[Biopython] Generative AI policy for contributions to Biopython

[Peter Cock]

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