Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-07-15

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All times shown according to UTC.

Time Nick Message
00:32 CIA-52 joined #bioclipse
04:25 egonw_ joined #bioclipse
04:41 egonw_ moin
04:41 zarah hello egonw_, you fantastic person you
05:21 egonw joined #bioclipse
06:45 olass joined #bioclipse
06:45 olass hi egonw
06:45 egonw ha olass
06:45 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
06:45 egonw @msg
06:45 zarah egonw: 20 h 50 m 29 s ago, jonalv said regarding "Making your own feature Git repository" I could be wrong but I think that if I first do 'git repack -ad' and the do 'git prune' then 'git prune' will never do anything.
06:45 zarah egonw: 16 h 40 m 44 s ago, jonalv said Why are org.openscience.cdk.annotation and org.openscience.cdk.ioformats in core instead of in cheminformatics?
06:45 zarah egonw: 16 h 36 m 11 s ago, jonalv said net.bioclipse.xom and probaly a few more are both in core and in cheminformatics for the moment. They need to be only at one place...
06:45 zarah egonw: 16 h 34 m 9 s ago, olass said net.bc.xom should only be in bioclipse.core repo
06:45 zarah egonw: 16 h 33 m 6 s ago, olass said don't forget you promised to fix the qsar repo
06:46 egonw @tell olass I did not forget about the qsar repo, and about to upload the fixes
06:46 zarah Consider it noted.
06:46 olass egonw: I'm here
06:46 zarah olass: You have new messages. Write '/msg zarah @messages' to read them.
06:46 egonw @tell olass I just sent an email a few minutes ago explaining what went wrong
06:46 zarah Consider it noted.
06:46 olass @clear
06:46 zarah olass: Messages cleared.
06:46 egonw olass: yeah, I know...
06:47 egonw you started it
06:47 egonw :)
06:47 olass did I?
06:47 olass yes, 16h ago
06:47 egonw indeed :)
06:47 olass sorry, after a @tell I can't remove it from zarah
06:47 * egonw just made another two Jmol releases
06:48 olass egonw: would a commit hook be possible for github > irc ?
06:48 olass I miss that feature...
06:49 olass now you have to guess when people have done something
06:49 olass yes, an email hook too would be desirable
06:49 egonw yes
06:50 egonw rednael is for that
06:50 egonw but has some bugs
06:50 egonw in the sense, that it stops working after a while...
06:50 olass yes, there is an RSS feed from github activity
06:50 egonw right
06:53 olass egonw: you, masak, and jonalv are now lieutenants on bioclipse.core in case you have not noticed that
06:53 egonw aya, captain!
06:53 egonw ummm
06:54 egonw aya, dictator!
06:55 * olass has always been jealous of dictators, swimming in money
06:57 egonw OK, let's try something...
06:57 egonw olass: in for a rollarcoaster ride?
06:57 olass woops
06:57 egonw please go to the github.com website
06:57 olass let's go!
06:57 egonw bioclipse.qsar repository
06:58 olass in my repo?
06:58 olass yes
06:58 olass done
06:58 olass we tried pulling in from Fork que yesterday, works nicely
06:59 egonw ok, excellent!
06:59 egonw please do the same from my bioclipse.qsar fork
06:59 olass hmm, I see red..
06:59 olass what does that mean?
06:59 olass needs a mege?
06:59 egonw dunno
07:00 egonw unfortunately, I cannot see what you see...
07:00 olass will try
07:00 egonw it normally does sort of a test run...
07:00 egonw but not sure how well it does that...
07:00 olass firt worked, the rest fails
07:01 olass failed
07:01 egonw :(
07:01 egonw ok, then you'll have to delete your old one, and fork from that again...
07:02 egonw but please wait until I verified no other plugin has 99+ commits
07:02 olass ok
07:02 olass let me know
07:02 * olass needs coffee to wake up
07:03 olass slept very badly tonight
07:03 olass it's so damn hot again here in SWE
07:03 olass how is NL?
07:03 egonw good
07:03 egonw moist :)
07:03 egonw we'll have 25 today
07:03 egonw likely 2-3 degrees warmer here in Eindhoven
07:10 egonw olass: qsar.ui was affected too...
07:10 egonw updated github...
07:10 egonw please make a fresh fork
07:28 olass ok
07:28 olass will I have to delete my old bioclipse.qsar first?
07:29 olass egonw?
07:29 egonw yes
07:29 olass ok
07:31 olass ok, forked
07:31 edrin joined #bioclipse
07:31 olass should I delete my local repo and clone a new?
07:32 egonw no, that should not be necessay
07:32 egonw just try a 'git pull'
07:32 olass ok
07:32 egonw since I started from the same git repos your old local clone was made from
07:32 egonw the hashes should be compatible
07:32 edrin hi
07:32 zarah hello edrin, you fantastic person you
07:32 edrin http://xkcd.com/610/
07:32 egonw olass: and that sentence should now actually make sense to you :)
07:33 olass egonw: do I need to cd bioclipse.qsar before 'git pull' ?
07:33 egonw yes
07:33 olass error: Entry 'plugins/net.bioclipse.qsar/src/net/bio​clipse/qsar/business/IQsarManager.java' not uptodate. Cannot merge.
07:34 olass can I force in some way?
07:34 olass or override?
07:34 olass I have local changes that I want to override
07:34 egonw you can 'stash' your local changes
07:34 egonw git stash
07:34 egonw then try git pull again
07:34 olass nah, want to remove them
07:35 egonw git checkout .
07:35 egonw (assuming you do not have anything staged yet)
07:35 olass yes
07:35 olass what is the dot?
07:35 egonw 'current folder'
07:36 olass did not work
07:36 olass # Your branch is behind 'origin/master' by 50 commits, and can be fast-forwarded.
07:36 egonw that sounds good
07:36 egonw try git pull again
07:36 olass hmm, seems git checkout . worked
07:37 olass nice
07:37 olass hmm, I got untracked bin dirs
07:37 olass how do I get rid of them?
07:37 olass some git ignore list?
07:37 olass how?
07:38 egonw .gitignore
07:38 egonw it is a text file
07:38 egonw just list the folder you want to ignore
07:40 olass I want to list all .bin
07:40 olass I want to list all bin dirs
07:41 olass I see ok
07:43 olass ah
07:44 * olass added, staged, committed, and pushed gitignore successfully
07:44 * olass is learning git, but it will take a while to master
07:47 sneumann joined #bioclipse
07:50 egonw olass++
07:50 olass :)
07:53 sneumann Hi, congrats to the BC2 release !
08:01 olass sneumann: thanks
08:01 olass now it's only bug fixing ;)
08:10 shk3 joined #bioclipse
08:20 egonw does someone know how to get Mylyn settings from one workspace to another?
