[Biopython-dev] Next release?

[Wibowo Arindrarto]

Hi Peter, Tiago, everyone

I'm almost close to finishing hmmer3.1b1 support in SearchIO. This
includes some updates so that our existing HMMER parsers can handle
the formats released in hmmer3.1b1 and also a new parser for a new
format (pfamtab) that hmmer3 now supports.

Fixes for the existing parser is completed. But for the new parser, I
think I need 2-3 days to finish and polish everything (test cases,
etc).

What do you (and everyone) think about waiting until pfamtab support
is completed? If this is not preferable, I can also push my fixes
without the new parser into our main branch and keep the new parser
for release after this.

Best,
Bow

On Sun, May 25, 2014 at 7:48 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> 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
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