Perl 6 - the future is here, just unevenly distributed

IRC log for #bioperl, 2017-09-12

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Time Nick Message
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01:55 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
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15:26 carandraug pyrimidine: hi
15:52 pyrimidine carandraug: hi, I'm, about to go into an online meeting but I'll have time in about 1 hr
15:52 pyrimidine Had a lot of things pop up this morning, planning for a trip and having to deal with last-minute visa stuff
15:53 carandraug ok. I think I will have 30min in 1 hour
15:53 carandraug by the way, I want to release two new distributions, for TCoffee and Clustalw
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18:00 carandraug pyrimidine: are you back?
18:13 pyrimidine yup, it's been a hellish day :P
18:14 pyrimidine have time?
18:14 carandraug a bit yeah
18:14 carandraug I will have to leave at 19:30
18:15 pyrimidine carandraug: not a problem
18:17 pyrimidine I'm wondering (sort term) whether it would be easier to just split out those modules in the Build.PL listed as having outside dependencies into separate distributions
18:17 pyrimidine *short term
18:18 carandraug you mean in bioperl-run?
18:18 pyrimidine bioperl-live
18:19 carandraug so what prorblem exactly are we discussing?
18:19 pyrimidine splitting out code
18:19 carandraug (I was finishing up the TCoffe and CLustalw out of bioperl-run so I need to change mindset)
18:19 pyrimidine ah, cool
18:20 pyrimidine are you leaving the Bio::AlignIO::clustal parser in bioperl or splitting it out?
18:20 carandraug so you are suggesting split bioperl-live based on a module dependencies rather than actual topic?
18:21 pyrimidine Not completely.
18:21 pyrimidine I think we use that as the general starting point.
18:21 carandraug yes, I am leaving the AlignIO::clustawl on bioperl-live. I am thinking that should go into a bio-alignio distribution
18:22 pyrimidine for example: XML::SAX::Writer is required by one parser (Bio::SeqIO::tigrxml), so split it out
18:22 pyrimidine if we find ones that group together, we would bundle them
18:23 carandraug no, I don't think that's a good idea. That will only make the bundle more difficult to install. Instead, just have a distribution with that module alone.
18:24 pyrimidine carandraug: I agree.  It only makes sense to group them if they are required to go together
18:25 pyrimidine like your PAML module group, right?
18:25 carandraug if we have a bundle bio-difficult, which has all the modules that are difficult to install on it, that will make it harder to develop. If instead we have one distribution for each of them, at least those interested on that module alone will be able to work on it.
18:25 pyrimidine oh yes, I agree with that :_
18:25 pyrimidine :)
18:26 pyrimidine the one I used (tigrxml) is a prime example of this
18:27 carandraug but honestly, I don't want to work on those modules. I have some I have interest on making it easier to develop and install. I want to split those and leave the rest on -live and -run.  The idea is that those interested on working specific module will do the split first
18:27 pyrimidine Moving Bio::Phylonetwork out as one functional distribution would remove a hand full of dependencies
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18:28 carandraug I have no opinion about Bio::Phylonetwork
18:29 pyrimidine That makes sense, though I think reducing the dependency overhead for core installation would go a long way to solving a lot of the current problems
18:30 pyrimidine (reply was to your 'but honestly' comment)
18:30 carandraug there isn't really a core install at the moment. There's is only -live. Which is why I want to have a Bio-Root that provides such a core installation
18:31 pyrimidine ah yes. This is one of the problems with bioperl, namely that no one has bothered to actually define 'what is core'.
18:31 pyrimidine I've had this discussion w/ Hilmar, Jason, Ewan, etc
18:31 pyrimidine I get different answers, but all of them agree that 'core' is more than Root
18:32 pyrimidine it also encompasses Seq, SeqFeature, Annotation: their interfaces and the generic implementations
18:32 carandraug may be. I have been thinking that core should also include a selection of *I classes although I don't have a strong opinion about which ones
18:33 carandraug but it's useful if the distribution is named after one of its modules, which is why I have been calling it Root
18:34 pyrimidine That makes sense; if it were larger than Root I would suggest calling it bioperl-core
18:34 pyrimidine but 'bioperl' to me is core, so it's a bit redundant :)
18:36 carandraug hmm... I think it may be useful to have bioperl only the name of the project. This could then encompass the collection of distributions developed by the project too
18:39 carandraug I have to go
18:39 pyrimidine I think we should look at that as an option, then a Bundle or Task package could mimic an older 'install everything' approach
18:39 pyrimidine ok
18:39 carandraug have you pushed everything to bioperl-run for the last release?
18:39 pyrimidine I'm working through one remaining bug on that, but it should go out today
18:40 carandraug ok
18:40 pyrimidine I think it's essentially fixed though
18:40 carandraug then after that, I would like to push the TCoffee and Clustalw release. I could remove the files.
18:41 carandraug then I will need PhyloBase and WrapperBase and I will be done with bioperl-run
18:42 carandraug not sure if those should go into a Bio-Tools-Run
18:42 carandraug or into a bio-root distribution
18:43 carandraug if you give me a list of modules for that root distribution, I will prepare it
18:43 carandraug bye bye now. Talk to you tomorrow
18:48 pyrimidine bye carandraug!  talk to you tomorrow
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22:29 carandraug pyrimidi_: are you still around?
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