Perl 6 - the future is here, just unevenly distributed

IRC log for #bioperl, 2017-09-13

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01:54 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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14:07 carandraug pyrimidine: ping
14:08 pyrimidine good morning (well, at least here in Illinois)
14:09 carandraug pyrimidine: well let's use UGT
14:10 carandraug UGT is [0] Universal Greeting Time: http://www.total-knowledge.com/~ilya/mips/ugt.html [1] When someone joins, it's morning. When someone parts, it's evening.
14:10 pyrimidine carandraug: works for me
14:15 carandraug pyrimidine: so let's talk about new distributions. What's the plan?
14:16 carandraug I have a Clustalw and TCoffee distributions ready to go
14:16 carandraug also, I was trying to understand bioperl github teams
14:16 pyrimidine are these from only bioperl-run, or do they include bioperl-live code?
14:17 carandraug pyrimidine: they include one example file from bioperl-live
14:17 pyrimidine script or data?
14:17 carandraug example
14:17 carandraug not a script
14:18 carandraug which on the new release would not exist since examples are documentation, and documentation goes into the module POD
14:18 pyrimidine oh, you mean in the 'examples' folder under 'align'
14:18 carandraug it was quite a long example 'examples/align/clustalw.pl'
14:19 carandraug yes, on the examples folder
14:19 pyrimidine the clustalw.pl script
14:19 pyrimidine ok
14:19 carandraug so they are not even installed in bin like the stuff under scripts
14:20 carandraug but as I mentioned yesterday, I will need to have a few more modules out of bioperl-run. These declare the interfaces, so I'm not sure what to do about them. Should they go into a Bio-Root distribution?
14:20 pyrimidine I would go ahead and pull those from bioperl-live and bioperl-run.  I can hold on a 1.7.2 release for bioperl-run until those are split out
14:21 carandraug I don't mind at all. You could make a 1.7.2 release now, and a 1.7.3 release tomorrow (not sure how difficult is to make a release from the -live and -run repos, the others use dzil, is very quick)
14:21 pyrimidine it's not terribly difficult, but no need if we're about to split out more code.
14:22 carandraug pyrimidine: so you're ok with me releasing https://github.com/bioperl/Bio-Tools-Run-Alignment-TCoffee and https://github.com/bioperl/Bio-Tools-Run-Alignment-Clustalw as they are now?
14:22 pyrimidine I would place the core wrapper modules into a different repo, not back in Bio-Root, since they are helper modules
14:23 pyrimidine yes, and 1.7.2 should be fine
14:24 pyrimidine Can you announce this on the list?
14:25 carandraug pyrimidine: what do you mean with core wrapper modules?
14:25 pyrimidine WrapperBase etc
14:25 carandraug so, where should they go? Bio-Tools-Run ?
14:25 pyrimidine yeah, I think that's fine
14:26 pyrimidine can you check whether there are bioperl-live modules still relying on them?  Otherwise they'll create a circular dependency
14:32 pyrimidine carandraug: a quick check seems to confirm WrapperBase and co. not used in bioperl-live (there are some hits in Bio::Root modules, but they are interface checks or in documentation)
14:32 carandraug pyrimidine: doesn't look like there's anything on bioperl-live that's dependent on PhyloBase, WrapperBase, AssemblerBase, or AnalysisFactory.
14:33 carandraug yes, I found them mentioned on bioperl-live documentation
14:33 pyrimidine carandraug: so, technically those can be split out as well, and we can add them as a dependency to bioperl-run
14:33 pyrimidine works for me
14:33 carandraug pyrimidine: however, why shouldn't they go in the same distribution as the rest of bioperl interfaces?
14:33 pyrimidine they could, but they are also quite specific to the tool wrappers
14:34 pyrimidine almost a separate set of helper modules
14:35 carandraug pyrimidine: but tool wrappers are also part of bioperl project.  So bioperl has a distribution that specifies interfaces which other bioperl modules implement.
14:36 pyrimidine right, but if we ever decided to change their functionality, their versioning (if packaged on their own) would be independent of the other core modules.
14:37 pyrimidine It really could go either way to be honest
14:38 carandraug pyrimidine: why would we want that? Sounds to me like it would be better to have all interfaces versioned together
14:39 pyrimidine I'm okay with that.  I think these were originally moved out of core into bioperl-run b/c they were only used for the bioperl-run wrappers
14:40 pyrimidine but if we want core to represent all the interfaces that works for me
14:40 carandraug ok. So let's say we then have a separate distribution for ontology. Will OntologyI go into the the bioperl interfaces distribution or into Bio-Ontology?
14:42 carandraug by the way, can you give me permissions on PAUSE to push the TCoffee and Clustalw distributions?
14:43 pyrimidine I think it would make sense to keep OntologyI in core.  Though to be honest I dont like the Java-like interfaces we have
14:44 pyrimidine I do agree w/ Lincoln's assessment of them (it's a 'contract' that defines the interface), just wish there were something else at the low level we could use instead.
14:45 pyrimidine on PAUSE now
14:47 pyrimidine Ok, you should have co-maint now
15:10 pyrimidine AFK FOR A BIT
15:13 pyrimidine Wow, that was a little shout-y
15:14 carandraug we had an emergency on the systems. Still not fixed, I might be gone for the rest of the day
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15:58 carandraug pyrimidine: problem solved. Do you have time to continue now?
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19:19 pyrimidine carandraug: missed your reply, good luck with the systems fun
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