Camelia, the Perl 6 bug

IRC log for #bioclipse, 2011-07-26

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All times shown according to UTC.

Time Nick Message
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07:49 egonw Gpox: I made a few commits to rdf.cquery
07:50 egonw jonalv: the PharmBio book Bioclipse extension → http://pele.farmbio.uu.se/jen​kins/job/bioclipse.pharmbio/
07:50 egonw versioned after the book, like the first extension for the 1.0 book
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07:52 egonw jonalv: ping
07:52 egonw jonalv: did you redo the image in section 5.1.2.1?
07:52 egonw it's wrong
07:52 egonw and must be fixed in 1.1
07:52 jonalv egonw: not seen that no
07:53 egonw I'll run git blame to see who made it... I don't think this is my version...
07:53 egonw too nice arrows :)
07:54 * jonalv doesn't even know what text it is. Only that he hasn't seen it :)
07:55 jonalv egonw: why is there a file named pharmbioCopy.tex?
07:56 egonw dunno
07:56 egonw was wondering too...
07:56 egonw not very version-controlish :)
07:57 jonalv egonw: how do you run blame when using git svn?
07:57 egonw the same
07:57 egonw but it lost history because of the dir rename
07:57 jonalv egonw: but then I have done everything..
07:58 jonalv oh
08:00 egonw patrick
08:00 egonw he did it
08:03 jonalv the copy?
08:03 egonw yeah, the current version
08:03 egonw and there is no source
08:04 jonalv source?
08:05 egonw have to save a bitmap
08:08 * jonalv has no idea what you are talking about now egonw
08:09 egonw no worries
08:10 jonalv egonw: what image are we talking about now?
08:10 egonw [07/26/11 09:52] <egonw> jonalv: did you redo the image in section 5.1.2.1?
08:10 jonalv ah I see, it's the same
08:10 egonw right
08:10 jonalv I understand now
08:11 jonalv is that what Patrik made?
08:11 egonw it seems so
08:11 jonalv I want to draw these sort of images using LaTeX one day
08:11 jonalv there seem to be a package fot it
08:12 egonw I'm fixing the images as bitmap now
08:14 jonalv oki
08:16 egonw btw, are you up in converting to biblatex for 2.0 ?
08:16 egonw there are so many inconsistencies in the biobliogrpahies...
08:16 egonw shall we consider for a sec?
08:16 jonalv hm, I haven't considered it
08:16 egonw biblatex is superior
08:16 jonalv to be honest I am not sure how much work it is
08:17 egonw that's why we consider...
08:17 egonw the .bib files do not change
08:17 jonalv I had some trouble with multiple bib files
08:17 egonw we hack the pharmbio.tex a bit
08:17 egonw and each chapter
08:17 egonw one sec...
08:17 jonalv egonw: have you done it with multiple?
08:17 egonw checking...
08:17 jonalv I am using one big merged one...
08:18 jonalv where I do it
08:18 egonw that we can do too
08:18 egonw \usepackage[style=chem-angew,hyperref,citestyle=n​umeric-comp,articletitle,sorting=none]{biblatex}
08:18 egonw \setlength{\bibitemsep}{0cm}
08:18 egonw \addbibresource{book.bib}
08:19 egonw that's what I have for the CDK book
08:19 jonalv yea I am just using the default style for the moment in mine. I haven't looked into that yet... :)
08:20 egonw I actually want to write a stylesheet for BMC journals...
08:20 egonw does not seem to exist yet
08:20 egonw but no clue when I have time for that :)
08:20 jonalv I just found age 219 in 1.1
08:20 jonalv that is terrible
08:20 egonw :)
08:20 jonalv can you see page 219?
08:21 egonw yeah, I found a few stupid typos in my chapters too yesterday
08:21 egonw mom, checking
08:21 egonw PDF or print?
08:21 egonw ah... 1.1 → PDF
08:21 jonalv pdf
08:21 egonw one sec
08:21 jonalv you were talking about terrible layout. This is what I call terrible layout
08:22 egonw hold on...
08:22 egonw building PDF
08:23 jonalv I hate that our grey boxes aren't floats
08:25 egonw ah, PDF done
08:25 egonw 219 book page...
08:26 egonw or 291th page of the PDF?
08:26 jonalv book page
08:26 egonw Ex 11-4
08:26 egonw yeah, I see it...
08:26 egonw that's ugly indeed
08:26 * jonalv has trouble with the other measurements.
08:27 jonalv there are other things in that chapter that are troublesmoe
08:27 jonalv but I think I have a fix now
08:27 egonw I think those two figures (11.4 and 11.5) should be pulled out of the ex box
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08:27 jonalv but they are part of the example
08:27 egonw so?
08:27 jonalv generally we have trouble with example boxes
08:27 jonalv so they should be in the box
08:28 jonalv the example boxes need a lot of fiddling
08:28 jonalv cause they are n't floats and they contain figures which aren't floats wither
08:29 egonw yeah, at some point I asked on tex.se.net on a good solution... but never got one
08:29 jonalv I can't think of one either
08:30 jonalv it's a complicated mix of floats
08:30 jonalv maybe a godd tex hacker could come up with something
08:30 jonalv does minipages supports floats?
08:30 jonalv I guess not
08:31 jonalv you sort of need connected minipages which support floats
08:31 egonw dunno
08:32 jonalv might be worth offering some points on bounty on such a question...
08:32 jonalv Just need to work on the formuation of the question...
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08:36 egonw Gpox: did olass talk with you about the deadline for the update site, etc?
08:36 egonw because that needs to be ready pretty soon too...
08:36 egonw Gpox: I did see a promising commit about the aggregated update site
08:37 egonw so, it seems you are close
08:37 egonw but the 2.0 book text needs matching updates
08:37 Gpox well it wont install new things
08:37 egonw and that deadline is Sept 1
08:37 egonw how so? what do you mean?
08:37 Gpox No repository found containing: osgi.bundle,net.bioclipse.cdk.j​chempaint.view,2.5.0.qualifier
08:39 egonw so, you mean, the agg update site is up and running, but no one can install anything from it, because this bundle is not found?
08:39 Gpox there is a lot of those lines, so something is wrong
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11:34 CIA-120 bioclipse.statistics: Valentin Georgiev master * rbed1689 / plugins/net.bioclipse.r.business/src/n​et/bioclipse/r/business/Activator.java : increased getJavaScriptRBusinessManager timeout to 60 sec - https://github.com/bioclipse/bioclipse.statistics​/commit/bed168959f91ab3ba82251d5526e0d93d8fe6a3b
11:38 CIA-120 bioclipse.rdf: Egon Willighagen 2.5.x * r50ce86f / (16 files in 3 dirs): Uploaded Pellet bug fix release 2.0.2 (was 2.0.0) - https://github.com/bioclipse/bioclipse.rdf/co​mmit/50ce86fc399dfafa28fdcfeeddd1cbd8433be21e
11:38 CIA-120 bioclipse.rdf: Egon Willighagen 2.5.x * rf23a945 / (2 files in 2 dirs): Factored out the method to convert Jena/SPARQL results into a StringMatrix - https://github.com/bioclipse/bioclipse.rdf/co​mmit/f23a94581e0ce14822eb55247b2dc780387b06d2
11:38 CIA-120 bioclipse.rdf: Egon Willighagen 2.5.x * rcec532a / (5 files in 3 dirs): Use StringMatrix for better integration in Bioclipse - https://github.com/bioclipse/bioclipse.rdf/co​mmit/cec532a69f8807ae49eb3c448b0367e911bdac1a
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12:20 zaetnick egonw: ping
12:20 egonw pong
12:21 zaetnick I updated my repo with the IRBusinessManager stuff
12:22 zaetnick and there is a problem with the net.bioclipse.r.business
12:22 zaetnick Missing Constraint: Require-Bundle:...
12:25 egonw and now?
12:26 zaetnick net.bioclipse.statistics; bundle-version="2.5.0"
12:26 zaetnick and BC starts without R
12:27 egonw please post the full error message to gist.github.com
12:27 egonw it seems to me you need to add a bundle to the deps somewhere
12:29 zaetnick do u mean the output in the eclipse console, because that's all I have
12:30 egonw turn on bioclipse logging
12:30 egonw make sure you have -consoleLog as option at the right palce
12:34 zaetnick well, added the ...statistics plug-in in the Run config and it's solved
12:34 zaetnick 10x
12:36 CIA-120 bioclipse.core: Arvid Berg 2.5.x * r6357bdb / plugins/net.bioclipse.browser.busin​ess/src/net/bioclipse/browser/busin​ess/business/IBrowserManager.java : Fixed javascript documentation for browser.scrapeWebpage - https://github.com/bioclipse/bioclipse.core/co​mmit/6357bdbceaab23efcad2d3a2f2053f5230213cdd
12:36 egonw good :)
12:36 * egonw thinks that the statistics feature may perhaps be part of the core platform ...
13:25 Gpox @tell jonalv This site works http://pele.farmbio.uu.se/buckminster/final/
13:25 zarah Consider it noted.
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13:30 CIA-120 bioclipse.pharmbio: Egon Willighagen master * r76413ed / (34 files in 6 dirs): Added data for the Molecular Descriptors chapter - https://github.com/bioclipse/bioclipse.pharmbio/​commit/76413ed5876f5fdf937e702c100fe45a22bc3ad6
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13:44 CIA-120 bioclipse.statistics: Christian Ander master * rcf38f66 / (6 files in 4 dirs): Added a Preference page - https://github.com/bioclipse/bioclipse.statistics​/commit/cf38f66eaaa79e2798e22f30049a43088a95dd4c
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