Camelia, the Perl 6 bug

IRC log for #cdk, 2010-01-29

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All times shown according to UTC.

Time Nick Message
06:19 egonw joined #cdk
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08:18 CIA-67 cdk: annulen * r15357 /jchempaint/trunk/src/main/org/opensci​ence/jchempaint/JChemPaintPanel.java: Use "Title" property in JChemPaintPanel
08:18 liz1 hi is anybody good at organic chem?
08:18 liz1 im really struggling with a problem
08:18 liz1 helloo??
08:20 sneumann joined #cdk
08:20 CIA-67 cdk: annulen * r15358 /jchempaint/trunk/src/main/org/openscience​/jchempaint/action/ChangeBondAction.java: Removed commented string
08:24 jbrefort joined #cdk
12:29 sneumann joined #cdk
12:48 * egonw turned on RixFM
13:49 markr joined #cdk
13:52 egonw hi markr!
13:52 * egonw is making progress, slowly, but steadily
13:53 egonw I'm working on the IGeneratorParameter patch
13:53 egonw which will phase out the RendererModel to a very large extend
13:53 egonw when those patches are updated, I'll focus on CDK master
13:53 egonw with the MDL stuff first...
13:54 egonw git seems to be smoother now, and splitting up patches does not have to be done manually anymore...
13:55 egonw the 'git mergetool' now sees that files no longer exist, and will directly ask if you want to keep the 'deleted' copy
13:55 egonw which is perfect for the current JCP set up
13:55 markr aha
13:55 markr I'll have a look at the mergetool
13:56 egonw I can highly recommend the combination with kdiff3
13:56 egonw which 'git mergetool' can use as GUI for merging patches
13:56 egonw did I show you kdiff3 when you were in Uppsala?
13:57 markr don't think so
13:57 markr but I have KDE running here..
13:57 egonw http://kdiff3.sourceforge.net/
13:57 zarah egonw's link is also http://tinyurl.com/syxv5
13:57 markr yep, seems to be installed by default
14:10 * egonw is compiling 9-render-impl-extra
14:12 egonw mmm
14:12 egonw what happened to render-impl-awt ??
14:13 egonw grmph... that got lost
14:13 egonw (not the patches, mind you)
14:13 egonw just the alias :)
14:14 * egonw is not please, as this will mess up the numbering :(
14:18 egonw ok, we now have a 9b :(
14:26 markr Sounds confusing !
14:29 egonw ok, almost done
14:37 jbrefort joined #cdk
14:41 egonw ok, done
14:41 egonw uploading to pele
15:05 egonw compiling CDK master
15:05 egonw markr: looking forward to comments from you and Stefan about the design of IRenderingParameter and current implementation in render-api and render-impl-*
15:26 egonw markr: ping
15:26 markr ping pong
15:26 egonw I think I found the cause of the master compile issue: missing patch
15:26 egonw it's a patch by me, small one...
15:26 egonw could you please review?
15:27 markr review how?
15:27 egonw I would email it
15:27 markr ok!
15:30 markr regarding your uload to pele, can we still see that through  http://pele.farmbio.uu.se/g​it/jchempaint-primary.git/ ?
15:30 zarah markr's link is also http://tinyurl.com/l7zegy
15:31 egonw yes, and no...
15:31 egonw different repos
15:31 egonw because of big rebase
15:31 egonw mom...
15:32 egonw http://pele.farmbio.uu.se/cgi-bin/gitw​eb.cgi?p=cdk-jchempaint.git;a=summary
15:32 zarah egonw's link is also http://tinyurl.com/y9hfxqd
15:32 egonw that's the web gui for the new repos
15:32 egonw link:
15:33 egonw http://pele.farmbio.uu.se/git/cdk-jchempaint.git/
15:33 zarah egonw's link is also http://tinyurl.com/ydn95m8
15:33 egonw but hang on
15:33 egonw as I have to update the refs...
15:33 egonw (meanwhile, patch sent...)
