Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-10-02

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Time Nick Message
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16:49 towodo reminder, PR review at 2:00
16:49 kcranstn_ ok. I will only have an hour
16:50 towodo there aren’t many, the queue was clear on Sunday
17:02 jimallman ah, i didn’t realize this was a standing weekly thing. neat!
17:59 kcranstn_ ok, where are we starting?
18:00 towodo ‘open all in tabs’  -> 9 tabs of PRs
18:00 towodo https://github.com/OpenTreeOfLife/opentree/pull/461
18:01 kcranstn_ I do not want that many tabs
18:01 towodo I’ll close the ones that have no PRs
18:02 towodo now only 5
18:02 kcranstn_ 461 looks harmless
18:02 towodo #461 depends on https://github.com/OpenTreeOfLife/phylesystem-api/pull/123 , let’s do that first
18:03 kcranstn_ ok
18:03 towodo looks good to me.
18:03 towodo #461 again
18:03 kcranstn_ it still looks harmless
18:04 kcranstn_ good?
18:04 travis-ci joined #opentreeoflife
18:04 travis-ci [travis-ci] OpenTreeOfLife/phylesystem-api#638 (master - 72779e6 : Karen Cranston): The build passed.
18:04 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/b1f23fb85243...72779e623040
18:04 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/36895665
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18:04 towodo I would like to deploy to ot17 & test but that would take about 3-4 minutes… I guess I can skip that
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18:05 towodo keeping a list of things to try out on ot17 before pushing to production
18:05 kcranstn_ ok
18:05 towodo https://github.com/OpenTreeOfLife/opentree/pull/462
18:06 towodo I did that one, so that when Mark started backups he’d get the scratch dirs
18:06 towodo mtholder, did you try the mirroring script?
18:06 towodo did I send you email about it even?
18:07 towodo well, this can’t break the production system, so I say merge
18:07 mtholder not yet. will do soon.
18:08 towodo kc, you’ve been doing the merges, I’ll get the next PR
18:08 towodo https://github.com/OpenTreeOfLife/opentree/pull/463
18:08 kcranstn_ it’s a hard job, pushing that merge button
18:08 towodo I haven’t had a chance to look at this.
18:09 kcranstn_ me neither
18:09 towodo give me a couple of minutes and I’ll put it on ot17
18:11 towodo pushed api, now pushing opentree…
18:12 towodo hmm… I don’t see checkboxes http://ot17.opentreeoflife.org/curator/study/view/pg_932/?tab=otu-mapping  maybe I screwed up deployment?…
18:13 kcranstn_ nope. I don’t see checkboxes
18:13 kcranstn_ did you deploy hte feature branch?
18:13 towodo I thought so
18:16 kcranstn_ testing on dev now, and finding some issues
18:16 jimallman branch designation should look like this:
18:16 jimallman opentree_branch opentree otu-mapping-simple-and-hungry
18:16 jimallman (in server-config file)
18:16 towodo yes, that’s what it says.
18:17 towodo Using branch otu-mapping-simple-and-hungry of repo opentree
18:17 towodo From https://github.com/OpenTreeOfLife/opentree
18:17 kcranstn_ select all -> map selected -> select none -> select one taxon -> map selected = nothing happens for the one taxon
18:17 towodo * [new branch]      also-mirror-scratch -> origin/also-mirror-scratch
18:17 towodo 196cf22..3846e72  master     -> origin/master
18:17 towodo * [new branch]      otu-mapping-simple-and-hungry -> origin/otu-mapping-simple-and-hungry
18:17 towodo * [new branch]      return-new-history-on-save -> origin/return-new-history-on-save
18:17 towodo Switched to a new branch 'otu-mapping-simple-and-hungry'
18:18 towodo oh well, will deal with it later, on my own time
18:19 towodo oh, i wasn’t logged in. duh
18:19 kcranstn_ ha
18:19 jimallman thank you! i just did the same on devtree...
