Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-01-20

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All times shown according to UTC.

Time Nick Message
07:32 Gpox joined #bioclipse
07:38 Gpoks joined #bioclipse
08:04 egonw joined #bioclipse
08:37 thomas_ku joined #bioclipse
08:59 Gpox left #bioclipse
09:00 Gpox joined #bioclipse
09:11 shk3 joined #bioclipse
09:18 olass joined #bioclipse
09:18 olass egonw: around?
09:19 egonw yes, sort of...
09:19 egonw was a rather late night yesterday
09:19 egonw but it was worthwhile :)
09:19 olass saw tha t2 plugin
09:19 olass nice
09:19 egonw yeah, really nice :)
09:19 egonw it's not quite perfect yet...
09:19 olass ok, now to some bc2 stuff
09:19 egonw but it works :)
09:20 olass according to me, we have a net.bc.cdk.jcp.business and net.bc.cdk.jcp.business.tests
09:20 egonw :)
09:20 egonw n.b.jcp and n.b.jcp.tests
09:20 egonw IIRC
09:20 olass arvid does not have the jcp.business plugin
09:20 egonw neither have I
09:20 olass IIRC?
09:20 egonw the jcp.busisness was merged with jcp itself
09:21 olass can you delete the jcp.bus and jcp.bus.tests from svn?
09:21 egonw because the interdepended on each other
09:21 egonw are they not?
09:21 egonw oh...
09:21 olass I see them
09:21 egonw ok, please file a bug report...
09:21 olass and please update the JCP and cheminfo features
09:21 egonw will fix it later this morning
09:21 olass for the friday release
09:22 olass are all plugin ID's up to date for cheminfo?
09:22 egonw I think so...
09:22 egonw what needs updating?
09:22 olass we should set date to 20090123 for the friday release
09:22 egonw version number?
09:23 olass for bioclipse plugins that is, not cdk plugins
09:23 egonw ok
09:23 egonw right
09:23 olass and
09:23 egonw that version will remain 1.1.4.something
09:23 olass ok
09:23 egonw what it is now
09:23 egonw btw, I hope to release 1.1.5 this week...
09:23 egonw and that would be the first 1.2.0 RC
09:23 olass should we rename feature cheminformatics to cheminformatics?
09:23 egonw no, not now
09:24 egonw in the future, I like that...
09:24 olass chemoinformatics -> cheminformatics I mean
09:24 olass ok
09:24 egonw but it is really not important
09:24 olass your decision
09:24 olass oh, when you update the features
09:24 egonw yes, hereby :)
09:24 olass will jcp feature be in cheminfo feature?
09:25 olass or separate?
09:25 egonw separate
09:25 olass you could make jcp feature an included feature in cheminfo if you like
09:25 egonw and the jcp feature should not go onto the main update site
09:25 olass but you see a use case where users like cheminformatics without JCP?
09:25 egonw yes
09:25 olass egonw: WHAT!?
09:26 egonw JCP is a simple 2D editor program
09:26 olass jcp not on update site?!
09:26 olass please explain now
09:26 egonw the feature, the editor is part of chemoinfo too
09:26 olass so a nested feature, right?
09:27 egonw the JCP feature is a planned JChemPaint perspective with just the basic editing features
09:27 egonw but without whatever...
09:27 egonw but since we do not have a proper perspective yet...
09:27 egonw it does not make sense to put that up...
09:27 edrin joined #bioclipse
09:27 olass so only ship cheminfo feature
09:27 edrin hi
09:27 olass with JCP in it
09:27 egonw yes
09:27 olass hi edrin
09:27 egonw hi edrin
09:27 olass egonw: agreed
09:27 edrin hi olass
09:27 edrin hi egonw
09:28 zarah hi edrin
09:29 edrin egonw: thanks, for the mail to WS-XMPP, very good :)
09:29 egonw good
10:06 olass egonw: around?
