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

[Ximin Luo]

+Vincent, the jalview maintainer

Andreas Tille:
> On Sat, Dec 10, 2016 at 03:37:00PM +0000, Ximin Luo wrote:
>> [..]
>>
>> 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.
> 
> I have asked Olivier about this.
> 
>> - biojava4-live is currently being worked on by the upstream developer. We're waiting to hear back from them.
> 
> Olivier has just uploaded a recent BioJava 4 version.  I think this one
> should be kept in Debian in any case.
>  
>> - 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:
> 
> From my *personal* and *uneducated* view its better to have a recent
> Jmol than an outdated Jalview.  While having also an updated Jalview
> would be the optimal approach I'm not sure (in other words I doubt)
> whether we will manage to package the missing dependencies:
>  
>>   https://anonscm.debian.org/cgit/pkg-java/jalview.git/tree/debian/TODO
>>
>>   fr.orsay.lri.varna.*
>>   htsjdk.samtools.*
> 
> This should be inside the libhtsjdk-java package.
> 
>>   org.biodas.jdas.*
>>   org.jfree.graphics2d.svg.*
>>

>From popcon:

600 https://qa.debian.org/popcon.php?package=jmol
300 https://qa.debian.org/popcon.php?package=jalview
70 https://qa.debian.org/popcon.php?package=biojava4-live
90 https://qa.debian.org/popcon.php?package=biojava3-live

>> So we have a few options:
>>
>> 1. Keep everything old in Debian, and SageMath out of Debian stable.
> 
> No.
> 

Thanks for this input, I also feel it doesn't make sense to add software that is already 4 years old to Debian stable, where newer versions exist. They will be 6 years old by the time a new stable comes out, the value to users would be very low.

>> 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.
> 
> 4. Update Jmol in Debian, and update biojava4 and drop outdated jalview
>    (by at least starting the new dependencies and trying to upgrade
>    jalview) and have the chance of SageMath entering Debian stable.
>  
>> 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.
> 
> May be 4 is a sensible compromise if we could live with backporting
> the latest version of Jalview later.
> 

I agree and I'll be happy to move forward on this. Reminding everyone of the release schedule: https://lists.debian.org/debian-devel-announce/2016/11/msg00002.html

- The deadline for packages-in-testing to be updated by a newer unstable version is ~Jan 25
- The deadline for new packages to enter testing, is ~Dec 25.
  - This includes packages that are in unstable, that were/will removed from testing for QA reasons. (e.g. Jmol 12)
  - This also includes time passing through the NEW queue, for new packages.

In summary:

- Jmol 14 must be uploaded to unstable by ~Dec 25
- biojava4, jalview must be uploaded to unstable by ~Jan 25
- jalview's extra dependencies must be uploaded to unstable (NEW) by ~Dec 20 or ideally earlier, to give FTP masters a few days to process it.

So it's much harder to make this work for jalview. Apologies in advance to any jalview Debian stable users that might be reading this.

X

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