Camelia, the Perl 6 bug

IRC log for #cdk, 2008-10-16

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Time Nick Message
05:29 thomasku joined #cdk
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06:39 thomasku moin
06:39 zarah hi thomasku
06:55 thomasku joined #cdk
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08:21 egonw hi shk3
08:21 egonw wiki time?
08:23 shk3 yes
08:23 shk3 what I worry about about
08:24 shk3 is how to make the wiki easily accesible
08:24 shk3 often, the problem with wikis is, you don't find things
08:24 shk3 can we have a menu in the left column?
08:25 carsten joined #cdk
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08:31 CIA-62 cdk: egonw * r12716 /cdk/branches/egonw-pka/src/main/org/opens​cience/cdk/charges/pka/PkaPredictor.java: Added full tree
08:33 egonw shk3: no idea
08:34 egonw let's first copy the pages... and we'll explore that option...
08:34 shk3 ok
08:37 shk3 how do we share things?
08:37 shk3 shall I do the jcp stuff?
08:37 egonw we have two old wikis...
08:37 egonw let's divide like that
08:38 egonw that is, you could port "almost"
08:38 egonw while I'd do http://cdk.wiki.sourceforge.net/
08:38 zarah egonw's link is also http://tinyurl.com/488db9
08:38 shk3 aren't tings from almost in the cdk wiki?
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08:41 egonw well...
08:41 egonw there is the Plone CDK webpage that needs porting
08:41 egonw and the wiki
08:41 shk3 yes
08:41 shk3 but didn't you copy the wiki from plone?
08:41 egonw no
08:41 shk3 just want to avoid we get things twice
08:42 shk3 ah
08:42 egonw the wiki was user oriented
08:42 egonw the webpage was the formal homepage
08:42 egonw http://www.steinbeck-molecula​r.de/cdk/index.php/Main_Page
08:42 zarah egonw's link is also http://tinyurl.com/4ajtwn
08:42 egonw that's the 'homepage'...
08:42 egonw which now happens to be a wiki
08:42 egonw btw, mind the spam on the front page
08:42 gilleain joined #cdk
08:43 egonw I think I've removed that earlier this week
08:43 egonw so might be spammed already again :(
08:43 egonw yes, spammed again yesterday
08:43 egonw so, many other pages migth be spammed too, so make sure to check the page history
08:43 egonw gilleain: please let me know which dates you can for a JChemPaint developers meeting
08:43 shk3 but steinbeck molecular wiki shouldn't have any content not in plone or sf wiki?
08:44 egonw I'm not sure how s-m.de/Main_Page compares to the old Plone
08:46 shk3 the same
08:47 shk3 plus same at the new wiki
08:47 egonw ok
08:47 egonw let's announce the page your editing here...
08:47 egonw title=Documentation
08:50 shk3 which page is that?
08:51 egonw https://apps.sourceforge.net/mediawi​ki/cdk/index.php?title=Documentation
08:51 egonw and now on to: title=Graph_Representation
08:53 egonw title=ChemFormats
08:55 shk3 title=JChemPaint
08:57 shk3 looks like angel wrote a completly new page on jcp
08:57 egonw yes, he did :)
08:57 egonw a nice one too :)
08:57 egonw nice to have him on board
08:58 shk3 cdk plugins are no longer existing, are they?
08:59 egonw title=Descriptor_Calculation
08:59 egonw no, CDK plugins are /dev/null
08:59 egonw well, it's called Bioclipse now :)
08:59 egonw rojasm: hi!
08:59 egonw rojasm: I learned yesterday about "git rebase"
09:00 egonw rojasm: if you want to synchronize your branch with the branch you branched from, then you should use "git rebase"
09:00 egonw rojasm: do: git rebase --help
09:00 egonw and check the schemas drawn
09:00 carsten IcedTea 1.3 is out. Guten Morgen :)
09:01 egonw hi carsten
09:01 egonw ah, sounds good!
09:01 egonw have not used it yet, though
09:03 carsten http://mail.openjdk.java.net/pipermail/​distro-pkg-dev/2008-October/003525.html
09:03 zarah carsten's link is also http://tinyurl.com/44w454
09:03 shk3 can I use html in the media wiki?
09:04 carsten egonw: I am still on OpenSUSE 10.3 and will skip OpenSUSE 11.0. I hope that with 11.1 Java will finally be faster :-) It is still very slow here no matter what others say.