15:33 egonw ok, hashes updated
15:34 egonw so easy to forget that :(
15:34 egonw need to add a line in my updatePele script...
15:40 Gpox joined #cdk
15:40 markr I applied your patch, but the compilation error is still there. Compiler doesn't recognize Rectangle2D..
15:42 egonw ah, right...
15:42 egonw that's because there are also a few missing imports :)
15:42 egonw should have mentioned that ...
15:42 egonw but the patch applies cleanly, not?
15:42 markr yes
15:43 egonw do you want me to fix the patch?
15:43 egonw (I can)
15:43 markr yep
15:43 egonw hang on
15:43 markr actually, for our jcp cdk branch we also applied something similar to GeometryTools
15:43 markr there was a whole bunch of lost patches we re-applied
15:44 markr you can find them in our html based repository
15:44 egonw yes, I think this might be one of the rewrites of patches by Stefan
15:44 markr right
15:44 markr the other ones are relevant too I think
15:44 markr well - I put them into our branch anyway
15:45 markr seemed to make jcp applet work better (and compile)
15:45 markr thanks for rewriting it anyway, I'll update our stuff to omit the one you now included in master
15:46 markr have a look at the other ones too if you don't mind
15:52 egonw will do
15:52 egonw was afk to fire up the fire place
15:52 egonw it's getting cold in the house
15:53 markr it's 25 degrees here in the UK
15:53 egonw below zero?
15:53 markr inside, that is
15:53 egonw or inside?
15:53 egonw ah :)
15:53 markr at least the snow is gone !
15:57 slyrus joined #cdk
15:57 egonw :)
15:57 egonw we just had another 30cm Tue :)
15:57 markr is the latest commit you done "Added dependency on IOldChemModelRelay which is needed at this level"
15:58 markr ?
15:58 markr regarding that IRenderingParameter.. which branch do we have to look
15:58 egonw yes, that's the latest patch 6f7dd179894d4aff47944cef124f25525e757ee1
15:59 egonw API for rendering parameters in branch: http://pele.farmbio.uu.se/cgi-bin/​gitweb.cgi?p=cdk-jchempaint.git;a=​shortlog;h=refs/heads/2-render-api
15:59 zarah egonw's link is also http://tinyurl.com/y93mjn4
16:00 egonw markr: new patch sent
16:00 * egonw hates multitasking
16:01 markr markr hates tasking
16:13 egonw markr: got your ebiPatches branch rebased on my master
16:14 markr I suppose the one for GeometrryTools failed though
16:14 egonw yes, but was easy to fix with 'git mergetool'
16:14 * egonw loves git
16:18 markr The patch you sent applies and compilation okay
16:18 egonw ok, please use the --amend --signoff
16:19 markr we would just have to check now which of the other GeometryTools patches should go in
16:20 egonw yes, but we'll run into that at some point anyway
16:20 egonw I'll start at the bottom of your branch
16:20 egonw looking at af0b87ed665cae068e12235ad88d6f2402e16f1d
16:21 egonw which looks good, and applies... now compiling and running tests
16:22 egonw markr: btw, feel free to use String.contains()
16:22 egonw instead of indexOf() != -1
16:22 markr okay
16:22 egonw I think that was introduced in Java5 already
16:22 egonw checking
16:22 egonw Since:
16:22 egonw 1.5
16:22 egonw yep
16:23 markr you could be looking at Stefan's patch btw; even when my name is on there, that could be because I rebased it
16:23 egonw that would normally not change the author's name
16:23 markr nah
16:24 markr it would if there's a conflict.. then I fix it, commit, skip and move on
16:24 egonw related... have a look at --author
16:24 egonw for 'git commit'
16:24 egonw rather useful
16:25 markr check
16:28 egonw let me know when you have the getRectangle2D() patched signed off
16:28 egonw then I can commit to the repos
16:28 egonw 'your' mdl stereo patch is fine AFAICS
16:35 CIA-67 cdk: shk3 * r15359 /cdk-web/trunk/src/ (7 files in 4 dirs): image rendering works
16:43 egonw looks like it worked fine
16:43 egonw pushing to github & sf
16:43 CIA-67 cdk: Egon Willighagen master * rda488c0 / (2 files in 2 dirs):
16:43 CIA-67 cdk: Added a helper method GeometryTools.getRectangle2D() to get the space occupied by an IAtomContainer
16:43 CIA-67 cdk: Signed-off-by: mark_rynbeek <markr@ebi.ac.uk> - http://bit.ly/aXHhhN
16:43 egonw there it is :)
16:49 egonw markr: second patch in the ebiPatches branch is not good
16:49 egonw d4c4a281ccffa432bd26e318af83d36bac1ab47b
16:49 egonw causes 6 failing unit tests in MDLV2000ReaderTest
16:49 egonw investigating...
