[Biojava-dev] Increasing Java version requirement for BioJava

Wed Jan 13 08:41:03 UTC 2016

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
> -----------------------------------------------------------------------
>
>
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> 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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