09:04 egonw shk3: http://meta.wikimedia.org/wiki/He​lp:Editing#Wiki_markups_and_codes
09:04 zarah egonw's link is also http://tinyurl.com/47b2f
09:04 egonw icedtea is slow?
09:04 egonw can't imagine that, being 95+% based on Sun's Java...
09:05 carsten no, suns java is slow!
09:06 egonw what are you using then?
09:06 carsten suns
09:06 egonw and what program?
09:06 carsten Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_16-b02)
09:06 carsten egonw: doesn't matter, for example bioclipse is slow
09:06 carsten cmaptools
09:07 egonw anyting RCP-based is a bad example
09:07 * carsten doesn't know what rcp is
09:07 egonw Eclipse-RCP is too resource comsuming indeed
09:07 egonw nothing to do with Java
09:07 egonw RCP ~= Qt
09:07 egonw nah, better
09:08 egonw RCP is like KDElibs
09:08 egonw with nepomuk strigi and the sorts
09:08 egonw all booted by default, full fledged
09:08 shk3 egonw: I am adding a DONE to the top of all transferred plone pages
09:08 egonw yeah, sure it's slow
09:08 egonw particularly with <1GB mem
09:08 egonw shk3: good idea
09:08 egonw will do that from now on too, then
09:09 carsten egonw: do you know cmaptools?
09:09 carsten really really good software
09:09 egonw no, URL?
09:09 carsten the GUI sucks hell but you can really get good results
09:10 carsten http://cmap.ihmc.us/
09:10 carsten not FOSS but free for academic wokr
09:12 egonw title=3D_rendering_with_Jmo
09:17 egonw title=Using_the_CDK_in_R
09:19 egonw title=Installation
09:24 shk3 hm, there is a jcp user guide in plone
09:24 shk3 which seems to be a copy of the help
09:24 shk3 that's prone to be outdated
09:25 shk3 I will say "look at the help", I think
09:25 egonw yes, makes sense
09:26 shk3 angel did something similar anyway
09:27 egonw yes, was thinking that too... though that might be more oriented at people integrating the applet?
09:32 gilleain title=Development
09:33 egonw title=CDKInstallationWindowsXP
09:37 egonw title=CDKTIPSTRICKS
09:41 shk3 egonw: do you know how to access sf shell?
09:41 shk3 wasn't projectname.sf.net?
09:42 egonw yes, think so
09:42 shk3 but  ssh -l shk3 cdk.sf.net doesn't work
09:42 shk3 it used to, I think
09:43 egonw same here
09:43 egonw check the docs
09:43 egonw I guess something has changed since they move to Chicago
09:43 shk3 can't find it there :-(
09:43 shk3 well, will do that later
09:49 egonw gilleain: ping
09:49 gilleain pong
09:49 egonw done with title=Development?
09:49 gilleain Yup.
09:49 egonw ok
09:49 egonw title=Development
09:49 gilleain Looking for things to move!
09:49 egonw (going to append bits from the wiki)
09:52 gilleain title=CDK_on_the_internet
09:52 gilleain (ok?)
09:52 egonw yes
09:53 gilleain Creating...
09:53 egonw if no one mentioned the title yet, or a different one after that, consider it unlocked
10:05 shk3 there is a bibliography for jcp in plone, which is a mixture of everything
10:05 shk3 what to do with this?
10:05 egonw URL?
10:06 shk3 http://almost.cubic.uni-koe​ln.de/cdk/jcp/bib/base_view
10:06 zarah shk3's link is also http://tinyurl.com/4chq5l
10:07 egonw title=Spring2007Workshop
10:07 egonw shk3: that needs to be copied...
10:07 egonw but requiring more work indeed :)
10:07 egonw it's good that we're doing this with three people
10:08 shk3 we have only one citations page in media wiki. right?
10:16 egonw dunno
10:18 shk3 well, we should, shouldn't we?
10:18 shk3 title=Applet_class_lists
10:18 egonw shk3: not sure...
10:19 egonw it would make quite sense to me to have a separate list for JCP related citations
10:21 egonw title=BSP200609
10:22 egonw crap
10:22 egonw now I get Internal Server Errors on the new wiki :(
10:22 shk3 title=Tests_for_JCP
10:24 egonw grmphh...