08:25 egonw olass: spam on blogspot for the 2.0 release post
08:25 egonw reported by jpansanel
08:25 egonw on #cdk
08:26 olass damn
08:26 olass how resolve?
08:26 egonw log in, go to blog post page
08:26 olass deleted comment
08:27 egonw ah, good
08:27 olass is that all we can do?
08:27 olass guess so...
08:29 egonw I'll have a look
08:31 jonalv joined #bioclipse
08:34 jonalv oh hai
08:34 zarah saluton jonalv
08:36 jonalv olass: around?
08:37 olass yes
08:37 olass egonw: We have a bag with hair-stuff here that you forgot on the island
08:37 olass I'll bring it to BMC
08:37 egonw ah, excellent
08:37 olass along with your t-shirt
08:37 egonw :)
08:37 egonw tack
08:37 * egonw is preparing for tea with cake
08:38 jonalv olass: we need to figure out a shared way of deliviring Birt to Brunn and ds..
08:39 olass indeed
08:39 olass how about thinking tomorrow at bmc?
08:39 egonw olass: I really would like you to resolve the issue around the missing 2.0.x branch
08:39 olass egonw: what!?
08:39 egonw where to commit bug fixes for 2.0.0 ?
08:39 olass git?
08:39 egonw yeah, fine
08:39 egonw but what branch
08:39 jonalv uhm 2.0?
08:40 olass please explain what you mean
08:40 egonw or do you plan to make 2.0.x from master ?
08:40 olass can we have branches in github?
08:40 egonw which would be disruptive...
08:40 olass egonw: I am new to github, don't forget
08:40 olass please advice
08:40 jonalv I think we should have a 2.0 branch for bug fixes and when we ah ve a couple we call tht 2.0.1 and move on...
08:40 egonw because there are API clean up planned to 2.1
08:40 egonw yes, github can do branches
08:40 olass egonw: indeed
08:41 olass so what do you suggest?
08:41 shk3 jonalv: you have a few minutes?
08:42 jonalv shk3: sure
08:42 egonw I have no particular preference for either SVN or Git branch
08:42 egonw but since we moved to GitHub, I think a git branch would be more logical
08:42 egonw more consistent
08:42 shk3 there seems to be no IPartialReturner interface
08:43 jonalv (egonw: You don't prefer a git branch before an svn branch? Who are you and what have you done to egonw?)
08:43 jonalv shk3: intresting, so what is there? :)
08:44 shk3 nothing similar
08:44 jonalv shk3: ah no the name is just Returner these days. Someone made change that name. I forgot
08:44 shk3 I thought the implementation has to look like this:
08:44 shk3 public void executeJob(SenecaJobSpecification jobSpec, IPartialReturner returner, IProgressMonitor monitor){
08:44 olass egonw: should I do a git branch of bioclipse.core in github and call it 2.0.x ?
08:45 shk3 ok
08:45 egonw yes, sounds good
08:45 olass ok
08:45 olass egonw: how do I do a branch?
08:45 shk3 jonalv: but IReturner is what I use for the method returning a complete result.
08:46 shk3 is this the same?
08:46 olass is a fork the same?
08:46 jonalv shk3: it has both a method partial return and a method complete return
08:46 egonw yes and no
08:46 egonw a fork is a branch under a new account
08:46 jonalv if you start doing partial returns you are not allowed to do complete return and vice versa
08:46 egonw but technically the same as a branch
08:46 egonw olass: not sure how to create a branch using the github website
08:47 egonw from the command line...
08:47 olass oh, there are service hooks :)
08:47 egonw (oh, that is new!)
08:47 olass CIA
08:47 olass irc
08:47 jonalv egonw: uhm I thought I could fork a complete repo with a zillion branches in them...
08:47 olass email
08:47 egonw olass: remember 1-fixFoo
08:47 olass nice!
08:47 olass ?
08:47 egonw upload a branch with
08:47 egonw git push 1-fixFoo
08:47 egonw and remove it with
08:47 egonw git push :1-fixFoo
08:47 egonw note the ':' in there...
08:47 egonw short for delete
08:47 olass oh, so I can create branches locally and push to github?
08:47 egonw yes
08:48 olass exciting
08:48 olass egonw: just to repeat, how do I create a branch?
08:48 olass git checkout -b "weee"
08:48 egonw yes
08:48 egonw that will create a branch from the current branch
08:48 egonw use instead:
08:49 egonw git checkout -b "weee" "branchToBranchFrom"
08:49 egonw to branch of branchToBranchFrom
08:49 olass well, I only have master
08:49 egonw ah, no :)
08:49 olass no?
08:49 egonw remember: git branch -r
08:49 egonw you can do:
08:49 olass ?
08:49 egonw git checkout -b "weee" origin/master
08:50 olass why?
08:50 olass is git pull not enough?
08:50 shk3 jonalv: IReturner has partialReturn and completeReturn
08:50 jonalv shk3: yup
08:51 shk3 so it seems to be the same
08:51 shk3 so how do I use these?
08:51 shk3 do I do partial returns and complete returns?
08:52 shk3 do I still need an interface method with an updatehook and returning bioclipsejob?
08:52 jonalv shk3: if you want to return all at once use complete return at the end of your method. If you wan to return partial returns while running yourr method use partial return whenever you ahve a result. For example i na loop
08:52 shk3 sorry, I am confused
08:52 shk3 ok
08:52 egonw olass: yes, it is...
08:53 shk3 this means i can just add this to my existing method?
08:53 shk3 no need for
08:53 jonalv shk3: hm I cam confused too. How do you signal that that was the last return? :)
08:53 shk3 There is also a pattern where the interface method takes a BioclipseJobUpdateHook and returns a BioclipseJob.
08:53 egonw olass: it's just that there is a bit more detail to 'there is only master' :)
08:53 jonalv shk3: you know there is no implemetned example of this...
08:53 shk3 jonalv: I don't know
08:53 shk3 you should ;-)
08:53 jonalv shk3: have a look at Testmanager.getBioObjects
08:53 jonalv it does returner.partialReturn a couple od times
08:55 shk3 which plugin is that in?
08:56 jonalv net.bioclipse.core.tests
08:58 shk3 ok
08:58 shk3 i have a look
08:59 shk3 it calls done();
09:00 jonalv shk3: that's a test related thing
09:00 jonalv shk3: ignore that :)
09:00 shk3 but this isn't for telling the last return, is it?
