Re: [Biopython] Planning Biopython 1.85

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Good news: The Biopython 1.85 release is done (bar the blog post and more
formal
announcement). The updated documentation is live:

https://biopython.org/docs/1.85/

This includes pre-compiled wheels for Python 3.13

Bad news: I couldn't get LaTeX to build the PDF version of the Tutorial as
I managed
for Biopython 1.84 from the Sphinx output. I suspect some package
incompatibility,
but after trying on two machines (one a fresh latex installation, the other
the one I
think I used last time) I gave up. This means there is NO bundled version
of the
Tutorial in the .zip or .tar.gz file this time. It might be worth having a
fresh look at the
PDF options from Sphinx nowadays...

Peter

On Tue, Dec 31, 2024 at 6:55=E2=80=AFPM Peter Cock <[email protected]=
om>
wrote:

> 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 <p.j.a.cock@googlemail=
.com>
> 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 a=
ny
>> 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@googlema=
il.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 o=
wn
>>> favorite new features.
>>>
>>> Peter
>>>
>>> On Mon, Sep 9, 2024 at 12:55=E2=80=AFPM Peter Cock <p.j.a.cock@googlema=
il.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 so=
me of
>>>> our legacy C code (since addressed) which complicates releasing a Biop=
ython
>>>> 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>Good news: The Biopython 1.85 release is done (bar th=
e blog post and more formal</div><div>announcement). The updated documentat=
ion is live:</div><div><br></div><div><a href=3D"https://biopython.org/docs=
/1.85/">https://biopython.org/docs/1.85/</a></div><div><br></div><div>This =
includes pre-compiled wheels for Python 3.13 <br></div><div><br></div><div>=
Bad news: I couldn&#39;t get LaTeX to build the PDF version of the Tutorial=
 as I managed</div><div>for Biopython 1.84 from the Sphinx output. I suspec=
t some package incompatibility,</div><div>but after trying on two machines =
(one a fresh latex installation, the other the one I</div><div>think I used=
 last time) I gave up. This means there is NO bundled version of the</div><=
div>Tutorial in the .zip or .tar.gz file this time. It might be worth havin=
g a fresh look at the</div><div>PDF options from Sphinx nowadays...<br></di=
v><div></div><div><br></div><div>Peter<br></div></div><br><div class=3D"gma=
il_quote gmail_quote_container"><div dir=3D"ltr" class=3D"gmail_attr">On Tu=
e, Dec 31, 2024 at 6:55=E2=80=AFPM Peter Cock &lt;<a href=3D"mailto:p.j.a.c=
[email protected]">[email protected]</a>&gt; wrote:<br></div><bloc=
kquote 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>The NumP=
y 2.2 issue is solved, and I hope to merge <a href=3D"https://github.com/bi=
opython/biopython/pull/4901" target=3D"_blank">https://github.com/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=
"><div dir=3D"ltr" class=3D"gmail_attr">On Wed, Dec 18, 2024 at 5:15=E2=80=
=AFPM Peter Cock &lt;<a href=3D"mailto:[email protected]" target=3D=
"_blank">[email protected]</a>&gt; wrote:<br></div><blockquote clas=
s=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-left:1px solid r=
gb(204,204,204);padding-left:1ex"><div dir=3D"ltr"><div>Hello all,</div><di=
v><br></div><div>My employer (currently University of Strathclyde) will be =
shut from next week</div><div>for Christmas, so I am hoping to do the Biopy=
thon 1.85 then.</div><div><br></div><div>There are a few GenBank issues I w=
ant to catch up on, and something breaking</div><div>with the recently rele=
ased NumPy 2.2 - but otherwise I am not aware of any</div><div>blocking iss=
ues. 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 overlooking 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_attr">On Tue, Sep=
 17, 2024 at 11:47=E2=80=AFAM Peter Cock &lt;<a href=3D"mailto:p.j.a.cock@g=
ooglemail.com" target=3D"_blank">[email protected]</a>&gt; wrote:<b=
r></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>Also, I think Biopython 1.85 should be our last release to support Pyt=
hon 3.9 (which we declared deprecated in Biopython 1.84).</div><div><br></d=
iv><div>One of the small cosmetic advantages of moving to Python 3.10 onwar=
d is more concise type annotation notation, but I&#39;m sure you all have y=
our 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:p.=
[email protected]" target=3D"_blank">[email protected]</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 di=
r=3D"ltr"><div>Dear Biopythoneers,</div><div><br></div><div>We released Bio=
python 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 thi=
s month.</div><div><br></div><div>There are practical reasons to do this to=
o - <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 lega=
cy C code (since addressed) which complicates releasing a Biopython 1.84 wh=
eel for Python 3.13. We can in principle release a Python 3.13 compatible r=
elease now (compiled against the release candidates ahead of the formal rel=
ease at the start of October).</div><div><br></div><div>However, as unfortu=
nately has become common, we have a backlog of open issues and open pull re=
quests. 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 he=
lp a volunteer do the release itself, although I see now that I didn&#39;t =
finish updating <a href=3D"https://biopython.org/wiki/Building_a_release" t=
arget=3D"_blank">https://biopython.org/wiki/Building_a_release</a> alongsid=
e doing Biopython 1.84 which changed the way the documentation is built and=
 published. By default, I&#39;ll do the Biopython 1.85 release 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>
</blockquote></div>

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