[Biopython] Planning Biopython 1.85

[Peter Cock]

We now have Python 3.13 versions on conda-forge as well (needed an extra
step I had
forgotten about), along side Python 3.9, 3.10, 3.11 and 3.12 which where up
the same
day.

Peter

On Wed, Jan 15, 2025 at 3:27 PM Peter Cock <p.j.a.cock at googlemail.com>
wrote:

> 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
>>>>>
>>>>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20250119/5edf0e49/attachment.htm>