[Debichem-devel] [Outreachy] pymol

Andreas Tille andreas at fam-tille.de
Wed Jul 27 19:57:29 UTC 2016

Hi Tanya,

I noticed you have created changelog entries for so you seem to
have managed to update the patches and build the new version, right?

Could you please merge both entries for (UNRELEASED) and

On Wed, Jul 27, 2016 at 07:44:51PM +0300, merlettaia wrote:
> Hi Andreas,
> For now I wrote simple test which runs over all .py and .pml scripts inside
> specific directory and tries to run them with pymol with -c flag (for now
> this script doesn't care if python errors appear during run - it only
> checks that pymol closes as expected). This is made because some of these
> scripts (located in `data` and `examples` directories in upstream source
> tree) use data from other directories in relative paths and write to the
> folder where they are located in. I symlink them to temporary directory. I
> haven't solved usage of files from relative paths yet, that's why this
> leads to python exceptions, but pymol still closes as expected.
> Incorrect paths are present in installed example scripts, for example, in
> /usr/share/doc/pymol/examples/generate_amber.py there is a line:
>     model= io.pdb.fromFile("../../test/dat/pept.pdb")
> Since in installation this path is incorrect, this script also raises
> python exception (but pymol command line closes as expected).

I admit I'm not fully sure if I understand all this but for me this
sounds like another quilt patch would be needed to fix the pathes.

> I don't know
> how to deal with these relative files. I can fix as many examples as I
> could to make them find input parameters correctly when they are installed,
> or write several examples by myself. What is a better solution?

Hard to say.  May be users might know some of these examples from
anywhere else than Debian and want to run these.  Moreover if you manage
to fix these examples this could be forwarded upstream which is in the
interest of all users.
> I've updated patches 22 and 31 and fixed several lintian warnings.

Very nice!
> Is this bug in the same state as it was?
> https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=506202 - I can fix it
> too, if no one fixed it yet.

Cool, I filed a bug 8 years ago.  I do not even remember. :-)  If there
is nothing in the bug log and neither in the packaging it is probably
not fixed.  I would not really call it a show stoper for an upload but
if you would fix this it would be nice.
> For now I'll add a testsuite for apbs (it will be very simple, but probably
> it would help make it work with pdb2pqr).

Very good job so far.

Thanks a lot for your work on this



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