[Debichem-devel] Jmol again

[Michael Banck]

Hi,

sorry for the late reply.

On Fri, Aug 20, 2010 at 04:08:14PM +0200, Georges Khaznadar wrote:
> Hello Michael,
> 
> Michael Banck a écrit :
> > On Mon, Aug 16, 2010 at 10:05:03PM +0200, Georges Khaznadar wrote:
> > > I would like to package Jmol, because it would be useful as a
> > > recommended package for two other packages which I maintain: wims and
> > > chemical-structures.
> > 
> > I see wims on packages.debian.org, but not chemical-structures, where is
> > that one maintained?
> 
> chemical-structures was formerly maintained in the non-official
> repository debian.ofset.org. Now I passed my AM, and I began uploading
> it as a NEW package, see
> http://qa.debian.org/developer.php?login=georgesk@ofset.org

You are welcome to team-maintain it in debichem.  We currently support
svn and git as VCSes, though most packages are in svn.  Let us know if
you encounter issues or just drop by in #debichem on irc.freenode.net.

> > I can add you to the alioth debichem team if you tell me your alioth ID,
> > or request to join.
> 
> This login used to be georgesk-guest; now it is georgesk.

I added you now, welcome!
 
> > > However there is a big license issue, as the sources contain a
> > > handful of jars coming from third parties, and only two of them seem to
> > > exist in already available packages.
> >  
> > Which ones?
> 
> Most are in the jars/ subdirectory.
> 
> > So far I succeeded (I think) in building jmol by doing a 
> > 
> > find . -name "*.jar" | xargs rm -f
> > 
> > in the clean target, followed by
> > 
> > ant -Dlib.dir=/usr/share/java -Dvecmath.jar=vecmath.jar
> > -Ditext.jar=itext1.jar -Dcommons-cli.jar=commons-cli.jar
> > 
> > in the build target, using libcommons-cli-java, libjaxp1.3-java,
> > libsaxon-java, libvecmath-java, libitext1-java as Build-Depends, see the
> > above packaging.
> 
> Thank you, I shall watch it carefully.
> 
> > However, there are also a couple of code-drops in the src/ directory
> > which are 3rd party, see below.
> > 
> > The other problem is that jmol's build system seems to combine all those
> > external jars into the main libjmol-java instead of linking to them, and
> > (as I am no Java expert) I have not found a work-around for this yet.
> 
> I am no more savvy in Java. My concern was just to be able to use Jmol as
> a dfsg-free piece of software, and to add features in my maintained
> packages, as they miss them, contrarily to the upstream archives, due to
> license issues.
> 
> > 
> > Anyway, my memory is a bit fuzzy on that as it has been a couple of
> > weeks.
> > 
> > > I saw that the packaging of Jmol had been discussed in the past in this
> > > mailing list. Had some solutions been suggested to package dependencies,
> > > or were some bad licenses discovered in them?
> > 
> > I have been going through them, and so far, I did not find any obviousy
> > non-free licenses.  However, Debconf of sort blocked further movement
> > here.
> > 
> > Personally, I don't think the non-linking of the jars is a very big
> > issue, however it would be nice to fix it.  Unfortunately, squeeze has
> > been frozen since, so we got lots of time to do so...
> 
> Then I suppose that Jmol's package can be released in main. If it is
> possible, please do so, and I will activate again Jmol's support in Wims
> and in Chemical-structures.

I think the way forward is merging what Daniel said he had - I was not
aware of his packaging tree.  Then, we should upload jmol.


Michael