Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-08-06

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All times shown according to UTC.

Time Nick Message
04:32 rojasm joined #bioclipse
05:46 egonw joined #bioclipse
06:18 Gpox joined #bioclipse
07:34 olas joined #bioclipse
07:34 olas hi all
07:34 zarah hi olas
07:34 olas zarah: dobar dan
07:34 zarah olas: please rephrase or stop trying to be witty :)
07:34 olas oh
07:37 rojasm joined #bioclipse
07:52 egonw joined #bioclipse
08:53 shk3 joined #bioclipse
08:56 masak joined #bioclipse
09:08 CIA-49 bioclipse: ospjuth * r6484 /bioclipse2/trunk/plugins/net.bi​oclipse.ui/META-INF/MANIFEST.MF: Updated version to alpha02.
09:09 masak olas: shouldn't that be alpha03?
09:11 olas sorry
09:11 egonw hehehe
09:11 olas had forgotten to commit that yesterday :-(
09:11 olas so missed the tag
09:12 olas alpha03 scheduled for friday :-)
09:12 * egonw likes this release soon, release often
09:12 olas which means I will update the Update Site then
09:13 masak olas: I mean, the next release is alpha03. might one not change the MANIFEST.MF to reflect that in the svn repository already, so that we don't have to remember it the day of the release?
09:14 olas masak: I like your idea
09:14 olas but only on the plugins that needs updating
09:14 masak I'd say net.bioclipse.ui is such a plugin
09:14 olas we only ship updated plugins in the updated features and feature-patches
09:14 olas masak: I agree
09:14 olas what is the difference with a generic solution and a general solution?
09:16 masak very slight
09:16 olas is there any?
09:16 masak but "generic solution" sounds more professional
09:16 CIA-49 bioclipse: ospjuth * r6485 /bioclipse2/trunk/plugins/net.bi​oclipse.ui/META-INF/MANIFEST.MF: Updated version to alpha03.
09:16 egonw I'd guess:
09:16 egonw generic: works for all
09:16 egonw general: applied to all
09:16 masak egonw: could be.
09:19 olas egonw: how is the atom typing going? Is it merged with trunk yet?
09:19 olas and did you test it with OB?
09:20 egonw olas: no, patch is awaiting review
09:20 egonw olas: not testted against OB yet
09:20 olas ETA?
09:20 egonw olas: email Rajarshi and tell him to review the patch :)
09:20 olas and testing?
09:20 egonw working on that
09:20 olas I know, that's not fun
09:21 olas but important
09:21 egonw no, and need to do that in trunk
09:21 egonw so, awaiting this review
09:21 gilleain joined #bioclipse
09:21 olas ok
09:21 egonw so, ping rguha
09:21 olas rguha works a lot
09:21 olas I'm sure he'll review the patch soon
09:21 egonw rguha and I had a very nice hack sessions last nite
09:22 egonw on CDK
09:22 olas aah
09:22 olas did you solve a lot?
09:22 egonw no
09:22 egonw :)
09:22 olas haha
09:22 olas but it was nice :-)
09:22 egonw we updated the APIs to support for (IAtom atom : molecule.atoms()) {}
09:22 egonw based on patches provided by Matt and Thomas
09:22 egonw (both who you do not know yet)
09:23 olas I see
09:23 egonw gilleain, olas:
09:23 egonw the key to this CML problem might be detection of @convention="" content
09:23 egonw not so much used yet
09:23 egonw but you should certainly include that in the scanner
09:23 egonw some people are using it...
09:24 egonw and CMLSpect certainly is
09:24 olas the only think I'd like to stress is that it must be super-fast
09:24 gilleain Definately.
09:24 egonw :)
09:24 egonw regarding that...
09:24 egonw don't do SAX
09:24 egonw use a pull parser
09:24 gilleain Okay.
09:24 egonw there is example code in the CDK
09:25 gilleain How extensible do you think it should be?
