[Biopython] Anyone using the multiple sequence alignment's add_sequence method?

[Peter Cock]

Hello all,

A long time ago back in Biopython 1.57 (April 2011) the .add_sequence method
of the MultipleSeqAlignment was deprecated, and we thought we removed it
in Biopython 1.69 (April 2017).

However, I messed up, and in the process of removing a legacy base class
left the .add_sequence method alive without a deprecation warning - which
we have only just noticed. Moreover, several of the doctest examples used
the "zombie" method to construct an alignment object in code.

The question now is do we go through the deprecation cycle again (leaving
in in place for at a year and least two releases with a warning), or just delete
the method in the next release?

https://biopython.org/wiki/Deprecation_policy
https://github.com/biopython/biopython/pull/3548

If anyone says they have been using it, we'll go for the (repeat) deprecation
route. Comments here, or on the pull request as appropriate.

Thank you,

Peter