Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-07-17

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Time Nick Message
00:11 mgerlich joined #bioclipse
00:11 zarah joined #bioclipse
06:45 olass joined #bioclipse
06:45 olass moi
06:45 olass moin
06:45 zarah saluton olass
07:26 sneumann joined #bioclipse
07:28 jonalv joined #bioclipse
07:28 jonalv o/
07:35 olass \o
07:39 shk3 joined #bioclipse
07:45 egonw joined #bioclipse
07:45 egonw moin
07:45 zarah privet egonw
07:54 olass egonw, jonav: I have some git questions
07:55 olass if I want to share a local branch with someone, how do I do that?
07:55 olass for example
07:55 olass I have rewritten bioclipse.ds in a local branch
07:55 egonw just like you shared the 2.0.x branch in github
07:55 olass hmm
07:56 olass when people do 'git pull' they get the ne wbranch?
07:56 egonw I think they do
07:56 egonw possible the need to do:
07:56 egonw git pull ssh://... newBranch
07:56 egonw and then make a local checkout with
07:57 egonw git checkout -b localNewBranch origin/newBranch
07:57 olass ok, another question
07:57 olass how to I see if I need to push?
07:57 egonw git status mentiones this, I think
07:57 egonw something like:
07:57 egonw you're ahead 5 commits
07:58 egonw or something like that
07:58 olass hmm
07:58 olass not in a local branch
08:01 olass egonw?
08:01 * olass is confused
08:01 egonw what do you mean with: [07/17/09 09:58] <olass> not in a local branch ?
08:02 olass I am standing in my local branch of bioclipse.ds
08:02 olass mbpro:bioclipse.ds ola$ git status
08:02 olass # On branch endpoints-refactoring
08:02 olass nothing to commit (working directory clean)
08:02 olass it is committed to the branch
08:02 egonw oh, right
08:02 olass what happens if I do git push?
08:02 egonw this will not say anything like 'x commit ahead' because there is no 'origin' to compare against at this moment
08:03 olass what happens if I do git push?
08:03 egonw depends on the exact full command...
08:03 olass just git push?
08:03 egonw git push ssh:// branchName
08:03 egonw btw, try this:
08:03 egonw git diff ..master
08:03 egonw I think...
08:03 egonw mom
08:04 olass very verbose..
08:04 egonw yeah, I think you can do the same with 'git log'
08:05 egonw normally use gitk for this
08:05 egonw gitx in your case, I guess
08:05 olass hmm
08:05 egonw but I don't know how gitx works...
08:06 egonw http://book.git-scm.com/3_comp​aring_commits_-_git_diff.html
08:06 zarah egonw's link is also http://tinyurl.com/lkpthp
08:06 egonw http://linux.yyz.us/git-howto.html#diff_branch
08:06 zarah egonw's link is also http://tinyurl.com/t8ya4
08:07 CIA-52 bioclipse.ds: Ola Spjuth master * re7cd5b0 / (6 files in 5 dirs): Updated extension point schema and extenions for the new endpoint element. - http://bit.ly/GNmL8
08:07 CIA-52 bioclipse.ds: Ola Spjuth master * r10939ab / .gitignore : Added .gitignore for the ds project. - http://bit.ly/LHvgi
08:07 CIA-52 bioclipse.ds: Ola Spjuth master * r3ab6116 / (20 files in 9 dirs): Some refactoring of model classes to more suitable packages and cleanup of unused code. - http://bit.ly/FMj1f
08:07 CIA-52 bioclipse.ds: Ola Spjuth master * r32eb286 / plugins/net.bioclipse.ds.bursi/plugin.xml : Updated manifest for refactored classes. - http://bit.ly/NkQT3
08:07 CIA-52 bioclipse.ds: Ola Spjuth master * raded6ae / (6 files in 5 dirs): Added 'visibility' attribute in DS to filter out consensus tests from DSView since they should not be shown there. - http://bit.ly/N45G5
08:20 olass @px thread
08:20 olass @pz thread
08:20 zarah [222] Ability to cancel a JS call tha... http://tinyurl.com/cdg6w5
08:20 zarah [1421] Can not open ActionHistory view   http://tinyurl.com/lj7z35
08:20 zarah [1326] Fix serialization/deserializat... http://tinyurl.com/msm3ak
08:20 zarah [950] Cleanup messy structure hangs b... http://tinyurl.com/mxcd5l
08:20 zarah [1163] Solve threading problem with c... http://tinyurl.com/kvx8we
08:20 zarah Entire list (12) at http://tinyurl.com/n2ohbs
08:23 egonw olass: can we start using Eclipse3.5?