18:19 jimallman we is expert users
18:19 kcranstn_ I got a 404 when I tried to log in
18:19 towodo click on ‘login’ at http://ot17.opentreeoflife.org/curator ==> 404
18:20 towodo click on ‘login’ from study => 404
18:20 towodo hmm...
18:20 jimallman we’ll need to register this as a new app on GitHub to log in (if it’s not already)
18:20 jimallman because its login URL is domain-specific
18:20 towodo but that’s ot17, it doesn’t have credentials.
18:20 kcranstn_ can we discuss the changes on dev for now?
18:21 kcranstn_ rather than debug deployment?
18:21 towodo yes.  i see the checkboxes
18:21 kcranstn_ I understand now why my previous attempt failed
18:21 * jimallman is retracing kcranstn’s steps above
18:21 kcranstn_ select all -> map selected -> select none -> select one taxon -> map selected = nothing happens for the one taxon
18:21 kcranstn_ if the taxon is “failed mapping” then nothing happens
18:22 kcranstn_ Q: about “approve and continue”
18:22 kcranstn_ “continue” = ??
18:23 kcranstn_ is it approve all or approve selected
18:23 kcranstn_ and does continue go to the next page?
18:23 jimallman current behavior is approve all proposed (single-option) mappings, which updates the list.
18:24 jimallman in the default filter “Unmapped OTUs first”, this brings a fresh set of unmapped OTUs into view.
18:24 kcranstn_ I think we should reserve “all” when we really mean “all
18:25 jimallman makes sense, “all” vs. “visible” vs. “selected”
18:26 kcranstn_ can we move all of the action buttons together (Map, Approve, Reject, Clear, Clear all)
18:26 kcranstn_ it is confusing that they are in three places
18:27 jimallman I can do that, but I’m trying to distinguish between actions that will move routine mapping forward, versus occasional + drastic actions like Clear *
18:27 jimallman i’ll take another swing at this
18:27 towodo yes, and they’re far down the window, so you have to slide the window to get to all the controls
18:27 kcranstn_ happy to talk through this over G+ if it helps
18:27 towodo looks like it’s going in the right direction
18:27 jimallman sure. after PR review?
18:29 towodo I think kc said she was busy at 3
18:29 kcranstn_ I have a meeting at 3, but it should be short
18:29 towodo ok, moving on
18:29 jimallman ok, i can meet at your convenience (just let me know when that mtg is over)
18:29 towodo https://github.com/OpenTreeOfLife/phylesystem-api/pull/124
18:30 kcranstn_ are we not merging 463?
18:30 kcranstn_ i.e. are there good things there that we should accept
18:30 towodo oh.  I don’t know, I guess it’s ok, and doesn’t seem to make anything worse, which is the criterion
18:30 towodo so merge it if you like
18:31 kcranstn_ ok. Then we can move forward without piling on and making that a huge PR
18:31 jimallman fwiw, the problem areas we discussed won’t require major surgery to change
18:32 towodo looking at #124 code
18:32 towodo long lines…
18:33 towodo it is possible in the github ui to scroll to the right, but it’s annoying
18:33 kcranstn_ your code has long lines
18:33 towodo mine? probably so, tell me and I’ll fix them
18:33 kcranstn_ whoops. no that wasn’t yours
18:33 jimallman i can wrap these if you like...
18:34 kcranstn_ sorry, towodo
18:34 jimallman them’s fightin words
18:34 towodo no need now, but in general keeping to github’s width would be helpful in PR reviews
18:34 jimallman noted
18:35 towodo (Hilmar made a big stink about this for one of the nescent informatics repos, so I’m not alone)
18:35 towodo this one looks fine to me
18:35 kcranstn_ actually, I think it was Todd communicated by Hilmar
18:35 kcranstn_ but, moving on...
18:35 towodo I’ll put this on my to-test list
18:36 towodo waiting for merge, or shall i do it?
18:36 kcranstn_ go ahead
18:36 jimallman i’ve tested this on dev, with a variety of URLs and good/bad DOIs
18:37 towodo great
18:37 jimallman so it should do no harm at least
18:37 towodo https://github.com/OpenTreeOfLife/taxomachine/pull/78
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18:38 travis-ci [travis-ci] OpenTreeOfLife/phylesystem-api#639 (master - 622eb67 : Jonathan A Rees): The build passed.
