Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-08-08

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

All times shown according to UTC.

Time Nick Message
05:07 masak joined #bioclipse
06:42 malick joined #bioclipse
07:05 Gpox joined #bioclipse
07:25 thomas_ku joined #bioclipse
07:42 egonw joined #bioclipse
07:52 olas joined #bioclipse
07:53 olas hi all
07:53 zarah hi olas
07:53 masak hi olas
07:53 zarah masak: You have new messages. Write '@messages' to read them.
07:53 masak @messages
07:53 zarah masak: olas said masak++ for icons!
07:53 zarah masak: olas said Feedback on icons: IMO carbon is too black compared to red/blue (who look a bit too bright IMO). It is also hard to distinguish between single-double-tripple bonds due to too thin lines (more focus on bonds than atoms in that case). But a very good start!
07:53 masak olas: sounds reasonable.
07:54 masak olas: how would I do to see the icons myself. it's easier to see what you mean if I see them in action.
07:54 olas was just about to suggest that
07:54 olas open a 2D mol in JCP
07:54 olas icons are in outline
07:55 olas I will today release a ne version of Bioclipse on SF (if all goes well)
07:55 masak olas: do you have an example of a 2D molecule in data,sampledata?
07:55 olas the new versioning will be 2.0.0.A20080808
07:55 olas masak: yes
07:55 masak olas++ # early and often
07:55 olas many
07:55 masak olas: such as?
07:55 olas under the folder 2D
07:55 masak oki
07:56 olas hm 2DStructures
07:56 olas any comments on the new versioning?
07:56 olas A is for alpha
07:56 olas Eclipse use M for milestones
07:57 olas but since we don't have milestones...
07:57 olas i suggest an A
07:57 masak olas: how will it sort compared to the old versioning?
07:57 olas not at all
07:57 olas it replaces
07:57 masak I mean...
07:57 olas hence we need a new BC on SF
07:57 olas yes?
07:57 masak will the version comparing thing in the downloader consider it a newer version, or and older?
07:58 olas no idea
07:58 masak that's all that matters
07:58 olas the idea is not to be backwards compatible at this point
07:58 masak so you don't want the newer version to supercede the older one?
07:58 olas in what respect?
07:58 masak when Bioclipse searches for updates, you don't want it to find your new version?
07:59 olas no
07:59 masak ok
07:59 olas I will not care about this at this point
07:59 masak I have no further questions. :)
07:59 olas hence we need to download a new version from SF
07:59 olas THEN the update site works
07:59 olas masak: it's either that or stick to alpha0X versioning
08:00 olas BUT we need a new version of SF anyway
08:00 olas logging is now fixed
08:00 olas and we need to add -Xmx256m to program arguments
08:00 masak olas: yes, it's either one or the other
08:00 olas I tested this and it cannot be contributed via update site
08:00 masak 256 Mb seems reasonable
08:00 olas good
08:00 olas I figured so too
08:01 olas if people want more, they can add it in the file bioclipse.ini
08:01 masak I agree about the colored atoms being too bright. I think the carbon is perfect, though
08:02 olas good
08:02 olas and the bonds?
08:02 olas you agree it's hard to see if it's 1,2 or 3?
08:02 masak olas: hold on, I'll find a molecule with triple bonds
08:02 gilleain joined #bioclipse
08:02 masak yes, it's too hard.
08:02 olas hi gilleain
08:03 gilleain hi, saw the bug report.
08:03 olas masak: I thought so too
08:03 olas well, it was just to say that you work on contenttypes :-)
08:03 gilleain Sure, that's fine.
08:05 olas masak: then you agree with me on the versioning?
08:05 olas jonalv, what do you say?
08:05 olas egonw, any comments from you?
08:05 jonalv joined #bioclipse
08:05 olas else I will commit
08:06 jonalv uhuh he will commit! :)
08:06 zarah jonalv: You have new messages. Write '@messages' to read them.
08:06 jonalv zarah: tell me
08:06 zarah jonalv: olas said I think you have a dependency in usermanager plugin to another plugin in the brunn feature, while the brunn feature depends on the usermanager feature
08:06 masak olas worked late yesterday :)
08:06 olas yes
08:06 olas jonalv: the new versioning will be 2.0.0.A20080808
08:06 olas or at least that's the proposal
08:06 jonalv oki
08:06 olas ok with you?
08:07 jonalv yea
08:07 olas just want some support before I commit :-)
08:07 olas right, here it comes
08:08 CIA-49 bioclipse: ospjuth * r6515 /bioclipse2/trunk/ (5 files in 4 dirs): Updated versioning to 2.0.0.A20080808. A stands for Alpha.
08:09 CIA-49 bioclipse: ospjuth * r6516 /bioclipse2/trunk/ (12 files in 10 dirs): Updated versioning to 2.0.0.A20080808. A stands for Alpha.
08:11 CIA-49 bioclipse: ospjuth * r6517 /bioclipse2/trunk/ (4 files in 4 dirs): Updated versioning to 2.0.0.A20080808. A stands for Alpha.
08:11 CIA-49 bioclipse: ospjuth * r6518 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk10/META-INF/MANIFEST.MF: Updated Eclipse plugin versioning to 1.0.0.A20080808. A stands for Alpha.
08:12 CIA-49 bioclipse: ospjuth * r6519 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Updated versioning to 2.0.0.A20080808. A stands for Alpha.
08:13 jonalv uhm olas maybe you didn't want to change version number of cdk? :)
08:15 olas nah, it's just the version of the CDK plugin
08:15 olas not the CDK
08:15 masak @update
08:15 CIA-49 bioclipse: carl_masak * r6520 /bot/trunk/zarah.pl: [zarah] joins in on thrice-repeated things uttered
08:15 olas and I kept the 1.1.0 for CDK trunk and 1.0.0 for cdk10
08:15 jonalv it's in the cdk repo...
