Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2015-01-08

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All times shown according to UTC.

Time Nick Message
00:16 kcranstn joined #opentreeoflife
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18:07 towodo kcranstn, jim & I are in hangout (via calendar)
18:10 jimallman joined #opentreeoflife
18:11 jimallman kcranstn, towodo: i’m here now, waiting for browser
19:01 kcranstn PR review!
19:03 towodo https://github.com/OpenTreeOfLife/opentree/pulls
19:03 * jimallman is grabbing some coffee, back in a minute!
19:03 towodo in 2000 I was peripherally involved in a ‘cobrowsing’ application in which your browser would be slaved to someone else’s
19:04 towodo that was back when IE had about 95% market penetration
19:04 kcranstn scary times
19:05 towodo these days you could probably implement it in javascript
19:05 jimallman yes, i remember Hipbone (great name) for co-browsing
19:05 pmidford2 Just checking in for the PR review
19:05 jimallman hi pmidford2 !
19:05 towodo hi
19:05 towodo ok, reverse chronological order
19:05 towodo https://github.com/OpenTreeOfLife/opentree/pull/495
19:06 jimallman i’m afraid this is still not ready for prime time.
19:06 towodo we should have an open issue list, or other kind of action item
19:06 towodo who does the next step?
19:06 towodo (takes)
19:06 towodo and what is it?
19:06 pmidford2 Is this being held up for stats from the other server?
19:07 jimallman i guess it’s on me (and possibly peter). lots of bogus data, the viz is still going through changes, and where this appears is up for discussion.
19:07 towodo ‘Sorry, we couldn't find this page.’
19:07 kcranstn I also get a 404
19:07 jimallman right, it’s on a branch
19:07 towodo if it were in production system, we’d be able to review it more reliably.  or I guess we could put it in the asterales system?
19:07 kcranstn can we get it up on dev?
19:08 towodo I think I’m voting for production, without tying it into the main application
19:08 jimallman so missing from the nav.. yes, i can work on this for next time.
19:08 towodo if it’s in dev it will just get overwritten next time jim deploys a different branch
19:08 towodo brb 1 minute. you two decide
19:09 kcranstn I like towodo ’s idea
19:09 jimallman ok, will do. (meanwhile, checking the possible branches for a momentary push to dev…_
19:10 towodo back
19:10 jimallman to my mind, this (stats page) is tangled up in the notion of release pages
19:10 kcranstn yes
19:10 towodo back
19:10 jimallman i feel like they could easily merge together, or either one could launch the other
19:10 pmidford2 I will put getting the data from the other server back on my current list
19:11 jimallman thanks peter! we’ll see some of the issues in the next PR
19:11 towodo so, jim to deploy on prod in current form, then KC to review - yes?
19:11 kcranstn yes
19:11 towodo ok, so I will merge it then
19:11 jimallman yes, but i might need to remove some nav/links first
19:12 jimallman easy fix, but it need to be done, else we’ll see About > Statistics in the main menu
19:12 kcranstn yes, please do make that change
19:12 towodo oh… so I should wait for that
19:12 jimallman https://github.com/OpenTreeOfLife/opentree/pull/495/files#r22673568
19:13 jimallman towodo: yes, please hold on (i’ll notify you when it’s done)
19:13 towodo ok. I will comment and then assign it to me (and reassign after)
19:13 jimallman this should not affect the order of merging later PRs
19:14 towodo right. moving on...
19:14 towodo https://github.com/OpenTreeOfLife/opentree/pull/498
19:14 jimallman since our last discussion, more recent work starts here: https://github.com/OpenTreeOfLife/opentree/pull/498#issuecomment-68031851
19:15 jimallman i took this through a few iterations over the holidays, scroll down for screenshots and discussion
19:15 kcranstn I like the area chart
19:16 towodo fine
19:16 jimallman yes, i thought that would be the most “natural” way to show progression
19:16 towodo this should help pmidford2
19:16 kcranstn yay! consensus!
19:16 jimallman hm, not sure what happens if we merge this PR (spans two branches??)
19:17 jimallman oh yeah, the area chart is a separate branch, so needs a separate PR
19:17 jimallman it’s based on this branch, so no work is lost
19:17 jimallman but i’ll need to spin up a new PR for it.
19:17 towodo right
19:18 towodo so, merge to master, or keep on dev?  — hey, this problem is exactly what dev branches are for!  maybe we should have one.
19:18 towodo (re previous quandary)
19:18 jimallman keep this un-merged, and use this one instad: https://github.com/OpenTreeOfLife/opentree/pull/536
19:18 towodo please add comment in other PR
19:18 jimallman (and again, there’s probably a nav link or two that needs to be purged here...)
