[Biojava-dev] Last call for 3.1.0 release

[Spencer Bliven]

I've submitted a paper on the CE-CP algorithm in the structure module, and
I would like to do a release of the dev-3.1.0 branch to include this. I've
cherry-picked a few bug fixes from the master branch, but left most things
for version 4.0.0. If anyone wants to get any backwards-compatible code
released in this branch, let me know before Monday.

The dev branch doesn't have the maven central configurations, so this will
be a traditional release on github/biojava.org.

-Spencer
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