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

[Michiel de Hoon]

Hi everybody,

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.

On a related point, the fact that we are deprecating Bio.ParserSupport (which was a painful process) suggests that having a new module Bio._utils with a set of generic utility functions is not a good idea.

Best,
-Michiel.