[Biopython] Generative AI policy for contributions to Biopython

Thu Jul 2 10:42:14 EDT 2026

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
>>> 
>>> 
>>> On Mon, Jun 1, 2026 at 7:31 AM Peter Cock <p.j.a.cock at googlemail.com> wrote:
>>>> 
>>>> I'm proposing some text in the CONTRIBUTING file to spell this out
>>>> this point explicitly:
>>>> 
>>>> https://github.com/biopython/biopython/pull/5229
>>>> 
>>>> Suggested changes welcome, ideally on that PR please.
>>>> 
>>>> I will probably follow that with a draft PR for a general no-AI stance.
>>>> 
>>>> Going back to the start of this thread, I wrote (spelling fixed):
>>>> 
>>>> https://mailman.open-bio.org/pipermail/biopython/2026-April/017113.html
>>>> 
>>>>> Would anyone like to speak in defense of accepting AI (assisted) PRs,
>>>>> and suggest an existing policy you would be happy we adopt or base
>>>>> ours on?
>>>> 
>>>> Would anyone want to draft a more moderate policy with limited AI use?
>>>> 
>>>> Thank you,
>>>> 
>>>> Peter
>>>> 
>>>> On Mon, Jun 1, 2026 at 3:09 PM Peter Cock <p.j.a.cock at googlemail.com> wrote:
>>>>> 
>>>>> This is a real issue - I added that tag to an old issue and with a
>>>>> week it had two likely AI generated PRs:
>>>>> https://github.com/biopython/biopython/issues/2116
>>>>> 
>>>>> Peter
>>>>> 
>>>>> On Fri, Apr 24, 2026 at 7:26 PM Peter Cock <p.j.a.cock at googlemail.com> wrote:
>>>>>> 
>>>>>> I just posted this on Mastodon (neither I nor Biopython or the OBF use X/Twitter
>>>>>> anymore):
>>>>>> 
>>>>>> https://fediscience.org/@pjacock/116143426085553346
>>>>>> 
>>>>>> And that reminded me of an earlier remark I made:
>>>>>> 
>>>>>>> Seems the recent #GenerativeAI #slop pull requests that I've looked at for
>>>>>>> #Biopython have preferentially targeted the "Good First Issues". We really
>>>>>>> wanted those to be onboarding ramps for new #OpenSource contributors -
>>>>>>> and not for padding anyone's GitHub profile or whatever the motivation here is.
>>>>>>> 
>>>>>>> So I think any formal policy will want to say explicitly #NoAI on those issues
>>>>>>> at the very least.
>>>>>> 
>>>>>> https://fediscience.org/@pjacock/116161804363016972
>>>>>> 
>>>>>> Peter
>>>>>> 
>>>>>> On Fri, Apr 24, 2026 at 11:16 AM Peter Cock <p.j.a.cock at googlemail.com> wrote:
>>>>>>> 
>>>>>>> Dear Biopythoneers,
>>>>>>> 
>>>>>>> We need to set out a generative AI policy for contributions to Biopython.
>>>>>>> 
>>>>>>> There are now multiple recent PRs submitted by new contributors which
>>>>>>> are openly using AI tools, more that I suspect are, and now even AI assisted
>>>>>>> PRs from past contributors (where CV padding or other external metrics
>>>>>>> are unlikely to be driving this). These are generally more work to review
>>>>>>> than human written PRs, and that is a growing issue.
>>>>>>> 
>>>>>>> I blogged about my views late last year - ending in the line "Right now, I
>>>>>>> still lean very much to saying no any PR using generative AI".
>>>>>>> 
>>>>>>> https://blastedbio.blogspot.com/2025/11/thoughts-on-generative-ai-contributions.html
>>>>>>> 
>>>>>>> Things will change (both tool capabilities, but also the social and legal
>>>>>>> interpetations) but that post still describes my views today - note I did
>>>>>>> not touch on the topic of communications there (see below).
>>>>>>> 
>>>>>>> Recently Linux adopted what has been described as a balanced stance
>>>>>>> treating it as a tool with very clear expectations that usage MUST be declared
>>>>>>> and that the human submitter is responsible for (quoting these four points):
>>>>>>> 
>>>>>>> * Reviewing all AI-generated code
>>>>>>> * Ensuring compliance with licensing requirements
>>>>>>> * Adding their own Signed-off-by tag to certify the DCO
>>>>>>> * Taking full responsibility for the contribution
>>>>>>> 
>>>>>>> https://docs.kernel.org/process/coding-assistants.html
>>>>>>> 
>>>>>>> That is pragmatic but ignores the legal and ethical minefield. We don't
>>>>>>> have a Developer Certificate of Origin (DCO), but I think the other
>>>>>>> points are a bare minimum for any Biopython policy.
>>>>>>> 
>>>>>>> Most of my personal open source projects have only had a very small
>>>>>>> number of contributors, and I am comfortable with outright rejecting
>>>>>>> generative AI. I know some of the past/current Biopython contributors
>>>>>>> are more willing to embrace this technology though - so I doubt support
>>>>>>> for a simple ban would be unanimous.
>>>>>>> 
>>>>>>> Speaking for a moment as the current Open Bioinformatics Foundation
>>>>>>> president, the board has discussed this and agreed not to try to micro
>>>>>>> manage the member projects. For reference, BioPerl have started
>>>>>>> https://github.com/bioperl/bioperl-live/issues/407 which has some
>>>>>>> excellent points and examples to consider.
>>>>>>> 
>>>>>>> In particular, this is not just a code or documentation changes issue - but
>>>>>>> also about the communication around any proposed change: the nature
>>>>>>> of the commit messages, pull request description, and discussion. This
>>>>>>> ties into the maintainers' burden - many of our recent AI generated PRs
>>>>>>> have fairy short code changes but the verbose text is exhausting to read
>>>>>>> and unhelpful. It has sometimes felt like I have been talking to an AI agent
>>>>>>> rather than a human - I actually liked the feeling of mentoring a new
>>>>>>> contributor and guiding them through minor hurdles to getting their
>>>>>>> change accepted, but you lose that with an AI agent inbetween you.
>>>>>>> 
>>>>>>> I therefore very much like this line from the curreth Codeberg policy:
>>>>>>> 
>>>>>>>> All communication, that includes: commit messages, pull request
>>>>>>>> messages, documentation, code comments and issues (and
>>>>>>>> comments on issues/pull requests), that is intended to be read
>>>>>>>> by people to understand your thoughts and work must not have
>>>>>>>> been generated with AI. We exclude machine translation and
>>>>>>>> tooling that helps with grammar and spelling check.
>>>>>>> 
>>>>>>> https://codeberg.org/comaps/Governance/src/branch/main/AI_USAGE.md
>>>>>>> 
>>>>>>> Would anyone like to speak in defence of accepting AI (assisted) PRs,
>>>>>>> and suggest an existing policy you would be happy we adopt or base
>>>>>>> ours on?
>>>>>>> 
>>>>>>> Or should I start drafting a more draconian but likely much shorter one -
>>>>>>> a few lines like this in the CONTRIBUTING file and/or PR template: No
>>>>>>> generative AI to be used in any Biopython contributions, with the exception
>>>>>>> of machine translation to/from English (where you might consider including
>>>>>>> your original language text as well).
>>>>>>> 
>>>>>>> Thank you,
>>>>>>> 
>>>>>>> Peter
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-- 
Hilmar Lapp -:- lappland.io

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