[Biojava-dev] Renaming BioJava3 packages & modules

[Jose Manuel Duarte]

> No, the pain is actually in the future.
>
> Consider:
>
> Project a has a dependency on biojava-legacy version 1.9.1, package
> names org.biojava.*
> Project b has a dependency on biojava3 version 3.1, package name also
> org.biojava3.*
> Project c has a dependency on projects a and b
>
> Project b updates their dependency on biojava3 to version 4.0, which
> doesn't necessarily mean a binary incompatible change for project b,
> but it means the transitive biojava3 packages are now org.biojava.*,
> same as biojava-legacy
>
> Project c now runs into RuntimeExceptions because some biojava3
> version 4.0 class clobbers a biojava-legacy version 1.9.1 class.

Alright, that is indeed a problem. So it means that for the new release 
we can't reuse any namespace ever used before.

>
> Commons Math and Commons Collections are other projects that have had
> to deal with this
>
> http://commons.apache.org/proper/commons-math/
> http://commons.apache.org/proper/commons-collections/
>
> Rather than move from package names org.biojava3 --> org.biojava
> perhaps we should consider going from org.biojava3 --> org.biojava4.

Instead of keeping a 3 or a 4, how about we use a new namespace, not 
used before and that doesn't refer to the release number?

If I understand it correctly, legacy was using:

org.biojava.bio.* and org.biojava.*

then Biojava 3 was using:

org.biojava3.* and org.biojava.bio.* (only in the structure module)

So there's not much left, but we could be creative for Biojava 4 and 
successors, some possibilities:

org.biojava.plus
org.biojava.obf
org.biojava.open
org.open-bio.biojava
org.obf.biojava
org.nbiojava
org.biojava.next
org.biojavaplus
org.biojava.bj


Or of course stay with the status quo and keep the 3 forever. I'm happy 
to compromise there, but surely one issue would have to be solved if 
taking that route: the structure module packages org.biojava.bio.* 
should be renamed to org.biojava3.* to be consistent. Also the tutorial 
would still need to be fixed in order not to mention Biojava 3, while 
explaining why the packages have the "3" in the name anyway.

Jose