[Biopython-dev] Bio.utils, Bio.PropertyManager, Bio.Encodings.IUPACEncoding, etc

[Peter]

On Wed, Sep 1, 2010 at 4:38 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>
> For Biopython 1.55 we explicitly declared Bio.utils, Bio.PropertyManager,
> and Bio.Encodings as obsolete. So, what do we do now? I'd like to declare
> them deprecated in Biopython 1.56, and remove them (and Bio.Translate
> and Bio.Transcribe) in Biopython 1.57. This is a quicker removal than usual,
> but I'd argue anyone using these modules would have already been getting
> deprecation warnings about Bio.Translate and Bio.Transcribe anyway.
>

I've marked them as deprecated, with an explicit DeprecationWarning in
Bio.utils, but not for Bio.PropertyManager and Bio.Encodings which would
be triggered by Bio.Alphabet.IUPAC.

http://github.com/biopython/biopython/commit/28a7daeef6ff57979ec08de62777528219976df7

Peter