Camelia, the Perl 6 bug

IRC log for #cdk, 2010-05-22

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All times shown according to UTC.

Time Nick Message
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14:59 CIA-47 cdk: Egon Willighagen master * r50b9e74 / (2 files):
14:59 CIA-47 cdk: Use interfaces instead of implementation
14:59 CIA-47 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/cmKgSq
14:59 CIA-47 cdk: Egon Willighagen master * rb82a2f6 / (2 files in 2 dirs):
14:59 CIA-47 cdk: Use an interface instead of an implementation as type
14:59 CIA-47 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/aegQKn
14:59 CIA-47 cdk: Egon Willighagen master * r6317be2 / src/main/org/openscience/cdk/​validate/BasicValidator.java :
14:59 CIA-47 cdk: Replaced use of implementations by interfaces
14:59 CIA-47 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/cZnlst
15:21 CIA-47 cdk: Egon Willighagen master * r648a2f4 / (4 files in 4 dirs):
15:21 CIA-47 cdk: A few more interfaces instead of implementations
15:21 CIA-47 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/cFeE7q
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16:00 slyrus egonw_: is http://github.com/egonw/cdk.git the best place to get cdk sources these days?
16:00 zarah slyrus's link is also http://tinyurl.com/37e7zym
16:14 egonw_ slyrus: yes, but
16:14 egonw_ while not official yet, I think we'll move to:
16:14 egonw_ http://github.com/cdk/cdk.git
16:14 slyrus ah, that would be a nice, logical place :)
16:14 egonw_ that one is in sync, and already used by the two commiters
16:14 slyrus and how about jchempaint?
16:14 egonw_ so, best yo just use that one
16:15 egonw_ to
16:15 slyrus great
16:15 egonw_ slyrus: depends on which JChemPaint you want to use
16:15 slyrus oops.. page doesn't exist
16:15 slyrus how many are there?
16:15 egonw_ http://github.com/cdk/cdk
16:15 egonw_ two
16:15 slyrus ah, right, thanks!
16:15 slyrus which one do I want to use?
16:16 egonw_ depends on the situation
16:16 egonw_ what would you like to do?
16:17 slyrus ah, you know, play around with it. draw some molecules. git (whoops, i mean get, i keep doing that...) familiar with how one builds cdk apps
16:17 slyrus my ulterior motive is that, kind of like the very nice R/CDK stuff, I really want to use cdk from some clojure code I'm putting together.
16:18 slyrus trying to write my own cdk-like library in common lisp proved to be just too much work
16:18 slyrus (but kinda fun though)
16:18 egonw_ then use the CDK-JChemPaint patch
16:18 slyrus is that on github?
16:19 egonw_ http://pele.farmbio.uu.se/cgi-bin/gitw​eb.cgi?p=cdk-jchempaint.git;a=summary
16:19 zarah egonw_'s link is also http://tinyurl.com/y9hfxqd
16:20 egonw_ clone URL: http://pele.farmbio.uu.se/git/cdk-jchempaint.git/
16:20 zarah egonw_'s link is also http://tinyurl.com/ydn95m8
16:20 slyrus excellent
16:20 egonw_ mind you...
16:20 egonw_ I have not had time recently to rebase on master...
16:20 egonw_ so, it's using a somewhat older CDK master version
16:21 slyrus oh...
16:21 egonw_ in particular CDK 1.3.4
16:21 egonw_ of 7 weeks ago
16:21 slyrus jcp comes with its own cdk? hmm... ok.
16:21 egonw_ so, not horribly old :)
16:21 egonw_ no, it's the main CDK master
16:21 egonw_ but not yet with the patches of the past 7 weeks
16:22 slyrus yes, but cloning the above jcp repo will give me another copy of (a slightly older) CDK master, right?
16:23 egonw_ yes, but an exact copy
16:23 slyrus well, that's a step in the right direction, at least!