10:07 egonw on phone
10:07 olass for the beta release, we have (IMO) 2 options for versioning
10:07 olass ex 1) 2.0.0.B20090123
10:07 olass ex 2) 2.0.0.v20090123
10:07 olass hmm, maybe 3
10:07 egonw no A?
10:07 olass A was for alpha
10:08 egonw ok...
10:08 egonw b for beta then
10:08 egonw B
10:08 olass ok
10:08 olass then v will be in release
10:09 egonw ok, sounds good
10:31 CIA-30 bioclipse: ospjuth * r8377 /bioclipse2/trunk/features/net.biocli​pse.structuredb_feature/feature.xml: Updated feature copyright and information.
10:32 CIA-30 bioclipse: ospjuth * r8378 /bioclipse2/trunk/features/net.bio​clipse.xws4j_feature/feature.xml: Updated feature deps, copyright and information.
10:57 CIA-30 bioclipse: ospjuth * r8379 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.ui/META-INF/MANIFEST.MF: Updated version to 2.0.0.B20090123.
10:57 olass egonw: please update the wiki pages http://wiki.bioclipse.net/index.php?title​=List_of_stable_managers_in_bioclipse_2.0 and http://wiki.bioclipse.net/index.p​hp?title=Bioclipse2_release_plan with info on new features and their respective tests.
10:57 zarah olass's link is also http://tinyurl.com/68dyxn
10:58 olass @tell zarah: which one of the links did you shorten?
10:58 zarah Consider it noted.
10:58 olass zarah: when will you tell zarah this?
10:58 zarah olass: are you talking to *me*?
10:59 olass @msg zarah
10:59 zarah olass: You have no new messages.
10:59 olass @help
10:59 zarah olass: avaliable commands are botsnack clear-messages google help hi karma messages pelezilla ping plan replan restart seen slap start stop tell thanks unplan
10:59 olass @help messages
10:59 zarah olass: avaliable commands are botsnack clear-messages google help hi karma messages pelezilla ping plan replan restart seen slap start stop tell thanks unplan
10:59 olass @thanks
10:59 zarah you're welcome, olass :)
10:59 olass @ping
10:59 zarah olass: pong
11:00 edrin @stop
11:00 zarah edrin: There's nothing to stop.
11:00 olass @are
11:00 olass :-)
11:00 edrin @restart
11:00 olass lunch!
11:02 egonw @lunch
11:16 egonw http://gitready.com/ -> daily Git tips
11:16 egonw apparently... just subscribed
11:40 CIA-30 joined #bioclipse
11:40 shk3 hi olass
11:45 shk3 edrin
11:45 shk3 anybody?
11:45 edrin yes
11:45 edrin hi
11:45 zarah hello edrin, you fantastic person you
11:45 shk3 why is zarah not greeting my this way?
11:46 shk3 well, anyway.
11:46 shk3 I try to do the dependencies for the speclipse feature
11:46 shk3 if I compute these using the compute button, it adds dependencies to plugins.
11:46 shk3 I would like to have dependencies to features.
11:47 shk3 anybody an idea about that?
11:47 olass shk3: I stay away from the compute button on deps
11:47 shk3 ah
11:47 olass remove all plugin deps
11:47 shk3 check it manually?
11:47 olass add manually the features
11:47 olass I do that
11:47 olass I think it's much cleaner
11:47 shk3 hm, I am afraid I miss something
11:47 olass then you need to test
11:47 shk3 yes, features are much cleaner
11:47 olass and add
11:48 shk3 hm, ok
11:48 shk3 there is a net.bc.xml feature
11:48 shk3 but this does not contain any of the bioclipse xml related plugins.
11:48 olass ask egonw about that
11:48 shk3 that's what I would have expected
11:48 shk3 ok
11:48 shk3 thanks
11:48 olass I'm not sure it's finished yet
11:49 shk3 ok
12:01 egonw the net.bc.xml feature (ola, that one should go onto the update site) ensures all required plugins are added to have a validating XML parser
12:01 egonw Speclipse may, but must not, depend on it...
