Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-05-08

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All times shown according to UTC.

Time Nick Message
04:22 egonw joined #bioclipse
05:24 egonw @tell olas http://chem-bla-ics.blogspot.com/2009/05/n​omination-cdk-for-sf-community-award.html
05:24 zarah egonw's link is also http://tinyurl.com/o766rq
05:24 zarah Consider it noted.
05:24 egonw @tell olas please do bioclipse too?
05:24 zarah Consider it noted.
06:18 olass joined #bioclipse
06:20 CIA-40 bioclipse: ospjuth * r10147 /bioclipse2/trunk/plugins/net.bioclipse.jmol/src​/net/bioclipse/jmol/views/JmolConsoleView.java: Added empty waitUnitilCommandFinished() in jmolConsoleView to make it compile.
06:29 olass hi
06:29 zarah hi olass
06:35 edrin joined #bioclipse
06:35 edrin hi
06:35 zarah ni hao edrin
06:36 paulymer_ joined #bioclipse
07:14 Gpox joined #bioclipse
07:26 CIA-40 bioclipse: lc69 * r10148 /bioclipse2/trunk/plugins/net​.bioclipse.ds.signsig.bursi/ (5 files in 4 dirs): Adding the bulk of the signature significance code. It is not working and needs to be adapted to the DS feature.
07:26 CIA-40 bioclipse: ospjuth * r10149 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/ (build.properties cheatsheets/tutorial.xml): Refactored step 7 into several parameters. Should resolve problems on windows.
07:29 egonw ha a commit from lars
07:30 egonw lc69++
07:42 sneumann morning zarah
07:42 sneumann hm, she's asleep ?
07:43 egonw seems so
07:45 rojasm joined #bioclipse
07:46 Gpox zarah: ping
07:46 zarah Gpox: pong
08:14 jonalv joined #bioclipse
08:27 shk3 joined #bioclipse
08:31 CIA-40 bioclipse: lc69 * r10150 /bioclipse2/trunk/plugins/net​.bioclipse.ds.signsig.bursi/ (6 files in 2 dirs): Added signature binary for linux 32 bit. It needs openbabel to run. Also, the libsvm model files are added and a tab-file that specifies the signatures that were created for the model.
08:36 CIA-40 bioclipse: lc69 * r10151 /bioclipse2/trunk/plugins/net.bioclipse.d​s.signsig.bursi/data/bursiSignsXYZ_1.tab: Added a space to test my committing abilities.
08:37 CIA-40 bioclipse: lc69 * r10152 /bioclipse2/trunk/plugins/net.bioclipse.d​s.signsig.bursi/data/bursiSignsXYZ_1.tab: Removed the space...
08:41 jonalv zarah: ping me when masak is online
08:41 zarah jonalv: ping
08:41 jonalv zarah: no
08:41 zarah jonalv: I see.
08:42 jonalv zarah: alert me when masak is online
08:42 zarah jonalv: that was not so easy for a little bot to understand
08:43 jonalv zarah: tell masak could you have a look at bug 1033?
08:43 zarah Consider it noted.
08:49 maclean joined #bioclipse
08:51 maclean shk3 : did you see that I made a seneca commit yesterday?
08:52 maclean I only want to draw your attention to it, to make sure that you update before making more changes, as it can be frustrating to find conflicts...
08:56 olass egonw: could I manually vote for bug 1034? I really need it...
08:56 egonw @pz 1034
08:56 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1034
08:57 maclean hmmm. I should remember to file a feature request for a "fromInChI" method.
08:58 egonw CDK does not have that for the current InChI version
08:59 maclean oh well, fair enough.
09:09 egonw you can still request it, of course
09:11 maclean it just won't happen? :)
09:11 egonw make it a Junior Job
09:11 egonw that helps
09:17 egonw olass: ack... working on 1034
09:17 olass egonw: thanks
09:22 CIA-40 bioclipse: egonw * r10153 /bioclipse2/trunk/ (2 files in 2 dirs): Fixed typo: Rad -> Read (fixes #1031)
09:22 zarah bug #1031 | http://tinyurl.com/ody5d8
09:28 shk3 hi olass
09:29 shk3 did you have your status meeting on wednesday?