08:24 olass I'd be happy if you tried it
08:24 olass maybe try java 1.6 at the same time?
08:24 olass we need someone on Mac to test it too
08:24 olass since there's where I expect most hassle will be
08:24 olass jonalv: do you feel the urge?
08:25 * olass does not have time for it
08:25 * jonalv is cleaning up his desktop in order to find the cnf tutorial papers... :)
08:27 jonalv olass: hm I guess I could but not right now. I want to get some order to structuredb now...
08:27 jonalv +my desktop...
08:27 olass sounds like a good prio
08:27 egonw joined #bioclipse
08:28 olass egonw: how about a 3.5 branch in bioclipse.core towards 3.5 and java 1.6?
08:28 egonw yes, good idea
08:28 olass please set it up if you like
08:28 egonw oh, goodies ... Java6
08:29 olass let's hope it works on Mac
08:29 olass :)
08:29 jonalv so do you think we should aim for this in 2.1?
08:34 * egonw has set up a 2.0.x branch for bioclipse.cheminformatics too
08:35 de__maas joined #bioclipse
08:40 egonw ha, de__maas!
08:42 de__maas Hi Egon, how's life?
08:44 egonw good
08:44 egonw went to the Efteling yesterday :)
08:44 de__maas LOL, so you @NL for the time being
08:46 egonw right
08:47 de__maas Well you've luck with the whether.
08:47 egonw that's why we went yesterday :)
08:47 de__maas I actually became a dad 3 weeks ago, so efteling is a bit fast.
08:48 egonw ah, congrats!
08:48 egonw well, next year should be fun
08:48 olass de__maas: congratulations!
08:48 egonw het sprookjesbos
08:49 * olass is slowly starting to like git
08:49 egonw been there, done that
08:49 * olass also likes coffee very much
08:49 egonw we told you so
08:49 olass I really like the offline commit function
08:50 egonw yes
08:50 egonw distributed systems are superior
08:50 olass but difficult to get into
08:51 de__maas Thx, sprookjesbos rules is does git.
08:51 de__maas olass: did you see the crash course?
08:53 olass de__maas: no
08:53 olass where is it?
08:53 de__maas http://git.or.cz/course/svn.html
08:53 zarah de__maas's link is also http://tinyurl.com/2coemo
08:53 de__maas But I guess you already passed this part.
08:55 olass de__maas: actually read that, was rather good
08:55 olass yes, passed it :)
08:57 olass egonw: how do you work with git on windows?
08:57 de__maas Using cygwin
08:57 de__maas some commands also run on cmd but not all.
08:58 de__maas There is a small gui but not really well.
08:58 olass oh
08:58 olass so git on win is complicated :(
08:59 * olass was just thinking of windows developers
08:59 olass I think edrin is on windows, right?
08:59 olass well, there is eGit for Eclipse
08:59 olass so you basically just need to be able to clone a repo and then use eGit
09:02 de__maas What I understood eGit is not quite there yet.
09:03 de__maas I'm on windows and I don't feel it's that big a problem. It does install a small version of cygwin for the interactive commands (opening vi)
09:24 olass ah
09:24 olass not bad then
09:24 * olass finds YourKit extremely nice!
09:25 olass integrates beautifully with Eclipse!
09:25 olass really good product
09:37 egonw joined #bioclipse
09:37 egonw sorry...
09:37 egonw network hickup
09:40 edrin joined #bioclipse
09:40 edrin hi
09:40 zarah saluton edrin
09:40 edrin http://xkcd.com/611/
09:53 egonw_ joined #bioclipse
09:58 egonw_ de__maas: I think they would certainly appreciate bug reports...
