Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-07-03

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All times shown according to UTC.

Time Nick Message
04:58 TR2N joined #bioclipse
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06:03 egonw moin
06:03 zarah privet egonw
06:53 olass joined #bioclipse
07:03 Gpox joined #bioclipse
07:03 olass egonw: XML-feature does not seem to work to download from update site using released RC5. Can you confirm?
07:04 olass anyway, it's experimental, but I guess I should remove it pending a fix
07:04 egonw will test
07:05 olass bug 1395
07:06 egonw got it
07:13 olass egonw: could you tag 2.0.0.RC5?
07:13 olass Aaah, rain in Stockholm! Long awaited!
07:13 egonw which commit ?
07:14 egonw yeah, some good rain too
07:14 olass egonw: current
07:14 egonw ack
07:14 olass only a few zarah commits sneaked in ;)
07:17 egonw tagging
07:18 CIA-52 bioclipse: egonw * r11600 /bioclipse2/tags/2.0.0.RC5/: Tagged 2.0.0.RC5
07:19 sneumann_ joined #bioclipse
07:21 olass @pz balloon virtual
07:21 zarah [1057] NPE when trying to create 3D c... http://tinyurl.com/qgrzh4
07:21 zarah Entire list at http://tinyurl.com/nujsh9
07:23 olass @pz 1057
07:23 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1057
07:25 egonw olass: ping
07:25 olass pong
07:25 egonw I think it should be enough to add org.eclipse.platform to the list up plugins, correct?
07:25 olass no idea
07:25 egonw and then we can make an update of the experimental update site...
07:25 egonw can we try that?
07:25 olass but a good start probably
07:26 olass sure
07:26 egonw btw, yes, I can confirm :)
07:26 olass can you verify it works from Eclipse?
07:26 olass running from features?
07:26 egonw umm...
07:26 egonw yes, can do that too...
07:26 olass please do
07:26 olass might be more deps
07:26 olass and building/updating update site takes a while
07:29 olass there is now: http://wiki.bioclipse.net/ind​ex.php?title=Known_Major_Bugs
07:29 zarah olass's link is also http://tinyurl.com/lnfkjs
07:29 olass and http://wiki.bioclipse.net/ind​ex.php?title=Intractable_Bugs
07:29 zarah olass's link is also http://tinyurl.com/bfhd57
07:30 olass plan to link to these in the release notes for 2.0
07:30 egonw I also not the Pellet feature not on the update site...
07:30 egonw we shouuld set up a wiki page for what goes onto what update site
07:30 egonw or does that already exist
07:31 olass egonw: in RC4 you said pellet feature should not be on update site, and it has never been
07:31 egonw did I?
07:31 olass please make up your mind
07:32 olass I don't mind putting it there if it works
07:32 olass after all, it's experimental
07:32 olass but you specifically said to me to not do it
07:32 egonw it works
07:32 olass is there  use case?
07:32 egonw yeah, maybe that was because I had not tested it yet
07:32 egonw yeah, I'm using it in metware
07:32 egonw and there is a gist
07:32 egonw will blog some more really soon
07:33 olass a wiki page would be nice too
07:33 egonw I'm on it
07:33 olass we should have a wiki page for all features
07:33 olass linking to the standalone help system on pele, which we should set up running
07:34 olass egonw: about bug 1393
07:34 olass can you comment?
07:34 olass is it fixed?
07:34 egonw no, that is not fixed yet
07:39 olass Thunderstorm in Stockholm. Me likey!
07:39 olass egonw: is it a blocker?
07:39 egonw XML feature works from inside eclipse
07:39 olass good
07:40 olass 1393 seems very important to me
07:40 * olass is going through the bug list
07:41 CIA-52 bioclipse: egonw * r11601 /bioclipse2/trunk/features/net.bi​oclipse.xml_feature/feature.xml: Added org.eclipse.platform plugin, hopefully fixing 'updating' the XML feature
07:42 egonw olass: I need to figure out first if CDK 1.2.3 allows saving of atom type info
07:42 olass oh
07:42 olass ok
07:42 egonw I am actually working on roundtripping a full CDK model, with *all* properties...
07:42 egonw but that is not finished yet
07:49 egonw ha, we're back on our schedule!
07:49 egonw wiki: "Bioclipse 2.0 Release Candidate 1 (RC1) is scheduled for June 4th (feature freeze). "
07:49 egonw hahahaha
07:58 rojasm joined #bioclipse
07:58 rojasm moin!
07:58 zarah oh hai rojasm
07:59 egonw hi rojasm
07:59 rojasm hi egonw: I sent a mail with the patch
07:59 egonw can you please add all patches to the patch tracker too?
07:59 rojasm yesterday but I realise that only to the cdk-devel@lists.sourceforge.net
07:59 rojasm ok
08:00 egonw for all your patches, please
08:04 rojasm but you meant for email to the cdk-patch@ or in the https://sourceforge.net/mailarchiv​e/forum.php?forum_name=cdk-patches page selfs
08:05 egonw no, please attach to the patch tracker reports
08:05 rojasm ok
08:08 egonw olass: http://wiki.bioclipse.net/index​.php?title=Bioclipse2_Features
08:08 zarah egonw's link is also http://tinyurl.com/kpcf4z
08:09 olass egonw: could we remove that page and generate something instead?
