Camelia, the Perl 6 bug

IRC log for #bioclipse, 2007-12-06

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All times shown according to UTC.

Time Nick Message
07:42 masak joined #bioclipse
08:12 steinbeck joined #bioclipse
08:13 egonw joined #bioclipse
08:27 olas_ joined #bioclipse
08:34 olas_ egonw: around?
08:34 CIA-19 bioclipse: ospjuth * r4400 /trunk/plugins/net.bioclipse.compute/ (icons/icon_wand.gif plugin.xml): New icon for compute wizard
08:34 olas_ egonw: I have soem questions for the 1.1.6 release
08:35 olas_ net.bioclipse.bibtex is required in spectrum feature, but is in playground
08:35 olas_ Should I remove dep or move bibtex to trunk/plugins?
08:35 olas_ Also, what about the CASE feature? Is that operational?
08:36 olas_ egonw: let me know when you get back
08:36 egonw mom, will move it to trunk/plugins
08:36 egonw no, CASE is still under development
08:36 olas_ please move it to playground/features
08:37 olas_ right?
08:40 steinbeck Yeah - bloody CASE feature - needs to be worked on :-)
08:41 egonw olas_: yes
08:41 egonw steinbeck: yes, we should try to set up a update site for the case too...
08:41 egonw but not on the main bioclipse site...
08:41 egonw not the same update site at least...
08:41 steinbeck yes - correct.
08:41 egonw steinbeck: still  haven't gotten around to trying the structgen when the code was just finished...
08:42 egonw to make sure nothing broke afterwards... or detect that at least...
08:42 steinbeck I'm currently writing stuff to participate in the first round to get EMBL phd students - CASE will be a topic
08:42 egonw steinbeck: I also suggest we set up an extension point for the structure generation, so that we can hook in molgen
08:42 steinbeck egonw: good point
08:42 egonw brb
08:42 steinbeck BTW, I saw the original SMOG code is freely availalbe
08:44 olas_ hi steinbeck
08:44 steinbeck hi olas_
08:44 egonw what was SMOG again?
08:44 olas_ congrats again to you steinbeck!
08:44 steinbeck SMOG was the code of a structure generator
08:44 steinbeck olas_: thanks
08:44 steinbeck egonw: ... on which the CDK one is based
08:45 olas_ egoonw: is move complete?
08:46 egonw wait... I got other things to do too, you know...
08:46 olas_ aah
08:46 egonw hang on...
08:46 olas_ I'll do it then
08:46 olas_ no worries
08:46 egonw stop
08:46 egonw on it
08:46 olas_ ok?
08:46 * olas_ is building bioclipse1.1.6
08:47 olas_ no worries, got some other things that needs fixing too
08:47 egonw olas_: bibtex *is* in trunk/plugins
08:47 olas_ hmm
08:47 olas_ indeed it is
08:47 olas_ strange
08:47 olas_ must be some other error then
08:48 olas_ egonw: what feature should bibtex go in?
08:48 egonw have a meeting in 10 minutes, which I still need to prepare...
08:48 egonw spectrum for now
08:48 olas_ ok
08:48 egonw it's used by submit-to-nmrshiftdb
08:50 olas_ ah
08:53 olas_ that was the problem, iwas not in spectrum feature
08:53 olas_ ok, fixed it
08:53 CIA-19 bioclipse: ospjuth * r4401 /trunk/features/net.bioclipse.​spectrum-feature/feature.xml: Added bibtex to spectrum feature
09:08 jonalv joined #bioclipse
09:12 CIA-19 bioclipse: ospjuth * r4402 /trunk/bioclipsUpdateSite/site.xml: Updated update-site
09:12 CIA-19 bioclipse: ospjuth * r4403 /trunk/plugins/net.bioclipse/s​rc/net/bioclipse/preferences/ (3 files): Updated preference pages to select first line and updated Text size in dialogs
09:16 CIA-19 bioclipse: ospjuth * r4404 /trunk/ (33 files in 33 dirs): Update for release 1.1.6: Version, provider, dependencies, removed unused views, updated icons
09:20 CIA-19 bioclipse: ospjuth * r4405 /trunk/plugins/net.bioclip​se.biojava.ui/plugin.xml: Removed unused view
09:21 CIA-19 bioclipse: ospjuth * r4406 /trunk/plugins/net.bioclipse.biojava.ui/ (META-INF/MANIFEST.MF plugin.xml): Removed duplicate progress view and updated version
09:22 CIA-19 bioclipse: ospjuth * r4407 /trunk/plugins/net.bioclipse.chart/ (icons/chart.jpg plugin.xml): New icon and name for chart view
09:23 CIA-19 bioclipse: ospjuth * r4408 /trunk/features/ (4 files in 4 dirs): Updated version and set features to depend on 1.1.6
09:24 CIA-19 bioclipse: ospjuth * r4409 /trunk/plugins/net.bioclipse.​cdk.ui/META-INF/MANIFEST.MF: Set version to 1.1.6
09:33 CIA-19 bioclipse: ospjuth * r4410 /trunk/plugins/net.bioclipse/ (about.mappings plugin.properties): Updated plugin version and main contributors in about text
09:50 CIA-19 bioclipse: ospjuth * r4411 /trunk/plugins/net.bioclipse/build.properties: Updated build for 1.1.6
09:58 CIA-19 bioclipse: ospjuth * r4412 /trunk/plugins/de.ipbhalle.msbi.mz​data.editor/META-INF/MANIFEST.MF: Removed org.eclipse.ui.editor as it depends on IDE. Don't know how many times I've done this, people keep adding it all the time...
