Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-06-15

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All times shown according to UTC.

Time Nick Message
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07:40 egonw jonalv: I have commited the test suite for the bioclipse manager
07:40 egonw there are two tests in it, please add yours
07:40 egonw yahoo!
07:40 egonw @pz 2000
07:40 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=2000
07:41 jonalv egonw++
07:42 egonw pelezilla++
07:44 egonw 2000 bug reports, 1459 fixed.
07:48 egonw Gpox: can you please have a look today at this patch:
07:48 egonw http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1997
07:48 zarah egonw's link is also http://tinyurl.com/2eolbmm
07:48 egonw and possible the related email to the cdk-jchempaint ML
07:50 Gpox I dont's see any path attached
07:50 egonw oh..
07:51 egonw crap..
07:51 Gpox a patch would be ok too
07:51 egonw so, attaching a patch when submitting the bug report is broken
07:51 egonw would also explain why ola's bug report did not have a patch
07:51 egonw damn
07:52 egonw Gpox: try now, please
07:54 egonw Gpox: otherwise... I have been unable so far to find the problem of the initial bonds being too small...
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08:13 jonalv AbstractBioclipsePlatformManagerPluginTest That name must be worthy of some price
08:13 egonw Gpox: doing heavy fixing of ControllerHub.cleanup()
08:13 egonw what a mess it is...
08:13 egonw who wrote that code???
08:14 egonw why is it, that if you want to get somethine done right, you have to do it yourself :(
08:15 jonalv "själv är bäste dräng"
08:19 * egonw is relocating to the BMC
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14:41 jonalv @pz version number
14:41 zarah [1657] running JavaScript from script... http://tinyurl.com/yab7mlc
14:41 zarah [1545] QSAR project xml source does n... http://tinyurl.com/35723s4
14:41 zarah Entire list at http://tinyurl.com/3xnh62y
14:42 jonalv @pz bioclipse.version
14:42 zarah jonalv: I couldn't find anything on 'bioclipse.version' in the database.
14:44 egonw @pz version
14:44 zarah [1934] QSAR-XMPP fails when molecules... http://tinyurl.com/2e68p7a
14:44 zarah [1537] Implement isValidDescriptorDef... http://tinyurl.com/2ufvn9a
14:44 zarah [1827] Old workspaces run from new ve... http://tinyurl.com/ycrf3me
14:44 zarah [1486] -q flag not recognized in some... http://tinyurl.com/359at7l
14:44 zarah [39] ChangeListeners of domainObjects    http://tinyurl.com/8fg5pb
14:44 zarah Entire list (21) at http://tinyurl.com/35gda8t
14:44 egonw @pz version bioclipse
14:44 zarah [1934] QSAR-XMPP fails when molecules... http://tinyurl.com/2e68p7a
14:44 zarah [1537] Implement isValidDescriptorDef... http://tinyurl.com/2ufvn9a
14:44 zarah [1827] Old workspaces run from new ve... http://tinyurl.com/ycrf3me
14:44 zarah [1486] -q flag not recognized in some... http://tinyurl.com/359at7l
14:44 zarah [39] ChangeListeners of domainObjects    http://tinyurl.com/8fg5pb
14:45 zarah Entire list (21) at http://tinyurl.com/35obu65
14:45 egonw @pz version egon
14:45 zarah [1537] Implement isValidDescriptorDef... http://tinyurl.com/2ufvn9a
14:45 zarah [1486] -q flag not recognized in some... http://tinyurl.com/359at7l
14:45 zarah [1657] running JavaScript from script... http://tinyurl.com/yab7mlc
14:45 zarah [1873] Preference for showing choose ... http://tinyurl.com/2uj45ae
14:45 zarah [1945] Which version to upload to Lab... http://tinyurl.com/3ysjm29
14:45 zarah Entire list at http://tinyurl.com/38gss7q
14:45 egonw @pz require
14:45 zarah [1942] new target platform does not s... http://tinyurl.com/35u3zts
14:45 zarah [1995] Metaprint2d fails on molecules... http://tinyurl.com/3y6g72h
14:45 zarah [2000] Bundle-RequiredExecutionEnviro... http://tinyurl.com/38u4he8
14:45 zarah [1537] Implement isValidDescriptorDef... http://tinyurl.com/2ufvn9a
14:45 zarah [836] Generate3D on ATP.mol in sample... http://tinyurl.com/32qhtsb
14:45 zarah Entire list (40) at http://tinyurl.com/36xl9dw
14:45 egonw @pz "bioclipse manager"
14:45 zarah [1658] Exceptions related to Virtual ... http://tinyurl.com/ygn8a73
14:45 zarah [1985] inchi fails on my mac             http://tinyurl.com/37yxp4c
14:45 zarah Entire list at http://tinyurl.com/2uw5hq4
14:46 masak @pz "chunky bacon"
14:46 zarah masak: I couldn't find anything on '"chunky bacon"' in the database.
