Re: [Biopython] Planning Biopython 1.85

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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=E2=80=AFPM Peter Cock <[email protected]=
om>
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 an=
y
> 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=E2=80=AFAM Peter Cock <p.j.a.cock@googlemai=
l.com>
> wrote:
>
>> Also, I think Biopython 1.85 should be our last release to support Pytho=
n
>> 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 ow=
n
>> favorite new features.
>>
>> Peter
>>
>> On Mon, Sep 9, 2024 at 12:55=E2=80=AFPM Peter Cock <p.j.a.cock@googlemai=
l.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 som=
e of
>>> our legacy C code (since addressed) which complicates releasing a Biopy=
thon
>>> 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 o=
f
>>> 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
>>>
>>>

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<div dir=3D"ltr"><div>The NumPy 2.2 issue is solved, and I hope to merge <a=
 href=3D"https://github.com/biopython/biopython/pull/4901">https://github.c=
om/biopython/biopython/pull/4901</a> but otherwise is there anything worth =
waiting on?</div><div></div><br><div>Peter<br></div></div><br><div class=3D=
"gmail_quote gmail_quote_container"><div dir=3D"ltr" class=3D"gmail_attr">O=
n Wed, Dec 18, 2024 at 5:15=E2=80=AFPM Peter Cock &lt;<a href=3D"mailto:p.j=
[email protected]">[email protected]</a>&gt; wrote:<br></div><=
blockquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-l=
eft:1px solid rgb(204,204,204);padding-left:1ex"><div dir=3D"ltr"><div>Hell=
o all,</div><div><br></div><div>My employer (currently University of Strath=
clyde) will be shut from next week</div><div>for Christmas, so I am hoping =
to do the Biopython 1.85 then.</div><div><br></div><div>There are a few Gen=
Bank issues I want to catch up on, and something breaking</div><div>with th=
e recently released NumPy 2.2 - but otherwise I am not aware of any</div><d=
iv>blocking issues. In particular, in my testing Python 3.13 is fine.<br></=
div><div><br></div><div>Please let us know if there is something I&#39;m ov=
erlooking here. Thanks!<br></div><div><br></div><div>Peter</div><div><br></=
div></div><br><div class=3D"gmail_quote"><div dir=3D"ltr" class=3D"gmail_at=
tr">On Tue, Sep 17, 2024 at 11:47=E2=80=AFAM Peter Cock &lt;<a href=3D"mail=
to:[email protected]" target=3D"_blank">[email protected]</=
a>&gt; wrote:<br></div><blockquote class=3D"gmail_quote" style=3D"margin:0p=
x 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><d=
iv dir=3D"ltr"><div>Also, I think Biopython 1.85 should be our last release=
 to support Python 3.9 (which we declared deprecated in Biopython 1.84).</d=
iv><div><br></div><div>One of the small cosmetic advantages of moving to Py=
thon 3.10 onward is more concise type annotation notation, but I&#39;m sure=
 you all have your own favorite new features.<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 Mon, Sep 9, 2024 at 12:55=E2=80=AFPM Peter Cock &lt;<a h=
ref=3D"mailto:[email protected]" target=3D"_blank">p.j.a.cock@googl=
email.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>Dear Biopythoneers,</div><div><br></div><d=
iv>We released Biopython 1.84 at the end of June, so three months later whi=
ch was our typical cadence in the past would put us due for another release=
 at the end of this month.</div><div><br></div><div>There are practical rea=
sons to do this too - <a href=3D"https://peps.python.org/pep-0719/" target=
=3D"_blank">https://peps.python.org/pep-0719/</a> - Python 3.13 is being re=
leased at the start of October, and there is a minor compilation problem wi=
th 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 Pytho=
n 3.13 compatible release now (compiled against the release candidates ahea=
d of the formal release at the start of October).</div><div><br></div><div>=
However, as unfortunately has become common, we have a backlog of open issu=
es and open pull requests. Please speak up with any key issues or overlooke=
d pull requests you think need to be addressed for Biopython 1.85, and if y=
ou can help review or tests them, even better!</div><div><br></div><div>I&#=
39;d be happy to help a volunteer do the release itself, although I see now=
 that I didn&#39;t finish updating <a href=3D"https://biopython.org/wiki/Bu=
ilding_a_release" target=3D"_blank">https://biopython.org/wiki/Building_a_r=
elease</a> alongside doing Biopython 1.84 which changed the way the documen=
tation is built and published. By default, I&#39;ll do the Biopython 1.85 r=
elease and get that how-to updated.<br></div><div><br></div><div>Thank you =
all,</div><div><br></div><div>Peter</div><div><br></div></div>
</blockquote></div>
</blockquote></div>
</blockquote></div>

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