Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2015-01-09

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All times shown according to UTC.

Time Nick Message
02:34 towodo joined #opentreeoflife
13:17 mtholder joined #opentreeoflife
13:48 kcranstn joined #opentreeoflife
14:33 josephwb joined #opentreeoflife
14:41 josephwb All: what package do you use for latex on Linux (Debian)?
14:42 kcranstn can’t help you with that. mtholder?
14:42 mtholder I'm not sure about debian (I run ubuntu). I'll look at what I installed...
14:42 josephwb thanks
14:45 mtholder I can't recall installing it.  where is what I get if I ask pdflatex its version:
14:45 mtholder $ pdflatex -version
14:45 mtholder pdfTeX 3.1415926-2.5-1.40.14 (TeX Live 2013/Debian)
14:45 mtholder kpathsea version 6.1.1
14:45 mtholder Copyright 2013 Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
14:45 mtholder There is NO warranty.  Redistribution of this software is
14:45 mtholder covered by the terms of both the pdfTeX copyright and
14:45 mtholder the Lesser GNU General Public License.
14:45 mtholder For more information about these matters, see the file
14:45 mtholder named COPYING and the pdfTeX source.
14:45 mtholder Primary author of pdfTeX: Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
14:45 mtholder Compiled with libpng 1.2.49; using libpng 1.2.50
14:45 mtholder Compiled with zlib 1.2.8; using zlib 1.2.8
14:45 mtholder Compiled with poppler version 0.24.5
14:45 mtholder Looks like I installed Kile at some point, but I was just checking it out.
14:46 mtholder Are you having problems installing, joesphwb?
14:46 mtholder josephwb that is
14:47 josephwb no problems, just wondering about vetted packages.
14:48 josephwb looks like i have that installed already. thanks.
14:49 josephwb must have come with debian.
14:54 josephwb i guess that comes from "texlive"; must be the standard package.
14:56 mtholder yes. a joy of LaTeX is it is remarkably standardized at this point
14:57 josephwb while i've got you, what do you use for mac? MacTeX is a behemoth; download is ~2.5 GB!
14:58 josephwb AND apparently has problems with Yosemite.
14:59 mtholder it is has been a few years since I installed on Mac. I think that I followed the instructions on http://pages.uoregon.edu/koch/texshop/
14:59 mtholder which looks like it recommends MacTeX...
15:00 kcranstn that’s what I use. No problems on yosemite
15:00 kcranstn using the instructions in mark’s link
15:01 josephwb thanks to both. seems like that might be it for mac. and yes, it is a spawn of MacTex.
15:01 josephwb as far as i can say.
15:02 mtholder TeXShop is the GUI editor. MacTeX is the backend + lots of packages, as I recall.
15:02 kcranstn yup
15:03 josephwb i am not limited in space; it is just an aesthetic repulsion to the size.
15:11 josephwb mtholder: i assume you use emacs/vi for actual editing?
15:11 mtholder yes.
15:11 mtholder latexmk -pvc -pdf myfile.tex
15:12 mtholder will run the compile whenever there is a change
15:12 josephwb nice
15:17 josephwb woah; lots of editors available: http://en.wikipedia.org/wiki/Comparison_of_TeX_editors
15:39 towodo joined #opentreeoflife
16:15 jimallman towodo: as we discussed, i’ve merged the otu-stats-area branch to devtree. This shows two of the proposed statistics pages at https://devtree.opentreeoflife.org/about/statistics (original mockup) and https://devtree.opentreeoflife.org/about/otu-statistics (with the more promising area chart).
16:16 jimallman these are listed in the About menu as ‘General statistics’ and ‘OTU Statistics’, respectively.
16:17 jimallman this weekend i’ll add dated markers for taxo and synth releases along the bottom axis of the area chart
16:19 jimallman (to be clear: this was done with the new workflow, merging my features to the development branch and deploying that to devtree)
16:20 towodo I wonder if we should send out a general call for review, or if it’s too early for that.
16:20 towodo what’s the red dot mean?
16:20 kcranstn that chart is HUGE
16:21 kcranstn I don’t think it is ready for general review
16:22 kcranstn I have a bunch of comments now that I see them live
16:22 kcranstn but yay! to get something up!
16:22 towodo me too
16:23 towodo it’s showing the analysis date, not the synthesis date where it says ‘synthesis date’
16:23 towodo probably too early for general review
16:24 kcranstn how do you want comments, jimallman?
16:25 jimallman good question.. we could resume the existing thread in the older pull request, or try a thread in the google group?
16:26 kcranstn I like it on github rather than the mailing list
16:26 jimallman lots of caveats here, incl. bogus data.
16:26 kcranstn my biggest general comment is that I don’t understand the purpose of the two pages (how is “statistics” different than “otu statistics”)
16:26 jimallman OK, we can start commenting on the newer PR: https://github.com/OpenTreeOfLife/opentree/pull/536
16:26 kcranstn thanks
16:27 towodo I don’t think we need the about/statics one
16:27 jimallman agreed, we only need one of these (preferably the one with area chart, in my opinion)
16:27 kcranstn replace with a release page
16:27 kcranstn about the synthetic tree, includes download links
16:28 jimallman i think the conversation here will circle around release pages (both types) and a main “history” page (area chart + release markers)
16:28 jimallman each page would link to the others
16:28 jimallman (i’ll get to work on nav and page designs for these)
16:31 kcranstn ok, left some comments
16:37 jimallman thanks, will respond shortly
16:49 kcranstn excited to get these up, though!
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21:45 josephwb just got an email from PNAS
21:47 kcranstn me too
21:47 josephwb did you bug them? i was just saying to stephen yesterday that we are due a response.
21:47 josephwb decision
21:50 kcranstn didn’t bug them
21:51 kcranstn We definitely need more detail about the choice and ranking of trees
21:51 josephwb i can't see any reviews or anything; just that revisions are necessary.
21:52 kcranstn oh, you must have got a different email
21:52 kcranstn just a sec
21:52 josephwb no links. nuthin.
22:03 towodo joined #opentreeoflife
22:09 kcranstn just sent
22:10 kcranstn both reviewers and the editor are anonymous. that is really frustrating.
22:11 josephwb thanks.
22:11 josephwb didn't they just change to double-blind review?
22:11 kcranstn did they?
22:11 josephwb i think i saw that somewhere...
22:11 josephwb emily-jane posted something
22:11 kcranstn the reviews mention smith et al
22:12 towodo it would not be hard for the reviewers to unblind themselves.
22:12 towodo in this case.
22:12 josephwb huh, yeah
22:13 towodo maybe in most cases… just find a few keywords and google
22:13 josephwb oh, AmNat
22:14 towodo the trick then would be to write in the style (or using same vocabulary) as someone whose papers get accepted (: cynicism)
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