Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-02-02

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All times shown according to UTC.

Time Nick Message
07:05 jonalv joined #bioclipse
07:30 Gpox joined #bioclipse
07:36 Gpoks joined #bioclipse
07:37 jonalv hi Gpoks, Gpox
07:38 Gpox hi
07:38 zarah saluton Gpox
08:14 egonw joined #bioclipse
08:15 egonw moin
08:15 zarah saluton egonw
08:15 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
08:15 egonw @msg
08:15 zarah egonw: 23 h 6 m 1 s ago, masak said re bugs.bioclipse.net: that was already fixed, but zarah needed a reboot :)
08:15 egonw @tell masak thanx!
08:15 zarah Consider it noted.
08:50 edrin joined #bioclipse
09:03 maclean joined #bioclipse
09:04 jonalv joined #bioclipse
09:04 jonalv oh hai
09:04 zarah hi jonalv
09:07 maclean oh
09:07 maclean hai
09:07 * maclean is feeling ill
09:07 jonalv ?
09:09 maclean ill? a kind of sickness, or unbalanced humours
09:09 maclean a malaise
09:11 jonalv okey
09:12 jonalv that can't be good
09:15 maclean it isn't. oh well, I'll survive :)
09:43 maclean joined #bioclipse
09:48 egonw jonalv: ping
09:48 jonalv egonw: pong
09:48 egonw jonalv: can  you come over to my room?
09:48 jonalv comming
09:57 shk3_ joined #bioclipse
10:02 CIA-55 bioclipse: egonw * r8535 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Defines a global NAMESPACE field
10:11 CIA-55 bioclipse: egonw * r8536 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (CDKManager.java ICDKManager.java): More conform expected API: now takes an IProgressMonitor (fixes #342)
10:11 zarah bug #342 | http://tinyurl.com/aqptmk
10:12 masak joined #bioclipse
10:15 shk3_ the pelezilla home page
10:15 shk3_ http://pele.farmbio.uu.se/cgi-bin/bugzilla/
10:15 zarah shk3_'s link is also http://tinyurl.com/6pp42l
10:15 shk3_ gives me a "you don't have permission"
10:15 masak @pz
10:15 zarah masak: Pelezilla is at http://bugs.bioclipse.net
10:15 masak shk3_: that's because you need an 'index.cgi' at the end.
10:16 shk3_ that's the link behind home on pelezilla
10:17 masak that link has an 'index.cgi' at the end.
10:18 masak egonw++ # for home page
10:18 shk3_ not for me
10:19 masak try reloading the page or something?
10:20 shk3_ stays withouth the index.cgi
10:20 shk3_ also after a search etc.
10:21 masak that's odd.
10:23 shk3_ anyway
10:36 maclean_ joined #bioclipse
10:40 jonalv egonw: I am trying to merge in yoiur changes now... :(
10:40 jonalv ...not so easy.,.. :(
10:40 egonw ack
10:40 egonw how so?
10:40 jonalv everything has changed in my version...
10:47 CIA-55 bioclipse: egonw * r8537 /bioclipse2/trunk/plugins/net.bioclipse.cdk.bus​iness.test/src/net/bioclipse/cdk/business/test/ (CDKManagerPluginTest.java CDKManagerTest.java): Compile fixes for commit 8536: API changes to match new manager convention
10:47 CIA-55 bioclipse: egonw * r8538 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.jchempaint/plugin.xml: Added tool tips
10:48 maclean_ ooh tooltips
10:51 CIA-55 bioclipse: egonw * r8539 /bioclipse2/trunk/plugins/net.​bioclipse.jmol/jars/Jmol.jar: Uploaded Jmol bug fix release 11.6.14 (fixes #338)
10:51 zarah bug #338 | http://tinyurl.com/daenlj
11:30 jonalv AAAAAAAHAHHHHHH
11:32 maclean_ A*H*?
11:38 shk3_ hi maclean_
11:38 shk3_ it's amazing
11:38 masak ^A+[AH]*$
11:39 maclean_ shk3: what's amazing? the snow?
11:39 shk3_ two centimeters of snow stop this country running
11:39 maclean_ masak: heh
11:39 jonalv I lost my changes
11:39 masak maclean_: ...but Perl 5 regexes are so 20th century. :P
11:39 * jonalv hates to do merging
11:40 maclean_ shk3 : also; leaves, wind, 'heatwaves' (>30 degrees C) :)
11:40 maclean_ masak: <A|H> |X| <R|G>
11:40 masak :D
11:41 maclean_ jonalv : were there a lot? :(
11:41 jonalv all I had done today
11:41 maclean_ gah.
