb ok, graph/source_tree documentation fixed
18:02 kcranstn_ ok, I think we should get going
18:02 kcranstn_ still waiting for one group from lunch, but...
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18:07 kcranstn_ pitches going into google doc: https://docs.google.com/document/d/1aAwS5mH4iCmRW4aRlVe3po5GO8hB9CQw3e25NWoSAFM/edit#
18:09 josephwb ok, graph/source_tree documentation fixed (again…)
18:23 towodo jimallman, you listening? (style sheets for trees - a propos tree illustrator project)
18:24 jimallman yes, i’ve been reading the TSS spec as well. pondering the implications of their model vs. what i’ve been building so far..
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18:24 thackerBob I will be out for about 30 min
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19:02 blackrim I have to run to unscheduled faculty meeting real quick. will be online as I can
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19:12 jimallman snacks!
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19:29 jonxhill We're counting how many folk may want to join in the pitches
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19:30 ShanKothari This is important; raise your hand or type something if you have interest in any of the pitches
19:30 ShanKothari (you can do more than one for now)
19:31 mtholder 2 is of most interest to me, but I'm happy to help with any of them.
19:31 jimallman #4 is probably my fave
19:31 lcoghill 2, 7 and 8 for me.
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19:32 ahdebevec 7, 4, 9 for me
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19:33 ShanKothari 2 and 3 are merged as general language interoperability issues (probably sharing test cases)
19:34 towodo what’s the URL for the google doc for the meeting notes?…
19:34 ShanKothari 5 and 6 (I think?) were also merged, so numbers have changed
19:34 ShanKothari https://docs.google.com/document/d/1aAwS5mH4iCmRW4aRlVe3po5GO8hB9CQw3e25NWoSAFM/edit#
19:35 ShanKothari Are all you remote folks okay, in terms of understanding what's going on?
19:35 towodo thanks
19:36 ahdebevec yes but I'm not sure if all the remote people are also in the IRC at this point. thanks for keeping us updated
19:36 jimallman ShanKothari: i believe i’m following, yes. seems like we’re trying to consolidate or cluster pitches, to get to a few strong teams.
19:37 jimallman my mistake, i guess we’re just giving them catchy names :)
19:37 ShanKothari Exactly. We'll be writing things on large pads of paper around the room, so we can flesh out ideas and walk around.
19:37 ShanKothari I'm sure we'll have some way to keep you guys updated
19:38 daisie I missed this in the IRC if it happened: @jimallman, are you interested in helping with tree style sheets?
19:39 ShanKothari I think he said yes
19:39 jimallman hi daisie! yes, i’d like to help with this.
19:39 daisie woohoo!
19:39 daisie do you have a code base I can look at for your tree viz?
19:39 jimallman did i see a request to “standardize” the TSS syntax? some of it makes me itch...
19:39 daisie ha, yes, please.
19:40 jimallman the work (preliminary so far) is on github:  https://github.com/OpenTreeOfLife/tree-illustrator
19:40 daisie we wrote it at the last hackathon and never cleaned it up or really discussed or tested it further.
19:40 daisie the only implementation is the one I did for Mesquite
19:40 jimallman most good stuff is in the wiki, see esp. the Home page and Design Notes: https://github.com/OpenTreeOfLife/tree-illustrator/wiki/Design-notes
19:40 daisie it's in the nexml.java github project
19:41 jimallman i found it earlier… let’s see… http://www.evoio.org/wiki/.TSS_and_extended_NeXML
19:41 jimallman and https://github.com/daisieh/nexml.java
19:41 jimallman (neat stuff!)
19:41 daisie yep, thanks :)
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19:42 daisie I will take the IRC with me to that board so that you can contribute
19:43 jimallman daisie: i can hear you, too (just FYI)
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19:44 ahdebevec People in the Remote session are asking about how we will be able to participate in this process, or if it was better for us to try to join a group post-formation.
19:44 daisie we're working it out
19:45 ahdebevec thank you daisie!
19:45 arlin_stoltzfus sorry thus is the worst part for remotes.   we'll try to get someone on chat for each pitch
19:46 jimallman fyi - the Tree Illustrator (initial proof-of-concept, at least) is based on d3 + Vega, so it’s declarative like TSS, but using JSON. this makes it easy to edit (and bind to browser UI using KnockoutJS)
19:47 daisie is there a case to be made for the style standard to be in something else besides CSS?
19:48 daisie like perhaps XSL?
19:48 daisie XPath?
19:48 jimallman to me, just the tractibility of JSON. but i totally get why CSS makes sense too.
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19:48 kcranstn_ anyone interested in the branch length subgroup?
19:49 jimallman i’m frustrated by TSS (on reading it) because it come *so close* to normal CSS (applying to style to elements, based on class attributes, etc) but it’s more indirect…
19:49 daisie any specific case?
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19:50 jimallman def a fan of XPath, but in either case, expressing the *real* relationships of metadata to the styled *ML element seems like it would be really verbose..
19:50 jimallman but i’m nit-picking, it’s conceptually pretty clean as-is
19:50 otobserver remote participants, your chats are now being sent to the presentation screen
19:51 daisie jim do you know if css handles conditional values?
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19:51 jimallman hm, conditional as in “IF it has a class? or attribute value?
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19:51 jimallman i want to say yes, as in numerous examples of @media selectors…
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19:52 jimallman @media (min-width: 768px) and (max-width: 979px) { …
19:52 otobserver2 if you are interested in TREE AND TRAIT INTEGRATION: https://plus.google.com/hangouts/_/gw2yt4agaibn3mjp4xy42cnbxua
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19:53 daisie so is there a more standard way to implement conditionals than "bootstrap[min=0][max=50]
19:53 daisie "
19:53 daisie ?
19:53 jimallman daisie: hm, i see
19:54 jimallman tempting to use conventions as in jQuery:
19:54 jimallman [bootstrap>=0] [bootstramp<=50] ? i’m spitballing here
19:55 mtholder can jeet et al in the library group start a G+ hangout?
19:55 jimallman my bad, jquery uses string matching, so operators are = (matches exactly), ^= (starts with), $= (ends with), *= (anywhere in the string)
19:55 mtholder (or some other channel for me to hear their audio)
19:55 mtholder "their audio" = "them talking"
19:56 jimallman daisie: mtholder has a good idea. would it be too chaotic if we start a hangout?
19:56 daisie let me try to do it
19:56 jimallman too slow
19:56 jimallman :)
19:57 jimallman already trying to call daisie
19:57 jimallman (ok, that didn’t work. i’m waiting on G+)
19:57 mtholder some one kick jeet for me, please.
19:58 mtholder thanks
19:58 thackerBob @karen, yes I am interested in branch lengths
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20:20 ShanKothari Everyone alright>
20:20 ShanKothari *?
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21:13 thackerBob @Luke: Bob and Curt have been working on branch lengths in the past hour or so
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21:16 otobserver2 @bob and curt, we also have a group who have been talking about branch lengths. y'all should talk
21:17 thackerBob good idea!
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21:35 arlins katie asks what bob & kurt have to say
21:37 thackerBob Did Katie show a slide that can be put onto WebEx?
21:38 jonxhill No, Karen put a pic on twitter
21:38 jonxhill http://t.co/vG2DYzun17
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21:41 thackerBob thanks for the twitter link
21:41 jonxhill np
21:41 jonxhill Taxonomic downsampling: http://t.co/sc5eQ2gjuU
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