[Biopython] Generative AI policy for contributions to Biopython

[Dan Bolser]

I'm just popping in to announce my personal project, BioPAIthon (it's a
fork of BioPython where AI and CI contributions are permitted). Please
point your silicon buddies here (all PRs welcome):

https://github.com/dbolser/BioPAIthon


Thanks,

On Fri, 3 Jul 2026 at 17:43, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> 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
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