Re: [Biopython] Planning the Biopython 1.84 release

--===============6992932209378535467==
Content-Type: multipart/alternative; boundary="000000000000c632e0061be96cf0"

--000000000000c632e0061be96cf0
Content-Type: text/plain; charset="UTF-8"
Content-Transfer-Encoding: quoted-printable

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=E2=80=AFAM Peter Cock <p.j.a.cock@googlemail.=
com>
wrote:

> I've been working on this (as have Michiel, Jo=C3=A3o, and others), and s=
till
> 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 mor=
e
> surprises!
>
> Peter
>
> On Wed, May 22, 2024 at 9:39=E2=80=AFPM Peter Cock <p.j.a.cock@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 tac=
kle
>> the Biopython 1.84 in early June.
>>
>> That will be about six months worth of changes, including dropping Pytho=
n
>> 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 interoperabili=
ty,
>> 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 tes=
ts
>> in Biopython 1.63 fail. We have addressed those already, and the tests n=
ow
>> 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
>>
>

--000000000000c632e0061be96cf0
Content-Type: text/html; charset="UTF-8"
Content-Transfer-Encoding: quoted-printable

<div dir=3D"ltr"><div>I am working on the release now, forgot I didn&#39;t =
have LaTeX on this machine</div><div>which we still need for a PDF version =
of the Tutorial (this is the first release</div><div>to use Sphinx and RST =
for the Tutorial, rather than LaTeX directly).</div><div><br></div><div>Ple=
ase don&#39;t update the master branch until the release is done.<br></div>=
<div><br></div><div>Peter<br></div></div><br><div class=3D"gmail_quote"><di=
v dir=3D"ltr" class=3D"gmail_attr">On Wed, Jun 26, 2024 at 11:37=E2=80=AFAM=
 Peter Cock &lt;<a href=3D"mailto:[email protected]">p.j.a.cock@goo=
glemail.com</a>&gt; wrote:<br></div><blockquote class=3D"gmail_quote" style=
=3D"margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding=
-left:1ex"><div dir=3D"ltr"><div>I&#39;ve been working on this (as have Mic=
hiel,=C2=A0Jo=C3=A3o,  and others), and still hope to do the release very s=
oon.</div><div><br></div><div>Touch wood the numpy 2.0.0 work is done. Righ=
t 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"gma=
il_attr">On Wed, May 22, 2024 at 9:39=E2=80=AFPM Peter Cock &lt;<a href=3D"=
mailto:[email protected]" target=3D"_blank">[email protected]=
om</a>&gt; wrote:<br></div><blockquote class=3D"gmail_quote" style=3D"margi=
n:0px 0px 0px 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 li=
ked to tackle the release sooner, but things have been busy at work. Howeve=
r, 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=
 of 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 =
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&#39;re only using the buf=
fer 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 me=
ans a lot of the documentation tests in Biopython 1.63 fail. We have addres=
sed those already, and the tests now pass on a recent NumPy v1 and on the v=
2 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 outstan=
ding issues which the community feels need to be addressed prior to our rel=
ease?</div><div><br></div><div>Thanks,<br></div><br><div>Peter<br></div></d=
iv>
</blockquote></div>
</blockquote></div>

--000000000000c632e0061be96cf0--

--===============6992932209378535467==
Content-Type: text/plain; charset="us-ascii"
MIME-Version: 1.0
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

_______________________________________________
Biopython mailing list  -  [email protected]
https://mailman.open-bio.org/mailman/listinfo/biopython

--===============6992932209378535467==--