Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-07-25

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All times shown according to UTC.

Time Nick Message
05:54 rojasm joined #bioclipse
06:10 Gpox joined #bioclipse
06:46 egonw joined #bioclipse
06:53 olas joined #bioclipse
06:53 olas hi all
06:53 zarah hi olas
06:58 egonw hi olas
06:59 egonw moin all
06:59 zarah hi egonw
07:04 olas hi egonw
07:13 egonw relocating... bbl
07:45 jonalv joined #bioclipse
07:56 jonalv What\s up with cdk? I can't even get it to compile now...
08:04 masak joined #bioclipse
08:38 malick left #bioclipse
09:12 edrin joined #bioclipse
09:12 edrin moin
09:12 zarah hi edrin
09:13 olas hi edrin
09:20 masak hi edrin
09:24 jonalv hi edrin
09:27 egonw joined #bioclipse
09:35 olas wb egonw
09:35 olas egonw: I had some nice discussions yesterday with goran who will work on Bioclipse-Q
09:36 olas I think he might want to contribute to cdk as well
09:36 olas he is in MD
09:36 olas and their Gaussian expert
09:36 olas he wanted to build a Gaussian plugin for Bioclipse
09:36 egonw sounds good
09:36 egonw I'm *so* looking forward to october!
09:36 olas :-)
09:37 egonw olas: please have him contact me, possibly via bioclipse-devel
09:37 egonw CDK has a Gaussian input file writer
09:37 egonw so, setting up a Gaussian job works quite nice with the CDK
09:40 olas we did see that
09:40 masak I've been thinking of contributing to CDK as well
09:40 egonw great
09:40 masak but mostly by cleaning up code :)
09:40 egonw that would be very much appreciated
09:41 egonw cleaning up the code is a lot of work
09:41 egonw and doesn't get you papers
09:41 masak I think it will have to happen after we've turned bc2 on the right keel code-wise, though
09:41 egonw so, I have been doing that in off hours mostly
09:41 egonw so slow progress only
09:41 masak I'd be happy to help
09:41 masak would be fun to automate, too
09:41 masak Perl scripting FTW
09:41 olas masak: is the pmd for bioclipse up and running?
09:42 olas url?
09:42 masak olas: it's up, but not running :)
09:42 masak http://pele.farmbio.uu.se/pmd/
09:42 zarah masak's link is also http://tinyurl.com/5943h4
09:42 masak we need to decide how best to present that information
09:42 olas not responding
09:42 olas works for you?
09:42 masak yes
09:43 olas aah
09:43 olas inside UU NW
09:43 olas we need to sort that out
09:43 masak indeed.
09:43 olas the UU IT dep need to open that up
09:43 olas will see to that next week
09:43 masak olas: can you ask them?
09:43 masak goodie
09:43 olas yes
09:44 olas via BMC comp dept
09:44 olas Anders is back from vac next week
09:44 masak vaccination? :)
09:44 olas will also get him to install ejabberd
09:45 olas for our future XMPP services :-)
09:45 masak 40k issues on PMD
09:45 olas edrin++ has a working implementation now that can be utilized
09:45 masak but 17k belong to CDK
09:53 olas egonw: cdk does not compile
09:53 olas SMARTSParserVisitor seems missing
09:53 olas any ideas?
09:53 egonw run ant's taks 'javacc'
09:54 olas oh
09:54 olas thx
09:54 jonalv I have tested that 3 times now... :(
09:54 jonalv it doesn't help me...
09:54 olas f5 after?
09:54 jonalv yes
09:54 egonw yes
09:54 jonalv and clean
09:55 jonalv hm gonna test updaete classpath too :)
09:55 jonalv nope
09:56 olas javacc does not create SmarrtsParserVisitor
09:56 stain we want to dump CVS for Taverna.. what should we use instead?
09:57 jonalv stain: svn?
09:57 olas SVN?
09:57 stain yeah..
09:57 egonw svnadmin
09:57 olas what's the alternatives?
09:57 stain I'm thinking of Mercurial and Git and such.. but I'm not sure how easy they are to use from Eclipse
09:57 egonw sorry... that kind of dump
09:57 jonalv svn, git, darcs, svk....
09:57 stain so I'm doing cvs2svn and trying to upload the svndump to SF now
09:57 jonalv many
09:58 stain too many..
09:58 egonw git has much better merge support
09:58 * masak likes git
09:58 * olas has never used git
09:58 stain git could also be powerful for people like you guys, in case you need to take some taverna code and patch it a bit
09:58 egonw but svn is easier to use
09:58 * jonalv doesn't like mergining in svn...
