Camelia, the Perl 6 bug

IRC log for #cdk, 2008-01-29

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All times shown according to UTC.

Time Nick Message
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08:48 CIA-18 bioclipse: j_viklund * r4826 /trunk/playground/plugins/net.bioclipse.paml/ (44 files in 20 dirs): Added plugin net.bioclipse.paml
09:06 CIA-18 bioclipse: jonalv * r4827 /branches/bioclipse2/ (8 files in 6 dirs): renamed net.bioclipse.core.buisness-​>net.bioclipse.core.business
09:24 egonw rojasm: let me know when you're around...
09:26 rojasm hi egonw
09:26 egonw hi rojasm
09:26 egonw you got my email?
09:26 rojasm I am reading now
09:27 rojasm For me is ok about the merge the reaction and the mf
09:28 egonw ack
09:29 rojasm I work now with that today. To finish the reaction tests
09:29 egonw OK, will make sure the mf/ branch works with trunk/ and run tests in both trunk/ and mf/
09:29 egonw to make sure no regressions are occuring
09:30 egonw I noticed that the [s+] atom type I added yesterday causes some 7-8 mercaptam unit tests to fail...
09:30 egonw charges...
09:30 egonw likely resonance structures now getting messed up...
09:31 rojasm ok! I will take account
09:33 CIA-18 cdk: miguelrojasch * r9959 /branches/miguelrojasch/mf/src/org/openscience/cd​k/test/formula/IsotopePatternGeneratorTest.java: replacing the form getting properties from getProperties().get() to getProperty()
09:34 steinbeck joined #cdk
09:34 egonw hi steinbeck
09:35 steinbeck Hi egonw
09:36 CIA-18 cdk: miguelrojasch * r9960 /branches/miguelrojasch/reaction/sr​c/org/openscience/cdk/test/tools/St​ructureResonanceGeneratorTest.java: added new tests to improve the generator.
09:48 egonw bbl
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09:52 thomas_ku moin
09:59 steinbeck moin thomas_ku
10:00 thomas_ku hi steinbeck
10:17 CIA-18 cdk: miguelrojasch * r9961 /branches/miguelrojasch/reaction/src/o​rg/openscience/cdk/test/reaction/type/ (24 files): added tests to recognize if the reactant molecule matches correctly into the CDKAtomTypes description.
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11:33 CIA-18 cdk: miguelrojasch * r9962 /branches/miguelrojasch/reaction/src/​org/openscience/cdk/test/reaction/typ​e/CleavageBondMultiReactionTest.java: removed smilesParser to create the IMolecule
11:41 CIA-18 bioclipse: ospjuth * r4828 /branches/bioclipse2/core/plu​gins/net.bioclipse.scripting/ (3 files in 3 dirs): Removed namespace EP.
11:42 CIA-18 bioclipse: ospjuth * r4829 /branches/bioclipse2/core/​plugins/net.bioclipse.ui/ (bioclipse.product plugin.xml): Update product and removed namespace extension.
12:07 rojasm joined #cdk
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12:35 egonw brilliant /. poll this week :)
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13:30 CIA-18 cdk: miguelrojasch * r9963 /branches/miguelrojasch/reaction/src/o​rg/openscience/cdk/test/reaction/type/ (15 files): removed using smilesparser to create IMolecule
13:49 CIA-18 cdk: egonw * r9964 /branches/miguelrojasch/mf/ (15 files in 10 dirs): Fixed dependencies
13:49 egonw steinbeck: did you notice how close we are to the 10k-th commit ?
13:49 egonw matter of days now
13:50 steinbeck no, did not realize that :-)
13:50 steinbeck I'm sure you are going to make it :-)
13:51 egonw I hope not
13:51 steinbeck don't you think it is an honor?
13:51 egonw oh sure
13:51 egonw leading the OHLOH stats is honor enough :)
13:51 steinbeck but you would wish it to be sign that others also contribute
13:51 steinbeck right
13:52 egonw well... leading implies some competition, so might not really be the right word :)
13:52 egonw quite so
13:54 egonw steinbeck: this has been a burning question here...
13:55 egonw is your group involved in BioMart development?
13:55 egonw and, what is your group already doing wrt metabolomics?
13:56 steinbeck We are going to develop the system that put all other groups out of business
13:56 steinbeck ...
13:56 steinbeck but seriously ...
13:57 steinbeck my teams and the group will be involved in a number of larger consortia that tackle metabolomis databases
13:57 steinbeck AFK
13:57 egonw I've shown you metware.sf.net ?