19:19 towodo so, we keep the dev machine current with the dev branch, merge manually to dev branch, and merge PRs to production branch in github UI
19:19 jimallman OK, closed (unmerged) and comment added that points to the new PR
19:20 towodo jimallman, could you live with that workflow? we had talked about a dev branch before and said we’d do it when we needed it. now we need it.
19:20 jimallman yes, i can work with that.
19:21 towodo so we could keep commits for review on dev, and not have them be overwritten by new branches
19:21 jimallman i’ve added a note to the new PR that i’ll need to sweep nav links before merging: https://github.com/OpenTreeOfLife/opentree/pull/536#issuecomment-69232931
19:21 jimallman towodo: understood. we have a few balls in the air, and lots to discuss.
19:22 towodo so, kcranst, if we go with that, change of plans, new features will ‘stick’ to the dev branch for review, and not go to prod until ready.
19:22 towodo kcranstn ^
19:22 kcranstn sounds good to me
19:22 towodo ok. I’ll send email to software group (opentree repo only for now) , writing out the workflow
19:22 towodo next…
19:22 towodo https://github.com/OpenTreeOfLife/opentree/pull/519
19:23 jimallman i have one more thought about this area chart… since it shows the complete (or lots of recent) history of the system, i’d like to add markers on the x axis that indicate releases (synthesis or taxonomy). clicking these markers would jump to the release page. so this viz becomes the top-level navigation of history and release info.
19:23 jimallman (sorry for the text bomb)
19:23 towodo want to close 495?
19:23 towodo sounds good
19:25 jimallman re: closing 495… i suppose it’s trumped by the area-chart viz. unless you think we’d want its more expansive “table” layout..?
19:25 kcranstn I think there are stats in the table for 495 that aren’t in the chart
19:25 kcranstn right?
19:25 jimallman true, we pounded on the viz to simplify stats.
19:25 towodo i think i was confused.
19:25 towodo you already closed the bar chart PR ?
19:26 kcranstn I like the viz for overall system-level stats (across taxonomy, phylesystem, synthetic tree)
19:26 jimallman towodo: yes, sorry about that. it seemed clearly trumped by area chart
19:26 jimallman but the discussion (and screenshots) there are useful. i’ll link back to them from the new PR
19:26 towodo ok good.
19:27 jimallman done
19:28 towodo 519…
19:28 jimallman from a suggestion by towodo. pretty easy to implement, and seems reliable in testing.
19:29 pmidford2 looks straightforward
19:29 kcranstn indeed. i am happy
19:29 towodo ok, i will merge
19:29 jimallman sweet!
19:29 towodo I wonder if github is down, or my dns, or something… is anyone else having trouble with github.com?
19:30 jimallman website is responding for me
19:30 towodo ah, just slow.
19:30 towodo https://github.com/OpenTreeOfLife/opentree/pull/528
19:30 towodo this looks great
19:30 kcranstn i like it!
19:31 towodo what makes it pop up?
19:31 jimallman text looks accurate? i’m not thrilled with the “tips”, but it’s really that vague..
19:31 jimallman this is triggered by a “Legend” button next to the argus zoom controls.. same style and color.
19:31 towodo oh, it should also explain the red hover stuff on the left, nobody gets that
19:32 towodo tip is fine I think
19:32 jimallman hm, ok. will add explanations for both node and edge highlights
19:32 kcranstn agreed
19:32 pmidford2 works for me
19:32 jimallman do you think people understand to click on a node to “go there”?
19:33 towodo comment added
19:33 towodo maybe not
19:33 jimallman i suppose it won’t hurt to add that too (show cursor over a node)
19:33 kcranstn i think people get the click nnode
19:34 towodo I’ve shown the UI to a few people and they don’t find it all self-evident… but clicking on a node might be too obvious to say
19:34 towodo not sure
19:34 jimallman easy enough to add it (room permitting)
19:34 towodo what makes this pop up?
19:35 towodo worried about mobile space constraints?
19:35 jimallman this is triggered by a “Legend” button next to the argus zoom controls.. same style and color.
