Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2015-07-23

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All times shown according to UTC.

Time Nick Message
12:47 kcranstn joined #opentreeoflife
16:05 kcranstn joined #opentreeoflife
16:19 kcranstn joined #opentreeoflife
16:50 kcranstn joined #opentreeoflife
17:21 pmidford2 joined #opentreeoflife
18:02 jimallman ready for PR review: https://github.com/pulls?user=OpenTreeOfLife
18:03 jar286 joined #opentreeoflife
18:03 jar286 ji
18:03 jar286 hi
18:04 kcranstn here
18:05 kcranstn v
18:05 kcranstn https://github.com/pulls?user=OpenTreeOfLife
18:05 jar286 https://github.com/OpenTreeOfLife/germinator/pull/20
18:05 jar286 damn, i’m trying to remember what i was thinking…
18:05 kcranstn still needs cleanup, can’t be merged
18:06 jar286 I have work in progress here.  Been changing those files.  Table until next time
18:06 jar286 added lots of tests
18:07 kcranstn ok
18:07 jar286 it’s at the top of my to-do list (well, under nagios)
18:08 jar286 https://github.com/OpenTreeOfLife/opentree/pull/679
18:09 jimallman “merged” about page is live on devtree: https://devtree.opentreeoflife.org/about/open-tree-of-life
18:09 jimallman (looks good to me)
18:09 kcranstn me too, but I am biased
18:10 jimallman hm, not sure the source code and visible tree agree
18:10 jar286 so we folded the curators category into the other groups?
18:10 kcranstn the curator list was manually generated and incomplete
18:10 * jimallman is looking for “Browse the tree and leave feedback” in the source.. not found
18:10 kcranstn and grad students and postdocs who were not curators got no mention
18:10 jimallman perhaps this edit was made directly in the ‘development’ branch?
18:11 jar286
18:11 jar286 kcranston wants to merge 2 commits into master from about_menu “
18:12 kcranstn yeah, I might have messed that up. was before jar286 pointed out developemnt branch instructions
18:12 jimallman this appears to be the misplaced commit: https://github.com/OpenTreeOfLife/opentree/commit/fa95a084cba26c31398a0557374a328061c4dd97
18:12 jimallman i only thought to check because i’ve made that mistake as well :)
18:13 jar286 that unquoted & really makes me squirm, but apparently it’s valid html5
18:13 kcranstn what unquoted?
18:13 jar286 <dt style="margin-left: 10px;">Postdocs & students </dt>
18:14 jar286 unescaped is what I meant
18:14 kcranstn should I change this to merge into development isntead?
18:14 jar286 no
18:14 jimallman we probably want to cherry-pick any misplaced commits back into your feature branch
18:15 jar286 development is just for testing.  one manually merges to it
18:15 jar286 where did you find fa95?
18:16 jimallman https://github.com/OpenTreeOfLife/opentree/commits/development
18:16 jimallman looking for kcranston’s recent commits that are not obviously merges
18:16 jar286 ah, i see in the development branch
18:16 jar286 yes, merge to feature branch (which the PR tracks)
18:17 kcranstn just a second
18:17 jar286 cherry pick is what I meant, I think
18:17 kcranstn *goes off to read cherry pick documentation"
18:19 jimallman when in doubt, check to see if a commit is already in your branch: https://github.com/OpenTreeOfLife/opentree/pull/679/commits
18:19 jimallman (it
18:20 jimallman (it’s not obvious, because simple commits from the feature branch will show up in ‘development’ after a merge)
18:21 kcranstn crap, I think I just globbered the style changes you made
18:22 kcranstn nope
18:23 kcranstn ok, that text is now in about_menu
18:23 kcranstn from commit fa
18:24 kcranstn 95
18:24 jimallman woot!
18:25 kcranstn ok, are we merging this to master or should I merge to development?
18:25 jimallman two more to check, please:
18:25 jimallman https://github.com/OpenTreeOfLife/opentree/commit/a4ad646203b05ec0178d041d0a5059163c9bacff
18:25 jimallman https://github.com/OpenTreeOfLife/opentree/commit/63f2b191114f9312c51adeb04f1de3eda7af4dfd
18:26 kcranstn both on about_menu
18:27 jar286 (we should be resetting development to master from time to time… not too important, but there’s a small risk of significant divergence)
18:27 jimallman agreed
18:27 kcranstn yup
18:27 jimallman kcranstn: i don’t see those commits here:  https://github.com/OpenTreeOfLife/opentree/pull/679/commits
18:28 jimallman (were they introduced prior to this branch’s creation? happy to be wrong here)
18:29 kcranstn https://github.com/OpenTreeOfLife/opentree/blob/about_menu/webapp/views/layout.html
18:29 kcranstn changes reflected in file
18:29 kcranstn confused
18:29 jimallman checking the blame here: https://github.com/OpenTreeOfLife/opentree/blame/about_menu/webapp/views/layout.html#L161
18:30 jimallman ah, it came from this prior PR (already merged): https://github.com/OpenTreeOfLife/opentree/pull/677
18:30 kcranstn whew
18:31 jimallman false alarm!  :D
18:31 kcranstn ok, so what are we doing with https://github.com/OpenTreeOfLife/opentree/pull/679
