Re: [Biopython] Planning Biopython 1.85

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We now have Python 3.13 versions on conda-forge as well (needed an extra
step I had
forgotten about), along side Python 3.9, 3.10, 3.11 and 3.12 which where up
the same
day.

Peter

On Wed, Jan 15, 2025 at 3:27=E2=80=AFPM Peter Cock <[email protected]=
om>
wrote:

> 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 a=
s
> 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 <p.j.a.cock@googlemail=
.com>
> 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@googlemai=
l.com>
>> wrote:
>>
>>> Hello all,
>>>
>>> My employer (currently University of Strathclyde) will be shut from nex=
t
>>> 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
>>> 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@googlem=
ail.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 i=
s
>>>> 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@googlem=
ail.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 anothe=
r
>>>>> 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 s=
ome of
>>>>> our legacy C code (since addressed) which complicates releasing a Bio=
python
>>>>> 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 ope=
n
>>>>> 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 se=
e
>>>>> 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 tha=
t
>>>>> how-to updated.
>>>>>
>>>>> Thank you all,
>>>>>
>>>>> Peter
>>>>>
>>>>>

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<div dir=3D"ltr"><div>We now have Python 3.13 versions on conda-forge as we=
ll (needed an extra step I had</div><div>forgotten about), along side Pytho=
n 3.9, 3.10, 3.11 and 3.12 which where up the same</div><div>day.</div><div=
><br></div><div>Peter<br></div></div><br><div class=3D"gmail_quote gmail_qu=
ote_container"><div dir=3D"ltr" class=3D"gmail_attr">On Wed, Jan 15, 2025 a=
t 3:27=E2=80=AFPM 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>Good news: The Biopython =
1.85 release is done (bar the blog post and more formal</div><div>announcem=
ent). The updated documentation is live:</div><div><br></div><div><a href=
=3D"https://biopython.org/docs/1.85/" target=3D"_blank">https://biopython.o=
rg/docs/1.85/</a></div><div><br></div><div>This includes pre-compiled wheel=
s for Python 3.13 <br></div><div><br></div><div>Bad news: I couldn&#39;t ge=
t LaTeX to build the PDF version of the Tutorial as I managed</div><div>for=
 Biopython 1.84 from the Sphinx output. I suspect some package incompatibil=
ity,</div><div>but after trying on two machines (one a fresh latex installa=
tion, 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 having a fresh look at the</div>=
<div>PDF options from Sphinx nowadays...<br></div><div></div><div><br></div=
><div>Peter<br></div></div><br><div class=3D"gmail_quote"><div dir=3D"ltr" =
class=3D"gmail_attr">On Tue, Dec 31, 2024 at 6:55=E2=80=AFPM Peter Cock &lt=
;<a href=3D"mailto:[email protected]" target=3D"_blank">p.j.a.cock@=
googlemail.com</a>&gt; wrote:<br></div><blockquote class=3D"gmail_quote" st=
yle=3D"margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padd=
ing-left:1ex"><div dir=3D"ltr"><div>The NumPy 2.2 issue is solved, and I ho=
pe to merge <a href=3D"https://github.com/biopython/biopython/pull/4901" ta=
rget=3D"_blank">https://github.com/biopython/biopython/pull/4901</a> but ot=
herwise 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"gma=
il_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]=
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>My employer (cu=
rrently University of Strathclyde) will be shut from next week</div><div>fo=
r Christmas, so I am hoping to do the Biopython 1.85 then.</div><div><br></=
div><div>There are a few GenBank issues I want to catch up on, and somethin=
g breaking</div><div>with the recently released NumPy 2.2 - but otherwise I=
 am not aware of any</div><div>blocking issues. In particular, in my testin=
g Python 3.13 is fine.<br></div><div><br></div><div>Please let us know if t=
here 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 d=
ir=3D"ltr" class=3D"gmail_attr">On Tue, Sep 17, 2024 at 11:47=E2=80=AFAM Pe=
ter Cock &lt;<a href=3D"mailto:[email protected]" target=3D"_blank"=
>[email protected]</a>&gt; wrote:<br></div><blockquote class=3D"gma=
il_quote" style=3D"margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,2=
04,204);padding-left:1ex"><div dir=3D"ltr"><div>Also, I think Biopython 1.8=
5 should be our last release to support Python 3.9 (which we declared depre=
cated in Biopython 1.84).</div><div><br></div><div>One of the small cosmeti=
c advantages of moving to Python 3.10 onward is more concise type annotatio=
n notation, but I&#39;m sure you all have your own favorite new features.<b=
r></div><div><br></div><div>Peter<br></div></div><br><div class=3D"gmail_qu=
ote"><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]" target=
=3D"_blank">[email protected]</a>&gt; wrote:<br></div><blockquote c=
lass=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-left:1px soli=
d rgb(204,204,204);padding-left:1ex"><div dir=3D"ltr"><div>Dear Biopythonee=
rs,</div><div><br></div><div>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.</div><div><br></div><d=
iv>There are practical reasons to do this too - <a href=3D"https://peps.pyt=
hon.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 min=
or compilation problem with some of our legacy C code (since addressed) whi=
ch 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 th=
e release candidates ahead of the formal release at the start of October).<=
/div><div><br></div><div>However, as unfortunately has become common, we ha=
ve a backlog of open issues and open pull requests. Please speak up with an=
y 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!</di=
v><div><br></div><div>I&#39;d be happy to help a volunteer do the release i=
tself, although I see now that I didn&#39;t finish updating <a href=3D"http=
s://biopython.org/wiki/Building_a_release" target=3D"_blank">https://biopyt=
hon.org/wiki/Building_a_release</a> alongside doing Biopython 1.84 which ch=
anged the way the documentation is built and published. By default, I&#39;l=
l 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>
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</blockquote></div>

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