09:00 shk3 so i was right
09:00 jonalv shk3: nope
09:00 shk3 looks like no signalling is needed
09:01 shk3 just call partialReturn as often as needed
09:01 shk3 I will try
09:02 shk3 it looks like there are two interface methods:
09:02 shk3 public void getBioObjects( IFile file,
09:02 shk3 BioclipseUIJob<List<IBioObject>> uiJob );
09:02 shk3 and
09:02 shk3 public void getBioObject( IFile file,
09:02 shk3 BioclipseJobUpdateHook h  );
09:03 shk3 which both end up in the same method of the implementation:
09:03 jonalv shk3: yes they are used internally
09:03 shk3 public void getBioObjects( IFile file,
09:03 shk3 IReturner returner,
09:03 shk3 IProgressMonitor monitor ) {
09:03 masak joined #bioclipse
09:03 jonalv masak: hi
09:03 shk3 ok, so I add a new interface method for the partial return and change my old implementation to use partialReturn
09:04 shk3 instead of completeReturn.
09:04 masak jonalv: oh hai
09:04 shk3 Is that reasonable?
09:04 jonalv shk3: I think I should try to work out a real example of how to use this. I just ahve not gotten a round tuit yet
09:05 shk3 that's what I try
09:05 shk3 but I need some idea what to do to do a real example
09:05 jonalv http://tinyurl.com/roundtuit
09:05 shk3 but I think I've got that now
09:07 jonalv shk3: sounds good
09:08 jonalv shk3: the idea is that you reimplement the partialReturn method in your own Returner when you call the manager method from the ui code...
09:10 shk3 my own returner?
09:10 shk3 Oh dear
09:10 jonalv shk3: :)
09:11 shk3 but don't I call the inferface method having a BioclipseJobUpdateHook
09:11 shk3 don't I need to implement that?
09:13 jonalv shk3: hm, yes and BioclipseJobUpdateHook implements IReturner
09:13 shk3 ah ok
09:13 olass egonw: how do I push my branch to github? I did not understand the 1- and : above
09:17 shk3 jonalv: ok, I can write code which compiles - let's see if it also works.
09:17 shk3 something I don't understand is this:
09:17 jonalv olass: 1- was part of the branch name
09:17 shk3 the two methods in the interface either returning complete result
09:17 shk3 or partial results
09:17 shk3 are implemented by the same method, right?
09:18 egonw olass: git push <branchToPush>
09:18 jonalv shk3: uhm namely which one?
09:18 olass ok, if I have a branch named 2.0.x, do I just do git push then?
09:18 olass ok
09:19 shk3 jonalv: in case of your TestManager it's
09:19 shk3 public void getBioObjects( IFile file,
09:19 shk3 IReturner returner,
09:19 shk3 IProgressMonitor monitor ) {
09:19 shk3 I think?
09:19 jonalv shk3: I don't understand what you mean
09:20 shk3 sorry
09:20 shk3 let's look at the ITestManager interface
09:20 jonalv shk3: yes
09:20 jonalv hi bioclipse-core
09:20 shk3 it has:
09:20 shk3 public void getBioObjects( IFile file,
09:20 shk3 BioclipseUIJob<List<IBioObject>> uiJob );
09:20 shk3
09:20 shk3 public void getBioObject( IFile file,
09:20 shk3 BioclipseJobUpdateHook h  );
09:20 shk3 right?
09:21 jonalv shk3: yes I am looking at hat now
09:21 shk3 btw, why is update hook not parametrized?
09:21 shk3 anyway
09:21 shk3 it seems they are both implemented by the
09:21 shk3 public void getBioObjects( IFile file,
09:21 shk3 IReturner returner,
09:21 shk3 IProgressMonitor monitor ) {
09:21 shk3 method in TestManager
09:22 jonalv shk3: in the manager?
09:22 jonalv shk3: yes
09:22 jonalv shk3: there is always only one method in the manager. That's at least what I am striving for. No code duplication...
09:22 olass hi
09:22 zarah privet olass
09:22 shk3 fint, but this method uses the partialstuff only
09:22 bioclipse-core joined #bioclipse
09:22 bioclipse-core bioclipse.core: 3jonalv master0 SHA1-997e06a
09:22 bioclipse-core Changed copyright year
09:22 bioclipse-core http://bit.ly/13h9z7
09:22 bioclipse-core bioclipse.core: 3Carl Masak master0 SHA1-79ed028
09:22 bioclipse-core [keep-clean.pl] removed fossil code
09:22 bioclipse-core http://bit.ly/PrwLE
09:22 bioclipse-core left #bioclipse
09:22 jonalv shk3: actually that is the main reason for all the mess. I really don't want code duplication...
09:22 shk3 so how is the one without the updatehook supposed to work?
09:23 shk3 I undestand this
09:23 shk3 the concept is great, I think
09:23 shk3 we just need to get it working in practice now ;-)
09:23 shk3 but I will try using the partialreturn in seneca for now
09:24 shk3 do you understand what it is I don't understand?
09:24 olass egonw, jonalv: help
09:24 olass mbpro:bioclipse.core ola$ git push 2.0.x
09:24 olass fatal: '2.0.x': unable to chdir or not a git archive
09:24 olass fatal: The remote end hung up unexpectedly
09:24 egonw ok, try it with adding the full remote URL
09:24 olass do I need to commit a branch?
09:24 masak olass: 'git push origin 2.0.x' ?
09:24 olass remote url?
09:25 egonw masak: yes, like that
09:25 masak just a guess.
09:25 egonw origin being an alias defined in .git/config
09:25 bioclipse-core joined #bioclipse
09:25 bioclipse-core left #bioclipse
09:25 olass yes
09:25 olass worked
09:25 jonalv shk3: maybe, it has been some time since I wrote this code and I have not used personally so I am not 100% sure about it... :)
09:25 olass but the irc hook does not seem to work that nicely
09:27 shk3 jonalv: Ok, I try running my stuff and will come back to you
09:27 jonalv egonw: have you fixed the plugin that where duplicated between core and cheminformatics?
09:27 jonalv shk3: good luck
09:27 egonw jonalv: no
09:27 egonw jonalv: did you file a bug report?
09:27 egonw I am updating my bug list
09:28 jonalv egonw: I used zarahs tell functionality to alert you to the problem...
09:28 jonalv :)
09:28 egonw yes, i noticed that
09:28 egonw but that gets lost in time
09:29 jonalv egonw: sry I have been away too long. It seems I ahve stopeed filing bug repports...
09:31 egonw olass: why not use CIA instead?
09:31 egonw http://cia.vc/stats/project​/bioclipse.cheminformatics
09:31 zarah egonw's link is also http://tinyurl.com/llpqby
09:31 olass how is that done?
09:31 egonw http://cia.vc/stats/project/bioclipse.core
09:31 zarah egonw's link is also http://tinyurl.com/mg6ajw
09:31 olass yes, will try that
09:31 egonw just enable the service on GitHub
09:32 olass ok
09:32 olass do I need a CIA account?
