Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-01-15

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All times shown according to UTC.

Time Nick Message
23:00 towodo jimallman: new pull request for your attention
23:00 jimallman towodo: ok, taking a look now...
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23:03 jimallman towodo: what does this expression in push.sh mean?
23:04 jimallman -r $OPENTREE_IDENTITY
23:04 jimallman ? checking for non-empty file?
23:05 jimallman ah, i think i found it ("true if file is readable")
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06:33 Topic for #opentreeoflife is now Open Tree Of Life | opentreeoflife.org | github.com/opentreeoflife | http://irclog.perlgeek.de/opentreeoflife/today
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14:51 josephwb1 phylografter is down. any idea when it will be back up?
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15:00 PEM If phylografter is down, Lyndon is probably the person to contact - I think Rick is still on travel.
15:01 kcranstn I think Mark emailed them yesterday
15:03 PEM He did, I don't think Lyndon responded.  I'll follow up with him.
15:04 josephwb1 it was down, then back up for a while.
15:04 josephwb1 yesterday
15:06 PEM So maybe he restarted it and it's down again.  Lyndon isn't on google either, so I'll try email
15:06 josephwb1 thanks peter
15:11 blackrim maybe we should try to get those folks on irc as well. especially since we are trying to get use to this as our quick communication and tool
15:13 PEM Lyndon was on irc for a while yesterday, so he may just be out this morning.
15:13 blackrim aha. got it. nevermind then
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16:18 Lyndon Does anyone know if there is a way to stop the timeout disconnect in IRC? It would make following the conversations throughout the day a little easier without having to constantly check the log.
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16:26 blackrim hm, what is the program you are using to connect?
16:26 Lyndon xchat on ubuntu
16:26 PEM Rick has brought phylografter back up
16:27 blackrim if you are looking for a gui, i wonder whether pidgin has the same timeout (maybe someone else knows). I am using irssi (on debian) which is command line but doesn't seem to have a timeout issue
16:28 Lyndon maybe i'll switch to a command line client then and see if that helps.
16:35 josephwb thanks rick
16:37 blackrim going to discussion group but not logging out, set myself as away though
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17:34 jimallman blackrim, Lyndon: irssi + gnu screen = awesome. captures everything, never times out...
17:36 lcoghill I'll give it a shot. Thanks Jim.
17:42 dukeleto lcoghill: just fyi, http://weechat.org/ is the successor of irssi and may be easier for you to install
17:43 lcoghill I'm using weechat atm, and it seems really nice. I didn't realize it was the successor of irssi though. It is really intuitive.
17:44 lcoghill I also haven't had any timeout issues with weechat yet.
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19:02 josephwb do we have a skype meeting today?
19:03 kcranstn no
19:03 josephwb ok, thanks. old calendar.
19:04 kcranstn friday and monday for software, thurs for all-hands
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19:09 travis-ci [travis-ci] OpenTreeOfLife/phylesystem#96 (master - 4ea4260 : josephwb): The build passed.
19:09 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/phylesystem/compare/deb7a0ee7937...4ea4260542cd
19:09 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem/builds/17014694
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19:10 blackrim fantastic! glad that it works. irssi is very nice. I feel like my 14 year old young hacker self on IRC all the time. thanks opentree!
19:22 blackrim jimallman: sorry, wasn't clear, my last comment was for you
19:23 jimallman thanks for the tip on weechat. i was not aware...
19:23 ruchi Hi Stephen, a question?
19:24 blackrim ruchi: sure
19:25 ruchi I have been looking at your PLOS 2013 paper "Analyzing and Synthesizing Phylogenies using....".
19:26 ruchi Some algorithmic details are missing but they are probbaly in it's supplement document.
19:26 ruchi So where can I find this supplement document?
19:26 blackrim aha, yes, so that is a mistake from a previous version. you are talking about the branch and bound algorithm?
19:27 ruchi yes
19:28 ruchi Is there more material out there that goes with this paper?
19:28 blackrim on revision they suggested not having a supp so we missed that sentence in there. however, i am happy to send along to you either the relevant java code in treemachine (or I have a python version as well if that is easier). it is something that we don't use for constructing the tree for opentree but for some of the other analyses that we do
19:29 blackrim i will go ahead and add that to my website for others that might be looking for it as well
19:30 ruchi is there a writeup of that algorithm?
19:31 blackrim no, they aren't novel, just standard branch and bound. nevertheless, the lack of detail in the paper is an error. If you would rather not see the code, I can give a write up of it
19:35 ruchi if there is a write up, please share it.
19:36 blackrim will do. I will get that to you and up on the website ASAP
19:37 ruchi Which website? (Sorry for so many questions)
19:37 blackrim no problem. on my http://blackrim.org/publications website
19:37 ruchi thanks
19:39 blackrim no problem. it was my bad anyway
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