09:59 CIA-19 bioclipse: ospjuth * r4413 /trunk/features/net.bioclipse.​spectrum-feature/feature.xml: Updated feature to not require ui.editor
10:07 EskilA joined #bioclipse
10:23 CIA-19 bioclipse: biocoder * r4414 /trunk/plugins/net.bioclipse.statistics/src/​net/bioclipse/editors/MatrixGridEditor.java: Removed debug output
10:46 CIA-19 bioclipse: biocoder * r4415 /trunk/plugins/net.bioclipse.chart/src​/net/bioclipse/chart/ChartUtils.java: Fixed a bug causing ClassCastException
10:47 steinbeck left #bioclipse
11:06 edrin joined #bioclipse
11:07 edrin hi
11:13 olas_ hi edrin
11:13 edrin hi olas
11:14 CIA-19 bioclipse: ospjuth * r4416 /trunk/plugins/net.bioclipse.descriptor/src/net​/bioclipse/jobs/DescriptorCalculationJob.java: Fixed a nasty bug that made editor open with unparsed input after close of first qsar_results.csv.
11:17 egonw olas_: did I write a QSAR tutorial?
11:17 olas_ yes, think so
11:17 egonw good :)
11:17 olas_ please update it
11:17 olas_ or verify that it's up2date
11:18 egonw it is
11:18 olas_ I'm working my way towards 1.1.6
11:18 olas_ good
11:18 egonw last time I made changes to the set up, at least
11:18 * olas_ is at lunch
11:18 egonw olas_: is 1.1.6 a good replacement for 1.0.x?
11:19 egonw I thinks it might be...
11:19 egonw that is, should 1.0.x users use 1.1.6 instead?
11:19 egonw if so... then version might be branded 1.2.0
11:19 egonw indicating that everyone should stop using the 1.0.x series
11:20 * egonw awaits Olas answer when he gets back from the sauna^W^Wlunch
11:57 olas_ joined #bioclipse
11:57 olas_ egonw: you have a good point
11:57 olas_ I think we should say that
11:57 olas_ even though it is not really stable
11:58 olas_ but we can always release 1.2.1 later if need be
11:58 olas_ I will update to 1.2.0 (that is quite some work actually)
12:00 edrin http://xkcd.com/350/
12:00 edrin ;)
12:00 edrin they are soo cool
12:00 egonw olas_: excellent
12:01 egonw yeah, very nice one
12:01 egonw edrin: thanx for that link
12:08 edrin :
12:08 edrin yeah :)
12:28 CIA-19 bioclipse: ospjuth * r4417 /trunk/plugins/ (3 files in 3 dirs): Resized icons to 16x16
13:00 CIA-19 bioclipse: ospjuth * r4419 /trunk/plugins/net.bioclipse.cdk.ui/src​/net/bioclipse/model/CDKResource.java: Removed question "would you like to switch to chemoinfo persp as it is in wrong place. Should be moved from parse to openEditor.
13:01 * olas_ is off for a short meeting
13:06 jonalv olas: ta med henne ned hit och häla på oxå?
