Camelia, the Perl 6 bug

IRC log for #cdk, 2007-11-23

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All times shown according to UTC.

Time Nick Message
05:34 masak joined #cdk
06:18 jbrefort joined #cdk
06:20 egonw_ joined #cdk
06:20 egonw_ moin
06:20 egonw_ busy this time of the morning
06:21 masak :)
07:33 miguelrojasc1 moin
07:40 egonw_ hi miguelrojasc1
08:19 egonw_ he, is there no one who want to help port some of the wiki pages??
08:45 miguelrojasc1 egonw_ do you mean with wiki pages?
08:45 miguelrojasc1 what do ..
08:46 egonw_ go to cdk.wiki.sf.net
08:46 egonw_ and open another tab for cdk.sf.net/wiki
08:46 egonw_ pick a missing missing on cdk.wiki.sf.net
08:46 egonw_ look that one up on cdk.sf.net/wiki
08:47 egonw_ pick := follow a broken link
08:47 egonw_ eg http://cdk.wiki.sourceforge.net/CDKInstallation
08:47 egonw_ then click 'Edit This Page'
08:48 egonw_ make sure to edit as text only
08:48 miguelrojasc1 wenn I put cdk.wiki.sf.net I relinked to http://sourceforge.net/
08:48 egonw_ oh...
08:48 egonw_ make that then:
08:48 egonw_ cdk.wiki.sourceforge.net?
08:48 egonw_ eg http://cdk.wiki.sourceforge.net/CDKInstallation
08:49 miguelrojasc1 ok
08:50 egonw_ miguelrojasc1: you need to make two minor tweaks to the code
08:51 egonw_ 1. reverse the ===='s   ... the old wiki the ====== should now be =, while ===== is now ==, etc
08:51 egonw_ h1 was ======, is now =
08:51 egonw_ <h2> was ===== is now ==
08:51 egonw_ 2. and... the spaces between '*' for list item need to be removed
08:52 egonw_ 2b. and second indent, for second level list items is now not extra whitespace, but ** etc
08:56 masak at least some of those things could be converted automatically with a few lines of perl
08:56 masak ...but you probably know that
08:56 masak is it a lot of text?
08:56 egonw_ yeah, but getting the source out and in is the time consuming part
08:56 egonw_ no, not a lot...
08:57 egonw_ just many pages
08:57 masak true
08:57 masak there's no export function or something?
08:57 masak a way to dump everything from the db?
08:57 egonw_ no idea
08:57 egonw_ and have not seen any way to import it into the new wiki db
09:01 CIA-16 joined #cdk
09:10 miguelrojasc1 egonw_ if remove the space between '*' it doesn't work fine but yes with spaces
09:11 egonw_ no, not between... before
09:12 egonw_ the '*' should be the first char of the line
09:12 miguelrojasc1 ack
09:13 masak joined #cdk
09:18 jonalv joined #cdk
09:28 miguelrojasc1 egonw: I am so slow. If I understood good You want to update the new wiki.cdk (http://cdk.wiki.sourceforge.net/) from the old (http://cdk.sourceforge.net/wiki/)
09:29 egonw_ not update...
09:29 egonw_ just copy the pages
09:29 egonw_ already copied many of them
09:29 egonw_ but some have not been transfered yet
09:29 egonw_ the pages that are already on cdk.wiki.sourceforge.net are OK
09:30 miguelrojasc1 ok, because I was checking some of them
09:30 egonw_ and do not have to be updated :)
09:30 miguelrojasc1 it was already copied
09:30 egonw_ sorry... should have been more clear...
09:30 miguelrojasc1 ok I look what not are
09:30 egonw_ yes... see the recent changes
09:30 miguelrojasc1 ok, I think now I understand :)
09:30 egonw_ that install page for which I gave the URL is one missing
09:31 egonw_ and http://cdk.wiki.sourceforge.net/RefactoringtheCDK
09:38 CIA-16 cdk: egonw * r9476 /branches/egonw/remove-non-cdkatomtype-code/src/ (8 files in 7 dirs): Synched with trunk up to 9475
09:40 egonw_ masak: cheers
09:40 egonw_ masak: that outcome sounds perfect
09:44 egonw_ miguelrojasc1: when you got a sec...
09:44 egonw_ about your branch...