10:24 egonw with the proper content you get a ISE :(
10:25 egonw ==Things *JChemPaint/Bioclipse Users* can do==
10:25 egonw don't copy paste that
10:25 egonw that won't work
10:27 egonw :(
10:29 shk3 title=Events
10:30 egonw shk3: please copy that into https://apps.sourceforge.net/mediawiki/​cdk/index.php?title=cdk:Current_events
10:43 egonw http://github.com/egonw/cdk/network
10:43 zarah egonw's link is also http://tinyurl.com/4okc8h
10:43 egonw there is some branching and merging there ! :)
10:43 egonw drag to slightly older history
10:43 egonw around the 10th
10:44 egonw is title=Literature done already?
10:44 egonw search does not give anything, so:
10:44 egonw title=Literature
10:45 gilleain I've been using the allpages (easier than search :)
10:45 gilleain https://apps.sourceforge.net/mediawiki​/cdk/index.php?title=Special:AllPages
10:45 egonw ah, good tip
10:47 shk3 title=Jcp_citations
10:52 shk3 who is a sysop on this wiki?
10:54 egonw chris, I guess
10:55 egonw he requested the hosted app
10:56 shk3 title=Software_using_CDK
10:57 shk3 is this "XB Edit" living somwhow?
10:57 shk3 don't think so, I would remove it.
10:58 egonw shk3: don't worry about page validation right now
10:58 egonw just copy/paste
10:58 egonw I'd say
10:58 egonw that's enough work for today, I guess
10:59 shk3 but it will then be forgotten forever again
10:59 shk3 google doesn't give anything except our page
10:59 zarah shk3: http://www.guardian.co.uk/lifeandstyl​e/2006/jun/25/foodanddrink.features6
10:59 egonw hahahah
11:00 gilleain a small effort to not copy/paste whole pages that will live on zombie-like seems worth it.
11:00 shk3 zarah: ?
11:00 zarah shk3: yes?
11:00 egonw it's making the decision that takes the time
11:00 egonw but you googled now...
11:00 egonw and you sounds sure about your removel
11:00 egonw so go ahead
11:00 shk3 we can make an "obsolete section"
11:00 egonw I heard some uncertainty at first
11:01 shk3 btw. jumbo is listed as "software using cdk"
11:01 shk3 is that true?
11:01 shk3 it's related, but not using, is it?
11:01 egonw yes, that is true
11:01 egonw it is
11:01 egonw cmldom is not
11:01 egonw but jumbo is
11:02 shk3 ah
11:02 gilleain Thus the whole cyclic dependencies discussion about cdk/cml.
11:03 egonw right
11:03 egonw hence the cdk-pom project in SVN
11:03 egonw which actually needs some love
11:03 egonw any love, erally
11:03 gilleain heh:
11:03 gilleain google InChI=1/CH4/h1H4
11:03 zarah gilleain: http://chem-bla-ics.blogspot.co​m/2007/02/invisible-inchis.html
11:03 egonw title=CDKFAQ
11:03 egonw cool :)
11:04 egonw yeah, my blog has a pretty decent google rank :)
11:05 gilleain ah, but if you do this:
11:05 gilleain google 1/CH4/h1H4
11:05 zarah gilleain: http://chem-bla-ics.blogspot.co​m/2007/02/invisible-inchis.html
11:05 gilleain Oh, wait!
11:05 gilleain I get chemspider in my browser :(
11:06 gilleain Must be google-tailored results...
11:13 egonw title=Features
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11:21 egonw title=Modules
11:21 gilleain title=ChangeLog
11:23 gilleain ISE!
11:23 gilleain Nooooooooo!
11:24 egonw right
11:24 egonw see above
11:24 egonw it's a key combination in the wiki source yuo entered
11:24 gilleain Indeed.
11:24 gilleain http://darthno.ytmnd.com/
11:24 egonw have not really fuond a pattern
11:24 egonw but & seems to be a problem
11:31 gilleain damn you changelog! I'm for lunching.
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12:15 gilleain Ah-ha! The problem line may have been :
12:15 gilleain "Insert from SMILES in JChemPaint now really inserts, instead of adding a new model. [egonw]"
12:15 gilleain weird.
12:17 egonw I guess the bracket
12:17 egonw I had it crash over a "= some header="
12:17 egonw really weird
12:18 gilleain But all the other lines had brackets...
