Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-07-18

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All times shown according to UTC.

Time Nick Message
07:54 egonw joined #bioclipse
09:03 egonw_ joined #bioclipse
10:58 egonw joined #bioclipse
11:29 egonw hi rojasm
11:30 rojasm hi egonw
11:30 rojasm I received you email
11:31 rojasm I have some lunch and I come later
11:31 egonw ack
14:30 rojasm joined #bioclipse
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15:31 olass joined #bioclipse
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17:03 egonw joined #bioclipse
17:16 olass hi egonw
17:18 olass egonw: I need help with git
17:19 olass how can I, from my forked bioclipse.cheminformatics, commit to your bioclipse.cheminformatics?
17:19 olass or should I do a pull request?
17:22 CIA-52 bioclipse.ds: Ola Spjuth master * r92458c7 / plugins/net.bioclipse.ds/src/net/​bioclipse/ds/ui/views/DSView.java : Check MolTable with now public method instead of JCPContext. - http://bit.ly/qnhJL
17:24 olass egonw: ping
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18:19 egonw joined #bioclipse
19:00 olass egonw: ping
19:13 miguelrojasch hi I download the new bioclipse2 from github. And I have some errors in the biojava plugin
19:13 miguelrojasch is it updated?
19:21 miguelrojasch is in github the specmol and spectrum plugin available?
19:26 egonw olass: pong
19:27 olass hi
19:27 zarah hi olass
19:27 egonw miguelrojasch: no, specmol and speclipse, etc are still in SVN
19:27 miguelrojasch oo
19:27 miguelrojasch ok
19:27 olass [19:20] < olass> how can I, from my forked bioclipse.cheminformatics, commit to your bioclipse.cheminformatics?
19:27 olass [19:20] < olass> or should I do a pull request?
19:28 egonw pull request
19:28 olass would be good if I could learn how to commit there too...
19:28 olass ok, will do pull request
19:29 olass egonw: pull request sent
19:31 egonw olass: I think you should have write access access...
19:32 olass so, how do I commit there then?
19:32 egonw change the orig URL in .git/config
19:32 egonw with a plain-text editor
19:33 egonw it should also be possible with 'git remote' I guess...
19:33 egonw but not sure about that syntax
19:33 olass ok, will ask jonalv then (he did it last week)
19:33 olass in the meantime, please tend to my pull request :)
19:34 egonw did you see my pull request for bioclipse.qsar?
19:34 olass no
19:35 olass I would like to get emails for pull requests
19:35 egonw yeah, same here
19:35 egonw that is probably configurable
19:36 egonw olass: which repos?
19:36 egonw ah, found it
19:36 egonw my 'inbox'
19:38 olass how do I pull your qsar stuff?
19:38 egonw good point
19:38 egonw no ide
19:38 egonw a
19:39 olass hmm
19:39 olass then I guess I can't pull
19:39 egonw trying to find the docs about it
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19:47 egonw olass: http://github.com/guides/pull-requests
19:47 zarah egonw's link is also http://tinyurl.com/3rold8
19:48 egonw ok... it seems that performing the merge after a pull is not possible via the website...
19:48 egonw olass: that above link has the commands...
19:50 * egonw now received an message from GitHub from olas :)
19:50 olass by email?
19:50 egonw yes
19:50 olass how did you set that up?
19:50 egonw I changed nothing
19:51 olass oh
19:51 olass it probaly goes to my gmail, which I don't check
19:51 olass right
19:51 egonw hahahaha
19:51 egonw ok
19:51 egonw olass: can you make sense from those lines in the guide ?
19:52 egonw on how you can reply to a pull request?
19:52 olass yes, think so
19:52 egonw with git remote add -f egonw git://github.com/egonw/bioclipse.qsar.git
19:52 egonw git checkout -b egonw/master
19:52 egonw git pull egonw master
19:53 egonw those things after the semi colon would likely be the latest hash...
19:53 egonw but just leaving it out, as I just did, would likely give you HEAD
19:53 egonw the next black section is about the merging into *your* master branch
19:53 egonw meanwhile, you can signof the patches
19:54 egonw to indicate you checked them
19:54 egonw (optional)
19:54 egonw with
19:54 egonw git commit --amend --signoff
19:54 egonw which you can probably also do with gitx
19:54 olass how do I review the patches? gitx?
19:54 egonw yes
19:54 egonw or from the command line
19:54 egonw with git log
19:55 egonw or: git diff master..otherBranch
19:55 olass how do I use gitx for this?
19:55 egonw click a 'commit' hash
19:55 egonw I guess...
19:55 egonw not sure...
19:55 egonw never used gitx
19:56 olass I want a nic eGUI for seeing changes
19:56 egonw gitk does that on my machine
19:56 egonw but the k is for KDE I think
19:56 olass right
19:56 egonw http://gitx.frim.nl/user_manual.html
19:56 zarah egonw's link is also http://tinyurl.com/mf5skv
19:56 egonw that's a user mamnual for gitx
19:57 egonw I think the 'The commit list' is the second you want to read now
19:57 egonw interesting user manual
19:58 olass gitx does this
19:58 egonw also lots of pointers to have gitx focus on differences between branches
20:00 egonw ok, gotta help my father-in-law with his new laptop...
20:00 egonw olass: btw, working on the descriptor ontology...
20:00 olass great!
20:00 egonw I seem to have lost a set of fixes...
20:00 egonw so, redoing those now
20:00 egonw no idea where those went :(
20:00 egonw anyway...
20:00 egonw more on that asap
20:00 olass egonw: will you be online tomorrow?
20:01 egonw yeah, likely part of the day
20:01 olass I really need those SPARQL queries
20:01 egonw but also going to see Harry Potter
20:01 olass to get me further
20:01 olass :)
20:01 egonw that Gist I gave you is working for me
20:01 olass yes
20:01 egonw the SPARQL is fine
20:01 olass but I filed a new bug
20:01 egonw ah, ok
20:01 olass for more extensive queries
20:01 egonw ok, good
20:02 egonw will reply after I fix up the current OWL again
20:02 egonw with the new classes...
20:02 olass oki
20:02 egonw will email asap
20:02 egonw at least the content is synchronized now
20:02 olass oh, I commented in bug 1107
20:02 egonw with some JOELib descriptors that were not in the CDK, nor in the BC version
20:02 egonw ack
20:02 olass for what I need
20:02 olass The gist was ncie to start with, I'd liek to request that, for each descriptor found, to get the name and id (instead of only the id).
20:02 olass Also, how do I get the name for a descriptor class (atomic/bond/molecular)?
20:03 egonw ack
20:03 olass oki
20:03 olass see you tomorrow
20:03 egonw bye for now
20:03 olass bye
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21:16 egonw joined #bioclipse
21:17 egonw olass: ping

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