Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-08-11

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All times shown according to UTC.

Time Nick Message
06:07 egonw joined #bioclipse
07:01 Gpox joined #bioclipse
07:25 Gpox joined #bioclipse
07:28 egonw joined #bioclipse
07:33 egonw_ joined #bioclipse
07:50 jonalv joined #bioclipse
07:50 jonalv oh hai
07:50 zarah hi jonalv
07:52 egonw hi jonalv
08:12 edrin joined #bioclipse
08:12 edrin moin
08:12 zarah oh hai edrin
08:29 masak joined #bioclipse
09:04 CIA-71 bioclipse.structuredb: jonalv master * r8b51f74 / plugins/net.bioclipse.struc​turedb/META-INF/MANIFEST.MF : fixed deps - http://bit.ly/9KGPO9
09:35 jonalv egonw: ping
09:39 egonw pong
09:40 jonalv egonw: regarding @bug 2010
09:40 jonalv zarah: you should handle that that would be awesome...
09:40 zarah jonalv: Hokay. You provide the commits, I provide the "should"-ing
09:40 jonalv @pz 2010
09:40 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=2010
09:41 jonalv zarah: yes some day I might...
09:41 zarah jonalv: I see.
09:41 jonalv egonw: I am thinking maybe create another method instead of changing behavior...
09:41 jonalv egonw: for the moment I ma thinking cdk.moleculesFromString
09:42 jonalv egonw: can you come up with a better (shorter) name?
09:42 jonalv egonw: and what do you generally think about it?
09:42 egonw cdk.moleculesFromString() works for me
09:43 * jonalv get's started then...
09:47 masak s/'//
09:47 egonw jonalv: seen the last PhD Comic?
09:47 egonw about the repulsor field
10:47 jonalv egonw: yes :)
11:14 sneumann is there an insinuation behind this ?!
11:15 * jonalv didn't dare to ask...
11:15 sneumann (yes, I looked the word up in a dictionary ...)
11:25 jonalv egonw: CAn you run the plugin tests for net.bioclipse.cdk.business?
11:25 * jonalv is havign some trouble
11:25 jonalv No Classloader found for plug-in net.bioclipse.cdk.business.test
11:26 egonw sneumann, jonalv: no insinuation... it's just a good perspective for reflection... I have not clue how jonalv orbits the mindspace
11:26 egonw jonalv: booting eclipse
11:29 jonalv egonw: it seems to be working now
11:29 jonalv egonw: thanks!
11:29 jonalv running plugin tests is not so easy it seems...
11:30 * egonw hates code that depends on eclipse running on my laptop
11:30 jonalv oh hang on
11:30 jonalv Could not get the CDK manager
11:31 jonalv hm the JavaCDKManager tests does not work but the JavaScriptCDKManager tests seems to run at least...
11:31 jonalv egonw: does all of them work of you?
11:35 egonw eclipse is still booting
11:51 egonw plugin unit tests are booting
11:52 egonw jonalv: I get 12 failures
11:52 jonalv hm intesring I git 5 failures and 2 errors
11:53 egonw 5 knows
11:53 jonalv Does it actually run all the JavaCDKMangerplutingTests?
11:53 egonw 224 (6 ignored)
11:53 jonalv 112/224 (3 ignored) for me
11:54 jonalv okey so it works better for you then...
12:30 jonalv egonw: okey now it runs all of the tests (I didn't change anything though)
12:30 * jonalv mumbles
12:30 jonalv 12 failures 4 errors
12:31 egonw lovely...
12:31 egonw one source of variance I have is /Virtual
12:31 egonw olass, Gpox: what is the state of the plans to replace that?
12:39 Gpox are you testing Virtual, why not use a propert workspace location in the tests?
12:41 egonw because the WS might not have a proper project
12:41 egonw which is why I asked about methods to create and destroy projects at some point
13:37 _ilbot2 joined #bioclipse
13:37 Topic for #bioclipseis now #bioclipse 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
14:05 egonw jonalv: ping
14:05 jonalv egonw: pong
14:05 egonw this is what I meant yesterday...
14:05 egonw if you make patches, make them as small as possible...
