[Biojava-dev] version 3.1.0 plans and deprecation

[Michael Heuer]

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