[Biopython-dev] Modules to be removed from Biopython

[Peter]

On Jul 22, 2008 Peter wrote:
> 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

I suggest we leave these four modules (Bio.expressions, Bio.config,
Bio.dbdefs and Bio.formatdefs) in for one more release, and then
remove them.

> 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.

I would like to deprecate Bio.Mindy and Bio.builders for the next
release.  Are there any comments - otherwise I'll post a message on
the main discussion list to check no-one objects there.  Should we
push for even more "spring cleaning" for the next release?  Another
candidate for deprecation is Bio.Decode, which doesn't seem to be used
by any of Biopython.

Peter