09:59 egonw_ you can file them here:
09:59 egonw_ http://code.google.com/p/egit/issues/list
09:59 zarah egonw_'s link is also http://tinyurl.com/mcgpge
10:06 rojasm joined #bioclipse
10:18 de__maas egonw_: bug report file I would, but I'm not using egit but just the command line version.
10:18 egonw_ ack, same here
10:18 egonw hi rojasm
10:18 egonw rojasm: looking forward to next week!
10:19 rojasm hi egonw
10:19 rojasm yes indeed
10:19 rojasm do you will come back Monday night to your place or
10:19 rojasm you want to stay in my place
10:19 egonw if possible, I prefer to stay over
10:19 rojasm of course
10:20 rojasm So all arranged
10:20 egonw saves me 5 hours of travel, and more time to talk, hack, and have beer (or equivalent)
10:20 egonw great
10:20 rojasm :)
10:20 rojasm what time will you be in Leiden!
10:24 * jonalv @ lunch
10:34 CIA-52 bioclipse.core: Egon Willighagen master * rf0b21a4 / plugins/net.bioclipse.core.tests/sr​c/net/bioclipse/core/MockIFile.java : Added new methods required by the IFile interface in Eclipse 3.5 - http://bit.ly/wdRcD
10:46 olass egonw: ping
10:46 egonw pong
10:46 olass how do I merge in my local branch into my local master, before a git push?
10:47 egonw git checkout master
10:47 egonw git pull
10:47 egonw if there are no new incoming patches...
10:47 egonw git merge branchToMerge
10:47 egonw if there are...
10:47 egonw do this:
10:47 egonw git checkout branchToMerge
10:47 egonw git rebase master
10:47 egonw git checkout master
10:48 egonw git merge branchToMerge
10:48 egonw note the 'git rebase'
10:48 olass Ok, thanks
10:48 olass I get the flow
10:48 olass will the branch disappear?
10:48 egonw that will basically create a new branch on the fly using the patches you already had in that branch
10:48 egonw no
10:48 egonw you can delete it after the push with:
10:48 egonw git branch -d branchToDelete
10:49 olass thx
10:49 egonw note the 'after'
10:49 olass yes
10:49 egonw otherwise we end up recovering dangling hashes :)
10:49 egonw olass: update in Eclipse 3.5
10:49 egonw only very few compile issues
10:49 egonw but
10:49 egonw there is some stuff with the .product
10:49 egonw reset target platform does not solve it...
10:49 egonw some stuff missing
10:50 olass yea, sounds logical
10:50 egonw probably renamed, or not part of the eclipse version I have now
10:50 olass since a new eclipse version, things will have changed
10:50 egonw e.g. equinox p2 stuff...
10:50 egonw org.eclipse.compare.core
10:50 egonw that's one
10:51 olass can I mege with gitx?
10:51 olass merge
10:51 egonw dunno
10:52 olass ok
10:53 olass should it not appear here?