19:35 jimallman yes, i’m trying to keep it narrow-ish for small screens
19:35 towodo good
19:36 jimallman sadly, this will take a little time to groom the graphics, so can’t merge yet
19:36 towodo added link to this IRC log
19:36 towodo i assigned you.  let’s move on
19:37 towodo https://github.com/OpenTreeOfLife/opentree/pull/532
19:37 jimallman these are convenience feature for faster OTU mapping (based on mtholder’s feedback)
19:38 towodo I feel I don’t need to review these
19:38 kcranstn merge
19:38 pmidford2 sure
19:39 jimallman all have been tested on devtree, no problems found so far
19:39 towodo hey, it would be cool if the app would tell you which github branch it was running
19:39 jimallman hm, that would be handy on dev
19:39 towodo merged
19:39 jimallman towodo: i’ll make a TODO for that
19:39 towodo https://github.com/OpenTreeOfLife/opentree/pull/533
19:41 jimallman this one needs discussion… see https://github.com/OpenTreeOfLife/opentree/issues/499 for discussion and screenshots
19:41 towodo yes, I was just looking there. I think the NexSON issue should be a separate PR
19:41 towodo so, leave the issue open, but close the PR
19:42 towodo this looks fabulous by the way
19:42 jimallman great! i like it too.
19:42 kcranstn +1
19:42 towodo ‘we can’t automatically merge’ - Jim can I get you to do this song and dance and merge it?
19:43 jimallman sure, right after we’re done here.
19:43 towodo right.
19:43 towodo assigned to you
19:43 towodo https://github.com/OpenTreeOfLife/opentree/pull/536 … we already talked about this
19:44 kcranstn I still like it
19:44 towodo need to merge to dev branch
19:44 jimallman yep, needs nav links removed.. and i’d like to try adding those markers for synth and taxo releases
19:44 jimallman (or i can keep the nav links, if we’re just taking this to dev)
19:44 towodo I will add comment to ask JA to merge to dev branch? or should I do it?
19:45 towodo maybe I should set up dev branch as it involves the deployment system
19:45 towodo so what don’t I take that on.  but leave the PR open for discussion.  OK?
19:45 jimallman sounds good. i’ll merge to dev once it’s ready, complete with nav links for now
19:46 towodo ok, then we can look at the PR again next week
19:47 towodo ok, I think that’s everything.  thanks
19:48 jimallman should we have a separate huddle on new or modified stats?
19:48 jimallman i’ll review the area-chart branch (most recent work) and see if things are truly missing, or just misnamed, etc.
19:49 jimallman or maybe i should wait for pmidford’s stats “from the other server” and see what’s there.
19:49 jimallman pmidford2: ^ (misspelled your nick)
19:50 pmidford2 It's going to look the same as the existing stats - there will be separate files.  I hadn't planned on merging them
19:50 pmidford2 Or, is there something I should be changing/adding?
19:54 towodo I still need to set up that ssh stuff… foo…
19:56 jimallman pmidford2: sorry, i’m hazy on this. i just know there’s a lot of placeholder data in the current pages.
19:57 jimallman i’ll review and see if what we need is there, but misnamed, etc
19:58 pmidford2 The format hasn't changed since mid-November; there should be a large, but boring data set on the dev machine at this point
19:58 jimallman cool :) will check that out
20:19 towodo jimallman, development branch created with a few of your unclosed PRs… going to push to devtree now
20:19 jimallman thanks, i’ll follow up with more later today.
20:21 jimallman can we bump production too? (opentree and phylesystem-api, anyway)
20:22 towodo sure… will get to it…
20:23 towodo ok, development branch deployed to devtree…
20:24 towodo phylesystem-api master deployed to production…
20:24 jimallman sweet, that should fix oti for new studies.
20:25 jimallman we should probably do the complete re-indexing command as well (i can do that if you’re busy)
20:25 pmidford2 towodo - trying to remember exactly what was needed for moving the stats onto production - is something like https://github.com/scponly/scponly/wiki what we're looking for?
20:39 towodo jimallman, https://docs.google.com/document/d/1k1NJhnE4I6Klw7u9RTpbrBgqfhWkvoR8N0fogQ29rEA/edit
20:39 towodo thought you might review first before I send it out to others
20:44 towodo pmidford2, looks like overkill to me
20:44 towodo I’m going to take another look at how rsync does it
20:44 pmidford2 towodo - ok
20:47 towodo pmidford2, I think this: http://www.guyrutenberg.com/2014/01/14/restricting-ssh-access-to-rsync/
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22:09 jimallman towodo: i’ve added some comments to the google doc.. i think some will find this dance confusing, but our only alternative is to liberally bump devtree from branch to branch.
22:09 towodo right.
22:10 towodo I set development to have no upstream branch.
22:10 towodo (agreeing with your comment)
22:14 towodo left out step: push F to github    - fixed
22:36 jimallman towodo: i’ve done the cleanup and merge of https://github.com/OpenTreeOfLife/opentree/pull/533, if you want to take a look.
22:37 jimallman (i can merge + push to devtree if you like)
22:38 towodo let me look a bit later. going to dinner now
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