[Biojava-dev] Renaming BioJava3 packages & modules

[Spencer Bliven]

Ok, the groupids seem all be 'org.biojava' now, so that part has already
been fixed. The org.biojava3 versions in my maven repository must have been
old.

However,  the artifactids do still contain biojava3, to match the module
names. So changing artifactids could be another point to add to the list.
IMO, they should match the module names.

On Fri, Oct 10, 2014 at 11:46 AM, Spencer Bliven <sbliven at ucsd.edu> wrote:

> Jose mentioned this a bit in the BioJava 4 release thread, but I think it
> deserves independent discussion.
>
> Due to historical reasons, the 'biojava3' identifier is used in several
> places in the project:
> - Most module names (except integration and protein-comparison-tool)
> - Some maven groupids (integration and biojava3-survival)
> - Most package names (except for parts of biojava3-structure and
> biojava3-structure-gui
>
> Aesthetically it would be nice to remove the 3 from all of these places
> given the plan for frequent major releases. It is simpler to be consistent
> and will prevent future confusion about why biojava v4+ still refers to
> biojava3. That said, there are downsides to the changes:
>
> - Changing groupids will require downstream projects to update their maven
> dependencies (although they have to update version numbers anyways)
> - Changing module names will be a major code rearrangement. It would
> probably require some moderately advanced git wrangling to merge branches
> and uncommitted code to the new master. Eclipse users would probably have
> to update their projects as well.
> - Removing the 3 from package names would require changing imports on all
> downstream projects. It might also cause conflicts with legacy packages
> which would break any projects that tried to include both biojava3 and
> biojava1 (a bad idea to start with, but I know of one case).
> - Changing package names requires carefully updating the Cookbook and
> tutorial by hand
> - All of this requires work from developers which could be better spent
> writing code
>
> My personal opinion: Changing all groupids to 'org.biojava' is a
> no-brainer. Changing module names is fair amount of work for us, but
> doesn't effect downstream projects much and now is the best time to do it.
> Changing package names completely breaks all downstream projects (even if
> it's easy to fix), which isn't worth it. If anyone asks we can just explain
> it's a historical thing.
>
> -Spencer
>
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