09:34 egonw I have one
09:34 olass ok, will register
09:38 stain is anyone of you in the US..?
09:38 stain I guess not
09:38 olass nope
09:38 olass not me
09:39 CIA-52 bioclipse.cheminformatics: Egon Willighagen master * rbaa743e / (13 files in 6 dirs): Removed plugin already available from the bioclipse.core dependency - http://bit.ly/nLaUw
09:39 stain I put our Taverna downloads on Google Code, but when trying to download them again I get about 10 kB/s.. not very usable :)
09:39 egonw olass: the GitHub-CIA bridge works lovely :)
09:39 olass I tried to register one for core, but it says you claimed it already
09:40 egonw ah, try again...
09:40 egonw I gave up ownership
09:40 jonalv hm I sort of liked the one where the bot was named after the repo... :)
09:40 olass still conflict
09:40 olass The bot you are requesting access to, bioclipse on Freenode, has been claimed exclusively by another user: Egon Willighagen.
09:41 egonw ok, then I will add bioclipse.core to that bot
09:41 olass ok
09:41 egonw done
09:41 egonw this is rather nifty
09:41 egonw github++
09:41 egonw cia++
09:42 olass does email work for you too?
09:42 olass seems to work
09:43 egonw saw your mail
09:43 egonw mine did not arrive because I had the email wrong :)
09:43 shk3 jonalv: looks good
09:44 shk3 it seems to work
09:44 jonalv shk3: it does? sounds cool
09:44 shk3 I only did a sort of test implementation, so I need to do the real stuff
09:44 jonalv \o/
09:44 shk3 but I am optimistic
09:44 shk3 at least I can return something piecewise
09:56 egonw olass: did you make hooks for .statistics and .qsar too?
09:56 olass I can
09:56 olass mom
09:58 CIA-52 bioclipse.rdf: Egon Willighagen master * re97121d / README : Added some dependency info - http://bit.ly/L2Acr
09:58 olass egonw: done for qsar and statistics
09:59 egonw good :)
09:59 olass egonw: should you not fork statistics and qsar from me?
10:00 egonw yes
10:00 egonw I do
10:00 egonw qsar I just updated :)
10:00 egonw stats I need to check
10:00 olass ok
10:41 shk3 hi jonalv
10:49 * jonalv is back
10:49 shk3 looks pretty good
10:49 jonalv shk3: okey
10:49 shk3 i still have problems with this "when are we finished"
10:50 shk3 when I execute the method,
10:50 shk3 I have the BioclipseJobUpdateHook
10:50 shk3 with its partialReturn method
10:50 shk3 I can update the ui in there.
10:50 shk3 fine so far.
10:50 jonalv shk3: yea, should we add some mechanic that says that it is finnished?
10:50 shk3 but I also want to collect stuff
10:51 shk3 and save as sdf
10:51 shk3 I think it would be necessary, yes.
10:51 shk3 because right now, i cannot see where/when I should call the save as sdf
10:51 jonalv shk3: I guess what you really want is writing the sdf file as you get result. |At least in the genreal case we don't want to have everything in memory...
10:52 shk3 had that idea as well
10:52 shk3 could do so
10:52 jonalv shk3: there is no cdk manager method for diong that yet is there?
10:52 shk3 but I also want to open the sd file
10:52 shk3 so when to do that?
10:52 jonalv open it?
10:52 shk3 an addToSdf method or so?
10:53 shk3 don't think so
10:53 shk3 open means
10:53 jonalv shk3: you should probably talk to gpox about this...
10:53 shk3 calling UIManager.open(sdfile)
10:53 jonalv he knows how the sdf editor works
10:53 shk3 ah, you mean the sdf editor should be dynamically updated as well?
10:54 jonalv shk3: that's the idea yea
10:54 shk3 that would be best, because then it would save me the view for display of intermediate stuff
10:54 shk3 ok, where is gpox?
10:54 * shk3 is calling gpox
10:55 shk3 jonalv: i will try to finish this and update the wiki
10:55 jonalv shk3: sounds great
10:55 shk3 the display is not needed for describing the manater mechanism, I think
10:55 jonalv shk3: sry?
10:56 shk3 I don't need to know how to do the sdf to do the wiki, i mean
10:56 jonalv shk3: okey
10:56 shk3 about the returner etc.
10:56 shk3 do you know if gpox will be around?
10:56 shk3 or is he on holiday?
10:56 jonalv shk3: no idea
10:56 jonalv olass: do you know when gpox will be back?
10:58 egonw I think first week of aug
10:59 shk3 jonalv: it might still be good to think about a finish notification
10:59 shk3 in other cases it might be needed
10:59 jonalv shk3: I could probably do that automagicly using aop
10:59 shk3 or usefull at least
10:59 shk3 automagically sounds good
11:00 olass jonalv: Gpox will be back in 2.5 weeks
11:00 jonalv We could add a method allRerturnsDone to the interface and call it after the method has finnisehd
11:00 shk3 olass: thanks
11:00 jonalv shk3: but do you really need it?
11:00 shk3 well, if gpox isn't here to discuss the sdf editor...
11:01 shk3 and I think we should have it
11:01 shk3 anyway
11:01 shk3 people might miss it
11:04 shk3 jonalv: another small problem I found is the following:
11:05 shk3 partialReturn and completeReturn have the same parameter T
11:05 jonalv shk3: yes?
11:05 shk3 in my case, completeReturn takes a List<IMolecule>
11:05 jonalv no
11:05 shk3 whereas partialReturn really only does a single IMolecule
11:05 shk3 I can use a list there
11:05 shk3 with one member
11:06 shk3 so no real problem
11:06 jonalv you don't use completeReturn at all in that case
11:06 jonalv you only use one of them not both
11:06 shk3 yes
11:06 shk3 but
11:06 shk3 there are the two methods in the interface
11:06 shk3 in my case
11:07 shk3 public BioclipseJob<IMolecule> executeJob(SenecaJobSpecification sjs, BioclipseJobUpdateHook<List<IMolecule>> hook);
11:07 shk3 and
11:07 shk3 public void executeJob(SenecaJobSpecification sjs, BioclipseUIJob<List<IMolecule>> uiJob);
11:07 shk3 both end up in the same implementation
11:07 shk3 at least that was my understanding
11:07 masak egonw: re http://wiki.bioclipse.net/index.php?title=G​it_Development#Strip_away_unwanted_plugins -- could you clarify the phrase "This is often an iteration do"?