08:15 zarah joined #bioclipse
08:15 olas I know
08:15 masak test
08:15 masak test
08:15 masak test
08:15 zarah test
08:15 masak zarah++
08:15 olas test
08:15 jonalv test
08:15 masak test
08:15 zarah test
08:15 olas test
08:15 olas test
08:15 olas test
08:15 olas tes
08:16 olas test
08:16 olas @test
08:16 olas zarah: test
08:16 zarah olas: please rephrase or stop trying to be witty :)
08:16 jonalv tes
08:16 jonalv tes
08:16 jonalv tes
08:16 zarah tes
08:16 olas zarah: you are stupid
08:16 zarah olas: you've just exceeded my capabilities :/
08:16 masak olas: she only repeats it the third time
08:16 masak after that, she's silent
08:16 olas wee
08:16 olas wee
08:16 olas wee
08:16 zarah wee
08:16 olas we
08:16 olas why?
08:17 masak olas: I liked it that way.
08:17 olas olas++
08:17 zarah shame on you, olas, giving yourself karma like that
08:17 olas olas++
08:17 zarah shame on you, olas, giving yourself karma like that
08:17 olas olas++
08:17 zarah shame on you, olas, giving yourself karma like that
08:17 zarah olas++
08:17 olas olas++
08:17 zarah shame on you, olas, giving yourself karma like that
08:17 olas olas++
08:17 zarah shame on you, olas, giving yourself karma like that
08:17 olas olas++
08:17 zarah shame on you, olas, giving yourself karma like that
08:17 olas olas++
08:17 olas olas++
08:17 zarah shame on you, olas, giving yourself karma like that
08:17 olas olas++
08:17 olas olas++
08:17 zarah shame on you, olas, giving yourself karma like that
08:17 olas olas++
08:17 olas olas++
08:17 zarah shame on you, olas, giving yourself karma like that
08:17 olas olas++
08:17 zarah shame on you, olas, giving yourself karma like that
08:17 masak olas: doesn't work. you know it.
08:17 zarah shame on you, olas, giving yourself karma like that
08:17 zarah shame on you, olas, giving yourself karma like that
08:17 zarah shame on you, olas, giving yourself karma like that
08:17 masak olas: you didn't get one karma point from all that :)
08:17 olas olas++
08:17 zarah shame on you, olas, giving yourself karma like that
08:17 olas olas++
08:17 zarah shame on you, olas, giving yourself karma like that
08:17 olas olas++
08:17 zarah shame on you, olas, giving yourself karma like that
08:17 zarah olas++
08:18 olas the last one?
08:18 masak nope
08:18 masak she just says it
08:18 olas :-(
08:18 jonalv zarah: shut up :)
08:18 zarah jonalv: :)
08:18 olas oh
08:18 masak she doesn't actually do anything
08:18 olas karma
08:18 zarah olas has a karma of 77
08:18 masak ???!?
08:18 olas nice
08:18 olas :-)
08:18 jonalv uhm?
08:18 masak what the...?
08:18 olas I've been a good boy
08:18 olas working late and all that
08:19 masak olas: something tells me that's undeserved
08:19 masak karma
08:19 zarah masak has a karma of 3
08:19 masak masak++
08:19 zarah shame on you, masak, giving yourself karma like that
08:19 masak karma
08:19 zarah masak has a karma of 3
08:19 olas zarah: do you think I deserve it?
08:19 zarah olas: please rephrase or stop trying to be witty :)
08:19 masak masak++
08:19 zarah shame on you, masak, giving yourself karma like that
08:19 masak masak++
08:19 zarah shame on you, masak, giving yourself karma like that
08:19 masak masak++
08:19 zarah shame on you, masak, giving yourself karma like that
08:19 zarah masak++
08:19 masak karma
08:19 zarah masak has a karma of 3
08:19 masak hm...
08:19 olas I guess she just likes me more
08:21 egonw no, I think I am the cute one :)
08:21 olas zarah: you are the cute one
08:21 zarah olas: no, YOU'RE the cute one! :)
08:21 olas egonw: you see?
08:22 olas karma egonw
08:22 zarah egonw has a karma of 0
08:22 egonw ah, that autoraises the karma?
08:22 olas karma olas
08:22 zarah olas has a karma of 77
08:22 egonw que???
08:22 egonw zarah: when did I loose my 367 karma of yesterday??
08:22 zarah egonw: I did not understand that
08:22 egonw sure, play to innocent one
08:22 olas zarah: do you like egonw?
08:22 zarah olas: I did not understand that
08:22 olas neither did I
08:23 masak egonw: we're investigating how the heck olas could have gotten 77 karma point all of a sudden
08:23 masak s/point/points/
08:23 olas I guess I have just done good in this channel
08:23 olas people give me olas++
08:23 zarah shame on you, olas, giving yourself karma like that
08:24 masak karma olas
08:24 zarah olas has a karma of 77
08:24 egonw commits?
08:24 masak olas: you've figured something out, that's for sure
08:24 masak egonw: commits don't count yet
08:24 masak unless 77 separate commits did 'olas++'
08:24 * olas suddenly likes zarah very much
08:26 egonw olas: I don't think the CDK plugins should follow the versioning of Bioclipse
08:27 olas egonw: I was afraid you'd say so
08:27 egonw but I don't have a good alternative either...
08:27 egonw olas: yeah, no worries...
08:27 olas but we need an incremented ID
08:27 egonw it's just in METINF
08:27 olas that's what I thought
08:27 egonw so, no conflicts...
08:27 olas so it's ok for now?
08:28 egonw yes
08:28 olas if we don't increment the ID, it will not be udpated from online updates
08:28 olas good
08:28 olas I kept the 1.0.0 and 1.1.0 parts...
