Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-04-07

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All times shown according to UTC.

Time Nick Message
04:43 masak joined #bioclipse
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07:18 olass joined #bioclipse
07:19 olass moin
07:19 zarah oh hai olass
07:19 edrin hi
07:19 zarah hi edrin
07:21 grandm44 joined #bioclipse
07:53 jonalv joined #bioclipse
07:54 jonalv o/
08:19 shk3 joined #bioclipse
08:24 CIA-58 bioclipse: goglepox * r9619 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk.jchempaint/ (4 files in 3 dirs): Added updateElement() to handler to sync what toolbar button is checked fixes bugs 514 & 541
08:43 CIA-58 bioclipse: shk3 * r9620 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.ui.sdfeditor/html/sdfEditor.html: added help
09:00 shk3 is there any reason why the new molecule from smiles is in net.bc.cdk.ui,
09:00 shk3 whereas the new molecule is net.bc.chemoinformatics?
09:17 egonw the first requires SMILES
09:17 egonw the second does not
09:17 egonw the first requires CDK
09:17 egonw the second does not
09:18 CIA-58 bioclipse: goglepox * r9621 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.jchempaint/plugin.xml:
09:18 CIA-58 bioclipse: Added editor id for cml, mdl & pubchem editors
09:18 CIA-58 bioclipse: fixes bug 719
09:18 zarah bug #719 | http://tinyurl.com/dlpgyt
09:20 CIA-58 bioclipse: shk3 * r9622 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.ui/html/maintopic.html: improved help
09:22 egonw shk3: can you please improve your commit messages too? please?
09:22 egonw shk3: don't say 'improved help'
09:22 egonw it's useless
09:22 egonw what did you change, and preferable indicating why that improves things
09:23 egonw please notice the difference with a random commit, say 9621
09:24 egonw which show what has changed: 'added editor id for cml, mdl & pubchem editor' and even a note on why that improved the code, i.e. fixes bug X
09:24 egonw we all now and then have bad commit messages... but your ranking the high score on useless commit messages by a lengthy distance to the runner up
09:25 egonw </rant>
09:26 masak I can think of situations where 'improved X' is about the only sensible thing that can be said in a commit comment. that said, I strive to write not only what I did (in the summary), but also why (in the body).
09:28 egonw masak: example?
09:28 egonw I may hope that any commit is an actual improvement
09:28 masak egonw: http://gist.github.com/91160
09:29 masak I often find git's short summary line length restrictive, but it also helps me think, and compress what I want to say.
09:29 egonw git's summary line??
09:29 egonw never heard of that...
09:29 egonw but
09:29 masak egonw: aye, it's something like 50 chars long.
09:29 egonw that commit message may be challenged in the summary, it has everything it takes inthe full message: the what and the why
09:31 shk3 I am doing my best on useless commit messages.
09:31 shk3 glad to see you appreciate that.
09:38 masak egonw: 50 chars, it seems.
09:39 egonw shk3: :)
09:39 masak though I have no sources to back that up, save for the way vim colours my commit messages.
09:39 egonw cytoscope update site: will it work in Bioclipse too?
09:39 egonw http://chianti.ucsd.edu/kono/cyide/
09:39 zarah egonw's link is also http://tinyurl.com/cug3nl
09:39 masak egonw: it was also vim that finally taught me not to write anything on the second line.
09:40 masak vim++
09:40 egonw ah, vim the pro-whitespace-nazi
09:40 masak well, it allows you to write anything.
