| Time |
S |
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/bioclipse/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/bi[…]e.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/inde[…]_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/inde[…]e=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-[…]w_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-[…]w_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.ds.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.bioclipse.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/biocli[…]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.c[…]ub-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.sourcefo[…]ipse2/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.sourcefor[…]ioclipse.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.sourcefor[…]ipse.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.bioclipse.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/net.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/net.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 |
|
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edrin left #bioclipse |
| 18:07 |
|
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egonw joined #bioclipse |
| 18:28 |
|
CIA-52 |
bioclipse: shk3 * r11690 /bioclipse2/trunk/plugins/net.bioclipse.seneca/src/net/bioclipse/seneca/ (10 files in 4 dirs): A temp/score graph is now displayed |
| 18:54 |
|
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masak left #bioclipse |
| 20:11 |
|
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sneumann joined #bioclipse |
| 20:14 |
|
olass |
egonw: awake? |