09:25 olas that's not overly important I think
09:25 egonw gilleain: not important
09:25 olas we can always implement new describers
09:25 gilleain So specific, and fast, rather than general and slow.
09:25 egonw I made the CDK CML reader super extendible
09:25 egonw but it's hardly used
09:25 olas gillean: right :-)
09:26 gilleain Okay, that's good to know.
09:26 * egonw has the feeling that gilleain is a real good addition to Chris' team :)
09:26 egonw gilleain++
09:27 gilleain Thanks.
09:27 egonw gilleain: looking forward to meeting you in person in a few weeks
09:28 gilleain Yes, that will be good.
09:28 olas egonw: I take it you will not come for EuroQSAR 2008?
09:28 egonw olas: no
09:28 egonw when was that?
09:29 egonw after Oct 1st?
09:29 olas 22-26 sept
09:29 egonw ah, no
09:29 egonw won't make that
09:29 olas pity
09:29 egonw yeah
09:29 olas Chris will be there
09:29 olas amongst others
09:29 olas some people from AZ will be there too
09:29 olas I will demo to them
09:29 egonw where is it?
09:29 olas which reminds me
09:29 olas Uppsala
09:30 egonw should be free for a dinner or two
09:30 egonw would love to meet up, particularly with the AZ people
09:30 olas when will you move in?
09:30 olas I need to implement QSAR in Bioclispe by then :-)
09:30 egonw Chris I'll see anyway some day again
09:30 olas we should try to set that up then
09:30 egonw 12 is our NL house packed up and moved into the truck
09:30 egonw they deliver on ...
09:30 olas we could have a Bioclipse dinner some evening
09:31 egonw a week later or so...
09:31 olas I'll arrange that
09:31 egonw and a Blue Obelisk meeting too
09:31 egonw with three Blue OBelisk awards winners around, one has too :)
09:31 olas haha
09:31 olas yes
09:31 olas sounds good
09:32 olas I don't think the conference will be overly good
09:32 egonw oh? :(
09:32 olas so I'm mostly interested in off-hours
09:32 egonw not as much audience, not being on a cruise ship?
09:32 olas Don't know
09:32 olas there are many important actore there
09:32 egonw and without turkish belly dancers (year before that...)
09:32 olas but, you know, a whole week :-(
09:33 * olas is tired of listening to presentations
09:33 egonw yeah, I will check if I can join in one conference day or so...
09:33 olas I'm mostly in it for the social networking
09:33 olas and to present a poster "QSAR in Bioclipse"
09:33 olas hmm
09:33 olas need to work on that
09:33 olas and the pcores
09:34 egonw cool social programme :)
09:34 olas oh?
09:36 egonw nice speaker line up too
09:40 jonalv joined #bioclipse
09:45 jonalv moin
09:45 zarah hi jonalv
10:07 * olas is off for a fancy lunch on the Kings Island (Kungsholmen) in Stockholm
10:12 jonalv joined #bioclipse
10:45 Laszlo joined #bioclipse
10:47 Laszlo left #bioclipse
10:57 gilleain What is the xom plugin used for? It's classes don't seem to be used anywhere...
10:59 masak gilleain: I believe olas can answer that when he gets back
10:59 gilleain Ah, okay, thanks.
11:00 shk3 it is just for providing the libraries
11:00 shk3 they should be used in cml plugin
11:01 shk3 and this is used e. g. in spectrum
11:01 egonw shk3: please check #cdk
11:01 gilleain hmm. I'll take a look at spectrum.
11:04 shk3 net.bc.cml depends on xom and uses it
11:08 jonalv cd q
11:21 masak jonalv: ~/q$ _
11:21 jonalv ls
11:22 masak jonalv:
11:22 jonalv mkdir r
11:22 masak jonalv:
11:22 jonalv cd r
11:22 masak jonalv: r
11:22 masak d'oh!
