[Neurodebian-devel] Debian packages for Stimfit

[Yaroslav Halchenko]

On Mon, 24 Jan 2011, Christoph Schmidt-Hieber wrote:
> Unfortunately, stimfit has a rather unusual structure that I'm not too happy with: "libstimfit" is not really a library in the sense that it could be used by anyone else. In fact, it's the full program that I had to split into a separate library so that it can be imported into the Python shell at runtime. If you wish, it's everything except of main().
> Now the problem is that I haven't found an elegant way to make the autotools chain understand that. At the moment, I'm linking explicitly during install (L27 in src/stfswig/Makefile.am)

> 	ln -f ${prefix}/lib/${STF_PYTHON_LIBNAME} ${PYTHON_SITE_PKG}/stimfit/_stf.so

> This hard links libstf.so.0.0.0 to _stf.so so that the Python shell can communicate with the running program.

thanks for the explanation -- it makes things clearer ;-)
since this library is not intended to be public, it better be hidden.
according to
http://www.debian.org/doc/debian-policy/ch-sharedlibs.html
,---
| 8.2 Shared library support files
| It is recommended that supporting files and run-time support programs
| that do not need to be invoked manually by users, but are nevertheless
| required for the package to function, be placed (if they are binary) in
| a subdirectory of /usr/lib, preferably under /usr/lib/package-name.
`---
thus logical location for it /usr/lib/stimfit  and both executable
stimfit and python extensions should be linked against it under coming
from that directory

if you 
ls -l /usr/lib/*/*.so
you will see plentiful of other packages doing the same

I guess the easiest solution is by providing -rpath to the linker and
since it is not public -- version is not per se needed, thus something
like

-Wl,-rpath,${prefix}/lib/aeskulap -avoid-version

in your configure.in

> I would suppose that this is why dh_shlibdeps complains about all these missing symbols because it is not aware of _stf.so?
probably ;-)

> This being said, the deb seems to run and install fine on current Ubuntu and Debian installs.
that is great -- but you do want to make build more robust and
standardized, right? ;-)

> One thing that I would like to add to the deb is the pure-python
>  stfio module. How would I add this to the deb? Create a new
> control/rules/etc. directory? Or add a package to the existing files?

you can build as many binary packages as you like from a single source
package, i.e. debian/control can contain many 'Package: ' entries, in
this case it should be python-stfio, Architecture: all (if it is
pure-python without extensions).  then, after things are built, unless
they get installed directly into debian/binarypackagename/,
usually they get placed under debian/tmp and you direct which things go
to which binary packages by creating debian/binarypackagename.install
files and (unless possible easily with .install files) - by moving
things into corresponding debian/binarypackagename/ subdirectories
within debian/rules.

just look into some package for how things done... e.g. libfann of
Christian seems to be clean enough, so

apt-get source libfann2

and see how things are sorted out 

-- 
Yaroslav O. Halchenko
Postdoctoral Fellow,   Department of Psychological and Brain Sciences
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik