[Biopython-dev] Code review request for phyloxml branch

[Eric Talevich]

On Mon, Jan 11, 2010 at 6:37 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> 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?

Er, sorry if I jumped the gun. I was eager to get this done before the
semester kicks in... anyway, these are the Git commands I used:

git checkout master
git pull upstream  # remote: biopython master
git checkout phyloxml
git merge master  # check that it merges cleanly
git checkout master
git merge phyloxml  # fast-forward
git push upstream master
git push origin master  # updating my own branches on github
git push origin phyloxml

It looks more reasonable in gitk; maybe the branches will separate
again later on GitHub when they're no longer equivalent, or when I
delete the 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).

I extracted test_Phylo_depend.py from test_Phylo and added tests at
the top level for networkx and either pygraphviz or pydot (since those
are also used by Bio/Phylo/Utils.py).

> 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.

Great, thanks!

Eric