12:01 egonw I guess not... as speclipse users are not expected to edit the XML source
12:01 egonw not the typical user...
12:02 egonw Speclipse users may, however, if they wish, install the feature, to add the validating XML editor functionality
12:02 egonw that's what the XML Feature is for
12:05 shk3 ah ok
12:05 shk3 I need to include all the xom, cml, xpp3 etc. stuff
12:06 shk3 shouldn't we have a feature for that?
12:08 * egonw checks if there is a CML Feature
12:08 egonw olas is not so keen on many features
12:12 shk3 well, if we want feature based distributions, every plugin must be member of at least one feature, right?
12:12 egonw yes
12:15 shk3 that doesn't seem to be the case right now
12:16 gilleain joined #bioclipse
12:18 egonw shk3: OK, was not aware of that... please file bug report for plugins you find that are not part of a BC2 feature
12:18 shk3 ok
12:26 shk3 ah, there is a net.bioclipse.cml_feature
12:28 shk3 what is net.bioclipse.feature-patch for?
12:48 egonw for allowing updating of the Bioclipse2 core
13:04 CIA-30 bioclipse: egonw * r8381 /bioclipse2/trunk/plugins/net.biocl​ipse.cdk.jchempaint.business.test/: Removed folder which git apparently had not done; it was replaced 5 days ago with net.bioclipse.cdk.jchempaint.test/
13:06 CIA-30 bioclipse: egonw * r8382 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.jchempaint.business/: Removed folder which git apparently had not done; code has been moved 7 weeks ago to net.bioclipse.cdk.jchempaint/
13:14 shk3 so feature-patch is feature_core?
13:14 egonw no
13:14 egonw it's a patch to the core feature
13:17 shk3 and which one is the core feature? can't find it
13:17 egonw net.bioclipse_feature
13:19 shk3 ah, overlooked that
13:21 maclean joined #bioclipse
13:22 maclean am I here?
13:22 maclean ack.
13:22 egonw :)
13:22 maclean I'm gilleain in the mornings, and maclean in the afternoons.
13:22 egonw actually... you're not here, but on #cdk
13:22 egonw why is that?
13:22 egonw does caffeine make that much difference?
13:23 maclean Disconnected at lunch time when pc goes to sleep
13:23 maclean :)
13:26 maclean There I go.
13:41 shk3 egonw: could you make me a member of the cdk group in launchpad?
13:41 egonw yes, think so...
13:41 egonw what's your account?
13:41 shk3 stefan-kuhn
13:44 egonw done
13:49 shk3 "Enable translation by following the Change details link on your project's overview page and selecting Translations for this project are done in Launchpad."
13:49 shk3 can you do that?
13:49 shk3 looks like I can't
13:49 egonw URL?
13:49 shk3 at least no change details link exists
13:49 shk3 https://help.launchpad.net​/Translations/YourProject
13:55 egonw busy
13:55 egonw on it
14:04 olass joined #bioclipse
14:04 egonw OK, try on this page:
14:04 olass hi
14:04 zarah oh hai olass
14:04 olass @ping
14:04 zarah olass: pong
14:04 egonw https://translations.launchpad.net/jchempaint
14:04 egonw click the trunk series link
14:04 egonw shk3: there you can upload the main .pot file (The english one)
14:05 egonw and .po files for localized translations
14:05 egonw hi olass
14:05 egonw olass: there is no cheminfo perspective yet, right?
14:05 olass hi egonw
14:05 egonw olass: doing that now
14:05 olass egonw: hmm, there should be
14:05 olass ok
14:05 egonw really?
14:05 olass might be lost in bc1 -> bc2
14:05 egonw yes, think so
14:05 shk3 egonw: I get "The jchempaint project is not set up for translation in Launchpad. "
14:05 egonw yeah, same here
14:06 egonw click the "jchempaint Series: trunk" link
14:06 egonw there is an upload field
14:07 shk3 can't find that link
14:07 shk3 do I need to be a member of jchempaint project to see it?
