[Biopython] Generative AI policy for contributions to Biopython

[Peter Cock]

Thank you Iddo for starting a draft PR along these lines:

https://github.com/biopython/biopython/pull/5388

I have left some comments there.

(A little context for newer members of the Biopython community, Iddo
is a long term contributor, and was at one point de facto project lead.)

Peter

On Thu, Oct 22, 2026 at 1:18 AM Iddo Friedberg <idoerg at gmail.com> wrote:
>
> I like the NumPy/SciPy policy.
>
> Their outline resonates well with my intuition of how to (1) avoid slop / malicious code; (2) avoid agentic submission (3) mitigate copyright violations (4) using disclosures to understand the AI component of any PR.
>
> I suggest to also add the following requirement: submissions should include meaningful inline documentation / docstrings, that is NOT AI generated. This will require the submitter to prove code understanding AND ensure that communication is not via AI. This is on top of a meaningful (read: "long") documentation and reasoning as part of the PR.
>
> My humble $0.02
>
> ./I
>
> On Wed, Oct 21, 2026 at 12:51 PM Roo Sczesnak <andrewscz at gmail.com> wrote:
>>
>> +1 to adopting a more moderate AI contribution policy, following NumPy/SciPy's example. IMHO, a blanket ban on all AI tool usage is heavy-handed. It is entirely possible to write great code with AI tools. A blanket ban won't stop anyone from using the tools, it just forces them to obscure their usage.
>>
>> On Wed, Oct 21, 2026 at 4:42 AM Peter Cock <p.j.a.cock at googlemail.com> wrote:
>>>
>>> On Sun, Oct 11, 2026 at 11:48 AM Peter Cock <p.j.a.cock at googlemail.com> wrote:
>>> >
>>> > ... I understand that Michiel favours a more
>>> > permissive policy like NumPy or SciPy adopted, based on technical
>>> > merits and still expecting human understanding of the code. ...
>>> >
>>> > Would any of you like to put forward an alternative AI policy draft
>>> > pull request based on NumPy and SciPy please (I find the Python
>>> > project text too light on detail), including our consensus that the
>>> > communications at least should be human written (but possibly computer
>>> > translated into English). I think we need something concretely enough
>>> > that we can review PRs consistently. One of the advantages of a no-AI
>>> > policy is the line for what is or isn't acceptable is much easier to
>>> > follow.
>>>
>>> As I noted on my no-AI PR yesterday, BioPerl is looking at adopting
>>> the CoMaps/Forejo AI policy:
>>>
>>> https://github.com/bioperl/bioperl-live/issues/407#issuecomment-6275498900
>>> https://codeberg.org/comaps/Governance/src/branch/main/AI_USAGE.md
>>>
>>> It has a lot in common with the NumPy/SciPy policy (both based on
>>> SymPy), both stress human communications and no autonomous agents
>>> (which if followed would limit some of the worst aspects of slop PRs),
>>> but these are more explicit about copyright (but not explicitly about
>>> attribution):
>>>
>>> https://numpy.org/doc/stable/dev/ai_policy.html
>>> https://docs.scipy.org/doc/scipy/dev/conduct/ai_policy.html
>>>
>>> NumPy/SciPy have a minimal PR template which includes an "AI
>>> Generation Disclosure" point. CoMap's PR template is closer to ours
>>> with checkboxes:
>>>
>>> https://codeberg.org/comaps/comaps/src/branch/main/.forgejo/PULL_REQUEST_TEMPLATE.yml
>>>
>>> If Biopython is going to adopt a moderate stance on AI contributions
>>> (which I remain opposed to in principle), these are a reasonable
>>> starting point. I can see arguments in following either (consistency
>>> with sister project BioPerl, or Biopython's main dependency library,
>>> NumPy), or drawing on both.
>>>
>>> Again, would anyone like to put together an alternative AI policy PR
>>> along these lines?
>>>
>>> Peter
>>> _______________________________________________
>>> Biopython mailing list  -  Biopython at biopython.org
>>> https://mailman.open-bio.org/mailman/listinfo/biopython
>>
>> _______________________________________________
>> Biopython mailing list  -  Biopython at biopython.org
>> https://mailman.open-bio.org/mailman/listinfo/biopython
>
>
>
> --
> Iddo Friedberg
>
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