09:31 olass no
09:31 olass on tuesday
09:32 olass release plans will hopefully be finalized next week
09:32 olass depending on how the NWO is coming along
09:32 olass and on external demands from our professor
09:33 shk3 sounds good
09:33 shk3 I really vote for the release asap
09:33 shk3 if everything is ready, of course
09:37 maclean shk3 : I made some small changes to how seneca uses the annealing engine. I was only really making the engine independent of eclipse code. It should still work the same.
09:37 shk3 ok
09:38 shk3 I will continue with the ui
09:38 maclean great.
09:38 maclean I tried out the drag and drop stuff, and got files like data.cml.cml when I dropped the data.cml on the field
09:39 maclean not sure why. I may have been doing it wrong.
09:39 maclean anyway, I'm going to try to gain admission to the central library (again) today, having only got a form yesterday...
09:41 shk3 i am still working on that
09:41 shk3 the .cml.cml will disappear
09:41 shk3 did you get teh form signed?
09:41 shk3 it should work then today
09:42 maclean he claimed that I didn't need it signed if I didn't need to look at manuscripts, we'll see.
09:42 shk3 ah hm
09:43 shk3 they told me something different
09:46 CIA-40 bioclipse: ospjuth * r10154 /bioclipse2/trunk/plugins/net.bioclipse.​ds.signsig.bursi/exec/signatures-macosx: Added signatures naive for mac os x.
09:47 CIA-40 bioclipse: ospjuth * r10155 /bioclipse2/trunk/plugins/net.bioclipse.​ds.signsig.bursi/permissions.properties: Added installation permissions for native signatures applications.
09:47 CIA-40 bioclipse: goglepox * r10156 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Corrected name in debuging output
09:48 CIA-40 bioclipse: goglepox * r10157 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java: Avoids the NPE from bug #1032 but return null if no model is active
09:48 zarah bug #1032 | http://tinyurl.com/r3eoo4
09:48 CIA-40 bioclipse: ospjuth * r10158 /bioclipse2/trunk/plugins/net.bioclip​se.ds.signsig.bursi/src/net/bioclipse​/ds/signsig/bursi/SignSIcRunner.java: Adapted runner for reading files defined in plugin and initialize on first run. Also writes temporary MDL file before prediction.
09:48 CIA-40 bioclipse: goglepox * r10159 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.ui.sdfeditor/src/net/bioclipse/cdk/ui/sd​feditor/editor/SDFIndexEditorModel.java:
09:48 CIA-40 bioclipse: Avoid index out of bounds exception
09:48 CIA-40 bioclipse: Only ty to remove '$$$$' at the end if they exists
09:50 CIA-40 bioclipse: ospjuth * r10160 /bioclipse2/trunk/plugins/net.bioclips​e.balloon.business/src/net/bioclipse/b​alloon/business/BalloonManager.java: Changed temp mdl file postfix from 'mdl' to '.mdl'.
09:51 CIA-40 bioclipse: ospjuth * r10161 /bioclipse2/trunk/plugins/net.bioclip​se.ds.signsig.bursi/src/net/bioclipse​/ds/signsig/bursi/SignSIcRunner.java: Changed temp mdl file postfix from '.mdl' to '.mol'.
09:53 CIA-40 bioclipse: goglepox * r10162 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.jchempaint/plugin.xml:
09:53 CIA-40 bioclipse: Added Backspace to keybindings for remove in JCP
09:53 CIA-40 bioclipse: Fixes bug #853
09:54 zarah bug #853 | http://tinyurl.com/dnyjbo
10:01 olass Gpox++ //Solving a lot of bugs today!
10:11 CIA-40 bioclipse: ospjuth * r10163 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/ (cheatsheets/xmppgists.xml plugin.xml): Added cheat sheet for downloading XMPP gists and opening them in editor.
10:17 olass @lunch
10:27 egonw @pz 1036
10:27 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1036
10:52 CIA-40 bioclipse: ospjuth * r10164 /bioclipse2/trunk/plugins/net.bioclip​se.chemoinformatics/build.properties: Added css folder to build.properties so logo for Chemoinformatics welcome contribution is added to exported packages.