12:18 egonw yeah, but that one did tooo
12:18 egonw it's fine on those other lines...
12:18 egonw it just can't be on that line
12:18 gilleain )
12:19 gilleain + :
12:19 gilleain aargh!
12:20 egonw gilleain: you did ChangeLog200607?
12:20 shk3 ok, all transferred from plone outsie the cdk section
12:20 gilleain Er, I'm doing ''a'' changelog, yes.
12:21 egonw :)
12:21 gilleain No,  mine is 20050826
12:21 gilleain Hmmm. Is this going to be done automatically?
12:24 egonw sort of
12:24 egonw git log > changelog.txt
12:24 gilleain then?
12:24 gilleain "upload changelog.txt"
12:24 gilleain ?
12:25 egonw then nothing...
12:25 egonw I once had such an upload script for Plone
12:25 egonw but we keep changing system again and again
12:25 egonw originally we had static pages
12:25 egonw of which the source was in SVN
12:25 gilleain Well, I say either have all changelogs in the wiki, or none.
12:25 egonw (well, CVS really :)
12:25 egonw and then this inclusion of the ChangeLog was fully automated
12:25 gilleain Or a link to nightly changelog (assuming it exists?)
12:26 egonw no such thing
12:26 gilleain Oh.
12:26 gilleain Well, I've had 5 ISEs on this changelog. It's getting tiresome.
12:26 egonw ah, not bad
12:26 egonw I had 10-ish on a page
12:27 egonw which was actually really short
12:27 gilleain Huh, annoying
12:27 egonw yes
12:32 egonw gilleain: ha, I got a new one: Method not Found
12:32 egonw upon hitting the 'Save' button
12:32 gilleain Ohh. A rare beast.
12:33 gilleain I wonder if sf's log files are filling up...
12:34 egonw I hope so
12:34 egonw maybe we reach the top 10 :)
12:34 gilleain heh
12:47 gilleain title=Interoperable OS Projects
12:47 gilleain (with tables : gulp!)
12:49 shk3 if anybody tries to use sf shell service, read this:
12:49 shk3 https://sourceforge.net/community/forum/​topic.php?id=3518&amp;page&amp;replies=1
12:49 shk3 I missed that, but it is an important change
12:51 egonw gilleain: yeah, I'm converting a table too :)
12:51 egonw title=Refactoring_of_the_kernel_classes
12:51 egonw forgot to mention that :)
12:54 gilleain hmmm. it does work, all the {| and |- stuff.
12:54 gilleain but it doesn't look so good.
13:06 shk3 I am trying to redirect the jchempaint.sf.net page
13:06 shk3 there is an index.html in the htdoc dir
13:07 shk3 but changing that has no effect.
13:07 shk3 does anybody know if there is another redirectin setting?
13:11 shk3 ok, solved
13:11 shk3 was caching
13:27 egonw gilleain: ping
13:31 gilleain yup.
13:33 gilleain pong.
13:33 gilleain ack.
13:34 egonw I'd like to see your branch and arvid branch merged next
13:34 egonw ... week
13:34 egonw we just discussed my patch
13:34 gilleain hahaaaha. unlikely I feel.
13:35 gilleain We have totally different architectures.
13:35 egonw and I asked him to integrate the rendering module (basic, reaction, controllerfeedback, highlight, ...) into his branch
13:35 gilleain (which Is my fault)
13:35 gilleain I like the Visitor pattern idea, though.
13:36 gilleain I might be wrong, I suppose.
13:36 egonw but I'm sure you can come up with a single design
13:36 egonw accomodation for both your and arvids idea, right?
13:36 gilleain Hmmm. Maaaaayybeee.
13:36 egonw OK, so please discuss how to do this on the list
13:37 egonw everyone is agreeing on the second week I proposed
13:37 egonw and we really should have a single design ready before that
13:37 egonw so we can use that meeting for making first releases
13:37 gilleain I'll take another look at his code, and try and work out if & how it is possible.
13:37 egonw of applet(s) and the SWT wisget(s) based onthe new design
13:37 gilleain Right, okay.
13:38 egonw OK, I'll focus a bit more on the mouse event -> controller -> edit actions -> CDK data model side
13:38 egonw and further hack on that
13:38 egonw which will actually include a scripting language...
