Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-03-23

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All times shown according to UTC.

Time Nick Message
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05:19 mtholder hi jimallman, It looks like I broke the api master branch in several spots. I'm working on getting backward-compatibility into peyotl. sorry.  soon (hopefully)
05:20 jimallman ok, no rush. i can work elsewhere if need be..
05:21 jimallman mtholder: ... but let me know if i can help
05:21 mtholder ok. what version of the phylesystem repo are you working with?
05:22 mtholder jimallman ^
05:22 jimallman hm, master i assume.
05:23 jimallman confirmed
05:23 jimallman (on my local)
05:23 mtholder sorry. I meant phylesystem or phylesystem_test or hbf_phylsystem_test
05:23 jimallman duh, and 'phylesystem'
05:23 jimallman :)
05:26 mtholder cool. thanks.
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05:32 travis-ci [travis-ci] OpenTreeOfLife/phylesystem#181 (master - 1d46623 : Mark T. Holder): The build passed.
05:32 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/phylesystem/compare/99793a6b47ee...1d46623f7657
05:32 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem/builds/21350580
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05:32 travis-ci [travis-ci] OpenTreeOfLife/phylesystem#178 (master - e4b5232 : Mark T. Holder): The build passed.
05:32 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/phylesystem/compare/9e205f03c75d...e4b52324e6c1
05:32 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem/builds/21350574
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05:33 travis-ci [travis-ci] OpenTreeOfLife/phylesystem#180 (master - 99793a6 : Some Author): The build passed.
05:33 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/phylesystem/compare/30a49a39b7ef...99793a6b47ee
05:33 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem/builds/21350578
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05:34 mtholder jimallman, you don't want/need to see these travis-ci updates for the phylesystem repo, do you?
05:35 jimallman no problem either way
05:35 jimallman ah, but i see your point. they're going to be increasingly frequent noise
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05:35 travis-ci [travis-ci] OpenTreeOfLife/phylesystem#182 (master - 5e78c19 : Mark T. Holder): The build passed.
05:35 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/phylesystem/compare/1d46623f7657...5e78c19992d6
05:35 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem/builds/21350654
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05:35 mtholder much of the .travis.yml seems outdated. I'm going to trash it from that repo...
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05:38 travis-ci [travis-ci] OpenTreeOfLife/phylesystem#185 (master - 1862d2b : Mark T. Holder): The build passed.
05:38 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/phylesystem/compare/1788eb17495a...1862d2b50e34
05:38 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem/builds/21350660
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05:39 travis-ci [travis-ci] OpenTreeOfLife/phylesystem#183 (master - 25a522b : Mark T. Holder): The build passed.
05:39 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/phylesystem/compare/5e78c19992d6...25a522ba32d5
05:39 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem/builds/21350656
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05:41 travis-ci [travis-ci] OpenTreeOfLife/phylesystem#186 (master - d816028 : Mark T. Holder): The build passed.
05:41 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/phylesystem/compare/1862d2b50e34...d816028f15c6
05:41 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem/builds/21350777
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06:00 mtholder jimallman: 2 questions: #1 would you mind testing against phylesystem_test rather than phylesystem?
06:01 jimallman sure, no problem
06:01 mtholder number 2: is having @root= true rather that @root="true" going to be a problem for you?
06:01 mtholder in nexson
06:02 jimallman i might need to tweak client-side JS to match, but not a big problem in any case (and it certainly sounds like an improvement)
06:02 mtholder stricter peyotl checking of booleans was causing it to reject some of the studies in phylesystem. I can loosen the strictness of the validator, or I can migrate all of the studies in phylesystem to use the boolean rather than string.
06:03 jimallman i like proper boolean values myself...
06:04 mtholder me too.
06:04 mtholder I'll convert phylesystem, but until I do it won't work with the latest peyotl.
06:05 mtholder and that change will require some scripting because phylografter is emitting the string form.
06:05 jimallman ok, so my setup for now should be phylesystem_test + peyotl master + api master?
06:06 mtholder I just pushed to peyotl and api master. with those fixes, that configuration is working for me.
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06:07 travis-ci [travis-ci] OpenTreeOfLife/api.opentreeoflife.org#420 (master - a48c696 : Mark T. Holder): The build passed.
06:07 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/api.opentreeoflife.org/compare/6a00bc7c772c...a48c69627aee
06:07 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/api.opentreeoflife.org/builds/21351530
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06:07 jimallman mtholder: sweet, will do as well
06:07 mtholder the only substantive change to api was "new_sha = gd.merge(branch_name)" instead of "gd.merge(branch_name)"
06:08 mtholder emily is working on the documentation for the local-dep branch that should be much more robust than the master branch.
06:09 mtholder it will require a couple of client-side changes, but I think they'll be not too hard, and unavoidable.
06:10 jimallman no prob, worth it to get to multiple repos... wait, what does "local-dep" mean?
06:10 mtholder sorry that is a branch on api
06:11 mtholder local is a peyotl branch and local-dep was the api branch that depends on it.
06:12 jimallman ah, got it
06:17 mtholder can the client code determine the user's github name? or is the auth info opaque to JS ?
06:18 mtholder in local-dep we are adding a struct to the return for GET that lists all of the WIPs for that study
06:19 mtholder but to be of most use to the JavaScript side, you'd need to be able to determine the curator's GH login name (because that is the start of their WIP name)
06:19 mtholder jimallman ^
06:20 jimallman yes, JS knows the logged-in (=GH) name and email
06:20 mtholder great.
06:20 jimallman and yes, that includes full (proper) name and GH userid/username
06:21 jimallman i'm off to bed, but will play with the latest in the AM. thanks!
06:21 mtholder good night. thanks .
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11:32 Topic for #opentreeoflife is now Open Tree Of Life | opentreeoflife.org | github.com/opentreeoflife | http://irclog.perlgeek.de/opentreeoflife/today
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19:18 travis-ci [travis-ci] OpenTreeOfLife/api.opentreeoflife.org#423 (local-dep - a4a1939 : Emily Jane McTavish): The build passed.
19:18 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/api.opentreeoflife.org/compare/677e0a9df2d4...a4a19392d267
19:18 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/api.opentreeoflife.org/builds/21377929
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23:54 mtholder jimallman: is that delete issue that you are seeing on your local machine or one of the ot servers?
23:54 jimallman on ot10 (working API for dev.opentreeoflife.org)
23:54 mtholder ok. I'll look at the config.
23:55 jimallman i can see that the global git config settings are correct on that box....
23:55 jimallman ...and that we're the right effective user (opentree), so it's pretty weird
23:55 jimallman fyi - i got past this with an ugly hack, adding username + email to the git_env like so:
23:55 jimallman git_env     = {"GIT_SSH": git_ssh, "PKEY": pkey, "GIT_COMMITTER_NAME": "OpenTree API", "GIT_COMMITTER_EMAIL": "api@opentreeoflife.org"}
23:56 jimallman but git should be picking that up from ~/.gitconfig instead, i would think
23:57 jimallman also fyi - once i got past that, there was an ugly conflict situation in two studies... so perhaps that error msg is a red herring?
23:58 mtholder perhaps. Is it possible that the key for phylesystem rather than phylesystem_test is deployed?
23:58 jimallman ! interesting! i didn't think to change that in server-config files!
23:58 jimallman ...checking now...
23:59 mtholder unfortunately, github won't let us reuse deploy keys
23:59 mtholder I just looked at it, and I think that is the problem.

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