Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-01-09

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All times shown according to UTC.

Time Nick Message
02:39 jimallman joined #otol
12:19 towodo joined #otol
14:09 _ilbot joined #otol
14:09 Topic for #otol is now #otol Open Tree Of Life | http://opentreeoflife.org/ | http://github.com/opentreeoflife | http://irclog.perlgeek.de/otol/today
15:02 jimallman joined #otol
18:06 transsib joined #otol
20:22 dukeleto joined #otol
21:46 mtholder joined #otol
21:46 towodo starting work on deployment branches
21:49 jimallman towodo: awesome, thanks!
21:50 jimallman i'm (finally) getting ready to integrate mark's newick-import code...
22:05 mtholder hi jim. fwiw, I just pushed a minor change to the NCL repo that is a dependency of that newick/NEXUS importing code.
22:07 mtholder jimallman: I forgot to prepend your nickname to that last message. IRC is only 26 years old. At some point I'll learn what I'm doing...
22:12 jimallman mtholder: sorry, i was in a hangout... reading now...
22:13 jimallman NCL repo = https://github.com/OpenTreeOfLife/2nexml  ???
22:15 jimallman mtholder: ^
22:16 jimallman it looks like we might need to add this to the deployment scripts (push.sh and related)...
22:20 dukeleto towodo: i am in the process of updating treenexus->phylesystem. Do you want me to rename treenexus_test to phylesystem_test ?
22:21 towodo That would be great, and now's the time. Thanks
22:27 dukeleto towodo: ok, it is renamed: https://github.com/OpenTreeOfLife/phylesystem_test
22:28 dukeleto towodo: as is treenexus: https://github.com/OpenTreeOfLife/phylesystem
22:28 dukeleto jimallman: ^^^
22:28 jimallman cool, thanks!
22:29 jimallman towodo: dukeleto: time to update some config files! i wonder if things on dev.opentreeoflife.org are broken already...
22:31 dukeleto towodo: https://github.com/OpenTreeOfLife/opentree/pull/177
22:31 dukeleto jimallman: the above PR will update the deployment code
22:31 dukeleto jimallman: i imagine that writes will attempt to push to the old repo address and return an error
22:32 jimallman i just saved study changes on dev... no apparent error in the browser.
22:32 jimallman and no recent commits in treenexus or treenexus_test on GH
22:32 dukeleto jimallman: that seems odd
22:33 dukeleto jimallman: going to ttps://github.com/OpenTreeOfLife/treenexus redirects to phylesystem
22:33 dukeleto jimallman: so perhaps the clone/push urls redirect as well
22:33 jimallman cool!
22:33 dukeleto jimallman: they indeed do
22:33 dukeleto jimallman: which is kind of nice
22:34 dukeleto jimallman: i just did a clone of treenexus_test
22:34 jimallman sweet! and there's my change on phylesystem_test, on the jimallman_study_9 branch (duh)
22:35 dukeleto jimallman: awesome
22:37 mtholder jimallman: Sorry. No the NCL repo is https://github.com/mtholder/ncl  That URL is in the install-ncl.sh script that is in the curator app. I agree that it will need to be incorporated into the deploy stuff. I have not learned the deploy system yet.
22:38 mtholder Notes in the opentree/curator/README.md on the branch about external-format-to-nexson branch.
22:39 jimallman mtholder: OK, I'll see if I can get things running. Once I understand all the moving parts, I should be able to wrangle the deployment side.
22:40 jimallman dukeleto: pls disregard my last GH comment.. I'll tweak the sample.config file myself.
22:40 jimallman no need for excessive bureaucracy... :-/
22:51 towodo dukeleto, I don't get how to refresh a git repository throwing away local changes.
22:51 towodo I'm getting "error: you need to resolve your current index first"  which I didn't expect
22:52 towodo I don't even know what it means
22:53 towodo and now I have "Cloning into 'phylesystem_test'...
22:53 towodo fatal: Not a git repository (or any of the parent directories): .git"
22:53 dukeleto towodo: hmmm
22:53 towodo shooting in the dark here
22:53 dukeleto towodo: what is the full command that you are trying?
22:54 towodo push.sh -c ot6.config       :)
22:54 towodo let me look. these are 2 distinct problems. 1st 1st
22:54 towodo it's in functions.sh if you want to look
22:55 towodo (cd $repo_dir; git checkout $branch; git checkout .; git pull)
22:55 dukeleto towodo: did you make changes in your deployed git repo on the server?
22:56 towodo I don't think so. Matter of personal policy. Double checking now.
22:56 towodo Changes to be committed:
22:56 towodo #
22:56 towodo #new file:   ws-tests/test_study_get_404.py
22:56 towodo I don't think I did that.
22:56 dukeleto towodo: that is in the api repo
22:57 towodo right, that's where the problem is
22:57 towodo I can't imagine how a file could have gotten added to the index
22:57 dukeleto towodo: sounds like the repo was attempting to be updated, and failed somehow
22:58 dukeleto towodo: that is from a commit from a few days ago
22:58 dukeleto towodo: the addition of that file, anyway
22:58 towodo could that have happened by interrupting the process?
22:58 dukeleto towodo: yes, i believe so
22:59 dukeleto towodo: if you did a cntrl-c (or similar) while it was pulling in new changes
22:59 towodo ok. so what do i do to discard the index? stash it?...

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