16:49 egonw but this is what reviewing patches makes so slow...
16:49 egonw too often, they do not work out of the box
16:50 egonw this is the patch:
16:50 markr sloppy
16:50 egonw commit a58db1fd1f62bb15de62e047e00fa717ced60109
16:50 egonw Author: Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>
16:50 egonw Date:   Fri Sep 4 18:04:57 2009 +0100
16:50 egonw MDL reading and writing valency
16:50 egonw in your branch
16:51 egonw at least one test is faulty itself...
16:51 egonw because the patch assumes something about the files (correctly, I think)...
16:51 egonw the file read is not really a MDL V2000 file, but an original MDL molfile
16:51 egonw pre-V2000
16:52 egonw but those tests should be fixed before...
16:52 egonw second failing unit test indicates it is a v2000 file, but not convinced yet...
16:53 egonw third is testing a MDL SD file...
16:53 egonw but still failing
16:53 egonw others are all instances of reportingly V2000, but really pre-v2000, I think
16:55 markr okay
16:55 CIA-67 cdk: mark_rynbeek master * re335bbc / (4 files in 3 dirs):
16:55 CIA-67 cdk: MDL reading and writing and stereo bond types
16:55 CIA-67 cdk: Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net> - http://bit.ly/cwrrZ4
16:57 markr We'll test those MDL patches first, we'll let you know when that's done then
16:57 egonw oh, btw...
16:58 egonw there are several patches by me in your branch...
16:58 egonw if you have reviewed them, please do the --signoff --amend thing
16:58 egonw then I know they are reviewed and can upload them to master
16:58 markr ok
16:58 egonw being in your branch, I assume you already had a look a them anyway
16:59 egonw do you have a unit test for: 6e8daf47116d2f472bb84d86015186ef8639f2e0
16:59 egonw ?
16:59 egonw otherwise, looks fine
17:00 egonw markr: wait...
17:00 egonw just found another patch by stefan, which is related to the failing unit tests...
17:00 egonw oh, bugger
17:00 egonw the above hash is of my version (rebased)
17:01 markr ah I had trouble finding those hashes
17:01 egonw so, rephrasing:
17:01 markr :D
17:01 egonw do you have a unit test for: 9e392e2aacf20047111d8ecdb1d807ca8b9d99ab
17:02 markr right that one
17:02 egonw the commit related to the failing unit tests is:
17:02 egonw f9178941d38e011b9244e2c87526d9b40b7a0d30
17:03 markr 9e392e2aacf20047111d8ecdb1d807ca8b9d99ab: no, don't think there's unit test
17:03 markr it's been a while
17:03 markr without the patch, you get a nullpointer I think
17:03 egonw yes, probably
17:03 egonw I think I saw that bug report
17:07 egonw ok, will report later tonite about the short lines issue...
17:07 egonw want to check up with the specs...
17:07 egonw I was working on a IO patch to support more in-depth error reporting and warning...
17:07 egonw perhaps I can combine things...