10:55 olass egonw: how did it go with remove hydrogens?
10:58 olass egonw: and you worked on 1019 (save FP as props). How did that go?
10:58 olass egonw: sorry to stress you
10:59 olass just wondering :)
11:24 egonw olass: ran into an unexpected CDK thingy...
11:24 olass oh?
11:24 egonw but think I have found the proper way of doing it
11:24 olass good
11:33 jonalv joined #bioclipse
11:37 CIA-40 bioclipse: ospjuth * r10165 /bioclipse2/trunk/plugins/net.bioclip​se.ds.signsig.bursi/src/net/bioclipse​/ds/signsig/bursi/SignSIcRunner.java: Implemented toString().
11:38 CIA-40 bioclipse: ospjuth * r10166 /bioclipse2/trunk/plugins/net.bi​oclipse.ds/src/net/bioclipse/ds/ (3 files in 2 dirs): Adapted TestRun to cache Editor instead of ICDKMolecule, and get the CDKMolecule when needed.
11:43 CIA-40 bioclipse: ospjuth * r10167 /bioclipse2/trunk/plugins/net.bioclipse.​ds.smarts/src/net/bioclipse/ds/smarts/mo​del/impl/SmartsMatchingTestMatch.java: refactored to extend SubStructureMatch
11:43 CIA-40 bioclipse: ospjuth * r10168 /bioclipse2/trunk/plugins/net.biocl​ipse.ds/src/net/bioclipse/ds/model/ (ISubstructureMatch.java ITestResult.java TestHelper.java): Restructured so interfaces has needed methods.
11:44 masak joined #bioclipse
11:45 CIA-40 bioclipse: ospjuth * r10169 /bioclipse2/trunk/plugins/net.bioclip​se.ds.signsig.bursi/src/net/bioclipse​/ds/signsig/bursi/SignSIcRunner.java: Changed name on bogus hit.
11:49 jonalv egonw: are you touching the branch?
11:49 egonw no, not right now
11:49 egonw was waiting for you to return
11:49 jonalv k good :)
11:49 jonalv ah
11:49 egonw and working on some bug reports by olass
11:49 olass egonw++
11:50 egonw jonalv: you want to rebase?
11:50 jonalv egonw: no not really
11:51 jonalv egonw: I think I will do that first thing monday if that is fine by you?
11:51 egonw sure
11:51 egonw so, how do we continue?
11:51 jonalv egonw: yea that's the question...
11:51 egonw did you do the refactoring of IJavaCDKManager and IJavaScriptCDKManager yet?
11:52 jonalv uhm I think so
11:52 CIA-40 bioclipse: egonw * r10170 /bioclipse2/trunk/plugins/ (4 files in 2 dirs): Implemented cdk.remove[Im|Ex]plicitHydrogens (fixes #1034)
11:52 zarah bug #1034 | http://tinyurl.com/o3n9ar
11:52 jonalv or no
11:52 jonalv or I mean
11:52 egonw :)
11:52 jonalv uhm which refactoring do you mean?
11:52 jonalv the big one is not done...
11:53 CIA-40 bioclipse: egonw * r10171 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.business/src/net/bioclip​se/cdk/business/ICDKManager.java: Fixed a typo: s instead of \s
11:54 CIA-40 bioclipse: egonw * r10172 /bioclipse2/trunk/plugins/net.biocli​pse.inchi.business/src/net/bioclipse​/inchi/business/InChIManager.java: Fixed returning of key, not InChI itself (fixes #1028)
11:54 zarah bug #1028 | http://tinyurl.com/pzgoxd
11:58 olass egonw: IMO we should only use IMolecule as parameters in CDKManager
11:58 olass do you disagree with this?
11:59 olass I mean, you do return an ICDKMolecule
11:59 olass if you did not, I can understand that parameter has to be ICDKMolecule
11:59 olass but as it is now, please accept IMolecule
11:59 olass it just makes it so much more useful
12:00 olass egonw: right?
12:02 egonw no, I agree
12:02 egonw but it needs clean up anyway...
