Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-04-24

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
01:04 zarah joined #bioclipse
06:53 egonw joined #bioclipse
07:03 Gpox joined #bioclipse
07:10 egonw hi Gpox
07:10 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
07:10 egonw @msg
07:10 zarah egonw: 1 d 16 h 38 m 20 s ago, sneumann said your links in the blog cdk#2 post are https: which require authentication.
07:13 olass joined #bioclipse
07:13 olass moin
07:13 zarah hello olass, you fantastic person you
07:13 zarah olass: You have new messages. Write '/msg zarah @messages' to read them.
07:13 egonw hi olass
07:13 olass @msg
07:13 zarah olass: 16 h 4 m 46 s ago, jonalv said have a look at bug 899
07:13 olass @bug 899
07:13 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=899
07:14 olass @tell jonalv: I have looked at bug 899. It is closed. Do you want me to reopen it?
07:14 zarah Consider it noted.
07:15 rojasm joined #bioclipse
08:10 shk3 joined #bioclipse
08:18 jonalv joined #bioclipse
08:24 masak joined #bioclipse
08:31 shk3 hi uppsala
08:31 egonw hi shk3
08:31 * masak waves from Uppsala
08:31 shk3 how is bioclipse doing?
08:31 shk3 anything I can help with?
08:31 masak documentation.
08:32 shk3 hm
08:32 egonw rojasm: http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=1725
08:32 zarah egonw's link is also http://tinyurl.com/cfpk56
08:32 egonw quote:
08:32 shk3 it's hard to write help for the plugins I didn't do
08:32 shk3 but I will have a look what I could do
08:32 egonw "The WebBook is Open Data which is where the spectra would go first/initially."
08:32 egonw talking about MS spectra
08:32 masak shk3: better to start with things you are familiar with, I think.
08:38 rojasm egonw looks great. But in this case it will be only EI MS spectra, isn't it
08:39 egonw dunno
08:39 egonw I'm right now writing up email to Steve
08:39 rojasm which make sense because it is more reproducible
08:39 jonalv shk3: I am pretty sure that we could use someone testing and hunting/reporting bugs
08:39 egonw rojasm: the ionization potentials you got from NIST WebBook too, right?
08:41 rojasm yes it was
08:41 shk3 how are the job things going?
08:43 jonalv shk3: I am just about to start it. There has however already turned up yet another feature request about them. olass want to be bale to get a callback on partial results for example to show found substructure during the search
08:43 jonalv shk3: so things are still sort of a moving target I would say...
08:43 jonalv they get better and better though :)
08:43 olass jonalv: we could push that to 2.1
08:43 olass if too hard
08:43 jonalv olass: no
08:43 olass ok :)
08:43 * olass is happy if this makes 2.0
08:43 olass that means less changes later
08:44 jonalv olass: I think it's time to do both that and the interface manager seperation now
08:44 olass jonalv++
08:44 jonalv I can imagine not all managers using this in the 2.0 release though...
08:44 olass yup
08:44 olass shk3: we'll have to live with changes now
08:44 olass there is no alternative
08:44 olass do not be upset about this
08:44 olass it is for the benefit of us all
08:45 egonw jonalv: can you give me an update? did you finishd transition of some managers?
08:45 shk3 don't worry
08:45 jonalv egonw: I am working on the gist manager
08:45 olass egonw: let's take this on tues next week
08:45 shk3 I just wait for you to come up with something
08:45 jonalv egonw: see my branch at pele
08:45 olass in a meting
08:45 egonw jonalv: URL?
08:45 egonw jonalv: nvm
08:45 egonw will find it
08:45 olass jonalv, egonw: meeting tuesday is fine with you two?
08:45 olass in the morning?
08:45 egonw olass: yes
08:45 jonalv pele:/var/www/gist/jonalv.gist or something like that
08:45 egonw olass: what about Thu
08:45 egonw ir that a holiday?
08:46 olass ?
08:46 egonw 30 Apr
08:46 olass ah
08:46 egonw burning things
08:46 olass no, don't think thur is holiday
08:46 olass fri is
08:46 egonw oh...
