[Biopython] Planning Biopython 1.72

[Peter Cock]

Those TODO items have all been done now. I'm proposing
a limited change to the Seq objects' __repr__ method to
hide the alphabet argument if the default was used:

https://github.com/biopython/biopython/pull/1687

Other than that, I think we are ready to do the Biopython 1.72
release...

Peter

On Tue, Jun 12, 2018 at 5:12 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> 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
>>
>>