[Biojava-l] [Biojava-dev] Increasing Java version requirement for BioJava

Wed Jan 13 06:58:57 UTC 2016

I hear a strong wish to upgrade to Java 1.8, but also a few voices about
being a bit more conservative.

On the RCSB PDB production servers we are for now still on Java 1.7.  We
are also re-distributing BioJava via Java Web Start to users out of which
1/4 are still on 1.7 as previously commented.  As such I can't support an
immediate jump to 1.8. However I propose the following procedure for the
next couple of months:

For the upcoming 4.2 release (scheduled for ~mid February) we migrate to
Java 1.7. After the 4.2 release becomes available, the master branch on
GitHub (i.e. the developmental code base) gets scheduled for the next major
5.0 release and starts using Java 1.8.

That way the future 5.0 release will be the first stable release using Java
1.8.  However all the active developers who want to start using the latest
Java features will be able to do so in about a month by using the latest
code from git.

Does this procedure find general agreement?

Andreas

On Tue, Jan 12, 2016 at 5:09 PM, Jose Duarte <jose.duarte at rcsb.org> wrote:

> Thanks Spencer for the nice summary!
>
> I'm going to give my vote to 1.8, because of all the new features and
> because I think we really need to move forward in this one.
>
> I would be in any case ready to compromise in 1.7 if we see that 1.8 will
> really cut off a significant amount of users. With the condition that the
> next release will then go to 1.8.
>
> The only thing I feel strongly against is staying in 1.6. Whatever we do
> we should avoid that.
>
> Jose
>
>
> On Tue, Jan 12, 2016 at 10:06 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
>
>> Based on some RCSB PDB analytics data, I'd estimate that about 2/3 of all
>> users are already on 1.8. However there is still a significant number of
>> users on 1.7 (somewhere around 1/4).
>>
>> As such my vote is to upgrade to 1.7 for now and move to 1.8 at some
>> point in the future, when 1.7 usage has declined further.
>>
>> Andreas
>>
>>
>>
>>
>>
>>
>> On Tue, Jan 12, 2016 at 8:56 AM, Terry Casstevens <tmc46 at cornell.edu>
>> wrote:
>>
>>> Dear Spencer,
>>>
>>> I'm the lead developer for the Tassel software, and we use the Biojava
>>> libraries.  We've required Java 8 for Tassel since August 2014.  If
>>> you change, some users will need to upgrade Java regardless.  I
>>> recommend going to Java 8.
>>>
>>> maizegenetics.net/tassel
>>>
>>> Best,
>>>
>>> Terry
>>>
>>>
>>> On Tue, Jan 12, 2016 at 7:16 AM, Spencer Bliven
>>> <spencer.bliven at gmail.com> wrote:
>>> > There has been some informal discussion of increasing the Java version
>>> > requirement for BioJava from the current Java 6 to either 7 or 8. It
>>> would
>>> > be great to hear from the larger BioJava community about whether this
>>> would
>>> > be a welcome change or not.
>>> >
>>> > I will start the discussion by listing what I see as the pros and cons
>>> of
>>> > setting each version as the minimum requirement for BioJava.
>>> >
>>> > Java 6:
>>> > ---------
>>> > + Greatest backwards compatibility
>>> > - No updates since Feb 2013*
>>> > - Some dependencies are not compatible, requiring the use of older
>>> versions
>>> > (currently only log4j, but could be others in the future)
>>> >
>>> > Java 7:
>>> > ---------
>>> > + Most popular version currently
>>> > + Some minor language features added
>>> > - No updates since Apr 2015*
>>> >
>>> > Java 8:
>>> > ---------
>>> > + Tons of awesome new programming features, e.g. lambda functions
>>> > + Only version supported by Oracle
>>> > - Not available for many systems
>>> >
>>> > * Note that all versions are backwards compatible, so you can always
>>> use a
>>> > more up-to-date JDK for downstream projects. Running outdated software
>>> is
>>> > generally a bad idea, so users are encouraged to use the Java 8 JRE,
>>> > regardless of the minimum BioJava requirement.
>>> >
>>> >
>>> > One thing I would like to get a sense of is how many BioJava users are
>>> still
>>> > using 6 and 7. @emckee2006 mentioned on github that they still have
>>> some
>>> > servers on 6. I know that getting Java 8 installed on CentOS is rather
>>> > painful, so probably some users haven't yet updated to 8.
>>> >
>>> > Let me know if I missed anything!
>>> >
>>> >
>>> > Cheers,
>>> >
>>> > Spencer
>>> >
>>> >
>>> >
>>> > _______________________________________________
>>> > biojava-dev mailing list
>>> > biojava-dev at mailman.open-bio.org
>>> > http://mailman.open-bio.org/mailman/listinfo/biojava-dev
>>> _______________________________________________
>>> biojava-dev mailing list
>>> biojava-dev at mailman.open-bio.org
>>> http://mailman.open-bio.org/mailman/listinfo/biojava-dev
>>>
>>
>>
>>
>> --
>> -----------------------------------------------------------------------
>> Dr. Andreas Prlic
>> RCSB PDB Protein Data Bank
>> Technical & Scientific Team Lead
>> University of California, San Diego
>>
>> Editor Software Section
>> PLOS Computational Biology
>>
>> BioJava Project Lead
>> -----------------------------------------------------------------------
>>
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at mailman.open-bio.org
>> http://mailman.open-bio.org/mailman/listinfo/biojava-dev
>>
>
>

-- 
-----------------------------------------------------------------------
Dr. Andreas Prlic
RCSB PDB Protein Data Bank
Technical & Scientific Team Lead
University of California, San Diego

Editor Software Section
PLOS Computational Biology

BioJava Project Lead
-----------------------------------------------------------------------
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