11:22 masak jonalv: ~/q/r$
11:22 jonalv vim test.pl
11:23 masak jonalv: [2;1H~[3;1H~
11:24 jonalv *lol
11:24 masak :)
11:24 masak jonalv: writing Perl, are we? :)
11:27 jonalv what? no I would never
11:27 jonalv wouldn't know how to
11:30 masak it's like riding a bike
11:33 CIA-49 bioclipse: jonalv * r6486 /bioclipse/trunk/playground/plugins/ (net.bioclipse.expression/ net.bioclipse.expression.tests/): Removed net.bioclipse.expression. It has a new home in the Brunn repo
11:33 jonalv masak: how can programming be like riding a bike?
11:33 masak jonalv: how can flying a helicopter be like riding a bike? I don't know.
11:44 CIA-49 bioclipse: carl_masak * r6487 /bioclipse2/trunk/plugins/net.bioc​lipse.biojava.ui/src/net/bioclipse​/biojava/ui/editors/Aligner.java:
11:44 CIA-49 bioclipse: [Aligner] various smaller tweaks to selection semantics
11:44 CIA-49 bioclipse: changed selection color to semi-transparent dark, jonalv++
11:44 masak feel free to play around with the new selection behavior and tell me how it feels.
11:45 masak in particualt, I hope to have eradicated all zero-area selections now
11:45 masak reports on edge case appreciated
12:18 olas masak: I will try it
12:18 olas what are the limits now?
12:18 CIA-49 bioclipse: ospjuth * r6488 /bioclipse2/trunk/bioclipse-updatesite/: Initial import.
12:19 olas (so I know where to push)
12:19 masak olas: there used to be a problem with zero-area selections.
12:19 masak I hope to have removed it.
12:19 masak beyond testing for that, please just play around and tell me your impressions
12:20 olas sure
12:20 masak the file opsd.fasta is the one I use to test things
12:20 masak it's in sequences/ in data.sampledata
12:20 olas right
12:20 olas masak: are there any actions?
12:20 masak olas: no.
12:20 olas like, different colorings?
12:20 olas ok
12:21 * olas is looking forward to testing it
12:21 olas hmm
12:21 olas is it a bad idea to have the update-site on SVN?
12:21 olas I thought it'd be a good idea
12:21 olas but it takes quite some time to commit...
12:21 olas hmm
12:22 olas maybe not the built features?
12:22 olas what do you think?
12:22 jonalv no probably not...
12:22 olas ok
12:22 olas canceling
12:22 * olas hates subversion
12:23 olas it wonät stop sending
12:23 masak heh
12:23 masak olas: I bet you're talking about subclipse again, not svn
12:23 olas right
12:23 olas definitely
12:23 olas subversion is nice!
12:24 olas subclipse sucks
12:24 * masak thought so
12:24 jonalv :)
12:25 jonalv stop using subclipse for big things then :)
12:25 olas good idea
12:25 olas jonalv: donät forget the skype conf at 16
12:25 olas grr
12:25 olas don't
12:26 jonalv olas: right thnaks for remining me
12:26 jonalv *reminding
12:26 olas let's remind each other at 16
12:26 olas hmm
12:26 olas do we have a skype "number" to call?
12:26 masak hm, maybe a zarah @remind feature? :)
12:26 olas would be nice
12:26 masak zarah: how about a @remind feature?
12:26 zarah masak: excuse me?
12:26 masak zarah: I said, how about a @remind feature?
12:26 zarah masak: you've just exceeded my capabilities :/
12:27 masak :)
12:27 jonalv olas: not sure
12:27 jonalv olas: I think so
12:27 olas zarah: slap himself
12:27 * zarah orders her trained monkeys to punch himself
12:27 olas hmm
12:27 olas @slap herself
12:27 zarah *SMACK*, *SLAM*, take that herself!
12:27 olas @slap herself
12:27 zarah stop telling me what to do
12:27 olas ?
12:28 olas @slap olas++
12:28 zarah shame on you, olas, giving yourself karma like that
12:28 zarah *SMACK*, *SLAM*, take that olas++!
