[Biojava-l] Increasing Java version requirement for BioJava

Wed Jan 13 13:23:42 UTC 2016

I vote for 1.8.
Moreover, I would like to remember that current snapshot version has API
changes that require a major version increase, according to semantic
versioning. So current GitHub code is 5.0 at my eyes, Do I have miss
something? What is going to be 4.2?

Il mercoledì 13 gennaio 2016, Spencer Bliven <spencer.bliven at gmail.com
<javascript:_e(%7B%7D,'cvml','spencer.bliven at gmail.com');>> ha scritto:

> I don't understand the logic behind requiring 1.7 support for the 4.2
> release. After all, we're not currently using any 1.7 features. I was under
> the impression that we were all discussing changing for the 5.0 release.
>
> -1 to changing away from 1.6 for the 4.2 release
> +1 to jumping to 1.8 for the following release
>
> -Spencer
>
> On Wed, Jan 13, 2016 at 8:08 AM, Steve Darnell <darnells at dnastar.com>
> wrote:
>
>> Hi Andreas,
>>
>>
>>
>> You have my support. That sounds like a fair migration plan. Do you have
>> a goal in mind for when a BioJava 5.0/Java 8 release could take place?
>>
>>
>>
>> -Steve
>>
>>
>>
>> *From:* biojava-dev [mailto:biojava-dev-bounces+darnells=
>> dnastar.com at mailman.open-bio.org] *On Behalf Of *Andreas Prlic
>> *Sent:* Wednesday, January 13, 2016 12:59 AM
>> *To:* Jose Duarte
>> *Cc:* biojava-dev; Biojava-l at lists.open-bio.org
>> *Subject:* Re: [Biojava-dev] Increasing Java version requirement for
>> BioJava
>>
>>
>>
>> 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
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>>
>>
>>
>>
>>
>> --
>>
>> -----------------------------------------------------------------------
>> 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
>> -----------------------------------------------------------------------
>>
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at mailman.open-bio.org
>> http://mailman.open-bio.org/mailman/listinfo/biojava-dev
>>
>
>
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