Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2015-02-19

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Time Nick Message
02:49 ilbot3 joined #opentreeoflife
02:49 Topic for #opentreeoflife is now Open Tree Of Life | opentreeoflife.org | github.com/opentreeoflife | http://irclog.perlgeek.de/opentreeoflife/today
04:30 jimallman joined #opentreeoflife
12:11 kcranstn joined #opentreeoflife
13:42 kcranstn joined #opentreeoflife
14:29 kcranstn joined #opentreeoflife
14:58 kcranstn josephwb - emailing that journal article
15:16 kcranstn joined #opentreeoflife
16:06 jimallman kcranstn: i’ve added issues based on your feedback. thanks!
16:06 kcranstn indeed
16:07 kcranstn emily jane pointed this out: https://devtree.opentreeoflife.org/curator/profile/torvalds
16:14 jimallman one of us! one of us!
16:15 jimallman that’s why I showed jeresig (creator of jQuery)
16:15 kcranstn somehow, that wasn’t as awesome as torvalds
16:17 kcranstn I seem to be providing all sorts of edge cases lately...
16:34 josephwb kcranstn is paup code open source yet?
16:37 kcranstn nope
16:37 kcranstn I harass Dave frequently ;)
16:37 josephwb hehe
16:38 josephwb but it will definitely be available in 2013, right? that is what i heard.
16:38 josephwb [not a typo]
16:38 josephwb [lame joke]
16:38 kcranstn definitely
16:39 josephwb paup is sometimes good for validating new code (i.e. same results)
16:40 josephwb would be nice to look at dave's implementation.
16:40 josephwb probably crazy-efficient
16:40 kcranstn probably
16:40 kcranstn I don’t know what he would say if you asked to see a specific part of the code
16:40 josephwb not that important
16:40 josephwb just curious
18:19 pmidford2 joined #opentreeoflife
19:01 * jimallman is standing by for PR review
19:02 jar286 joined #opentreeoflife
19:02 kcranstn here!
19:02 jar286 here.
19:02 jimallman reminder: https://github.com/pulls?user=OpenTreeOfLife
19:03 pmidford2 here
19:03 jar286 bottom to top
19:03 jar286 skip phylografter
19:03 jar286 kfoney ‘patching’ - file is in wrong format, no response to gentle nags
19:04 jimallman ok to wait on this? or can/should we attempt a fix?
19:04 jar286 I’ve moved a bunch of similar files on master to ‘.hold’ and smasher then ignores them…
19:04 jar286 so the files are there ready to be fixed by not screwing up the build
19:05 jar286 I tried to fix one of the other files and lost patience.  lots of emacs keyboard macros
19:05 kcranstn ack
19:05 jar286 she used spaces instead of tabs.  it’s a terrible UI, too hard for biologists to master
19:06 jar286 I’ll just move the file to .hold and close the issue
19:06 jar286 (later)
19:06 jar286 otu stats still simmering?
19:07 pmidford2 I've made a history file and am in the process of checking it out
19:07 jimallman yes. i’ve pulled the latest from master...
19:07 jar286 ‘needs discussion’ 7 days ago
19:07 jimallman and am buiilding some of the new requrements by hand (JSON history of OT versions by date)
19:07 jimallman miles to go, i’m afraid
19:08 jar286 OTT dates are all in the files/ott index pages
19:08 jimallman OTT versions, that is
19:08 jar286 page
19:08 jimallman yes, got ‘em
19:08 jar286 writing scripts to process OTT files is pretty simple (mostly)
19:08 kcranstn why the miles?
19:08 jimallman i’d like to add a label ‘statistics’ in the issue tracker, just to corral this
19:09 pmidford2 When my phylesystem history file is ready, where should it go?
19:09 jar286 ‘miles’?
19:09 jimallman miles = missing artifacts for synth releases, old history (previous synthesis releases and taxo versions)… a few other TODOs on the release pages on dev
19:10 jimallman pmidford2: “history file” is different from phylesystem.json (existing stats)?
19:10 pmidford2 This is the reconstructed file - I could just append it to the existing file, maybe that's enough
19:11 jar286 pmidford2, doesn’t matter too much where they go, just so they don’t get lost… maybe germinator repo?
19:11 pmidford2 jar286 - ok
19:11 jimallman ah, i see. yes, appending (as if it had been added with the new tools) makes sense to me
19:11 jar286 yes
19:11 pmidford2 ok, will do
19:12 jimallman i believe i have the breadcrumbs i need to tie OT versions to synth releases, so i have work to do
19:12 pmidford2 I'll stash it in germinator as well (along with the tool)
19:12 jar286 no particular comments on 536 from last week
19:13 jar286 the april synth used OTT 2.6
19:13 jar286 the earlier of the two used 2.6, i should say. the later one used 2.8
19:14 * jimallman nods
19:14 jar286 can we move on?
