[Biopython-dev] Next release?

[Peter Cock]

On Sun, May 25, 2014 at 2:49 PM, Tiago Antao <tra at popgen.net> wrote:
> 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

Regarding 1 & 2, does the README file cover this now?
https://github.com/biopython/biopython/commit/d60f0fe4445e178f63458eabfdc69f1309a93ddf

Regarding 3, that is up to you. Un-deprecating the code is fine
from my point of view.

Peter