Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-08-05

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All times shown according to UTC.

Time Nick Message
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07:51 olas hi all
07:51 zarah hi olas
07:51 olas zarah: dz
07:51 zarah you're welcome, olas :)
07:51 olas zarah: any messages for me?
07:51 zarah olas: you've just exceeded my capabilities :/
07:52 olas zarah: messages
07:52 zarah olas: You have no new messages.
07:52 olas :-(
07:52 masak joined #bioclipse
07:52 olas hi masak
07:53 * olas is rewriting chemical selections in Bioclipse
07:53 olas this time I will make it right!
07:53 olas grr
07:53 olas there are so many ways of selecting/updating/highlighting
07:54 * masak is rewriting the multiple aligner to make use of biojava
07:54 masak the code is much prettier now
07:54 zarah masak: You have new messages. Write '@messages' to read them.
07:55 masak aw, ok
07:55 masak @massage
07:55 zarah masak: jonalv said I fear the Bioclipse alpha 01 tag you made is broken since the cdk svn:externals in it probably points to trunk. Or did you remember to change that to the current version at that time?
07:55 zarah masak: olas said I'd like to be able to start my sentences with help, and propose @help to lead to zarah help
07:55 zarah masak: egonw said that zarah did not tinyurl the link https://bugs.launchpad.net/debia​n/+source/sun-java5/+bug/162232
07:55 masak help does this trigger?
07:55 zarah masak: avaliable commands are clear-messages google help hi karma messages restart seen slap tell thanks
07:56 masak yeah, that's bad
07:56 masak olas: will change
07:56 masak @tell jonalv no, I did not remember to freeze cdk. never too late, though
07:56 zarah Consider it noted.
07:58 masak @tell egonw zarah is using the latest within URL-recognizing technology. I'm not sure there's a lot I can do if it doesn't recognize stuff. my guess is that the plusses confuse things; most probably a plus is not really allowed within a URL, but browsers handle them behind the scenes. or something.
07:58 zarah Consider it noted.
07:58 masak zarah++
07:59 egonw que???
07:59 egonw + are certainly allows in URLs !
07:59 egonw it's part of the specs
07:59 egonw query part
08:01 jonalv joined #bioclipse
08:01 jonalv moin
08:01 zarah hi jonalv
08:01 zarah jonalv: You have new messages. Write '@messages' to read them.
08:01 jonalv zarah: tell me
08:01 zarah jonalv: masak said no, I did not remember to freeze cdk. never too late, though
08:15 masak egonw: you're most likely right. I don't know why she didn't match on it. I've noticed it for some URLs too, but so far haven't seen a pattern
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08:16 egonw masak: hahahah... that was a funny statement :)
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08:52 masak egonw: unintentionally so :)
08:56 * masak is becoming fond of BioJava's data model
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09:02 egonw olas: subversive plugins have license texts with multiple licenses
09:02 egonw seems not that uncommon
09:04 CIA-49 bioclipse: carl_masak * r6461 /bioclipse2/trunk/plugins/net.bioc​lipse.biojava.ui/src/net/bioclipse​/biojava/ui/editors/Aligner.java:
09:04 CIA-49 bioclipse: [Aligner] home-brewed brittle parser replaced by Biojava
09:04 CIA-49 bioclipse: call to IOTools.readFastaProtein()
09:11 olas masak: do you use BiojavaX?
09:12 olas it has a reader that detects diferent formats
09:12 masak olas: aye
09:12 olas but I guess you knew that?
09:12 masak but I'm not there yet
09:12 CIA-49 bioclipse: carl_masak * r6462 /bioclipse2/trunk/plugins/net.bioc​lipse.biojava.ui/src/net/bioclipse​/biojava/ui/editors/Aligner.java: [Aligner] adapted comments, corrected indentation
09:12 olas right, sorry :-)
09:12 masak olas: I'm learning as we speak
09:48 CIA-49 bioclipse: carl_masak * r6463 /bioclipse2/trunk/plugins/net.bioc​lipse.biojava.ui/src/net/bioclipse​/biojava/ui/editors/Aligner.java: [Aligner] moved some boilerplate into a generating method
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10:37 CIA-49 bioclipse: ospjuth * r6464 /bioclipse2/trunk/plugins/net.bioclipse.cdk10.​jchempaint/src/net/bioclipse/cdk10/jchempaint/ (5 files in 3 dirs): Synchronized selections between JCP, outline, and 2dView. Also clears views on editor close.
