[Debian-science-sagemath] Jmol transition?

[Ximin Luo]

I updated libnaga-java to 3.0 in Debian. However Jmol itself is not possible to package.

I've filed a bug about it here:

https://sourceforge.net/p/jmol/bugs/587/

Let's see how they respond...

Also I was wrong about "it hasn't been updated in years", that was just due to debian/watch being out-of-date and not detecting the new versions. Looks like it's still pretty active.

X

François Bissey:
> That package traditionally gave me a lot of troubles. Because
> I am not a java guy and none of my occasional helpers is either.
> As it is jmol has three main elements as I see it 
> jspecview a separate package
> jmol proper
> jsmol a javascript version of jmol produced from jmol.
> Plus some other smaller java dependencies. jsmol as far as I
> can see is difficult to produce from source on linux - I think
> upstream uses a windows program to “compile it”.
> So lately I just shipped jmol as a binary package. 
> 
> François
> 
>> On 22/10/2016, at 06:33, Ximin Luo <infinity0 at debian.org> wrote:
>>
>> Tobias Hansen:
>>> I just realized that Jmol may also need a transition, if we want to
>>> update the package properly. :(
>>>
>>> It has these reverse dependencies:
>>>
>>> # Broken Depends:
>>> biojava3-live: libbiojava3.0-java
>>> biojava4-live: libbiojava4.0-java
>>> jalview: jalview
>>>
>>> # Broken Build-Depends:
>>> biojava3-live: libjmol-java
>>> biojava4-live: libjmol-java
>>> jalview: jmol-applet (>= 12.1.42)
>>>         libjmol-java (>= 12.1.42)
>>>
>>> But somehow I think spending a lot of time working on Jmol would be too
>>> much of a distraction. Can we just bundle the stuff we need with sage?
>>>
>>
>> I have already hacked this into the sagemath package (in sagemath-deps / sagemath-deps-common) but this has zero chance of passing NEW.
>>
>> I have some experience with java packaging, I can try to pick this up over the next week. The good thing is this package hasn't been updated in a few years so at least we're not trying to hit a moving target. The bad thing is this package hasn't been updated in a few years so probably all its dependencies are "too new" now.
>>
>> Andreas, could you tell us some more details that need to be done? Just on a quick build attempt I can see the following:
>>
>> - probably need to do something about that ugly jsmol.zip
>> - build requires you to press <enter>, this can probably easily be fixed
>> - build fails to compile due to (probably) mismatching naga API, more research needed to see if this is easily fixable.
>>
>> I see earlier on in this bug thread other people mentioned jmolspec and jspecview, has that issue been resolved?
>>
>> X
>>
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