[Neurodebian-devel] Debian packages for Stimfit

[Yaroslav Halchenko]

On Sat, 05 Feb 2011, Christoph Schmidt-Hieber wrote:
> there's been some progress with the packaging:

GREAT! thanks! I will have a look later on

> >$> objdump -t /usr/lib/python2.6/dist-packages/stimfit/_stf.so | grep _ZN9Recording9SetFitEndEi
> >0000000000000000         *UND*  0000000000000000              _ZN9Recording9SetFitEndEi
> >$> objdump -t /usr/lib/stimfit/libstf.so | grep _ZN9Recording9SetFitEndEi
> >0000000000000000         *UND*  0000000000000000              _ZN9Recording9SetFitEndEi

> >and there is more of them:
> >dpkg-shlibdeps: warning: 48 other similar warnings have been skipped (use -v to see them all).

> These warnings are still present after adding -fPIC. Supposedly because _stf.so is only loaded by Python at runtime?
;-) -fPIC is not the cause for them

> No, stimfit isn't using stfio. stfio is a standalone Python
> module for reading files, while Stimfit is a GUI program that happens to
> have an embedded Python shell. They're just using the same file reading
> library.
ok -- what is that library?  ;) is its absence as a library is the
reason for above UNDs? ;-)  Let me requote my previous email:

    ... there would be ./usr/lib/stimfit/libstf.so  which would
    absorbs all the code (e.g. like recording.*) which will be used (linked
    dynamically) by both _stf.so and bin/stimfit

    and definitions present in /usr/lib/stimfit/libstf.so would be defined


> I've added python-stfio to the Recommends for Stimfit.

If not used it could simply be Suggests or absent at all ;-)

> I've added the missing parts to debian/copyright.
> The Axon Instruments/Molecular Devices code is still a problem. While most files mention:

> "Permission is granted to freely to use, modify and copy the code in this file." (sic!)

> this sentence is missing in a few other files. At best, they simply forgot to put it in. I'll try to get a reply from Molecular Devices (they've bought up Axon Instruments).

yes -- sounds like it was just forgotten indeed.  Thanks for the emails

btw please adjust years in debian/copyright for axon/, seem to be
1993-2000

besides being legal information on original dates of copyright, it often
gives an idea on how old project(s) are ;-)


> >* is test.h5  which you use in ./src/stfswig/unittest_stfio.py  too big
> > to be included at least into version control repository?
> >  >...<
> > would you mind sharing some way some other samples files to test
> > functionality of stimfit/python-stfio ?
> >* are there any other tests available besides the above?
> Shame on me, unit testing is pathetic at the moment. We'll try to add some more testing on the long run.

some are better than nothing -- so what about test.h5 file?


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