11:42 jonalv mhm
11:42 jonalv please nobody touch the cdkmanager... :)
11:42 jonalv ...until I have managed to commit...
11:42 jonalv ...someday next week...
11:42 jonalv ...or not...
11:42 jonalv :)
11:43 * jonalv has to many things going on right now...
11:53 masak @plan old bc2
11:53 zarah masak: bc2/console-egonw-single-line-refactor: 2 h planned, 21 h 53 m elapsed
11:53 zarah masak: bc2/managerdocs-finder: 1 h 30 m planned, 1 h 37 m elapsed
11:53 zarah masak: bc2/managerdocs-finder-html-skin: 1 h 15 m planned, 1 h 15 m elapsed
11:53 zarah masak: bc2/scriptconsole-backspace-bug: 30 m planned, 2 m elapsed
11:53 zarah masak: bc2/scriptconsole-literal-tab-bug: 30 m planned, 15 m elapsed
11:54 masak @start managerdocs-finder-h..
11:54 zarah masak: Starting task 'bc2/managerdocs-finder-html-skin'.
11:58 shk3_ maclean, masak: is there a method in swt-based jchempaint
11:58 egonw joined #bioclipse
11:58 shk3_ to get screen coords from world coords?
11:58 * masak doesn't know
11:58 masak maybe Gpox knows.
11:58 shk3_ i. e. the inverse of getCoorFromScreen
11:59 masak @stop
11:59 zarah masak: Stopping task 'bc2/managerdocs-finder-html-skin' after 5 m at 1 h 20 m out of 1 h 15 m (106%).
11:59 masak jonalv: fixed the \n problem you reported. http://pele.farmbio.uu.se/manager-docs/
11:59 zarah masak's link is also http://tinyurl.com/aqykgf
12:00 egonw what is IMoleculeManager?
12:00 CIA-55 bioclipse: carl_masak * r8540 /bioclipse2/trunk/manager-apidocs/render-as-html: [managerdocs] replace \n with <br> in HTML output
12:01 egonw masak: please add the namespace for the managers
12:01 masak egonw: IMoleculeManager was an early experiment with CDK interaction, I think.
12:01 masak egonw: good idea.
12:01 egonw I guess these docs are for users, right?
12:02 masak jonalv++ also suggested that I use the manager names, not the names of the interfaces.
12:02 masak egonw: guess so.
12:02 egonw I also suggest a link to gist scripts for that manager:
12:02 egonw (via delicious)
12:02 egonw delicious.com/tags/bioclip​se+gist+manager:NAMESPACE
12:02 masak um. patches welcome.
12:06 maclean_ shk3: there should be, it's in the interface
12:07 shk3_ which interface?
12:07 shk3_ well, let's have a look at this tomorrow
12:07 shk3_ I working round it right now
12:07 maclean_ okey
12:08 maclean_ If my newest branch were merged, you would have this method in the renderer...
12:10 maclean_ hmmm
12:10 maclean_ there is no method how odd
12:11 shk3_ i get confused so let's have a look together
12:12 maclean_ ok
12:21 shk3_ "
12:21 shk3_ I have just been informed by security that the campus buses will be
12:21 shk3_ leaving 4 hours earlier than normal. So the first one will leave at
12:21 shk3_ 13.30 and the last at 16.30.
12:21 shk3_ "
12:21 shk3_ all this because of a little snow...
12:22 egonw hahaha
12:22 egonw well, with those narrow english roads...
12:22 egonw a little slip can already be fatal
12:22 egonw and UK cars do not have winter tires, I guess...
12:22 egonw same in NL, btw
12:23 egonw except for the so narrow raods
12:24 maclean_ also, you can drive on the frozen canals in NL. :)
12:24 egonw no
12:24 egonw sorry
12:24 egonw that would mean we could skate on the ice too
12:24 egonw seldom
12:25 egonw this year a few days... the last time before that 12 years earlier
12:26 egonw downloads for BC2 beta are pretty good :)
12:26 egonw 140 downloads or so...
12:26 egonw in just one week
12:26 egonw for a beta
12:26 olass joined #bioclipse
12:26 maclean_ good
12:29 olass hi
12:29 zarah oh hai olass
12:29 CIA-55 bioclipse: ospjuth * r8541 /bioclipse2/trunk/plugins/net.bio​clipse.xom/META-INF/MANIFEST.MF: Set version of XOM plugin to 1.1. Reference: bug #278 (now closed).