08:46 olass I have not yet decided if I should take thurs off but probably
08:47 jonalv egonw: well put it this way, I won't get much done that day...
08:48 * egonw is invited for burning stuff ... so won't do much either
08:48 egonw other than putting fire to things
08:48 egonw (not sure what those things are)
08:48 egonw because our x-mas tree is long time gone :)
08:48 egonw but don't care either
08:48 jonalv hehe but isn't that at the evening?
08:48 egonw putting fire to things is alwyas fun
08:49 egonw jonalv: no clue :)
08:49 egonw I'm new here
08:49 jonalv I thought it would be...
08:52 sneumann Hi
08:52 zarah hi sneumann
08:52 sneumann [10:43] <olass> jonalv: we could push that to 2.1
08:52 sneumann [10:43] <jonalv> olass: no
08:53 sneumann I remeber a few articles e.g. on lwn.net
08:53 sneumann on development strategies and releases et al
08:53 jonalv sneumann: hi
08:53 sneumann with a few examples:
08:53 jonalv sneumann: okey
08:53 jonalv :)
08:53 sneumann KDE4 broken -> 4.2 usable
08:53 sneumann Python 3.0 broken
08:54 jonalv oh I see...
08:54 sneumann and 3.1 to be release before regular schedule
08:54 sneumann such that 3.1 becomes usable
08:54 sneumann but at least you get 3.0 out of the door
08:54 sneumann and currently the discussion how gnome 3 will do that
08:54 sneumann so my interpretation is:
08:54 sneumann bc2 will be a major change in the architecture
08:55 sneumann so my 2c: get that out of the door rather sooner than later
08:55 sneumann and push these "nice to have" features
08:55 sneumann into 2.1
08:56 sneumann otherwise you'll end up with bc2 beta19
08:56 jonalv okey put it like this then: I am doing this now for the gist manager and the inchi manager in a branch. If they work we merge it into master for the 2.0 release and perhaps redo the cdk manager according to this scheme. If not we put it in 2.1...
08:56 sneumann I have no clue what your're talking about,
08:56 sneumann because Im watching you from very far away
08:57 sneumann which also means that I am not in the position to tell what's right to do
08:57 sneumann but just giving points to think about.
08:57 sneumann to quote some blog I read recently
08:57 sneumann whatever happens at a given time was the right thing(tm)
08:57 sneumann or something like that ...
08:57 jonalv sneumann: No I am probbaly the only one with enough insight in what I am doing. But your point is good and I will try to make sure it's well tested before I merge my branch into master
08:58 sneumann because Im watching you from very far away
08:58 egonw :)
08:58 jonalv anyway I am going to work on this now.
08:58 sneumann where you== whole BC development team
08:58 egonw 2 hours by RyanAir
08:58 jonalv sneumann: so where are you? :)
08:58 sneumann home == www.ipb-halle.de
08:59 sneumann and not BC developer and not even regular BC user
08:59 olass sneumann: thanks for your input
08:59 sneumann but friend of shk3 and egonw and talking about things every now and then
08:59 olass it's valuable
08:59 olass and I completely agree with you
08:59 egonw "and not even regular BC user" *yet*
09:00 egonw I think I'll get sneumann beta testing when I finally get around makin that Metabolomics feature
09:00 sneumann Yes, we were talking about getting features for LC/MS into BC2 (or BC2.1 for that matter ;-)
09:01 sneumann BTW: we're among the people who do XCMS for MS processing
09:01 sneumann which is an R / Bioconductor package
09:01 egonw sneumann: regarding that...
09:01 egonw have you tried running XCMS inside BC2 yet?
09:01 egonw masak: do we have a demo script that takes data from the JS to the R console and back?
09:02 egonw use case is fairly simple:
09:02 masak egonw: no. sounds worthwhile, though.
09:02 egonw 1. store RAW data in a Bioclipse project
09:02 egonw 2. process those files with R console using the XCMS package
09:02 egonw 3. move the extracted MF info to the JS console
09:03 egonw 4. use PubChem/ChemSpider/CDK code to work with the MF info from the JS console
09:03 olass egonw: R connsole is unfortunately broken in release
09:03 masak :(
09:03 jonalv olass: broken how?