09:45 miguelrojasc1 yes I finish some copy-paste I we can discass it
09:46 egonw_ ack
09:46 CIA-16 cdk: egonw * r9477 /branches/egonw/remove-non-cdkatomtype-code.patch: Updated patch: zero regressions now, and because I did not receive any comments I will apply it to trunk now...
09:46 miguelrojasc1 the table are changing as well between the new and old version.
09:47 egonw_ indeed... sorry, forgot about that...
09:47 egonw_ | becomes ||
09:47 egonw_ something like that...
09:51 masak egonw_: mediawiki syntax? yes, it's | at the start of a line and || further in
09:52 masak ...so the syntax for new cells is really \n| or ||
09:56 egonw_ masak: wikispaces == mediawiki?
09:57 masak no idea
09:57 masak but maybe that part of table syntax is the same? if not, ignore my comment :)
09:59 miguelrojasc1 one remarak each new ** the word size will be small. Is there not a way to say the word size should remain the same size
10:00 egonw_ no, that's a downside indeed...
10:00 egonw_ noted that too
10:04 CIA-16 cdk: egonw * r9478 /trunk/cdk/src/org/openscience/cdk/ (44 files in 24 dirs): Applied patch from branches/egonw/remove-non-cdkatomtype-code
10:05 miguelrojasc1 what is the new writing for <code> ?
10:05 egonw_ {{
10:05 egonw_ and }} for </code>
10:06 miguelrojasc1 ok
10:06 CIA-16 cdk: egonw * r9479 /branches/egonw/ (2 files in 2 dirs): Removed branch now that it is applied to trunk/
10:07 miguelrojasc1 I found
10:07 miguelrojasc1 [[code]]
10:07 miguelrojasc1 blabla
10:07 miguelrojasc1 [[code]]
10:08 egonw_ as new syntax?
10:08 egonw_ {{ strictly is <pre>
10:10 miguelrojasc1 I think that {{ put the words as a code and [[code]] put the blue box
10:10 egonw_ latter is better
10:15 egonw_ did not know about that syntax...
10:17 CIA-16 bioclipse: jonalv * r4321 /trunk/playground/plugins/net.bioclipse.expres​sion.tests/src/net/bioclipse/expression/tests/ (CalculatorBaseTest.java FunctionsTest.java): Added tests for a bug found while doing live demo. (Never do live demo...)
10:21 CIA-16 bioclipse: carl_masak * r4322 /trunk/playground/plugins/net.bioclip​se.expression.tests/src/net/bioclipse​/expression/tests/FunctionsTest.java:
10:21 CIA-16 bioclipse: [FunctionsTest.java]
10:21 CIA-16 bioclipse: * removed nasty @Overrides attribute
10:31 CIA-16 cdk: egonw * r9480 /branches/egonw/ibondorder/ (53 files in 28 dirs): Synchronized with trunk rev 9479
10:47 CIA-16 bioclipse: carl_masak * r4323 /trunk/plugins/net.bioclips​e.rhino/src/net/bioclipse/ (8 files in 3 dirs):
10:47 CIA-16 bioclipse: [net.bioclipse.rhino]
10:47 CIA-16 bioclipse: * renamed IScriptProvider -> INamespaceProvider
10:47 CIA-16 bioclipse: * (because that's what it provides)
10:47 CIA-16 bioclipse: * this change is a backport form bc2
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11:17 jpansanel moin
11:18 egonw_ hi jpansanel
12:36 CIA-16 blueobelisk: pansanel * r175 /structures/trunk/src/amino_acids/D-arginine: Moving to common name
12:37 CIA-16 blueobelisk: pansanel * r176 /structures/trunk/src/amino_acids/2R-2-amino-​5-diaminomethylideneaminopentanoic_acid.cml: Replacing IUPAC name by usual name
12:38 CIA-16 blueobelisk: pansanel * r177 /structures/trunk/src/amino_acids/ (D-arginine D-arginine.cml): Adding missing extension
12:44 egonw_ jpansanel: that was not using svn move, was it?
12:59 jpansanel it was using svn mv
13:00 * egonw_ is puzzled why it gave two commits...
13:00 egonw_ not that it really matters...
13:10 jpansanel egonw : because I've done two commits
13:11 jpansanel I've many things to commit into the amino_acids repository
13:11 jpansanel I've rename each file according the usual name.
