Re: [Biopython] Planning Biopython 1.85

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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 breakin=
g
with the recently released NumPy 2.2 - but otherwise I am not aware of any
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@googlemail.=
com>
wrote:

> Also, I think Biopython 1.85 should be our last release to support Python
> 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 own
> favorite new features.
>
> Peter
>
> On Mon, Sep 9, 2024 at 12:55=E2=80=AFPM Peter Cock <p.j.a.cock@googlemail=
.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 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 Python 3.13
>> compatible release now (compiled against the release candidates ahead of
>> 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>Hello all,</div><div><br></div><div>My employer (curr=
ently University of Strathclyde) will be shut from next week</div><div>for =
Christmas, so I am hoping to do the Biopython 1.85 then.</div><div><br></di=
v><div>There are a few GenBank issues I want to catch up on, and something =
breaking</div><div>with the recently released NumPy 2.2 - but otherwise I a=
m not aware of any</div><div>blocking issues. In particular, in my testing =
Python 3.13 is fine.<br></div><div><br></div><div>Please let us know if the=
re is something I&#39;m overlooking here. Thanks!<br></div><div><br></div><=
div>Peter</div><div><br></div></div><br><div class=3D"gmail_quote gmail_quo=
te_container"><div dir=3D"ltr" class=3D"gmail_attr">On Tue, Sep 17, 2024 at=
 11:47=E2=80=AFAM Peter Cock &lt;<a href=3D"mailto:[email protected]=
m">[email protected]</a>&gt; wrote:<br></div><blockquote class=3D"g=
mail_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>Also, I think Biopython 1=
.85 should be our last release to support Python 3.9 (which we declared dep=
recated in Biopython 1.84).</div><div><br></div><div>One of the small cosme=
tic advantages of moving to Python 3.10 onward is more concise type annotat=
ion 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 href=3D"mailto:[email protected]" tar=
get=3D"_blank">[email protected]</a>&gt; wrote:<br></div><blockquot=
e class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-left:1px s=
olid rgb(204,204,204);padding-left:1ex"><div dir=3D"ltr"><div>Dear Biopytho=
neers,</div><div><br></div><div>We released Biopython 1.84 at the end of Ju=
ne, so three months later which was our typical cadence in the past would p=
ut us due for another release at the end of this month.</div><div><br></div=
><div>There are practical reasons 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 released at the start of October, and there is a =
minor compilation problem with 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 Python 3.13 compatible release now (compiled against=
 the release candidates ahead 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 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!<=
/div><div><br></div><div>I&#39;d be happy to help a volunteer do the releas=
e itself, although I see now that I didn&#39;t finish updating <a href=3D"h=
ttps://biopython.org/wiki/Building_a_release" target=3D"_blank">https://bio=
python.org/wiki/Building_a_release</a> alongside doing Biopython 1.84 which=
 changed the way the documentation is built and published. By default, I&#3=
9;ll do the Biopython 1.85 release and get that how-to updated.<br></div><d=
iv><br></div><div>Thank you all,</div><div><br></div><div>Peter</div><div><=
br></div></div>
</blockquote></div>
</blockquote></div>

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