08:28 olas is that OK?
08:28 egonw yes, that's the proper choice
08:28 egonw actually...
08:28 olas egonw: where di src/data go?
08:28 egonw the first should be:
08:28 egonw 1.0.3.something
08:28 olas ok
08:28 olas will fix that
08:28 egonw thanx
08:28 olas about trunk
08:29 olas src/data?
08:29 olas where is that now?
08:29 egonw oh, sybyl atom types is in trunk now
08:29 olas good
08:29 egonw so, will try to this OB validation this weekend
08:29 masak olas: we've figured out how you eleveted your karma.
08:29 olas great
08:29 masak olas: resetting.
08:29 egonw ah, that moved into src/test
08:29 olas ok
08:29 masak @refresh
08:29 olas masak: what do you mean?
08:29 masak jonalv++
08:30 masak @update
08:30 zarah joined #bioclipse
08:30 masak karma olas
08:30 zarah olas has a karma of 78
08:30 masak dang.
08:30 olas nice
08:30 egonw karma
08:30 zarah egonw has a karma of 0
08:30 egonw that's not fixed either :)
08:30 masak egonw: will fix that :)
08:31 masak ah, we'll do like this.
08:31 olas egonw: so no data is needed at runtime?
08:31 masak we'll take the old karma file and use that
08:31 egonw not from src/test/data
08:31 egonw that's only test data
08:31 olas is there a src/main/data now?
08:31 egonw thanx to your bug report :)
08:31 egonw no, that's all deep inside the org.openscience tree
08:31 olas ok, good
08:32 shk3 joined #bioclipse
08:33 masak @update
08:33 zarah joined #bioclipse
08:33 masak karma olas
08:33 zarah olas has a karma of 14
08:33 masak karma egonw
08:33 zarah egonw has a karma of 5
08:33 masak back to normal
08:33 olas NOOOOOOO
08:33 masak olas: and don't do that again
08:33 olas where did my karma go?
08:33 olas ???
08:33 masak we know you've been cheating.
08:33 olas do what?
08:34 olas now I wouldn't
08:34 masak you left proof all over the logs
08:34 masak at least be a bit discrete :)
08:34 olas logs?
08:34 olas you have logs?
08:34 masak you bet
08:34 masak so behave!
08:35 olas masak++ for that
08:35 * olas will behave
08:42 jonalv olas: HAve you been looking at my brunn problems
08:42 jonalv I can't find any dependency to a Brunn plugin from the Usermanagerplugin...
08:43 CIA-49 bioclipse: carl_masak * r6521 /bot/trunk/zarah.pl: [zarah] logs implemented -- so that olas will behave
08:43 masak olas: I can't believe you fell for that one
08:43 masak _now_ we have logs
08:44 masak @update
08:44 zarah joined #bioclipse
08:44 olas masak--
08:44 jonalv lol
08:44 jonalv masak++
08:44 masak olas: you can't win.
08:44 olas you got a masak + + for logs before
08:44 masak olas: chalk that up for making you confess.
08:45 masak that's worth a karma point :)
08:45 olas hahaha
08:45 olas you still have NO idea how I di it :-)
08:45 jonalv olas: about Brunn?
08:45 jonalv olas: you probably used another name and did it from #farmbio
08:45 masak olas: let me guess: you logged in on #farmbio as another nick and plusplussed olas
08:45 jonalv That would have worked anyway....
08:45 olas oh
08:46 olas never thought of that
08:46 olas that would have been much easier
08:46 jonalv &me hopes you did something way more complicated:)
08:46 olas /me=>:)
08:47 * olas = O:)
08:47 masak noobs. :)
08:47 jonalv olas: did you have a look at brunn?
08:48 olas no
08:48 olas building new Bioclipse
08:48 olas hmm
08:49 olas what is the Version and BuildID of Eclipse?
08:49 jonalv olas: can you help me after that?
08:49 olas did you get my msg?
08:50 olas was it incorrect?
08:50 olas what are the deps from usermanager
08:51 jonalv org.eclipse.ui,
08:51 jonalv net.bioclipse.core,
08:51 jonalv net.bioclipse.ui,
08:51 jonalv net.bioclipse.scripting,
08:51 jonalv org.eclipse.core.resources,
08:51 jonalv org.eclipse.core.runtime,
08:51 jonalv org.eclipse.core.runtime.compatibility.auth,
08:51 jonalv org.springframework.bundle.spring.aop,
08:51 jonalv net.sf.cglib,
08:51 jonalv net.bioclipse.logger
08:51 olas what is keyring then?
08:52 * jonalv updated classpath on plugins and now nothing works... :(
08:52 olas clean
08:52 jonalv olas: keyring?
08:52 olas versions are updated
08:52 olas didnät it complain about keyring yesterday?
08:52 jonalv fixed that
08:53 jonalv now there's just the circle it;s complaining about
08:53 olas paste the circle here
08:53 CIA-49 bioclipse: ospjuth * r6522 /bioclipse2/trunk/plugins/net.biocli​pse.data.sampledata/about.mappings: Updated version.
08:54 * jonalv managed to break org.openscience.cdk by updating classpath...
08:54 CIA-49 bioclipse: ospjuth * r6523 /bioclipse2/trunk/plugins/net.​bioclipse.ui/build.properties: Added branding to build.
08:55 olas jonalv: I did that too
08:55 olas the solution is:
08:55 olas right-click org.op.cdk
08:55 olas properties
08:55 olas Java build path
08:55 olas remove src/data
08:55 olas for some reason that didn't happen when PDE > update classpath
08:56 gilleain weird.
08:56 jonalv olas: how do I remove it?
08:56 gilleain apparently it is legal java to have a semicolon after the method body.
