[Biopython-dev] Modules to be removed from Biopython

[Peter]

On June 27, Michiel wrote:
> ..., there is also a set of interconnected modules where it's not 100%
> clear if they can be removed without causing some surprises:
> Bio.builders
> Bio.config
> Bio.dbdefs
> Bio.formatdefs
> Bio.dbdefs
> Bio.expressions
> Bio.FormatIO  [already deprecated and removed]
> Bio.Std
> Bio.StdHandler
> It is probably OK to remove these, since these were deprecated we did
> not get a barrage of complaints from our users. Personally, I think it is
> important to keep the code base clean, so I am in favor of removing
> these (and see if anybody complains; in that case, we can always put
> these modules back in and make a new release). But I can live with
> keeping these modules for another release round. If anybody thinks
> that that would be better, please let us know.

Bio.expressions was already deprecated, and seems to be a dependency
of the following modules, which I have now explicitly deprecated in
CVS:

Bio.expressions (deprecated in Biopython 1.44)
Bio.config
Bio.dbdefs
Bio.formatdefs
Bio.dbdefs

It probably would be fine to remove these five modules now
(Bio.expressions, Bio.config, Bio.dbdefs, Bio.formatdefs and
Bio.dbdefs), since the indirect warning from Bio.expressions should
have alerted anyone who was using them.  Or we can ship one more
release with them included?

Moving on, Bio.Std and Bio.StdHandler appear to be used by:
- Bio.expressions (deprecated in Biopython 1.44)
- Bio.config (now deprecated in CVS)
- Bio.builders (used by Mindy)
- Bio.Mindy (used by Bio.config which is now deprecated)

As far as I can tell, other historic usage of Mindy (e.g. in Bio.Fasta
and Bio.GenBank) has already been deprecated and removed.  I think it
would therefore also be safe to deprecate these four together
(Bio.expressions, Bio.config, Bio.builders and Bio.Mindy), or start by
deprecating Bio.Mindy on its own.

Peter