14:07 egonw should be on: https://translations.launchpad.net/jchempaint
14:07 egonw yes, maybe
14:07 egonw but "CDK Developers" is owner
14:07 egonw so, I though it should have showed up for you...
14:07 egonw mom
14:08 shk3 might be oversight from my side
14:09 egonw will try to upload it myself...
14:09 egonw hang on
14:10 egonw can't find where to add you as project member...
14:13 egonw shk3: OK, will take a while... will report later
14:14 shk3 thanks anyway
14:16 egonw shk3: https://translations.launchpad​.net/jchempaint/trunk/+imports
14:16 egonw it needs approval by launchpad
14:18 shk3 so we have to wait?
14:18 egonw yes
14:21 shk3 ok
14:39 egonw olass: ping
14:45 shk3 updated bc
14:45 shk3 errors in webservices
14:45 shk3 net.bioclipse.ui.Activator.getDefault().CONSOLE.
14:46 shk3 CONSOLE cannot be resolved
14:46 egonw file a bug report, assigned to edrin and cc jonalv
14:46 egonw and masak
14:46 olass egonw: pong
14:47 egonw branding of the cheminfo feature
14:47 egonw is now done by the cdk.ui plugin
14:47 egonw but should be n.b.chemoinfo, right?
14:47 egonw don't think any branding is actually done... or?
14:47 egonw what sort of branding could I expect?
14:53 CIA-30 bioclipse: egonw * r8383 /bioclipse2/trunk/features/net.bioclips​e.chemoinformatics_feature/feature.xml: Added info on license of plugins included in this feature (fixes #13)
14:53 zarah bug #013 | http://tinyurl.com/7z5q8o
14:53 olass shk3: egonw: the branding is the feature image and the fact that name of the branding plugin appears as the name of the feature (unlogical, I know)
14:53 egonw ok, good
14:54 egonw will port that from cdk.ui to chemoinformatics then
14:54 olass egonw: yes, branding should be in n.bc.chemoinfo IMO too
14:54 olass good
14:56 shk3 is it not possible in bugzilla to choose assignees from a list or so?
14:56 shk3 if not, what's edrin's email?
14:57 egonw you can do that with Mylyn in Eclipse
14:57 egonw Ctrl-space
14:57 shk3 sorry, I don't want to bother with that mylyn stuff
14:58 egonw then make a list of all bug reports
14:58 egonw and look up edrin's email
15:01 shk3 aliban@gmx.net
15:02 CIA-30 bioclipse: ospjuth * r8384 /bioclipse2/trunk/plugins/net.bi​oclipse.ui/META-INF/MANIFEST.MF: Updated version to 2.0.0.B20090123.
15:03 CIA-30 bioclipse: ospjuth * r8385 /bioclipse2/trunk/plugins/net.bioclip​se.ui.business/META-INF/MANIFEST.MF: Updated version to 2.0.0.B20090123.
15:04 CIA-30 bioclipse: shk3 * r8386 /bioclipse2/trunk/features/net.biocl​ipse.speclipse_feature/feature.xml: prepared for upcoming release
15:06 olass egonw: what is org.xmlcml.cmlxom in externals?
15:06 egonw CMLXOM
15:07 egonw PMRs CML library
15:07 olass it is not listed on http://wiki.bioclipse.net/index.p​hp?title=Bioclipse2_release_plan
15:07 zarah olass's link is also http://tinyurl.com/5guree
15:07 olass should we not have it in release?
15:07 egonw we should
15:07 olass egonw: please update that page
15:07 egonw it's part of the chemoinfo featue
15:07 olass so no CML feature?
15:07 olass and no XML feature?
15:08 egonw [13:01:04] <egonw> the net.bc.xml feature (ola, that one should go onto the update site) ensures all required plugins are added to have a validating XML parser
15:08 olass Ok, could you please update that wiki page? I am following it for the release... need it up to date
15:09 * olass is checking out all plugins for the release from SVN
15:09 olass and all features
15:11 olass egonw: I guess rdf-feature not in release?