09:59 olas egonw: could you locate SMARTSParserVisitor for us?
09:59 egonw yeah, working on it
10:00 olas thx
10:34 egonw joined #bioclipse
10:43 jonalv CIA-40: out on some secret mission again?
10:44 olas I got cdk to compile now
10:46 egonw olas: sorry, in the middle of other stuff now...
10:46 egonw so, I'm quite slow with things today
10:46 olas no worries
10:46 olas I solved it
10:51 egonw what was the problem?
10:53 olas no idea
10:54 olas update/refresh/classpath/clean/target platform or something like that
10:54 olas on arbitrary, repeated order
10:55 egonw ok, the regular eclipse stuff :)
10:56 olas think so
10:57 olas I built and tested chemoinformatics feature containing cdk and cdk10. It works from an update site now :-)
10:58 egonw excellent!
10:58 egonw olas++
10:59 * olas is testing and reporting bugs
10:59 olas looks promising
10:59 olas hopefully alpha01-release next week
11:00 egonw cool
11:00 olas @masak status on JSEditor?
11:00 olas @ask masak: Status on JSEditor?
11:00 zarah Consider it noted.
11:40 berry joined #bioclipse
11:58 masak @clear
11:58 zarah Messages cleared.
11:58 olas edrin: next release is scheduled for next friday
11:58 masak olas: I don't know, really
11:58 olas august 1.
11:58 olas masak: did you see all updated bugs?
11:58 masak olas: I'm ready to install and try it out, but I haven't figured out how
11:58 masak olas: yes, excellent
11:58 olas let me know if you need assistance
11:59 masak olas: I will
11:59 olas but I have a lot of things to finish before next friday :-)
11:59 olas we should all try to focus on the release as much as possible
11:59 olas and file/close bugs asap
12:00 masak yes
12:15 jonalv I still don't hava a compiling cdk
12:15 jonalv what am I doing wrong?
12:15 jonalv I think I have tried everything...
12:16 jonalv olas: Where can I find the list of lpugins which will be in the alpha release?
12:17 olas hmm
12:17 olas will add to wiki
12:17 jonalv it's more or less the two created features right?
12:18 olas yes
12:18 jonalv structuredb is in the chominformatics feature...
12:20 jonalv I will remove cdk and redownload it. I can't get it to woek...
12:21 olas run clean + javacc
12:21 olas f5
12:21 olas update CP
12:21 olas f5
12:23 olas jonalv: added to wiki
12:23 olas http://wiki.bioclipse.net/index.p​hp?title=Bioclipse2_release_plan
12:23 zarah olas's link is also http://tinyurl.com/5guree
12:23 olas thanks zarah
12:23 olas zarah: thanks
12:23 zarah you're welcome, olas :)
12:23 olas @dz
12:23 zarah you're welcome, olas :)
12:24 masak @dz
12:24 zarah no, YOU'RE the cute one! :)
12:24 masak :)
12:27 jonalv finally after having checked out a fresh cdk it compiles :)
12:28 olas nice
12:28 olas jonalv: please comment on bugs with group 2.0-alpha
12:28 jonalv I think I hava
12:28 olas release should be next friday
12:28 olas August 1st
12:28 olas it will require some work next week
12:28 jonalv I have commented on all bugs I have, haven't I?
12:29 olas good
12:29 jonalv or did I miss something?
12:29 olas dunno
12:29 olas is it feasible to release next friday?
12:29 olas I think so
12:29 masak perhaps
12:29 jonalv perhaps
12:29 olas if bugs are too extensive, we just postpone them
12:29 masak if everything works smoothly with JSDT
12:29 jonalv everything won't be topp notch though...
12:30 olas but let's have it as a goal
12:30 olas no worries
12:30 olas it's an alpha release :-)
12:30 jonalv I am not sure I will get taht AOP jobs up[ and running but maybe
12:30 olas but it should RUN
12:30 olas let's see how it works out
12:31 masak ok, so JSDT seems to be a part of ATF (Ajax Toolkit Framework), which is a part of WTP (Web Tools Platform). _that's_ why you can't just download JSDT standalone...
12:32 olas I think it might be troublesome to factor out that JSEditor
12:32 jonalv I have collected a bunch of tests. Many of them fails. Right now I am blaming a lot if it on cdk...
12:32 olas is the SF one bad?
