Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2015-08-20

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All times shown according to UTC.

Time Nick Message
00:57 jimallman joined #opentreeoflife
12:02 kcranstn joined #opentreeoflife
12:16 kcranstn I can’t load the webapp (strangely enough, I *can* load curator)
12:20 kcranstn seem to be issues with login (again, only webapp, not curator)
12:20 kcranstn hanging
12:22 kcranstn very, very slow
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14:17 pmidford2 joined #opentreeoflife
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15:07 kcranstn jimallman re: pair programming. Want to tackle auto visibility of feeback form OR quality scores?
15:07 jimallman yes, webapp is very slow for me too. i need to move the initial request for tree ids to the client-side, to better isolate which server is the problem.
15:07 kcranstn or we could tackle that
15:08 jimallman yes, any of these would be worthy targets.
15:08 jimallman quality score feels timely, and should be an easy win
15:08 kcranstn ok
15:08 kcranstn I’ll take a look at that code this afternoon / tomorrow morning
15:09 jimallman i’m working through the stats/progress changes from yesterday’s meeting (some changes are already visible on devtree). testing pmidford’s latest stats now…
15:10 kcranstn yay
15:15 pmidford2 joined #opentreeoflife
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18:02 * jimallman is almost ready for PR review, pushing latest work to devtree...
18:03 kcranstn joined #opentreeoflife
18:03 kcranstn let me know when you are ready
18:03 kcranstn no rush
18:03 jimallman devtree now has the new stuff
18:04 jimallman so i’m ready
18:04 kcranstn is the stats stuff on development, or on its own branch?
18:04 pmidford2 jimallan - the synthesis changes we've been discussing this morning won't be ready for the PR review.  Maybe we can merge tomorrow or in KS.
18:04 pmidford2 jimallman ^
18:05 jimallman kcranstn: the feature branch is otu-stats-area, but the latest is merged into development branch as well
18:05 kcranstn cool
18:05 kcranstn shall we postpone the stats review until tomorrow?
18:06 jimallman pmidford2: understood. for now my manually-tweaked stats file is on devtree: http://devtree.opentreeoflife.org/static/statistics/synthesis.json
18:06 jimallman postponing is fine with me
18:06 jimallman i’ve been pestering pmidford2 with tweaks and requests..  :-/
18:06 pmidford2 Ok, I should have the fixable things ready for tomorrow.
18:07 pmidford2 Maybe even later this afternoon for people to look at
18:07 jimallman neat!
18:08 jimallman did we ever settle on where we’re putting “proper” release docs for each synthesis release?
18:08 jimallman i’m assuming markdown on Github, as we’ve done for OTT versions
18:08 kcranstn I don’t think we decided on a repo. No one had strong feelings. Germinator?
18:09 jimallman works for me. maybe there’s not that much to say..?
18:09 kcranstn not at the moment, but hoping that will improve over time (i.e. reports on tests of inclusion and monophyly)
18:10 kcranstn new trees not in past versions
18:10 kcranstn method changes
18:10 jimallman OK. we can start with minimal placeholders and reminiscences…
18:10 kcranstn :)
18:10 jimallman kcranstn: if possible, i’d like to quickly review (and hopefully merge) this one, which gives us release notes for ott2.7: https://github.com/OpenTreeOfLife/reference-taxonomy/pull/157
18:11 kcranstn I was just looking at that. seems ok to me
18:11 jimallman me too.
18:11 jimallman love the download links here
18:13 kcranstn ok to merge?
18:13 pmidford2 works for me too
18:13 jimallman please do
18:13 kcranstn ok, done
18:14 jimallman et voila!   https://devtree.opentreeoflife.org/about/taxonomy-version/ott2.7
18:14 jimallman no more nagging messages
18:14 kcranstn nice
18:16 jimallman there are a few other snack-sized PRs here if we want to keep going… or tomorrow’s fine of course
18:16 kcranstn sure, let’s do a few more
18:19 jimallman this addresses josephwb’s mysterious inability to save a study (adds client-side validation): https://github.com/OpenTreeOfLife/opentree/pull/709
18:19 jimallman we’re actually incredibly liberal about accepting incomplete submissions, so it just checks for an integer in Study Year
18:20 josephwb +1
18:21 kcranstn I am ok with this (when we talk tomorrow about study quality, we might revisit what other changes might be helpful)
18:21 pmidford2 I guess this is all we need for now
18:21 jimallman yeah, i’m just tracking the existing server-side validation, to avoid cryptic error messages.
18:22 kcranstn ok, merging
18:22 jimallman we could add more restrictions here, but i’d like to maintain parity with the server
18:22 kcranstn agreed
18:23 jimallman https://github.com/OpenTreeOfLife/opentree/pull/708 just addresses a long-standing annoyance (empty footer message on page load)
18:23 kcranstn yes!
18:23 jimallman i thought you’d like this one :)
18:24 kcranstn done
18:24 jimallman i found the answer in web2py, it was confused by the bit of markup i’d added here
18:25 jimallman https://github.com/OpenTreeOfLife/opentree/pull/706 is a mtholder fix, a better response code for missing PhyloPic images
18:25 kcranstn nice
18:25 jimallman i believe this will have no visible effect to an end user, just better diagnostic information for us
18:26 pmidford2 Looks good
18:26 jimallman agreed
18:29 jimallman kcranstn, ok for me to merge?
18:29 kcranstn yup
18:30 jimallman https://github.com/OpenTreeOfLife/opentree/pull/703 is kcranstn’s safety measure, to avoid immense Newick downloads (at least until we find a better way)
18:30 kcranstn yeah, it’s a hack
18:31 jimallman hm, i guess i’d like to tweak the removed “inner” comment delimiters to be more clear…
18:31 jimallman so we can restore them later.
18:31 jimallman i sometimes change /* to **, or separate them as / *
18:32 * jimallman is testing this now…
18:34 josephwb jimallman sourceToMetaMap is fixed on dev
18:34 jimallman cool! thanks
18:35 josephwb i checked and it is compatible with prod DB too
18:35 jimallman kcranstn, pmidford2: please refresh to see my change (no ill effects): https://github.com/OpenTreeOfLife/opentree/pull/703/files
18:36 kcranstn looks good, thanks
18:36 pmidford2 yes, think that's a bit clearer.  Ok to merge.
18:36 jimallman +1 to merge
18:37 jimallman i’ll do it…
18:37 kcranstn go ahead
18:37 jimallman done
18:38 jimallman https://github.com/OpenTreeOfLife/opentree/pull/700 fixes an oversight on my part (broken taxon search in About pages of main webapp)
18:38 jimallman i’m surprised we haven’t got a bug report on this..
18:38 jimallman (except for my own, i mean)
18:39 pmidford2 Is most of this change a cut and paste?
18:39 jimallman exactly. sorry for all the visual noise, it’s the very same code in a new file
18:44 jimallman modesty prevents me from merging this… (hint)
18:44 kcranstn ok, merging
18:45 jimallman https://github.com/OpenTreeOfLife/files.opentreeoflife.org/pull/2 is a tiny fix to a release date on files.opentreeoflife.org (wrong year)
18:45 kcranstn nice catch
18:46 kcranstn I think we can merge this
18:46 pmidford2 yes
18:46 kcranstn ok, so we can discuss stats page tomorrow?
18:46 jimallman sounds good.
18:46 pmidford2 Agree, when would be good?
18:47 kcranstn same time?
18:47 pmidford2 works
18:47 jimallman sounds good to me.
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