10:56 CIA-49 bioclipse: shk3 * r6465 /bioclipse2/trunk/plugins/net.bioclipse.spectrum/ (4 files in 3 dirs): working on the spectrum editor
11:41 edrin joined #bioclipse
11:41 edrin hi
11:41 zarah hi edrin
11:57 olas hi edrin
11:57 olas did you start with an outline for XMPP based services?
11:58 * olas is eager to start
13:13 masak olas: re "it has a reader that detects diferent formats":
13:14 masak I've tried it now, and it doesn't recognize my protein Fasta file
13:14 gilleain is it preferable to use only pre-java5 code in bioclipse, or to use things like loop iterators and autounboxing?
13:14 masak gilleain: feel free.
13:14 masak we're using Java 5 here.
13:15 gilleain Okay, cool. I'll try to resist adding "this" everywhere - a bad habit from python...
13:16 masak :)
13:16 shk3 I think bioclipse needs java5 in many places, doesn't it?
13:16 masak shk3: most likely.
13:16 shk3 e. g. cdk trunk needs it and this is a central component
13:16 gilleain oh, what, for annotations?
13:24 shk3 can be used, i would say
13:24 shk3 but never really cared about annotations
13:30 jonalv joined #bioclipse
13:35 jonalv uhm net.bioclipse.jmol and net.bioclipse.spectrum is not compiling for me. Should they?
13:36 jonalv zarah?
13:36 zarah jonalv: yes?
13:36 jonalv zarah: good
13:36 zarah jonalv: excuse me?
13:36 shk3 spectrum should
13:36 jonalv zarah: you are excused
13:36 zarah jonalv: oh, thank you, thank you!
13:37 jonalv shk3: I wonder what might have gone wrong then...
13:37 shk3 jonalv: looks like there was a problem with commit
13:37 shk3 jcamp library is not under snv control
13:37 jonalv uhm okey
13:37 shk3 it was, and i updated it
13:37 shk3 checking for this
13:38 jonalv as for jmol that's olas right?
13:38 shk3 jonalv: please try update
13:40 jonalv shk3: now it compiles :)
13:43 shk3 ah
13:43 shk3 no idea how the update became a delete...
13:44 jonalv :)
13:56 olas joined #bioclipse
13:57 jonalv olas: what\s up with jmol?
13:58 olas not much
13:58 jonalv it doesn't compile for me...
13:58 olas aha
13:59 olas please update
14:00 olas update CP
14:00 olas or clean
14:03 jonalv now it seems to work
14:04 olas gotcha
14:09 masak olas: I'm re-adding sequences/ that you removed from n.b.data.sampledata, since I use it for Aligner testing. is that in order?
14:12 olas sure
14:12 olas but please do not re-add it in plugin.xml yet
14:12 olas not until we have the bioinfo plugin/feature out
14:12 jonalv uhm how would that work?
14:12 olas just donät add it in plugin.xml
14:13 olas easy
14:13 masak olas: well, that's kind of pointless, isn't it?
14:13 jonalv but how can I then use it?
14:13 olas why add it if we don't have a plugin out that can make use of it?
14:13 masak are you saying people who want to test the Aligner should copy the files manually?
14:13 olas jonalv: just copy/paste it into the WS
14:13 olas yup
14:14 olas IMO
14:14 jonalv Because I need it inorder to test masaks work
14:14 olas if you place it in sampledata
14:14 masak olas: I think we might as well enable it in plugins.xml too
14:14 olas then jonalv can just copy and paste it in
14:14 masak until next release
14:14 olas no
14:14 masak then more people can test it
14:14 masak easily
14:14 olas I'm making the next patch now
14:14 masak oh?
