[Biopython] Planning Biopython 1.87

[Peter Cock]

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