[Debichem-devel] Will we manage to upgrade jmol

[Andreas Tille]

Hi Ximin,

On Thu, Dec 08, 2016 at 04:08:00PM +0000, Ximin Luo wrote:
> Andreas Tille:
> >     [javac]   first method:  notifyEnabled(CBK) in JmolCallbackListener
> >     [javac]   second method: notifyEnabled(EnumCallback) in MyJmolStatusListener
> >     [javac] Note: /build/biojava3-live-3.1.0+dfsg/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/JmolPanel.java uses or overrides a deprecated API.
> >     [javac] Note: Recompile with -Xlint:deprecation for details.
> >     [javac] Note: Some input files use unchecked or unsafe operations.
> >     [javac] Note: Recompile with -Xlint:unchecked for details.
> >     [javac] 9 errors
> > 
> > BUILD FAILED
> > /build/biojava3-live-3.1.0+dfsg/biojava3-structure-gui/build.xml:73: Compile failed; see the compiler error output for details.
> > 
> 
> This basically means that Jmol changed its API between version 12 and 14. I don't think I messed up the packaging, the missing things like org.jmol.constant.EnumCallback are not even in the current source code.

While I have no idea about BioJava itself I can confirm that BioJava3 is
in (very) low maintenance and has not seen any release for years - so
your explanation sounds quite probable.
 
> Someone will have to go through the changes and make biojava3-live work with Jmol 14 again, this involves Java coding. What I normally do is grep the source code to see if there's anything "similar" in the current source. Or perhaps upstream has a patch, commit, or ticket lying around somewhere where this is already done or half-done.
> 
> To avoid problems like this in the future, it's recommended to only use things that are clearly labeled as public API. The current version of Jmol has a src/org/jmol/api/ directory, perhaps you can edit the currently-failing code to use this instead.
> 
> Or, if it is already an old/abandoned project (I notice that biojava4-live exists too) I suggest to consider just removing it from Debian.

Yes, BioJava 4 exists and is packaged.  Olivier is working on the latest
upstream version - thus I did not tested Jmol with this since the
packaging is currently in flux.  I fully trust Olivier to decide whether
to remove BioJava3 from Debian or whether it is worth to find a solution
for the issue above.  I'd be personally in favour of getting a recent
Jmol and drop BioJava3.
 
> > BTW, if it helps I could migrate biojava3-live from SVN to Git if this
> > might be more convenient for interested people to directly change things
> > in VCS.
> > 
> 
> That would help me if I had time to work on it, but probably not directly on the code, for another few weeks. 

Olivier, if you confirm that it is worth keeping BioJava3 I'd volunteer to
do this.

Kind regards

      Andreas. 

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