15:11 egonw correct
15:15 jonalv joined #bioclipse
15:15 jonalv hi
15:15 zarah ni hao jonalv
15:20 olass hi jonalv
15:20 olass edrin: around?
15:21 olass egonw: no CML feature in release? Should it go in chemoinformatics feature?
15:21 * olass is confused here
15:21 olass jonalv: please update site http://wiki.bioclipse.net/index.php?t​itle=Bioclipse2_release_plan#Contents
15:21 zarah olass's link is also http://tinyurl.com/5guree
15:21 olass structuredb entry
15:21 shk3 we need cml
15:22 shk3 I think
15:22 jonalv olass: I don't understand what I should do...
15:22 olass add plugins included in structuredb feature
15:23 olass to give an overview
15:23 jonalv dependenices_
15:23 jonalv ah plguins
15:23 jonalv not dependencies then?
15:28 olass jonalv: Do like all other features on the page, list the bioclipse-relevant plugins and omit spring+eclipse plugins
15:30 olass FYI: I will release with latest stable release of Eclipse, 3.4.1
15:30 jonalv and if they are bioclipse relevant Spring plugins?
15:43 CIA-30 bioclipse: ospjuth * r8387 /bioclipse2/trunk/plugins/net.biocli​pse.encryption/META-INF/MANIFEST.MF: Updated version to 2.0.0.B20090123.
15:43 CIA-30 bioclipse: jonalv * r8388 /bioclipse2/trunk/features/net.biocli​pse.structuredb_feature/feature.xml: removed usermanager from structuredb feature
15:48 shk3 olass: sorry, one more question
15:48 shk3 do you have a minute?
15:49 olass go on
15:49 olass busy with jonalv but please go ahead
15:49 shk3 ok
15:49 shk3 I want to test a save method in a plugin test
15:49 shk3 it gets the file name
15:49 shk3 so I do
15:49 shk3 spectrummanager.saveSpectrum(spectrum, "/Virtual/testSaveSpectrum.dx", SpectrumEditor.JCAMP_TYPE);
15:50 shk3 this failes because Virtual is not found
15:50 shk3 for cdkmangertest
15:50 shk3 this
15:50 shk3 cdk.saveMolecule(propane, "/Virtual/testSaveMolecule.mol", ICDKManager.mol);
15:50 shk3 works
15:50 shk3 what am I doing wrong?
15:50 shk3 any setup or so required?
15:51 egonw shk3: if olas can't answer it now, file a bug report, and I'll have a look at your source code
15:51 shk3 ok
15:51 shk3 will do so
15:51 olass shk3: this is not my doing
15:51 shk3 if nobody has an idea
15:52 shk3 ok
15:52 shk3 will file a bug report
15:52 egonw olass: what is a 'org.eclipse.ui.contexts' ?
15:52 olass egonw: Are you working with CDKManager?
15:52 egonw not right now
15:52 olass egonw: we donät use it currently
15:53 olass but it is in principle, you could work in a 'context'
15:53 olass and have UI customized for this
15:53 olass like 'bioinformaytics' I guess
15:53 maclean context != perspective?
15:54 egonw ok, so something above perspective even?
15:54 shk3 <olass> egonw: we donät use it currently
15:54 shk3 decent languages have umlaute, I suppose
15:54 olass :-)
15:54 maclean sensible languages have eliminated all diacritics.
15:54 egonw which language doesn't?
15:54 olass maclean: I agree, its confusing
15:54 olass haven't gripped it 100% yet
15:55 egonw sensible countries have also eliminated all critics
15:55 maclean North Korea? Zimbabwe?
15:56 maclean hhmm:
15:56 maclean http://pookzilla.net/wp/2006/10/co​ntext-capability-and-perspective/
15:56 zarah maclean's link is also http://tinyurl.com/75eq22
15:58 maclean sorry, that page doesn't actually explain contexts, only capabilities (!!)