13:06 jonalv hälsa
13:07 jonalv ups wrong channel? (at least wrong language..)
13:12 * jonalv is off buying coca cola (kaskelot it's your fault...)
13:17 thomas_ku joined #bioclipse
13:23 EskilA jag testade att bygga en jar av grid från repot, men det gjorde ingen skillnad på selektion
13:27 jonalv posta bugg eller till mejllistn då
13:53 CIA-19 bioclipse: jonalv * r4420 /branches/bioclipse2/bioinformatics/pl​ugins/net.bioclipse.biojava.business/ (9 files in 4 dirs): Now the spring-osgi bundle can be started from console at least...
13:59 egonw olas_: will be away for a party the rest of the day...
13:59 egonw will be back online tomorrow
14:15 masak joined #bioclipse
14:25 jonalv I just realised why I get a deadlock when starting the plugins
14:25 jonalv ÄI think scripting will become a plugin of it' ows on bc2
14:31 * jonalv and masak++ will now refactor out the scripting into a plugin of it's own.
14:37 olas_ great
15:00 masak hmm
15:01 masak upon investigating ScriptingTools, I suspect it should be moved to net.bioclipse.ui
15:01 olas_ hmm eller hrrmmm?
15:01 masak olas_: just hmm
15:04 olas_ ok, just wanted to check
15:04 jonalv what's the difference?
15:04 edrin olas_: are there already any instructions on how to make a plugin for bc2?
15:05 CIA-19 bioclipse: ospjuth * r4422 /trunk/plugins/net.bioclipse/about.mappings: Updated about text to 1.2.0
15:05 EskilA joined #bioclipse
15:05 CIA-19 bioclipse: ospjuth * r4423 /trunk/plugins/net.bioclipse.webservices/src​/net/bioclipse/plugins/bc_webservices/wizard​s/wizardpages/EBIWSDbfetchWizardPage.java: Fixed bug that broke download of PDB if uppercase ID in query
15:05 edrin i was about to port the rhino plugin to bc2 however i am a little bit confused with the naming conaventions (where are they?) and svn structure of bc2
15:05 olas_ edrin: well...
15:06 olas_ edrin: for porting scripting languages, talk to masak
15:06 olas_ I think the JS is already ported :-)
15:06 jonalv edrin: what does the rhino plugin do?
15:06 * jonalv thought we already ran rhino...
15:06 edrin jonalv: it runs java script scripts
15:06 masak did somebody mention scripting? :)
15:07 olas_ edrin: generally about BC2 is that all plugins should be able to run in Eclipse
15:07 olas_ masak is working hard on scripting
15:07 olas_ in BC2
15:07 masak edrin: the names are changing as we speak
15:07 jonalv edrin: masak and I are refactoring the scripting stuff in bc2 right now so the question is somewhat complex...
15:07 olas_ and masak + jonalv will build into scripting into the core of Bioclipse2
15:07 masak I'm not sure it's possible to contribute today unless you're in Uppsala
15:07 edrin it's nearly impossible to write code for bc then...
15:07 masak in this office, in fact
15:07 masak edrin: yes, sorry
15:08 masak it's a sea of change right now
15:08 olas_ edrin: how is XMPP coming along?
15:08 masak we're hoping it's for the better
15:08 edrin currently it's not because I am doing experiments
15:08 masak edrin: if it's any consolation, I'm also eager to see your file scripting included in bc2. I will get on it as soon as I can
15:11 CIA-19 bioclipse: jonalv * r4424 /branches/bioclipse2/core/plugins/net.bioclips​e.core/src/net/bioclipse/core/Activator.java: Added the start() method to the Activator in core which someone removed in some commit just reasonly...
15:11 jonalv Yes we have acommit bot!
15:16 CIA-19 bioclipse: ospjuth * r4425 /trunk/plugins/net.bioclipse.biojava.ui/src/net/​bioclipse/extensions/PDBSequenceExtractor.java: Replaced sysout with logger.debug
15:19 olas_ masak: please make sure that the wiki gets updated with the latest info about the scripting in bc2
15:19 olas_ when you're done, thaat is
15:20 masak olas_: ok
15:21 CIA-19 bioclipse: ospjuth * r4426 /trunk/bioclipsUpdateSite/site.xml: Updated for 1.2.0 features
15:31 CIA-19 bioclipse: ospjuth * r4427 /trunk/plugins/net.bioclipse/bioclipse.product: Updated product for 1.2.0
15:33 CIA-19 bioclipse: ospjuth * r4428 /trunk/features/net.bioclipse.data.d​rugbank-feature/feature.properties: Updated drugbank feature to be named drugbank feature and not BODR
15:46 CIA-19 bioclipse: carl_masak * r4429 /branches/bioclipse2/core/plug​ins/net.bioclipse.scripting/: Initial import.