08:57 jonalv ah from the source tab
08:57 jonalv olas: thanks olas++
08:58 CIA-49 bioclipse: ospjuth * r6524 /bioclipse2/trunk/features/net.b​ioclipse.sampledata/feature.xml: Added size to feature.
08:58 jonalv olas: Problems during export
08:58 jonalv A cycle was detected when generating the classpath net.bioclipse.brunn.core_0.1.0, net.bioclipse.usermanager_0.1.1, net.bioclipse.core_2.0.0.A20080808, org.springframework.bundle.spring.beans_2.5.1, org.springframework.bundle.spring.core_2.5.1, net.bioclipse.brunn.core_0.1.0.
08:59 olas if you put usermanager in brunn feature, it works?
09:00 jonalv does that mean that  org.springframework.bundle.spring.core_2.5.1 has a dependency to net.bioclipse.brunn.core_0.1.0? Becasue I am pretty sure it doesn't...
09:00 jonalv olas: I don't know
09:00 olas test
09:00 olas I have never seen this
09:00 jonalv I don't think I can do that for license reasons though...
09:00 masak jonalv: http://sourceforge.net/projects/pastebot/
09:00 zarah masak's link is also http://tinyurl.com/rnu6b
09:00 olas you have some dep wrong somewhere I assume
09:02 olas masak: can we run it on pele?
09:02 olas looks good
09:02 masak olas: I think so.
09:02 jonalv olas: it doesn't work either...
09:02 masak though I'd like to integrate it into zarah if possible
09:03 jonalv Problems during export
09:03 jonalv A cycle was detected when generating the classpath net.bioclipse.usermanager_0.1.1, net.bioclipse.core_2.0.0.A20080808, org.springframework.bundle.spring.beans_2.5.1, org.springframework.bundle.spring.core_2.5.1, net.bioclipse.brunn.core_0.1.0, net.bioclipse.usermanager_0.1.1.
09:03 jonalv
09:03 jonalv
09:04 olas hmm
09:05 olas check the deps of all those plugins
09:05 jonalv I have done that... :(
09:05 jonalv but I must have misssed something I guess...
09:07 stain you need Spring! ;)
09:07 stain oh wait..
09:07 masak olas: when selecting atoms in the outline, they are highlighted in the jcp editor, but not vice versa? is there a technical limitation involved, or is it just a missing feature?
09:08 olas missing feature
09:08 olas was implemented in bc1
09:08 olas a bug
09:09 olas is it filed?
09:09 olas if not, please file it
09:09 * masak files
09:12 CIA-49 bioclipse: ospjuth * r6525 /bioclipse2/trunk/features/net.bioclips​e.chemoinformatics-feature/feature.xml: Updated to correct size.
09:12 CIA-49 bioclipse: ospjuth * r6526 /bioclipse2/trunk/features/net.b​ioclipse.sampledata/feature.xml: Updated to correct size.
09:12 CIA-49 bioclipse: ospjuth * r6527 /bioclipse2/trunk/plugins/net.bi​oclipse.ui/META-INF/MANIFEST.MF: Set correct provider and version.
09:12 CIA-49 bioclipse: ospjuth * r6528 /bioclipse2/trunk/plugins/n​et.bioclipse.ui/plugin.xml: Updated abouttext with version.
09:12 olas CIA bot backlogging :-)
09:13 CIA-49 bioclipse: ospjuth * r6529 /bioclipse2/trunk/plugins/net.b​ioclipse.ui/bioclipse.product: Updated abouttext with version in product as well.
09:13 olas I fel ready for Bioclipse alpha 2
09:14 olas is it OK to call it alpha2 on SF or should I name it 2.0.0.A20080808?
09:14 olas egonw?
09:14 * jonalv has a track now on his circle
09:14 egonw alpha2 is fine
09:14 olas ok
09:14 olas jonalv: go go!
09:16 olas no more commits to come?
09:16 olas masak?
09:16 olas jonalv?
09:16 olas shk3?
09:16 masak olas: many more commits on the way
09:16 jonalv olas: no I don't think so. logging is still working? :)
09:17 masak I have about 300 commits planned for the coming year. possible more
09:17 olas uhm
09:17 olas masak: more, please
09:17 masak :)
09:17 olas :-)
09:17 * jonalv is working on Brunn today
09:17 masak olas: quality, not quantity
09:17 olas ok
09:17 olas toffifee, not marabou
09:17 * masak is working on KI this morning
09:17 olas right
09:17 olas then off we go
09:18 * olas is exporting alpha02
09:18 olas jonalv: I need you to just see if it runs on linux/win
09:18 olas ok?
09:18 jonalv sure, what?
09:18 jonalv your export?
09:18 olas alpha02
09:18 olas yes
09:18 jonalv okey, you hvae it now?
09:19 olas will send you URL to it when ready
09:19 jonalv good
09:19 olas 10 mins
09:19 * jonalv starts up Pan then :)
09:19 olas lol
09:20 olas Pan needs 10 minutes to start
09:20 olas like an old Xerox machine
09:20 olas do you need "startkablar" as well?
09:20 olas of a defibrilator?
09:20 olas of=or
09:22 jonalv nah perhaps not 10 mins but I miust say that the best thing with nox is that it 'insta-starts' :)
09:22 masak olas: 'jump start cables'
09:23 olas aah
09:23 olas now I remember
09:23 * masak just found out
09:33 egonw olas: don't expect me to say much more than that for the time being...
09:33 egonw :)
09:36 olas time to learn ;-)
09:37 olas you can at least listen in
09:37 jonalv olas: when I build amn update site, where does the things I have bult end up? :)
09:38 olas in the update-site project
09:38 olas it creates two folders, features and plugins
09:38 jonalv ah
09:38 jonalv okey
09:38 jonalv and two xml files
09:39 olas copy all files+folders from the update site project to a web dir
09:39 olas that's it
10:14 CIA-49 bioclipse: ospjuth * r6530 /bioclipse2/trunk/bioclipse-updatesite/site.xml: Updated for rel 20080808.
