Camelia, the Perl 6 bug

IRC log for #cdk, 2009-04-24

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All times shown according to UTC.

Time Nick Message
01:04 zarah joined #cdk
05:01 bag joined #cdk
05:45 jbrefort joined #cdk
06:53 egonw joined #cdk
07:03 Gpox joined #cdk
07:15 rojasm joined #cdk
07:17 rojasm Hi all
07:17 zarah oh hai rojasm
07:21 rojasm someone knows where is registered the LoggingTool file in cdk
07:23 egonw grep the build/*.javafiles
07:23 rojasm oo thanks egonw
08:07 jpansanel moin moin
08:10 shk3 joined #cdk
08:18 jonalv joined #cdk
08:30 egonw shk3: fixed that launchpad issue
08:31 shk3 thanks
08:31 egonw sorry about that
08:31 egonw was not aware that account expired by default
08:31 egonw it's now set to never expire
09:05 CIA-58 cdk: shk3 * r14564 /jchempaint/trunk/src/main/org/openscienc​e/jchempaint/application/JChemPaint.java: more i18n
09:19 CIA-58 cdk: shk3 * r14565 /jchempaint/trunk/src/main/org/openscience​/jchempaint/dialog/editor/AtomEditor.java: isotope numbers can now also be set via atom dialog
10:18 rednael joined #cdk
12:40 jonalv joined #cdk
13:18 rajarshi joined #cdk
13:19 egonw hi rajarshi
13:19 rajarshi egonw: hi
13:21 rajarshi looks like you had a useful workshop
13:21 egonw rajarshi: which patch contains that EState changes?
13:21 egonw cannot find it...
13:21 rajarshi sorry - something weird happended during pull
13:21 rajarshi i think it's best to use --no-commit with pull, so the merge does not take place
13:22 rajarshi I reran the pull and your patch looks fine - I can go ahead and commit to master (?)
13:22 egonw shit
13:22 egonw wanted to ask about that
13:23 egonw maybe it should go into the nightly project really
13:23 rajarshi hmm, makes sense if it is to be included as part of the nightly build
13:23 rajarshi there's no other use for it, right?
13:23 egonw well, I can imagine it is for use for people with just the project
13:24 egonw like ant -f javadoc.xml html
13:24 rajarshi yeah, that makes sense
13:24 rajarshi then lets place it in master
13:24 egonw yes, the workshop was superb
13:24 egonw not the branch?
13:24 egonw not cdk-1.2.x?
13:24 rajarshi i think master is more suitable - it's totally new feature
13:25 egonw true
13:25 egonw I guess we will have 1.4 before all major API changes...
13:25 egonw with vflib etc too
13:26 egonw maybe that is better than trying to squeeze in too many new features into 1.2
13:26 rajarshi I agree  -1.2 is stable and good
13:26 rajarshi and we had discussed just porting bug fixes into 1.2.x
13:27 egonw and then we can think about how to do major API changes later
13:27 rajarshi right
13:27 egonw that will be in a branch to start with anyway
13:27 egonw ok
13:27 egonw ok, please apply then
13:27 egonw to master
13:29 egonw btw, I just realize a downside of cdk-patches...
13:29 egonw we should discuss them there
13:29 egonw but on cdk-devel
13:29 egonw and only submit reviewed patches there
13:29 egonw or so...
13:29 rajarshi what downside?
13:29 egonw otherwise we have to ask all developers to subscribe to cdk-patches too
13:29 egonw or is that OK?
13:30 rajarshi hmm, good point
13:31 rajarshi I think the idea of sending the final patch to cdk-patches is good - makes life easier for reviewers
13:32 rajarshi also, we should have the protocol to specifically indicate which branch the patch is for
13:32 egonw yes...
13:32 egonw email subject line:
13:32 egonw prepend with [master] or [cdk-1.2.x]
13:32 rajarshi at least somewhere in the mail
13:32 egonw ?
