[Biopython-dev] Deprecated code

[Peter]

On Sat, Aug 28, 2010 at 1:21 PM, Michiel de Hoon wrote:
> I finished adding the deprecation warnings and removing deprecated
> code as discussed, except for these three:
>
> Bio.Transcribe
> Bio.Translate
> BioSQL.BioSeqDatabase.open_database: driver="psycopg" option
>
> For last one, I wasn't sure how to appropriately remove this option from
> the code. Maybe somebody more familiar with BioSQL can take care of this?

I could do that - or maybe Cymon if he has time.

> For Bio.Transcribe and Bio.Translate, it turned out that Bio/Encodings
> /IUPACEncoding.py still use these modules. I don't know if
> Bio.Encodings.IUPACEncoding is still being used. It's only imported
> from Bio.Alphabet.IUPAC, but it doesn't seem to be actually used there.
> Bio.Encodings itself is not being imported anywhere in Biopython.
>
> Can we declare Bio.Encodings obsolete? Or can we just remove this
> module together with Bio.Transcribe, Bio.Translate?

This is also tied in with Bio.PropertyManager and thus Bio.utils - it
is probably best to mark these and Bio.Encodings as obsolete, leave
Bio.Transcribe and Bio.Translate as deprecated, and review this after
Biopython 1.55 is out.

Peter