12:28 jonalv zarah: price heself
12:28 zarah jonalv: please rephrase or stop trying to be witty :)
12:28 masak olas: that doesn't work
12:28 olas hmm, did see that
12:28 jonalv zarah: help
12:28 zarah jonalv: avaliable commands are clear-messages google help hi karma messages restart seen slap tell thanks
12:28 masak help
12:28 zarah masak: avaliable commands are clear-messages google help hi karma messages restart seen slap tell thanks
12:28 masak gotta fix that
12:29 olas thanks
12:29 olas @thanks
12:29 zarah you're welcome, olas :)
12:29 olas zarah: for what?
12:29 zarah olas: excuse me?
12:29 olas zarah: are you just a bot?
12:29 zarah olas: I did not understand that
12:29 CIA-49 bioclipse: ospjuth * r6489 /bioclipse2/trunk/bioclipse-updatesite/ (23 files in 3 dirs): Added contents as of alpha02. Seems reasonable to have this on SVN as well.
12:31 CIA-49 bioclipse: carl_masak * r6490 /bot/trunk/zarah.pl: [zarah] @help is no longer a bare command
12:31 CIA-49 bioclipse: carl_masak * r6491 /bioclipse2/trunk/plugins/net.bioc​lipse.biojava.ui/src/net/bioclipse​/biojava/ui/editors/Aligner.java: [Aligner] selections can now be moved
12:31 jonalv help
12:31 zarah jonalv: avaliable commands are clear-messages google help hi karma messages restart seen slap tell thanks
12:31 jonalv @restart
12:32 zarah joined #bioclipse
12:32 jonalv help
12:32 jonalv @help
12:32 masak zarah++
12:32 zarah jonalv: avaliable commands are clear-messages google help hi karma messages restart seen slap tell thanks
12:32 olas @help jonalv
12:32 zarah olas: avaliable commands are clear-messages google help hi karma messages restart seen slap tell thanks
12:32 jonalv thanks masak
12:32 CIA-49 bioclipse: ospjuth * r6492 /bioclipse2/trunk/bioclipse-updatesite/ (. features/ plugins/): Removed features and plugins dir. Can be built from site.xml.
12:32 jonalv @thanks masak
12:32 zarah you're welcome, jonalv :)
12:32 jonalv lol
12:32 masak hm
12:33 egonw @seen rguha
12:33 zarah I have not seen rguha
12:34 jonalv @seen zarah
12:34 zarah jonalv: I'm right here
12:37 CIA-49 bioclipse: carl_masak * r6493 /bot/trunk/zarah.pl: [zarah] now thanks a person if such is supplied
12:38 olas @thank masak
12:38 olas @thanks masak for that
12:38 zarah you're welcome, olas :)
12:38 masak @update
12:39 zarah joined #bioclipse
12:39 olas @thanks masak for that
12:39 zarah masak for that: olas says thank you
12:39 jonalv thanks masak++
12:39 jonalv @thanks masak++
12:39 zarah masak++: jonalv says thank you
12:39 masak :)
12:39 olas @thanks olas++
12:39 zarah shame on you, olas, giving yourself karma like that
12:39 zarah olas++: olas says thank you
12:39 olas karma olas
12:39 zarah olas has a karma of 1
12:39 masak olas: that did not work
12:39 olas 1!?!?!?
12:40 masak olas: we lost the original karma file the other day
12:40 masak will merge as soon as we get it back
12:40 olas how?
12:40 olas mm
12:40 masak olas: addition.
12:40 jonalv gatekeepter lost power
12:40 masak olas: still, there's no possible way you can give yourself karma. I promise.
12:40 jonalv zarah is on pele now
12:40 zarah jonalv: I did not understand that
12:40 jonalv zarah: oh shut up
12:40 zarah jonalv: :)
12:48 jonalv olas: did you find any skupe name?