12:33 olas SF JSEditor that is
12:33 olas jonalv: submit bugs, assign to egonw (seems shk3 is on vacation)
12:33 olas group 2.0-alpha
12:33 olas jonalv: or you could blame it on the rain
12:34 jonalv yea it's too hot today
12:37 masak olas: we'll see
12:37 masak we definitely want many of those features
13:51 masak olas: I have now succeeded in downloading and testing WTP
13:51 masak it looks nice
13:52 CIA-40 bioclipse: jonalv * r6258 /bioclipse2/trunk/plugins/net.biocl​ipse.core.tests/src/net/bioclipse/ (4 files): Added tests in net.bioclipse.core.tests to the "all tests test suite"
14:00 rojasm joined #bioclipse
14:05 rojasm joined #bioclipse
14:16 olas masak: WTP is nice
14:16 masak olas: do you know where I can get at the source_
14:16 masak ?
14:16 olas but we don't want to ship Bioclipse with WTP, just the JSEditor
14:16 olas oh
14:16 olas check it our from eclipse cvs
14:16 masak olas: yes, I'm planning to steal the source
14:16 olas mom
14:16 masak olas: how do I do that?
14:17 olas mom
14:17 olas I always need to look that up as well
14:17 olas well
14:17 olas there's another way
14:17 olas open view Plug-ins
14:17 olas right-click desired plugin, choose 'import as source'
14:18 olas if you have the source downloaded
14:18 olas else, grab it from CVS
14:18 olas http://wiki.eclipse.org/index.php/CVS_Howto
14:18 zarah olas's link is also http://tinyurl.com/ma38l
14:18 masak olas: dz
14:18 olas commit bot broken?
14:22 masak CIA-40: vacation?
14:25 masak jonalv and I are discussing clear and print right now
14:25 masak maybe we should create a separate bug ticket for that
14:25 olas good idea
14:25 masak there's a trick we need to learn to make it work
14:25 * masak writes the ticket
14:25 olas then a new bug seems appripriate
14:25 olas you need a ticket to ride
14:28 masak she's got a ticket to ride
14:29 olas a ticket to the blue?
14:37 masak olas: I would like categories bc_scripting, bc_ui and bc_structuredb
14:38 masak olas: also, bc_rhino should go away
14:38 masak (with all its bugs moved to bc_scripting)
14:39 olas ok
14:39 masak olas++
14:44 olas done
14:44 olas gotta run now
14:44 olas CUall on monday
14:44 olas will be in UA at BMC then
14:44 olas bye
14:44 olas left #bioclipse
14:44 jonalv oki bye
14:44 jonalv :(
14:50 masak @tell olas maybe org.openscience.cdk shouldn't be in plugins/ after all. it's not a bc2 plugin, net.bioclipse.cdk.* are.
14:50 zarah Consider it noted.
15:08 jonalv det aer det som aer grejjen, vi jobbar intensivt :)
15:08 jonalv ups wrong channel
15:08 jonalv that was for #farmbio...
15:13 edrin left #bioclipse
15:22 masak great success!
15:23 masak I managed to connect to the CVS repository of Web Tools Platform
15:23 jonalv yey
15:23 masak they have more plugins than we do! :)
15:24 jonalv hehe
15:25 masak orders of magnitude more...
15:27 egonw yeah, nothing wrong with each third party jar in a separate plugin
15:27 egonw I have been saying that all along
15:28 egonw :)
15:30 masak I'm officially lost again
15:30 masak there's just too much
15:30 masak I'm looking for a class that could contain a Javascript editor
15:31 masak but I can't find a suitable plugin to look inside
15:33 masak hold on... here's a trail that looks promising
16:01 masak nope, false alarm :/
16:24 CIA-40 bioclipse: jonalv * r6260 /bioclipse2/trunk/plugins/net.bioclipse​.jmol/src/net/bioclipse/jmol/business/ (IJmolManager.java JmolManager.java):
16:24 CIA-40 bioclipse: [jmol manager]
16:24 CIA-40 bioclipse: made the load method use string path and IFile. Also made all within 80 cols.
16:29 CIA-40 bioclipse: goglepox * r6248 /bioclipse2/trunk/plugins/net.bioclip​se.core/src/net/bioclipse/core/intern​al/filesystem/memory/MemoryTree.java: Added generics to a List
16:29 CIA-40 bioclipse: goglepox * r6272 /bioclipse2/trunk/plugins/net.bioclipse​.cdk10.jchempaint/src/net/bioclipse/cdk​10/jchempaint/ui/editor/JCPPage.java: Fixed dirty flag
16:33 CIA-40 bioclipse: carl_masak * r6253 /bioclipse2/trunk/_playground_/net.bi​oclipse.pkpd/src/net/bioclipse/pkpd/ (4 files in 3 dirs):
16:33 CIA-40 bioclipse: [net.bioclipse.pkpd]
16:33 CIA-40 bioclipse: * a few PMD fixes
16:33 CIA-40 bioclipse: ospjuth * r6251 /bioclipse2/trunk/plugins/net.bi​oclipse.ui/META-INF/MANIFEST.MF: Cleaned up manifest runtime exports.
