Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-04-17

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Time Nick Message
05:52 Gpox joined #bioclipse
06:28 ilogger2 joined #bioclipse
06:39 olass joined #bioclipse
06:48 olass moin
06:48 zarah privet olass
06:48 CIA-73 bioclipse: ospjuth * r9864 /bioclipse2/trunk/plugins/net.bioclip​se.data/data/Javascripts/buildmol.js: Updated buildmol.js in sampledata to gist fork 96594
07:33 CIA-73 bioclipse: ospjuth * r9865 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/sr​c/net/bioclipse/xws4j/DefaultClientCurator.java: Reformulated error message and corrected a spelling error when no XMP account data was available.
08:17 edrin joined #bioclipse
08:19 shk3 joined #bioclipse
08:51 egonw joined #bioclipse
08:51 egonw moin
08:51 zarah oh hai egonw
08:51 edrin hi egonw
08:55 olass moin egonw
08:55 edrin hi olass
08:55 olass hi edrin
09:00 CIA-73 bioclipse: goglepox * r9866 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java:
09:00 CIA-73 bioclipse: Show generator extentions by default in editor
09:00 CIA-73 bioclipse: resolves bug #931
09:00 zarah bug #931 | http://tinyurl.com/cvgvb8
09:00 CIA-73 bioclipse: goglepox * r9867 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk.jchempaint/ (3 files in 2 dirs):
09:00 CIA-73 bioclipse: Added generator extention to show center of mass
09:00 CIA-73 bioclipse: fixes bug #930
09:00 zarah bug #930 | http://tinyurl.com/c66nux
09:01 egonw olass: you think they can type the scripts on on slide in one minute?
09:10 olass egonw: that's why I have all in sampledata
09:10 olass to run
09:10 olass and as gists
09:10 egonw right
09:10 olass running a script isvery fast once you get the hang of it
09:10 egonw but still :)
09:10 egonw they have plenty to think about when going home
09:11 egonw did you test my fork?
09:11 olass no
09:11 olass I expect it to work :)
09:11 egonw good enough for me
09:11 egonw can you actually apply the changes from my fork to your gist?
09:11 egonw was wondering about that
09:12 olass no idea
09:12 olass I will have cheat sheets so users can re-do all steps when going home or on spare time if I run out of time
09:12 egonw shk3: ping
09:12 olass 'better to have more and skip parts than too little
09:12 olass I will hold 45 mins
09:12 egonw shk3: you mean, both mark and chris are out of office until monday?
09:13 egonw olass: mmm... I will have lots to do then...
09:13 olass what you mean?
09:13 egonw with my material...
09:13 olass I thought you were finished with it
09:14 egonw shk3: ping
09:16 shk3 hi egonw
09:16 shk3 yes
09:16 egonw hej
09:16 egonw ah, ok
09:17 egonw let's see what we can do on Monday then...
09:17 shk3 mark and christoph are both away
09:17 shk3 yes
09:17 shk3 the planning seems a bit tight
09:17 egonw will arrive on Sunday
09:17 shk3 okay
09:17 egonw but also need to sit down with the KNIME people to get CDK 1.2.1 in there
09:17 egonw shk3: the other things is
09:18 egonw that your commit to split up those two unit tests did not make it to your online cdk.git yet
09:18 egonw that is, just pulled from the online local-cdk-1.2.x branch, but no commit to split them up
09:18 shk3 hm
09:19 shk3 what do I ned to do?
09:19 shk3 I commited locally
09:19 shk3 and did a push.
09:19 egonw do another push
09:19 shk3 anything else?
09:19 egonw that should be fine
09:19 egonw you were in the correct branch?
09:19 egonw when you pushed?
09:20 shk3 yes
09:20 egonw mmm...
09:20 shk3 git branch
09:20 egonw maybe this needs to git-update-server-info too
09:20 shk3 * local-cdk-1.2.x
09:20 egonw did you do that?
09:20 shk3 yes
09:20 shk3 git push tells me:
09:20 shk3 Everything up-to-date
09:21 egonw did you also run on the server that git-update again?
09:21 egonw if I check the info/refs
09:21 egonw it points to the "new files" commit
09:21 egonw not to any new commit you may have pushed
09:21 shk3 just ran that
09:22 egonw OK; it has now changed
09:22 egonw will now pull again
09:22 shk3 ah
09:22 shk3 so I need to run update-server after push?
