[Biopython] Planning Biopython 1.72

[Peter Cock]

Hi all,

Bow has removed the experimental warning from SearchIO :)

I don't think we're going to make any alphabet changes
for Biopython 1.72, but I would urge people to look at
https://github.com/biopython/biopython/issues/1674 and
https://github.com/biopython/biopython/issues/1681 for
comment.

Separately, I solved why the Tutorial's online Entrez tests
had stopped working. We have to run the online tests
'by hand' since TravisCI and AppVeyor are setup to only
run the offline tests.

The new pairwise alignment module is in, although it needs
a NEWS file entry and some minor tweaks to make its pretty
alignment string output match the rest of Biopython:

https://github.com/biopython/biopython/pull/1655

I'm intending to merge the SeqFeature translation:

https://github.com/biopython/biopython/pull/1509

Thanks everyone who has worked on these changes
and all other others already in the repository - unless
anyone speaks up that could be everything for
Biopython 1.72.

Regards,

Peter

On Tue, Jun 5, 2018 at 9:58 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> Thanks Bow - do you want to do a pull request removing the
> experimental warning (and the bits in the tests to ignore it),
> or should I?
>
> Another interesting proposal is from Michiel about hiding
> the alphabet in the Seq object's __repr__ output:
>
> https://github.com/biopython/biopython/issues/1674
>
> Peter
>
>
> On Mon, Jun 4, 2018 at 10:39 PM, Wibowo Arindrarto <w.arindrarto at gmail.com>
> wrote:
>>
>> Hi Peter, everyone,
>>
>> It's been a while that the warning exists for SearchIO. I think it can
>> be lifted for the next release as I don't expect any major changes to
>> the API anytime soon.
>>
>> The index_db() PR also seems like a good inclusion for the next release.
>>
>> Cheers,
>> Bow
>> On Mon, Jun 4, 2018 at 2:13 PM Peter Cock <p.j.a.cock at googlemail.com>
>> wrote:
>> >
>> > Dear Biopythoneers,
>> >
>> > I am hoping we can release Biopython 1.72 in the next
>> > week or two - mainly so I can include this work in the
>> > Biopython Project Update talk at GCCBOSC 2018:
>> >
>> > https://gccbosc2018.sched.com/
>> >
>> > To that end, are there any outstanding issues or pending
>> > pull requests which we ought to address now? e.g. these
>> > seem worth including:
>> >
>> > https://github.com/biopython/biopython/pull/1655
>> > New pairwise alignment module
>> >
>> > https://github.com/biopython/biopython/pull/1509
>> > Add translate method to Bio.SeqFeature
>> >
>> > https://github.com/biopython/biopython/pull/1619
>> > Preserve on-disk order in SeqIO & SearchIO indexes
>> > (Does anyone want to try benchmarking the changes?)
>> >
>> > Bow - can we remove the experimental warning from
>> > Bio.SearchIO now?
>> >
>> > Thanks,
>> >
>> > Peter
>> > _______________________________________________
>> > Biopython mailing list  -  Biopython at mailman.open-bio.org
>> > http://mailman.open-bio.org/mailman/listinfo/biopython
>
>