08:09 olass I am getting tired of updating wiki pages...
08:09 egonw yes, possibly
08:09 egonw are the update site projects in SVN?
08:10 olass yes
08:10 shk3 joined #bioclipse
08:10 olass bioclipse-updatesite and experimental-updatesite
08:19 mgerlich joined #bioclipse
08:19 egonw olass: file a bug report, please
08:23 olass ok
08:25 olass egonw: do we have an HTML page for each feature, specifying its license etc?
08:25 olass and the plugins it contains?
08:27 olass guess not
08:27 olass filed as bug 1399
08:32 egonw no, we do not yet
08:32 egonw this too can be autogenerated
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09:51 masak joined #bioclipse
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11:13 CIA-52 bioclipse: goglepox * r11602 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java:
11:13 CIA-52 bioclipse: Add default tooltip
11:13 CIA-52 bioclipse: Solves bug #1401
11:13 zarah bug #1401 | http://tinyurl.com/l464k7
11:17 egonw can I do something like
11:17 egonw Class<? implements Foo> ?
11:18 olass Gpox is the master of generics here...
11:18 egonw Gpox++
11:18 olass egonw: where can I get a >Gb SDF?
11:18 egonw for introducing '...' in the CDK
11:18 egonw PubChem
11:18 olass @gg pubchem download
11:18 zarah olass: http://pubchem.ncbi.nlm.nih.go​v/pc_fetch/pc_fetch-help.html
11:19 egonw to be precise:
11:19 Gpox I don't see anything wrong wit it but it is all about context with generics
11:19 egonw ftp://ftp.ncbi.nih.gov/pubche​m/Compound/CURRENT-Full/SDF/
11:19 egonw olass: you'll need to gunzip them, and concatenate a few
11:20 egonw Gpox: ok, will try, tack!
11:20 olass how do a concatenate files?
11:20 egonw cat Compound_foo_bar.sdf > large.sdf
11:20 egonw cat Compound_foo2_bar2.sdf >> large.sdf
11:20 olass ok
11:20 olass thx
11:20 olass hmm
11:20 olass I need quite many of them
11:21 egonw > := write to file
11:21 egonw >> := append to file
11:21 egonw so, mind the '>>' :)
11:21 egonw well, you can do this:
11:21 egonw take one file
11:21 egonw and double it each time
11:21 egonw cat Compound_foo2_bar2.sdf >> large.sdf
11:21 egonw cat large.sdf > large2.sdf
11:21 egonw cat large.sdf >> large2.sdf
11:21 egonw and then iterate
11:22 egonw cat large2.sdf > large3.sdf
11:22 egonw cat large2.sdf >> large3.sdf
11:22 egonw so, lots of compound duplicates
11:22 egonw but that does not matter in this situation
11:22 olass right
11:22 egonw should get you to any size in reasonable time :)
11:22 olass hmm, this will take a while...
11:22 egonw or write a simple script to do it
11:23 egonw masak: you can help with a Perl(6) one liner?
11:23 olass concatenate all files in a dir to a large one
11:23 egonw iterater of all Compound_*.sdf.gz files, gunzip and append, until result.sdf > 1GB
11:23 egonw masak: I would certainly reblog that for a wider audience...
11:24 olass egonw: reblogging is living on other peoples fame, does not sound nice
11:24 egonw yes, you have asses and asses...
11:24 egonw reblogging can also be:
11:25 egonw Look what Carl has written a brilliant Perl6 one liner:
11:25 egonw that's called attribution
11:25 egonw not quite uncommon among scientists
11:25 olass I guess..
11:25 olass I've seen many blogs where people just copy stuff that other people has done without proper credit
11:26 egonw true
11:26 egonw being a scientist requires some training
11:26 olass indeed
11:26 egonw they have institutes for that, IIRC :)
11:26 olass :)
11:26 egonw anyway... you bring up a nice socialogical point...
11:26 egonw scientists think of blogs as something different
11:27 egonw and do no consider science best-practices to apply
11:27 egonw same for software...
11:28 olass masak: about that perl one-liner...
11:28 olass is it easy to do?
11:36 egonw OK, back to JCP work
11:36 egonw going to write a ILogger patch for the CDK
11:37 egonw that sould also enable using the Bioclipse logging framework for the CDK feature
12:08 CIA-52 bioclipse: goglepox * r11603 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java:
12:08 CIA-52 bioclipse: Added ToolTip and removed DefaultToolTip class
12:08 CIA-52 bioclipse: Solves bug #1403 & #1401
12:08 zarah bug #1403 | http://tinyurl.com/l5ov3a
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12:17 olass Gpox++ //tooltips much better now!
