[Biopython] Planning the Biopython 1.84 release

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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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<div dir=3D"ltr"><div>Hello all,</div><div><br></div><div>I would have like=
d 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.</div><div><br></div><div>That will be about six months worth o=
f changes, including dropping Python 3.8 support and deprecating Python 3.9=
 support.<br></div><div><br></div><div>It is worth noting this coincides wi=
th 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&#39;re only using the buffe=
r 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 mean=
s a lot of the documentation tests in Biopython 1.63 fail. We have addresse=
d 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 N=
umPy for our next release.</div><div><br></div><div>Are there any outstandi=
ng issues which the community feels need to be addressed prior to our relea=
se?</div><div><br></div><div>Thanks,<br></div><br><div>Peter<br></div></div=
>

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