13:33 rajarshi easy to foget that the branch has to be in the subject
13:34 egonw true
13:34 rajarshi so anywhere in the email - saves having to ask
13:34 egonw but same for body of email
13:39 rednael [master] Added links to PMD pages  http://cdk.git.sourceforge.net/git/g​itweb.cgi?p=cdk;a=commitdiff;h=71492​aaba87c58eba2fa417a156e30f1e318cafa
13:39 rednael [master] Added link to JUnit stats  http://cdk.git.sourceforge.net/git/g​itweb.cgi?p=cdk;a=commitdiff;h=d2c5d​a2c8e957a11d30cae1d22e25fdacf7efa78
13:39 zarah rednael's link is also http://tinyurl.com/d8b3sk
13:39 rednael [master] Added list of classes in the module, with links to Nightly@Pele  http://cdk.git.sourceforge.net/git/g​itweb.cgi?p=cdk;a=commitdiff;h=fe51d​197fb7f7bb06761013e19c88fe03c000f05
13:39 rednael [master] Added set up for creating module HTML pages  http://cdk.git.sourceforge.net/git/g​itweb.cgi?p=cdk;a=commitdiff;h=05480​3c5905eb146765e0999766ceb8e2df0d6ef
13:39 rednael [master] Added set up for creating module HTML pages  http://cdk.git.sourceforge.net/git/g​itweb.cgi?p=cdk;a=commitdiff;h=8e183​f959c769bf91e25b136d6ce2d7e737f9554
13:39 zarah rednael's link is also http://tinyurl.com/d6bfcq
13:39 zarah rednael's link is also http://tinyurl.com/dz9c8n
13:39 zarah rednael's link is also http://tinyurl.com/dkcm3d
13:39 zarah rednael's link is also http://tinyurl.com/cv973l
13:39 rajarshi ok, your patches are in
13:44 egonw ah, nice
13:45 egonw rednael in action :)
13:50 edrin joined #cdk
13:50 edrin hi
13:50 zarah saluton edrin
13:51 edrin rajarshi: did finally compile an xws service?
13:51 rajarshi aah, no :(
13:51 edrin i mean, did running one work out
13:51 rajarshi got sidetracked with RDF & SPARQL
13:51 edrin ah ok
13:51 edrin ok
13:57 rednael [master] Merge branch 'master' of ssh://egonw@cdk.git.sourceforge.net/gitroot/cdk  http://cdk.git.sourceforge.net/git/g​itweb.cgi?p=cdk;a=commitdiff;h=0b67a​53c7762c431595ac6b6d9b195ac0e62a045
13:57 rednael [master] Added unit test for bug 1579235, which checks for aromaticity in indolizine  http://cdk.git.sourceforge.net/git/g​itweb.cgi?p=cdk;a=commitdiff;h=4f90d​ada96f58e93fd9182028b5c4643a77ba9e8
13:57 zarah rednael's link is also http://tinyurl.com/dayuch
13:57 rednael [master] Updated code to use 1.5 idioms and remove use of Iterator  http://cdk.git.sourceforge.net/git/g​itweb.cgi?p=cdk;a=commitdiff;h=51ad2​b65b82409cd92c09ed3f1c29880beba94a1
13:57 rednael [master] Updated build system to take into account non public classes as well. Also updated...   http://cdk.git.sourceforge.net/git/g​itweb.cgi?p=cdk;a=commitdiff;h=9b379​db0874f487c7dd17302ab883c252bfa1da7
13:57 zarah rednael's link is also http://tinyurl.com/d7dcoe
13:57 zarah rednael's link is also http://tinyurl.com/cbx6wm
13:57 zarah rednael's link is also http://tinyurl.com/djzjb3
14:07 egonw rajarshi: I see three Rajarshi patches on SF master now
14:08 rajarshi rajarshi: right, those correspond to the 3 patches I attached to the mail
14:09 rajarshi actully I only see 2 followed by a merge
14:09 egonw a bit further down is the other
14:09 egonw that's I think because I forgot the rebase
14:10 rajarshi aah, got it
14:10 rajarshi so the patches I inlcuded links for haven't made it in, right?
14:10 egonw and then it probably uses data to see what order to apply the patches
14:10 egonw I commented on one patch
14:10 egonw miguel on another one
14:10 egonw and there was one duplicate AFAICS
14:11 egonw the one which fixed the MakeJavaFilesFiles
14:11 rajarshi your email said that http://rguha.net/tmp/0001-Converted-cdk.​svnrev-tags-to-cdk.githash-tags.patchwas applied?