14:14 olas (as in almost now)
14:14 * masak didn't know
14:15 olas bugfixes
14:15 jonalv alpha02 commiing today then? :)
14:15 olas no
14:15 olas just on updatesite
14:15 jonalv no?
14:15 olas we have online updates
14:15 jonalv so what are you calling this version then?
14:15 olas it's not a version
14:15 olas not a feature version
14:15 olas plugins get incremented
14:15 olas if they are updated
14:16 olas but not a Bioclipse version
14:16 jonalv the plugins need a new version number don't they?
14:16 olas plugins have individual versions
14:16 olas yes
14:16 jonalv and you named all alpha01 last time so what are you namining them now if not alpha02?
14:16 olas We cannot have plugin ids and feature ids synchronized
14:16 olas or 20080805 or similar
14:17 olas jonalv: does it matter?
14:17 jonalv olas: yea I am curious
14:17 olas ok
14:17 olas I think we should do like eclipse releases does
14:17 jonalv olas: why don't you wanan tell me? :(
14:17 olas use dates
14:17 olas I just did
14:17 masak I like dates
14:17 jonalv dates are nice
14:17 masak they are automatically ordered
14:17 olas ok with you then?
14:18 masak yes, sure
14:18 olas hmm
14:18 jonalv so the new plugins will be called>
14:18 olas you'll see :-)
14:18 masak though I naturally dislike the policy of plugin.xml that will make life harder for my testers :)
14:19 olas then release a feature
14:19 jonalv can't the plugin.xml in biojava.ui have those lines instead?
14:19 olas sure
14:19 masak jonalv: care to fix?
14:19 olas but you need an additional wizard too I suppose
14:19 olas hmm
14:20 jonalv I am not sure how it works... I just wondereed...
14:20 olas maybe not
14:20 olas you have to test
14:20 olas could work
14:49 gilleain right.
14:49 gilleain there is now a CmlFileDescriber.
14:59 gilleain hmmm. there is an import statement for the quicktime package in the JmolView.
14:59 gilleain Since I can comment it out without error, I guess it isn't needed?
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15:05 jonalv olas: I fixed logging :)
15:05 olas NICE
15:05 jonalv commit pending
15:05 olas jonalv++
15:05 olas damn
15:05 olas I just updated bc :-)
15:05 olas so too late
15:05 olas but jonalv++ anyways
15:05 jonalv lol
15:05 masak jonalv++ # definitely
15:05 olas send email to rklancer that you fixed it
15:05 masak olas: then we can look forward to an alpha-03 soon? :)
15:06 egonw 03?
15:06 olas yup
15:06 egonw ah, ic, that commit :)
15:06 egonw tag?
15:06 olas egonw: we will move to date versioning
15:06 olas but not today
15:06 egonw ah, great!
15:06 egonw oh...
15:07 olas that requires a newe release
15:07 masak olas: should I make a tag?
15:07 egonw no worries :)
15:07 olas so you have to wait until beta
15:07 egonw yeah, fine
15:07 olas masak: please do
15:07 olas hm
15:07 olas let me test it first...
15:08 * jonalv really must switch to checking out only trunk...
15:08 olas yes
15:08 olas please make tag
15:08 olas I can confirm update is working :-)
15:09 masak olas: I'll make the tag from before jonalv++'s commit
15:09 olas good
15:09 olas there will be many new alphaxx coming out
15:10 olas today was just a start to test it
15:10 olas and it worked out just fine :-)
15:10 masak olas++
15:10 olas now: time for some serious jogging
15:10 egonw will alpha02 be availalbe from the update site too?
15:10 masak jog++
15:10 egonw or does not have to download a new version?
15:10 egonw (just wondering, not a feature request :)
15:11 olas no
15:11 olas no new version
15:11 olas will update automatically
15:11 olas on startup
15:11 olas AND
15:11 olas new version of chemoinfo feature on update site
15:11 olas bye for now
15:11 egonw bye
15:11 egonw thanx
15:42 gilleain Right. CML files with multiple molecules should now show in sdf.
15:42 gilleain I think there might be some mileage in having multiple structure icons.
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