Camelia, the Perl 6 bug

IRC log for #bioperl, 2013-04-04

| Channels | #bioperl index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
01:27 looper joined #bioperl
01:54 scottcain joined #bioperl
06:18 bbb joined #bioperl
07:44 aleimba joined #bioperl
08:06 _ilbot joined #bioperl
08:06 Topic for #bioperl is now Be patient! People chat here daily, but not necessarily the minute or hour you wandered in. Leave your IRC client connected. | http://bioperl.org/wiki/IRC#Getting_help | http://www.bioperl.org/wiki/Using_Git | nopaste to gist.github.com
10:16 looper joined #bioperl
13:53 carandraug joined #bioperl
13:53 carandraug joined #bioperl
14:26 denisboyun joined #bioperl
16:05 rbuels carandraug++ # carrying on with dist splitting
16:08 carandraug rbuels, I'm looking at the wiki page. You were the mentor 2 years ago. What went wrong?
16:09 rbuels carandraug: nothing went wrong, just couldn't keep the momentum up
16:09 carandraug rbuels, ok. Well, I'm trying to make this really easy now. Running "dzil release" is as easy as it gets
16:10 rbuels yarp.
16:11 carandraug I ahve doubts about one thing though. Should I start splitting from the core or from the outer rings? Splitting from the outer circles, means that there's no need to release bioperl-live at the same time
16:11 rbuels carandraug: it's best to split from the core outward, because if you don't, you have to keep updating the dependencies of things you have already split off
16:12 rbuels (i think)
16:12 rbuels but obviously it doesn't matter that much if you feel you can keep up with updating dependencies
16:12 carandraug rbuels, I don't think that's true because a new smaller distribution is dependent on indivudla modules, not on another distributinos
16:13 carandraug rbuels, so, for example, Bio-Biblio is dependent on Bio::Root::Root, not no the BioPerl distribution. When Bio-Root gets released, nothing changes.
16:15 rbuels carandraug: *if* the dependencies of the split-off distributions are well-characterized to the point of listing all the individual modules, yes.  but that's rather hard to do; can't always be done automatically
16:15 carandraug rbuels, they are. Because it's done by dzil
16:16 carandraug rbuels, the list of dependencies is huge though, it lists use utf8, utf strict, etc...
16:16 rbuels carandraug: the automatic dep discovery in dzil isn't perfect though; be careful
16:17 carandraug rbuels, well, when bugs come I will fix them :p
16:17 rbuels fair enough  :-)
16:17 carandraug a bug about, the dependency X is not listed is the least of the concerns
16:18 * leont is considering a plugin to remove core dependencies from the prereqs
16:36 denisboyun_ joined #bioperl
16:39 aleimba joined #bioperl
17:15 Ulti left #bioperl
17:37 denisboyun_ joined #bioperl
17:41 denisboyun_ joined #bioperl
17:47 github [bioperl-live] carandraug pushed 1 new commit to master: https://github.com/bioperl/bioperl-live/comm​it/ee8b48d583f07b575a0c77e7c458c687cbe97b11
17:47 github bioperl-live/master ee8b48d Carnë Draug: maint: remove files that have been moved to a separate Bio-Coordinate distribution
18:01 denisboyun_ joined #bioperl
18:24 denisboyun_ joined #bioperl
18:36 denisboyun_ joined #bioperl
18:45 carandraug rbuels, hey! Could you give me permissions to push to bio-coordinate?
18:46 carandraug rbuels, I believe the problem may the same that Bio-Root had. "that one repo didn't have team set, just owners." by cjfields
18:46 carandraug rbuels, if so, my guess is that the other repos created at the time, will have the same problem.
18:46 * rbuels looks
18:47 carandraug I have made a bunch of changes to it, after I push, Bio-coordinates is ready for release with dzil
18:49 rbuels carandraug: ok it's got bioperl-team on it now
18:52 carandraug rbuels, thanks
18:52 carandraug rbuels, could you check the other repos as well, please? I'll be doing them as I can
18:52 rbuels carandraug: yeah i just did.  a few others needed it too
18:52 rbuels carandraug: i think i got them all though
18:54 carandraug rbuels, cool. Thank you
19:22 deafferret rbuels++ # does Ace Hood proud
21:08 scottcain joined #bioperl
21:26 carandraug joined #bioperl
21:32 carandraug rbuels, I'm confused about Bio-Range and Bio-Location. Could you explain please?
21:33 rbuels carandraug: they're just Bio::Range::*
21:33 rbuels carandraug: er, wait, there's no Bio-Location dist, is there?
21:33 carandraug rbuels, but they used to be Bio::Location and they're still there on the repository
21:34 rbuels carandraug: there was no module renaming.  only splitting.
21:34 carandraug rbuels, no. But there's the Bio::Location modules
21:34 rbuels carandraug: oh.  what's the difference between a Bio::Range and a Bio::Location?
21:34 rbuels is that the question?
21:34 carandraug rbuels, so basically, all the Bio::Location modules are to be renamed to Bio::Range?
21:34 rbuels carandraug: no, there's no renaming.
21:34 carandraug rbuels, yes. What is going on that repository?
21:35 rbuels carandraug: read the pod for Bio::Location and Bio::Range stuff. they're not the same thing at all
21:36 carandraug rbuels, even the modules in Bio/Range are declared as Bio::Location. By the way, that repo didn't kept the history from bioperl-live. I could merge them like I did with Bio-FeatureIO but that's a lot of work. Since it only has 4 commits, could you remove it and I make a fresh clean one?
21:37 rbuels carandraug: eh, i just put you on the owners team, so you can do it
21:37 carandraug the POD for Bio::Range::Atomic and Bio::Location::Atomic are the same
21:37 rbuels carandraug: sounds like something got messed up during the split
21:38 carandraug rbuels, and there is no Bio::Range::* on bioperl-live. Git log suggests there never was
21:38 rbuels carandraug: there's just Bio::Range and Bio::RangeI
21:38 rbuels carandraug: https://github.com/bioperl/biope​rl-live/blob/master/Bio/Range.pm
21:39 rbuels carandraug: https://github.com/bioperl/bioper​l-live/blob/master/Bio/RangeI.pm
21:39 carandraug rbuels, yes. But no Bio::Range::* like it appears on Bio-Range distribution
21:39 rbuels carandraug: probably sheena messed up something in copying stuff
21:39 rbuels and i didn't notice
21:40 rbuels carandraug: the Range/ dir in that repository looks like a copy of the Location/ dir
21:40 rbuels which isn't right
21:40 rbuels carandraug: so just delete that repository if you want and re-do it correctly
21:41 carandraug rbuels, ah! ok. Yes, that was my question. I was wondering if there was some plan to rename the modules and change their API, something like that
21:41 rbuels lol renaming modules and changing APIs is not in the cards for bioperl.
21:42 carandraug rbuels, hmmm... splitting is good but I'm not sure if Bio::Range and Bio::Location should exist in Bio-Seq distribution
21:42 rbuels carandraug: sure, whatever you want
21:43 rbuels carandraug: but then all the annotation stuff would depend on Bio-Seq
21:43 rbuels (is that avoidable?  maybe not)
21:44 carandraug annotation can in theory exist disconnected from a sequence but does it actually exist that way in real life?
21:44 rbuels carandraug: only thing that matters is the module dependency tree
21:44 carandraug rbuels, what's the point of having an annotation if you don't have the thing you're annotating?
21:47 * rbuels has no opinion about that
21:55 byte48 joined #bioperl

| Channels | #bioperl index | Today | | Search | Google Search | Plain-Text | summary