14:11 zarah rajarshi's link is also http://tinyurl.com/df3vg5
14:11 egonw no, not that one...
14:11 egonw grmph...
14:11 egonw mom
14:12 egonw my bad
14:12 egonw that explains the duplicate
14:12 egonw I had been looking at attached #1 twice
14:12 egonw sorry about that
14:13 rajarshi np
14:13 rajarshi so just to be in sync
14:13 rajarshi patch links 1 and  2 are yet to be applied, right?
14:14 egonw yes
14:14 egonw so does 3
14:15 rajarshi well, we decided to drop 3, since it's actually not an SVN change
14:17 egonw ok
14:17 egonw rojasm: please see rajarshi reply to your question
14:24 shk3 does anybody know if the IteratingMDLReader is supposed to read sdf properties?
14:26 egonw it is
14:26 egonw (supposed to)
14:26 shk3 hm, looking at code it looks like only the first one is read
14:26 shk3 I am looking into that
14:26 shk3 the chebi people are having trouble
14:30 egonw checking
14:30 shk3 ah no
14:30 shk3 looks good
14:31 shk3 problem seems to be in the file
14:32 egonw confirmed
14:32 egonw wrote a unit test and no fail
14:34 egonw patch send to cdk-devel
14:45 egonw http://depth-first.com/articles/2009​/04/24/the-first-inchikey-collision
14:45 zarah egonw's link is also http://tinyurl.com/crb9ow
14:46 egonw ah...
14:46 egonw not really one found :(
14:47 egonw rajarshi: your latest email is a third patch in the svn/git javadoc tag series?
14:48 egonw will apply them
14:48 * egonw is looking that Mark's AllRingFinder patch
14:48 rajarshi correct
14:48 rajarshi apply it last
14:48 de__maas joined #cdk
14:50 egonw rajarshi: after pulling someone's patch to a local branch of master
14:50 egonw ... it can help to do a rebase master directly after that
14:50 egonw or did we say that already?
14:50 egonw we did...
14:50 rajarshi yes
14:50 egonw nevermind
14:50 rajarshi and then co master and pull from the local branch
14:50 rajarshi btw, was your sdf unit test for master? or 1.2.x?
14:51 egonw grmph :)
14:51 egonw 1.2.x
14:51 rajarshi ok
14:51 egonw sorry
14:54 rajarshi rebase update. The correct sequence of actions for a given patch is:
14:54 rajarshi # on branch 1.2.x
14:54 rajarshi git checkout -b newPatch
14:54 rajarshi git am -s patch_file
14:54 rajarshi git checout 1.2.x
14:54 rajarshi git rebase newPatch
14:56 egonw sure?
14:56 egonw rebase cdk-1.2.x on the patch?
14:56 rajarshi yes
14:56 egonw yeah, possible
14:56 rajarshi rebase the patch on cdk-1.2.x says that everything is upto date
14:57 egonw ic
14:59 rednael [cdk-1.2.x] Added a unit test to ensure SD fields are read for all molecules  http://cdk.git.sourceforge.net/git/g​itweb.cgi?p=cdk;a=commitdiff;h=989bf​872b8b83e44a7424c504b14c74302f83c09
15:00 zarah rednael's link is also http://tinyurl.com/d8qa9h
15:00 rajarshi do you know how to remove a head from SF? I add one (cdk.1.2.x by mistake)
15:02 rednael [master] Merge branch 'cdk-1.2.x'  http://cdk.git.sourceforge.net/git/g​itweb.cgi?p=cdk;a=commitdiff;h=a7687​3ade0875f4859a1fe7dc4f5f1bd0161fc2f
15:02 rednael [master] Added a unit test to ensure SD fields are read for all molecules  http://cdk.git.sourceforge.net/git/g​itweb.cgi?p=cdk;a=commitdiff;h=989bf​872b8b83e44a7424c504b14c74302f83c09
15:02 rednael [master] split up test  http://cdk.git.sourceforge.net/git/g​itweb.cgi?p=cdk;a=commitdiff;h=8ed3f​fdd1f623fbac13c1af545811a6bf1cf7a65
