Re: [Biopython] Planning Biopython 1.85

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Hi Sean,

One idea would be scanning over the open issues and pull requests - fresh
eyes are always useful, even if you focus on topics you are familiar with.
There are likely issues which have been resolved but never got closed, and
pull requests which stalled with blocking issues never addressed. In some
cases they might be worth reviving, but in others we should probably close
them. And on a more positive note, there may be some forgotten pull
requests which are in fact ready to merge with passing tests, which just
need flagging for a developer to merge (although they may need to update
some style issues as our checks have gotten stricter over the years).

Peter

On Thu, Sep 12, 2024 at 8:37=E2=80=AFPM Sean Brimer <[email protected]> wr=
ote:

> Hi Peter,
>
> I have been using Biopython for several years now and I would like to
> contribute to the maintenance of it. I'm not a formally trained programme=
r
> so I'm not sure if I have the needed skills for everything but I'm very
> happy to try! My background is a wet bench virologist who learned to code
> enough to get his work completed. I'm looking to work on a project that
> would allow me to stay practiced and to improve my overall skills.
>
> If you think there could be a place here for me I would love to help.
>
> Cheers,
> Sean Brimer
>
> On Mon, Sep 9, 2024 at 6:55=E2=80=AFAM 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
>>
>> _______________________________________________
>> Biopython mailing list  -  [email protected]
>> https://mailman.open-bio.org/mailman/listinfo/biopython
>>
>

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<div dir=3D"ltr"><div>Hi Sean,</div><div><br></div><div>One idea would be s=
canning over the open issues and pull requests - fresh eyes are always usef=
ul, even if you focus on topics you are familiar with. There are likely iss=
ues which have been resolved but never got closed, and pull requests which =
stalled with blocking issues never addressed. In some cases they might be w=
orth reviving, but in others we should probably close them. And on a more p=
ositive note, there may be some forgotten pull requests which are in fact r=
eady to merge with passing tests, which just need flagging for a developer =
to merge (although they may need to update some style issues as our checks =
have gotten stricter over the years).<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 Thu, Sep 12, 2024 at 8:37=E2=80=AFPM Sean Brimer &lt;<a href=3D"m=
ailto:[email protected]">[email protected]</a>&gt; wrote:<br></div><block=
quote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-left:1=
px solid rgb(204,204,204);padding-left:1ex"><div dir=3D"ltr"><div>Hi Peter,=
 <br></div><div><br></div><div>I have been using Biopython for several year=
s now and I would like to contribute to the maintenance of it. I&#39;m not =
a formally trained programmer so I&#39;m not sure if I have the needed skil=
ls for everything but I&#39;m very happy to try! My background is a wet ben=
ch virologist who learned to code enough to get his work completed. I&#39;m=
 looking to work on a project that would allow me to stay practiced and to =
improve my overall skills.</div><div><br></div><div>If you think there coul=
d be a place here for me I would love to help. <br></div><div><br></div><di=
v>Cheers, <br></div><div>Sean Brimer<br></div></div><br><div class=3D"gmail=
_quote"><div dir=3D"ltr" class=3D"gmail_attr">On Mon, Sep 9, 2024 at 6:55=
=E2=80=AFAM 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>
_______________________________________________<br>
Biopython mailing list=C2=A0 -=C2=A0 <a href=3D"mailto:Biopython@biopython.=
org" target=3D"_blank">[email protected]</a><br>
<a href=3D"https://mailman.open-bio.org/mailman/listinfo/biopython" rel=3D"=
noreferrer" target=3D"_blank">https://mailman.open-bio.org/mailman/listinfo=
/biopython</a><br>
</blockquote></div>
</blockquote></div>

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

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