19:15 pmidford2 sure
19:15 jar286 https://github.com/OpenTreeOfLife/opentree/pull/597
19:16 jimallman this is the fix for our mysterious failure on production vs. dev, for cached API calls
19:16 jar286 will add a comment about asterales system
19:16 jimallman also patched an occasionaly error sending POST responses to OPTIONS calls
19:16 jimallman definitely recommend merging this
19:17 jar286 doing so now
19:18 jar286 github changed their site… merging now makes the issue disappear from issue list immediately - no need to refresh the page
19:18 jar286 https://github.com/OpenTreeOfLife/opentree/pull/598
19:19 jimallman this reflects our latest decisions on  tree properties (working on devtree)… maybe not ready for production
19:19 jimallman since it modifies Nexson piecemeal in the curation app.
19:19 jar286 this didn’t get kcranstn’s review
19:19 jimallman might be better to convert all Nexson in the corpus to the new schema?
19:19 kcranstn I dropped the ball here, because I wanted to have some discussion on the MIAPA list before we finalized our decision
19:20 jimallman right, and there are a couple of minor questions about the new fields: https://github.com/OpenTreeOfLife/opentree/issues/552#issuecomment-74100943
19:20 kcranstn I don’t feel like this is the last word on this
19:20 jar286 then we should probably leave it open
19:20 jimallman agreed, and review/modify on dev
19:20 kcranstn yes, please
19:21 jar286 added comment.  moving on
19:21 pmidford2 agree
19:21 jar286 https://github.com/OpenTreeOfLife/reference-taxonomy/pull/126
19:21 josephwb can we hold off on altering nexsons until we get a new synth tree/revisions submitted?
19:21 kcranstn yes
19:22 kcranstn moving onto worms...
19:22 kcranstn is there a summary of how the incorporation of worms affects OTT?
19:22 jar286 no
19:22 kcranstn i.e. how do we decide if we should merge this
19:22 jimallman just curious: why remove the nematode test?
19:23 jar286 I don’t think it worked any more, and it was superseded by the asterales test
19:23 jimallman ah, ok
19:23 jar286 hard to say about QC. we’ve never had a good way to evaluate taxonomy versions
19:23 jar286 my main measure it looking carefully at the deprecated taxa list.
19:24 kcranstn where is that list?
19:24 jar286 it’s in deprecated.tsv (the whole thing) or otu_deprecated.tsv (just the ids that are OTUs in studies)
19:24 jar286 in the dump
19:25 jimallman some of these whitespace changes are weirding me out.. but if python isn’t complaining, it’s OK by me.
19:26 kcranstn should probably send a review notification to the main opentreeoflife list with links to the summary files (new taxa, deprecated taxa, etc)
19:26 jar286 it would be nice if argus worked with taxomachine like it used to
19:26 jar286 then we could set up a server for review
19:27 jimallman i can look into that if you like. i know some of the taxo-code is still in there...
19:27 jimallman (in the argus JavaScript, i mean)
19:27 kcranstn hmmm… not sure that is highest priority
19:27 jar286 I wonder if we should put it off
19:27 jar286 2.9 isn’t needed for submission
19:28 jar286 the reason I did it was for the EOL links
19:28 kcranstn wonder how long it would take to build a simple ncbi-style browse for the taxonomy?
19:28 jar286 the hard part is deciding on a platform
19:28 kcranstn (again, not high priority)
19:28 jar286 I’ve often been tempted to write one
19:28 jimallman jump to small HTML pages per taxon, you mean? might be easier to do a single viz
19:29 jar286 there’s stephen’s thing, maybe that would work
19:29 kcranstn easier to build, or easier for people to use?
19:29 jimallman both, i think
19:29 jimallman but yes, stephen’s d3 viz might be closest
19:30 kcranstn ok, getting sidetracked
19:30 jar286 moving on, leaving this open
19:31 jimallman https://github.com/OpenTreeOfLife/opentree/pull/609
19:31 jimallman this handles the wacky bug that kcranstn was seeing in Chrome in our load testing
19:31 kcranstn are you calling my browser dumb?
19:31 kcranstn ;)
19:31 jimallman let’s say “addled”
19:32 jimallman if cookies+data (and therefore the History API) are disabled, this will Do The Right Thing
19:32 kcranstn yay
19:32 jimallman goes through all the normal steps, but keeps a stale URL in the address bar.
19:32 jar286 merge?