12:29 zarah bug #278 | http://tinyurl.com/bewtdy
12:31 CIA-55 bioclipse: goglepox * r8542 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MoleculeTableContentProvider.java: Some formatting changes
12:32 olass egonw: around?
12:32 egonw yes
12:32 egonw for 15 minutes or so
12:32 egonw then appointment
12:32 olass I am thinking of refactoring out docs/cheatsheets/intro pages etc to a net.bioclipse.help plugin
12:32 edrin left #bioclipse
12:32 olass like eclispe does it :-)
12:33 olass well, eclipse anyway
12:33 egonw ah, you read: http://blog.eclipse-tips.com/2009/01/t​op-10-mistakes-in-eclipse-plug-in.html
12:33 zarah egonw's link is also http://tinyurl.com/d982dn
12:33 egonw item 8 in particular :)
12:33 olass no
12:33 olass will do now
12:33 olass nah
12:33 olass anyways
12:33 egonw :)
12:34 olass I think this is the only help plugin we should have
12:34 egonw the reversioning is sort of bad practice...
12:34 egonw caused by things
12:34 egonw because we did not put the XOM lib in its separate plugin...
12:34 olass and that other plugins should NOT have separate docs plugins
12:34 egonw anyways...
12:34 olass egonw: what you mean?
12:34 egonw nevermind
12:34 egonw let's talk .help...
12:34 olass xom lib is in a plugin
12:34 egonw why should speclipse help be in bioclipse.help?
12:34 olass that plugin is now versioned 1.1
12:35 olass no
12:35 egonw olass: yes, never mind
12:35 olass it should definitely not
12:35 olass my point is
12:35 olass speclipse should have its help in the speclipse plugins
12:35 olass not create a speclipse.help plugin
12:35 olass but the Bioclipse platform has so many docs
12:35 olass that it makes sense to have a plugin of its own
12:36 olass you agree?
12:36 egonw I do not understand the difference
12:36 egonw if speclipse has tons of docs...
12:36 olass ?
12:36 olass it doesn't
12:36 egonw why should it not make that decision too?
12:36 olass sure
12:36 olass but right now I'm talking about
12:37 olass egonw: sorry to have brought this up for discussion.
12:37 olass I think only I confused you
12:37 olass nvm
12:38 * olass has been working on docs over the weekend
12:38 olass sooo boring
12:39 jonalv bit rot, Bioclipse haz it :)
12:41 maclean_ uh-oh. I prescribe a healthy refactoring.
12:41 jonalv I hvae reached c'est end of c'est file
12:42 egonw bbl
12:42 maclean_ c'est?
12:42 CIA-55 bioclipse: ospjuth * r8543 /bioclipse2/trunk/ (3 files in 3 dirs): Updated dep to XOM version 1.1 after reversioning.
12:43 maclean_ C'est le fin de la dossier?
12:45 masak jonalv: worst use of "c'est" EVAR.
12:45 jonalv woho
12:47 CIA-55 bioclipse: jonalv * r8544 /bioclipse2/trunk/plugins/net.bioclip​se.structuredb/META-INF/MANIFEST.MF: Now structuredb at least starts. Seems like I removed a little too much in last commit. It does however not build now during export to update site. I don't know what to do...
12:47 CIA-55 bioclipse: jonalv * r8545 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Started work on reindentation of the cdkmanager. A number of unlucky events had made it a terrible read indentation-wise.
12:47 CIA-55 bioclipse: jonalv * r8546 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: continued reindentation and cleanup up in the cdk manager
12:48 CIA-55 bioclipse: jonalv * r8547 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: finished fixing indentation of the cdkmanager
12:58 maclean_ (syntax fixes)++
13:03 shk3_ how are menus built in Biolipcse-Jchempaint?
13:03 shk3_ hard coded?
13:04 shk3_ or is there a config file?
