[Biopython-dev] [biopython] Bugfix in test_Phylo; branch length formatter for Newick trees (#7)

Peter Cock p.j.a.cock at googlemail.com
Sun Jun 5 20:11:26 UTC 2011

On Sun, Jun 5, 2011 at 7:53 PM, Eric Talevich wrote:
>> There's an issue with naming -- I called the argument "format_support"
>> because all the other arguments refer to confidence as "support", since they
>> were all copied from Bio.Nexus. The Bio.Phylo Clade attribute this affects
>> is called "confidence", though. It's confusing either way. Thoughts &
>> suggestions?
> To follow up on that last bit, would anyone be opposed to
> deprecating/renaming the other arguments in NewickIO functions to
> change all references from "support" to "confidence"? The keyword
> arguments are a little esoteric, I think; can we try a 1-release (or
> even 0-release) deprecation cycle here?

Do you think you could have both arg names supported in 1.58
(with a deprecation warning if the old names are used)?

If so, and you post this to the main list and get no objections,
I'm open to adding a deprecation warning in 1.58 (which could
be relatively soon, before BOSC/ISMB would be my guess) and
dropping the old names in 1.59.


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