18:38 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/72779e623040...622eb674dc61
18:38 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/36898232
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18:38 towodo innocuous, merge it, but I ought to test the case of zero trees (which is the one that confused me)
18:38 kcranstn_ ah, it’s travis. Happily building away
18:38 towodo umm.. in fact, let’s delay this one, I’ll add the request now
18:39 towodo ok, leaving taxo $78 open
18:39 towodo #78
18:39 towodo https://github.com/OpenTreeOfLife/treemachine/pull/145
18:40 towodo hmm… I believe this one, will add it to to-test list
18:40 kcranstn_ ok
18:40 towodo merging
18:41 towodo https://github.com/OpenTreeOfLife/reference-taxonomy/pulls
18:41 towodo not part of production system, we probably don’t need to look at it.
18:42 towodo unless someone wants to.
18:42 kcranstn_ nah
18:43 towodo ok, then we’re done
18:43 kcranstn_ w00t!
18:43 kcranstn_ this is definitely better than letting them pile up
18:45 jimallman regarding milestones, i’m still chugging through the stuff marked ‘columbus day’.. am i correct that these are the most pressing?
18:45 jimallman https://github.com/OpenTreeOfLife/opentree/issues?q=is%3Aopen+is%3Aissue+milestone%3A%22Columbus+Day%22
18:45 * jimallman is current working on #376
18:46 kcranstn_ yes!
18:46 jimallman re: # 44 (Visually distinguish phylogeny edges from taxonomy edges)… Cody had requested that the argus tree view use standard colors (black on white).. i’m inclined to do this while i’m in the argus code… Thoughts?
18:47 kcranstn_ yes, I think that’s a good idea
18:47 jimallman (my original rationale for shades of brown was to distinguish the tree view from all the other visual “boxes” in view, but that’s moot now that argus basically fills the window)
18:48 jimallman cool. shouldn’t take long at all.
18:48 kcranstn_ what’s your plan for the lines?
18:49 kcranstn_ I just gave a demo today for a class I was teaching, and people had that “I’ll believe you when you say there are different kinds of lines, but I just don’t see them” look
18:49 jimallman i was going to try color change first, to see if solid vs. dotted is more prominent. we could also change thickness (nice), or double the lines (i think), or add an accent color for phylo-edges, if that seems appropriate.
18:50 jimallman agreed that the distinction is way too subtle now
18:50 kcranstn_ I don’t like the colour-only idea
18:50 kcranstn_ unless we are sure that it will be visible to the colourblind
18:50 kcranstn_ colour + thickness or colour + style
18:51 jimallman agreed. a medium-value color would read as gray at least, but would have the opposite “emphasis” from what we intent (muted phylo-edges).
18:51 kcranstn_ we want the phylo edges to stand out, for sure
18:51 kcranstn_ feel free to send some screencaps while you experiment
18:52 jimallman agreed. i’ll start with color+style, then color+thickness if that doesn’t pop
18:52 jimallman ah, will do (screencaps)!
18:52 jimallman will also need to “play with the zoom” and see what holds up.
18:52 jimallman at different zoom levels, i mean
18:54 jimallman hm, Cody raises an interesting point in this issue: https://github.com/OpenTreeOfLife/opentree/issues/44#issuecomment-29080423
18:54 jimallman tl;dr, he wants to distinguish phylo-only, taxo-only, phylo+taxo
18:55 jimallman edges
18:55 kcranstn_ I saw that
18:55 jimallman three kinds of edges. i’ll see if can “double” edges to accomplish this
18:56 kcranstn_ I suspect this might be hard
18:57 jimallman i think the supporting data is handy, but yes, the drawing operations might be tricky. but i’ll know quickly and can bail if it’s not coming easily.
18:59 towodo commented on #376
19:05 jimallman yes, i’m working on a design that makes this distinction clear (should have this up for review shortly)
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