[Biopython-dev] Modules to be removed from Biopython

[Peter]

>> But, 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
>> 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.
>
> Given some of these are very interconnected, I would be inclined to leave
> them in for one more release.  However I'm content to see them go.  If no
> one else has any  qualms, then please carry on.

Now that Biopython 1.47 is out, its probably time to remove
Bio.expressions (deprecated in 1.44) and explicitly deprecate the
rest:

Bio.builders
Bio.config
Bio.dbdefs
Bio.formatdefs
Bio.Std
Bio.StdHandler
(plus Bio.Writer which is part this "Bioformat" code base?)

The final entry from your list, Bio.FormatIO, has already been removed.

Peter