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

Eric Talevich eric.talevich at gmail.com
Sat Jun 18 19:13:34 UTC 2011

On Sun, Jun 5, 2011 at 4:11 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> 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.
I posted this to the main list about a week ago, and haven't heard anything
since then, so I committed the change:

The new keyword argument names replace the old names in the argument, and
then the old ones reappear at the end of the argument list, with default
values "None". If existing scripts use positional arguments without the
keyword, it will still work fine without triggering a warning; if they use
the old name it triggers a warning.


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