12:02 egonw thought about this while cycling home yesterday
12:02 egonw there are things I don't like about the current design
12:04 olass ok...
12:04 CIA-40 bioclipse: ospjuth * r10173 /bioclipse2/trunk/plugins/net.bioclip​se.ds.signsig.bursi/src/net/bioclipse​/ds/signsig/bursi/SignSIcRunner.java: Use new cdk methods (egonw++) removeImplicitHydrogens and removeExplicitHydrogens.
12:05 egonw sorry phone
12:06 egonw e.g. overloading of ICDKMolecule and IMolecule with .getFormatRepresentation()
12:06 egonw instead, I like more the ISMILESMolecule
12:06 egonw stuff...
12:06 egonw so that .getAdapter() can be used to provide things like that
12:06 egonw and have each impl (Jmol, CDK, ...) provide whatever they can
12:07 egonw and all managers can use whatever intermediate format they understand
12:07 jonalv uhm the Smilesmolcuel is dead
12:07 jonalv let it rest in peace
12:07 egonw jonalv: that was a mistake, I think
12:07 jonalv oh?
12:07 egonw I want to go even further and have too:
12:07 egonw CMLMolecule
12:08 egonw MDLMolfileMolecule
12:08 egonw and whatever else we support
12:08 jonalv egonw: go right ahead. you gonna create managers for each of them as well?
12:08 egonw managers? why?
12:08 egonw manager is for functionality
12:09 egonw IMOlecule of for data models
12:09 egonw manager is for algorithms
12:09 egonw IMOlecule of for data representation
12:09 egonw those things are different
12:11 jonalv egonw: of course but for instantiating them
12:12 egonw ah, ok, agreed
12:12 egonw yes, sure
12:12 egonw but we have those already, anyway
12:12 egonw CMLManager
12:12 egonw CDKManager
12:12 egonw JmolManager
12:12 jonalv egonw: I mean you don't have to. I just wondered if you where planning to...
12:15 Gpox you could have it like this IMolecule.getAdapter(org...cdk.IMolecule.class) to get a CDK representation
12:16 egonw Gpox: indeed
12:16 egonw and things like:
12:16 egonw IMOlecule.getAdapter(ICMLMolecule.class)
12:16 egonw to get a CML represntation
12:16 CIA-40 bioclipse: ospjuth * r10174 /bioclipse2/trunk/plugins/net.bioclipse.ds/ (5 files in 3 dirs): Added propertysource for matches to show in proeprties view.
12:16 egonw which returns null if the XXXXMolecule cannot save as CML
12:20 CIA-40 bioclipse: egonw * r10175 /bioclipse2/trunk/plugins/net.bioclipse.cdk​.debug/src/net/bioclipse/cdkdebug/business/ (CDKDebugManager.java ICDKDebugManager.java): cdx.debug() and cdx.diff() now return the output, instead of directly printing to the console (fixes #1029)
12:20 zarah bug #1029 | http://tinyurl.com/qqdnlj
12:21 egonw jonalv: ping
12:21 jonalv egonw: pong
12:21 egonw branch 7?
12:21 jonalv jupp
12:21 egonw OK
12:22 jonalv hang on and I will push my latest stuff
12:22 egonw ok
12:22 jonalv now
12:22 egonw cfdd3fb77a2ba275ef3973bb7f7f2cbf9a1d8849 ?
12:22 egonw that's your latest commit?
12:22 CIA-40 bioclipse: ospjuth * r10176 /bioclipse2/trunk/plugins/net.biocl​ipse.ds/src/net/bioclipse/ds/model/ (SubStructureMatch.java SubStructureMatchPropertySource.java): Added propertysource for substructurematches to show matching atoms in properties view.
12:23 jonalv egonw: yup
12:25 * jonalv digs in on the CDKManager and it's interface now
12:25 egonw shall we do this together?
12:25 jonalv egonw: uhm on distance?
12:25 jonalv egonw: aren't you home?
12:25 egonw yes
12:26 jonalv egonw: so how do you suggest we do that then?
12:26 jonalv egonw: are all the debug tests passing now?
12:26 egonw dunno
12:26 egonw should I test?