10:53 * olass is waiting
10:53 olass well, seemed to work
10:54 olass but no messages here
10:54 olass that happened earlier
10:56 CIA-52 bioclipse.core: jonalv master * r2390557 / plugins/net.bioclipse.core/src/net​/bioclipse/recording/History.java : store max 100 events in action history. Fixes bug: #1419 - http://bit.ly/10VJdz
10:56 CIA-52 bioclipse.core: Egon Willighagen master * rf0b21a4 / plugins/net.bioclipse.core.tests/sr​c/net/bioclipse/core/MockIFile.java : Added new methods required by the IFile interface in Eclipse 3.5 - http://bit.ly/wdRcD
10:56 zarah bug #1419 | http://tinyurl.com/mnk8gg
10:56 CIA-52 bioclipse.cheminformatics: Egon Willighagen 2.0.x * r7ab1ff0 / plugins/net.bioclipse.webservi​ces.tests/META-INF/MANIFEST.MF : Added missing (implicit) dependency which Eclipse 3.5 complains about - http://bit.ly/nANqJ
10:56 CIA-52 bioclipse.cheminformatics: Egon Willighagen 2.0.x * r00e818b / plugins/net.bioclipse.cdk.business.te​st/src/net/bioclipse/cdk/business/tes​t/AbstractCDKManagerPluginTest.java : Force compare int with int, instead of relying on autoboxing - http://bit.ly/BKRGL
10:56 CIA-52 bioclipse.cheminformatics: Egon Willighagen master * r8da8eee / plugins/net.bioclipse.webservi​ces.tests/META-INF/MANIFEST.MF : Added missing (implicit) dependency which Eclipse 3.5 complains about - http://bit.ly/1fpQ3c
10:56 CIA-52 bioclipse.cheminformatics: Egon Willighagen master * ra0d1350 / plugins/net.bioclipse.cdk.business.te​st/src/net/bioclipse/cdk/business/tes​t/AbstractCDKManagerPluginTest.java : Force compare int with int, instead of relying on autoboxing - http://bit.ly/1MMJgd
10:56 CIA-52 bioclipse.ds: Ola Spjuth master * r088b306 / (6 files in 5 dirs): Deprecated the cone attribute in extension point schema and ignored it in implementations. We now always clone the CDKMolecule before a test is run in DSView. - http://bit.ly/1orGzp
10:56 CIA-52 bioclipse.ds: Ola Spjuth master * r1fe27d7 / (4 files in 2 dirs): Deleted old extension point net.bioclipse.ds.tests and corresponding schema. Also renamed schema for new EP to not include redundant namespace. - http://bit.ly/XSeMi
10:57 egonw crap
10:57 CIA-52 bioclipse.cheminformatics: Egon Willighagen 2.0.x * ra8dd95d / plugins/net.bioclipse.webservi​ces.tests/META-INF/MANIFEST.MF :
10:57 CIA-52 bioclipse.cheminformatics: Revert "Added missing (implicit) dependency which Eclipse 3.5 complains about"
10:57 CIA-52 bioclipse.cheminformatics: This reverts commit 7ab1ff0ef4914b62aed05437963af552b354998a. - http://bit.ly/9ORPP
10:57 CIA-52 bioclipse.cheminformatics: Egon Willighagen 2.0.x * r39d5163 / plugins/net.bioclipse.cdk.business.te​st/src/net/bioclipse/cdk/business/tes​t/AbstractCDKManagerPluginTest.java :
10:57 CIA-52 bioclipse.cheminformatics: Revert "Force compare int with int, instead of relying on autoboxing"
10:58 CIA-52 bioclipse.cheminformatics: This reverts commit 00e818bcb9a9dbf676cb3fb9ea512d1d9835a7ce. - http://bit.ly/NXFL5
10:58 egonw ok, lunch time
11:00 CIA-52 bioclipse.ds: Ola Spjuth master * rcad9215 / plugins/net.bioclipse.ds.lipinski/plugin.xml : Updated lipinsky test with a new endpoint 'Informative' for new DS EP. - http://bit.ly/P8EnA
11:15 * jonalv is back from lunch\
11:18 * egonw will do a balloon git
11:19 olass egonw: thanks
11:19 olass bioclipse.balloon
11:20 egonw ack
11:29 CIA-52 bioclipse: shk3 * r11692 /bioclipse2/trunk/plugins/net.bioclipse.seneca/ (3 files in 3 dirs): slight improvement with score handling
11:34 jonalv egonw: how do you hook in these CIA bots to do commit reporting. It would be sort of nice to have one for structuredb as well... :)
11:34 egonw github -> bioclipse.structuredb -> admin -> hooks
11:34 egonw enable CIA end email
11:35 egonw (email for bioclipse-commit)
11:36 egonw and after that, try a commit
11:36 jonalv egonw: but how should CIA be confgiured?
11:36 egonw no need for that
11:37 egonw the local bot already knows about the bioclipse.structuredb project
11:37 jonalv egonw: how can it?
11:37 egonw because I made it aware for it...
11:37 jonalv egonw: so I can't do that?
11:37 egonw no
11:38 egonw because the only options are:
11:38 egonw everyone can change it, one person can change it
11:38 egonw and I don't like the first
11:45 rojasm joined #bioclipse
11:46 rojasm left #bioclipse
11:52 egonw jonalv: is it working?
11:52 jonalv egonw: don't know yet
11:52 egonw de__maas: btw, looking forward to your hearing about your experiences with SDF in the 2.0.0 release
11:52 egonw olass: http://github.com/egonw/bio​clipse.balloon/tree/master
11:52 zarah egonw's link is also http://tinyurl.com/lzol5g
11:53 olass egonw: forked
11:54 olass egonw: and cloned
11:54 egonw :)
11:54 olass egonw++ //Thanks for this
11:54 * egonw hears the joy of git sounding through olas irc messages :)
11:55 olass indeed, I am getting sort of used to it (git)
11:55 egonw good
11:56 egonw the learning curve of git is not so high nowadays
11:56 olass egonw: turned on CIA and email for bioclipse.balloon now too
11:57 egonw good
11:57 olass testing...
11:57 CIA-52 bioclipse.balloon: ospjuth master * rc4849eb / plugins/net.bioclipse.jnati/.classpath :
11:57 CIA-52 bioclipse.balloon: Added executable file permissions on PDE build using a permissions.properties file.
11:57 CIA-52 bioclipse.balloon: git-svn-id: https://bioclipse.svn.sourceforge.net/s​vnroot/bioclipse/bioclipse2/trunk@9698 fcb5ba71-d80d-0410-8237-ba3920747fcc - http://bit.ly/h3weJ
11:57 CIA-52 bioclipse.balloon: ospjuth master * r6e53015 / plugins/net.bioclipse.jnati/.set​tings/org.eclipse.jdt.core.prefs :
11:57 CIA-52 bioclipse.balloon: Set version to 2.0.0.RC1 for release candidate 1.
11:57 CIA-52 bioclipse.balloon: git-svn-id: https://bioclipse.svn.sourceforge.net/s​vnroot/bioclipse/bioclipse2/trunk@10945 fcb5ba71-d80d-0410-8237-ba3920747fcc - http://bit.ly/150qjK
11:57 olass yes, seems to work
11:59 CIA-52 bioclipse.core: jonalv master * ra9cb9d6 / plugins/net.bioclipse.core/src/net/bio​clipse/recording/RecordingAdvice.java : indentation - http://bit.ly/18TQYL
11:59 CIA-52 bioclipse.core: jonalv master * r695a3ba / plugins/net.bioclipse.core.tests/sr​c/net/bioclipse/core/MockIFile.java : Merge branch 'master' of git@github.com:olas/bioclipse.core - http://bit.ly/141ipA
11:59 CIA-52 bioclipse.structuredb: jonalv master * r483b429 / (70 files in 10 dirs): Changed copyright header for all files in structuredb plugin - http://bit.ly/18acRN
11:59 CIA-52 bioclipse.structuredb: jonalv master * r13b1ac8 / plugins/net.bioclipse.struc​turedb/META-INF/MANIFEST.MF : structuredb no longer requires net.bioclipse.services (no longer compiles either though...) - http://bit.ly/18XHxP
11:59 CIA-52 bioclipse.structuredb: jonalv master * rcec859f / plugins/net.bioclipse.structuredb/​.settings/org.eclipse.jdt.ui.prefs : some strange prefs file. Mgiht as well commit it... - http://bit.ly/en8eg
11:59 jonalv hm what was that merge all about?
12:00 jonalv egonw: structuredb is hooked to CIA anyway. But I don't get that merge...
12:00 jonalv why is it there?
12:02 rojasm joined #bioclipse
12:02 egonw jonalv: please make sure to update from github before you commit your local changes
12:02 egonw it now merged your local branch with the upstream branch
12:02 egonw like with SVN
12:02 jonalv egonw: ah, but that can't be avoided...
12:02 egonw it is best practise to first 'svn up' before you 'svn commit'...
12:02 egonw yes, it can
12:03 jonalv egonw: what does svn have to do with this?
12:03 egonw just 'git pull' before 'git push'
12:03 jonalv egonw: I am pretty sure I did
12:03 egonw the will remove redundant merging of branches
12:04 egonw oh, and I think all .settings/ folders should be removed from the repository
12:04 jonalv egonw: but I did. I always pull before I push
12:04 egonw booting gitk to confirm...