11:07 zarah masak's link is also http://tinyurl.com/mqpa8m
11:08 shk3 the implementation is
11:08 shk3 public void executeJob( SenecaJobSpecification jobSpec,
11:08 shk3 IReturner<List<IMolecule>> returner,
11:08 shk3 IProgressMonitor monitor)
11:08 shk3 throws BioclipseException{
11:08 egonw hi masak
11:08 masak egonw: oh hai
11:08 shk3 if the interface methods do not both have List<IMolecule>,
11:08 jonalv shk3: I am not sure that returner should work on a list if you want to partial returns
11:08 shk3 they can't use that same implementation, can they?
11:09 egonw masak: for your purpose, I recommend the other option
11:09 masak egonw: understood.
11:09 masak egonw: but I still think the sentence is less than awesome.
11:09 jonalv shk3: they can use the same implementation.
11:09 shk3 but if both interface methods end up in that implementation,
11:09 shk3 the implementation most have the smalles common denominator, so to say
11:09 egonw masak: yes, fixed that
11:09 jonalv shk3: there is code that collects all partial returns in to one big return and return them as a list...
11:10 shk3 ah
11:10 masak egonw: thanks.
11:10 shk3 so the implementation ca be IReturner<IMolecule>
11:10 jonalv shk3: it's a bit messy... :)
11:10 shk3 and will serve both interface methods?
11:10 jonalv shk3: yes that's the idea. (if it hasn't changed)
11:10 masak egonw: 'This is often an iteration'. do you mean to say that one of the below commands is often run several times?
11:10 jonalv shk3: exactly
11:10 shk3 and the interface mehtods have
11:11 egonw masak: yes
11:11 shk3 BioclipseJobUpdateHook<IMolecule>
11:11 shk3 and
11:11 masak which one? the second?
11:11 shk3 BioclipseUIJob<List<IMolecule>>
11:11 shk3 ?
11:11 egonw because the command line becomes very length
11:11 egonw +y
11:11 egonw masak: so you remove plugin set by plugin set
11:12 shk3 ok, will try that later
11:14 jonalv olass, egonw: Is the ds project on github yet?
11:14 olass NO
11:14 olass svn
11:14 olass sorry, didn't mean to shout
11:14 masak :)
11:14 jonalv olass: will it be moved soon?
11:14 olass no idea
11:14 egonw olass: you will maintain that one, right?
11:14 olass yes
11:15 olass but no idea how to move it
11:15 olass besides, rewriting it now
11:15 egonw I do
11:15 olass so move has to wait
11:15 egonw I can do it...
11:15 olass ok, will let you know
11:15 olass when I have committed
11:15 egonw will move things on a rather pragmatic basis
11:15 egonw ack
11:15 olass meaning...?
11:16 egonw jonalv, masak, olass: shall I give a short tutorial how I suggest how you could do it?
11:16 masak sure.
11:16 jonalv egonw: what is "it"?
11:16 olass egonw: summarize on a wiki page please
11:16 egonw move stuff from svn to a git repository
11:16 egonw olass: already there
11:17 masak olass: http://wiki.bioclipse.net/ind​ex.php?title=Git_Development
11:17 zarah masak's link is also http://tinyurl.com/mqpa8m
11:17 jonalv egonw: oh I have sort of done that using your first trick on that wiki page
11:17 egonw but some live session is always more usefull
11:17 egonw oh, wow!
11:17 egonw I know how much work that is :)
11:17 * masak is just about to create a biojava git repo
11:17 egonw the second option is much quicker when you have just a few plugins to port
11:17 jonalv egonw: I have realised that I didn't manage to totally get rid of all extra history though.. :(
11:17 olass I'd rather wait until I have something to move
11:17 olass doing other stuff now
11:18 jonalv egonw: but it will have to be enough...
11:18 edrin masak: what is the status of biojava? is it still actively developed?
11:18 olass edrin: very much so
11:18 masak edrin: it has been low-prio'd for 2.0, but it's the focus of upcoming releases.
11:19 edrin ok
11:19 olass masak: I take it he was asking about the biojava project, not the biojava plugin
11:19 edrin masak: ah, no I meant if the biojava project itself is still active... a few years ago it appeared a little bit "inactive", but most likely i was wrong
11:20 edrin olass: yes
11:20 masak edrin: oh, I think it's still quite active.
11:20 edrin they published in bioinfo last year
11:20 edrin yes
11:20 jonalv olass: didn't you talk about them planning a rewrite called biojava 3?
11:21 olass yes
11:22 olass I am listening in to their mailing list
11:22 edrin olass: why are they planning a rewrite?
11:22 olass why not?
11:23 olass extend functionality, improved interfaces, better API bla bla...
11:23 olass you can ALWAYS rewrite
11:23 masak (doesn't mean you always should)
11:23 olass indeed
11:23 edrin yep
11:23 edrin :)
11:23 masak rewriting is hard.
11:23 egonw jonalv: I do not fully understand your problem with removing history?
11:24 jonalv egonw: I could only remove history for the plugins that were left in the svn repo at the time that I did the convertion. The rest is still in the history for strucutredb...
11:25 egonw that sounds good
11:25 jonalv egonw: there was no way to know what I should purge from history since they were removed in HEAD...
11:25 jonalv egonw: good?
11:25 jonalv egonw: well I guess I managed to make the repo smaller but not as small as it could theoretically be...
11:27 egonw jonalv: then try the other approach
11:27 masak the other approach seems to skirt that problem, yes.
11:28 jonalv egonw: nah I think I can live with this. Maybe nest time...
11:28 egonw ack :)
11:28 jonalv egonw: it's just some extra unnecessairly history... :)
11:29 egonw yes, which can be some few tens of MBs
11:30 egonw ok, gone for lunch now
11:30 * masak just realized that there's no net.bioclipse.bioinformatics feature yet
11:30 masak :)
11:30 masak so, what do we envision would go into such a feature?
11:30 masak biojava...
11:30 masak anything else?
11:34 egonw whole genome browsing
11:35 olass masak: we should have a net.bioclipse.bioinformatics plugin
11:35 olass defining content types menus and categories for bioinformatics
11:35 olass similar to net.bioclipse.cheminformatics plugin
11:35 egonw http://www.broadinstitute.org/annotation/argo/
11:35 zarah egonw's link is also http://tinyurl.com/kpbm2p
11:35 egonw which is lgpl
11:35 jonalv who here knows the jchempaint widget?
11:35 egonw OK, really at lunch now
11:36 jonalv Will a new thread be spawned when I draw a new atom?
11:37 masak olass: aye, I like.
11:38 masak no, my question was more: are there any existing plugins that should be ported to the bioclipse.bioinformatics git repo?
11:39 olass no
11:39 olass biojava
11:39 olass aligner
11:39 olass no more for now I think
11:40 masak aligner sleeps in biojava.ui, methinks.
11:40 * masak checks
11:40 masak aye, it does.