16:23 egonw_ yes, one I worked hard for :)
16:24 egonw_ and I'm happy to hear you share the view of that being important :)
16:25 slyrus in my idealized, fantasy, drive-by coding world, one would do: git clone <cdk>; git clone <jcp>; cd cdk ; ant ; cd ../<jcp> ; ant -Dsomemagicflagtotelljcpwheretofindcdk ; and have a current, workingish, cdk and jcp :)
16:25 slyrus but it sounds like things have gotten much closer to this then the were 9 months ago
16:25 egonw mind you, cdk-jchempaint is the underlying JChemPaint technology
16:25 egonw not the JChemPaint applet, nor Swing app
16:26 slyrus which lives in cdk itself?
16:26 slyrus (the cdk-jchempaint bit, that is)
16:27 CIA-2 cdk: Egon Willighagen master * rad2bd3e / src/main/org/openscience/cdk/qsar/descrip​tors/molecular/RuleOfFiveDescriptor.java :
16:27 CIA-2 cdk: Replaced outdated URL with entry in WikiPedia (fixes #3002741)
16:27 CIA-2 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/czspVB
16:27 CIA-2 cdk: Egon Willighagen master * r2f56fd6 / src/main/org/openscience/cdk/qsar/descrip​tors/molecular/RuleOfFiveDescriptor.java : Merge branch 'cdk-1.2.x' - http://bit.ly/b93fRS
16:28 egonw the JCP architecture lives in the CDK library indeed
16:28 egonw it's the org.openscience.cdk.control
16:28 egonw and the org.openscience.cdk.render packages
16:28 slyrus great
16:30 s9asad joined #cdk
16:30 slyrus so now that I have that cdk-jchempaint, where do I find the swing app and the applet?
16:30 egonw ah, that's another story...
16:31 egonw those are based on a different branch, one I do not know the details of...
16:31 slyrus oh... so you mean instead of cloning that other repo I could have just done git checkout c4b4c482fa8f7c31597c93d34e4388c437e6b8ea in the other repo and gotten the same thing?
16:32 slyrus ah. do I take it you don't actually use the swing app?
16:32 egonw http://pele.farmbio.uu.se/cgi-bin/gitwe​b.cgi?p=cdk-jchempaint.git;a=commit;h=8​eb5771caba6185151fc06404ddee6a35f838206
16:32 zarah egonw's link is also http://tinyurl.com/2cm5r22
16:32 egonw that patch actually...
16:32 egonw that's what defines CDK-JChemPaint 9
16:33 egonw slyrus: the EBI team responsibility for that...
16:33 egonw Uppsala focuses on the SWT version
16:33 egonw which we use in Bioclipse
16:34 slyrus oh, ok. sounds like i should figure out how to get bioclipse working then.d
16:35 egonw clojure in Eclipse would be nice
16:35 egonw if clojure has a JSR 2xx impl... for scripting...
16:37 egonw there is: http://github.com/pmf/clojure-jsr223
16:37 zarah egonw's link is also http://tinyurl.com/2eccxyv
16:37 egonw but
16:37 egonw there is Scheme
16:38 egonw which is a Lisp dialect
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16:38 egonw and JSR 223 based... should not be too difficult to add support to Bioclipse, if I understood correctly
16:38 egonw hi s9asad
16:38 s9asad Hi Egon
16:40 slyrus egonw: for some reason the tags after cdk-jchempaint-5 don't show up when I pull from http://pele.farmbio.uu.se/git/cdk-jchempaint.git/
16:40 zarah slyrus's link is also http://tinyurl.com/ydn95m8
16:41 slyrus do I need to apply a patch?
16:41 egonw oh bugger...
16:41 egonw mom
16:43 egonw mmmm
16:44 egonw ok, for now, please use the hash:
16:44 egonw 8eb5771caba6185151fc06404ddee6a35f838206
16:44 egonw cannot see anything wrong... :(
16:46 slyrus fatal: reference is not a tree: 8eb5771caba6185151fc06404ddee6a35f838206
16:48 egonw weird
16:49 egonw ok, try this...
