[Biopython-dev] Code review request for phyloxml branch

[Peter]

On Sun, Jan 10, 2010 at 10:02 PM, Eric Talevich <eric.talevich at gmail.com> wrote:
>
> OK -- I pulled the latest from biopython/biopython on GitHub, merged
> my phyloxml branch into my master branch, and pushed it all back to
> biopython. Bio.Phylo is now part of Biopython!

Wow - that was quicker than I expected. As an aside, do you know
why there seem to be three main branches in the history now?
I guess this was the "original" master, your local master, and your
phyloxml branch?

One minor thing - test_Phylo.py needs to be tweaked to raise a
MissingExternalDependencyError if NetworkX isn't installed. That
way the run_tests.py script will treat it as a skipped test instead of
a failed test. Alternatively, if this is just a small part of the test,
maybe split test_Phylo.py into two files (e.g. add a new file
test_Phylo_NeworkX.py which needs the dependency).

And how's this for a draft entry in the NEWS file?

New module Bio.Phylo includes support for reading, writing and working with
phylogenetic trees from Newick, Nexus and PhyloXML files. This was work by
Eric Talevich on a Google Summer of Code 2009 project, under The National
Evolutionary Synthesis Center (NESCent), mentored by Brad Chapman and
Christian Zmasek.

Peter