Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2015-07-17

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All times shown according to UTC.

Time Nick Message
01:01 jar286 joined #opentreeoflife
01:08 jar286 jimallman, hi
01:26 jar286 joined #opentreeoflife
01:40 jar286 got it
01:48 ilbot3 joined #opentreeoflife
01:48 Topic for #opentreeoflife is now Open Tree Of Life | opentreeoflife.org | github.com/opentreeoflife | http://irclog.perlgeek.de/opentreeoflife/today
05:29 ilbot3 joined #opentreeoflife
05:29 Topic for #opentreeoflife is now Open Tree Of Life | opentreeoflife.org | github.com/opentreeoflife | http://irclog.perlgeek.de/opentreeoflife/today
11:24 jar286 joined #opentreeoflife
13:24 kcranstn joined #opentreeoflife
13:49 kcranstn joined #opentreeoflife
13:51 kcranstn getting a maintenance notice for editing studies on devtree. That expected?
14:28 kcranstn joined #opentreeoflife
14:37 kcranstn joined #opentreeoflife
14:56 jimallman hi kcranston, i just noticed your msg. sounds like a quick test made during yesterday’s deployment.
14:59 jimallman i’ve removed the curation blocker on devtree.
14:59 kcranstn joined #opentreeoflife
15:00 jimallman hi kcranston, i just noticed your msg above about blocked curation. it was a quick test made during yesterday’s deployment.
15:00 jimallman i’ve removed the curation blocker on devtree.
15:21 kcranstn cool, thanks
15:21 kcranstn changes to licensing look good
15:22 kcranstn I have a question about the Feedback form (the localcomments plugin that shows up in various places throughout the site)
15:41 kcranstn joined #opentreeoflife
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18:21 jar286 joined #opentreeoflife
18:36 jimallman joined #opentreeoflife
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19:47 kcranstn jimallman?
20:10 jar286 kcranstn?
20:10 kcranstn hey there
20:10 kcranstn I had a question abotu the feedback form
20:10 jar286 hi , I had a thought about the site
20:10 jar286 feedback 1st then
20:10 jar286 ?
20:10 kcranstn oops, you are jar286, not jimallman
20:11 kcranstn what’s up?
20:11 jar286 I am jar286, yes
20:11 jar286 I think it’s hard for someone arriving at the tree browser to know what the site is about
20:11 kcranstn agreed
20:11 jar286 they will click on about, I think
20:12 kcranstn maybe
20:12 jar286 well… assume they do
20:12 kcranstn assumed
20:12 jar286 that could have 1-2 paras talking about the purpose of the tree and the relationship between browser & curator
20:12 jar286 that would be enough
20:12 jar286 the rules of the game
20:12 kcranstn good idea
20:13 kcranstn I can add that to my recent PR
20:13 jar286 did you deploy on dev? I don’t see it
20:13 jar286 I should dig up the workflow description I wrote up earlier and put it on the opentree wiki
20:14 jar286 so you can know what to do if you don’t remember
20:17 jar286 email “suggested workflow for new 'development' branch in opentree repo” 1/8
20:23 kcranstn I need to remind myself how to deploy on dev
20:23 kcranstn it’s been a while
20:26 kcranstn have we been doing this?
20:26 jar286 https://github.com/OpenTreeOfLife/opentree/wiki/Suggested-workflow-using-%27development%27-branch-in-opentree-repo
20:27 jar286 yes, we have
20:27 kcranstn oops
20:27 kcranstn and by “we” you mostly mean “jimallman"
20:28 jar286 at least jim has.  for now it’s the opentree repo only
20:28 jar286 yes
20:28 kcranstn where are the docs for deploying to dev?
20:28 kcranstn ah, I see 2.vi.2
20:30 jar286 copied from google doc to wiki
20:30 kcranstn path is no longer opentree/deploy
20:30 jar286 isn’t it?  haven’t changed that yet
20:31 kcranstn assuming that work being in done in opentree repo, then path is simply deploy
20:31 jar286 I’ll tweak it
20:31 kcranstn (confusing because there is opentree/deploy and opentree/opentree in the repo)
20:32 jar286 oh I see
20:32 jar286 should be better now
20:32 kcranstn yes
20:33 jar286 expanded ‘this’ just following
20:35 jar286 the rules-of-game should set expectations around delays between tree submission and appearance in browser
20:35 jar286 i.e. somewhere between ‘never’ and ‘daily’
20:41 * jimallman just got back to the office, catching up now...
20:42 kcranstn hey jimallman!
20:42 jimallman howdy!
20:43 kcranstn I am re-learning the push-to-development workflow
20:44 jimallman cool. sorry about the opentree/opentree path, it’s quite annoying (esp. since we alias as ‘webapp’ in web2py/applications)
20:44 jimallman regrets, i’ve had a few
20:44 kcranstn np
20:45 jimallman regarding the “pulse” of the project (submissions leading maybe/eventually to impact on synth-tree), i’m hoping the progress page will illustrate this rhythm too.
20:45 kcranstn zsh: no such file or directory: ./deploy.sh