12:49 CIA-49 bioclipse: carl_masak * r6494 /bot/trunk/zarah.pl: [zarah] refuses to thank a person from erself
12:49 egonw guys, we're not enough looking for Bioclipse on google: http://www.google.com/insights/search/#cat=&q​=bioclipse&geo=&date=&clp=&cmpt=q
12:49 zarah egonw's link is also http://tinyurl.com/6ydgly
12:49 masak @update
12:50 egonw @google bioclipse download
12:50 zarah joined #bioclipse
12:50 egonw hahah
12:50 egonw bad timing
12:50 egonw @google bioclipse download
12:50 masak :)
12:50 zarah egonw: I can't do that; complain with masak and jonalv
12:50 masak egonw: sorry :/
12:50 masak not there yet.
12:50 egonw ah, that explains ;)
12:50 masak @thank egonw
12:50 zarah egonw: masak says thank you
12:50 masak @thank masak
12:50 zarah masak: you can thank yourself!
12:50 masak @thank me
12:50 zarah masak: you can thank yourself!
12:50 masak :)
12:50 masak zarah++
12:58 olas @thank olas++
12:58 zarah shame on you, olas, giving yourself karma like that
12:58 zarah olas: you can thank yourself!
12:58 olas thank you olas
12:58 olas zarah: dz
12:58 zarah you're welcome, olas :)
12:58 rojasm joined #bioclipse
13:07 CIA-49 bioclipse: ospjuth * r6495 /bioclipse2/trunk/bioclipse-updatesite/ (artifacts.xml content.xml): Updated update-site.
13:15 jonalv olas: sry did you or did you not have the skype name?
13:17 olas jonalv: I asked you
13:17 olas I have none
13:17 jonalv troublesome... :)
13:18 olas oh
13:18 olas found it
13:18 olas daveneti
13:19 gilleain joined #bioclipse
13:20 * jonalv <- maing tea
13:20 olas hi gilleain
13:20 gilleain hi
13:20 zarah hi gilleain
13:20 olas hi zarah
13:21 olas gilleain: in respond to your email:
13:21 gilleain yes,
13:21 olas you could also implement a new describer
13:21 olas extends XMLContentDescriber
13:21 olas whatever you like
13:21 olas let me know if I can assist
13:21 gilleain Okay. I've been looking at pullparsers.
13:22 olas but I'm no good with XML, better ask eginw there
13:22 gilleain Oh, right. Okay.
13:22 olas egonw that is
13:22 gilleain I'll give it a go, and let you know if I run into difficulties.
13:22 olas sounds excellent
13:22 olas looking forward to testing it
13:23 olas are all OK with requiring -Xmx1024M with Bioclipse by default?
13:24 olas I have a use case that requires some memory
13:24 olas egonw,jonalv,masak: what do you think?
13:25 egonw people with less memory will not run into problems?
13:25 olas they will I guess
13:25 olas and I assume that is the problem
13:26 olas hmm
13:26 olas maybe not a good idea after all
13:26 olas just don't know how to deal with the case of ONE product (with -Xmx settings) and multiple settings requiring different amount of memory
13:27 olas can -Xmx be set at runtime?
13:29 masak olas: my guess is no
13:29 jonalv olas: there might be soime other setting that's greedy but I don't know
13:31 shk3 question:
13:31 shk3 how is child parsing handled in bc2?
13:32 shk3 will there be/is there a system similar to bc1?
13:32 olas shk3: no
13:32 olas I suspect you refer to teh Navigator expanding into children?
13:33 olas or are you talking about the Outline showing children to the open editor?
