Camelia, the Perl 6 bug

IRC log for #bioruby, 2013-04-21

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All times shown according to UTC.

Time Nick Message
02:34 shevy joined #bioruby
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06:11 pjotrp hi!
06:15 pjotrparrot joined #bioruby
06:17 robsyme Hi Pjotr!
06:17 robsyme I'm looking at biogems.info now.
06:17 pjotrparrot it is a nice day (outside) :)
06:18 pjotrparrot just noticed the IRC channel in not mentioned on the bioruby.org page
06:18 pjotrparrot well, not directly
06:19 robsyme It's a beautiful day here too. Might have to duck away this afternoon for the beach :)
06:19 robsyme I can't get the site to build without errors at the moment, but will add irc link as soon as it assembles cleanly
06:20 pjotrparrot errors?
06:21 pjotrparrot haml, or the script?
06:21 robsyme Just started, so probably something wrong with my setup. One sc
06:21 robsyme *sec
06:26 pjotrparrot I am having my wakeup coffee, will fire up biogems build after. Think I was using 1.9.2 last time
06:26 robsyme Looks like it might be malformed xml at Clayton's blog
06:26 robsyme What is the difference between pjotr and pjotrparrot?
06:26 agarie_ joined #bioruby
06:31 pjotrparrot 2 machines
06:31 robsyme Aha.
06:31 robsyme Does this look broken to you:
06:31 robsyme https://gist.github.com/robsyme/5428695
06:32 pjotrparrot that explains the news feed is so short on the live site
06:32 robsyme I'll just rescue from parsing errors and then just move on to the next blog
06:33 pjotrparrot yeah, that should be the behaviour
06:34 pjotrparrot with a message to stderr
06:37 pjotrparrot I see it too - it is in my mail from the generator
06:37 pjotrparrot Missing end tag for 'hr' (got "body")
06:38 robsyme Yeah, but I'm not sure where this 'hr' is in the feed.
06:42 pjotrparrot probably in the message clayton wrote
06:42 pjotrparrot I'll look into it
06:42 pjotrparrot need to add a few more feeds too
06:50 pjotrparrot mruby looks interesting
06:53 robsyme Wow, I hadn't seen that.
06:53 robsyme http://qiezi.me/projects/mruby-web-irb/mruby.html#
06:53 robsyme Awesome.
06:55 pjotrparrot great find :). That means we can display bioinformatics examples in the browser too
06:57 robsyme Indeed
06:57 robsyme https://github.com/xxuejie/webruby
06:57 robsyme Although I think we'd be limited to the subset of mruby. I'm not sure how far that gets us.
06:58 pjotrparrot the things we do with JS these days...
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07:00 pjotrparrot I am not sure what the subset is,  but it is probably a good idea to stick to it. One reason mruby is there is that Ruby is 'overdesigned'.
07:01 pjotrparrot not that mruby is going to replace ruby
07:02 pjotrparrot but for (new) examples, we should be able to reduce to a minimum instruction set
07:04 robsyme It would be fun to see how far we could get.
07:17 pjotrparrot I intend to fetch latest github commits dynamically
07:17 pjotrparrot for biogems.info
07:18 robsyme And issues?
07:18 pjotrparrot maybe
07:19 pjotrparrot github does not like being hammered
07:21 robsyme How much traffic does biogems.info attract?
07:26 pjotrparrot not much
07:26 pjotrparrot but I think it is critical traffic
07:26 pjotrparrot for one, since it exists bioruby downloads have gone through the roof
07:34 robsyme Does biogems.info rebuild itself every day/week?
07:37 pjotrparrot 3x per day
07:41 pjotrp First pull reguest merged...
07:44 rgirish28 joined #bioruby
07:45 pjotrp about 400 hits per day
07:46 pjotrp incl. search engines etc.
07:47 robsyme Ok
07:50 pjotrp I can mail the log, if you want
07:54 fstrozzi joined #bioruby
07:54 pjotrp hello Italy!
07:54 fstrozzi hello
07:55 fstrozzi how is it going ?
07:55 robsyme Hi Francesco
07:56 fstrozzi HI Rob! How are you ?
07:56 robsyme Fantastic :)
07:56 fstrozzi Great!
08:01 robsyme Hey Pjotr, are you using version 1.0.0 of bundler as the gemfile suggests?
08:01 pjotrp let me check
08:02 pjotrp the build script is create_website.sh
08:02 pjotrp bundler (1.1.5)
08:03 arrigoni joined #bioruby
08:03 pjotrp according to bundle list
08:03 robsyme Cool
08:04 pjotrp the Gemfile needs to be updated, but now jeweler balks
08:04 fstrozzi not really started using Ruby 2.0 guys, but jeweler gave me some troubles even with Ruby 1.9.3 and JRuby
08:05 robsyme Yeah, I'm getting loads of complaints from jeweller. Downgrading to ancient versions of bundler seems to work, but it's obviously not ideal
08:05 fstrozzi yeah
08:05 pjotrp I don't need jeweler with staticmatic, so removed it
08:05 pjotrp testing...