09:03 masak I didn't know that.
09:03 egonw masak--
09:03 olass well
09:03 olass I haven't reported it
09:03 egonw ok, ok
09:03 egonw masak++
09:03 olass but please try
09:03 masak :/
09:04 olass I could not say why
09:04 olass masak: have you expoerted bioclipse any time?
09:04 masak olass: no.
09:04 olass if not, I'll take that bug
09:04 olass which I report now
09:05 masak excellent.
09:05 olass (please try in the release and correct me if I'm wrong)
09:05 olass debugging things that fail in release is a pain...
09:05 olass you need to add sysout and export betwen fixing things
09:05 olass no debugging :(
09:05 masak I read this blog post yesterday. http://www.modernperlbooks.com/mt/200​9/04/the-release-candidate-trap.html
09:05 zarah masak's link is also http://tinyurl.com/ckedvp
09:06 masak lots of things relevant for us.
09:06 masak some traps we don't fall into, such as the QA trap.
09:06 masak but that's mainly because we're small and not a company. :)
09:06 egonw hahaha...
09:06 egonw like companies do much better
09:06 egonw Vista :)
09:06 masak that's what I'm saying.
09:07 masak we're avoiding that mistake by not being a company.
09:07 egonw ah, in that way
09:07 egonw we're just delaying ad infinity
09:07 * egonw enjoying messing up yet another language
09:07 masak I'd describe us as "release-averse".
09:30 CIA-73 bioclipse: shk3 * r9917 /bioclipse2/trunk/plugins/net.bioclipse.​nmrshiftdb/src/net/bioclipse/nmrshiftdb/ (2 files in 2 dirs): changed server, corrected typo
09:38 CIA-73 bioclipse: shk3 * r9918 /bioclipse2/trunk/plugins/net.biocli​pse.chemoinformatics/cheatsheets/Gen​eralChemoinformaticsCheatSheet.xml: some typos etc. in the cheat sheet.
09:42 shk3 two questions with respect to jcp:
09:42 shk3 1. There are stil two definitions of the jcp editor in the plugin.xml, one unused, it seems.
09:42 shk3 Shouldn't we just remove the unused one?
09:43 shk3 2. Shouldn't jcp be registered with net.bioclipse.cdk.ui.moleculeType in addition to the types it handles?
09:43 shk3 ok, I go to the look and look for answers when coming back...
09:48 shk3 hm, no answers?
09:50 egonw shk3: about 1, file a bug report for Gpox
09:50 egonw 2: no, don't think so
09:50 egonw because there still is IO involved which the editor must support
09:51 shk3 right
09:51 shk3 but we are not handling quite a few formats which cdk/jcp could handle
09:51 shk3 ok, looking at the formats, I see some problems
09:51 shk3 rxn is in
09:51 shk3 but jcp in bc does not do reactions right now
09:52 egonw rxn should indeed not be there yet
09:52 egonw file a bug report for that
09:59 shk3 ok
09:59 Gpox shk3: about 1. where did you find the second definition?
10:00 shk3 in the plugin.xml
10:00 shk3 line 28
10:01 shk3 just files bug #968
10:01 shk3 files=filed
10:01 shk3 I would love to do the save as dialog
10:01 edrin joined #bioclipse
10:01 shk3 since I think this is really important
10:01 edrin hi
10:01 zarah saluton edrin
10:01 shk3 does anybody have an idea how that can be done?
10:02 shk3 do we need a new dialog
10:02 egonw you'll have to look at the Eclipse dialog sources
10:02 shk3 or can the existing one be changed?
10:02 egonw and start from there
10:02 Gpox there are 5 definitions for JCP-editor, they do nothing yet
10:02 shk3 you mean modifying their source?
10:03 shk3 right, and the first has no content-type associated
10:03 shk3 that was for Gpox
10:03 egonw shk3: metadata tabs specific for a particular format are planned
10:03 shk3 and the four other editor definitions could become one, I think
10:04 shk3 metadata tabs?
10:04 egonw Title:
10:05 egonw Created With:
10:05 egonw Author:
10:05 egonw like the first three lines in MDL molfiles, e.g.
10:06 shk3 in the jcp editor, you mean?