09:40 masak but it colours it white-on-red. :)
09:46 CIA-58 bioclipse: goglepox * r9623 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java:
09:46 CIA-58 bioclipse: Changed context menu to use a single id
09:46 CIA-58 bioclipse: By default it uses the editor's id for menu contributions
09:46 CIA-58 bioclipse: this don't work when we several editors with different ids using the same context menu
11:01 edrin joined #bioclipse
11:17 CIA-58 bioclipse: shk3 * r9624 /bioclipse2/trunk/plugins/net.bioclip​se.cdk.jchempaint/doc/jcpPlugin.html: there was incorrect html in jcp help
11:31 shk3 joined #bioclipse
11:32 edrin hi
11:32 zarah hi edrin
11:36 CIA-58 bioclipse: goglepox * r9625 /bioclipse2/trunk/plugins/ (5 files in 2 dirs): Extracted SDFileIndex from CDKManager to it's own file
12:39 CIA-58 bioclipse: jonalv * r9626 /bioclipse2/trunk/plugins/net.bioclipse.jmol/ (8 files in 6 dirs): Jmol script errors occurring when running jmol.run from the JavaScript console should be echoed to the JavaScript console now. Attempt at fixing bug 726.
12:39 zarah bug #726 | http://tinyurl.com/djac7c
12:54 masak if you ask me, $HOME/Library/Application\ Support/Bioclipse/Default\ Workspace is an excellent location for a workspace.
12:54 masak $HOME/bioclipse-workspace is not.
12:55 shk3 java.lang.RuntimeException: This manager method should not be called, loadMolecules(IFile, BioclipseUIJob)
12:55 CIA-58 bioclipse: ospjuth * r9627 /bioclipse2/trunk/plugins/net.bioclipse.q​sar.ui/src/net/bioclipse/qsar/ui/editors/ (InformationPage.java QsarEditor.java): Added an Information Tab, but commented it out since it is not yet operational.
12:55 shk3 does this mean I should use loadMolecule(IFile,  BioclipseUIJob) now?
12:56 shk3 what is BioclipseUIJob?
12:56 * jonalv goes and hides
12:58 shk3 no
12:58 shk3 better help me
13:00 shk3 I just need to load the molecule.
13:00 shk3 I need to work with that in the code
13:00 shk3 having this in a job is of no use.
13:00 shk3 what shall I do?
13:02 shk3 btw, a quick search shows that loadMolecules(IFile) is used in other places as well.
13:02 Gpox what loadMolecule(IFile, BioclipseUIJob) allows you do ui stuff runInUI() when the call is finished and you can use get the return value with getReturnValue()
13:03 shk3 do you have an example?
13:03 Gpox JChemPaintEditr uses it
13:04 shk3 right
13:04 shk3 code is
13:04 shk3 public void runInUI() {
13:04 shk3 model = getReturnValue();
13:05 shk3 so this line is executed after the job is finished?
13:05 Gpox MoleculesEditor.getIndexFromInput dose too
13:05 Gpox yes in the UI thread
13:06 CIA-58 bioclipse: ospjuth * r9628 /bioclipse2/trunk/plugins/ (48 files in 17 dirs): Updated copyright text.
13:06 shk3 hm
13:06 shk3 but the other code will run on
13:06 shk3 which means I cannot rely on the result being available
13:07 Gpox thats right
13:27 * jonalv is back
13:44 jonalv olas regarding bug number
13:44 jonalv @pz 737
13:44 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=737
13:44 olass yes?
13:44 jonalv olass: are there some further instructions somewhere?
13:45 * jonalv has no idea how the Help system works...
13:45 olass you mena, how extensive it should be?
13:45 olass oh
13:45 olass see wiki
13:45 olass http://wiki.bioclipse.net/index.php?title=Writi​ng_documentation_and_help_for_Bioclipse_plugins
13:45 zarah olass's link is also http://tinyurl.com/cne2sb
13:45 olass http://wiki.bioclipse.net/index.php​?title=How_to_add_help_to_a_plugin
13:45 zarah olass's link is also http://tinyurl.com/chsmnz
13:46 olass see links on the bottom of the latest page
13:46 olass it is really simple
13:46 jonalv okey will have a look at it
13:53 CIA-58 bioclipse: ospjuth * r9629 /bioclipse2/trunk/plugins/net.bioclipse.bibtexml/ (META-INF/MANIFEST.MF plugin.properties): Set version to 2.0.0.B20090407, cleaned up manifest and build.props.
