Camelia, the Perl 6 bug

IRC log for #cdk, 2011-09-05

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All times shown according to UTC.

Time Nick Message
03:51 sneumann_ joined #cdk
05:11 egonw joined #cdk
05:27 sneumann_ joined #cdk
07:03 Gpox joined #cdk
08:12 jonalv joined #cdk
11:14 jbrefort joined #cdk
12:22 jonalv egonw: ping
12:23 egonw pong
12:23 jonalv egonw: what is cheminf.bibx?
12:23 egonw see somewhere in cdk/docs
12:24 jonalv egonw: I don't understand
12:25 jonalv there is a doc directory in CDK but I don't understand what in there can help me
12:25 jonalv can't finds a docs directory
12:25 egonw well, the cheminf.bibx file
12:25 egonw cdk/doc
12:26 egonw duh...
12:26 jonalv uhm, okey
12:26 jonalv there si a README file talking about endnote
12:26 jonalv I don't have Endnote isn't that expensive?
12:26 egonw ug... endnote??
12:26 egonw who wrote that??
12:27 egonw I don't have endnote
12:27 jonalv okey so that's okey then.
12:27 jonalv So I should do something here?
12:27 egonw yes
12:28 jonalv like add the ref to the file? :)
12:28 egonw @cdk.cite refers to a bibtex key
12:28 egonw the full entry is in that bibtexml file
12:28 jonalv oh, that's
12:28 jonalv I don't know what that is
12:29 jonalv does, javadoc building read this?
12:29 egonw I'm sure you get it right when you looked at the file
12:29 jonalv What reads this?
12:31 jonalv egonw: I am gonna rebase my branch, is that evil?
12:31 egonw no
12:32 egonw not if you inform people using that branch
12:32 egonw alternatively...
12:32 egonw you create a new branch
12:32 jonalv egonw: consider yourself informed :)
12:32 egonw about what?
12:32 jonalv egonw: the rebase
12:32 egonw (bwahahaha)
12:32 jonalv bah
12:35 jonalv egonw: but cdk cite is a javadoc thing or a class annotation?
12:35 egonw javadoc
12:35 egonw plenty of examples in around in the CDK JavaDoc
12:35 jonalv I can't fint any reference example
12:36 jonalv ah thre we go
12:36 egonw an grep
12:36 egonw man grep
12:37 jonalv I don't know how to use Eclipse search apparently
12:37 jonalv jonalv--
12:43 jonalv egonw: that bibtex file is not in standard bibtex format but some sort of xml. How do I translate from my the bibtex format I downloaded from the publisher into what that file uses?
12:46 egonw look at the content
12:46 egonw it's not any sort of xml... it's bibtexml
12:46 jonalv egonw: you suggest manually?
12:48 egonw that's what I always do
12:48 jonalv oh
12:48 jonalv I see
12:49 jonalv makes me wonder why you are using the xml format in the first place honeslty
12:49 egonw because writing a parser is *much* easier
12:49 egonw I had absolutely 0% interest in writing a bibtex parser
12:50 jonalv well now you have to do it manually everytime you add something new + it's quite a treshold for new developers
12:50 jonalv but yea I sort of see what you mean
12:51 egonw oh, seriously? if a developer cannot edit a plain text file...
12:52 jonalv well, it's not Java, it could be argued to be a completely new language
12:52 jonalv + for some reason Eclipse is not recognising it as XML so I have to this in a standard text editor :(
13:00 jonalv uhm hang on, is "cdk.module a javadoc comment as well?
13:01 jonalv what has that go to do with javadoc?
13:06 egonw 1. class annotation does not end up in the JavaDoc (and users want to know which class is in which jar)
13:06 egonw 2. class annotation did not even exist before we started using cdk.module
13:06 jonalv ah so it's old stuff
13:06 jonalv well I can live with that I guess
13:07 jonalv egonw: I am thinking more about that license
13:07 egonw no, the electrons get refreshed frequently
13:07 jonalv egonw: maybe it's not a good idea to change the license?
13:07 egonw sorry... you're jumping to fast
13:08 jonalv ah, yea they get refreshed but it's like the guards in the Vatican, they get refereshed by yound people but they still were clothes looking the same
13:08 jonalv but we digress
13:08 jonalv egonw: Can a fingerprint in CDK be licensed as public domain?
13:09 jonalv egonw: If so maybe the KlekothaRoth one should be that?
13:10 egonw yeah, I think so
13:18 jonalv egonw: do you know of any other cdk component being licensed as public domain?
13:19 egonw search for MIT
13:19 jonalv egonw: but MIT license is not the same, is it?
13:20 egonw no, different license
13:20 egonw oh, sorry... misread
13:20 egonw specific as pub domain...
13:20 egonw that I am not sure
13:20 jonalv I am jsut wondering about what to write in the header
13:20 jonalv public domain is sort of no copyright at all
13:21 egonw rigth
13:21 egonw so, you only need to make the statement that it is...
13:21 egonw I suggest to copy/paste from the padel website:
13:21 egonw "The source code is released as public domain."
13:21 egonw so, strictly speaking you also remove the (C) Copyrigh bit from the first line
13:21 jonalv yea, fair enough
13:22 jonalv yup
13:22 egonw just list years, author names
13:22 egonw but leaving that line there is fine with me too...
13:22 egonw if you state it is public domain, it will be clear
13:24 jonalv oki
13:30 jonalv egonw: okey, whenever you have some time feel free to have a loog at: https://github.com/jonalv/cdk/tree/KlekotaRoth
13:30 jonalv *look
13:50 egonw OJDCheck results:
13:50 egonw 2  org.openscience.cdk.fingerpr​int.KlekotaRothFingerprinter  26  Missing @cdk.githash tag.
13:51 egonw 1  org.openscience.cdk.fingerpr​int.KlekotaRothFingerprinter  26  No class documentation given.
13:51 egonw 1  org.openscience.cdk.fingerpr​int.KlekotaRothFingerprinter  4900  No documentation given for the method getFingerprint().
13:51 egonw 1  org.openscience.cdk.fingerpr​int.KlekotaRothFingerprinter  4905  No documentation given for the method getSize().
13:51 egonw unit test coverage:
13:51 egonw fingerprint.KlekotaRothFingerprinter#getSize() does not have a test method
13:51 egonw fingerprint.KlekotaRothFingerprint​er#getFingerprint(IAtomContainer) does not have a test method
13:51 egonw fingerprint.KlekotaRothFingerprinter did not have a TestClass annotation
13:51 egonw (may simply be missing @TestMethod|Class annotation)
13:53 egonw and three PMD violations
13:53 egonw ant -Dmodule=fingerprint qa-module
13:53 egonw (so, yes, it compiles fine now :)
13:54 egonw jonalv: I'll leave some comments... on how to address these things
14:05 egonw OK, comments added
17:25 sneumann_ joined #cdk
21:24 CIA-38 cdk: Egon Willighagen cdk-1.4.x * r82c2c4a / src/test/org/openscience/cdk/atom​type/CDKAtomTypeMatcherTest.java :
21:24 CIA-38 cdk: Unit test for one of the current S atom types
21:24 CIA-38 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://git.io/MTiFGw

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