10:06 shk3 ok
10:06 shk3 obviously, you can keep the different editors
10:06 shk3 was just something which came to my mind when looking at it.
10:08 egonw well, there is some controversy here on having multiple editors too...
10:08 egonw so, no worries there...
10:15 CIA-73 bioclipse: shk3 * r9919 /bioclipse2/trunk/plugins/net.biocli​pse.spectrum/src/net/bioclipse/spect​rum/wizards/NewSpectrumWizard.java: explicit instanceof avoids classcastexception
10:18 rednael joined #bioclipse
10:22 rednael [Leander Git] Added a very basic command line wrapper for starting rednael  http://github.com/egonw/rednael/commit/2​ecaea14052f6fee3283a4fe3d20137384e7ec88
10:22 rednael [Leander Git] Ignore autogenerated .class files  http://github.com/egonw/rednael/commit/9​5feab56ac0be2267eb7e8324946203e4121a55a
10:22 zarah rednael's link is also http://tinyurl.com/c9ekm6
10:22 zarah rednael's link is also http://tinyurl.com/def9gg
12:18 CIA-73 bioclipse: carl_masak * r9920 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java:
12:18 CIA-73 bioclipse: [JsConsoleView] double \n between method candidates
12:18 CIA-73 bioclipse: Fixes bug #907.
12:18 zarah bug #907 | http://tinyurl.com/cfe2zm
12:18 masak @pz ignores
12:19 zarah [841] Pasting commands in JsConsole t... http://tinyurl.com/c7z6ua
12:19 zarah [795] Balloon ignores value given for... http://tinyurl.com/cgcwnk
12:19 zarah Entire list at http://tinyurl.com/c8ecqb
12:19 masak @pz //
12:19 zarah [898] Adapt scripts on http://wiki.bi... http://tinyurl.com/cugxk5
12:19 zarah [949] Home link broken                   http://tinyurl.com/d8355h
12:19 zarah [800] Refactor ValidateCMLManager int... http://tinyurl.com/c6u9hj
12:19 zarah [804] Refactor SpectrumManager into t... http://tinyurl.com/d99dnq
12:19 zarah [805] Refactor SpecmolManager into th... http://tinyurl.com/c4yf5o
12:19 zarah Entire list (54) at http://tinyurl.com/cqgnlh
12:40 jonalv joined #bioclipse
12:41 * jonalv hates his computer. Been with the nice admin for an eternity. Now he gave up for today...
12:41 jonalv mac--
12:54 sneumann Hi again,
12:54 sneumann just as further reading here the article I mentioned this morning
12:54 sneumann http://lwn.net/Articles/317900/
12:54 zarah sneumann's link is also http://tinyurl.com/cdr4rx
12:54 sneumann quoting:
12:54 sneumann There are others who argue that the 3.0 series should be abandoned entirely in the near term. Rather than have a 3.0.1 with substantial changes from
12:55 sneumann 3.0—including the incompatible removal of cmp()—3.1 should be released quickly so that it is the release targeted by developers.
12:55 sneumann where "developers" here means "users".
12:55 sneumann So long,
12:55 sneumann Steffen
13:04 egonw :)
13:04 egonw CDK has the concept of developer versions...
13:04 egonw so does Linux
13:04 egonw where 2.odd is developers oriented
13:05 egonw and 2.even is for users
13:05 egonw CDK, likewise, has had 1.0 and 1.2 for users, and 1.1 for developers
13:08 CIA-73 bioclipse: shk3 * r9921 /bioclipse2/trunk/plugins/net​.bioclipse.data.seneca/data/ (4 files in 4 dirs): changed the examples to actually run
14:02 CIA-73 bioclipse: shk3 * r9922 /bioclipse2/trunk/plugins/net.biocli​pse.seneca/src/net/bioclipse/seneca/ (2 files in 2 dirs): the randomstructuregenerator based jobs now actually run. code still ugly
14:18 jonalv bah I am trying to write tests for aop stuff. Not easy... :(
15:16 edrin left #bioclipse
15:27 rojasm left #bioclipse
16:46 * jonalv gives up for today now
16:46 jonalv cya

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary