[Biopython-dev] Bio.Entrez and the depreciated pm* functions

[Peter]

Hi Michiel (et al),

I have a query regarding the transition from Bio.WWW.NCBI to Bio.Entrez

I notice you've marked several of the functions in Bio.Entrez with
depreciation warnings as the NCBI has retired the associated APIs.
i.e. pmfetch, pmqty and pmneighbor  (while the whole of Bio.WWW.NCBI
is deprecated).

Anyone using Bio.WWW.NCBI.pmfetch, Bio.WWW.NCBI.pmqty and
Bio.WWW.NCBI.pmneighbor will get a deprecation warning from
Bio.WWW.NCBI, then if try switch to Bio.Entrez.pmfetch,
Bio.Entrez.pmqty and Bio.Entrez.pmneighbor they still get warnings.

Do you think we can just remove pmfetch, pmqty and pmneighbor from
Bio.Entrez so that it starts out "clean", and adjust the warning from
Bio.WWW.NCBI as follows:

import warnings
warnings.warn("Bio.WWW.NCBI is deprecated. The functions are now
available from Bio.Entrez, except for the pm* functions which the NCBI
have retired.", DeprecationWarning)

What do you think?

Peter