<div dir="ltr"><div>Nearly done, up on PyPI now. The packaging changes mean a bunch of weird errors from the build and upload process if the tooling isn't all up to date.</div><div><br></div><div><a href="https://pypi.org/project/biopython/1.87/">https://pypi.org/project/biopython/1.87/</a></div><div><br></div><div>Peter</div><div><br></div></div><br><div class="gmail_quote gmail_quote_container"><div dir="ltr" class="gmail_attr">On Thu, Mar 19, 2026 at 9:38 AM Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com">p.j.a.cock@googlemail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">I made that change last week, and have just tested the wheel building:<br>
<a href="https://github.com/biopython/biopython-wheels/actions" rel="noreferrer" target="_blank">https://github.com/biopython/biopython-wheels/actions</a><br>
<br>
Other than the loss of Intel macOS wheels (as the runners we used to use<br>
have been retired), that all looks good.<br>
<br>
I propose to do the Biopython 1.87 release today/tomorrow, and so ask<br>
those with merge permissions to hold off till that's done.<br>
<br>
Thank you,<br>
<br>
Peter<br>
<br>
<br>
Peter<br>
<br>
<br>
<br>
On Wed, Mar 4, 2026 at 11:13 AM Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com" target="_blank">p.j.a.cock@googlemail.com</a>> wrote:<br>
><br>
> We're still blocking on a NumPy 2.4 incompatibility:<br>
> <a href="https://github.com/biopython/biopython/issues/5135" rel="noreferrer" target="_blank">https://github.com/biopython/biopython/issues/5135</a><br>
><br>
> I am strongly leaning to the quick fix of changing the failing test in<br>
> #5161 (with the possibility of a better fix late), but want a consesus<br>
> or at least another voice in favour. If anyone using the vector<br>
> classes in Bio.PDB had some input that would be useful.<br>
><br>
> Peter<br>
><br>
> On Fri, Jan 23, 2026 at 10:11 AM Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com" target="_blank">p.j.a.cock@googlemail.com</a>> wrote:<br>
> ><br>
> > Also <a href="https://github.com/biopython/biopython/issues/5109" rel="noreferrer" target="_blank">https://github.com/biopython/biopython/issues/5109</a> which Michiel has been working on.<br>
> ><br>
> > Peter<br>
> ><br>
> > On Wed, Jan 21, 2026 at 2:29 PM Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com" target="_blank">p.j.a.cock@googlemail.com</a>> wrote:<br>
> >><br>
> >> Dear Biopythoneers,<br>
> >><br>
> >> I think once the following are resolved (they have pull requests), we should do the next release:<br>
> >><br>
> >> * NumPy 2.4 compatibility<br>
> >>    <a href="https://github.com/biopython/biopython/issues/5135" rel="noreferrer" target="_blank">https://github.com/biopython/biopython/issues/5135</a><br>
> >><br>
> >> * Using pyproject.toml rather than setup.py<br>
> >>    <a href="https://github.com/biopython/biopython/pull/5142" rel="noreferrer" target="_blank">https://github.com/biopython/biopython/pull/5142</a><br>
> >><br>
> >> Ideally sooner rather than later as the PDB _ATOM_FORMAT_STRING glitch introduced in Biopython 1.86 seems to be hitting a lot of people:<br>
> >> <a href="https://github.com/biopython/biopython/issues/5097" rel="noreferrer" target="_blank">https://github.com/biopython/biopython/issues/5097</a><br>
> >><br>
> >> Is there anything else you think is urgent enough to wait on?<br>
> >><br>
> >> Thanks,<br>
> >><br>
> >> Peter<br>
</blockquote></div>