12:06 jonalv egonw: If you don't believe me: http://pastebin.com/d748fec05
12:07 egonw ok, please post the content of your bpull and bpush scripts
12:07 jonalv egonw: hang on
12:07 jonalv egonw: you can see that it does a pull from bioclipse.core though...
12:08 egonw it does not say in what branches you pull and push
12:08 egonw so, not enough info
12:08 jonalv egonw: http://wiki.bioclipse.net/index.php?t​itle=Git_Development#Pushing_and_pull​ing_multiple_repositories_in_one_go
12:08 zarah jonalv's link is also http://tinyurl.com/mqpa8m
12:08 jonalv egonw: branches? I am only working in master I think
12:08 jonalv or
12:08 jonalv hm...
12:10 egonw well...
12:10 egonw run gitk
12:10 jonalv egonw: I can't
12:10 egonw and you'll see that your commits repeatedly introduce branching
12:10 egonw gitx
12:10 jonalv KDE refuses to build on this machine...
12:11 jonalv egonw: what does that mean?
12:11 egonw you can see it here too:
12:11 egonw http://github.com/olas/bioclipse.core/network
12:11 zarah egonw's link is also http://tinyurl.com/m2qx5z
12:12 egonw I think
12:12 egonw anyway...
12:12 egonw not sure what your scripts does...
12:12 jonalv egonw: okey why is this? Can it really be avoided?
12:12 egonw but the 'merge' commits are caused by merging branches
12:13 egonw which are typically caused by inproper getting upstream patches in your local history
12:13 jonalv egonw: my scripts does what I would do manually if I didn't have them...
12:14 egonw http://github.com/olas/bioclipse.core/commi​t/695a3bae11b47d2507f336c988a2a00aa357343a
12:14 zarah egonw's link is also http://tinyurl.com/m329ne
12:14 egonw something like that can and should be prevented
12:14 egonw I like a linear history
12:14 jonalv egonw: but that is not the commit that branched. That commit merged...
12:15 egonw but this is olas' branch...
12:15 egonw yes
12:15 egonw so?
12:15 jonalv I want to know why this occured
12:15 egonw so, please review your local state before you push
12:16 egonw I can't explain either...
12:16 egonw too little information
12:16 jonalv when I look at the network page it more looks like you created the branch
12:16 egonw remote debugging is difficult
12:17 egonw what does your 'git branch -r' say for you?
12:17 egonw yeah, I don't quite understand what that page shows either...
12:18 jonalv origin/2.0.x
12:18 jonalv origin/HEAD
12:18 jonalv origin/master
12:18 egonw from that one, it seems you are working in the 2.0.x branch
12:18 egonw can you pastebin your .git/config ?
12:18 jonalv egonw: no I am in master
12:19 egonw yeah, same here...
12:19 jonalv egonw: http://pastebin.com/d1226ae70
12:19 egonw yeah, that looks the same as mine
12:20 egonw so, what the network shows here...
12:20 egonw is that a branching occured
12:20 egonw depending on who of use commited first, created the branch in the history
12:20 egonw your commit was made at your machine before mine
12:20 egonw making it show up before mine in time in the Network Graph
12:21 jonalv oh welll, I guess we can come back to this if it ovvurs again...
12:22 jonalv It's not like the end of the world really...
12:22 egonw but your push was after mine
12:22 egonw at least, according to the CIA
12:23 egonw yeah, it's no big deal
12:23 egonw but it explains why you see that merge commit
12:38 de__maas egonw: MoleculeTableEditor, really lookes good. I just opened a SD-file of 206960 records (10mg stock database) in about 15 seconds. Also noticed that the smiles also created correct molecules.
12:39 egonw how large is that file? in MB?
12:40 de__maas 658 MB
12:41 egonw ok, good
12:41 de__maas real fast PC. Did anything change on the smile parser site?
12:42 egonw it's now in a thread
12:42 de__maas Is deduceBondOrder working any faster?
12:42 egonw but the same code
12:42 egonw no
12:43 de__maas Because when I get a smile file from a partner/customer I convert it to SD-file using openbabel and apply the CDK for 2D coordinates.
