[Biopython] Planning Biopython 1.85

[Peter Cock]

Good news: The Biopython 1.85 release is done (bar the blog post and more
formal
announcement). The updated documentation is live:

https://biopython.org/docs/1.85/

This includes pre-compiled wheels for Python 3.13

Bad news: I couldn't get LaTeX to build the PDF version of the Tutorial as
I managed
for Biopython 1.84 from the Sphinx output. I suspect some package
incompatibility,
but after trying on two machines (one a fresh latex installation, the other
the one I
think I used last time) I gave up. This means there is NO bundled version
of the
Tutorial in the .zip or .tar.gz file this time. It might be worth having a
fresh look at the
PDF options from Sphinx nowadays...

Peter

On Tue, Dec 31, 2024 at 6:55 PM Peter Cock <p.j.a.cock at googlemail.com>
wrote:

> 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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