[Debian-science-sagemath] jmol: diff for NMU version 12.2.32+dfsg2-1.1

[Ximin Luo]

+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.
> 
> X
> 

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