10:16 EskilA joined #bioclipse
11:01 egonw_ joined #bioclipse
11:01 * olas is uploading alpha02 to SF
11:01 olas takes a while
11:01 olas 214 Mb to upload
11:03 CIA-49 bioclipse: carl_masak * r6531 /bioclipse2/tags/2.0-alpha-20080808/: This is Bioclipse 2.0-alpha-20080808.
11:03 olas masak++
11:03 masak olas: next time I'll let you do it. It's not that hard :)
11:04 masak svn cp https://bioclipse.svn.sourcefor​ge.net/svnroot/bioclipse/trunk https://bioclipse.svn.sourceforge.net/sv​nroot/bioclipse/tags/2.0-alpha-20080808
11:04 masak that's all
11:05 * olas must install leopard soon
11:07 egonw_ yes, you should
11:07 egonw_ can you finally set up some vmwares
11:09 olas vmwares?
11:09 CIA-49 bioclipse: shk3 * r6532 /bioclipse2/trunk/plugins/net.bioclipse.spectrum/ (10 files in 5 dirs): added a basic outline
11:11 gilleain The new CmlFileDescriber is ready, with shiny new XPP innards. I've just missed a release, though, have I?
11:12 olas unfortunately, yes
11:12 olas but no problems
11:13 olas we'll just release a feature patch :-)
11:13 olas gilleain: please commit and let me try it out
11:13 gilleain Also, I wanted to ask - is there much duplication of jar file dependancies?
11:13 olas some I'd say
11:13 olas but no too much
11:13 gilleain Committing...
11:14 olas were you thinking of something in particular?
11:14 egonw_ depends on the amount of plugins
11:14 gilleain Well, I've just duplicated the xpp3 jar.
11:14 egonw_ :)
11:15 gilleain But, obviously if a plugin needs it, then it needs it.
11:15 egonw_ xpp3 is not so large though
11:15 egonw_ but versioning might be a problem
11:15 egonw_ it has been for years with Xerces
11:15 gilleain I guess the packaged bioclipse doesn't have duplication.
11:15 shk3 perhaps we could put it in net.bc.xom and make this a "xml library plugin"
11:15 egonw_ so, ideally xpp3 would be a separate plugin
11:15 egonw_ gilleain: yes, it will
11:15 olas shk3: not a bad idea
11:15 shk3 that's what I would call plugin explosion
11:16 olas suggest the basic stuff that several plugins use to go in the core
11:16 olas and with core I mean a core resources plugin, as shk3 suggests
11:16 jonalv why are people so afraid of this plugin explosion thing people are talking about?
11:16 olas and only have a single plugin if the jar is large
11:16 egonw_ ok, let's call it net.xml.dump or so
11:16 egonw_ jonalv: no idea
11:16 gilleain jonalv: It makes the codebase harder to grasp.
11:16 olas A LOT harder
11:16 egonw_ jonalv: I see no problem with a few more pluing you never have to change
11:17 egonw_ gilleain: harder than import nu.xom;
11:17 olas I hate scrolling in my workspace
11:17 egonw_ and import bla.xpp3; ??
11:17 jonalv I think it can be the other way around... Small plugins are easier to grasp
11:17 egonw_ jonalv: indeed
11:17 egonw_ jonalv++
11:17 egonw_ and easier to maintain
11:18 jonalv olas: linux version works
11:18 olas good
11:18 olas uploading to SF as we speak
11:18 olas ETA 20 mins or so
11:18 gilleain I suppose.
11:19 olas gilleain: please commit now with duplicated jar
11:19 olas and we can refactor it later
11:19 egonw it also reduced bandwith on the update server
11:19 egonw 30kB does not sounds like much...
11:19 egonw but times 10k Bioclipse installs
11:19 olas XML parsing is central for Bioclipse, and I could envision it being imported in core.
11:20 egonw I can even imagine it already is packaged by the Eclipse people
11:20 olas egonw: if you want to reduce BW, decrease the size of CDK
11:20 egonw olas: right... I'd love too...
11:20 olas it is 37 Mb now
11:20 egonw first TODO in october
11:20 olas cdk10 is 17
11:20 egonw one CDK module, one plugin
11:30 gilleain jonalv: this change to the log4j version number in the net.bioclipe.ui manifest gives me an error : how is it fixed?
11:30 jonalv d'oh
11:30 jonalv uhm what error? :)
11:31 gilleain I get an 'unsatisfied constraint' error.
11:31 gilleain Perhaps I have a different version of log4j?
11:31 jonalv maybe
11:32 jonalv IS  htere a way that I can reproduce this error?
11:32 gilleain Well, probably not. I suspect I just have to fiddle with the build settings.
11:32 CIA-49 bioclipse: carl_masak * r6533 /bioclipse2/tags/2.0-alpha-20080808/externals/: Fixed external cdk in the new tag at r11964.
11:36 * olas will be here until 15.00 CET today
11:38 CIA-49 bioclipse: shk3 * r6534 /bioclipse2/trunk/plugins/net.bioclips​e.spectrum/src/net/bioclipse/spectrum/ (editor/SpectrumEditor.java outline/SpectrumOutlinePage.java): outline is updated when spectrum is changed
11:38 olas ok, alpha02 release is online
11:44 olas ML sent
11:44 olas blog written
11:44 olas Bioclipse.net updated
11:44 olas wiki updated
11:44 olas great
11:44 jonalv olas: great :)
11:44 olas it's early friday today :-)
11:45 masak olas++ # early and often
11:45 olas karma
11:45 zarah olas has a karma of 17
11:46 jonalv karma
11:46 zarah jonalv has a karma of 21
11:46 * olas recalls the old days when he had karma 77+...
