Camelia, the Perl 6 bug

IRC log for #cdk, 2008-09-10

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All times shown according to UTC.

Time Nick Message
01:13 CIA-14 cdk: rajarshi * r12255 /cdk/branches/cdk-1.2.x/src​/main/org/openscience/cdk/ (15 files in 7 dirs): Fixed a bunch of Javadoc errors
01:34 CIA-14 cdk: rajarshi * r12256 /cdk/branches/cdk-1.2.x/src​/main/org/openscience/cdk/ (geometry/GeometryTools.java inchi/InChIGeneratorFactory.java): Fixed a bunch of Javadoc errors, cleaned up code
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06:13 CIA-14 cdk: egonw * r12257 /jchempaint/trunk/src/main/org/openscience/cdk/ (. applications/ applications/swing/ applications/undoredo/): Copied application class from cdk to jchempaint (which will be removed from cdk upon the next merge with the 1.2.x branch)
06:14 CIA-14 cdk: egonw * r12258 /cdk/branches/cdk-1.2.x/src/main/org/ope​nscience/cdk/io/cml/CMLCoreModule.java: Code clean up: new Integer -> Integer.valueOf; some minor JavaDoc cleanup
06:16 CIA-14 cdk: egonw * r12259 /cdk/branches/cdk-1.2.x/ (52 files in 10 dirs): Removed a application classes; they get restored elsewhere at a later stage
06:17 CIA-14 cdk: egonw * r12260 /cdk/branches/cdk-1.2.x/build.props: Removed cdk prefix which gets added anyway
06:18 CIA-14 cdk: egonw * r12261 /cdk/branches/cdk-1.2.x/src/ma​in/org/openscience/cdk/config/ (3 files in 2 dirs): Some Vector -> List cleanup
06:28 carsten joined #cdk
06:34 CIA-14 cdk: egonw * r12262 /cdk/trunk/src/ (39 files in 6 dirs): Updated and added copyright notices to the appropriate classes
06:34 CIA-14 cdk: egonw * r12263 /cdk/trunk/src/main/org/openscience/cdk/is​omorphism/UniversalIsomorphismTester.java: Fixed the return value in getIsomorphAtomsMap. Fixes bug #2028685
06:35 CIA-14 cdk: egonw * r12264 /cdk/trunk/src/main/org/ope​nscience/cdk/RingSet.java: Removed redundant casts
06:35 egonw joined #cdk
06:36 CIA-14 cdk: egonw * r12265 /cdk/trunk/src/ (3 files in 3 dirs):
06:36 CIA-14 cdk: Added a method to IRingSet that allows you to add a single ring to the set.
06:36 CIA-14 cdk: Implemented the method in RingSet and updated the test to properly test for
06:36 CIA-14 cdk: clone, rather than just assertTrue (which was not really a test). Fixes bug
06:36 CIA-14 cdk: #2099919
06:37 CIA-14 cdk: egonw * r12266 /cdk/trunk/src/main/org/ope​nscience/cdk/RingSet.java:
06:37 CIA-14 cdk: Updated the clone method since it was duplicating the rings. This is because
06:37 CIA-14 cdk: IRingSet is a child of IAtomContainerSet so super.clone() already clones all the
06:37 CIA-14 cdk: atom containers in the set. Thus when RingSet copied over all the atom
06:37 CIA-14 cdk: containers, we end up with duplicates.