16:49 egonw take the cdk-1.3.4 patch from github.com/cdk/cdk
16:49 egonw and download the patches from sf.net/projects/cdk
16:52 slyrus perhaps i should just try to get bioclipse working instead
16:54 egonw yeah, most welcome!
17:03 s9asad HI Egon could you please try to commit this patch https://sourceforge.net/tracker/ind​ex.php?func=detail&amp;aid=3005633&​amp;group_id=20024&amp;atid=320024
17:09 CIA-2 cdk: Egon Willighagen master * r5193626 / (2 files in 2 dirs): Emergency fix: IAminoAcid instead of AminoAcid - http://bit.ly/9wyzxe
17:11 egonw s9asad: it applies
17:11 s9asad thanks
17:13 egonw but I do not have time right now to review it
17:13 egonw a quick observation is that I do not see unit tests for the two new public methods
17:13 egonw and:
17:13 egonw +     * @see Added by Asad since CDK one doesn't pick up the correct changes
17:14 egonw the @see is for pointing to a class or method
17:14 egonw not for comments
17:14 egonw +                int IndexI = source.getAtomNumber(sourceAtom);
17:14 egonw +                int IndexJ = target.getAtomNumber(targetAtom);
17:15 egonw variables should start with a lower case
17:15 egonw -    @Test
17:15 egonw +    public void testQueryAtomCount() throws CDKException {
17:15 egonw method does not seem to have @Test annotation...
17:15 egonw actually, the next does not seem so either:
17:15 egonw +    }
17:15 egonw +
17:15 egonw public void testMatchCount() throws CDKException {
17:16 s9asad thanks I will resubmit the patch once I have fixed them
17:16 egonw or as add on patch
17:18 slyrus hmm... it looks like the trees for http://pele.farmbio.uu.se/git/cdk-jchempaint.git/ and http://pele.farmbio.uu.se/cgi-bin/gitw​eb.cgi?p=cdk-jchempaint.git;a=summary are a bit different. the heads on the gitweb page don't match the branches
17:18 zarah slyrus's link is also http://tinyurl.com/ydn95m8
17:18 s9asad okay I will submit an addon path
17:19 s9asad so will you push this and then follow with add on or I should submit then together ?
17:20 egonw add the extra patch to the patch tracker
17:20 egonw I'm leaving for dinner soon
17:21 slyrus egonw: thanks for your help!
17:21 egonw slyrus: for bioclipse questions, please join #bioclipse
17:21 slyrus ok. I'll probably play around with the core cdk stuff for a while first though.
17:21 egonw ok
17:21 egonw you know where to find me
17:22 egonw and feel most free to blog your findings and ideas
17:22 slyrus thanks! it's been too long since i've had time for hacking and blogging!
17:22 egonw :)
17:25 s9asad sumitted the addons
17:26 s9asad submitted the add on patches on the tracker
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20:38 CIA-2 cdk: Syed Asad Rahman master * r5bd8d64 / (2 files in 2 dirs):
20:38 CIA-2 cdk: fixed makeAtomsMapOfBondsMap with test
20:38 CIA-2 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/d81I4r
20:38 CIA-2 cdk: Syed Asad Rahman master * r4bdce61 / (2 files in 2 dirs):
20:38 CIA-2 cdk: add on patches
20:38 CIA-2 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/crmkqs
20:38 CIA-2 cdk: Syed Asad Rahman master * r32cb936 / src/test/org/openscience/cdk/smsd/al​gorithm/cdk/CDKRMapHandlerTest.java :
20:38 CIA-2 cdk: updated test cases Signed-off-by: Syed Asad Rahman <s9asad@gmail.com>
20:38 CIA-2 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/bO3Yd6
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