17:08 egonw called for dinner now
17:08 egonw bbl
17:08 markr c u
17:29 bag joined #cdk
18:03 CIA-67 cdk: shk3 * r15360 /cdk/branches/shk3-structgen/src/main/org​/openscience/cdk/structgen/deterministic/ (DeterministcGeneratorTest.java DeterministicGenerator.java): JTree based display included
19:02 sneumann joined #cdk
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20:09 CIA-67 cdk: mark_rynbeek master * r354e93f / (3 files in 3 dirs):
20:09 CIA-67 cdk: MDLV2000Reader throws exception for query bond types
20:09 CIA-67 cdk: Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net> - http://bit.ly/9lzoho
20:43 sneumann_ joined #cdk
20:46 CIA-67 cdk: Egon Willighagen master * ra30ca3e / src/test/org/openscience/cdk/t​ools/CDKHydrogenAdderTest.java : Added unit test for adding hydrogens to IPseudoAtom, which current causes a NPE - http://bit.ly/bPDlOH
20:46 CIA-67 cdk: mark_rynbeek master * r7074cf5 / src/main/org/openscience/cdk​/tools/CDKHydrogenAdder.java :
20:46 CIA-67 cdk: CDKHydrogenAdder should not attempt addImplicitHydrogen for pseudo atoms in an atom container
20:46 CIA-67 cdk: Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net> - http://bit.ly/aKe5ut
23:27 CIA-67 cdk: dleidert * r157 /trunk/chemical-mime-data/html_docs/index.html: Added lang and xml:lang attributes. Moved image styling to CSS.
23:30 CIA-67 cdk: dleidert * r158 /trunk/chemical-mime-data/ (ChangeLog html_docs/cmd.css):
23:30 CIA-67 cdk: 2010-01-30 Daniel Leidert <daniel.leidert@wgdd.de>
23:30 CIA-67 cdk:  * html_docs/index.html: Added lang and xml:lang attributes. Moved image
23:30 CIA-67 cdk:  styling to CSS.
23:30 CIA-67 cdk:  * html_docs/cmd.css (p span.sfnet img): Image shouldn't have border.
23:36 CIA-67 cdk: dleidert * r159 /trunk/chemical-mime-data/src/ (Makefile.am chemical-mime-database.xml.in):
23:36 CIA-67 cdk: 2010-01-30 Daniel Leidert <daniel.leidert@wgdd.de>
23:36 CIA-67 cdk:  * src/Makefile.am (XMLLINT_FLAGS): Added --noent switch to resolve
23:36 CIA-67 cdk:  entities.
23:36 CIA-67 cdk:  * src/chemical-mime-database.xml.in (chemical/x-jcamp-dx): Added
23:36 CIA-67 cdk:  specification URL.
23:37 CIA-67 cdk: dleidert * r160 /trunk/chemical-mime-data/ChangeLog:
23:37 CIA-67 cdk: 2010-01-30 Daniel Leidert <daniel.leidert@wgdd.de>
23:37 CIA-67 cdk:  * src/Makefile.am (XMLLINT_FLAGS): Added --noent switch to resolve
23:37 CIA-67 cdk:  entities.
23:37 CIA-67 cdk:  * src/chemical-mime-database.xml.in (chemical/x-jcamp-dx): Added
23:37 CIA-67 cdk:  specification URL.
23:39 CIA-67 cdk: dleidert * r161 /trunk/chemical-mime-data/po/: Ignore .intltool-merge-cache.
23:43 CIA-67 cdk: dleidert * r162 /trunk/chemical-mime-data/ (ChangeLog xsl/cmd_website.xsl):
23:43 CIA-67 cdk: 2010-01-30 Daniel Leidert <daniel.leidert@wgdd.de>
23:43 CIA-67 cdk:  * xsl/cmd_website.xsl (html.content): Added lang and xml:lang
23:43 CIA-67 cdk:  attributes to <html>.
23:43 CIA-67 cdk:  (html.content.table.mime.head, html.content.table.mime.supported)
23:43 CIA-67 cdk:  (html.content.table.mime.unsupported): Some usability improvements.
23:46 CIA-67 cdk: dleidert * r163 /trunk/chemical-mime-data/src/: Ignore src/chemical-mime-database.xml.

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