11:42 olass ok
11:44 masak so, biojava, then.
11:44 masak convenient. :)
11:50 masak it's working! \o/
11:50 masak egonw++
12:02 * jonalv is working on getting used with github
12:02 CIA-52 bioclipse.core: Egon Willighagen master * rbc6a4b6 / (13 files in 5 dirs): Added a 'bioclipse' manager to provide some helper methods oriented at users who like more info (addresses #1284) - http://bit.ly/b60Nq
12:02 jonalv hm |used to
12:02 zarah bug #1284 | http://tinyurl.com/n8cmkk
12:03 masak jonalv: tho' "working on getting used" was fun, too. :)
12:03 jonalv masak: bah
12:03 olass jonalv: I have more problems with the dispatcher when invoking methods as jobs from another thread
12:04 olass will show you tomorrow
12:04 jonalv olass: exciting :)
12:04 olass right...
12:05 masak http://github.com/masak/bioclipse.bioinformatics/
12:05 zarah masak's link is also http://tinyurl.com/ll4k7x
12:05 masak \o/
12:05 olass masak++
12:05 * olass is forking
12:05 jonalv olass++
12:05 masak jonalv++
12:05 olass jonalv: for what?
12:05 jonalv masak: what for?
12:06 masak olass: far whot?
12:06 jonalv *lol*
12:06 olass *grmf*
12:06 olass *murmel*
12:06 masak *plmk*
12:10 olass hmm, the javadispatcher is in serious need of some fising...
12:10 jonalv is that fisting?
12:10 olass na
12:10 olass fixing I guess
12:11 jonalv olass: file bugs with instructions for how to reproduce
12:11 olass I have already
12:11 jonalv olass: oh I thought you wanted to beat it :)
12:11 egonw joined #bioclipse
12:11 olass would indeed be nice too
12:11 jonalv olass: you have?
12:11 jonalv olass: uhm what bug ticket would that be? :)
12:11 olass I showed it to you on monday
12:11 olass I even showed how to reproduce
12:11 jonalv @pz 1367
12:11 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1367
12:12 olass there you have it
12:12 jonalv it is blocked by
12:12 jonalv @pz 1417
12:12 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1417
12:12 jonalv :)
12:12 olass no
12:12 olass incorrect
12:12 * jonalv ducks and covers
12:12 jonalv olass: incorrect?
12:12 olass look again
12:12 olass jonalv: please fix the bug
12:13 olass it is critical
12:13 masak <olass> I even showed how to reproduce
12:13 jonalv olass: I can't reproduce it
12:13 masak hehe
12:13 olass jonalv: are you serious?
12:13 jonalv olass: yes, I need ds to reproduce. I don't have ds
12:13 olass CHECK OUT FROM SVN
12:14 jonalv olass: are you saying that I have to combine svn and git now?
12:14 masak http://xkcd.com/583/
12:14 olass YES
12:14 masak jonalv: being a bit difficult, are we? :)
12:14 olass it's egonw's fault, live with it
12:14 masak jonalv: how's that policy of yours going?
12:14 jonalv masak: it's being put to the test as we speak actually
12:14 olass jonalv: I am sitting here waiting for you to fix it and you do nothing??
12:14 masak jonalv: :)
12:14 jonalv masak: it's a bit early to say if it will hold
12:15 olass for 2 days??
12:15 jonalv olass: what two days?
12:15 olass tuesday and wed
12:15 olass are you just watch
12:15 olass ing
12:15 masak well, one and a half in that case.
12:15 olass ok 1.5
12:15 olass seriously
12:15 olass I am blocked by this bug
12:15 jonalv olass: yea that's right I ahve been doing nothing at all since I came back to from vacation. That's right
12:16 olass please PLEASE
12:16 * olass is about to give up
12:16 jonalv olass: nevermind figuring out github, mocing structuredb to github, mocing brunn to github
12:16 jonalv |moving
12:16 jonalv olass: I thought that project were being moved as we are speaking
12:16 jonalv I ahve moved all my projects
12:16 olass no, please backlog
12:16 jonalv olass: I thought the idea was to move now...
12:17 olass no
12:17 olass please backlog
12:17 olass [13:15] < olass> besides, rewriting it now
12:17 olass [13:15] < egonw> I do
12:17 olass [13:15] < olass> so move has to wait
12:17 olass [13:16] < egonw> I can do it...
12:17 olass [13:16] < olass> ok, will let you know
12:17 olass [13:16] < olass> when I have committed
12:17 olass DS will not be moved until it works
12:18 olass and this is pending the dispatcher
12:18 masak deadlock!
12:18 jonalv masak: indeed
12:18 olass how so?
12:18 olass what blocks jonalv from fixing the bug?
12:18 masak olass: A waiting for B waiting for A.
12:18 olass not git
12:18 masak olass: his principles, it seems.
12:18 olass jonalv: I donät have time for this
12:19 masak .oO( donut )
12:19 egonw I'll set up bioclipse.ds for jonalv
12:19 masak egonw++
12:19 jonalv olass: I don't want to spend time running both systems when we are going to move anyway...
12:19 olass egonw: please don't
12:19 egonw and will port olas patches later
12:19 olass egonw: ok
12:19 olass jonalv: eat dirt
12:19 egonw olass: please file me a bug report when those patches are done
12:19 olass egonw: will do
12:19 * jonalv is glad olass is in Stockholm and he in Uppsala :)
12:19 * egonw is (meanwhile) release Jmol 11.8 RC2
12:20 egonw releasING
12:20 olass egonw: you did not respond to my email on qsar
12:20 jonalv masak: to answer your question. Quite well it seems ;)
12:20 * egonw is happy to have a multithreading core
12:20 masak jonalv: :P
12:20 egonw olass: correct...
12:20 olass jonalv: ok, you are making my work so much harder. Happy now?
12:21 masak olass: I'm looking at him. he's happy. :)
12:21 olass thanks
12:21 * olass is not happy
12:21 * masak pats olass
12:21 masak there, there.
12:21 olass @slap jonalv
12:21 * zarah smacks jonalv about with a large trout
12:21 olass @slap jonalv
12:21 * zarah jabs jonalv with a C pointer
12:21 masak *lol*
12:21 jonalv non ot the trout
12:21 olass @slap jonalv
12:21 * zarah loves jonalv, so no slapping
12:21 olass @slap jonalv
12:21 * zarah locks up jonalv in a Monad
12:22 olass @slap jonalv
12:22 zarah @slap jonalv
12:22 * zarah pulls jonalv through the Evil Mangler
12:22 olass that's what I was after
12:22 masak oh no, not the Evil Mangler!