15:46 CIA-19 bioclipse: carl_masak * r4430 /branches/bioclipse2/core/plu​gins/net.bioclipse.scripting/ (23 files in 8 dirs): Initial import.
15:48 CIA-19 bioclipse: carl_masak * r4431 /branches/bioclipse2/core/plugins​/net.bioclipse.scripting.tests/: Initial import.
15:48 CIA-19 bioclipse: carl_masak * r4432 /branches/bioclipse2/core/plugin​s/net.bioclipse.scripting.tests/ (10 files in 6 dirs): Initial import.
15:49 CIA-19 bioclipse: carl_masak * r4433 /branches/bioclipse2/core/plugins/ (11 files in 9 dirs):
15:49 CIA-19 bioclipse: * moved scripting out of net.bioclipse.core
15:49 CIA-19 bioclipse: * jonalv++
15:56 jonalv YES SPRING OSGI IS NOW WORKING FOR ME!
15:56 jonalv sorry for screaming... but it's a big moment... :)
15:57 jonalv commit comming real soon now... :)
16:01 CIA-19 bioclipse: jonalv * r4434 /branches/bioclipse2/ (4 files in 3 dirs):
16:01 CIA-19 bioclipse: [net.bioclipse.ui]
16:01 CIA-19 bioclipse: Added config.ini which starts the spring osgi bundle
16:01 CIA-19 bioclipse: [net.bioclipse.biojava.business]
16:01 CIA-19 bioclipse: Changed to work with the movement of the scripting parts
16:01 CIA-19 bioclipse: In general the fact that scripting is a separate plugin means that the deadlock occuring when starting bioclipse with spring osgi is no more and things are now working
16:02 masak yay!
16:02 masak jonalv++
16:06 olas_ excellent!
16:11 * olas_ has just released Bioclipse1.2.0RC1
16:17 masak yipes! :)
16:17 masak any CHANGELOG?
16:19 olas_ nope
16:19 olas_ not yet
16:19 olas_ (and will be very small)
16:19 olas_ please help me write it
16:20 masak well, what's changed? :)
16:26 olas_ what have you changed?
16:27 olas_ please test as much as you can
16:27 olas_ charts
16:27 olas_ matrices
16:27 olas_ js/rhico console
16:27 olas_ rhino
16:28 masak oki
16:29 jonalv olas: vi behöver prata om huir den här "inspelningen av anrop" ska gå till egentligen?
16:29 jonalv wow wrong language...
16:29 jonalv sry
17:06 CIA-19 bioclipse: jonalv * r4435 /branches/bioclipse2/core/plugins/ (2 files in 2 dirs): Removed special config.ini from net.bioclipse.ui. The activator in net.bioclipse.core now starts the org.springframework.osgi.bundle.extender bundle if it finds it
18:17 test joined #bioclipse
18:17 Topic for #bioclipseis now An open source workbench for chemo- and bioinformatics - http://www.bioclipse.net/ | BiclipseWiki => http://wiki.bioclipse.net/ !! | logs => http://colabti.de/irclogge​r/irclogger_logs/bioclipse & http://moritz.faui2k3.org/irc​log/out.pl?channel=bioclipse | Dieter wrote an article for Eclipse Magazine: http://eclipse-magazin.de/itr/ausg​aben/psecom,id,359,nodeid,228.html
18:17 Topic for #bioclipseis now An open source workbench for chemo- and bioinformatics - http://www.bioclipse.net/ | BiclipseWiki => http://wiki.bioclipse.net/ !! | logs => http://colabti.de/irclogge​r/irclogger_logs/bioclipse & http://moritz.faui2k3.org/irc​log/out.pl?channel=bioclipse | Dieter wrote an article for Eclipse Magazine: http://eclipse-magazin.de/itr/ausg​aben/psecom,id,359,nodeid,228.html
18:29 edrin left #bioclipse
19:06 edrin joined #bioclipse
19:27 CIA-31 joined #bioclipse

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