Path: csiph.com!news.mixmin.net!aioe.org!bofh.it!news.nic.it!robomod From: Nilesh Patra Newsgroups: linux.debian.devel.mentors,linux.debian.maint.python Subject: Re: [RFC] python-cobra, python3-sbml5 Date: Sun, 05 Apr 2020 13:00:02 +0200 Message-ID: References: X-Mailbox-Line: From debian-mentors-request@lists.debian.org Sun Apr 5 10:51:36 2020 Old-Return-Path: X-Amavis-Spam-Status: No, score=-2.849 tagged_above=-10000 required=5.3 tests=[BAYES_00=-2, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, FOURLA=0.1, FREEMAIL_ENVFROM_END_DIGIT=0.25, FREEMAIL_FROM=0.001, HTML_MESSAGE=2, LDO_WHITELIST=-5, MEDS2=2, RCVD_IN_DNSWL_NONE=-0.0001] autolearn=no autolearn_force=no X-Policyd-Weight: using cached result; rate: -5.5 Dkim-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc; bh=up84OrDookzkK2442c36qqKqpkIAAyJDqOCAmGTnnlk=; b=esOQn6FE84dCwuIxjirtUI7wU9zP1d7zfBp3kyVVScmMYhdZUybF46wPBZrV49TNNB fd/oOfQYiADjw7zRMR7jyfzJgrd4KG1ffBwRdnOhnoWVzCtIxGIdV7/ojrraWvh8q9y2 HURUCgnirbANADJtk3bsMCJDh2bEvKrs5Ai9A/xYS2Kcdsv+nIO6bNg8gj1JZF5G5ft0 sjX/meRdd004HHVMx8Sdu+YFJ2zNss3nZe0o6C8ZU+RLu/BTwdCQFIM3BV84wC4pQMBM NGowSj+QqQ3YilwMdEDlqOcm0w/IK+iLMNEIy99MakYEIk0BC7Us6Bc15muTlpjgbe6I rinw== X-Google-Dkim-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=up84OrDookzkK2442c36qqKqpkIAAyJDqOCAmGTnnlk=; b=qh2uFRWQ/SQclt5rZffhydwDuxcjGKkLJ4gbuH7Li6FHDepiQezp9IQ7gVxluGKxwk djgGOfooyd1x6T4jE9KP/+zQiGA83Pa74cgJsTAAj/+twEItyak1usdpip7DQTuVJGzv ffmFLqgdtLRMX+JCx3Liozo96aoz7dfKzzzRG3eBo605EXoW5kPHV5yZCI21pVk8QXZf GgSQybl88KMho5dwtVVqDYNEEs/Dj6emIWOwSNgv7Mzegq6J7V6BypjjQIWdqOMfQje8 H1s0C5gVBJKhLOH4D993+wbMSL7dyoC7Jf0iH/ZzDlHZw8jnTvCJcwfZ4L4uMsFq3YZY RHHw== X-Gm-Message-State: AGi0PuZgBIs6p+C9sBgPvdKdQsIv4rZWQ0PO5t5UlIWArrLRWZ6BlOKD RTTLtfmMUi+wNhDqVCfyJh6+lWIB5QU7zpsRdMI= X-Google-SMTP-Source: APiQypK3HP1ilEL5Cjn0ShhtVtXoGOujFhwa3rbZUtUmIPoikabdW4VswY9MtciG/7KZqqSGOSHSRaDzHXiwwr6otzk= X-Received: by 2002:a67:f993:: with SMTP id b19mr11493930vsq.117.1586082934063; Sun, 05 Apr 2020 03:35:34 -0700 (PDT) MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="000000000000de86c605a288b53f" X-Mailing-List: archive/latest/102231 List-ID: List-URL: List-Archive: https://lists.debian.org/msgid-search/CAJN1929YXQk3dv2OMmYG_R8xmZhLMJUmNixMwM-gw6d=xEk9GA@mail.gmail.com Approved: robomod@news.nic.it Lines: 141 Organization: linux.* mail to news gateway Sender: robomod@news.nic.it X-Original-Cc: debian-mentors@lists.debian.org, Debian Python X-Original-Date: Sun, 5 Apr 2020 16:05:21 +0530 X-Original-Message-ID: X-Original-References: <20200405061355.GI7599@an3as.eu> <20200405102025.GO7599@an3as.eu> Xref: csiph.com linux.debian.devel.mentors:43517 linux.debian.maint.python:12429 --000000000000de86c605a288b53f Content-Type: text/plain; charset="UTF-8" On Sun, 5 Apr 2020, 15:50 Andreas Tille, 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 > --000000000000de86c605a288b53f Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable


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 p= ython3-sbml5 as a
> > > provide) package. When I dug into looking at libsbml, I noti= ced 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 i= s really
> > autogenerated what about re-generating it with swig-4?
>
> I think there's a miscommunication here. The file in the archive(o= n doing
> $apt source python3-sbml5) is generated with swig-4 already, while it&= #39;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?=C2=A0 Did I now understood=
correctly?

Yep.
That's my _suspicion_ though, tha= t the rest of the upstream code isn't compatible with the new version, = and there are API changes needed.
Hence I sent the m= ail 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.=C2=A0 I'm doing so in other source tarba= lls
for instance with cython files to be absolutely sure that this code
is regenerated.=C2=A0 This would probably not solve the build issue but mig= ht
be a good idea in general.=C2=A0 What do you think?
<= /div>

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 no= t seem DFSG compliant.
Not really sure what to do he= re.

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