12:27 CIA-52 bioclipse: goglepox * r11604 /bioclipse2/trunk/plugins/net.bioclipse.cdk​.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfe​ditor/business/MoleculeTableManager.java:
12:27 CIA-52 bioclipse: Added code to handle cancelation of a job
12:27 CIA-52 bioclipse: fixes bug #1405
12:27 zarah bug #1405 | http://tinyurl.com/mx7zfw
12:28 masak I think we should remove the "Latest news" section on the frontpage of wiki.bioclipse.net
12:28 masak its latest three news items are about 1.2.0, beta4, and beta5.
12:29 masak people might think those are actually the latest releases.
12:29 olass masak++ //good idea
12:29 * masak goes ahead and removes it
12:30 * olass beat you to it
12:30 masak olass: please update http://bioclipse.net/ with the RC5 news.
12:30 olass yes
12:30 olass did I miss that?
12:30 masak aye
12:30 olass sorry
12:31 masak np
12:31 masak JFDI :)
12:31 masak I think it might be a good idea to keep the 'Latest news' heading, but to link to bioclipse.net
12:34 olass maybe
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13:23 CIA-52 bioclipse: goglepox * r11605 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.ui.sdfeditor/src/net/bioclipse/cdk/u​i/sdfeditor/editor/MoleculesEditor.java:
13:23 CIA-52 bioclipse: Cancel parsing and indexing jobs when editor is closed
13:23 CIA-52 bioclipse: Solves bug #1404
13:23 zarah bug #1404 | http://tinyurl.com/ncsjok
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14:37 egonw olass: you want this for Bioclipse too: http://maps.google.com/maps/ms?ie=UTF8&amp;hl=​en&amp;msa=0&amp;ll=59.843036,17.634666&amp;sp​n=0.003967,0.019076&amp;t=h&amp;z=16&amp;msid=​103733862046497992978.00046dce090029ceed81d
14:37 zarah egonw's link is also http://tinyurl.com/mznpkz
14:37 egonw or variants?
14:37 egonw like: Google Map of Update Sites
14:37 egonw (yes, it's Friday afternoon :)
14:53 maclean joined #bioclipse
14:53 maclean hi
14:53 zarah oh hai maclean
14:53 masak \o/
14:53 maclean hi ceiling zarah
14:54 maclean o/
14:54 maclean I have a question : should I be able to save from jmol?
14:55 maclean in rc4, that is.
14:55 maclean or can I do this from the jmol console?
14:55 egonw neither
14:55 egonw because we have no IJmolMolecule yet
14:55 egonw scheduled for 2.1
14:55 maclean ohhhhh.
14:55 maclean rightho.
14:55 egonw sorry about that
14:56 egonw Jmol is a viewer
14:56 maclean no problem :)
14:56 egonw but we appreciate the need
14:56 egonw I want it too
14:56 maclean and a pony?
14:56 maclean :)
14:56 egonw no, they eat too much
14:56 masak do they ever!
14:57 maclean oh, egonw : saw the Renderer refactoring - looks good
14:58 maclean http://gilleain.tumblr.com/post/134803493
14:58 zarah maclean's link is also http://tinyurl.com/mg9dv3
15:01 olass we should be able to save state in jmol
15:01 olass at least I think that jmol supports saving the state
15:02 egonw yes, it should
15:02 maclean yeees. there's a save command.
15:02 egonw but save != save state
15:02 maclean http://chemapps.stolaf.edu/jmo​l/docs/index.htm?command=save
15:02 zarah maclean's link is also http://tinyurl.com/mxr8jz
15:02 olass ok, will need to sign off for today
15:02 olass Gpox: happy holidays!
15:03 olass bye for today
15:03 * olass will now prepare dinner
15:03 olass bye
15:53 maclean joined #bioclipse
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15:55 edrin hi
15:55 zarah privet edrin
16:00 masak ni hao edrin
16:01 egonw hi edrin
16:22 CIA-52 bioclipse: goglepox * r11606 /bioclipse2/trunk/plugins/net.bioclipse.cdk​.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfe​ditor/business/MoleculeTableManager.java:
16:22 CIA-52 bioclipse: Changed proggress calcualtions
16:22 CIA-52 bioclipse: Solves bug #1406
16:22 zarah bug #1406 | http://tinyurl.com/nzymo6
16:23 CIA-52 bioclipse: goglepox * r11607 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui​.sdfeditor/src/net/bioclipse/cdk/ui/sdfeditor/ (2 files in 2 dirs):
16:23 CIA-52 bioclipse: Created MolTableSelection and return it for multiple selections in MolTable
16:23 CIA-52 bioclipse: This is to stop the property view from picking up
16:23 CIA-52 bioclipse: and starting calculating jobs for every structure
16:23 CIA-52 bioclipse: in large selections.
16:24 CIA-52 bioclipse: goglepox * r11608 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui.sdfeditor/ (4 files in 4 dirs):
16:24 CIA-52 bioclipse: Changed moltable selection to be one item in a structure selection
16:24 CIA-52 bioclipse: This is so the visibleWhen will work.
16:24 CIA-52 bioclipse: This fixes the extract option in the context menu
16:24 CIA-52 bioclipse: Also added fix so molTable.saveSDF work
16:24 CIA-52 bioclipse: with non SDFIndexEditorModel IMoleculesEditorModels
16:28 Gpox bye, cya in four weeks
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