13:11 jpansanel It's easier then for the user
13:11 egonw_ if you did only two commits, why are there commit reve 175, 176, and 177?
13:12 egonw_ yes, agreed
13:13 CIA-16 cdk: egonw * r9481 /branches/egonw/ibondorder/src/org/openscience/​cdk/test/atomtype/CDKAtomTypeMatcherTest.java: Added extra test case
13:14 CIA-16 cdk: egonw * r9482 /branches/egonw/ibondorder/src/org/opensci​ence/cdk/atomtype/CDKAtomTypeMatcher.java: Further tuned/fixed N atom types
13:15 CIA-16 cdk: egonw * r9483 /branches/egonw/ibondorder/src/org/​openscience/cdk/test/isomorphism/Un​iversalIsomorphismTesterTest.java: Removed a test, because I don't agree with the aromaticity which is really being tested :(
13:15 masak joined #cdk
13:15 carsten joined #cdk
13:16 egonw_ hi carsten
13:17 jpansanel hi
13:17 egonw_ carsten: is it normal that kalzium4kde4 always shows a popup for element properties?
13:17 egonw_ that's quite annoying IMHO
13:24 CIA-16 bioclipse: ospjuth * r4324 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.jmol/ (6 files in 4 dirs): JmolEditor now populates Outline with Model/BioPolymer/Monomer. It also listens to selections of 1-N Monomers and highlights them in JmolEditor, JmolView.
13:24 carsten jpansanel: moin!
13:24 carsten jpansanel: hey, chem-file will be installed by default on our school PCs!
13:24 carsten so will Avogadro
13:25 jpansanel cool !
13:25 jpansanel carsten : I've added some german translation for aminoacids
13:25 carsten yes, a bit i18n is missing
13:26 carsten Monoisotopic Weight: 17.0265491 g/mol
13:26 CIA-16 blueobelisk: pansanel * r178 /structures/trunk/src/amino_​acids/D-allo-isoleucine.cml: Fixing IUPAC name
13:26 carsten Monoisotopisches Gewicht
13:26 carsten jpansanel: ^^^
13:26 jpansanel ok
13:26 carsten can you change that?
13:26 egonw_ miguelrojasc1: thanx for the wiki help
13:26 jpansanel yes, I can
13:26 carsten Formula: H3N
13:26 carsten That is "Formel"
13:27 carsten Struktur Laden
13:27 carsten Small "l" → Struktur laden
13:27 egonw_ carsten: you don't have BO SVN write access?
13:27 carsten that is all in BO?
13:27 carsten Where?
13:28 egonw_ [14:26] <CIA-16> blueobelisk: pansanel * r178 /structures/trunk/src/amino_​acids/D-allo-isoleucine.cml: Fixing IUPAC name
13:28 egonw_ or are you talking about mychem?
13:28 egonw_ not, right... the webpage with structures, not?
13:29 CIA-16 blueobelisk: pansanel * r179 /structures/trunk/xml/l10n.xml: Fixing german translations
13:29 jpansanel carsten : fix
13:30 CIA-16 blueobelisk: cniehaus * r180 /structures/trunk/xml/l10n.xml: For testing: The space was not needed
13:30 carsten well, the space in the xml was unneeded, my commit was ok
13:31 carsten wait... jpansanel: is a space before a : needed in french?
13:32 jpansanel yes, the space is needed in french
13:33 jpansanel carsten : I'll make a demo CD for this project
13:33 CIA-16 blueobelisk: cniehaus * r181 /structures/trunk/xml/l10n.xml: fix the fix and fix another string (for real)
13:34 jpansanel with an embedded web browser and openbabel
13:35 carsten and avogadro, please
13:38 carsten jpansanel: http://chem-file.sourceforge.n​et/data/alkanes/index_de.html has an error
13:38 carsten >Nonane
13:38 carsten why the >?            I don't see where the html code is...
13:38 carsten --> I cannot fix it
13:44 CIA-16 blueobelisk: pansanel * r182 /structures/trunk/src/amino_acids/ (82 files):
13:44 CIA-16 blueobelisk: Renaming each file according the usual name
13:44 CIA-16 blueobelisk: Adding missing french and german translations
13:44 jpansanel carsten : because I've fix it yeasterday and I did not regenerate the HTML pages
13:46 CIA-16 cdk: egonw * r9484 /trunk/cdk/src/org/openscience/cdk/ (2 files in 2 dirs): Applied N atom typing fix from my ibondorder branch
13:47 thomas_ku joined #cdk
13:47 miguelrojasc1 egonw around?
