Re: Help needed with python-cobra and python-pyani

[Andrius Merkys <merkys@debian.org>]

Hello,

On 2022-11-24 06:31, Nilesh Patra wrote:
> > python-pyani
> This is because python3-biopython does not vendor shared object libs
> for python3.11 yet
>
> $ apt-file list python3-biopython | grep '_align'
> ...
> python3-biopython:/usr/lib/python3/dist-packages/Bio/Align/_aligners.cpython-310-x86_64-linux-gnu.so
> python3-biopython:/usr/lib/python3/dist-packages/Bio/Align/_aligners.cpython-39-x86_64-linux-gnu.so
>
> There are two ways to fix this:
>
> 1. Run tests only for default python3-dev version
> 2. Re-compile biopython to vendor 3.11 bindings, but this has issues
> at present due to t-coffee bug.
>
> I have pushed something that implements 1.) to salsa, please check.

I have packages that also suffer from python3-biopython not supporting 
python3.11. Since the real blocker here is t-coffee, I would prefer 
option 2 over 1, as option 2 would unblock other packages en route.

Best,
Andrius