11:46 egonw karma
11:46 zarah egonw has a karma of 5
11:46 zarah karma
11:46 olas haha
11:46 masak olas: that was before we put you under strict surveillance
11:46 olas karma zarah
11:46 zarah zarah has a karma of 17
11:46 egonw zarah has no karma?
11:46 zarah egonw: eh... wha'?
11:47 malick left #bioclipse
11:52 masak @update
11:52 zarah joined #bioclipse
11:52 masak test
11:52 masak test
11:53 masak test
11:53 zarah test
11:53 masak karma
11:53 zarah masak has a karma of 18
11:53 masak karma
11:53 zarah masak has a karma of 18
11:53 masak karma
11:53 zarah masak has a karma of 18
11:53 masak zarah++
11:53 masak karma zarah
11:53 zarah zarah has a karma of 18
11:53 masak zarah: we're very much alike, you and I :)
11:53 zarah masak: I'm just a bot, you expect me to understand that?
11:53 masak zarah: no.
11:53 zarah masak: I see.
11:54 CIA-49 bioclipse: carl_masak * r6535 /bot/trunk/zarah.pl:
11:54 CIA-49 bioclipse: [zarah] now does not repeat things that match against other behavior,
11:54 CIA-49 bioclipse: for example "karma"
12:10 CIA-49 bioclipse: ospjuth * r6536 /bioclipse2/trunk/plugins/net.bioclipse.ui/src/ne​t/bioclipse/ui/ApplicationActionBarAdvisor.java: Removed unwanted menu options in Bioclipse: "Open File...", "Convert file delimiters", and gotoLastPosition.
12:10 CIA-49 bioclipse: ospjuth * r6537 /bioclipse2/trunk/plugins/net.bioclipse.ui/src/ne​t/bioclipse/ui/ApplicationActionBarAdvisor.java: Hunted down warnings due to restrictions.
12:10 masak olas: no "Open File..."?
12:11 olas very annoying
12:11 olas have you EVER used it?
12:12 egonw masak: Import?
12:13 masak egonw: aye, probably better
12:13 masak olas: no, I haven't
12:17 olas :-)
12:19 * gilleain is a fool. it was a conflict problem.
12:22 gilleain committed.
12:24 egonw gilleain: what revision?
12:25 egonw because in 6539 you commits a SVN conflict
12:25 gilleain Oh. Sorry.
12:25 egonw in net.bioclipse.ui/build.properties
12:25 gilleain Curses.
12:25 masak is that even possible?
12:25 masak ah well, maybe if you `svn resolve` a file by mistake
12:26 masak s/resolve/resolved/
12:26 gilleain Sigh.
12:26 * masak pats gilleain consolingly
12:27 egonw btw, this is the first time that I see the use of pointers in Java code !
12:27 masak o_O
12:27 gilleain Pointers? Where <_< >_>
12:27 masak real pointers?
12:27 egonw search:
12:27 egonw sorry, goto statements
12:27 egonw those pointers :)
12:27 gilleain Oh. Break labels.
12:27 egonw and "breal search;"
12:28 gilleain I see what I've done to the build.properties.
12:28 masak egonw: if you call 'break' statements 'goto' statements, you'd have to include 'if' and 'while' in that group too. so no, it's not the first time you see them :)
12:29 egonw not entirely, I think...
12:29 egonw with if/while it is well defined where you go...
12:29 egonw a label can be anywhere
12:29 masak egonw: no, not in Java
12:29 egonw like a true old days BASIC goto
12:30 egonw ah, ok...
12:30 masak it's not like that.
12:30 gilleain Right. I've fixed it. So: recommit, right?
12:30 egonw well, as said, it's the first time I see them :)
12:30 egonw gilleain: yes
12:30 egonw I'm not fond of labels in general
12:30 gilleain Neither am I, particularly. There may be a better solution.
12:31 masak egonw: http://java.sun.com/docs/books/jls/se​cond_edition/html/statements.doc.html
12:31 zarah masak's link is also http://tinyurl.com/8m642
12:31 masak egonw: labels in Java are actually very nice.
12:31 egonw I typically us outside the while a 'boolean done = false; while(!done && parser.next() != etc etc'
12:31 masak just because they are so managed and harmless
12:32 egonw in this case, I'd actually test for </molecule>
12:32 masak egonw: I used to think like that. then I met with the Perl model of doing things
12:32 egonw perl is 'quick and dirty'
12:33 gilleain Actually, one thing that it doesn't handle is the @convention that you mentioned.
12:33 gilleain I saw a file with @convention=pdb, with nested molecule tags.
12:33 masak egonw: I think that's a matter of how you use it.
12:33 egonw gilleain: and you can easier use:
12:34 egonw getAttribute(nsString, localNamsString)
12:34 egonw then you do not have to iterate over all attributes and use the bool searching...
12:35 gilleain True.
12:36 shk3 I saw there are quite a few bug reports for jcp
12:36 egonw which is why we are rewriting it :)
12:36 shk3 should we invest time in cdk10 jchempaint or will there be the trunk based one soon
12:36 shk3 ?
12:37 shk3 bug reports in bioclipse for jcp, I mean
12:37 olas Gpox is working on an SWT implementation
12:37 olas the cdk10 version should be in a sort of "minimum working state"
12:37 olas until replaced
12:37 olas it WILL be replaced before 2.0
12:38 olas and cdk10 WILL be removed then
12:38 olas ah, that will be a beautiful day :-)
12:38 * olas has to leave soon
12:39 masak olas: if the version you just released is known as alpha02, what was it that I tagged as alpha02 a few days ago?