13:47 thomas_ku moin
13:47 miguelrojasc1 hei thomas_ku
13:47 egonw_ miguelrojasc1: yes
13:48 miguelrojasc1 is for you ok if we pospone the metting on 7th for 14th
13:48 egonw_ miguelrojasc1: now would be a good time to synchronize your branch with trunk/
13:48 miguelrojasc1 ok
13:48 egonw_ yes, 14th is fine
13:49 miguelrojasc1 ok, perfect I spoke with Piotr and he said also is good
13:49 miguelrojasc1 We can do it now
13:49 egonw_ who will come, you, Theo, Piotr?
13:49 miguelrojasc1 only Piotr
13:49 egonw_ ok
13:50 egonw_ brb
13:50 jbrefort joined #cdk
13:50 CIA-16 blueobelisk: pansanel * r183 /structures/trunk/src/amino_acids/ (19 files): Fixing IUPAC names
13:51 miguelrojasc1 Ok I try now. And see how many errors I have :)
13:52 jonalv_ joined #cdk
13:53 CIA-16 bioclipse: carl_masak * r4325 /trunk/plugins/net.bioclipse.rhino/src/net/​bioclipse/views/ScriptingConsoleView.java:
13:53 CIA-16 bioclipse: [ScriptingConsoleView.java]
13:53 CIA-16 bioclipse: * fixed backspace bug
13:58 egonw_ miguelrojasc1: you know how to use 'svn merge'?
13:59 miguelrojasc1 what was the exact command that I have to used emerge or compare
13:59 miguelrojasc1 :)
13:59 miguelrojasc1 that was the question
13:59 miguelrojasc1 :)
13:59 egonw_ svn merge -r X:HEAD https://.../../cdk/trunk
13:59 miguelrojasc1 I tried to find if Eclipse has some help
13:59 egonw_ where X is to be determined
13:59 egonw_ and ../../ the regular URL bits
13:59 egonw_ I'll check X
14:00 * egonw_ types svn log -r 9400:HEAD
14:01 egonw_ and looks for some commit message like 'synched with trunk'
14:01 egonw_ ... nothing found
14:02 * egonw_ types svn log -r 9300:9400
14:02 miguelrojasc1 done
14:02 egonw_ what?
14:03 miguelrojasc1 nothing
14:03 miguelrojasc1 what I have to do ist Merge
14:03 miguelrojasc1 from trunk/cdk to brunch/miguelrojasch/mf
14:04 egonw_ ah... but you have not commited yet?
14:04 miguelrojasc1 nooooooooooo
14:05 miguelrojasc1 :) I make some times disaster but I this time not yet :)
14:06 miguelrojasc1 I will compare with trunk and syncronize
14:06 miguelrojasc1 I think is the easier way for me
14:07 egonw_ I can also show you what to type
14:08 miguelrojasc1 ok
14:09 miguelrojasc1 because I don't find some tipp in internet
14:09 egonw_ there have not changes been commited before, have there?
14:09 egonw_ ok, you're on the command line now...
14:09 egonw_ do this:
14:09 egonw_ cd mf
14:09 miguelrojasc1 done
14:10 egonw_ svn merge -r 9335:HEAD https://cdk.svn.sourceforge​.net/svnroot/cdk/trunk/cdk
14:10 egonw_ 9335 is the revision when the branch was made
14:10 egonw_ no syncs were done before...
14:10 egonw_ and HEAd is the latest version of anythings in SVN
14:11 egonw_ and it will apply ('merge') all commits made to any file below cdk/trunk/cdk
14:12 miguelrojasc1 If I understood good. It will merge from cdk/trunk/cdk -> cdk/branches/miguelrojasch/mf
14:12 miguelrojasc1 or from cdk/trunk/cdk -> to my directory
14:13 egonw_ to your directory...
14:13 egonw_ so that you can check compile conflicts first... and then commit
14:14 miguelrojasc1 perfect
14:14 egonw_ with a message like "Applied changes in trunk for rev 9335:9484"
14:14 egonw_ I'm sure there will be compile problems...
