Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-11-21

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All times shown according to UTC.

Time Nick Message
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14:00 mtholder kcranston. So I know that we just did PRs yesterday. but there is a new one (well 3 technically): https://github.com/OpenTreeOfLife/peyotl/pull/65
14:00 kcranstn I am seeing them pile into my inbox ;)
14:00 kcranstn that one starts very canadian. Is that why you want me to review it?
14:01 mtholder I wrestled with that one a lot this morning. If we can merge it, the others will look reasonable.
14:02 kcranstn merged
14:03 mtholder thanks.
14:03 mtholder I assume you saw this: http://programmers.stackexchange.com/questions/1483/do-people-in-non-english-speaking-countries-code-in-english/5576#5576
14:04 kcranstn I had not. Thanks, eh.
14:05 kcranstn “This question exists because it has historical significance, but it is not considered a good, on-topic question for this site”
14:07 mtholder for some definitions of "historical significance" ....
14:07 kcranstn = funny ha ha
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14:11 mtholder sorry. I hit the wrong branch on a new PR and then deleted. I'm putting the two that I added about 30 minutes ago back.
14:12 mtholder (they looked like a mess before karen merged their parent).
14:12 towodo I’m going to deploy yesterday’s stuff to ot10
14:13 mtholder OK. to "devapi" or api?
14:13 mtholder nm
14:13 mtholder ot10 = devapi
14:14 towodo I will deploy to production (api) on Sunday (if I’m not preoccupied with family the whole day)
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15:11 towodo kcranstn, note that the counts I sent you are for all nodes, not just tips
15:11 kcranstn argh!
15:11 kcranstn damn
15:12 josephwb Regarding the non-executable scripts: they should all be changed.
15:12 josephwb Don't know what went wrong
15:12 josephwb Not very useful if not executable.
15:12 towodo agree, but they are the *only* changes in that commit, so it really looks as if stephen wanted them to be nonexecutable
15:13 josephwb I can ask him.
15:13 towodo I changed the deployment system to not depend on their executability
15:13 josephwb Stephen is in a meeting; I will ask him when he is free.
15:14 towodo fyi, just deployed latest treemachine master head to devapi
15:14 josephwb Been a while since I've been on IRC. Good to see our friend ilbot3 still joins us.
15:14 josephwb ^o)
15:15 towodo didn’t push phylesystem-api as it was already up to date. similarly peyotl
15:15 kcranstn towodo - I just realized that the numbers from NCBI suffer from the same flaw
15:16 kcranstn the taxonomy records link on the NCBI pages counts *all* descendent nodes, not just tips
15:16 towodo opentree has a testing branch. jimallman, any chance you could merge master into tree-conflict-view and re-push tree-conflict-view to devtree? (or maybe you already did?)
15:17 towodo I can do tip counts for both ncbi and ott if you like
15:17 kcranstn that would be fantastic
15:17 jimallman towodo: glad to do that
15:17 jimallman (merge master and re-push, i mean)
15:17 kcranstn that = tip counts
15:17 kcranstn I guess I should have been suspicious abotu those numbers when I made the figure
15:18 jimallman towodo: looks like it was already up to date.. re-pushing just to be sure.
15:18 towodo right I didn’t check
15:19 towodo kcranstn, should I count tips for the version of ncbi that went into ott 2.8 / synthesis, or for a current ncbi?
15:19 towodo I guess the former
15:22 towodo jimallman, I think I forgot that we didn’t do any opentree merges yesterday. but redeploying is good because that gets us up to date with peyotl
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15:38 kcranstn towodo - the version that went into ott 2.8 / synthesis
15:38 towodo right, doing that now
15:38 kcranstn can you also send me the script / commands that you used to do that (or put them in the wiki / docs)
15:48 towodo email sent.
15:48 towodo will need some work before ready for general consumption
15:49 towodo numbers are interesting but not so surprising… gbif has a lot of insects
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17:08 mtholder I now have dependency graphs on the bottom of: http://opentreeoflife.github.io/peyotl/subpackages . May be helpful when trying to figure out if a change in peyotl will affect a service. (the graphs will get stale, though)
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17:12 towodo mtholder, isn’t there some dependency path from curator to phylesystem?
17:12 mtholder no The javascript talks to the phylesystem-api.
17:12 mtholder the plot just shows the python code in the curator.
17:13 mtholder the python in the curator only does translation to NexSON (which the curator JS then deposits in the phylesystem-api services)
17:13 mtholder I'll note that on the page, though. Thanks.
17:14 towodo I see, I was in effect expecting a blue arrow from blue box curator to blue box phylesystem-api.
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22:12 towodo pmidford2, wanna talk about taxonomy some time?
22:13 towodo I’m out from under other stuff a bit
22:14 pmidford2 Yes, probably not tonight, but Monday would work for me.
22:14 towodo mon morning is clear for me. 10?
22:16 pmidford2 10 should work, I'm still doing PT, but should be back by 9:30.
22:17 towodo ok
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