09:23 egonw yes, apparently
09:23 egonw this is the thing
09:23 egonw in git, everything is a blob
09:23 egonw and every blog has a hash
09:23 egonw blob
09:23 egonw ok, let me rephrase that
09:23 egonw in git, everything is a commit
09:23 egonw and every commit has a hash
09:23 egonw a branch is nothing more than a commit
09:23 egonw each commit has a parent
09:24 egonw which is how one sees the rhree of branches
09:24 egonw so, when you make a new commit
09:24 egonw the branch hash has to be updated to match that last commit
09:24 egonw shk3: run gitk
09:24 egonw and you will see that the commits have labels
09:24 egonw and that's about what it is...
09:25 egonw the whole commit history is merely a huge commit tree
09:25 egonw with labels here and there indicating what it is
09:25 shk3 I am happy as long as it works...
09:26 egonw sometimes it helps understanding what is going on...
09:26 egonw in deciding what to do next
09:26 egonw how to fix something
09:26 shk3 My brain is stuffed up with understanding
09:26 egonw ok, can I ask one more commit?
09:27 egonw add @cdk.bug annotation to the second unit test too...
09:27 shk3 sure
09:30 egonw shk3: update the wiki about still having to run git-update-server-info
09:30 shk3 will do so
09:35 CIA-73 bioclipse: ospjuth * r9868 /bioclipse2/trunk/plugins/n​et.bioclipse.scripting.ui/ (4 files in 3 dirs): Added a ScriptAction that allows custom scripts to be executed from a CheatSheet. Required a public method addition on ScriptingConsoleView, filed a refactoring bug for this as 940.
09:39 shk3 the info is already in the wiki
09:39 shk3 but I added a comment on the path, which confused me when I tried, perhaps this helps others.
09:44 egonw thanx
09:44 egonw I rewrote it to give more detail
09:47 CIA-73 bioclipse: ospjuth * r9869 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/actions/ScriptAction.java: Follow eclipse guidelines and report IAction.notifyResult(success) for ScriptAction.
10:06 shk3 egonw: I think there was some confusion
10:06 shk3 you were talking about that mark rorster, right?
10:06 shk3 forster
10:06 egonw yes
10:06 egonw that mark
10:06 shk3 I thought about mark rijnbeek
10:06 shk3 no idea about the other mark
10:06 egonw ah, ok
10:07 egonw http://cdk.git.sourceforge.net/git/gitweb.c​gi?p=cdk;a=shortlog;h=refs/heads/cdk-1.2.x
10:07 zarah egonw's link is also http://tinyurl.com/coyy7s
10:07 egonw 1.2.1 tagged
10:16 egonw and released
10:58 olass egonw++
10:58 CIA-73 bioclipse: ospjuth * r9870 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/actions/ScriptAction.java: Notify result on correct place, after all commands are successfully executed.
11:14 egonw groovy++
11:14 maclean joined #bioclipse
11:14 maclean ahh. that's better.
11:15 egonw :)
11:15 CIA-73 bioclipse: ospjuth * r9871 /bioclipse2/trunk/plugins/net.bioclip​se.doc/html/scriptingBioclipse.html: Wrote a VERY basic guide to scripting in Bioclipse.
11:39 maclean egonw : about the Strand/Chain renaming - do you want me to do it on cdk-1.2.x
11:39 egonw I think master
11:39 egonw cdk-1.2.x should be API stable
11:39 maclean right.
11:39 maclean I think I understand.
11:40 maclean for some reason, this RCS stuff gets me horribly confused.
11:40 egonw :)
11:42 maclean not really. more like ":(" than ":)"
11:42 egonw groovy seriously rocks
11:42 maclean it's okay.
11:42 maclean its not python
11:43 maclean if masak were here, he would probably say "it's not perl 5/6"
11:44 maclean egonw : what are you using groovy to do?
11:44 egonw oh, everyone is going to use Groovy next week
11:44 egonw everyone := all workshop participants
11:45 egonw and now using it to make a distrib with example code
11:45 maclean that first sentence sounded a little sinister, I'm glad you specified who 'everyone' was :)
11:46 maclean like you had sort of mind-ray that was going to convert the world to using groovy.
11:46 maclean are you doing a tutorial or something?
11:49 egonw what makes you think that?
11:49 egonw you did not peek at the programme, did oyu?
11:49 maclean Not at all actually, perhaps I should...
12:23 CIA-73 bioclipse: ospjuth * r9872 /bioclipse2/trunk/plugins/net.bioclipse.sc​ripting.ui/cheatsheets/usingJSConsole.xml: Updated help ref in cheatsheet since moved to net.bc.doc plugin.
12:39 egonw (groovy+ant)++
12:39 egonw I'm so done with Perl
12:46 maclean If I never have to type the word 'Chain' again, I will be happy.
12:52 CIA-73 bioclipse: ospjuth * r9873 /bioclipse2/trunk/plugins/net.bioclipse​.webservices/src/net/bioclipse/webservi​ces/business/WebservicesManager.java: Added functionality to increment filename if file exists on PDB download.
12:55 egonw 29 lines to extract the used CDK version, find all code snippets used in the book, and copy them into a snippet folder
12:55 * egonw is pretty impressed
12:56 egonw 28
12:56 egonw with 5 emtpy lines
12:56 egonw and pretty printed
13:07 maclean does anyone else find that renaming by refactoring is broken in the latest eclipse?
13:08 egonw no, have not encountered that
13:09 maclean it's really annoying it does things like throw up a dialog saying some mysterious thing ("variable does not exist") and then leaves everything in a partially renamed state.
13:09 maclean I'm now using find/replace, as that is more reliable :(
13:11 egonw OK, time to update my course material for CDK 1.2.1
13:12 maclean remember to s/Strand/Chain/...
13:12 egonw in my material?
13:12 egonw no PDB stuff in there
13:12 maclean I'm joking :)
13:12 egonw not yet at least
13:12 egonw seriously...
13:12 egonw my build system would complain
13:12 egonw and fail to generate a PDF
13:13 egonw I don't think I even could forget
13:15 egonw git (quote):
13:15 egonw #       renamed:    cdk-1.2.0.jar -> cdk-1.2.1.jar
13:15 egonw :)
13:15 egonw I know it's just a bug fix release... but... but ...
13:15 maclean well that was easy.
13:16 egonw OK, here goes
13:16 egonw recompiling the PDF against CDK 1.2.1
13:49 CIA-73 bioclipse: ospjuth * r9874 /bioclipse2/trunk/plugins/net.​bioclipse.tutorials.cdkws09/: Initial import: Plugin to hold cheat sheet for CDKWS09.
13:51 CIA-73 bioclipse: ospjuth * r9875 /bioclipse2/trunk/plugins/net​.bioclipse.tutorials.cdkws09/ (16 files in 9 dirs): Added a composite cheatsheet for the CDKWS09.
13:52 CIA-73 bioclipse: ospjuth * r9876 /bioclipse2/trunk/plugins/net.bioclipse.tutor​ials.cdkws09/cheatsheets/basicScripting.xml: Added a cheatsheet for basic scripting in Bioclipse.
13:52 CIA-73 bioclipse: ospjuth * r9877 /bioclipse2/trunk/plugins/net.bioclipse.t​utorials.cdkws09/cheatsheets/basicIO.xml: Added a cheat sheet for CDK I/O.
13:53 CIA-73 bioclipse: ospjuth * r9878 /bioclipse2/trunk/plugins/net.bioclipse.tutor​ials.cdkws09/cheatsheets/editrunscripts.xml: Added a cheat sheet for editing and running scripts + gists in Bioclipse.
13:53 CIA-73 bioclipse: ospjuth * r9879 /bioclipse2/trunk/plugins/net.bioclipse.tutori​als.cdkws09/cheatsheets/sampleCDKscripts.xml: Added cheat sheet for downloading and running sample CDK scripts.
13:54 CIA-73 bioclipse: ospjuth * r9880 /bioclipse2/trunk/plugins/net.bioclipse.tu​torials.cdkws09/cheatsheets/calcprops.xml: Added cheatsheet for calculating properties (descriptors), use QSAR project, and analyze with R.
13:54 olass *puh*
13:56 maclean *puh*?
13:56 CIA-73 bioclipse: ospjuth * r9881 /bioclipse2/trunk/features/ne​t.bioclipse.cdkws09-feature/: Initial import: Feature to hold CDKWS09 plugin.
13:56 CIA-73 bioclipse: ospjuth * r9882 /bioclipse2/trunk/features/ne​t.bioclipse.cdkws09-feature/ (.project build.properties feature.xml): Added cdkws09 plugin and feature deps.
13:57 CIA-73 bioclipse: ospjuth * r9883 /bioclipse2/trunk/features/net.biocli​pse.experimental_feature/feature.xml: Updated feature metadata.
13:58 CIA-73 bioclipse: ospjuth * r9884 /bioclipse2/trunk/features/net.bi​oclipse.rdf_feature/feature.xml: Set version to beta4.
14:00 CIA-73 bioclipse: ospjuth * r9885 /bioclipse2/trunk/features/ (2 files in 2 dirs): Updated metadata and copyright info.
14:15 CIA-73 bioclipse: ospjuth * r9886 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.jchempaint/plugin.xml: Commented out the generated demonstration star. Very nice, but need to make a release now.