14:46 egonw jonalv: I'm starting to wonder, if that bioclipse.version() feature request was ever filed :)
14:46 jonalv egonw: I found a bug report with a slighly different probl;em definition
14:46 jonalv egonw: I will close that one when I am done
14:47 egonw pz number?
14:47 jonalv @pz 1941
14:47 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1941
14:48 jonalv egonw: do you want me to add it to 2.4 btw?
14:48 egonw jonalv: yes please
14:48 egonw btw, yes, that seems the right report
14:49 jonalv I jsut have rewrite everything since I realised we want exceptions and not booleans
14:50 egonw which would stop the script running?
14:50 egonw make sense, I guess
14:51 jonalv yea
15:13 egonw masak: Linus: "See? All the rules really are pretty simple." :)
15:13 masak yup.
15:18 CIA-69 bioclipse.core: jonalv 2.4.x * r251832b / (3 files in 2 dirs):
15:18 CIA-69 bioclipse.core: implemented bioclipse.requireVersion method
15:18 CIA-69 bioclipse.core: fixes bug: 1941# - http://bit.ly/9ifKW8
15:18 zarah bug #1941 | http://tinyurl.com/39vlkbl
15:18 egonw jonalv++ (many thanx!)
15:22 egonw jonalv: can I ask you to please split up those unit tests?
15:22 jonalv egonw: uhm do I have to?
15:23 egonw jonalv: and use the JUnit annotation @Test(expected=Exception) and drop the try/catch wrapping?
15:23 egonw no, I can do it too...
15:23 jonalv egonw: it's sort of a pain to create so many test methods isn't it?
15:24 jonalv egonw: is that how you think it should be written?
15:24 egonw yes, a unit test is supposed to be the smallest test you can do
15:24 egonw and there are many small tests you can do
15:24 egonw e.g. test that requireVersion("998,999", "999.999") fails for 2.2.0.testRunning
15:25 jonalv hm I am afraid I have been damaged by some other testing framework
15:25 egonw it is testing som corner case
15:25 egonw the nice thing is, you can then even give the test() method a nice name like:
15:25 egonw testOutOfRangeVersions()
15:25 egonw and make the core more self-descriptive
15:25 jonalv yea but as it is not there is one test method for each method
15:25 egonw helps me now, and yourself in the future
15:26 egonw where is that suggested?
15:26 egonw try {
15:26 egonw 167
15:26 egonw +            bioclipse.requireVersion( "a.b.c", "c.d.e" );
15:26 egonw -> public void testFailOnNonNumericalInput() {
15:27 jonalv egonw: are you already rewriting my test code?
15:27 egonw btw, cool use of System.setProperty() :)
15:27 egonw no
15:29 jonalv okey
15:29 * jonalv might be guilty of caring more about the 'actual code' than the test code
15:30 * egonw seems to remember jonalv complaining about people not testing their code?? :)
15:30 jonalv but I did test, right?
15:39 egonw should I only care about testing what I did?
15:42 jonalv egonw: no, you mean that you have tested my code and found it lacking?
15:42 jonalv egonw: if so could you please file me a bug report?
15:50 jonalv egonw: quick question
15:51 jonalv egonw: are we running org.openscience.cdk in Bioclipse?
15:51 jonalv I mean that spefick bundle
15:51 jonalv |specific
15:51 egonw no
15:51 egonw and
15:51 egonw no
15:51 jonalv egonw: is there a reason not to?
15:51 egonw no: I have only reviewed your code, not run it yet
15:51 egonw no: we are not using org.openscience.cdk itself
15:52 egonw which is a plugin with all of the CDK
15:52 egonw instead, we cherrypick CDK modules
15:52 jonalv oh
15:52 jonalv I am trying to add a dep to smarts matching stuff and I seem to fail to understand how cdk works... :(
15:59 egonw jonalv:
15:59 egonw @pz 2001
15:59 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=2001
16:20 CIA-69 bioclipse.cheminformatics: Egon Willighagen 2.4.x * rd98b748 / plugins/net.bioclipse.cdk.jchempaint.view/src/ne​t/bioclipse/cdk/jchempaint/view/SWTRenderer.java : Implement visit(TextGroupElement) to draw with a solid background - http://bit.ly/c0WTOh
16:20 CIA-69 bioclipse.cheminformatics: jonalv 2.4.x * rde960fe / (2 files in 2 dirs):
16:20 CIA-69 bioclipse.cheminformatics: Added CDKException message text in SMARTS dialog
16:20 CIA-69 bioclipse.cheminformatics: Fixes bug: 1197 - http://bit.ly/az3NVg
16:20 zarah bug #1197 | http://tinyurl.com/39qs837
16:21 jonalv \o/
16:21 jonalv :)
16:22 * jonalv gives up for today
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