[Biopython] Planning Biopython 1.85

[Peter Cock]

The NumPy 2.2 issue is solved, and I hope to merge
https://github.com/biopython/biopython/pull/4901 but otherwise is there
anything worth waiting on?

Peter

On Wed, Dec 18, 2024 at 5:15 PM Peter Cock <p.j.a.cock at googlemail.com>
wrote:

> 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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