12:22 olass jonalv: let me know when the bug is fixed
12:22 jonalv the evil mangler is just so evil
12:22 * olass will quit his work until then
12:22 olass thanks jonalv
12:42 egonw masak: is jonalv in the same room as you are?
12:43 masak egonw: aye, here in the office.
12:43 egonw can you give him this URL:
12:43 egonw http://github.com/egonw/bioclipse.ds/tree/master
12:43 zarah egonw's link is also http://tinyurl.com/lw39x8
12:44 masak egonw: sent.
12:44 egonw tack
12:45 masak egonw: he tells me to say 'thanks'.
12:46 egonw tell him he's welcome
12:47 CIA-52 bioclipse: ospjuth * r11672 /bioclipse2/trunk/plugins/ (4 files in 4 dirs): Removed deprecated DS plugins.
12:48 CIA-52 bioclipse: ospjuth * r11673 /bioclipse2/trunk/plugins/net.bioclipse.ds.bursi/: Initial import.
12:50 CIA-52 bioclipse: ospjuth * r11674 /bioclipse2/trunk/plugins/net.bioclipse.ds.bursi/ (28 files in 11 dirs): Refactored all bursi tests into one data plugin.
12:52 CIA-52 bioclipse: ospjuth * r11675 /bioclipse2/trunk/plugins/net.bioclipse.ds/ (50 files in 12 dirs): Refactored all base tests (SMARTS, SDFile, pos/neg) to this plugin. Also new improved extension point net.bioclipse.decisionsupport. Sort of a rewrite of all DS test impls to get clean API and improved functionality.
12:52 CIA-52 bioclipse: ospjuth * r11676 /bioclipse2/trunk/plugins/net.bioclipse.d​s.lipinski/src/net/bioclipse/ds/lipinski/ (Activator.java impl/RuleOfFiveTest.java): Updated for new API and EP.
12:53 CIA-52 bioclipse: ospjuth * r11677 /bioclipse2/trunk/plugins/net.bioclipse.ds.birt/ (16 files in 6 dirs): Updated for new API and EP. Also added copyright.
12:55 olass joined #bioclipse
12:55 CIA-52 bioclipse: ospjuth * r11678 /bioclipse2/trunk/features/net.b​ioclipse.ds_feature/feature.xml: Updated feature for new DS plugin structure.
12:56 olass egonw: ok, done committing to DS SVN
12:56 olass egonw: you can now safely move ds to git
12:56 olass egonw++ //thanks for the help
12:59 * olass hopes that this means jonalv can attack the bug
12:59 olass @seen jonalv
12:59 zarah jonalv was last seen 36 m 38 s ago in #bioclipse saying 'the evil mangler is just so evil'
12:59 olass did jonalv get stuck in the mangler?
13:00 olass masak: where is jonalv?
13:00 masak olass: he disappeared, says he's working on your bug.
13:01 olass jonalv++
13:01 * olass has cooled down a bit
13:01 olass egonw: ping
13:01 masak olass: egonw, meanwhile, has ported .ds to github.
13:02 olass egonw: did you get my recent commits there?
13:02 olass up to 11678
13:03 egonw mom, in a conf call
13:03 olass oki
13:21 CIA-52 bioclipse: shk3 * r11679 /bioclipse2/trunk/plugins/net.bioclipse.seneca/ (18 files in 9 dirs): best structure so far is now displayed while running job
13:37 * egonw is porting the recent .ds patches from SVN to Git
13:39 olass egonw: let me know when done so I can fork
13:40 * olass is looking forward to continue working in a git branch
13:44 egonw http://github.com/egonw/bioclipse.ds/tree/master
13:44 zarah egonw's link is also http://tinyurl.com/lw39x8
13:45 egonw please verify your most recent patches are there...
13:45 egonw via http://github.com/egonw/bi​oclipse.ds/commits/master
13:45 zarah egonw's link is also http://tinyurl.com/nzlbjd
13:54 olass looks good
13:54 olass forking
13:54 olass will clone and test to run
13:59 olass egonw: seems to work fine!
13:59 egonw good
13:59 egonw please set up email and cia commit messages
14:00 olass @tell jonalv DS is now moved to git
14:00 zarah Consider it noted.
14:02 olass [16:00] < egonw> please set up email and cia commit messages < done. Please add CIA bot
14:03 egonw done
14:24 CIA-52 bioclipse: egonw * r11680 /bioclipse2/trunk/ (93 files in 24 dirs): Removed plugins and features now available from http://github.com/egonw/bioclipse.rdf/tree/master
14:24 zarah CIA-52's link is also http://tinyurl.com/lo8kq6
15:09 * olass and git are still not friends
15:09 masak olass: it took me a month or so to become comfortable with git.
15:10 * olass will require more help tomorrow
15:10 masak I'll be away tomorrow, but jonalv will help you.
15:10 olass sounds good
15:11 olass wish him luck with that nasty bug he's on to
15:11 * olass will be back later
15:11 olass afk
15:22 egonw I will be afk tomorrow too
15:25 CIA-52 bioclipse: egonw * r11681 /bioclipse2/trunk/ (8 files in 8 dirs): Removed plugins which are available from http://github.com/egonw/bioclipse.rdf/tree/master
15:25 zarah CIA-52's link is also http://tinyurl.com/lo8kq6
15:36 masak http://chem-bla-ics.blogspot.com/2009/07/​bioclipse-moving-to-github-cia-hooks.html # egonw++
15:36 zarah masak's link is also http://tinyurl.com/lrqeju
15:37 masak egonw: you listed bioclipse.cheminformatics twice! :)
15:37 masak I mean, come on. we know you think it's important, but...
15:37 egonw ah, copy/paste error...
15:37 egonw really
15:37 masak :P
15:37 egonw really!
15:37 masak right.
15:37 * masak is making a lot of copy-paste errors right now
15:38 masak creating many similar tests
15:38 masak static typing is saving me all the time.
15:41 egonw wondering what is gonna happen now...
15:43 egonw maybe CIA is slow again...
15:44 masak hm, I can't really see how to convert an RNA sequence to DNA using BioJava...
15:47 CIA-52 bioclipse.rdf: egonw master * rf6087d3 / (3 files):
15:47 CIA-52 bioclipse.rdf: Feature for this RDF-backed version
15:47 CIA-52 bioclipse.rdf: git-svn-id: https://bioclipse.svn.sourceforge.net/s​vnroot/bioclipse/bioclipse2/trunk@10825 fcb5ba71-d80d-0410-8237-ba3920747fcc - http://bit.ly/D9Iku
15:49 CIA-52 bioclipse.rdf: Egon Willighagen master * r5fcca86 / README : Updated info: n.b.structuredb.rdf depends on net.bioclipse.structuredb - http://bit.ly/Azifi
15:50 CIA-52 bioclipse: egonw * r11682 /bioclipse2/trunk/ (6 files in 6 dirs): Removed plugins and features that are now available from http://github.com/egonw/bioclipse.rdf/tree/master
15:50 zarah CIA-52's link is also http://tinyurl.com/lo8kq6
15:51 egonw masak: please remove plugins now available from git from the SVN repos
15:51 egonw @tell jonalv please remove plugins now available from git from the SVN repos
15:51 zarah Consider it noted.
