[Biopython] Planning the Biopython 1.84 release

[Peter Cock]

I am working on the release now, forgot I didn't have LaTeX on this machine
which we still need for a PDF version of the Tutorial (this is the first
release
to use Sphinx and RST for the Tutorial, rather than LaTeX directly).

Please don't update the master branch until the release is done.

Peter

On Wed, Jun 26, 2024 at 11:37 AM Peter Cock <p.j.a.cock at googlemail.com>
wrote:

> I've been working on this (as have Michiel, João, and others), and still
> hope to do the release very soon.
>
> Touch wood the numpy 2.0.0 work is done. Right now I'm fixing a minor
> regression with the new scipy 1.14.0 release, and hoping there are no more
> surprises!
>
> Peter
>
> On Wed, May 22, 2024 at 9:39 PM Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
>
>> Hello all,
>>
>> I would have liked to tackle the release sooner, but things have been
>> busy at work. However, I will be on leave soon and should be able to tackle
>> the Biopython 1.84 in early June.
>>
>> That will be about six months worth of changes, including dropping Python
>> 3.8 support and deprecating Python 3.9 support.
>>
>> It is worth noting this coincides with the release of NumPy 2.0. We have
>> lots of code using NumPy, including C code, which was a major concern as
>> there are C API breakages with NumPy 2.0. However, rather than the full
>> NumPy C API, we're only using the buffer API designed for interoperability,
>> so I believe that does not affect us. What does affect us are changes to
>> the NumPy scalar repr output, which means a lot of the documentation tests
>> in Biopython 1.63 fail. We have addressed those already, and the tests now
>> pass on a recent NumPy v1 and on the v2 release candidate. i.e. I am not
>> aware of any blocking issues relating to NumPy for our next release.
>>
>> Are there any outstanding issues which the community feels need to be
>> addressed prior to our release?
>>
>> Thanks,
>>
>> Peter
>>
>
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