14:06 egonw your patch changes the implementation of code all over the place :)
14:06 egonw do I have you vouch that it will not break anything?
14:06 jonalv egonw: the first commit is all the actual work
14:06 jonalv egonw: the second one is just white space
14:06 egonw yes, I know
14:07 egonw that's not what I'm talking about
14:07 egonw this is:
14:07 jonalv egonw: and yes it got big but none if it was unnecessary
14:07 egonw -    public List<ICDKMolecule> loadMolecules( IFile file,
14:07 egonw +    public List<ICDKMolecule> loadMolecules( InputStream contents,
14:07 egonw [08/11/10 16:06] <egonw> do I have you vouch that it will not break anything?
14:07 jonalv egonw: right, but there still is a method taking an IFIle it just got moved around so the diff doesn't pick it up...
14:08 egonw it will not break anything in 2.4.x?
14:08 jonalv egonw: and what if I wouch that it does not and then it does indeed break something? No one can promise that a certain piece of code breaks nothing. All I can say is that I ahve done my best and run the tests...
14:09 egonw ok, let me rephrase that...
14:09 jonalv egonw: oh you don't need to add it to 2.4.x branch
14:09 egonw if it does break something, you will help fix it?
14:09 egonw *if*
14:09 olass yes, I also suggest only master
14:09 jonalv I am not expecting this to go into 2.4.1 but 2.6.0...
14:10 egonw ack
14:10 egonw ok, good
14:10 jonalv egonw: can that work?
14:11 jonalv (I thought I wrote that in the pull request...)
14:11 egonw yes, I see that now...
14:11 jonalv also there will come another patch building on that one, any day now..
14:11 egonw :)
14:11 egonw seriously, the patch looks pretty useful, even as backport to 2.4.x
14:13 jonalv egonw: it doesn't really add anything worth backporting if you ask me. It's just a base for my next patch...
14:16 egonw ack
14:25 CIA-71 bioclipse.ds: Ola Spjuth master * rdd54420 / (3 files): Updated DS safety reports. - http://bit.ly/bDKUrY
14:25 CIA-71 bioclipse.ds: Ola Spjuth master * rc5af339 / plugins/net.bioclipse.ds.ui/src/ne​t/bioclipse/ds/ui/ImageHelper.java : Corrected ImageHelper to produce better images. - http://bit.ly/cwt2dr
14:25 CIA-71 bioclipse.ds: Ola Spjuth master * r1ac6ea3 / plugins/net.bioclipse.ds.common/src/net/biocl​ipse/ds/matcher/SDFPosNegNearestMatchFP.java : Turned on debugging since FP parsing now is fixed. - http://bit.ly/beVpUK
14:26 CIA-71 bioclipse.ds: Ola Spjuth master * rdd54420 / (3 files): Updated DS safety reports. - http://bit.ly/bDKUrY
14:26 CIA-71 bioclipse.ds: Ola Spjuth master * rc5af339 / plugins/net.bioclipse.ds.ui/src/ne​t/bioclipse/ds/ui/ImageHelper.java : Corrected ImageHelper to produce better images. - http://bit.ly/cwt2dr
14:26 CIA-71 bioclipse.ds: Ola Spjuth master * r1ac6ea3 / plugins/net.bioclipse.ds.common/src/net/biocl​ipse/ds/matcher/SDFPosNegNearestMatchFP.java : Turned on debugging since FP parsing now is fixed. - http://bit.ly/beVpUK
14:26 olass egonw: ping
14:26 olass for emails to commit-ml, does CIA fix that or do we use a hook in github?
14:27 egonw hook
14:27 olass ack
14:27 egonw that's what my reposes had
14:28 olass egonw: I am deleting my repos and forking agin from bioclipse organization
14:28 olass I suggest you do the same
14:28 egonw ask me after Boston
14:28 egonw going nuts here
14:29 olass at least, please do not fork from my repos but instead fork bioclipse repos
14:29 samuell joined #bioclipse
14:29 jonalv hi samuell
14:29 * olass likes nuts
14:29 samuell hi jonalv
14:29 jonalv mmmm nuts
14:29 egonw olass: sure
14:29 samuell you all get notifications about new posts in the forum, right?
14:29 olass samuell: dunno...