15:02 zarah rednael's link is also http://tinyurl.com/c4566z
15:02 rednael [master] new files  http://cdk.git.sourceforge.net/git/g​itweb.cgi?p=cdk;a=commitdiff;h=ca9cd​9d151c1c58941000d81f83b2e3a23be19de
15:02 zarah rednael's link is also http://tinyurl.com/d8qa9h
15:02 rednael [master] more tests for cml reading  http://cdk.git.sourceforge.net/git/g​itweb.cgi?p=cdk;a=commitdiff;h=43eca​b43550141eeb3bf8d9e47c9abf09183680b
15:02 zarah rednael's link is also http://tinyurl.com/csmt3l
15:02 rednael [master] Added unit test for #1848591: incorrect Murcko framework  http://cdk.git.sourceforge.net/git/g​itweb.cgi?p=cdk;a=commitdiff;h=f4cf3​8a066471e52f20fab892f9f29fd025105a6
15:02 zarah rednael's link is also http://tinyurl.com/d3lgxu
15:02 rednael [master] Fixed cast, remove redundant full package name  http://cdk.git.sourceforge.net/git/g​itweb.cgi?p=cdk;a=commitdiff;h=bd26c​b09c860eba066cdd39e118fb53b45887321
15:02 zarah rednael's link is also http://tinyurl.com/cutra7
15:02 rednael [master] Added unit test for #2692107  http://cdk.git.sourceforge.net/git/g​itweb.cgi?p=cdk;a=commitdiff;h=46d9d​c934c3be598279be5316a381690263a3831
15:02 rednael [master] Fixed typo: missing 's'  http://cdk.git.sourceforge.net/git/g​itweb.cgi?p=cdk;a=commitdiff;h=f68be​1abc61099e2409e531816d3b353dc198afd
15:02 zarah rednael's link is also http://tinyurl.com/dcus8o
15:02 zarah rednael's link is also http://tinyurl.com/dzzskz
15:02 zarah rednael's link is also http://tinyurl.com/da5m8p
15:02 zarah rednael's link is also http://tinyurl.com/ctux2a
15:04 shk3 egonw: we should add a comment to the iteratingMDLReader that it reads sdf properties into molecule properties.
15:04 shk3 right now, this is not clear from javadoc, as far as I can see.
15:11 rajarshi egonw: is the threading patch for 1.2.x? or master?
15:11 egonw 1.2.x
15:11 rajarshi ok
15:11 egonw so, needs another reviewer
15:12 egonw shk3: ummm... yes, we could add that
15:12 egonw shk3: curious...
15:12 egonw where would one be looking otherwise?
15:12 egonw doesn't it make sense ot have molecular properties in IMolecule.getProperties() ?
15:12 shk3 hä?
15:12 shk3 that's how it's done, isnt't it?
15:13 egonw AFAIK
15:13 egonw but why is that confusing?
15:13 shk3 oh, not at all
15:13 shk3 just not every user might know
15:14 shk3 but more important would be that properties are read at all
15:14 shk3 and then it's easy to say where they are read to
15:14 shk3 isn't it?
15:15 egonw yes, sounds fine
15:16 edrin left #cdk
15:20 rajarshi egonw: trying to pull the threading branch. says an't find remote 8-threadingTag
15:20 egonw confirmed
15:20 egonw mom
15:21 egonw fixed
15:21 egonw sorry
15:22 rajarshi ok got it
15:22 egonw ok, will do some house holding now
15:22 egonw but slowly this whole patching things is getting easier
15:23 rajarshi svn was the dark ages :)
15:23 egonw hehehe
15:23 egonw ok, bbl
15:27 rojasm left #cdk
15:43 egonw back
15:44 rajarshi commented on the threading tag patch
15:44 egonw and I replied
15:57 egonw dinner time
15:57 egonw rajarshi: I reviewed your pcore patch
15:57 egonw comments in patch tracker
15:57 egonw bbl tonite
15:58 rajarshi thanks
16:02 de__maas left #cdk
18:05 bag joined #cdk

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