14:13 CIA-18 cdk: egonw * r9965 /branches/miguelrojasch/mf/ (89 files in 33 dirs): Synchronized with trunk 9869:9964
14:13 rojasm perfekt. Thanks egonw
14:13 rojasm k=>c
14:15 egonw going to a meeting
14:15 egonw will be back later
14:16 egonw rojasm: will compare unit tests results later tonight, and if OK, I'll merge mf with trunk
14:16 egonw cu later
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15:33 CIA-18 bioclipse: ospjuth * r4830 /branches/bioclipse2/core/p​lugins/net.bioclipse.core/ (3 files in 3 dirs): Removed logging from core. Use net.bioclipse.logging instead.
15:34 CIA-18 bioclipse: ospjuth * r4831 /branches/bioclipse2/core/plugins/ne​t.bioclipse.ui/META-INF/MANIFEST.MF: Import net.bioclipse.logging.
15:35 CIA-18 cdk: miguelrojasch * r9966 /branches/miguelrojasch/react​ion/src/org/openscience/cdk/ (2 files in 2 dirs): corrected the reaction which failed
16:19 rojasm left #cdk
17:28 CIA-18 jmol: nicove * r8938 /trunk/Jmol-FAH/projects/ (p2586.xyz.gz p4122.xyz.gz): Folding@Home
17:30 Annzi left #cdk
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17:43 egonw here goes
17:43 egonw the big mf/ patch
17:45 CIA-18 cdk: egonw * r9967 /trunk/cdk/ (112 files in 21 dirs): Applied the mf/ branch to trunk/
17:49 CIA-18 cdk: egonw * r9968 /branches/miguelrojasch/mf/: Removed branch, now that it is applied to trunk/
17:54 CIA-18 bioclipse: Annzi * r4832 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.moss/ (5 files in 2 dirs): Sample wizards has been created are not functional at the moment
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18:06 CIA-18 cdk: egonw * r9969 /trunk/cdk/src/org/openscience/cdk/t​est/tools/CDKHydrogenAdderTest.java: Added test for mercaptan
18:08 carsten egonw: moin
18:08 carsten already tried KDE4?
18:08 egonw hi carsten
18:08 egonw yeah, sure
18:08 egonw did not read my blog?
18:08 egonw kemistrydesktop
18:09 carsten oops, seems i missed it
18:09 egonw http://kemistry-desktop.blogspot.com/200​8/01/kde-400-no-yukuake-for-kubuntu.html
18:09 carsten 4.0.1 is beeing tagged tomorrow
18:09 egonw many bug fixes?
18:09 egonw did those plasma task features make a backport?
18:09 egonw e.g. that multiline thingy
18:11 carsten http://www.kde.org/announcements/c​hangelogs/changelog4_0to4_0_1.php
18:12 carsten egonw: but the changelog is work in progress
18:12 egonw quite a few indeed
18:12 egonw in so short time :)
18:13 * carsten hopes Nokia, pardon, TT, will shop Qt 4.4beta1 soon
18:13 egonw :)
18:14 egonw btw, why?
18:14 egonw will that make KDE 4.0 even shinier?
18:15 carsten no, but 4.1
18:15 egonw how so?
18:15 carsten as soon as b1 is out we will depend on it
18:15 egonw what does it add?
18:16 carsten 4.4 adds a lot of thing, the most im portant is this "widget on a QGraphicsView" thing Plasma and KOffice rely on
18:16 carsten that will allow several 1000 LOC to be removed from plasma
18:16 carsten also, it adds WebKit!
18:16 egonw ah...
18:16 egonw that's interesting...
18:21 carsten In Feb 2008 there will be the next KDEPIM-Metting (Osnabrück again). I hope they will accomplish certain things :-)
18:21 carsten Like: Making KMail work
18:23 egonw :)
18:23 egonw yes, that would be great
18:23 egonw I like KDE4 quite a lot
18:24 egonw actually... running it as my main desktop
18:24 egonw except for my laptop
18:24 egonw it seems not to recover well from a suspend
18:24 egonw but don't use that on my desktop :)
18:24 egonw the 3D effects are brilliant
18:24 egonw more useful than compiz
18:24 egonw and simple/basic
18:25 carsten indeed. Will, I want to wait for 4.1 until moving to kde4
18:25 CIA-18 cdk: egonw * r9970 /trunk/cdk/src/org/openscience/cdk/test/ (2 files in 2 dirs): Added unit tests for S atom matching problem introduced in commit 9958
18:25 carsten but 401 seems to be important as well, the changelog is just a tip of the iceberg
18:25 carsten alone in kdeedu are ~50 or something fixes
18:25 egonw :)
18:25 carsten I bet 100+ in libs and the same for base
18:26 egonw yeah
18:27 CIA-18 cdk: egonw * r9971 /trunk/cdk/src/org/openscience/cdk​/atomtype/CDKAtomTypeMatcher.java: Fixed the perception of S.3 when hybridization was set, closes the bug introduced in commit 9958
18:27 egonw OK, got to leave
18:27 egonw bye
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