18:31 jar286 ha.  ok, someone merge it
18:31 jimallman on that note, i say we should merge this guy
18:31 jar286 jim?
18:32 * jimallman nods
18:32 jimallman done!
18:33 jimallman #680 (search by study ID) is available for review on devtree
18:34 jar286 ‘our desire to hide "internal" identifiers’   - what ‘we’, white man
18:35 jimallman ? i thought you were among the “we”…
18:35 jimallman we’ve had this conversation about node ids, but i guess those are ephemeral as well as “internal”
18:36 jar286 the goal is to make their use unnecessary. but I like seeing the numbers at NCBI taxonomy and elsewhere. hate having to copy it from mouseovers or view source or url bars.   node ids are completely different, the problem is not that they’re seen in the UI, it’s that they’re seen in the API
18:36 jar286 ‘their use’ = at the UI
18:37 jimallman ok, i think i follow (will ponder)
18:38 kcranstn this PR looks good, though
18:38 jar286 identity confusions are common, important to provide every possible bit of help.  node ids do not help with identity since they are unstable
18:38 * jimallman nods
18:38 jimallman +1 to merge
18:39 kcranstn merged
18:39 jar286 looking, i’m sure it’s fine
18:41 jar286 I’m being a bit slow here.
18:42 jimallman left #opentreeoflife
18:42 jar286 what do I do to see it in action?
18:42 jar286 oops he’s gone
18:43 kcranstn https://tree.opentreeoflife.org/curator
18:43 kcranstn search for ‘pg_112’
18:43 jar286 oh i get it
18:43 jar286 but when you arrive, you can’t see the study id
18:43 jimallman joined #opentreeoflife
18:43 jimallman sorry, i accidentally closed my window :-/
18:43 jar286 (you can scroll right on the url bar, if you know how to do that)
18:43 kcranstn no change to the study list page
18:44 jar286 no change to the study view page either
18:44 jimallman you should see the study ID (right aligned) when you expand a study in the list
18:44 kcranstn that link should have been devtree
18:44 jar286 right, got that
18:45 jar286 it’s great as far as it goes, but I would make sure the study id is displayed on the individual study page too
18:46 jimallman by expand, i mean click  [
18:46 jar286 otherwise you don’t know what the id is, if you wanted to remember it for future use
18:46 jimallman [show details]
18:46 jimallman re: showing the ID on the single-study page, gotcha. OK if it’s kind of subdued as in the study list?
18:46 jar286 yes
18:47 kcranstn yes
18:47 jar286 why is there a url underneath ‘Viewing study’, by the way? redundant with metadata view
18:47 jar286 unneede consumption of valuable vertical space
18:49 jimallman i do not recall the rationale. happy to remove it (though this was a nice line to include a right-aligned study ID)
18:49 jimallman i could add the study ID under the Metadata tab as well, i suppose
18:50 jar286 hmm.
18:50 jar286 url not so important, just metadata,  but study id is a bit more important.  dunno.  not a critical decision
18:51 jar286 would work either way
18:51 kcranstn I’d take out the URL and save that space. Add studyID to metadata (but closer to bottom)
18:51 jimallman agreed… shall i make these changes now, or ping later for a merge?
18:51 jar286 later
18:51 kcranstn feels like we could shrink the vertical spacing on the metadata tab
18:51 kcranstn later
18:53 jimallman re: spacing, i think this was set to work well when editing. i should be able to compress is slightly for the read-only view.
18:53 kcranstn ah, good point
18:53 jimallman ok, will check in soon with these changes for review
18:53 kcranstn now priority
18:53 kcranstn low
18:54 jimallman understood (but i’m already halfway done!)
18:59 kcranstn so everything else here stalled? https://github.com/pulls?user=OpenTreeOfLife
19:01 pmidford2 Rick's never responded on #127; it is probably moot by now.
19:01 pmidford2 Rich
19:01 jar286 yes
19:01 jar286 stalled
19:02 jar286 maybe the long-term prs should be closed until review is wanted
19:02 kcranstn I think that’s a good idea
19:02 jar286 as long as there are issues for them all
19:04 kcranstn ok, I am closing https://github.com/OpenTreeOfLife/opentree/pull/598
19:04 kcranstn there are two related (open) issues
19:05 kcranstn and this certainly requires discussion before implementing changes
19:05 jar286 dealt with 2 of them
19:08 jimallman single-study page changes (closer spacing for View vs. Edit, removed DOI from header, added Study ID to Metadata) are visible now on devtree
19:09 jimallman i didn’t realize kcranstn was clobbering the ‘search-studies-by-id’ branch, so it looks like i’ve resurrected it :-/
19:09 jimallman https://github.com/OpenTreeOfLife/opentree/pull/682
19:12 kcranstn is this deployed?
19:12 kcranstn (sorry about the branch)
19:12 jimallman deployed on devtree, PR is ready to merge to master
19:13 kcranstn merged
19:13 kcranstn deleting branch...
23:10 kcranstn joined #opentreeoflife
23:41 jar286_ joined #opentreeoflife

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