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

Eric Talevich eric.talevich at gmail.com
Sun Jun 5 18:53:58 UTC 2011

On Sun, Jun 5, 2011 at 12:09 PM, Eric Talevich <eric.talevich at gmail.com>wrote:

> This commit should fix both those issues:
> https://github.com/biopython/biopython/commit/4ce56619cb13e27659927707e2979807d37b26b0
> 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?


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