13:05 maclean_ there's some stuff in n.bc.cdk.jcp/plugin.xml
13:05 maclean_ don't know if it's the menus, but looks like
13:09 Gpox yes, it is all built in the plugin.xml
13:09 shk3_ hm
13:11 shk3_ olas assigned me the task to make the menu context specific
13:11 shk3_ can't see right now how to do this with the built-in popup menu
13:12 shk3_ there might be a possibility
13:12 * shk3_ is researching
13:14 Gpox you can put 'visibleWhen' on a menu item
13:14 sneumann joined #bioclipse
13:16 shk3_ visibleWhen
13:16 shk3_ hm
13:17 shk3_ but they would need to depend on selection in jcpeditor
13:17 shk3_ but i could perhaps set menu items visible=false from the jcp editor
13:20 olass shk3_: http://wiki.bioclipse.net/index.php?title=​How_to_add_menus_and_actions#Add_context_m​enu_for_file_extension_and_text_selection
13:20 zarah olass's link is also http://tinyurl.com/55gl83
13:21 olass also see links in bottom of that page
13:21 shk3_ hm, but that's in the navigator?
13:25 olass what is?
13:25 olass Selections are general for Eclipse
13:26 olass Navigator just implements a SelectionProvider
13:26 shk3_ hm, ok
13:33 CIA-55 bioclipse: goglepox * r8548 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui.sdf​editor/src/net/bioclipse/cdk/ui/sdfeditor/editor/ (4 files): Moved Row and Header from MoleculesEditor to MoleculeTableViewer
13:35 rojasm joined #bioclipse
13:49 shk3_ "Please note that the DiNA will be closing at 2.00pm today due to the extreme weather."
13:55 masak haha
14:20 Gpox shk3_: still working on bug 327?
14:20 shk3_ yes
14:21 shk3_ updating my workspace right now
14:21 shk3_ I got the impression I need to make the editor a selctionprovider
14:21 shk3_ and could then test that in
14:21 shk3_ visiblewhen
14:23 Gpox I should probably have that bug, there already is a selection provider and it adapts to selection. The problem is that a atom is always returned when no bond is highlighted or something like that
14:25 shk3_ go ahead please
14:32 CIA-55 bioclipse: shk3 * r8549 /bioclipse2/trunk/plugins/net.bioclipse.bibtex/ (2 files in 2 dirs): removed version requirement for net.bc.xom
14:33 masak @start managerdocs-finder
14:33 zarah masak: Starting task 'bc2/managerdocs-finder'.
14:33 CIA-55 bioclipse: shk3 * r8550 /bioclipse2/trunk/plugins/net.biocli​pse.nmrshiftdb/META-INF/MANIFEST.MF: removed version requirement for net.bc.xom
14:36 CIA-55 bioclipse: shk3 * r8551 /bioclipse2/trunk/plugins/net.biocl​ipse.spectrum/META-INF/MANIFEST.MF: removed version requirement for net.bc.xom
14:36 CIA-55 bioclipse: shk3 * r8552 /bioclipse2/trunk/plugins/net.bioclip​se.specmol.test/META-INF/MANIFEST.MF: removed version requirement for net.bc.xom
14:37 CIA-55 bioclipse: shk3 * r8553 /bioclipse2/trunk/plugins/n​et.bioclipse.spectrum.test/ (.classpath META-INF/MANIFEST.MF): removed version requirement for net.bc.xom
14:44 olass Gpox (or anyone else): If I am in a Wizard, how can I get the ID (as defined in the manifest) for this Wizard?
14:49 masak @start managerdocs-finder-html..
14:49 zarah masak: Stopping task 'bc2/managerdocs-finder'. Starting task 'bc2/managerdocs-finder-html-skin'.
14:50 shk3_ I am leaving due to extreme weather conditions
14:51 masak shk3_: enjoy the outside.
14:51 masak ...wading throught the two centimeters.
14:51 shk3_ extreme weather conditions==light snowfall, no wind
14:52 masak aye.
14:52 shk3_ might be 3 centimeters now
14:52 masak well, that's another matter entirely, then!
14:59 masak @stop
14:59 zarah masak: Stopping task 'bc2/managerdocs-finder-html-skin' after 10 m at 1 h 30 m out of 1 h 15 m (120%).
15:00 CIA-55 bioclipse: carl_masak * r8554 /bioclipse2/trunk/manager-apido​cs/parse-file-for-annotations: [manager-docs] now find the manager class too
15:00 CIA-55 bioclipse: carl_masak * r8555 /bioclipse2/trunk/manager-apidocs/render-as-html: [managerdocs] now shows the manager class name in the title
15:51 egonw olass: ping
15:51 egonw olass: what is the exact release plan for BC 2.0.0?
15:51 egonw another beta I guess?
15:51 egonw when, and when the RCs and final release?
15:51 egonw I need this info to assign bug/wishlist reports to milestones
15:57 olass egonw: are you serious?