12:40 shk3 olas: looking forwar to that day as well
12:41 olas masak: well, it seemed confisuing to release first alpha01 , then alpha04
12:41 olas so alpha02 is 20+080808
12:41 olas I know, not perfect
12:41 jonalv olas seems to love to confuse me and masak with version numberings :)
12:41 olas yup
12:41 * olas really likes that
12:42 jonalv wha will the name of the new tag be then?
12:42 * olas is still a bit angry that jonalv and masak cut his karma
12:42 olas it was well deserved
12:42 egonw people are twittering about Bioclipse
12:42 egonw well... BioClipse actually
12:42 egonw :)
12:42 olas twittering?
12:42 jonalv olas: maybe if you gloat a bit about how you did it you will feels better :)
12:42 egonw yeah, twitter.something
12:42 egonw I don't use it
12:43 olas twitter means complain?
12:43 egonw it's in between IRC and blogging
12:43 jonalv BioClipse?
12:43 egonw http://twitter.com/
12:43 masak olas: twitter is a mode of communication
12:43 masak it's a lifestyle
12:43 masak a time drain
12:43 masak the new black
12:44 masak tweet
12:44 masak tweet
12:44 masak tweet
12:44 zarah tweet
12:44 masak :)
12:44 olas how can I twitter?
12:44 masak olas: just join
12:44 jonalv egonw: what have your twitter radar picked up so far?
12:44 olas do I need to buy a twitterer?
12:44 masak it's free
12:45 olas egonw: what do people twitter about?
12:45 egonw http://www.neoformix.com/Projects/Twi​tterStreamGraphs/view.php?q=bioclipse
12:45 zarah egonw's link is also http://tinyurl.com/6z3son
12:46 gilleain What a weird visualization.
12:46 egonw cool one
12:46 egonw the bigger a 'peak' the more twittering about the subject
12:47 egonw each term related to the query gets a 'band in time'...
12:47 egonw the bigger ones with a label
12:47 olas gotta go now
12:47 gilleain Ah, it's clearer for a more popular topic.
12:47 olas bye all
12:47 egonw olas: have a nice weekend
12:47 gilleain bye.
12:47 olas have a nice weekend
12:47 olas cu monday
12:47 olas left #bioclipse
12:47 egonw gilleain: yes it is :)
12:58 * masak likes this page: http://nat.org/blog/?p=825
13:01 CIA-49 bioclipse: jonalv * r6538 /bioclipse2/trunk/features/net.bicli​pse.usermanager-feature/feature.xml: Made Brunn update site work with Bioclipse 2
13:10 edrin joined #bioclipse
13:10 edrin hi
13:10 zarah hi edrin
13:16 masak hi edrin
13:17 jonalv hi edrin
13:18 masak hi edrin
13:18 zarah hi edrin
13:18 jonalv hi edrin :)
13:18 egonw zarah: why do you repeat everything that has been said 3 times??
13:18 zarah egonw: eh... wha'?
13:18 egonw that's annoying
13:18 egonw zarah--
13:18 jonalv egonw: I think it's funny :)
13:19 egonw jonalv--
13:19 masak :)
13:20 jonalv (It was masak who implemetned it...)
13:21 masak I like it, too.
13:21 egonw masak-- (twice really)
13:21 egonw for liking it, and implementing it :)
13:22 masak :)
13:22 egonw oh, so ola just did:
13:22 egonw olas++
13:22 egonw olas++
13:22 egonw olas++
13:22 zarah olas++
13:22 egonw ic, now I understand :)
13:22 masak olas--
13:22 masak olas--
13:22 masak olas--
13:22 zarah olas--
13:23 masak egonw: I'm not sure you do. you can't increase your own karma, period.
13:24 fatbastard egonw++
13:24 fatbastard karme egonw
13:24 fatbastard karma egonw
13:24 zarah egonw has a karma of 6
13:24 fatbastard egonw++
13:24 fatbastard karma egonw
13:24 zarah egonw has a karma of 7
13:24 egonw yeah, the karme is just a gimick...
13:24 masak ...except that way, of course
13:24 egonw s/e/a/
13:24 gilleain Karma fraud!
13:24 masak egonw--
13:24 masak egonw--
13:24 shk3 egonw--
13:24 zarah egonw--
13:24 shk3 egonw--
13:25 shk3 egonw--
13:25 masak haha
13:25 egonw no, I like it much more that zarah tracks commit stats
13:25 egonw though surely one can fake that too...
13:25 egonw karma
13:25 zarah egonw has a karma of 2
13:25 egonw :(
13:25 masak egonw: tracks commit stats?
13:25 masak she doesn't.
13:25 egonw at least you can't mess with my LaunchPad karma
13:25 jonalv with great power comes great responisbility
13:25 egonw s/that/if/ :
13:26 egonw no, I like it much more if zarah tracks commit stats
13:26 masak ah
13:26 jonalv egonw: That means that we can't give you karma either...
13:26 masak yes, I'd like that too
13:26 sneumann joined #bioclipse
13:27 egonw masak:
13:27 egonw [15:26] <egonw> karma fun at #bioclipse :)
13:27 egonw [15:26] <zarah> fun at #bioclipse :) has a karma of 0
13:27 jonalv haha
13:27 sneumann left #bioclipse
13:27 masak egonw: that's a feature :)
13:32 masak sooner or later I'll implement (the ability to mod up several words)++
13:33 masak karma the ability to mod up several words
13:33 zarah the ability to mod up several words has a karma of 0
13:34 masak karma nobody
13:34 zarah nobody has a karma of 0
13:34 masak karma everybody
13:34 zarah everybody has a karma of 0
13:35 masak karma bioclipse
13:35 zarah bioclipse has a karma of 0
13:35 masak karma karma
13:35 zarah karma has a karma of 0
13:35 masak karma has a karma of 0
13:35 zarah has a karma of 0 has a karma of 0
13:36 masak karma 0 fo amrak a sah
13:36 zarah 0 fo amrak a sah has a karma of 0
13:37 jonalv having fun?