13:38 gilleain Cool.
13:39 gilleain I guess I have been doing core stuff. But then so has Arvid.
13:39 gilleain Hmmm.
13:40 egonw yes, right
13:40 egonw so now you and him would do got to pick the best, or integrate the best bits, into a single final design
13:40 egonw arvid also asked me for demo data
13:40 egonw which highlight the primary rendeing functionality requirements...
13:40 egonw and will do that asap
13:41 egonw with some screenshots where possible
13:41 gilleain Yes. I was thinking about a table, linked to mini-applets.
13:41 egonw as much as possible
13:41 egonw yes
13:41 egonw but the mini-applets would require a final design and implementation :)
13:41 gilleain Like "zoom" -> zoom applet
13:41 egonw hence screenshot :)
13:41 gilleain True.
13:41 gilleain True.
13:41 egonw OK, excellent
13:41 egonw while at it...
13:42 egonw I'll also draft a paper
13:42 egonw that will keep us focused on the goal :)
13:42 gilleain for sure.
13:42 egonw btw, having major trouble getting a table in the new wiki :(
13:43 egonw getting "No such method" all over the place
13:43 gilleain Really. Mine worked, but looked crap.
13:43 egonw for just adding one well-formated row :(
13:43 gilleain Also, I've just used vi to regex-replace html to wiki markup. Seems...wrong...somehow.
13:44 gilleain Table tags also work, btw.
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13:53 egonw grpmh...
13:53 gilleain grmph?
13:54 egonw WTF???!?!?!?!
13:54 egonw it just crashes in the simplest text-only content
13:54 egonw SF--
13:55 egonw gilleain or shk3:
13:55 egonw might one of you attempt to complete the table:
13:55 egonw https://apps.sourceforge.net/mediawiki/cdk/ind​ex.php?title=Refactoring_of_the_kernel_classes
13:55 egonw source:
13:55 egonw http://cdk.wiki.sourceforge.​net/refactoringkernelclasses
13:55 zarah egonw's link is also http://tinyurl.com/4wlhzp
13:55 gilleain I'll take a gander.
13:56 egonw thanx!
14:10 egonw shk3: ping
14:10 gilleain getting there...
14:10 egonw did the redirect work?
14:10 egonw for jcp and cdk?
14:11 shk3 only did jcp
14:11 shk3 is there one for cdk?
14:11 shk3 mom
14:11 egonw I'll fix those
14:12 shk3 I can change the one on cdk.sf.net
14:12 egonw I'm on it
14:12 shk3 ok
14:14 egonw fixed
14:15 shk3 great
14:30 gilleain The fabled "Method Not Implemented"!
14:30 egonw gilleain: does it work for you? with the table?
14:31 egonw ???
14:31 egonw stupid, isn't it?
14:31 gilleain I think the wiki is trying to call the getAllAtoms() method...
14:31 gilleain :)
14:32 shk3 guys, what are you doing?
14:32 shk3 I didn't have any problems
14:33 gilleain Well, you were not editing this table...
14:33 egonw shk3: maybe you want ot have a try? :)
14:34 gilleain It would be nice if the error message told what line was the problem.
14:37 egonw yes
14:38 egonw I have been adding things row by row
14:38 gilleain Ack. Effort duplication!
14:38 egonw but had some rows with nothing really different (in term of type of chars) than other rows
14:38 egonw but it still failed
14:38 gilleain I have the whole table here.
14:38 egonw no, that was before I gave up and asked you
14:38 gilleain But, it fails.
14:38 gilleain oh right.
14:38 gilleain Yes, just saved to notepad.
14:40 gilleain hmmm. some kind of binary search seems in order.
14:46 gilleain Aha!
14:47 gilleain "|IRingSet||ringAlreadyInSet()||(moves to manipulator)||Done (r7015)"
14:47 egonw so, what's wrong with that?
14:47 egonw does it really try to execute on of those things?
14:47 egonw wuold be really funny
14:47 gilleain No idea.
14:48 gilleain It might be the "(moves to manipulator)"..
14:49 gilleain Right, I've saved it, I'll try to get that row in somehow.
14:51 gilleain Yup. "(stuff in brackets)" also triggers a Method Not Implemented.
14:51 egonw got to catch my bus
14:52 gilleain bye.
14:52 egonw I'll be back on Monday
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