12:43 egonw that should work
12:43 egonw just open the .smi file in BC2
12:44 de__maas last time I checked OpenBabel gave me better results.
12:44 de__maas But it does not generate 2D coordinates.
12:45 egonw bug reports always most welcome
12:47 de__maas Shure, when I have a good case I will file it.
13:04 CIA-52 bioclipse.structuredb: jonalv master * r20989c1 / (10 files in 4 dirs):
13:04 CIA-52 bioclipse.structuredb: Working on rewriting StructureDB to work with new unfinnished
13:04 CIA-52 bioclipse.structuredb: net.bioclipse.databases plugin instead of net.bioclipse.services which seems to
13:04 CIA-52 bioclipse.structuredb: be dieing or perhaps is dead. All model classes will stand by them self now
13:04 CIA-52 bioclipse.structuredb: instead of extending a class from that services plugin. With this commit it at
13:04 CIA-52 bioclipse.structuredb: least compiles again but I have not even attempted to start it. -
13:04 CIA-52 bioclipse.structuredb: http://bit.ly/6wprl
13:37 olass egonw: ping
13:38 olass the CIA bot seems not to work so good. I just pushed quite some commits in bioclipse.ds but they don't show up here
13:38 olass also, no emails to commit list
13:39 olass however, trying the "test hook" makes them appear here
13:39 olass could it be a setting not to show when too many commits at the same time?
13:39 olass egonw: can you investigate?
13:40 egonw mmm
13:40 egonw it is in the list for the bot
13:40 egonw http://cia.vc/stats/project/bioclipse.ds
13:40 zarah egonw's link is also http://tinyurl.com/lznwhq
14:10 CIA-52 bioclipse.core: jonalv master * r3e077ac / (4 files in 3 dirs): Created CNF for showing databases - http://bit.ly/fCTRz
14:10 CIA-52 bioclipse.structuredb: jonalv master * r835ed99 / plugins/net.bioclipse.struc​turedb/META-INF/MANIFEST.MF : net.bioclipse.structuredb requires net.bioclipse.databases - http://bit.ly/edJRk
14:10 CIA-52 bioclipse.structuredb: jonalv master * rbe857b5 / plugins/net.bioclipse.structuredb/src/net/bioclips​e/structuredb/viewer/DatabaseContentProvider.java : Updated content provider for working with databases view - http://bit.ly/6AxJV
14:10 CIA-52 bioclipse.structuredb: jonalv master * r8cea1e7 / plugins/net.bioclipse.structuredb/plugin.xml : hooked in structuredb into the databases view - http://bit.ly/yOm4R
14:10 olass jonalv: any progress?
14:11 jonalv olass: yes
14:11 egonw joined #bioclipse
14:11 olass nice :)
14:11 jonalv the databaess view shows the data now
14:11 olass cool
14:11 jonalv next step is to get the listeners to work and update when things changes I guess
14:11 olass yes
14:11 olass and to allow queries etc
14:11 jonalv yea >(
14:12 jonalv hm
14:12 egonw jonalv++
14:12 olass hmm, how did I remove a branch again?
14:13 egonw put a ':' in front of the branch name
14:13 olass git branch :BranchToDelete
14:13 olass ?
14:14 jonalv hm the molecules editor connection is broken too. It is no longer possible to open things in it from Structuredb...
14:15 egonw olass: ah no...
14:15 egonw sorry... thinking about remote
14:16 egonw remove / remote
14:16 egonw git branch -d branchToDelete
14:16 olass jonalv: things very likely has changed
14:16 jonalv yea
14:16 jonalv they have it seems...
14:16 olass egonw: ok, and how did I make sure no differences between two branches?
14:16 olass gitt diff branchname?
14:16 egonw git diff master..otherBranch
14:16 egonw git log master..otherBranch
14:17 olass ok
14:17 jonalv olass: do you know if the CNF structure can have that feature where you "go into" a child in a tree and look at the tree with that as root?
14:17 olass It's called 'drill down', and yes
14:18 jonalv olass: I am thinking that we might want that...