13:37 masak yes :)
13:41 CIA-49 bioclipse: gilleain * r6540 /bioclipse2/trunk/plugins/net.​bioclipse.ui/build.properties: Fixed a broken conflict resolution.
13:44 egonw the transparent windows feature of KDE 4.1 is so nice!
13:44 egonw it's amazing how I can just monitor all windows (even if behind each other)
13:45 egonw except for the window I am currently working in, which is opaque
13:53 CIA-49 bioclipse: gilleain * r6541 /bioclipse2/trunk/plugins/net.bioclipse.ui/src/net​/bioclipse/ui/contenttypes/CmlFileDescriber.java: Minor edit to make the code clearer.
13:57 CIA-49 bioclipse: gilleain * r6539 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (6 files in 4 dirs): Changed the CmlFileDescriber to use the XmlPullParser (xpp), also added the jar as a library dependency.
14:02 masak http://www.marriedtothesea.c​om/072408/home-gymnasium.gif
14:02 zarah masak's link is also http://tinyurl.com/623kpe
14:03 gilleain Married to the sea plus-plus.
14:03 edrin hm
14:03 masak aye :)
14:04 CIA-49 bioclipse: shk3 * r6542 /bioclipse2/trunk/plugins/net.biocl​ipse.spectrum/src/net/bioclipse/spe​ctrum/editor/PeakCellModifier.java: handles non-numerical input
14:08 masak http://www.marriedtothesea​.com/071808/weiner-hat.gif
14:08 zarah masak's link is also http://tinyurl.com/67k845
14:12 masak haha -- http://www.marriedtothesea.com/07​1308/whered-you-get-that-fish.gif
14:12 zarah masak's link is also http://tinyurl.com/6l822v
15:00 CIA-49 bioclipse: shk3 * r6543 /bioclipse2/trunk/plugins/net.biocl​ipse.spectrum/src/net/bioclipse/spe​ctrum/editor/PeakCellModifier.java: looks like you need a refresh now after the edit. took me a while to find that out.
15:00 CIA-49 bioclipse: carl_masak * r6544 /bioclipse2/trunk/plugins/net.bi​oclipse.cdk10.jchempaint/icons/ (15 files): [n.b.cdk10.jcp] new/modified icons
15:23 edrin hm, btw...
15:23 edrin where is ola today?
15:24 shk3 he already started the weekend
15:24 edrin oh
15:24 edrin heh
15:24 edrin i currently have power work month
15:25 shk3 you told that
15:25 shk3 don't work too much
15:26 edrin 2 x weekend service .... 1 week stay-ready service, diagnostics every morning and every afternoon
15:27 CIA-49 bioclipse: shk3 * r6545 /bioclipse2/trunk/plugins/net.bioclipse.sp​ectrum/src/net/bioclipse/spectrum/editor/ (PeakCellModifier.java PeakTableViewer.java): changes in the table get actually propageted to the resource
15:53 CIA-49 bioclipse: jonalv * r6546 /bioclipse2/trunk/plugins/net.bioclipse.data​.sampledata/src/net/bioclipse/data/sampledat​a/wizards/NewSampleDataProjectWizard.java: When creating sampledata project "Sample Data" is suggested as project name unless a project with that name already exists.
16:01 edrin left #bioclipse
16:01 edrin joined #bioclipse
16:01 jonalv edrin: hi
16:01 edrin hi
16:01 zarah hi edrin
16:02 CIA-49 bioclipse: jonalv * r6547 /bioclipse2/trunk/plugins/net.bioclip​se.data.sampledata/data/Javascripts/ (extractsmiles.js extractsmilesAndMass.js):
16:02 CIA-49 bioclipse: Rewrote example java scripts to look for example sdf in "Sample Data" (which
16:02 CIA-49 bioclipse: will exists if the name hasn't been changed in the create sample data wizard).
16:02 CIA-49 bioclipse: This means that the example java scripts will work out of box as long as no
16:02 CIA-49 bioclipse: fiddling around is done. :)
16:02 jonalv edrin: friday night and you are here too? :)
16:02 edrin sure
16:02 edrin still working somehow
16:40 CIA-49 bioclipse: jonalv * r6548 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.business/src/net/bioclip​se/cdk/business/ICDKManager.java: [cdk manager] Wording in help annotations
16:40 CIA-49 bioclipse: carl_masak * r6549 /bioclipse2/trunk/plugins/net.bioclipse.cdk10.jche​mpaint/src/net/bioclipse/cdk10/jchempaint/outline/ (StructureContentProvider.java StructureLabelProvider.java): [n.b.cdk10.jcp.outline] many touch-ups to GUI look and to source code
16:41 masak @tell olas I made new icons, but I didn't stop there -- I changed a few things around in StuctureContentProvider.java and StructureLabelProvider.java. thought I'd tell you since the classes has your name on them. so be sure to update before you do any changes of your own.
16:41 zarah Consider it noted.
16:56 CIA-49 bioclipse: shk3 * r6550 /bioclipse2/trunk/plugins/net.bioclipse.spectrum/ (4 files in 3 dirs): better outline, also added a content type, but that doesn't work
17:33 edrin left #bioclipse
22:48 ChanServ joined #bioclipse
22:48 zarah joined #bioclipse
22:49 thomas_ku joined #bioclipse
22:49 ilogger2 joined #bioclipse
22:49 CIA-49 joined #bioclipse
22:49 stain joined #bioclipse
23:13 edrin joined #bioclipse
23:45 CIA-50 joined #bioclipse

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