[Biopython] Planning Biopython 1.72

[Peter Cock]

I'm part way though the release now, and for future reference
I think I would now be able to simplify the build instructions
as well...

The first hurdle is with the wheel building, it looks like I need
to debug this cryptic error:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
AttributeError: 'module' object has no attribute 'version'

https://travis-ci.org/biopython/biopython-wheels/builds/395521793

Depending on the timing, and assuming it works fine which it
should do based on Python 3.7.0rc1, we may later want to add
wheels for Python 3.7 from Biopython 1.72.

Otherwise official support for Python 3.7 will come with the
release of Biopython 1.73 instead.

Peter

On Thu, Jun 14, 2018 at 11:02 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> 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
>>>
>>>