From p.j.a.cock at googlemail.com  Wed Mar  4 06:13:11 2026
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 4 Mar 2026 11:13:11 +0000
Subject: [Biopython] Planning Biopython 1.87
In-Reply-To: <CAKVJ-_7k_aWauBBMRmTBbZqCX=6kAa2tFghzjbT-BAgETJxYgg@mail.gmail.com>
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 <CAKVJ-_7k_aWauBBMRmTBbZqCX=6kAa2tFghzjbT-BAgETJxYgg@mail.gmail.com>
Message-ID: <CAKVJ-_7V-G845E1UZyAs1izk5Zp-3MFW8D3MpuKrmcsS2jiFyA@mail.gmail.com>

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

From p.j.a.cock at googlemail.com  Wed Mar  4 11:26:39 2026
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 4 Mar 2026 16:26:39 +0000
Subject: [Biopython] Biopython and AI PRs,
 Fwd: Current policy on AI-generated code in NumPy
In-Reply-To: <ddad78fd-8af8-408c-8612-b7ff87bc4be1@gmail.com>
References: <CAGY4rcVcZ79m_YeoiiA8hei4YSqB7wiNEAznRik=vafrk2TyNQ@mail.gmail.com>
 <ddad78fd-8af8-408c-8612-b7ff87bc4be1@gmail.com>
Message-ID: <CAKVJ-_5D05d-F=sQ0qQPKf98_OJr=sL6FmMCw8U25EQ_tCUGBg@mail.gmail.com>

Dear Biopythoneers,

The email I am forwarding below should be on their webarchive shortly,
some action points from NumPy's recent long thread on AI-generated
pull requests:

https://mail.python.org/archives/list/numpy-discussion at python.org/thread/LAR7P3KQWHWAIKYSHTS2MY7X4HUBVA3L/?sort=date

I am watching the evolving policy with the expectation that this will
likey be a role model for Open Source in Python libraries, and that
Biopython will need to take action too.

See also https://github.com/biopython/biopython/pull/5171 regarding our
own PR template, and my blog post from late last year:

https://blastedbio.blogspot.com/2025/11/thoughts-on-generative-ai-contributions.html

Best,

Peter

P.S. Cross reference for BioPerl:

https://github.com/bioperl/bioperl-live/issues/407

---------- Forwarded message ---------
From: Matti Picus via NumPy-Discussion <numpy-discussion at python.org>
Date: Wed, Mar 4, 2026 at 3:29?PM
Subject: [Numpy-discussion] Re: Current policy on AI-generated code in NumPy
To: <numpy-discussion at python.org>
Cc: Matti Picus <matti.picus at gmail.com>


The NumPy steering council thanks the participants in this thread. We think it
has raised a several important points, which we propose to tackle
separately by opening a number of PRs to NumPy's PR template and
documentation (using, if needed, new, targeted threads on the
numpy-discussion mailing
list).  Specifically,

- A PR to the PR template to ask first-time contributors to introduce
themselves and how they use NumPy, as a way to signal that we value the
human connection.

- A PR to the documentation which points contributors to guidelines
for responsible use of AI, such as the SciPy policy
https://scipy.github.io/devdocs/dev/conduct/ai_policy.html. The PR
will mention the nice list Melissa put together
https://github.com/melissawm/open-source-ai-contribution-policies?tab=readme-ov-file.

- Once we have a guideline, a PR to add checkboxes to the PR template
for disclosure in accordance with the guideline.

- A PR to add another checkbox for taking responsibility for releasing
the code under NumPy?s license in accordance with the guidelines and other
documentation. (Done separately as the discussion so far suggests this may
need most thought in terms of phrasing and examples.)

We envision that the PR template checkboxes and information will be used
as a tool for code reviewers to accept or reject the PR based on the
guidelines. The Steering Council remains available to help resolve any
controversial disputes.

We do not propose to reach a prescriptive yes/no on AI, since we feel
like leaving the
actual decision in the hands of the reviewers makes it easier to evolve
policy with time.
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