[Biopython] Biopython and AI PRs, Fwd: Current policy on AI-generated code in NumPy

[Peter Cock]

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@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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