16:33 CIA-40 bioclipse: jonalv * r6261 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.business/src/net/bioclip​se/cdk/business/ICDKManager.java: [cdk-manager] Went through and fixed which methods are published and which methods are recorded
16:34 CIA-40 bioclipse: ospjuth * r6250 /bioclipse2/trunk/plugins/net.bioclipse.ui/src/net​/bioclipse/ui/wizards/NewQSARRProjectWizard.java: Removed unused wizard.
16:34 CIA-40 bioclipse: ospjuth * r6252 /bioclipse2/trunk/plugins/net.biocli​pse.core.tests/META-INF/MANIFEST.MF: Removed dep to biojava.business as this should not be in core.tests.
16:34 CIA-40 bioclipse: ospjuth * r6262 /bioclipse2/trunk/plugins/net.bioclipse.cdk10.​jchempaint/src/net/bioclipse/cdk10/jchempaint/ (4 files in 4 dirs):
16:34 CIA-40 bioclipse: Extract Abstract class for JCPEditors, let MDLMolfileEditor and CMLfileEditor
16:34 CIA-40 bioclipse: extend this. Also added support to provide selections from AbstractJCPEditor.
16:34 CIA-40 bioclipse: Now, 2DView displays chem structure when opened, and also if JCP is active
16:34 CIA-40 bioclipse: editor. Solves 2027731.
16:34 CIA-40 bioclipse: goglepox * r6263 /bioclipse2/trunk/plugins/net.biocli​pse.core.tests/src/net/bioclipse/cor​e/ResourcePathTransformerTest.java: Fixed failed test because hardcoded path to test file, and made it a little more resistant to changes.
16:35 CIA-40 bioclipse: ospjuth * r6264 /bioclipse2/trunk/features/net.bioclips​e.chemoinformatics-feature/feature.xml: Removed cdk10 from feature as mol content is not supported in 2.0-alpha. Should anyway be done in cdk.ui, not cdk10.ui.
16:35 CIA-40 bioclipse: ospjuth * r6265 /bioclipse2/trunk/features/​net.bioclipse.sampledata/: Initial import.
16:35 CIA-40 bioclipse: ospjuth * r6266 /bioclipse2/trunk/features​/net.bioclipse.sampledata/ (.project build.properties feature.xml): Added feature for sample data.
16:36 CIA-40 bioclipse: ospjuth * r6257 /bioclipse2/trunk/features/net.​bioclipse-feature/feature.xml: Added net.bioclipse.scripting.ui.
16:36 CIA-40 bioclipse: ospjuth * r6267 /bioclipse2/trunk/plugins/net.bioclip​se.ui/src/net/bioclipse/ui/wizards/: Removed empty package.
16:36 CIA-40 bioclipse: ospjuth * r6255 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk.ui/src/org/: Removed unused package from old JCP.
16:37 CIA-40 bioclipse: ospjuth * r6268 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk10.jchempaint/plugin.xml: Made cdk10-based 2Dview default and set in Chemoinformatics category.
16:37 CIA-40 bioclipse: ospjuth * r6269 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui/plugin.xml: Commented out cdk-based 2DView as it is not working for the moment. Will be re-introduced when fixed, see bug 2027732.
16:38 CIA-40 bioclipse: ospjuth * r6270 /bioclipse2/trunk/plugins/ne​t.bioclipse.jmol/plugin.xml: Moved jmolView to chemoinformatics category (until we find a better category). Solves 2027688.
16:38 CIA-40 bioclipse: jonalv * r6249 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business.test/build.properties: fixed build properties
16:40 CIA-40 bioclipse: jonalv * r6271 /bioclipse2/trunk/plugins/net.bioclipse.cor​e/src/net/bioclipse/recording/History.java: Added asyncExec on history view update
16:58 CIA-40 bioclipse: ospjuth * r6254 /bioclipse2/trunk/plugins/net.bioclipse.c​dk.ui/src/net/bioclipse/cdk/ui/editors/: Removed unused, old editor classes.
18:53 egonw joined #bioclipse
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