[Biopython] Generative AI policy for contributions to Biopython

[Peter Cock]

Hello Ant,

I on the other hand rather hope the current AI-assisted coding boom is
just a passing trend, and will be looked back on like asbestos - with
similar long term problems cleaning buildings/code bases contaminated
with its usage. The metaphor here works for both the legal minefield
and vibe coding quality side - but the later may be a short term issue
if the tools improve.

But if you're right, and we adopt a strict no-AI policy now, and
things move on and the legal issues settle quickly, moving towards a
policy something like that would be a sensible future choice.

Peter

On Thu, Jul 2, 2026 at 4:19 PM Anthony Underwood <email2ants at gmail.com> wrote:
>
> Dear Biopython maintainers,
>
> Thank you for setting out the contributing guidelines so clearly, especially the licensing and practical points. I wanted to raise a friendly but genuine concern about the blanket ban on LLM and generative AI use for contributions and community communication.
>
> I understand and share some of the underlying worries: copyright provenance of generated code, licensing compatibility, and the review burden on maintainers are all real issues. However, I think the current policy, as written, risks being unworkable in practice and could quietly undermine the project rather than protect it.
>
> AI-assisted coding is not a passing trend. It is now standard practice across academic labs, research institutes, and commercial biotech and pharma organisations, including in bioinformatics specifically. Most active contributors, whether they disclose it or not, are very likely using code completion, refactoring assistance, or LLM-based debugging as part of their normal workflow. A strict ban is difficult to enforce and, if taken literally, would exclude a large and growing share of the contributor base, including experienced developers who use these tools responsibly.
>
> I would encourage the maintainers to consider reframing the policy rather than prohibiting AI use outright. A more workable approach might treat AI tools the way many teams already do: as a junior coder whose output always requires review, testing, and sign-off by the human contributor before submission. Under that framing, the responsibility and accountability stay exactly where they already sit, with the person submitting the pull request, while acknowledging the reality of how code gets written today. This could be paired with a disclosure requirement (similar to the translation exception already in the policy) rather than a ban, which would also make the licensing and provenance questions easier to track rather than harder.
>
> I raise this constructively and with real respect for the work the maintainers do keeping Biopython healthy. I would be glad to help think through wording for a revised policy if that would be useful, and I am happy to discuss further on the mailing list or wherever is most appropriate.
>
> Best regards,
> Ant
>
> On Thu, 2 Jul 2026 at 15:42, Hilmar Lapp <hlapp at drycafe.net> wrote:
>>
>> I left one comment.
>>
>> As a more general comment, a No AI policy as is here will require most if not all future contributors to do their Biopython development under an environment entirely disconnected and divergent from what they would be using for anything else they do professionally. (I don’t think there’ll be any company or even academic lab in the future that can afford not to *require* their software developers to use AI-assisted coding. This is already the case in the teams I’m involved in, and they are all academic.)
>>
>> So this will be an interesting experiment in whether and how AI-assisted coding policies affect sustainability and viability of projects.
>>
>>  -hilmar
>>
>> On Jul 2, 2026, at 8:02 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>>
>> One typo fix later, that's no longer a draft policy - but it is
>> waiting on some approval reviews from others with commit permissions
>> please.
>>
>> Peter
>>
>> On Mon, Jun 22, 2026 at 9:56 AM Peter Cock <p.j.a.cock at googlemail.com> wrote:
>>
>>
>> Feedback welcomed on this new draft PR for an explicit no-AI policy:
>>
>> https://github.com/biopython/biopython/pull/5241
>>
>> I had one interesting comment over the weekend on Mastodon where I
>> asked about the AGENTS file text and if it was too whimsical (humour
>> is even harder with an international audience):
>>
>> https://fediscience.org/@pjacock/116782003665914065
>>
>> https://illuminant.asjo.org/user/asjo/object/156156
>>
>> I fear it is too whimsical.
>>
>> It will be appreciated by people who tend to agree, and those who
>> don't - for whom the message is - will read it as their belief being
>> ridiculed in an unserious manner.
>>
>> It is a fun idea, though :-)
>>
>>
>> Peter
>>
>> On Sat, Jun 6, 2026 at 10:13 AM Peter Cock <p.j.a.cock at googlemail.com> wrote:
>>
>>
>> Assuming no objections I'm planning to merge
>> https://github.com/biopython/biopython/pull/5229
>> on Monday (a week for comment seems fine).
>>
>> Then on to the broader AI policy...
>>
>> Thanks,
>>
>> Peter