15:59 shk3 just updating the list of stable managers
15:59 shk3 what does something like
15:59 shk3 InChIManagerPluginTests: 9/9, 0
15:59 shk3 mean?
15:59 shk3 what is 9/9 and 0?
16:00 egonw read explanation earlier on the page
16:00 egonw (unless someone removed that)
16:01 shk3 ah, it's before the TOC.
16:01 shk3 didn't look there
16:12 edrin olass: i am here now for short
16:13 olass edrin: what does your JS editor do apart from the JS editor in bc2?
16:13 olass I donät want to add your jseditor to beta release on friday
16:13 olass just FYI
16:13 edrin nothing
16:13 olass we need to agree on one JSEditor
16:14 olass edrin: ok
16:14 olass I will just ignore it then?
16:14 egonw olass: ping
16:14 olass pong
16:14 egonw in .chemoinformatics feature.xml
16:14 edrin it's just an editor. right now it pushs stuff to its own rhino instance. (in main thread or optionally in its own thread
16:14 egonw I get a lot of warnings about plugins elements not having @unpack="false"
16:14 egonw any reason not to add that?
16:14 egonw I actually like to see them as pluginbla.jar instead of folder
16:15 olass egonw: no idea about that
16:15 olass I agree with you too
16:15 egonw ok
16:15 olass jar is nicer
16:15 olass but no idea
16:15 olass maybe ask on eclipse ML?
16:16 edrin olass: i could make the editor to push scripts to the rhino implementation of bc2 core, of course, but i would need the stuff to return proper debug info...
16:16 edrin on the other hand, calling rhino is not much magic on its own, the managers are working, too
16:17 olass ok
16:17 olass just so we agree on it
16:17 edrin olass: not to put it in bc2?
16:17 olass yes
16:17 olass not in released features at least
16:17 edrin i dont mind
16:17 olass other alternative is to replace the existing jseditor
16:18 olass which I don't mind either
16:18 olass but it must work with managers
16:18 edrin i think the current editor is a discontinued buggy sf project
16:18 olass it is
16:18 olass if you want to extend yours to be better, that would indeed be great!
16:18 edrin the editor in rhino is working with the managers and it returns helpful error messages with line numbers
16:19 edrin i mean the editor in the "rhino" plugin
16:19 edrin maybe i should rename it to net.bioclipse.jseditor or something
16:20 edrin olass: what does masak like?
16:20 olass toffefee!
16:20 olass :-)
16:21 olass edrin: that is the name of the jseditor in bc2 trunk now
16:21 edrin ok
16:21 olass please talk to masak about what jseditor should go in friday release
16:21 edrin well, what do you think? do you want to replace the current jseditor with the one in xws/ ?
16:22 edrin ok
16:22 olass I leave that to you and masak
16:22 olass not my decision
16:22 olass masak is in charge of that
16:22 olass so you need to talk to him
16:22 edrin k
16:22 olass send him an email please
16:23 * olass got so many things before the release
16:23 olass I just want things to work
16:23 edrin it's a beta, right?
16:23 olass yes
16:23 olass bugs are very OK
16:23 edrin olass: i think it works nicely, did you try ?
16:23 olass but I'd like to start getting a stable list of plugins
16:23 olass yes
16:24 edrin sure
16:24 olass but the old one was just as nice
16:24 olass I saw no improvement
16:24 olass aoart from the console
16:24 olass and the old one had an outline as well
16:24 edrin the old one wont be extensible much i thing
16:24 olass agreed
16:24 egonw grmph...
16:24 egonw the chemoinfo perspective does not show up :(
16:25 olass edrin: if you have intentions to extend it, then we should definitely replace it
16:25 edrin sure, i want to extend it
16:25 olass bad chemoinfo persp
16:25 olass be nice to egonw
16:27 olass jonalv: resolving a conflict in the feature.xml...
16:28 CIA-30 bioclipse: egonw * r8389 /bioclipse2/trunk/ (7 files in 6 dirs): Copied chemoinformatics perspective code from Bioclipse1, but needs fixing.
