[Biojava-dev] version 3.1.0 plans and deprecation

[Andreas Prlic]

I do like semantic versioning and I believe it would make it easier for
users to understand how significant changes are between releases.

There is nothing preventing us from jumping to "4.0" instead of "3.1" . As
such I'd say let's start to use semantic versioning starting with next
release. This would make the next release the 4.0.0 release.

That leaves the question what to do about your case, where you need to
remove code due to the deprecation of code in an external library. Since we
are making a major version change anyways, let's move forward fast and
delete and replace the related code.

Andreas


On Tue, Apr 1, 2014 at 6:22 PM, Michael Heuer <heuermh at gmail.com> wrote:

> Hello devs,
>
> Biojava has never followed the semantic versioning specification
>
> http://semver.org/
>
> in that MAJOR version is set in stone due to the abandoned biojava2
> effort and binary incompatible changes have been allowed to take place
> between MINOR version changes (and perhaps even between PATCH
> versions, although I'm not sure I can find any examples).
>
> I need to make some changes to the org.biojava3.sequencing.io.fastq
> package, e.g.
>
>
> http://www.biojava.org/docs/api/org/biojava3/sequencing/io/fastq/FastqReader.html#parse(com.google.common.io.InputSupplier,%20org.biojava3.sequencing.io.fastq.ParseListener)
>
> because InputSupplier and related have been deprecated and scheduled
> for removal from Guava.
>
> "This interface is scheduled for removal in June 2015."
>
> http://docs.guava-libraries.googlecode.com/git-history/v16.0.1/javadoc/com/google/common/io/InputSupplier.html
>
>
> 3.0.8 --> 3.1.0 has been proposed because some deprecated biojava3
> code is ready to be removed.  I am wondering how I should coordinate
> the changes to io.fastq, deprecate in 3.0.9 and remove in 3.1.0, or
> deprecate in 3.1.0 and remove in 3.2.0?  Similarly in biojava-legacy,
> deprecate in 1.8.6 and remove in 1.9 or deprecate in 1.9 and remove in
> 1.10?
>
> Or should biojava3 at least move to semantic versioning from this
> point forward and jump to 4.0 instead of 3.1.0?
>
> Thanks,
>
>    michael
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>



-- 
-----------------------------------------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
-----------------------------------------------------------------------