12:27 jonalv egonw: they don't for me...
12:27 jonalv If you run the AllNewWorldOrdersTests suite you get a good feeling for our current situation...
12:28 jonalv 82 error for 200 tests
12:29 jonalv egonw: my suggestion is that you fix the debug manager and I start with the cdkmanager
12:29 egonw OK
12:29 jonalv egonw: I am going to change the layout as welll so please excuse me... :)
12:29 egonw what is there to fix about the debug manager?
12:29 egonw layout?
12:29 jonalv egonw: does all the tests pass for you?
12:29 egonw ah, separate commit please
12:29 jonalv egonw: they don't for me...
12:30 egonw mom, will try
12:30 egonw eclipse is still rebuilding
12:30 CIA-40 bioclipse: ospjuth * r10177 /bioclipse2/trunk/plugins/net.bi​oclipse.ds/src/net/bioclipse/ds/ (3 files in 2 dirs): Added TestRun properties and display no hits in label of viewer.
12:31 jonalv egonw: but it's not a seperate thing. I must fix the indentation while refactoring otherwise I might refactor wrong and I don't wanna fix infentation for things that I am gonna remove anyway... :(
12:31 egonw as long if you do not reindent line *without* code changes, I am happy
12:31 edrin joined #bioclipse
12:33 jonalv egonw: well I don't think I will manage to do that. I have stuff hrere that is indented to the wrong level and I am not gonna leave it like that sosumi ;)
12:33 egonw ok
12:33 egonw I don't want to slow you down in this refactoring
12:47 jonalv egonw: cdkmanager loadmolecules method
12:47 egonw yes
12:47 jonalv there is a catch CDKException and print stacktrace there
12:48 jonalv egonw: could you see if throwing a Bioclipseexception wrapping the CDKException is an option?
12:48 egonw yes, I got no problem with that
12:48 jonalv egonw: or I will leave a comment for you and give you a bug...
12:49 jonalv egonw: oh you know where it is?
12:49 egonw OK, file a bug report
12:53 egonw jonalv: CDKDebugManager needs fixes from BC2 SVN
12:53 egonw so, cannot continue that until Monday
12:53 jonalv egonw: okey I will rebase later today when I have a coupel of minutes
12:53 egonw jonalv: pushed one commit to 7
12:54 jonalv ah
12:54 jonalv egonw: the indentation status of the cdkmanager is bad...
12:54 egonw sure
12:54 egonw 100 people worked on it
12:54 jonalv I don't think I can fix it all now..
12:54 egonw no, please don't
12:54 egonw only if it makes you help understand the code
12:54 jonalv I will do the worst...
13:03 CIA-40 bioclipse: egonw * r10178 /bioclipse2/trunk/plugins/net.bioclipse.cdk​.debug/src/net/bioclipse/cdkdebug/business/ (CDKDebugManager.java ICDKDebugManager.java): Fixed cdx.perceiveCDKAtomTypes() to return the output instead of direct output to the JS console
13:09 * jonalv is reading cdkmanager code and he is gettign scared
13:10 * jonalv hopes it is well tested...
13:11 jonalv forexample there's a zillion cdk.saveMolecule method whitch call eachother in a mazelike pattern...
13:12 jonalv hm "mazelike" can you say that?
13:12 jonalv :)
13:12 egonw oh, I know...
13:12 egonw it's a mess
13:12 egonw and I have not clue about how well it is tested
13:12 egonw as the tests don't work :)
13:12 jonalv and I am removing half of them now so I hope we have tests for them... :)
13:13 egonw good
13:13 CIA-40 bioclipse: ospjuth * r10179 /bioclipse2/trunk/plugins/ (12 files in 6 dirs): Updated icons for tests.
13:13 jonalv egonw: we should probably do a little bit of pairwise code reviewing of this class soemtime...
13:14 egonw yes
13:14 egonw but when?
13:14 jonalv egonw: next week? :)
13:14 egonw I won't be at BCM next week
13:14 egonw BMC
13:14 jonalv ah yea I forgot
13:14 jonalv so some other time then...
13:15 jonalv at least the tests run now in this branch
13:15 jonalv although quite a few of them is failing...
