Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-11-28

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All times shown according to UTC.

Time Nick Message
06:24 Gpox joined #bioclipse
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09:11 jonalv joined #bioclipse
09:28 shk3 joined #bioclipse
09:29 jonalv hi
09:29 zarah hi jonalv
09:38 shk3 hi
09:39 zarah hi shk3
10:00 egonw joined #bioclipse
10:00 egonw moin
10:00 zarah hi egonw
10:00 egonw Gpox, jonalv: I'll come to your room in a few minutes
10:01 jonalv egonw: roger
10:05 shk3 hi egonw
10:45 CIA-30 joined #bioclipse
11:02 shk3 egonw?
11:02 egonw yes
11:03 shk3 good morning
11:03 shk3 two questions:
11:03 egonw moin :)
11:04 shk3 I found a lot of classes for the validate stuff are not longer in cdk.jcp-primary
11:04 shk3 any reason for this?
11:04 egonw what stuff?
11:04 shk3 and i found you copied org.os.cdk.applications.swing and undoredo packages to jcp
11:05 shk3 but they are not used right now.
11:05 shk3 valencychecker
11:05 shk3 PDBValidator
11:05 shk3 ValencyValidator
11:05 egonw valencychecker -> CDKValencyChecker, I think
11:06 shk3 ah yes, there is a cdkvalencychecker
11:07 egonw PDBValidator was not used at all
11:07 egonw ValencyValidator was broken because of valencychecker -> CDKValencyChecker
11:08 egonw if you want it reinstated, please file a bug report, and I'll replace the functionality with new code
11:08 shk3 well, we have a validate action in jcp
11:08 egonw then file a bug report
11:09 egonw the cdk.application.swing classes were used by previous JCP version
11:09 egonw so, that's why I moved it into jchempaint/trunk
11:09 egonw same for undoredo...
11:10 shk3 yes
11:10 shk3 but there are other classes used by jcp as well and not in there
11:10 shk3 might be usefull to only put in what we actually use
11:11 egonw not sure what you want to propose
11:12 shk3 remove these packages and only copy in individual classes we actually use in new jcp
11:12 shk3 (I put in dialogs etc. when needed anyway)
11:13 egonw yes, sounds fine... if you make a branch first, we can easily copy them back in later
11:14 shk3 i will try the applet build today, I think
11:15 shk3 arent't these classes in cdk-1.0 anyway? do we need a branch?
11:15 egonw you can check
11:15 egonw jchempaint is copied from JCP 2.3
11:15 egonw while cdk1.0 contained JCP 2.2
11:16 egonw so, no, they generally are not in cdk1.0, because things evolved since cdk1.0 was branched
11:16 egonw but, you can check if they are the same
11:16 shk3 where is jcp 2.3 from?
11:16 egonw that was from cdk trunk
11:17 shk3 cdk trunk contains jcp stuff?
11:17 shk3 I thought it doesn't?
11:17 egonw not anymore, I think
11:17 egonw maybe 2.4 was made from cdk1.2.x already?
11:17 shk3 but cdk1.2 has no jcp stuff, does it?
11:18 egonw well, you have to check SVN history to see the fine prints
11:18 egonw I don't know it in detail
11:18 shk3 ok
11:18 shk3 what happened to MACiEReader?
11:19 egonw removed
11:19 egonw outdated, unsupported
11:19 egonw broken
11:19 shk3 the pdbvalidator uses it
11:19 egonw well, that would explain why I removed that one too
11:19 egonw PDBValidator was not doing really shoking
11:20 egonw it only checked it PDBLocatorAtom was using a reasonable label
11:20 shk3 so i am leaving it our for now
11:20 egonw yes, that's fine
11:21 egonw ok, really need to get some work done now
11:21 egonw if you find more things you have questions about...
11:21 egonw please file them as bug reports...
11:23 shk3 gilliean and me thought it would be time for filing missing stuff as bug reports anyway
11:23 egonw yes, sounds like a good plan
11:24 shk3 and I will publish a release
11:24 egonw good
11:24 shk3 so that people downloading development can see something
11:24 shk3 we made good progress
11:24 egonw please tag jchempaint/ and the jchempaint-primary/ branch
11:25 egonw yes, think so too...
11:25 egonw http://cdk.svn.sourceforge.net/​viewvc/cdk/jchempaint/branches/
11:25 zarah egonw's link is also http://tinyurl.com/5rnanf
11:25 egonw http://cdk.svn.sourceforge.net/vie​wvc/cdk/jchempaint/branches/2.5.1
11:25 zarah egonw's link is also http://tinyurl.com/6hmvj8
11:25 egonw please tag jchempaint like that
11:25 egonw I forgot to do that for 2.5.0
11:25 egonw bla
11:26 egonw wrong one
11:26 egonw http://cdk.svn.sourceforge.net/v​iewvc/cdk/jchempaint/tags/2.5.1
11:26 zarah egonw's link is also http://tinyurl.com/5nqpxo
11:26 egonw tags/ not branches/
11:27 egonw and: svn cp cdk/branches/jchempaint-primary cdk/tags/jchempaint-2.5.1
11:28 shk3 yes, we should have done a tag for 2.5.0
11:28 shk3 but forgot that as well
11:28 shk3 realized too late
11:28 egonw yeah... same here
11:29 egonw I think can one copy a specific revision too...
11:29 egonw will check that out later
11:29 gilleain joined #bioclipse
11:31 egonw jonalv: ok, it seems it already is using the NoNotification data classes...
11:31 egonw so nothing can be gained there
12:59 jonalv joined #bioclipse
12:59 jonalv oh hai
12:59 zarah hi jonalv
13:15 gilleain joined #bioclipse
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13:58 jonalv @pele
13:58 zarah jonalv: Pelezilla is at http://pele.farmbio.uu.se/​cgi-bin/bugzilla/index.cgi
13:58 jonalv @ pele 5
13:58 jonalv @pele 5
13:58 zarah http://tinyurl.com/5jmqq5
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14:24 egonw jonalv: here goes...
14:24 egonw it's downloaded much of the new packages
14:24 jonalv egonw: okey
15:03 edrin hi
15:03 zarah hi edrin
15:59 egonw guys
16:00 egonw we're working on pele
16:00 egonw and installing bugzilla3
16:00 egonw but's this takes a while
16:00 egonw *and*
16:00 egonw we need at some point port the old data :(
16:43 egonw @pz manager
16:51 egonw OK, pelezilla is upgraded and graphics works now
16:51 egonw bye all
16:53 CIA-30 bioclipse: egonw * r7894 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Added StructureDBManager coverage test
16:58 CIA-30 bioclipse: jonalv * r7895 /bioclipse2/trunk/plugins/ (7 files in 4 dirs):
16:58 CIA-30 bioclipse: [structuredb]
16:58 CIA-30 bioclipse: Activator - increased timeout for waiting for Spring to build the manager
16:58 CIA-30 bioclipse: manager - removed noSMILESAnnotation creation on import from sdf
16:58 CIA-30 bioclipse: User - removed createdBaseObjects, it was a memory leak
18:22 edrin left #bioclipse
19:37 gilleain joined #bioclipse
20:27 zarah joined #bioclipse
22:21 edrin joined #bioclipse
23:45 CIA-30 bioclipse: edrin_t * r7896 /xws/tags/xws4j/:
23:46 CIA-30 bioclipse: edrin_t * r7897 /xws/tags/ (xws4j/ xws4j-08.11.17/):

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