[Biopython] Planning Biopython 1.87

[Peter Cock]

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.

https://pypi.org/project/biopython/1.87/

Peter


On Thu, Mar 19, 2026 at 9:38 AM Peter Cock <p.j.a.cock at googlemail.com>
wrote:

> I made that change last week, and have just tested the wheel building:
> https://github.com/biopython/biopython-wheels/actions
>
> Other than the loss of Intel macOS wheels (as the runners we used to use
> have been retired), that all looks good.
>
> I propose to do the Biopython 1.87 release today/tomorrow, and so ask
> those with merge permissions to hold off till that's done.
>
> Thank you,
>
> Peter
>
>
> Peter
>
>
>
> On Wed, Mar 4, 2026 at 11:13 AM Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
> >
> > We're still blocking on a NumPy 2.4 incompatibility:
> > https://github.com/biopython/biopython/issues/5135
> >
> > I am strongly leaning to the quick fix of changing the failing test in
> > #5161 (with the possibility of a better fix late), but want a consesus
> > or at least another voice in favour. If anyone using the vector
> > classes in Bio.PDB had some input that would be useful.
> >
> > Peter
> >
> > On Fri, Jan 23, 2026 at 10:11 AM Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
> > >
> > > Also https://github.com/biopython/biopython/issues/5109 which Michiel
> has been working on.
> > >
> > > Peter
> > >
> > > On Wed, Jan 21, 2026 at 2:29 PM Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
> > >>
> > >> Dear Biopythoneers,
> > >>
> > >> I think once the following are resolved (they have pull requests), we
> should do the next release:
> > >>
> > >> * NumPy 2.4 compatibility
> > >>    https://github.com/biopython/biopython/issues/5135
> > >>
> > >> * Using pyproject.toml rather than setup.py
> > >>    https://github.com/biopython/biopython/pull/5142
> > >>
> > >> 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:
> > >> https://github.com/biopython/biopython/issues/5097
> > >>
> > >> Is there anything else you think is urgent enough to wait on?
> > >>
> > >> Thanks,
> > >>
> > >> Peter
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20260330/d3c63fe3/attachment.htm>