15:51 masak egonw: gotcha.
15:58 jonalv joined #bioclipse
15:58 jonalv olass: oh so you are back?
15:58 zarah jonalv: You have new messages. Write '/msg zarah @messages' to read them.
15:58 jonalv zarah: just tell me...
15:58 zarah jonalv: 1 h 58 m 19 s ago, olass said DS is now moved to git
15:58 zarah jonalv: 6 m 56 s ago, egonw said please remove plugins now available from git from the SVN repos
15:59 jonalv egonw: what particaular plugin are you refering to? I thought I had done that...
15:59 jonalv olass: I have made some progress with that bug. But only some.
16:00 jonalv olass: However it seems to me like you have a memory leak because I can only run about 20 runs of that green play button then Bioclispe becomes _very_ slow
16:04 egonw jonalv: structuredb
16:04 CIA-52 bioclipse: carl_masak * r11683 /bioclipse2/trunk/plugins/ (86 files in 27 dirs): [n.b.biojava*] these plugins have moved to github -- removing
16:05 jonalv egonw: I am quite sure I ahve removed that...
16:05 jonalv egonw: strange...
16:06 egonw masak: mmm... your folders persist
16:06 egonw http://bioclipse.svn.sourceforge.n​et/viewvc/bioclipse/bioclipse2/tru​nk/plugins/net.bioclipse.biojava/
16:06 zarah egonw's link is also http://tinyurl.com/mm8wlx
16:06 egonw jonalv: maybe that is the case for you too?
16:06 egonw http://bioclipse.svn.sourceforge.ne​t/viewvc/bioclipse/bioclipse2/trunk​/plugins/net.bioclipse.structuredb/
16:06 zarah egonw's link is also http://tinyurl.com/lopb9f
16:06 egonw yes, it seems so
16:07 jonalv egonw: sry?
16:07 egonw try the URL
16:07 masak egonw: well, I did remove them.
16:08 masak egonw: is there something else I can do?
16:08 egonw you used git-svn ?
16:08 egonw you can try SVN
16:08 egonw (no shouting intended)
16:08 masak :)
16:08 masak none heard.
16:09 egonw yeah, NL-SE is quite some distance :)
16:09 masak how's vacation, by the way?
16:09 egonw no, no
16:09 egonw no vacation yet
16:09 egonw just working at home
16:09 masak oh.
16:09 egonw it's just that my current home is not the regular enköping kommun :)
16:10 jonalv egonw: so is only the folder left but everything else gone?
16:10 masak "Toto, I don't think we're in Enköping anymore."
16:10 egonw yes, think so
16:10 jonalv egonw: because on my computer the folders are gone...
16:10 egonw git-svn too?
16:10 jonalv egonw: yes what else? :)
16:11 egonw jonalv: use svn
16:11 jonalv egonw: I don't think I know how to do that :)
16:11 masak what's this new SVN craze all of a sudden?
16:12 egonw well, google... pay me off... but please make sure to get rid of those empty folders
16:12 masak egonw: I'm updating the svn wc now, and I see my folders being deleted.
16:13 egonw wc?
16:13 masak working copy.
16:13 * jonalv does 'svn up', guess that will take till tomorrow or so...
16:13 masak it's taking quite some time, yes.
16:13 egonw masak: well, the repository disagrees....
16:13 masak good thing we're not using SVN...
16:14 masak egonw: ok, but if they're really gone from my SVN working copy, I won't be able to remove them...
16:14 egonw yes you will
16:14 egonw try harder
16:14 egonw try this:
16:14 egonw svn remove https://bioclipse.svn.sf.net/....
16:14 egonw that is...
16:14 egonw do the commit directly on the remote repository
16:14 jonalv egonw: wow that looks dangerous
16:14 egonw this does not require a wc
16:15 jonalv "svn: Failed to add file 'trunk/plugins/net.bioclip​se.tests/userManager.dat': object of the same name already exists"
16:15 egonw well spoken by a git addict
16:15 jonalv I am not doing this all over
16:15 masak egonw: trying again.
16:15 jonalv can someone that has a working svn-- do it for me please?
16:15 CIA-52 bioclipse: carl_masak * r11684 /bioclipse2/trunk/plugins/ (5 files in 5 dirs): [n.b.biojava*] really removed plugins
16:15 egonw jonalv: please catch up with IRC...
16:15 egonw you do not need a wc
16:15 jonalv egonw: I don't?
16:16 egonw nope
16:16 masak ah, so all the files were gone, but empty directories remained?
16:16 jonalv egonw: then how do I see what I am doing?
16:16 egonw masak: correct
16:16 masak I did not realize that.
16:16 masak it all makes sense now.
16:16 egonw jonalv: you watch IRC and stop when people start shouting ?
16:16 masak git-svn does not delete directories.
16:16 egonw masak: right :)
16:16 jonalv git-svn--
16:16 * egonw has to go for dinner now
16:16 jonalv (git-svn)--
16:17 egonw bbl
16:24 CIA-52 bioclipse: jonalv * r11685 /bioclipse2/trunk/plugins/n​et.bioclipse.structuredb/: Really removinG Structuredb
16:32 CIA-52 bioclipse: jonalv * r11686 /bioclipse2/trunk/plugins/net.​bioclipse.structuredb.tests/: Really removed structuredb
16:34 CIA-52 bioclipse: jonalv * r11687 /bioclipse2/trunk/plugins/net.bioclipse.hsqldb/: Really removed strucutredb
16:35 CIA-52 bioclipse: jonalv * r11688 /bioclipse2/trunk/plugins/n​et.bioclipse.hsqldb.tests/: REally removed structuredb
16:36 CIA-52 bioclipse: jonalv * r11689 /bioclipse2/trunk/features/net.​bioclipse.structuredb_feature/: Really removed structuredb
16:37 * jonalv quit
17:19 edrin left #bioclipse
18:07 egonw joined #bioclipse
18:28 CIA-52 bioclipse: shk3 * r11690 /bioclipse2/trunk/plugins/net.biocli​pse.seneca/src/net/bioclipse/seneca/ (10 files in 4 dirs): A temp/score graph is now displayed
18:54 masak left #bioclipse
20:11 sneumann joined #bioclipse
20:14 olass egonw: awake?

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