Camelia, the Perl 6 bug

IRC log for #bioclipse, 2012-03-26

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
04:48 egonw joined #bioclipse
05:31 sneumann joined #bioclipse
06:28 konditorn joined #bioclipse
07:09 Gpox joined #bioclipse
07:29 egonw joined #bioclipse
07:30 egonw joined #bioclipse
07:52 egonw Gpox: one more hour, and I will submit renderextra as patch to cdk-1.4.x
07:52 egonw got anything to add?
08:08 amarillion joined #bioclipse
08:17 Gpox egonw: yes I do
08:35 zaetnick joined #bioclipse
10:42 egonw Gpox: good... here's is what I have right now: (a few patches pending)
10:42 egonw https://github.com/egonw/cdk​/commits/100-14x-renderextra
10:45 egonw Gpox: there are a few failing unit tests...
10:45 egonw but before I fix those, I like to see your patches
10:45 egonw are those online?
10:45 egonw so that I can pull them in?
10:56 Gpox http://pele.farmbio.uu.se/gitweb/?p=biocli​pse-cdk.git;a=shortlog;h=refs/heads/patch
10:56 zarah Gpox's link is also http://tinyurl.com/6uvmtb9
10:57 Gpox that is what I have right now. Been trying to clean it up and separate it
11:02 egonw thanx!
11:02 egonw Gpox: quick question... can you update the first two to have a commit message?
11:02 egonw http://pele.farmbio.uu.se/gitweb/?p​=bioclipse-cdk.git;a=commit;h=6b5c9​b199eb8835a889838d5c609fc631f4278b1
11:02 zarah egonw's link is also http://tinyurl.com/7ds96sf
11:03 egonw and
11:03 egonw http://pele.farmbio.uu.se/gitweb/?p​=bioclipse-cdk.git;a=commit;h=f0da1​d1aa35c5101b14415042644b48186195db3
11:03 zarah egonw's link is also http://tinyurl.com/79huh7j
11:03 egonw the first I can review for cdk-1.4.x now
11:03 egonw I will do the same with the others that are for renderbasic
11:11 Gpox egonw: http://pele.farmbio.uu.se/gitweb/?p=biocli​pse-cdk.git;a=shortlog;h=refs/heads/patch2
11:11 zarah Gpox's link is also http://tinyurl.com/82trfyo
13:26 egonw Gpox: two renderbasic patches reviewed...
13:26 egonw I'm now looking at the last one...
13:27 egonw can that not be fixed too by changing line 60 and assign a new Rectangle2D.Double()
13:27 egonw and union with the rectangle for the moleculeSet at line 62?
13:30 Gpox yeah , non need for the union at line 62
13:48 egonw if we do, we can remove one if statement from the next block
13:51 zaetnick egonw: ping
14:03 egonw pong
14:11 zaetnick egonw: I'm trying to help Apilak
14:11 egonw thanx, appreciated
14:11 zaetnick egonw: but this groovy snippet does't work
14:12 zaetnick how should I get the smiles variable
14:12 egonw the reason for a move to groovy is only that I have no idea how to read line by line of the .smi file in JavaScript
14:12 zaetnick I see
14:12 egonw right, that I did not implement...
14:12 egonw Java regex will work
14:13 zaetnick why do we take only smiles and name columns
14:13 zaetnick to make it faster?
14:15 egonw we need to see which SMILES strings cause trouble (read: cannot be read in Bioclipse)
14:15 egonw the other info is not important for that
14:15 zaetnick ok
14:15 egonw String.split() ?
14:15 egonw that should work too
14:16 zaetnick file = new File("/apilak/test.smi")
14:16 zaetnick file.eachLine { line ->
14:16 zaetnick js.say(line)
14:16 zaetnick }
14:16 zaetnick shouldn't this just print the lines one by one
14:16 egonw yes
14:16 zaetnick javax.script.ScriptException: javax.script.ScriptException: java.io.FileNotFoundException: /apilak/test.smi (No such file or directory)
14:16 egonw (assuming the path is correct)
14:16 egonw ah... there you have it :)
14:17 egonw /home/apilak/test.smi ?
14:17 zaetnick I need the absolute path?
14:19 zaetnick ok, so far so good
14:21 zaetnick ok egonw, thanks for now, I hope that's enough
14:21 zaetnick egonw++
14:31 egonw Gpox: ping? what shall we do with that last patch then?
14:32 Gpox the important thing is not to return null
14:33 egonw shall I send you a counter patch then?
14:37 egonw Gpox: https://github.com/egonw/cdk/commit/d9​07d018424d1265ee758171b49a45a2056a5cd8
14:37 egonw do you like that patch? if so, please sign it off
14:45 Gpox egonw: yes it is good. What do I do with it after sign off?
14:46 egonw email it to me, or whatever you find easiest :)
14:46 egonw I'll pull that patch, and push it to cdk-1.4.x
14:48 Apilak joined #bioclipse
14:48 egonw hi Apilak!
14:48 Apilak hi
14:48 egonw welcome!
14:48 zarah oh hai Apilak
14:49 Apilak Thank you
14:49 egonw Apilak: zarah is a IRC bot...
14:49 egonw zaetnick is valentin
14:49 Apilak OK
14:49 egonw stain_: ping
14:49 egonw stain_: got me some PDF perhaps on OAM, which AO is merging with?
14:50 egonw something I can read on the train?
14:50 egonw Gpox: thanx
14:55 egonw Gpox: commited all three renderbasic patches
14:55 egonw I will apply the others by you to that 100-14x-... branch
14:55 egonw on the way home
15:03 Apilak joined #bioclipse
15:16 egonw Gpox: I will ignore this patch: http://pele.farmbio.uu.se/gitweb/?p​=bioclipse-cdk.git;a=patch;h=d1c5bd​609ea1be1e35ea2985872b2c7d9c75c2d1
15:16 zarah egonw's link is also http://tinyurl.com/czcg6y9
15:16 egonw :)
15:17 egonw Gpox: do you want me to rewrite that one into something that does compile?
15:17 Gpox yes pleas :)
15:21 egonw OK
15:22 egonw I download those from the patch2 branch, and I will look at those on the train home
15:22 egonw and then submit the renderextra patch for review
15:22 egonw hooray!
15:22 egonw Gpox++ (thanx for the great work!)
15:30 konditorn left #bioclipse
16:52 sneumann joined #bioclipse
17:05 zaetnick joined #bioclipse
17:22 egonw joined #bioclipse

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary