[Biopython-dev] Deprecating Bio.ParserSupport, Bio.Blast.NCBIStandalone

[Wibowo Arindrarto]

Hi everyone,

>> Bio.ParserSupport has had a PendingDeprecationWarning since Biopython
>> 1.59, so we may consider upgrading this to a BiopythonDeprecationWarning in
>> Biopython 1.61 before removing Bio.ParserSupport. The only tricky point is
>> that then we would also have to upgrade the PendingDeprecationWarning in
>> Bio/Blast/NCBIStandalone.py to a BiopythonDeprecationWarning, as that code
>> relies on Bio.ParserSupport. Bio.Blast.NCBIStandalone has had this
>> PendingDeprecationWarning since Biopython release 1.56.
>>
>> Any objections? This may help giving Bow's Bio.SearchIO module some more
>> prominence.
>
> Bow's SearchIO is using Bio.Blast.NCBIStandalone to handle plain text,
> https://github.com/biopython/biopython/blob/master/Bio/SearchIO/BlastIO/blast_text.py
>
> We'd discussed a new parser targeting just the plain text from BLAST+
> (and if not too different maybe the final legacy BLAST release), which
> should be less diverse that the current range of BLAST quirks built up
> over the years.

Yes. Until such a parser is ready, Bio.ParserSupport is still needed.
We may still deprecate it from the visible / public namespace and move
it into a private module, though. If we are also deprecating
Bio.BLAST, then moving Bio.BLAST.NCBIStandalone into a private module
as well seems like an ok fix for the time being.

regards,
Bow