Groups > linux.debian.devel.mentors > #43498

[RFC] python-cobra, python3-sbml5

From	Nilesh Patra <npatra974@gmail.com>
Newsgroups	linux.debian.devel.mentors, linux.debian.maint.python
Subject	[RFC] python-cobra, python3-sbml5
Date	2020-04-04 15:50 +0200
Message-ID	<zRRln-15B-1@gated-at.bofh.it> (permalink)
Organization	linux.* mail to news gateway

Cross-posted to 2 groups.

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Hi,
Currently python-cobra FTBFS reported here [1].

>From the logs, in the last message[2] it looks like an import-error for
'_libsbml' file which corresponds to libsbml (with python3-sbml5 as a
provide) package. When I dug into looking at libsbml, I noticed that the
relevant file (libsbml.py) which throws error
is generated with swig-3.0 by the upstream [3]

While the same file in the apt archive (observed after $apt source
python3-sbml5) seems to be generated with swig-4.0, and that's the current
swig version in Debian now.

When I compared, the one generated with swig 4.0 looks pretty different
from the one generated by swig 3.0.
I "suspect" that the error is due to the swig version change to 4.0, and
corresponding API changes.

I would really appreciate if I could have more folks "confirm" that this is
the case, and I'm not missing out on anything else.
I'll then file a report upstream then, asking for corresponding code
changes needed for swig 4.0.

[1]: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=955656

[2]: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=955656#10

[3]:
https://salsa.debian.org/med-team/libsbml/-/blob/master/src/bindings/python/libsbml.py?expanded=true&viewer=simple

Thanks and regards
Nilesh

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[RFC] python-cobra, python3-sbml5 Nilesh Patra <npatra974@gmail.com> - 2020-04-04 15:50 +0200
  Re: [RFC] python-cobra, python3-sbml5 Andrey Rahmatullin <wrar@debian.org> - 2020-04-04 17:30 +0200
  Re: [RFC] python-cobra, python3-sbml5 Andreas Tille <andreas@fam-tille.de> - 2020-04-05 08:40 +0200
    Re: [RFC] python-cobra, python3-sbml5 Nilesh Patra <npatra974@gmail.com> - 2020-04-05 12:30 +0200
      Re: [RFC] python-cobra, python3-sbml5 Andreas Tille <andreas@an3as.eu> - 2020-04-05 12:30 +0200
        Re: [RFC] python-cobra, python3-sbml5 Nilesh Patra <npatra974@gmail.com> - 2020-04-05 13:00 +0200

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