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Re: [RFC] python-cobra, python3-sbml5

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On Sun, 5 Apr 2020, 15:50 Andreas Tille, <andreas@an3as.eu> wrote:

> On Sun, Apr 05, 2020 at 03:40:56PM +0530, Nilesh Patra wrote:
> > > > '_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]
> > >
> > > I admit I'm absolutely naive about swig - but if libsbml.py is really
> > > autogenerated what about re-generating it with swig-4?
> >
> > I think there's a miscommunication here. The file in the archive(on doing
> > $apt source python3-sbml5) is generated with swig-4 already, while it's
> > generated with swig-3 upstream.
> > Hence the issue.
>
> Ahhh, so it is regenerated in the Debian package build process but it
> conflicts with other parts of the upstream code?  Did I now understood
> correctly?
>

Yep.
That's my _suspicion_ though, that the rest of the upstream code isn't
compatible with the new version, and there are API changes needed.
Hence I sent the mail to confirm if I'm thinking in the right direction.


> I wonder if we should exclude this kind of autogenerated code inside
> the source tarball since we are repackaging the source anyway to exclude
> some files for policy reasons.  I'm doing so in other source tarballs
> for instance with cython files to be absolutely sure that this code
> is regenerated.  This would probably not solve the build issue but might
> be a good idea in general.  What do you think?
>

It seems like libsbml.py would be needed by the rest of the code. So we can
maybe keep the upstream's generated code and not generate it on our own -
this however does not seem DFSG compliant.
Not really sure what to do here.


> Kind regards
>
>       Andreas.
>
> > > > [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
>
> --
> http://fam-tille.de
>

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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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