14:18 CIA-73 bioclipse: goglepox * r9887 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java: Copying atomcontainer's properties
14:25 egonw olass: how's the release getting along?
14:25 egonw update
14:25 olass working on it
14:25 olass updating IDs
14:25 egonw saw that...
14:25 egonw difficulties?
14:25 egonw or just the regular?
14:26 olass just the regular :)
14:26 olass nothing much yet
14:27 CIA-73 bioclipse: ospjuth * r9888 /bioclipse2/trunk/ (37 files in 36 dirs): Updated plugin version to 2.0.0.B20090417
14:28 CIA-73 bioclipse: ospjuth * r9889 /bioclipse2/trunk/plugins/ (11 files in 11 dirs): Updated qsar plugins version to 2.0.0.B20090417
14:29 CIA-73 bioclipse: ospjuth * r9890 /bioclipse2/trunk/features/ (12 files in 12 dirs): Updated feature versions to 2.0.0.B20090417
14:29 CIA-73 bioclipse: ospjuth * r9891 /bioclipse2/trunk/plugins/ (6 files in 6 dirs): Updated balloon versions to 2.0.0.B20090417
14:30 CIA-73 bioclipse: ospjuth * r9892 /bioclipse2/trunk/ (7 files in 7 dirs): Updated experimental versions to 2.0.0.B20090417
14:34 CIA-73 bioclipse: ospjuth * r9893 /bioclipse2/trunk/plugins/net.b​ioclipse.ui/bioclipse.product: Updated feature version too.
14:35 CIA-73 bioclipse: ospjuth * r9894 /bioclipse2/trunk/plugins/ (6 files in 6 dirs): Updated xmpp versions to 2.0.0.B20090417
14:45 CIA-73 bioclipse: ospjuth * r9895 /bioclipse2/trunk/features/net.bioc​lipse.cdkws09-feature/feature.xml: Updated cdkws09 versions to 2.0.0.B20090417
15:25 edrin joined #bioclipse
15:34 edrin hi again
15:36 edrin1 joined #bioclipse
15:38 CIA-73 bioclipse: ospjuth * r9896 /bioclipse2/trunk/features/ (9 files in 9 dirs): Updated feature dependencies.
15:40 CIA-73 bioclipse: ospjuth * r9897 /bioclipse2/trunk/features/ (3 files in 3 dirs): Updated feature dependencies.
15:47 CIA-73 bioclipse: goglepox * r9898 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java: Copy properties from cdk-molecule to chemodel's atom containers when update is called
16:41 CIA-73 bioclipse: goglepox * r9899 /bioclipse2/trunk/ (2 files in 2 dirs): Displays the whole moleucle when opend
16:47 CIA-73 bioclipse: goglepox * r9900 /bioclipse2/trunk/cdk-externals/tr​unk/org.openscience.cdk.control/sr​c/org/openscience/cdk/controller/ (HighlightModule.java ZoomModule.java): Added check for null to avoid NPE
17:00 olass damn
17:00 olass it did not work :(
17:00 olass god damn release
17:00 olass will build again :(
18:15 Gpox joined #bioclipse
18:22 CIA-73 bioclipse: goglepox * r9901 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java:
18:22 CIA-73 bioclipse: Added x,y to center model
18:22 CIA-73 bioclipse: All of the sample molecules looks good
18:47 olass @tell egonw maybe you can hepl with bug 944? Maybe we can adjust the gist as a quikc fix...
18:47 zarah Consider it noted.
18:59 Gpox joined #bioclipse
19:03 maclean joined #bioclipse
19:03 maclean Gpox  or olass : around?
19:04 Gpox a litle
19:04 maclean bioclipse-jcp looks much better now, but I have a one-line change that would center on opening
19:04 maclean renderer.setDrawCenter(c.width / 2d, c.height / 2d);
19:04 maclean in the paint(GC gc) method of the editor
19:05 maclean line 310 or so.
19:05 maclean but I don't know if this behaviour is required or not
19:06 Gpox it would center every redraw
19:06 Gpox it would jump around
19:06 maclean it doesnt seem to
19:07 maclean you can move the molecule around, and it stays where you put it
19:08 maclean without this line, all molecules are in the top left corner, which looks okay, but not great.
19:10 maclean well, anyway. great work on fixing it.
19:10 maclean got to go.
19:10 Gpox it breaks the scrolling
19:10 maclean it does?
19:11 maclean well scrolling never seemed to work well, I'm testing it
19:11 maclean oh right.
19:12 maclean hmmm.
19:12 maclean dammit I wish this rendering stuff would just work
19:13 maclean sigh

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