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Bug#1068032: stimfit 0.16.4-1.1 packaged for debian

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  Bug#1068032: stimfit 0.16.4-1.1 packaged for debian Matthias Klumpp <mak@debian.org> - 2025-02-03 17:10 +0100
    Bug#1068032: stimfit 0.16.4-1.1 packaged for debian Matthias Klumpp <mak@debian.org> - 2025-02-04 01:40 +0100
      Bug#1068032: stimfit 0.16.4-1.1 packaged for debian Matthias Klumpp <mak@debian.org> - 2025-02-06 16:20 +0100
        Bug#1068032: stimfit 0.16.4-1.1 packaged for debian Matthias Klumpp <mak@debian.org> - 2025-02-07 02:00 +0100
          Bug#1068032: stimfit 0.16.4-1.1 packaged for debian Matthias Klumpp <mak@debian.org> - 2025-02-07 14:10 +0100
            Bug#1068032: stimfit 0.16.4-1.1 packaged for debian Matthias Klumpp <mak@debian.org> - 2025-02-10 14:40 +0100

#1231604 — Bug#1068032: stimfit 0.16.4-1.1 packaged for debian

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Hi everyone!

Thanks for maintaining stimfit and resolving this issue!

On Sun, 18 Aug 2024 10:52:27 +0200 Christoph Schmidt-Hieber <christsc@gmx.de>
wrote:
> Dear all,
>
> Apologies for the slow response, I was on holidays.
>
> I have just accepted Alois' pull request on the GitHub repo.

Will the package be uploaded to Debian soon? There's a lot of changes in
the Git repo (which is a bit hard to find without the Vcs-Browser tag
set...) that would make sense to have in Debian...
Please let me know if you need any help :-)

Cheers,
Matthias

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#1231665

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Am Mo., 3. Feb. 2025 um 18:45 Uhr schrieb Alois Schlögl <
alois.schloegl@gmail.com>:

> [...]
> Dear Matthias,
>
>
> thanks for your offer to help. From my point of view, this would be
> appreciated.
> Please find below my assessment of the state of stimfit in debian:
>
> - It should be possible bring stimfit 0.16.4-1.1 into bookworm-backports
> as is.
>
> - Concerning sid, this might be tricky because of the current dependency
> on the old distutils. At this time, I'm not positive that I could do the
> migration to numpy>=2 and the new distutils within the time frame of the
> release of trixie. If you know how to address this, your contribution is
> most welcome.
>

Oh wow, this is a lot more than I expected, and that also explains why the
package isn't in unstable yet...
I can have a look though!

- What is possible is disabling the embedded python (using "./configure
> --disable-python ..."). That's what we call "stimfit-lite" on the
> project homepage https://github.com/neurodroid/stimfit . What I can
> offer is preparing an upload for a stimfit-lite (w/o python support) for
> Debian.
> - This would mean that the debian package "python3-stfio" would not be
> available. Some of its functionality could be replaced by python3-biosig
> <https://packages.debian.org/unstable/python3-biosig> . [1] provides
> some starting points how to do this. However, full compatibility is not
> available at this time.
>

Our lab uses python3-stfio specifically to load CED binary CFS files, which
as far as I know can't be reliably done with any other tool. So, it would
be neat to keep that support. Migrating Python build systems is just about
the least fun thing I can imagine, but the Numpy transition might not be
too bad depending on how stimfit uses it (I have done that in a different
project and it was simple, however, usage of the API was also fairly basic
there).

I'll have a look...

Best,
    Matthias

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#1232005

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Hi Christoph!

Thank you so much, that's amazing - looks like it was quite a bit of work!
Do you want to upload the package (do you need sponsorship for that?).
I can also test it, if needed.