08:05 fstrozzi fine
08:05 robsyme excellent
08:05 pjotrp biogems plugs it in automatically
08:06 fstrozzi hi alberto!
08:06 pjotrp updated on github
08:08 robsyme This is great. Really testing my git-foo :)
08:08 pjotrp Rob and I are working on biogems.info
08:08 pjotrp what are the things we should work on today?"
08:08 pjotrp My main warts are:
08:08 pjotrp 1. The bioruby.org web page
08:09 pjotrp 2. bioruby-gem is failing on Travis
08:09 pjotrp 3. Some biogem.info issues
08:10 pjotrp I would be really happy if these get fixed soon
08:12 pjotrp robsyme, note I do not build the site using staticmatic
08:12 robsyme wait, what?
08:12 pjotrp darn, let me rephrase that :)
08:13 pjotrp ./create_website.sh --test
08:13 pjotrp staticmatic preview website/
08:13 pjotrp visit localhost:3000
08:13 robsyme with bundle exec prefix?
08:13 pjotrp no
08:14 pjotrp should do
08:14 pjotrp moment
08:15 pjotrp yes, that should work
08:17 pjotrp sigh. staticmatic is getting stale. Last update 2010
08:17 robsyme Could think about Rack app. Middleman can do static sites very well.
08:17 robsyme Too much for today though.
08:18 pjotrp yeah - well, as long as staticmatic gets the job done...
08:18 pjotrp Ruby is in version hell
08:19 pjotrp does not bode well - when I look at the Python guys, for example
08:21 robsyme what does the --test flag do? I can't see it getting picked up anywhere.
08:26 pjotrp it is in the Ruby code
08:26 pjotrp just parses a few gems, instead of all
08:27 pjotrp just found out how I can fetch the issue list again
08:27 pjotrp curl https://api.github.com/repos​/pjotrp/biogems.info/issues
08:27 robsyme Sorry, yes.
08:30 pjotrp robsyme: merged
08:35 pjotrp hmmm
08:35 pjotrp merge_rss_feeds': undefined method `items' for nil:NilClass
08:35 robsyme hmm
08:35 robsyme let me check
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08:37 ilpuccio ciao
08:37 fstrozzi ciao
08:40 pjotrp how is the weather in Italy. Here it is so nice it hurts to be inside ;)
08:41 pjotrp Yippie - biogems.info shows issues again (in testing)
08:42 fstrozzi mm weather not so good here
08:42 pjotrp good for hacking ;)
08:43 ilpuccio I can not hack for long today I must visit my bro H
08:43 fstrozzi yeah I have to leave too in about an hour
08:43 ilpuccio btw the main advantage of using jeweler was the creation of the github repo and the version management
08:43 fstrozzi will be good if we can talk of GSoC
08:44 pjotrp sure
08:44 pjotrp ilpuccio, versioning is bundler, right?
08:44 pjotrp github management we could duplicate ourselves - or minimalise it
08:45 pjotrp I think jeweler is moving forward - but josh is very busy
08:46 ilpuccio pjotrp it has only build install release
08:47 pjotrp github api allows fetching the stars through
08:47 pjotrp curl https://api.github.com/repos/pjotr​p/bioruby-logger-plugin/stargazers
08:47 pjotrp cool
08:47 pjotrp ilpuccio: what more do we need?
08:50 ilpuccio not so much I think. easy version upgrade, automatic creation of github repo.
08:50 ilpuccio about github we must choose the library http://developer.github.com/v3/libraries/
08:51 ilpuccio onces we decided it I can star coding. I already looked at bundler code and I must figure out how to ack the templates or adding our customs
08:51 ilpuccio then it is a matter of creating a rake file with our functionalities
08:52 ilpuccio and we need a library for git
08:52 pjotrp ok
08:53 pjotrp how much work is that?
08:54 ilpuccio I would say 3 days full time work for a fresh release
08:54 pjotrp ouch
08:55 ilpuccio maybe less
08:55 pjotrp and hacking jeweler to work again?
08:56 ilpuccio don't know I must try
08:56 ilpuccio there is a patch on github
08:58 ilpuccio let's do in this way, today I try to patch jeweler we'll se what came out.
08:58 ilpuccio actually it is just a matter of supporting ruby 2.0
08:59 ilpuccio about GSoC
09:00 pjotrp 2.0 support will come
09:00 pjotrp I think enough people use jeweller
09:03 pjotrp maybe biogem can stick to 1.9.x until 2.0 is working with jeweller
09:03 pjotrp I sure would like to get travis set to green again!
09:05 ilpuccio ok so we can fix bugs for 1.9 and then move to 2.0
09:07 ilpuccio GSoC, Alberto is going to present to sciruby a proposal about data mining
09:08 pjotrp awesome
09:08 ilpuccio I didn't see much attention to it but I was to have a proposal similar to the Clayton
09:09 pjotrp agree on fixing for 1.9
09:09 pjotrp I think it is good enough
09:10 pjotrp Coding 3 days to help just a few people is too much
09:11 ilpuccio ok and maybe after that we could star moving forward and shift from jeweler
09:12 pjotrp let's keep some momentum this year
09:12 pjotrp when things are broken, everything deteriorates
09:13 fstrozzi agree
09:13 fstrozzi how many gsoc proposals have arrived from students ?