14:15 egonw_ no, actually not ... :)
14:15 miguelrojasc1 >:O
14:17 egonw_ let me know when you're done...
14:17 egonw_ then we can talk about the other thing about the branch I wanted you to talk with you about
14:18 miguelrojasc1 done
14:21 egonw_ time for a commit then?
15:04 CIA-16 cdk: miguelrojasch * r9485 /branches/miguelrojasch/mf/ (75 files in 39 dirs): updated from cdk/trunk/cdk
15:07 egonw_ miguelrojasc1: would have been better if you had included the version to which it updated...
15:07 egonw_ now one has to guess that it was 9484
15:07 egonw_ no severe problem, but something to remember
15:19 miguelrojasc1 I ok sorry
15:21 egonw_ no worries
15:21 egonw_ just a tip
15:21 egonw_ OK, I got some comments on the code (don't I always...)
15:21 egonw_ may I put them in the source code as "// FIXME:"
15:22 egonw_ then you can use the Eclipse 'Tasks' view, to look at them
15:22 egonw_ I'll add "MF" in the comment too, so that you can use the 'Tasks' filtering to just see those I added...
15:24 miguelrojasc1 Ok, sounds good
15:38 egonw_ OK, test suite results look quite good: 2 fails out of 73
15:47 dleidert joined #cdk
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16:15 egonw_ miguelrojasc1: OK, comments commited
16:15 CIA-16 cdk: egonw * r9486 /branches/miguelrojasch/mf​/src/org/openscience/cdk/ (8 files in 4 dirs): Comments on the code
16:18 CIA-16 cdk: egonw * r9487 /branches/miguelrojasch/mf/src/org/opensc​ience/cdk/formula/MassToFormulaTool.java: Two more comments I forgot to save
16:24 egonw_ going to log out
16:24 egonw_ cu later
16:32 CIA-16 bioclipse: carl_masak * r4326 /trunk/playground/plugins/net.biocl​ipse.base2/src/net/bioclipse/base2/ (model/Assay.java model/Experiment.java views/TreeView.java):
16:32 CIA-16 bioclipse: [net.bioclipse.base2.model]
16:32 CIA-16 bioclipse: * added Experiment and Assay
16:32 CIA-16 bioclipse: [net.bioclipse.base2.views.TreeView]
16:32 CIA-16 bioclipse: * new, better mockup
16:33 CIA-16 bioclipse: * shiny new icons
16:36 CIA-16 bioclipse: carl_masak * r4327 /trunk/plugins/net.bioclipse.webservic​es/src/net/bioclipse/plugins/bc_webser​vices/scripts/WebservicesTools.java:
16:36 CIA-16 bioclipse: [WebservicesTools.java]
16:36 CIA-16 bioclipse: * chased name refactoring from net.bioclipse.rhino
17:03 CIA-16 bioclipse: carl_masak * r4328 /trunk/playground/plugins/net.bioclipse.expressi​on/src/net/bioclipse/expression/Calculator.java:
17:03 CIA-16 bioclipse: [Calculator.java]
17:03 CIA-16 bioclipse: * fixed illegal characters bug
17:03 CIA-16 bioclipse: * all tests now pass
18:39 jbrefort joined #cdk
18:49 CIA-16 jmol: hansonr * r8655 /trunk/Jmol/src/org/jmol/ (4 files in 2 dirs): version=11.3.48_dev # bug fix: antialiasDisplay changes during spinning (or any rendering) causes null pointer error
18:50 egonw_ joined #cdk
19:06 Zappacky joined #cdk
19:06 Zappacky left #cdk
19:06 egonw_ Zappacky??
19:08 LaserJock hi egonw_
19:09 egonw_ hi
19:39 * egonw_ is introducing a new CDK module: atomtype
20:30 edrin joined #cdk
21:19 CIA-16 cdk: egonw * r9488 /trunk/cdk/ (40 files in 9 dirs): Set up the atomtype module
22:00 CIA-16 blueobelisk: pansanel * r184 /structures/trunk/src/carbo​xylic_acids/malic_acid.cml: switching to usual name
22:11 CIA-16 blueobelisk: pansanel * r185 /structures/trunk/src/carbohydrates/index.xml: Some missing french translation have been added
23:55 dleidert joined #cdk

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