06:37 * egonw is merging cdk1.2.x/ into trunk
06:38 CIA-14 cdk: egonw * r12267 /cdk/trunk/src/ (3 files in 3 dirs): The commit that added a method to the IRingSet interface to add a single ring was unnecessary since we can use addAtomContainer from the super class to add a single ring. Removed the extraneous method
06:40 CIA-14 cdk: egonw * r12268 /cdk/trunk/src/main/org/ope​nscience/cdk/RingSet.java: Updated Javadocs
06:41 CIA-14 cdk: egonw * r12269 /cdk/trunk/src/main/org/openscien​ce/cdk/interfaces/IRingSet.java: Updated Javadocs
06:43 CIA-14 cdk: egonw * r12270 /cdk/trunk/src/ (7 files in 2 dirs): Added missing unit tests
06:45 CIA-14 cdk: egonw * r12271 /cdk/trunk/src/main/org/op​enscience/cdk/fingerprint/ (4 files): Fixed errors in test annotations
06:46 CIA-14 cdk: egonw * r12272 /cdk/trunk/src/ (2 files in 2 dirs): Added unit test and fixed annotations
06:48 CIA-14 cdk: egonw * r12273 /cdk/trunk/src/main/org/openscience/cdk/ (8 files in 3 dirs): Some PMD code clean up
06:49 CIA-14 cdk: egonw * r12274 /cdk/trunk/src/main/org/openscience/cdk/ (15 files in 7 dirs): Fixed a bunch of Javadoc errors
06:50 CIA-14 cdk: egonw * r12275 /cdk/trunk/src/main/org/openscience/cdk/ (geometry/GeometryTools.java inchi/InChIGeneratorFactory.java): Fixed a bunch of Javadoc errors, cleaned up code
06:51 CIA-14 cdk: egonw * r12276 /cdk/trunk/src/main/org/openscien​ce/cdk/io/cml/CMLCoreModule.java: Code clean up: new Integer -> Integer.valueOf; some minor JavaDoc cleanup
06:54 CIA-14 cdk: egonw * r12277 /cdk/trunk/ (52 files in 10 dirs): Removed a application classes; they get restored elsewhere at a later stage
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09:05 egonw rojasm: ping
09:05 egonw rojasm: git is very good at merging branches
09:05 egonw we can now backport specific patches from trunk to a branch
09:05 egonw and still merge later without to much trouble...
09:07 egonw rojasm, shk3: http://beta.friendfeed.com/ro​oms/chemistry-development-kit
09:07 egonw new bug reports, commit messages and other CDK News goes there
09:08 rojasm Hi egon
09:08 rojasm I see you blog and Christoph about that
09:08 rojasm I have to merge again the last update of Reaction ontologies
09:09 egonw right
09:09 egonw rojasm: I'm moving houses now, so quite distracted...
09:09 egonw but ping me if you need help...
09:09 egonw if I can, I'll help
09:11 rojasm perfect! thanks
09:16 CIA-14 cdk: thomaskuhn * r12278 /cdk-taverna-paper/trunk/cd​k-taverna/bmc_article.tex: Edit the article a bit
09:17 rojasm new member of friendfeed.com/rooms/chemistry-development-kit
09:34 CIA-14 cdk: egonw * r12279 /cdk/branches/cdk-1.2.x/src/main/org/open​science/cdk/controller/UndoAdapter.java: Added missing class
10:51 shk3 rojasm: do you seem my private chat?
10:59 thomas_ku joined #cdk
10:59 thomas_ku moin
11:00 zarah hi thomas_ku
11:21 rojasm hi shk3
11:21 rojasm yes now
12:38 rojasm egonw: the UndoAdapter is missed in trunk too
12:38 rojasm undoAdapter class
13:53 egonw joined #cdk
13:54 jonalv anyone here that's good with maven?
13:55 jonalv or rather: can you help me wioth maven?
13:55 egonw thomas_ku uses maven
13:55 thomas_ku I am here what's the problem?
13:55 egonw jonalv is trying to build cmldom
13:56 egonw which uses maven
13:56 thomas_ku but I have to say the I am not really an expert
13:56 jonalv I have managed to install maven using macports
13:56 egonw maven2, right?
13:56 thomas_ku ok can you do a mvn -version?
13:56 jonalv uhm hang on
13:57 jonalv 1.0.2
13:57 jonalv is that wrong?
13:57 thomas_ku this should give you the mvn version and the java version
13:57 egonw I think so
13:57 thomas_ku not sure
13:57 thomas_ku I am using maven 2
13:57 thomas_ku and get the version number 2.0.8
13:57 thomas_ku so it depends on which version cmldom is using
13:58 egonw all I remember was that maven2 was way better than maven1
13:58 egonw so I assume too much changed between versions
13:58 jonalv okey now I ahve version 2.0.6 too
13:58 jonalv that shoudl work right?
13:58 thomas_ku thats true but maven one is not compatible to maven 2
13:59 thomas_ku I would think so
13:59 jonalv good, what do I do now?
14:00 thomas_ku you have to go the the folder of cmldom where the pom.xml file is located
14:00 jonalv uhm is it now jumbo54?
