[Biopython] Anyone using the multiple sequence alignment's add_sequence method?
Peter Cock <[email protected]> Fri, 14 May 2021 10:13:26 +0100
| Newsgroups | gmane.comp.python.bio.general |
|---|---|
| Message-ID | <CAKVJ-_4csAwwerOvTgSg+=UhQtuZw8Mj2FU_6Lc47VAqmvWMPA@mail.gmail.com> |
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 _______________________________________________ Biopython mailing list - [email protected] https://mailman.open-bio.org/mailman/listinfo/biopython