13:54 CIA-58 bioclipse: ospjuth * r9630 /bioclipse2/trunk/plugins/n​et.bioclipse.bibtexml.edit/ (META-INF/MANIFEST.MF plugin.properties): Set version to 2.0.0.B20090407, cleaned up manifest and build.props.
13:55 CIA-58 bioclipse: ospjuth * r9631 /bioclipse2/trunk/plugins/net.biocl​ipse.cdk.qsar/META-INF/MANIFEST.MF: Set version to 2.0.0.B20090407, cleaned up manifest and build.props.
13:56 CIA-58 bioclipse: ospjuth * r9632 /bioclipse2/trunk/plugins/net.bioclipse.chart/ (META-INF/MANIFEST.MF logger.properties): Set version to 2.0.0.B20090407.
13:57 CIA-58 bioclipse: ospjuth * r9633 /bioclipse2/trunk/plugins/net.bio​clipse.qsar/META-INF/MANIFEST.MF: Set version to 2.0.0.B20090407.
13:57 egonw ha, beta5?
13:59 CIA-58 bioclipse: ospjuth * r9634 /bioclipse2/trunk/plugins/net.biocli​pse.qsar.model/META-INF/MANIFEST.MF: Set version to 2.0.0.B20090407.
13:59 CIA-58 bioclipse: ospjuth * r9635 /bioclipse2/trunk/plugins/net.bioclipse​.qsar.model.edit/META-INF/MANIFEST.MF: Set version to 2.0.0.B20090407.
14:00 CIA-58 bioclipse: ospjuth * r9636 /bioclipse2/trunk/plugins/net.biocl​ipse.qsar.ui/META-INF/MANIFEST.MF: Set version to 2.0.0.B20090407.
14:01 CIA-58 bioclipse: ospjuth * r9637 /bioclipse2/trunk/plugins/​net.bioclipse.statistics/ (META-INF/MANIFEST.MF logger.properties): Set version to 2.0.0.B20090407. Removed old logger.properties from bc1.
14:02 ilbot2 joined #bioclipse
14:02 Topic for #bioclipseis now An open source workbench for chem- and bioinformatics - http://www.bioclipse.net/ | BioclipseWiki => http://wiki.bioclipse.net/ !! | logs => http://colabti.org/irclogge​r/irclogger_logs/bioclipse & http://moritz.faui2k3.org/irc​log/out.pl?channel=bioclipse || Bioclipse2 beta released! See http://bioclipse.blogspot.com/
14:02 CIA-58 bioclipse: ospjuth * r9638 /bioclipse2/trunk/plugins/ne​t.bioclipse.statistics.jama/ (META-INF/MANIFEST.MF logger.properties): Updated version to follow Jama library version, currently 1.0.1.
14:08 olass as you might have guessed, it's (hopefully) release today
14:08 olass will be a new Sourceforge bundle too
14:09 olass beta4 is in the pipe ;)
14:09 CIA-58 bioclipse: shk3 * r9639 /bioclipse2/trunk/plugins/net.biocli​pse.spectrum/src/net/bioclipse/spect​rum/business/SpectrumManager.java: changed loadMolecule(IFile) to loadMolecule(IFile, BiocliposeUIJob)
14:10 CIA-58 bioclipse: shk3 * r9640 /bioclipse2/trunk/plugins/net.biocl​ipse.specmol/src/net/bioclipse/spec​mol/wizards/NewSpecMolWizard.java: changed loadMolecule(IFile) to loadMolecule(IFile, BiocliposeUIJob)
14:11 CIA-58 bioclipse: shk3 * r9641 /bioclipse2/trunk/plugins/net.bioclipse.nmrs​hiftdb/src/net/bioclipse/nmrshiftdb/wizards/ (3 files): changed loadMolecule(IFile) to loadMolecule(IFile, BiocliposeUIJob)
14:11 olass shk3: around?
14:12 shk3 yes
14:12 olass Did you add CheatSheetAction to net.bioclipse.chemoinformatics?
14:14 shk3 yes
14:14 olass what does it do?
14:14 olass the name does not say anything...
14:15 olass it seems to contain duplicate code to run softweare update
14:15 olass that is really out of place
14:16 olass besides
14:16 olass this really looks like my code from another plugin
14:16 shk3 well, there might be other actions triggered from the cheatsheet
14:16 shk3 mom
14:16 shk3 I had the pattern to have one CheatSheetAction per plugin
14:16 CIA-58 bioclipse: ospjuth * r9642 /bioclipse2/trunk/plugins/ (8 files in 8 dirs): Set version to 2.0.0.B20090407.
14:16 olass did you just copy my code and set yourself as authoir to it?
14:17 shk3 and put in all action triggered by cheatsheet
14:17 shk3 mom
14:17 shk3 to sort out the code duplication is on my agenda
14:17 shk3 sorry for submitting half-finished stuff
14:17 olass shk3: Code duplication creates a lot of redundant code
14:17 olass shk3: please donät do it again :)
14:17 shk3 good definition
14:17 olass and problems
14:18 olass and hassles
14:18 olass shk3: and please never copy my code and set yourself as author again
14:18 olass that is really bad mannors
14:18 olass manors
14:18 olass I appreciate you helping with cheatsheets
14:18 olass but not in this way
14:19 olass link code, donät duplicate
14:19 shk3 btw, there seems to be a code duplication in UpdateAction and SoftwareUpdatesAction in net.bc.ui
14:19 olass file a bug
14:19 shk3 that was one of the reasons I was confused
14:19 olass and please rename classes to resemble what they do
14:19 jonalv olass: but there exists a Jmol help. What is it you want me to do?
14:19 olass CheatSheetAction is really not saying anything
14:20 shk3 well, but the cheatsheetaction class really contains cheat sheet actions
14:20 olass jonalv: does reading the jmol help say everything you like it to?
14:20 shk3 this _is_ what the class does
14:20 jonalv olass: uhm, no... :)
14:20 olass shk3: no, it contains an UpdateAction
14:20 olass that is way different
14:20 shk3 but potentially, there will me more cheat sheet actions
14:20 shk3 and they will all be in that class
14:20 olass shk3: With that definition you could call every class "class"
14:21 shk3 that right now, there is only one is by accident
14:21 shk3 don't think so
14:21 shk3 but I don't want to discuss this
14:21 shk3 I will rename it
14:21 olass shk3: and please, no code duplication
14:21 shk3 but if later, other actions are added
14:21 olass (I've said it many times now :))
14:21 shk3 _do not tell m to rename the class_
14:22 shk3 if you do this, I will get out my device which allows you to stab people into their face over the internet
14:22 olass oops...
14:22 * olass hides under the desk
14:25 * egonw is really looking forward to a patch-based Bioclipse development model where patches are developed until everyone is happy...
14:25 egonw it does not speed up development directly
14:26 egonw but makes the model by which people peer review more transparent, and more pleasent
14:27 egonw and likely development versions in the repository more stable too
14:27 egonw (well, inherent to less direct patches, I guess)
14:32 CIA-58 bioclipse: shk3 * r9643 /bioclipse2/trunk/plugins/net​.bioclipse.chemoinformatics/ (2 files in 2 dirs): removed all that stuff
14:55 masak egonw: any idea how to set svn props via git-svn?
14:55 egonw no
14:56 masak there's 'propget', but no 'propset'.
14:58 masak the reason I'm asking is that small GIF files are treated as text, their contents annoyingly barfed out in the commit mails.
14:58 masak a well-placed propset would prevent that.
15:02 CIA-58 bioclipse: ospjuth * r9644 /bioclipse2/trunk/plugins/ (7 files in 7 dirs): Set version to 2.0.0.B20090407.
15:02 CIA-58 bioclipse: carl_masak * r9645 /bioclipse2/trunk/plugins/net.b​ioclipse.cdk.jchempaint/icons/ (doc_mol_2d.png doc_mol_2d.xcf):
15:02 CIA-58 bioclipse: [n.b.cdk.jcp] new JCP icon
15:02 CIA-58 bioclipse: This is an early release, to see what people think. In case you're wondering,
15:02 CIA-58 bioclipse: the icon depicts a shiny grey atom being colored red (jchem-PAINT, get it?)