13:17 egonw OK, can you commit and please rebase?
13:17 egonw then I can join in the fun
13:17 jonalv uhm okey
13:18 jonalv getNoMolecules is an intersting method
13:19 * olass hides
13:21 * jonalv has to merge ICDKManager now... :(
13:21 egonw there should only be new methods
13:21 egonw no changed old methods, I think
13:22 jonalv okey
13:22 jonalv that might be true
13:22 CIA-40 bioclipse: ospjuth * r10180 /bioclipse2/trunk/plugins/net.bioclipse.d​s.smarts/src/net/bioclipse/ds/smarts/mode​l/impl/SmartsInclusiveExclusiveTest.java: Better debugging for failing SMARTS.
13:23 * jonalv needs a better merge tool
13:23 jonalv right now he is alternating between vim and opendiff for different situations
13:23 jonalv need one that is good for all cases...
13:26 CIA-40 bioclipse: ospjuth * r10181 /bioclipse2/trunk/plugins/net.bioclipse.ds/s​rc/net/bioclipse/ds/ui/views/TestsView.java: Fixed corner case when closing one of multiple editors without activating the next. Seems part.closed can be called after part.open.
13:30 jonalv olass: I have problems
13:30 jonalv olass: in seneca
13:31 jonalv egonw: actually you are the @author of the file
13:31 egonw yes, CUBIC work :)
13:31 jonalv the StochasticStructureElucidationJob
13:31 egonw what's up?
13:31 jonalv it needs merging...
13:31 egonw yeah, that needs refactoring anyway
13:31 olass jonalv: seneca is not our business
13:31 olass it is an EBI project
13:31 egonw not 2.0 material anyway
13:31 jonalv egonw: I don't have a clue on how to merge it...
13:32 olass we should not spend time on it
13:32 egonw jonalv: no worries
13:32 olass jonalv: ignore it
13:32 jonalv egonw: yes worries
13:32 egonw olass: agreed
13:32 jonalv olass: how
13:32 jonalv olass: how do I ingore it?
13:32 olass ?
13:32 egonw jonalv: I'm sure I'll discuss it next week
13:32 * olass ignores that question
13:32 jonalv olass: how do I ignore it? I must merge it
13:32 olass why?
13:32 egonw with Stefan/Gilleain at EBI
13:32 jonalv olass: because it's ion my branch
13:32 egonw jonalv: close project
13:33 olass remove it from your workspace if you like
13:33 egonw move to outdated :)
13:33 olass yes
13:33 jonalv olass: it does not work that way...
13:33 egonw jonalv: seriously
13:33 egonw close project
13:33 olass jonalv: then I cannot help
13:33 egonw ignore the compile errors...
13:33 jonalv egonw: what do you suggest that I do?
13:33 olass lol
13:33 olass [15:36] < egonw> close project
13:33 egonw keep the original version of SVN
13:33 jonalv egonw: I am getting HUGE merge errors
13:34 egonw simply, don't merge that file
13:34 jonalv olass: what does "close project mean?:
13:34 egonw why did you touch it anyway?
13:34 egonw skype ?
13:34 jonalv egonw: I am pretty sure I ahven\t touched it
13:34 egonw yes, I understand
13:34 egonw so, something else must be going on
13:34 egonw skype?
13:34 olass jonalv: right-click "close project"
13:35 egonw olass: no, actually not
13:35 jonalv olass: I am not in Eclipse
13:35 egonw olass: this is when doing merging
13:35 egonw to closing project does not really help at this point yet
13:35 egonw only when the 'merge' is done
13:35 * olass cannot help with merging
13:35 jonalv egonw: sure let\s skype
13:35 * olass should learn how to merge post 2.0
13:35 jonalv olass: I am sure you could if it would actually have been you changes but it appears that's not the case...
13:36 olass ok
14:00 egonw jonalv:
14:01 egonw git checkout -b testFoo GistManagerRefactoring7
14:01 egonw git rebase master
14:02 olass joined #bioclipse
14:02 egonw jonalv: kdiff3
14:17 egonw https://sourceforge.net/project/sho​wfiles.php?group_id=58666&amp;packa​ge_id=54597&amp;release_id=665583
14:17 egonw http://kdiff3.sourceforge.net/
14:17 zarah egonw's link is also http://tinyurl.com/syxv5
14:18 jonalv mesa
14:36 Gpox jonalv: in opendiff in the middle at the bottom there is a dot, drag it up and you will get the preview window
14:36 Gpox http://stephenwoods.net/2009/03/​09/the-mystery-of-filemergeappz/
14:36 jonalv zarah: ask olass why does not cdk.getNoMolecules work with an IFile?
14:36 zarah Gpox's link is also http://tinyurl.com/o39gmm
14:36 zarah Consider it noted.
14:37 jonalv Gpox: but can you edit the result as well?
14:37 Gpox yes
14:37 jonalv hm
14:37 jonalv intresting
14:37 Gpox the actions drop down to the right is also usefull
14:38 jonalv hm I guess I will have to give it another try then. But I am still trying to install KDE... :)
14:57 egonw https://bugs.eclipse.org/b​ugs/show_bug.cgi?id=271054
14:57 jonalv egonw: when you get back please fit the access stuffs on pele
14:57 jonalv |fix
14:58 egonw fortunately we don't nick name releases :)
14:58 egonw jonalv: acj
14:58 egonw ack
14:58 jonalv egonw: we need to solve this in some more permanent way...
14:58 egonw yes, we should
14:58 egonw Gpox: you know that perhaps?
14:59 egonw how to have git over ssh:// properly set chgrp ?
14:59 egonw and g+w ?
14:59 egonw jonalv: should be fixed now
14:59 egonw jonalv: I can do a crontab which runs every five minutes?
15:00 jonalv egonw: lol
15:01 jonalv egonw: is that the best way of doing it?
15:01 egonw no
15:01 egonw nasty workaround
15:01 egonw but would work
15:02 egonw as long if we can wait 5 minutes between one others commit :)
15:02 jonalv if you feel that you wnat to do a nasty workaround then go right ahead. I will balem you when it fails though :)
15:02 * jonalv is happy that neiother masak nor gillean is arounf to balem him ;)
15:03 jonalv |around
15:03 egonw :)
15:05 egonw BTW, CDKDebugManager tests are sort of working again
15:05 egonw 8/18 fails
15:05 egonw but no longer because of misuse of the JS manager :)
15:05 egonw 6 file not founds
15:05 jonalv okey
15:05 egonw other two because of using the CDK manager
15:07 jonalv egonw: that build failed now :)
15:08 * jonalv gives that up for npw
15:08 jonalv |now
15:09 * jonalv dig into the ICDKManager now instead
15:10 egonw ok
15:12 jonalv this time I am gonna start by only doing layout stuff
15:12 jonalv at least I will try :)
15:16 Gpox you have done this right? git repo-config core.sharedRepository true
15:18 CIA-40 bioclipse: egonw * r10182 /bioclipse2/trunk/plugins/ (6 files in 5 dirs): Added ICDKMolecule cached InChI and InChIKey (fixes #1020)
15:18 zarah bug #1020 | http://tinyurl.com/ochsey
15:42 CIA-40 bioclipse: goglepox * r10183 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java: Added support for adapting selection to IAtomContainer and view as external selection
15:43 CIA-40 bioclipse: goglepox * r10184 /bioclipse2/trunk/plugins/net.bioclipse.ds/ (2 files in 2 dirs): Added adapter stub for IAtomContainer
15:47 CIA-40 bioclipse: goglepox * r10185 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java: Fixed wrong variable used to check for null
15:54 CIA-40 bioclipse: goglepox * r10186 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java:
15:54 CIA-40 bioclipse: Run structure changed event in ui thead
15:54 CIA-40 bioclipse: Fixes bug #1035
15:54 zarah bug #1035 | http://tinyurl.com/oh6zfg
16:34 edrin egonw: ping
16:34 edrin jonalv: are you there?
16:42 egonw was away
16:42 egonw briefly back
16:42 edrin ok
17:34 edrin left #bioclipse
23:47 edrin joined #bioclipse

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