[Neurodebian-devel] Debian packages for Stimfit

[Christoph Schmidt-Hieber]

On Sat, 5 Feb 2011, Yaroslav Halchenko wrote:
> On Sat, 05 Feb 2011, Christoph Schmidt-Hieber wrote:
>> 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:

Sorry for being unclear: stfio and stimfit are using the same file reading source code, but can't use the same binaries, mostly because some GUI elements such as progress dialogs get compiled for stimfit but not for stfio.
On the long run, I agree it would be good to have a single file reading library (libstfio) used by stimfit and stfio, but this would require some more extensive restructuring of the code.

>    ... 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 can't follow you here: _stf.so is now a symbolic link to libstf.so, i.e. both Python (via _stf.so) as well as bin/stimfit are using the same libstf.so

>> I've added python-stfio to the Recommends for Stimfit.
>
> If not used it could simply be Suggests or absent at all ;-)

Fixed (r471)

>> 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 ;-)

Added (r471)

>>> * 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?

Added to repository (r472).

Best,
Christoph