13:33 olas shk3: please describe your use case
13:34 shk3 no use case
13:35 shk3 net.bc.xom has code only used for child handling in bc1
13:35 shk3 so I am wondering if this should be kept in bc2
13:35 shk3 use case would be e. g. the specmol resource
13:37 olas that does not tell me much
13:37 egonw olas: navigator stuff
13:37 olas please explain more elaborate what you want to achieve
13:37 egonw he's refering to the childresourcecreator EP I set up for BC1
13:37 olas ok, expand in navigator
13:37 olas that is skipped in bc2
13:37 olas we use the Eclipse commonnavigator
13:37 egonw obsolete, better
13:37 olas right
13:38 olas the code for parsing can be re-used
13:38 olas but the actual hook-in into Bioclipse is done via some other extension points
13:39 olas Gpox++ promised to look into keeping track of parsed models since we want them to be shared between Navigator and any open Editors
13:39 shk3 I just looked at the xom plugin, it just contains the library and some unused code
13:39 shk3 so I thought to merge it into cml plugin
13:39 shk3 in bc1, the code was just used in child handling
13:39 shk3 but if we need this, we can put it in cml as well
13:40 shk3 so I think I will do this
13:40 shk3 one less plugin is good
13:40 egonw no, please don't
13:40 egonw I was using xom for other plugins too
13:40 shk3 ok
13:40 egonw where I don't depend on CML
13:40 egonw one less plugin is *not* good
13:40 egonw modularization is much better
13:40 shk3 depends on
13:41 shk3 looked like only be used in cml
13:41 egonw no, don't think so
13:41 egonw modularizatino is always better
13:50 * olas hates plugin explosion
13:51 masak it's the Eclipse way!
13:51 egonw explosions are cool!
13:51 egonw particularly if they are not too close
13:51 gilleain It does seem odd that it is a plugin, and not in the core, if it is used by multiple other plugins.
13:52 egonw core should not be a big monolitic thing
13:52 egonw then we can't share things with other projects
13:52 egonw xom is a 3rd party lib
13:52 gilleain Sure, I see.
13:52 egonw a quite general one, btw
13:52 egonw it'll be increasingly used
13:53 gilleain I've been looking at the webpages for it, its' interesting.
13:53 egonw ideally, the xom.nu people themselves would maintain the plugin...
13:53 egonw yeah, it's a nice DOM
13:54 gilleain By the way, do you have a suggested pull-parser?
13:54 gilleain There's a sun one, and this xmlpp one.
13:55 egonw yes, for the CDK I use...
13:55 egonw mom, looking it up ... :)
13:55 egonw xpp3
13:55 egonw http://www.extreme.indiana.edu/xgws/xsoap/xpp/
13:55 zarah egonw's link is also http://tinyurl.com/9ss2l
13:56 gilleain right, yes, that's the one I've been looking at.
13:56 gilleain my only worry was that development seemed to have stopped in 2006, but it might have just reached near-completion.
13:58 egonw for me it does what it should do...
13:58 gilleain I see the jar in the cdk referenced libs. I'll use it, thanks.
13:59 egonw it's used in the PubChem XML readers
14:00 gilleain Like PubChemXMLHelper, yes.
14:03 CIA-49 bioclipse: carl_masak * r6496 /bioclipse2/trunk/plugins/net.bioc​lipse.biojava.ui/src/net/bioclipse​/biojava/ui/editors/Aligner.java: [Aligner] fixed typo in expression; commented heavily
14:21 olas what is the ' called?
14:21 gilleain Quote mark, i think.
14:21 olas thx
14:22 masak olas: it's "quote" or "apostrophe"
14:39 ilogger2 joined #bioclipse
15:21 olas left #bioclipse
16:52 CIA-49 bioclipse: shk3 * r6497 /bioclipse2/trunk/plugins/n​et.bioclipse.spectrum/src/ (7 files in 2 dirs): the synchronisation of pages seems to work
16:55 malick left #bioclipse
17:16 olas joined #bioclipse
17:16 olas hi
17:16 zarah hi olas
18:44 CIA-49 bioclipse: ospjuth * r6498 /bioclipse2/trunk/plugins/net.b​ioclipse.ui/bioclipse.product: Added -Xmx256M to VM args.
19:39 egonw joined #bioclipse
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21:42 rojasm joined #bioclipse
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