Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-09-10

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All times shown according to UTC.

Time Nick Message
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10:08 travis-ci [travis-ci] OpenTreeOfLife/phylesystem-api#594 (alert-clogged-push - b6b9276 : Mark T. Holder): The build passed.
10:08 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/3b86ab07e83d^...b6b9276b1d65
10:08 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/34897253
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11:03 josephwb morning ilbot3
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11:42 travis-ci [travis-ci] OpenTreeOfLife/phylesystem-api#596 (master - a70e7b9 : Mark T. Holder): The build passed.
11:42 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/8f49d0884be5...a70e7b9ea3fb
11:42 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/34903491
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11:45 travis-ci [travis-ci] OpenTreeOfLife/phylesystem-api#597 (alert-clogged-push - 30bfa65 : Mark T. Holder): The build passed.
11:45 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/b6b9276b1d65...30bfa6517bd2
11:45 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/34903597
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13:14 towodo today I think I understand merge commits (when they’re made & when not)
13:14 towodo mtholder, have you been deploying your PR branches to ot10?
14:07 josephwb jimallman and towodo: i am keeping arguson as a hidden format for the subtree method (that is, complete below a given node)
14:07 josephwb i do not have it as a possible (even hidden) format for 1) induced subtree or 2) source tree
14:07 josephwb is that ok?
14:08 josephwb i.e. only newick for the 2 latter ones
14:09 jimallman josephwb: for now at least, we don’t use argus to view source trees. i’m not sure what you mean by induced subtree..
14:10 josephwb that's funny
14:10 josephwb we talked a lot about what would be the most clear name
14:10 josephwb i was outvoted on that one
14:10 josephwb it is a subsetted tree
14:10 josephwb pruned tree
14:11 jimallman ah yes, with just selected tips and necessary internal nodes, right?
14:11 josephwb yes
14:11 josephwb i figured arguson is only useful for the tree viewer (i.e. to you)
14:11 josephwb no i won't support it for the things that won't be viewed in the treeviewer
14:12 jimallman yeah, my brain wants to say “sparse subtree”, or “selective subtree”… but without the use case, it’s a hard idea to get across..
14:12 josephwb let's not open this back up
14:12 josephwb please
14:12 josephwb i think i got my answer
14:12 * jimallman withdraws the previous statement
14:12 josephwb thanks jimallman
14:13 jimallman i’m pretty sure we’ll be sunsetting argus ASAP, yes
14:13 josephwb :^)
14:21 mtholder sorry for the lag, towodo. No I have not deployed the PR commits. let me look into doing that now...
14:31 towodo just that I’d rather not push to production anything that’s not already deployed to development
14:40 mtholder sure.
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14:50 mtholder redeploying phylesytem-api to ot10...
15:00 towodo jimallman, i sent email about ‘induced’
15:06 mtholder OK, towodo. the branch for the PR is on ot10, and all of my tests in phylesystem-api/ws-tests when run against that instance.
15:06 towodo excellent thanks
15:17 * jimallman likes towodo’s “induced” email, much appreciated
15:19 josephwb don't know about the "authoritative source" though. one was a mathematician (not a phylogeneticist), the other was a tree viewer. i'm fine with the name, but it is not used in the field.
15:45 josephwb playing with Dendroscope. seems to use "induced" in a very different way
15:45 josephwb that is: the select tips, and all intervening tips
15:46 josephwb so, basically, "get the MRCA of selected taxa, and return the complete subtree below that node"
15:46 towodo oh.
15:47 towodo jimallman, I’ve just had a confusion over branches in config files… I did a push expecting ‘master’ to be pushed, but ot16.config said ‘Cavia’
15:47 towodo reverting to master…
15:47 josephwb i think the term is fine, but the precedence is not
15:48 towodo personally I don’t think it needs precedent other than a few hundred years of mathematician-speak
15:48 jimallman towodo: sorry for the confusion. i’ve tended to push any changes to the dev configuration, since we originally talked about it as accurately the currently deployed system.
15:49 jimallman but yeah, that should have been changed back to master (and pushed to dev) before now.
15:49 towodo either we keep ‘master’ as the branch in the config file, or i’ll have to remember to check the config file every time I push. not sure which is better
15:50 jimallman i’m a fan of the “de facto approach (
15:50 * jimallman is garbling
15:50 jimallman … since we might go for awhile with an experiment feature branch on dev* servers.
15:51 towodo we could keep the checked-in config file saying ‘master’ always, and have people modify that in their own checkout repos
15:52 jimallman the problem is that we’re all sharing a single dev/test system, i worry about surprise changes if 2+ people are pushing to dev* and >poof< What happened to my feature branch?
15:53 towodo having to pull/push the deployed-systems repo on every branch change (and after every PR merge) is a pain
15:53 towodo maybe we could keep the branch choices in google docs :)
15:53 jimallman or right here on IRC. yeah, that’s the ticket.
15:54 jimallman the proper solution is easy building of additional test systems using vagrant/docker/etc
15:54 towodo the hard part is the databases, not the code
15:55 towodo i guess the asterales system might solve that problem
15:55 jimallman hm, i see your point
15:56 towodo the other option is a development branch
15:56 towodo (we’ve been over this before)
15:59 jimallman i expect there will be n development branches, as people work on different features and fixes
15:59 * jimallman doesn’t mean to go through all this again… back to work!
16:00 towodo no, i mean a development branch from which the shared dev instances are deployed
16:00 towodo so, ‘master’ as the branch in the dev system config files, right?
16:02 jimallman sure, let’s keep things simple and see what happens.
16:14 towodo ok, assigned that deployed-systems PR to you…
16:55 towodo I will henceforth check to see what’s deployed on dev before clobbering it
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18:51 josephwb hey jimallman
18:52 jimallman josephwb: howdy
18:52 jimallman i hope your synthesis is going more smoothly now
18:52 josephwb um, i think i will send this one through email
18:52 jimallman ok
18:53 josephwb just want karen and jonathan to weigh in, and they are not here now
18:53 * jimallman is expecting salty language now
18:53 josephwb nothing like that
18:54 josephwb we have an extract subtree service that has 2 args that only apply to you (format and max_depth)
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18:54 josephwb i have been working with hiding them
18:54 josephwb talked it over with cody
18:54 josephwb thought of making a separate service for you, but cody pointed out that you could just use the v1 service
18:55 jimallman undocumented options seem reasonable to me, if we’re not intending them to be used normally. or yes, v1 service is fine for now, but i think we’re planning to sunset v1 eventually, yes?
18:57 josephwb but arguson is also going away. isn't it?
18:58 jimallman that’s the plan, but it’s going to be with us for awhile
18:58 josephwb ok, i think email will settle this
19:02 josephwb email sent
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