15:57 olass http://wiki.bioclipse.net/index.p​hp?title=Bioclipse2_release_plan
15:57 zarah olass's link is also http://tinyurl.com/5guree
15:57 olass it's been there for months...
15:57 olass weeks
15:57 egonw right...
15:57 egonw with varying dates...
15:57 olass well
15:57 egonw these are the final ones?
15:58 olass yes
15:58 egonw good :)
15:58 olass hopefully we can sketch on that tomorrow
15:58 olass not final
15:58 * egonw is not asking for delay or so...
15:58 olass well, I want us together to decide a final date tomorrow based on the bug lists
15:58 olass hard for me to decide
15:59 olass I can just judge my own buglist
15:59 egonw seems to me quite a few reports are wishlist reports
15:59 olass which is tight, but possible
15:59 egonw I'm fine with whatever schedule
15:59 olass egonw: really?
15:59 olass egonw: what do you mean fine with whatever schedule?
15:59 egonw I do not have the illusion that after 2.0.0 will can sit back and relaz :)
16:00 olass egonw: so you think we could release a 2.0 tomorrow inthe current state?!?
16:00 olass seriously...
16:00 egonw no, that's not what I mean...
16:00 olass we should be able to fulfill the use cases on the wiki
16:00 egonw but if you would decide that, I would back that up
16:00 olass :-)
16:01 * olass is glad for the support
16:01 egonw my point is the opposite
16:01 egonw there is so much more we can do...
16:01 egonw 2.0.0 is just the start
16:01 egonw not the end
16:01 olass I couldn't agree more
16:01 olass but
16:01 olass I have the feeling that after 2.0 people will sort of focus on more remote tasks and bug fixing will be slower than now
16:02 olass hence we really need to hunt down the basic stuff now
16:02 olass 2.0 must be able to do the basics
16:02 olass not fancy stuff
16:02 olass 2.0 feb 11th is maybe too soon
16:02 egonw fancy/basics are not really identifiables
16:03 olass I know :-)
16:03 olass but that's what we defined in the use cases
16:03 olass when we can check all those, 2.0 can be released
16:03 olass (or remove use cases in the worst case)
16:04 egonw I'll annotate Bioclipse_2.0_Cheminformatics
16:04 egonw with the state on things
16:04 olass egonw: any more comments on http://wiki.bioclipse.net/index.ph​p?title=Molecular_coordinate_rules ?
16:04 zarah olass's link is also http://tinyurl.com/d8gwhe
16:04 egonw and point to gists...
16:04 olass ok
16:04 olass gists for javascripts?
16:04 egonw updated that wiki page with my comments
16:16 olass great
16:16 CIA-55 bioclipse: ospjuth * r8556 /bioclipse2/trunk/plugins/net.bioclipse.data/: Initial import.
16:18 CIA-55 bioclipse: ospjuth * r8557 /bioclipse2/trunk/plugins/net.bioclipse.data/ (49 files in 16 dirs):
16:18 CIA-55 bioclipse: Working on bug 361: Refactor sample data into 2 plugins
16:18 CIA-55 bioclipse: http://pele.farmbio.uu.se/bugs/show_bug.cgi?id=361
16:18 zarah bug #361 | http://tinyurl.com/d2fosz
16:18 zarah CIA-55's link is also http://tinyurl.com/bbtmrw
16:29 maclean joined #bioclipse
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16:34 _jandar left #bioclipse
16:47 CIA-55 bioclipse: ospjuth * r8558 /bioclipse2/trunk/plugins/ne​t.bioclipse.data.sampledata/ (8 files in 5 dirs): Refactored out wizard to general data plugin. Solves bug #361.
16:47 zarah bug #361 | http://tinyurl.com/d2fosz
17:17 rojasm left #bioclipse
17:43 rojasm joined #bioclipse
17:46 egonw hi rojasm!
17:47 rojasm hi egon
17:49 rojasm With Metware means will you continue working?
17:51 egonw possibly...
17:52 egonw will certainly try to get funding...
17:52 egonw and spend time on it nevertheless...
17:52 egonw but at least keep on working on it for the papers we had/have in mind
17:54 egonw bbl
17:55 rojasm mmm! how was the presentation of Margriet?
18:12 CIA-55 bioclipse: egonw * r8559 /bioclipse2/trunk/cdk-externals/trunk/ (42 files in 42 dirs): No longer includes the bin in the export (fixes #287)
18:12 zarah bug #287 | http://tinyurl.com/dkxhxz
18:37 sneumann joined #bioclipse
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