20:46 jar286 yes, but I think it needs to be mentioned up front, even if it’s just ‘see the progress page’ … not sure that will quite do right now
20:46 kcranstn push.sh?
20:46 jimallman jar286: agreed..
20:46 jimallman kcranstn: yes, you should have deploy/push.sh
20:46 jar286 I think current directory has to be deploy/
20:47 kcranstn I do, but that doesn’t match the documentation at https://github.com/OpenTreeOfLife/opentree/wiki/Suggested-workflow-using-%27development%27-branch-in-opentree-repo
20:47 jimallman typically we run the push.sh command from deploy/, yes.
20:47 jimallman also assumes that deployed-systems (repo) is cloned alongside opentree repo
20:47 kcranstn the docs refer to deploy.sh, not push.sh
20:47 jimallman wow
20:47 jar286 ergo, ./push.sh -c ../../etc
20:47 jar286 that’s a bug
20:47 jar286 will fix now
20:47 jimallman indeed, i’ll change this now (unless someone’s already editing here)
20:48 kcranstn ok, deploying to devtree
20:48 kcranstn (not editing)
20:48 jar286 fixed
20:48 * jimallman nods
20:50 kcranstn https://devtree.opentreeoflife.org/about/open-tree-of-life
20:51 kcranstn I would love to put those headers (Postdocs, Developers, etc) above the lists, rather than beside,but not sure how
20:51 jimallman it’s a little dry, but i like it!
20:51 jimallman ah, i’ll take a look
20:51 kcranstn thanks
20:52 jar286 that looks pretty good
20:52 jar286 do we still say 11 PIs even though the original grant period is over?
20:54 jimallman the ‘dl-horizontal’ class is the culprit. remove this, then adjust the margins/padding to taste.
20:54 jimallman glad to do this. which branch are you working on?
20:58 kcranstn about_menu
20:58 kcranstn yes, let’s leave that part about the 11 PIs
20:58 kcranstn I don’t want to get into details about supplement
20:58 kcranstn and the work you see is from the main grant (at least at this point)
20:59 jar286 ok.
21:04 jar286 kcranstn, I wrote down some thoughts re reconciling the 2 views on the project, and advice to curators, and put them in the all-hands agenda doc
21:05 kcranstn i think that the “closer to the truth” part will be contentious
21:05 kcranstn is this on the agenda for discussion next week?
21:06 jar286 it’s science.  wanting the truth is inherent
21:06 jar286 there is a truth, after all.  we just don’t know it.
21:06 kcranstn I just think that first statement might lead us down a rabbit hole of “is there really a tree” rather than to the discussion that (I think) you want to have
21:06 jar286 there really is a tree, except for LGT
21:07 jimallman see revised About layout: https://devtree.opentreeoflife.org/about/open-tree-of-life
21:07 kcranstn much better, thanks
21:08 jar286 first statement is important (IMO) to frame the whole discussion.
21:09 kcranstn just saying that it is going to lead to a wordsmithing discussion
21:09 jar286 we’re trying to find out the truth, what happened historically.
21:09 jar286 this is not for public , sorry if I implied that
21:09 kcranstn that is not the important discussion to have
21:09 jar286 this is for discussion between us
21:10 kcranstn us = ??
21:10 kcranstn everyone on the wednesday hangout?
21:10 jar286 yes
21:11 kcranstn I suspect that #1 will lead to much discussion that might distract from the real purpose of putting that on the agenda
21:11 kcranstn at least worded in that way
21:11 kcranstn (look, it is already happening with just two of us)
21:11 jar286 how can one disagree that there is a matter of fact to what happened?
21:12 jar286 it’s just very hard to reconstruct.  that’s what science is about
21:12 kcranstn endless debates in phylogenetics about whether there is a tree at all + discussion about never being able to know the truth about the tree
21:12 jar286 I didn’t say there was a tree.
21:12 jar286 and I didn’t say truth was knowable.
21:12 kcranstn oh, just “truth” in general? about everything? ;)
21:13 jar286 about evolution.  I can put that in if it helps
21:13 jimallman things will look very different once synthesis is easy+accessible. many trees can be put forward for comparison and discussion, no (less) implied “blessing” on our published draft tree.
21:22 jar286 whenever I write something like this I usually write a paragraph or two to get myself thinking in the right frame of mind, like a runway.  I usually delete them later
21:23 jar286 s/whenever/when/
22:05 jar286 joined #opentreeoflife
22:29 jimallman hi jar286 . i’ve lost track of the information about the August meeting in Kansas. do you have a link?
22:39 jar286 hang on
22:40 jar286 no link.   aug 25-27
22:40 jar286 did you talk to karen about it?
22:41 jar286 lawrence ks.  fly to MCI

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