Re: Help needed with python-cobra and python-pyani
Hi Nilesh,
thanks a lot for having a look.
Am Thu, Nov 24, 2022 at 10:01:47AM +0530 schrieb Nilesh Patra:
> On Wed, Nov 23, 2022 at 09:01:40PM +0100, Andreas Tille wrote:
> > python-cobra
>
> It seems like that the interpreter is having trouble referencing the
> name variable. I tried using getName instead of that which gets the
> test passing but I'm not very sure if it serves the purpose well.
>
> Pushed this change to salsa, but please review.
I've forwarded you change to upstream[1] to evaluate the change (which
looks perfectly sensible to me). There is a remaining (and unrelated)
autopkgtest error[2]:
E ModuleNotFoundError: No module named '_libsbml'
which is caused by the fact that python3-sbml5 can only deal with one
Python3 version. Thus I will restrict the test to default Python3 and
upload to unstable.
> > 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.
Makes sense. I've added a FIXME to d/control which should create
sufficient noise in the future to revert that change once it is not
needed any more.
Kind regards
Andreas.
[1] https://github.com/opencobra/cobrapy/issues/1302
[2] https://salsa.debian.org/med-team/python-cobra/-/jobs/3565917
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