14:30 egonw samuell: have not seen one
14:30 egonw hi samuell
14:30 jonalv samuell: uhm yea now that you say it...
14:30 jonalv |mention it
14:30 samuell hi egonw
14:30 egonw samuell: please check if all your repositories wrt your research project are now on github.com/bioclipse
14:30 samuell Hmm . I get them ...
14:30 jonalv lookjs like spam
14:30 egonw samuell: at your earliest convenient time
14:30 samuell egonw: Ok!
14:31 samuell sounds like a good thing to collect them
14:31 samuell in one repo
14:31 samuell jonalv: Yea, there was one spam I think
14:31 samuell but at least one real post
14:31 jonalv samuell: when I click on the read more link in google reader I get acces denied though
14:32 jonalv samuell: is that becasue you have removed it?
14:32 samuell jonalv: Ok, humm...
14:32 samuell Ah, yes
14:32 samuell the "california drivecs platelet" sth, yes :)
14:35 CIA-71 bioclipse.cheminformatics: jonalv master * r2353a78 / (3 files in 2 dirs): whitespace fix -- Removed trailing whitespaces (+72 more commits...) - http://bit.ly/ad9rxZ
14:35 olass egonw: did you show jonalv how to edit CIA settings?
14:36 olass I will need some additions
14:36 olass and you seem pretty stressed...
14:36 jonalv olass: yes but he did not give me his password...
14:36 olass egonw: could you please do that?
14:36 egonw olass: yes
14:36 egonw why?
14:36 egonw ('m going to give him my password
14:36 olass so he can make changes when you are away..?
14:36 egonw he can get an account himself
14:36 jonalv I amn not sure I want egons passwrods...
14:37 egonw quite so
14:37 egonw I'd be looking at jonalv every and each time something goes wrong
14:37 olass can jonalv make changes with his own account?
14:37 egonw he would have the pwds after all :)
14:37 olass sounds excellent
14:37 jonalv I don't think so now
14:37 egonw olass: I think I need to show you too how the system works
14:37 jonalv but that could be changed?
14:37 egonw jonalv: please show ola how it works
14:37 egonw jonalv: I think you could even just define a new bot
14:38 egonw jonalv: did you try that yet?
14:38 olass egonw: I'd like us to have only one CIA bot...
14:38 jonalv egonw: then we would have two?
14:38 jonalv egonw: what was the adress of that page again? :)
14:38 egonw I'm also more than fine of donating the bot to jonalv
14:38 egonw jonalv: shall we do it like that?
14:38 jonalv egonw: sure, that works
14:40 jonalv egonw: but how?
14:40 egonw jonalv: what's your cia.vc account name?
14:40 jonalv jonalv
14:40 olass egonw: is the CIA bot better than the github IRCbot?
14:41 egonw guess so
14:41 egonw otherwise we would not be using the CIA bot
14:41 egonw or?
14:41 olass well, I have not tried the other so cannot say
14:41 jonalv egonw: well haven't we been using CIA since way beofee git?
14:41 olass I suppose you have
14:41 egonw notice: bioclipse.cheminformatics master branch is open for 2.6 development
14:41 olass egonw: sounds fair
14:42 egonw jonalv-- (for asking nasty questions)
14:42 olass I thnk that should go for all repos
14:42 olass same is core repo
14:42 olass 2.6
14:42 olass devel
14:58 edrin huh
14:59 jonalv olass was playing it seems...
15:16 CIA-71 bioclipse.cheminformatics: jonalv master * r17dc48e / (3 files in 2 dirs):
15:16 CIA-71 bioclipse.cheminformatics: PasteAsNew now handles multi mol sdf content
15:16 CIA-71 bioclipse.cheminformatics: The paste as new function now correctly handles strings containing multiple molecules such as for example a copied sdf file. This relates to bug: #1812 - http://bit.ly/cHikHT
15:17 zarah bug #1812 | http://tinyurl.com/2wzvotz
15:27 CIA-71 bioclipse.brunn: jonalv master * r1448f60 / (3 files in 2 dirs): removed strange project related artifacts - http://bit.ly/blf0gw
15:30 egonw_ joined #bioclipse
16:24 egonw_ joined #bioclipse

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