16:28 olass egonw: should we have org.opensci.cdk.ioformats in bioclipse feature!?
16:28 CIA-30 bioclipse: egonw * r8390 /bioclipse2/trunk/features/net.bioclips​e.chemoinformatics_feature/feature.xml: Don't unpack CDK plugins; add two missing plugins (cdk.annotation and cdk.ioformats); fixed name of jcp plugin to have no .business
16:29 egonw olass: yes
16:29 olass why?
16:29 egonw format detection
16:29 olass is that not chemoinfo specific?
16:29 CIA-30 bioclipse: egonw * r8391 /bioclipse2/trunk/plugins/net.bioclipse.ch​emoinformatics/src/net/bioclipse/chemoinfo​rmatics/ChemoinformaticsPerspective.java: Perspective now based on the Default, but adds wizard shortcuts, etc... well, should, because it doesn't :(
16:29 olass why not in chemoinfo feature?
16:30 egonw because now the default bioclipse recognizes what something is...
16:30 olass and?
16:30 egonw and it could, theoretically, indicate, hej... I see you have this file type... install that feature to open it in Bioclipse
16:30 olass ok
16:30 olass btw, did you get the property to show up in properties view?
16:30 egonw no, not yet
16:30 olass you got my pointers to tabbed properties?
16:31 egonw should file a bug report for that
16:31 egonw yes
16:31 olass ok, good
16:31 olass ok
16:31 olass adding the plugins to core feature
16:31 egonw yes, cdk.ioformats and cdk.annotation
16:31 egonw two really small plugins
16:31 olass 4
16:31 egonw 4kB... might be, no idea
16:31 olass gist as well
16:31 olass 4 plugins
16:31 egonw ah, yes, please
16:32 olass id="org.openscience.cdk.ioformats"
16:32 olass id="net.bioclipse.ioformats"
16:32 olass id="org.openscience.cdk.annotation"
16:32 olass id="net.bioclipse.gist"
16:32 egonw yes, think so
16:32 olass in the future, please update wiki page too when updating the feature
16:32 olass the core feature is my responsibility :-)
16:32 egonw we really need to have web pages autogenerated for this...
16:32 olass indeed
16:32 egonw I though I had added them to feature.xml already...
16:32 egonw sorry about that
16:32 olass no, they were
16:33 olass wiki was not
16:33 egonw ah, ok
16:34 jonalv olass: Do you want me to add org.appache.commons.codec to that web page under the structuredb feature or do you want me to leave that one out?
16:34 olass leave it
16:34 olass only plugins in our repo
16:34 jonalv aha oki
16:35 CIA-30 bioclipse: ospjuth * r8392 /bioclipse2/trunk/features/net.​bioclipse_feature/feature.xml: Added dep to plugins encryption and usermanager + updated version to beta release.
16:36 olass jonalv: ok, feature updated in r8392
16:37 * jonalv rebaes svn
16:37 olass hmm, no
16:37 olass seems my commit was lost
16:37 * olass hates SVN sometimes
16:40 jonalv olass: I din't think so it works for me now... :)
16:41 olass true
16:41 * olass hates subclipse
16:44 * egonw is going for dinner now
17:00 maclean jonalv : about org.apache.commons.codec - I get a missing dependency on it whenever I start up.
17:03 maclean Erk. Now I get 'Manifest has no main section'. I reverted.
17:04 maclean Ahhh. Now, on update it is back on 'missing constraint'.
17:17 jonalv maclean: what are yoiutrying to run?
17:17 jonalv how do I get my mac to not use acrobat reader for opening pdfs?
17:19 CIA-30 bioclipse: shk3 * r8393 /bioclipse2/trunk/plugins/net.biocl​ipse.specmol/src/net/bioclipse/spec​mol/business/ISpecmolManager.java: corrected comment
17:19 maclean jonalv : well structuredb wants the encryption plugin, and that wants the commons.codec
17:20 maclean Also, I don't know, pdfs always open in Preview.app for me.
