[Biopython-dev] Next release?

Wibowo Arindrarto w.arindrarto at gmail.com
Mon May 26 15:53:15 UTC 2014


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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