19:32 jimallman if that’s not acceptable, it could instead jump to the new URL
19:32 kcranstn yup
19:32 jar286 done
19:34 jar286 I’m going to close the earlier of the two WoRMS PRs since its two commits are incorporated in the later one
19:34 jimallman hm, looks like i should have made a proper PR in opentree, which also has a branch for ‘comment on delete study’
19:35 jar286 feel free…
19:36 jar286 https://github.com/OpenTreeOfLife/peyotl/pull/116
19:36 kcranstn looks straightforward to me
19:36 jimallman done: https://github.com/OpenTreeOfLife/opentree/pull/613
19:37 jar286 I’m going to assume #116 is well tested. Looks simple enough
19:38 jar286 merging…
19:38 pmidford2 agree
19:39 * jimallman nods
19:39 jar286 https://github.com/OpenTreeOfLife/phylesystem-api/pull/143
19:40 jar286 test is much bigger than change
19:40 jimallman looks tested as well
19:40 jar286 I’ll assume this is fine. test gives confidence
19:40 jar286 merging…
19:40 kcranstn +1
19:40 pmidford2 agree about test
19:40 jar286 https://github.com/OpenTreeOfLife/opentree/pull/613
19:41 jimallman this was previously tested in the client, just gathers and supplies a message on deletion
19:42 jar286 the delete doesn’t happen until after the comment is entered, right? and you can cancel?
19:42 jimallman UI screenshot here: https://github.com/OpenTreeOfLife/opentree/issues/486
19:42 jimallman yes to both
19:42 travis-ci joined #opentreeoflife
19:42 travis-ci OpenTreeOfLife/phylesystem-api#682 (master - b4d5a3f : Jonathan A Rees): The build passed.
19:42 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/2a05b8333ad0...b4d5a3f4d767
19:42 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/51420642
19:42 travis-ci left #opentreeoflife
19:43 jar286 wait… is this live on devtree?
19:43 jimallman travis is like Kramer, sliding in the door….
19:43 jar286 I just deleted a study and it didn’t ask for a comment
19:44 jimallman i believe i held it back, since we didn’t have the backend support for it
19:44 jimallman tested UI in my local
19:44 jimallman i assumed(!) that snacktavish tested the full setup, but maybe not
19:44 jar286 ahh… maybe it shouldn’t be merged until we’ve done a full test
19:45 jimallman ok, pretty sure the changes in peyotl and phylesystem-api will treat the message as optional (and supply a default deletion message)
19:45 jimallman so no harm done in taking it slow
19:45 jar286 yes, i saw that in the sources
19:45 jar286 we can deploy the new peyotl and phylesystem-api to dev, then do the curator test
19:46 * jimallman nods
19:46 jimallman testing (after PR review) should be quick, if you want to consider merging this later today
19:47 jar286 we’re done with reviews for now.  might as well do it right now
19:47 jar286 would you like to do the dev deploy honors?
19:47 jimallman sure
19:50 jimallman merging comment-on-delete-study into development, pushing now…
19:51 jimallman (in devtree, that is… devapi is next)
19:52 jar286 it occurs to me, how will anyone ever see these comments? browsing git history on github?
19:53 jimallman :D  good point. yes, that’s about it!
19:53 jimallman unless we want to leave a visible “ghost”, but even that will be confusing in the case of duplicates
19:54 jimallman testing deletion of a junk study on devtree…
19:56 jimallman “Cancel” button canceled without incident, and Delete seems to have worked (checking on GitHub now…)
19:57 kcranstn joined #opentreeoflife
19:57 jimallman hm, my comments didn’t make it. good call on holding this back
19:57 jimallman https://github.com/OpenTreeOfLife/phylesystem-0/commit/e58fd4354585f49fd9363d000b5c45c7c2273e60
20:00 jimallman the comment in delete request looks ok. i’ll chase this down and report in the issue tracker
20:09 jar286 I create a study and save it, and click on ‘delete’, and nothing happens
20:10 jar286 delete study doesn’t do anything for me now, jimallman
20:10 jimallman very odd. will investigate!
20:11 jar286 in FF
20:11 jimallman thanks.
20:12 jimallman stepping away for coffee, back in a bit…
20:35 jar286 jimallman ?
20:35 jimallman yes
20:36 jar286 I’ll redeploy api (production) now
20:36 jar286 it’s that time
20:37 jimallman ah yes. still chasing weirdness in study deletion on dev…
20:40 jar286 smoke tests pass
20:40 jar286 on to tree.opentreeoflife.org
20:41 jimallman by the way, i can’t reproduce your FF bug (create new study, delete does nothing)… it works for me (albeit without preserving my commit msg)
20:41 jar286 maybe I need to clear cache
20:42 jar286 yes, that was it
20:44 jar286 minor annoyance: once the blue-i appears, there’s no way to make it go away
20:45 jimallman hmm. it should disappear on mouse-out, but sometimes this event is not detected.
21:08 jimallman i’m getting normal behavior (no more surprises) on production in tree view, curation app.
21:09 pmidford2 joined #opentreeoflife
22:04 jimallman jar286: i found and fixed the problem with deleting on devtree:  https://github.com/OpenTreeOfLife/phylesystem-0/commit/672c179fd5516b2acd92b7375bbfd9c523aca1d8
22:05 jimallman it was just a git failure (didn’t pull master branch) due to my manual “hot fix” from last week. this logs a very subtle ‘*** git failure ***’ message that didn’t catch my eye. i think we might need dramatic ASCII art for these. :)
22:06 jar286 whew
23:25 kcranstn joined #opentreeoflife

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