Re: [Biopython] Planning the Biopython 1.84 release

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I've been working on this (as have Michiel, Jo=C3=A3o, and others), and sti=
ll
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=E2=80=AFPM Peter Cock <[email protected]=
om>
wrote:

> Hello all,
>
> I would have liked to tackle the release sooner, but things have been bus=
y
> at work. However, I will be on leave soon and should be able to tackle th=
e
> 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 interoperabilit=
y,
> 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 test=
s
> in Biopython 1.63 fail. We have addressed those already, and the tests no=
w
> 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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<div dir=3D"ltr"><div>I&#39;ve been working on this (as have Michiel,=C2=A0=
Jo=C3=A3o,  and others), and still hope to do the release very soon.</div><=
div><br></div><div>Touch wood the numpy 2.0.0 work is done. Right now I&#39=
;m fixing a minor regression with the new scipy 1.14.0 release, and hoping =
there are no more surprises!<br></div><div><br></div><div>Peter<br></div></=
div><br><div class=3D"gmail_quote"><div dir=3D"ltr" class=3D"gmail_attr">On=
 Wed, May 22, 2024 at 9:39=E2=80=AFPM Peter Cock &lt;<a href=3D"mailto:p.j.=
[email protected]" target=3D"_blank">[email protected]</a>&gt; =
wrote:<br></div><blockquote class=3D"gmail_quote" style=3D"margin:0px 0px 0=
px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir=
=3D"ltr"><div>Hello all,</div><div><br></div><div>I would have liked to tac=
kle 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 J=
une.</div><div><br></div><div>That will be about six months worth of change=
s, including dropping Python 3.8 support and deprecating Python 3.9 support=
.<br></div><div><br></div><div>It is worth noting this coincides with the r=
elease of NumPy 2.0. We have lots of code using NumPy, including C code, wh=
ich was a major concern as there are C API breakages with NumPy 2.0. Howeve=
r, rather than the full NumPy C API, we&#39;re only using the buffer API de=
signed for interoperability, so I believe that does not affect us. What doe=
s 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.</div><div><br></div><div>Are there any outstanding issue=
s which the community feels need to be addressed prior to our release?</div=
><div><br></div><div>Thanks,<br></div><br><div>Peter<br></div></div>
</blockquote></div>

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