[Biopython] Planning Biopython 1.87

[Peter Cock]

The 'easy' script tweak to the documentation deployment took me longer
than I expected, hard to debug except live as the condition I wanted
to check was specifically the window when the master branch had a
release version number. Anyway, done now and the release process has
one less manual step now.

Does anyone want to turn this into a blog post?:
https://mailman.open-bio.org/pipermail/biopython-announce/2026-March/000195.html

See https://github.com/OBF/OBF.github.io/blob/main/content/posts/YYYY-MM-DD-event-fellowship-blog-template.md
and https://github.com/OBF/OBF.github.io/blob/main/content/posts/2025-10-29-biopython-1-86-released.md
for guideance on the Hugo setup, and make a pull request.

Thanks,

Peter


On Mon, Mar 30, 2026 at 12:39 PM Peter Cock <p.j.a.cock at googlemail.com> wrote:
>
> 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