[Debichem-devel] jmol: diff for NMU version 12.2.32+dfsg2-1.1

[tony mancill]

On Sat, Dec 10, 2016 at 03:38:00PM +0000, Ximin Luo wrote:
> +debian-science-sagemath as well
> 
> Ximin Luo:
> > tony mancill:
> >> [..]
> >>
> >> This upload was rejected due to a lintian error that existed in the
> >> source package before I added the patch.  Since NMUs are supposed to
> >> be very targeted, the rejection puts us in an odd place.  Will the
> >> upload to experimental [1] find its way into unstable before the
> >> freeze, or should I try again with 12.2.32?
> >>
> > 
> > Hi Tony and everyone else I added:
> > 
> > That depends on what DebiChem, Debian Med, and the Debian Java Team collectively want.
> > 
> > jmol has three reverse dependencies. The new upload, jmol 14, breaks all of them.
> > 
> > - biojava3-live can feasibly be dropped from Debian.
> > 
> > - biojava4-live is currently being worked on by the upstream developer. We're waiting to hear back from them.
> > 
> > - jalview's current version doesn't work with jmol 14, but the new version does. I started packaging it, but it adds several other dependencies not in Debian. Most of them seem bio related:
> > 
> >   https://anonscm.debian.org/cgit/pkg-java/jalview.git/tree/debian/TODO
> > 
> >   fr.orsay.lri.varna.*
> >   htsjdk.samtools.*
> >   org.biodas.jdas.*
> >   org.jfree.graphics2d.svg.*
> > 
> > So we have a few options:
> > 
> > 1. Keep everything old in Debian, and SageMath out of Debian stable.
> > 2. Update Jmol in Debian, with a chance of SageMath entering Debian stable, but drop biojava4 and jalview from Debian stable. (They can remain broken in unstable, with a chance of fixing them later, ofc)
> > 3. Update Jmol in Debian, and update biojava4 and jalview as well.
> > 
> > If I work on (3) I don't think I will have any time to properly work on (2), but that is where my main personal interest lies. I'm also wondering what you all prefer, too.

Hi Ximin,

If the consensus is that there is value keeping the old package in
Debian for this release cycle, I think I can work on (1).  The upload
would be the prior NMU + swapping out the JSON library for a non-evil
implementation.  I just did the same port for JabRef (by way of
unirest-java), and it's not too difficult.

Cheers,
tony
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