[Biojava-dev] BioJava 3 current status

[Andreas Prlic]

Hi Pedro,


> 1. You mention SVN above, but I also see an active git repository at github.
>   Is that only a mirror, and active development occurs at biojava.org's svn repo?

Yes, git is only a mirror. The main development happens in an ssh
protected SVN, which is replicated onto the anonymous SVN and git
servers (within one hour after a commit).

> 2. Are all non biojava3-prefixed modules in the Maven repository not suitable to use with Biojava 3?
>   Eg., biosql, das, etc.

In an ideal world we would have a clear separation of biojava 3 and
biojava 1.  However the way things are at the present there is some
mix and  there is still legacy code in SVN. e.g. the module "core" is
essentially a lot of biojava1.7. It is up to the module maintainers to
upgrade their code. We will need to take a decision soon if we want to
drop all legacy code from SVN and only support biojava3 based code
from that point on. ( need to do a dependency analysis how many
modules are still depending on the old core).

> 3. Will the Maven repository eventually also host releases, not just snapshots?

yes

>   How far along would a release be?

We have not set a date at the present.  I will write a proposal about
the next steps to the mailing list soon and then this is up for
discussion. Having said this, several people are using the current SVN
checkouts in production environments and what seems mostly missing is
lots of documentation...

> To provide some context, I've started coding on 'Bioclojure', and my strategy is to position my efforts downstream from Biojava (3).

Excellent! Are you planning to add additional functionality or is it
mainly a wrapper for biojava?

> To that end, I'm trying to figure out the best way to pull development snapshots and stable releases from you guys, as well as
> your current state of affairs in the porting of biojava1/biojavax to biojava3.

The automated build system pushes any successful build to

http://www.biojava.org/download/maven/

This means all libraries that are available from there are guaranteed
to pass the junit tests and compile correctly.

Andreas