14:00 thomas_ku this is normaly the root folder of the project
14:00 jonalv |not
14:00 jonalv I thought I where building jumbo
14:00 jonalv not cmldom
14:00 thomas_ku no idea what you want to build
14:01 jonalv but yea I have a pom.xml here
14:01 thomas_ku thats good
14:01 thomas_ku than you can use the "mvn package"
14:01 thomas_ku to build a jar file
14:02 thomas_ku or the "mvn install" to install the builded packge to you local maven repository
14:02 jonalv and it will put the jar file in the current directory?
14:02 thomas_ku it will put the jar file into the target folder I think
14:02 jonalv uhm hang on. My local maven resoitpry? what's this?
14:02 jonalv uhm target folder?
14:02 jonalv and what's that?
14:03 thomas_ku if you do the mvn package maven will create a folder called target within the root folder of the project
14:03 jonalv k
14:03 thomas_ku if you do mvn install maven will install the lip with its configuration files into a local maven repository
14:03 * jonalv is doing the mvn package command :)
14:04 thomas_ku there is a very handy maven book freely available on the web
14:04 thomas_ku mom
14:04 jonalv no no I jsut want the crash course :)
14:05 thomas_ku ok
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14:05 jonalv how big is that book?
14:05 thomas_ku mom
14:06 thomas_ku http://www.i-proving.ca/download/Technologies/Mave​n/Maven+Resources/BetterBuildsWithMaven-1.0.2.pdf
14:07 jonalv 300 pages...
14:08 jonalv uhm might as wwlll buy the book as print that I think :)
14:12 thomas_ku I found the book quite usefull if you want to start using maven
14:12 thomas_ku but you will not need everything from it. It is only interessting if you really want to use maven for your projects
14:13 jonalv I just keep stumbling upon maven for building stuffs...
14:16 thomas_ku I till need some time on the first use of maven to download all the needed libs...
14:16 egonw jonalv: does cmldom not come with an INSTALL describing what you need to do?
14:17 jonalv it doesn't say anything about maven
14:17 egonw jonalv: btw, the current Jumbo basically is a cmlxom (the XOM-based DOM for CML) + extra algorithms (aka the new jumbo)
14:18 egonw this split up is needed to solve a circular dependency
14:18 jonalv egonw: it is jumbo54 I want right?
14:18 egonw not sure
14:18 CIA-14 cdk: egonw * r12280 /cdk/trunk/src/main/org/openscienc​e/cdk/controller/UndoAdapter.java: Added missing class
14:20 egonw bbl
14:20 egonw jonalv: but I think so
14:20 jonalv [ERROR] BUILD FAILURE
14:21 jonalv suprise! :(
14:23 jonalv It complains about not finding org.xmlcml.cml things whcih sort of was what I though I was building...
14:24 jonalv but I am not suprised. This is what always happend when I try using maven.
14:27 thomas_ku no idea why it cant find this things. do you know if these classes are within the project you try to build?
14:27 jonalv no idea actually
14:28 jonalv I am trying to use this as a black box but for the moment it's a broken black box so I guess I will have to open it up soon... :/
14:28 thomas_ku I fear you have to
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16:07 CIA-14 cdk: shk3 * r12281 /cdk/branches/cdk-1.0.x/ (EditorApplet.html build-applet.xml): building applet works with manual indexing. see the build.applet comments for details
16:11 jonalv thomas_ku: I thought you said it would build a jar file for me. I can't find one... :(
16:12 jonalv uhm there it is. Rather Eclipse can't find it... :(
16:15 jonalv no it wasn't there
16:33 jonalv I hate maven... :(
16:52 thomas_ku sorry jonalv
16:53 thomas_ku was away and have to go now
16:53 thomas_ku will be online tomorrow afternoon
16:58 jonalv okey, thanks anyway and see you :)
17:21 jonalv :q
17:21 jonalv >q
17:21 jonalv lol sry
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19:26 CIA-14 cdk: egonw * r12282 /cdk-eclipse/trunk/src/ (8 files in 7 dirs): Initial code for creating eclipse projects
19:59 CIA-14 cdk: egonw * r12283 /cdk-eclipse/trunk/ (5 files in 2 dirs): Wrapped with a Ant build.xml script

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