[Biopython] Planning Biopython 1.85

[Peter Cock]

Hello all,

My employer (currently University of Strathclyde) will be shut from next
week
for Christmas, so I am hoping to do the Biopython 1.85 then.

There are a few GenBank issues I want to catch up on, and something breaking
with the recently released NumPy 2.2 - but otherwise I am not aware of any
blocking issues. In particular, in my testing Python 3.13 is fine.

Please let us know if there is something I'm overlooking here. Thanks!

Peter


On Tue, Sep 17, 2024 at 11:47 AM Peter Cock <p.j.a.cock at googlemail.com>
wrote:

> Also, I think Biopython 1.85 should be our last release to support Python
> 3.9 (which we declared deprecated in Biopython 1.84).
>
> One of the small cosmetic advantages of moving to Python 3.10 onward is
> more concise type annotation notation, but I'm sure you all have your own
> favorite new features.
>
> Peter
>
> On Mon, Sep 9, 2024 at 12:55 PM Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
>
>> Dear Biopythoneers,
>>
>> We released Biopython 1.84 at the end of June, so three months later
>> which was our typical cadence in the past would put us due for another
>> release at the end of this month.
>>
>> There are practical reasons to do this too -
>> https://peps.python.org/pep-0719/ - Python 3.13 is being released at the
>> start of October, and there is a minor compilation problem with some of our
>> legacy C code (since addressed) which complicates releasing a Biopython
>> 1.84 wheel for Python 3.13. We can in principle release a Python 3.13
>> compatible release now (compiled against the release candidates ahead of
>> the formal release at the start of October).
>>
>> However, as unfortunately has become common, we have a backlog of open
>> issues and open pull requests. Please speak up with any key issues or
>> overlooked pull requests you think need to be addressed for Biopython 1.85,
>> and if you can help review or tests them, even better!
>>
>> I'd be happy to help a volunteer do the release itself, although I see
>> now that I didn't finish updating
>> https://biopython.org/wiki/Building_a_release alongside doing Biopython
>> 1.84 which changed the way the documentation is built and published. By
>> default, I'll do the Biopython 1.85 release and get that how-to updated.
>>
>> Thank you all,
>>
>> Peter
>>
>>
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