[Biopython-dev] Next release?

[Tiago Antao]

On Sun, 25 May 2014 14:28:11 +0100
Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Sun, May 25, 2014 at 1:47 PM, Tiago Antao <tra at popgen.net> wrote:
> Probably yes, but it has shown us some gaps in test coverage. Apart
> from the strings/unicode issues in Bio.Phylo, what is worrying you?


1. Regarding Bio.Phylo - I have not much to say in terms of "worrying".
I do not use the module, I cannot assess of the importance of the
remaining issues. What I can say is this (which is completely
unrelated to releasing a new version):
    NetworkX depends on modules (for graphviz rendering) that are not
python 3 compatible. Things seem to be a mess on that front. I think I
will spend some time digging down on the projects that are still not
python 3 compatible. Yes, there are pygraphviz and pydot versions for
Python3, but they simply crash/fail/throw exceptions with Phylo (I am
strongly convinced that this is not a Phylo problem). So, given that I
have spent so much time converting projects for 2 to 3, I will track
this down as it might not be very complicated for me.
    Again, this has nothing to do with biopython or biopython
releasing. Just something elsewhere that needs to be sorted out for
proper Phylo support on 3.

2. Regarding BioSQL. I think it is great that we now support MySQL on
Python 3 also. Maybe, after this release, we can think of deprecating
MySQLDB??

3. What worries me is that I have had a few reports that fastsimcoal2
might not approximate the same results as simcoal2 for unlinked
markers. So, I am considering proposing the undeprecation of the
simcoal2 code (and re-instating the test also)...

Your Python 3 zealot (ex-Jython zealot),
Tiago