14:19 egonw bah...
14:19 egonw network connectivity is rather unstable today... :(
14:32 jonalv hm I just realised I ahve no idea how to force the CNF to update when data changes
14:47 de__maas left #bioclipse
15:18 CIA-52 bioclipse: egonw * r11693 /bioclipse2/trunk/ (8 files in 8 dirs): Removed plugins now available from the Git repository at http://github.com/olas/bio​clipse.balloon/tree/master
15:18 zarah CIA-52's link is also http://tinyurl.com/m5flxa
15:23 CIA-52 bioclipse: egonw * r11694 /bioclipse2/trunk/ (7 files in 7 dirs): Removed plugins now available from the Git repository at http://github.com/olas/bioclipse.ds/tree/master
15:23 zarah CIA-52's link is also http://tinyurl.com/nl8eta
15:27 * jonalv is totally stuck. Updating CNF trees appharently isn't so easy.
15:37 egonw is this the bioclipse navigator widget?
15:38 egonw ui.foo() updates that CNF, not?
15:39 jonalv egonw: no this is the databases navigator widget
15:39 egonw but maybe the code is still helpful?
15:39 jonalv egonw: I am afraid that that one is updated automgicly with resourcechangelisteners deep in the CNF code...
15:40 egonw ic
15:40 jonalv but correct me if I am wrong
15:41 egonw I have no clue
15:41 egonw never done any CNF stuff
15:41 egonw rojasm: ping... around?
15:41 jonalv I am beginning to think that an extension point just for "update the viewer" callbacks is the only solution.... :(
15:42 jonalv or I could just hard-code all of it inside my model and get a really ugly big monster of code...
15:42 jonalv :(
15:43 jonalv not even the Eclipse people had any ideas...
15:44 * jonalv reads "Listeners considered harmful: The 'whiteboard' pattern" in desperate hope that it will trigger some ideas...
16:09 * jonalv gives up for today. Hopefully some brilliant idea will pop up when he get's back to this problem after a weekend...
16:11 CIA-52 bioclipse.structuredb: jonalv master * ra49ac30 / plugins/net.bioclipse.structuredb/plugin.xml : Changed to a better name for navigatorContent from Structuredb - http://bit.ly/17VLF5
17:39 edrin left #bioclipse
18:36 sneumann joined #bioclipse
19:21 CIA-52 bioclipse: egonw * r11695 /bioclipse2/trunk/plugins/ (3 files in 3 dirs): Removed plugins available from http://github.com/olas/bioclipse.statistics/tree/​95abc3f03e096875bbf465ee9915ed36065402f2/plugins
19:21 zarah CIA-52's link is also http://tinyurl.com/kr9c23
19:25 CIA-52 bioclipse: egonw * r11696 /bioclipse2/trunk/plugins/ (9 files in 9 dirs): Removed plugins available from http://github.com/olas/bioclipse.qsar/tree/master
19:25 zarah CIA-52's link is also http://tinyurl.com/m935yy
19:31 egonw joined #bioclipse
19:40 CIA-52 bioclipse: egonw * r11697 /bioclipse2/trunk/ (10 files in 10 dirs): Removed plugins and feature that are soon available as bioclipse.medea from GitHub
19:59 egonw olass: http://github.com/egonw/bioclipse.data/tree/master
19:59 zarah egonw's link is also http://tinyurl.com/n79wq8
20:01 CIA-52 bioclipse: egonw * r11698 /bioclipse2/trunk/ (4 files in 4 dirs): Removed data now available from http://github.com/egonw/bioclipse.data/tree/master
20:01 zarah CIA-52's link is also http://tinyurl.com/n79wq8
20:05 egonw olass: http://github.com/egonw/biocl​ipse.experimental/tree/master
20:05 zarah egonw's link is also http://tinyurl.com/n5a3q6
20:06 CIA-52 bioclipse: egonw * r11699 /bioclipse2/trunk/ (2 files in 2 dirs): Removed data now available from http://github.com/egonw/biocl​ipse.experimental/tree/master
20:06 zarah CIA-52's link is also http://tinyurl.com/n5a3q6
20:07 egonw olass: ping

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