17:22 maclean http://onflash.org/ted/2007/08/osx-​open-with-and-always-open-with.php
17:22 zarah maclean's link is also http://tinyurl.com/8tqdhr
17:22 jonalv maclean: strange I just had structuredb up and running...
17:22 maclean (I didn't know this!)
17:22 CIA-30 bioclipse: shk3 * r8394 /bioclipse2/trunk/plugins/n​et.bioclipse.specmol.test/: Initial import.
17:23 maclean jonalv : that link was for you, btw.
17:23 maclean also, it just complains about it, I guess that it is still running somehow.
17:23 jonalv maclean: I got help from Martin here... :)
17:24 jonalv oh
17:24 CIA-30 bioclipse: shk3 * r8395 /bioclipse2/trunk/plugins/n​et.bioclipse.specmol.test/ (17 files in 10 dirs): Initial import.
17:29 jonalv I have to leave now
17:29 jonalv maclean: I hope you find a solution
17:29 maclean thanks, it's not a pressing need, so don't worry about it.
18:14 edrin egonw: I fully agree that integration of gist into bc will make it "much" more powerful
18:15 edrin *much*
18:15 egonw good, because the gist plugin will be part of the next release :)
18:15 edrin egonw: but for this a contemporary data container is required
18:15 egonw a what?
18:15 edrin and recursive script invocation
18:16 edrin some kind of local (simple!) database
18:16 edrin where one can push the results to
18:16 edrin and request them from other scripts...
18:16 edrin and/or the possibility to call other scripts from a script
18:16 edrin and pass data
18:17 edrin and get the outcome of this call
18:17 edrin this way you drag and drop your codish work
18:18 egonw yes, sounds good
18:19 egonw please write it up as use case in the wiki
18:19 shk3 is the new renderer able to do atom numbers?
18:19 shk3 I would need that in the specmol editor
18:19 egonw no, don't think so
18:21 shk3 hm, do you think I could do this?
18:21 shk3 didn't work on the renderer till now
18:23 egonw yes, please do make a branch and add it...
18:23 egonw gilleain and Gpox can then pull, review and apply your patches
18:31 gilleain joined #bioclipse
19:27 edrin left #bioclipse
19:36 CIA-30 bioclipse: egonw * r8396 /bioclipse2/trunk/features/net.biocl​ipse.jchempaint_feature/feature.xml: Don't unpack CDK jars; net.bioclipse.ui.* version updates for Fri release
19:36 CIA-30 bioclipse: egonw * r8397 /bioclipse2/trunk/features/net.bioclips​e.chemoinformatics_feature/feature.xml: Require Fri release of Bioclipse core; removed duplicate cdk.jchempaint entry
20:10 ChanServ joined #bioclipse
20:10 stain joined #bioclipse
20:17 CIA-30 bioclipse: egonw * r8398 /bioclipse2/trunk/ (2 files in 2 dirs): Added missing dependencies, which no error messages were send to STDOUT; export all packages of the chemoinfo plugin. The ChemoInfo perspective finally shows up (fixes #271)
20:17 zarah bug #271 | http://tinyurl.com/89fchr
20:55 CIA-30 bioclipse: egonw * r8399 /bioclipse2/trunk/plugins/net.bioc​lipse.chemoinformatics/plugin.xml: Added icons and prefered perspective to New CML|MDL wizards
21:56 edrin joined #bioclipse
22:01 CIA-30 bioclipse: edrin_t * r8400 /bioclipse2/trunk/plugins/net.bioclipse​.xws4j/src/net/bioclipse/xws4j/views/se​rvicediscovery/BindingGenerator.java:
22:09 edrin hi
22:09 zarah oh hai edrin
22:26 CIA-30 bioclipse: edrin_t * r8401 /bioclipse2/trunk/plugins/net.bioclipse.w​ebservices/src/net/bioclipse/webservices/ (3 files in 3 dirs):

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