Best,
    Matthias

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#1232059

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Am Do., 6. Feb. 2025 um 20:25 Uhr schrieb Christoph Schmidt-Hieber <
christsc@gmx.de>:

> Hi Matthias
>
> > On 6 Feb 2025, at 16:08, Matthias Klumpp <mak@debian.org> wrote:
> >
> > Thank you so much, that's amazing - looks like it was quite a bit of
> work!
> > Do you want to upload the package (do you need sponsorship for that?).
>
> I vaguely remember using debian mentors many years ago, is this still
> active?
>
> > I can also test it, if needed.
>
> Yes that would be appreciated


mentors.d.n should still work fine, if you upload the package there*, I can
have a look! :-)*

*Best,*
*    Matthias*

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#1232139

Am Fr., 7. Feb. 2025 um 11:49 Uhr schrieb Christoph Schmidt-Hieber
<christsc@gmx.de>:
>
>
> > On 7 Feb 2025, at 01:50, Matthias Klumpp <mak@debian.org> wrote:
> >
> > [...]
> > Yes that would be appreciated
> >
> > mentors.d.n should still work fine, if you upload the package there, I can have a look! :-)
> >
>
> Here you go:
> https://mentors.debian.net/package/stimfit/
>

Nice, thank you!
The package could really need a bit of modernization, but that can be
done iteratively and demanding this now for what is essentially a
bugfix to the archive wouldn't be fair.
Still, can you make these changes for me please?
* Change the pkg-config build dependency to pkgconf? (without it,
we'll immediately get a bug report against the package about this
post-upload)
* Please drop the build-dependency on dh-autoreconf
* Please modernize the debian/watch file a little, this should work
and shouldn't catch "debian-suffixed" versions:
```
version=4

opts=filenamemangle=s/.+\/v?(\d\S+)\.tar\.gz/stimfit-$1\.tar\.gz/ \
  https://github.com/neurodroid/stimfit/tags .*/v?(\d[\d.]+)\.tar\.gz
```
* Please replace Priority: extra in stimfit-dbg with "optional" as
priority (in the long run, now that we have automatic debug symbols,
the package could even be replaced, but no rush!)

Those are the most pressing things, in the long run it would be very
nice to also update to a much higher debhelper version and simplify
d/rules with dh sequencer, and also to bump the standards version.
Maybe it would also be worth considering to you to maintain the
packaging in a Git repository on Salsa, maybe even under the science
team umbrella? => https://salsa.debian.org/science-team/
That would make it a lot easier to collaborate, and you could set the
Vcs-* fields for a bit more automated QA.
But that's optional :-)

I think with these changes, the package is good to go! Can you make
them and reupload to mentors? (I'll just run a few tests on the Python
module still before uploading)

Thank you for all the work!!
Cheers,
    Matthias

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#1232621

Am Mo., 10. Feb. 2025 um 07:43 Uhr schrieb Christoph Schmidt-Hieber
<christsc@gmx.de>:
> > On 9 Feb 2025, at 20:31, Matthias Klumpp <mak@debian.org> wrote:
> >
> > It looks like in order to get stimfit back into the next Debian
> > release, it will unfortunately also need to be ported from sip4 to
> > sip6, as sip4 does not work with Python 3.12+ anymore...
> > See https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1059648 which is
> > currently holding up the migration of stimfit.
> >
>
> Fixed:
> https://github.com/neurodroid/stimfit/commit/705cb1e2
>
> > For the next upload, it would also be nice to provide an icon for the
> > desktop-entry file, so the AppStream error goes away:
> > https://appstream.debian.org/sid/main/issues/stimfit.html
> > (you may even want to switch to only using the desktop-entry file,
> > dropping the menu file)
> >
>
> Done:
> https://github.com/neurodroid/stimfit/commit/85ab2247
>
> Should I prepare a new package version?

Yes, please! This totally warrants a new upload :-)
Thanks for all the work, that's super nice! You can also make the
upload "medium" priority, that's the new default (and would be totally
find here, so the package migrates to testing again a bit faster).

Cheers,
    Matthias

-- 
I welcome VSRE emails. See http://vsre.info/

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