09:14 pjotrp it is just starting
09:14 fstrozzi ok
09:24 ilpuccio i must leave
09:24 pjotrp enjoy the rain
09:24 ilpuccio ahahah
09:24 ilpuccio :(
09:25 pjotrp I'll keep going - maybe a 2 hour bike run in the afternoon
09:41 fstrozzi I have to leave too
09:41 fstrozzi see you guys
09:41 fstrozzi : )
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12:10 robsyme Are you still around pjotr?
12:36 pjotrp yes
12:36 pjotrp going for a bike run shortly
12:36 pjotrp been fixing biogems.info - it is looking better
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13:00 joachim hello. sorry, i am late to the party.
13:02 pjotrparrot hi
13:04 pjotrparrot joachim: some work has been done, especially by Rob and myself
13:04 joachim i am fixing my biogems gem "biointerchange" today. i broke it this week. i check how those changes will show up on the reworked biogems site. if i encounter workflow issues, then i put them in the biogems wiki again...
13:04 joachim sounds okay?
13:07 pjotrparrot great
13:07 pjotrparrot http://www.biogems.info/ is showing github stargazers now :)
13:07 pjotrparrot they are not all fetched because github allows 60 queries per hour(!)
13:08 pjotrparrot will fix that soon using authentication
13:08 pjotrparrot also the news feed is showing more RSS sources now
13:11 robsyme Heya joachim. Had to duck away to get some food. Great work Pjotr.
13:17 joachim hi rob!
13:17 joachim is anyone working on refactoring the web-site layout? i got quite some experience with bootstrap from twitter over the last two years and it can spice things up quite a bit. just wondering...
13:20 robsyme I'm also a huge fan of frameworks like bootstrap.
13:21 robsyme I'm just finishing up a redesign built on Zurb Foundation (preview.robsyme.com - all critique welcome).
13:22 joachim yeah. i was skeptical at first, but there is a new version of bootstrap out now (well, not that new anymore...) which really makes it easy to create a slick looking site...
13:23 joachim rob: nice animated dna "worms"... :)
13:24 robsyme Cheers :)
13:30 robsyme I think it would be nice if biogems also promoted github.com/helios/bioruby-gem itself (show basic install and gem creation etc).
13:34 robsyme Perhaps give this page more attention: http://www.biogems.info/howto.html
13:35 robsyme I suppose there is a list of existing issues to tackle as well: https://github.com/pjotrp/biogems.info/issues
13:45 robsyme I've got to go now, but I'll be back here regularly for the next couple of weeks (the prof is out of the country). Thanks for organising Pjotr!
13:46 robsyme Now that I've got the hang of the biogems.info base, expect more pull requests!
13:46 robsyme Night joachim.
13:47 joachim see you.
13:47 robsyme left #bioruby
14:02 pjotrparrot great :)
14:03 pjotrparrot I'll me sure to keep involved too
14:03 pjotrparrot me? make
14:06 pjotrparrot the way forward with the website is to create a prototype
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15:24 michaelbarton Hi
15:25 michaelbarton Is there anything to help with?
15:38 michaelbarton Where is biogem.info hosted?
15:44 arrigoni joined #bioruby
15:50 pjotrparrot source is on github
15:50 pjotrparrot https://github.com/pjotrp/biogems.info
15:51 pjotrparrot as well as issues
15:51 pjotrparrot but it may be interesting on fixing bioruby-gem itself for 1.9
15:52 pjotrparrot which is at https://github.com/helios/bioruby-gem
15:52 pjotrparrot with issues ;)
16:08 michaelbarton I think I found the ivars problem
16:09 pjotrparrot it has to do with gem version, right?
16:09 michaelbarton Let me push a fix quickly
16:10 michaelbarton I have to leave now, but this might be a start
16:10 pjotrparrot tnx!
16:10 michaelbarton https://github.com/michaelbarton/biogems.info/c​ommit/23332476c938205b8350fa5a5a00696d6d5e4288
16:11 michaelbarton It still fails but it's a general idea thing
16:11 michaelbarton *think
16:11 michaelbarton Sorry but I have to go
16:11 pjotrparrot ok
16:11 michaelbarton Might be a start
16:11 michaelbarton Bye!
16:11 pjotrparrot bye
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19:35 michaelbarton I'll try to continue to tackle this ivars problem
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20:40 michaelbarton I've started trying to simplify the generation of all the required files
20:40 michaelbarton https://github.com/michaelbarton/b​iogems.info/tree/refactor/rakefile
20:50 michaelbarton Replace two scripts with a Rakefile - https://github.com/michaelbarton/bio​gems.info/compare/refactor;rakefile
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