15:02 CIA-58 bioclipse: by a paintbrush. Comments welcome.
15:08 CIA-58 bioclipse: ospjuth * r9646 /bioclipse2/trunk/ (20 files in 19 dirs): Set version to 2.0.0.B20090407. Fixed build.props with items that were missed in some occasions.
15:17 CIA-58 bioclipse: ospjuth * r9647 /bioclipse2/trunk/plugins/net.bioclipse.cdk.debug/ (4 files in 2 dirs): Added feature branding icon.
15:17 CIA-58 bioclipse: ospjuth * r9648 /bioclipse2/trunk/plugins/net​.bioclipse.chemoinformatics/ (about.ini icons/chemistry_32.jpeg): Added feature branding icon.
15:17 CIA-58 bioclipse: ospjuth * r9649 /bioclipse2/trunk/plugins/net.bioc​lipse.data.blueobelisk/about.ini: Added feature branding icon.
15:18 CIA-58 bioclipse: ospjuth * r9650 /bioclipse2/trunk/features/net.bi​oclipse.cdk_feature/feature.xml: Set version to 2.0.0.B20090407.
15:18 CIA-58 bioclipse: ospjuth * r9651 /bioclipse2/trunk/features/net.bioclips​e.chemoinformatics_feature/feature.xml: Set version to 2.0.0.B20090407.
15:19 CIA-58 bioclipse: ospjuth * r9652 /bioclipse2/trunk/features/net.bioc​lipse.drugbank_feature/feature.xml: Set version to 2.0.0.B20090407.
15:21 CIA-58 bioclipse: ospjuth * r9653 /bioclipse2/trunk/features/net.bi​oclipse.qsar_feature/feature.xml: Set version to 2.0.0.B20090407 and updated license/copright statement in feature to EPL.
15:23 CIA-58 bioclipse: ospjuth * r9654 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui/ (about.ini about.mappings about.properties): Removed unused about classes.
15:24 CIA-58 bioclipse: ospjuth * r9655 /bioclipse2/trunk/plugins/net​.bioclipse.qsar.ui/about.ini: Added feature branding icon.
15:33 CIA-58 bioclipse: ospjuth * r9656 /bioclipse2/trunk/features/ (4 files in 4 dirs): Set version to 2.0.0.B20090407 and updated some licenses and deps in feature.
15:33 CIA-58 bioclipse: ospjuth * r9657 /bioclipse2/trunk/features/net.​bioclipse_feature/feature.xml: Set version to 2.0.0.B20090407 and updated some licenses and deps in feature.
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16:22 CIA-58 bioclipse: jonalv * r9658 /bioclipse2/trunk/plugins/ne​t.bioclipse.jmol/plugin.xml: Unified look of Jmol menu action labels.
16:23 CIA-58 bioclipse: jonalv * r9659 /bioclipse2/trunk/plugins/net.bio​clipse.jmol/doc/jmolEditor.html: Wrote help for the Jmol editor. The Jmol menu is at least explained in shortest possible way now.
16:47 edrin left #bioclipse
17:08 egonw hhhhhhhhhhhhhhhffffffffffffffffffffffffffffffffff​ffffffffuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuööööööööö​öööööööööööööööööööööäääääääääääääääääääääääääää
17:14 rajarshi egon, interesting :)
18:41 egonw :)
18:41 egonw that was Fientje
18:41 rajarshi :)
18:42 rajarshi btw, the diff problem is fixed
18:49 egonw oh? how?
18:50 rajarshi IntegerDifference was comapring refs rather than value
18:50 rajarshi see bug comment for the bit branch that firxes this
18:51 rajarshi sorry,git branch
18:58 egonw OK, copied your git repos
18:58 egonw ok, stupid me...
18:58 egonw there are enough important bug fixes/reports around for 1.2.1
18:58 egonw and hope to release that before the workshop...
19:01 egonw I'm watching some tv now
19:01 egonw will apply patch later
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