[Debichem-devel] [Outreachy] pymol

Tue Aug 16 17:01:46 UTC 2016

Hi Andreas,

Could you please take a look at pymol?
I made almost everything possible, except solving this warnings (but I can
fix them too):

   I: pymol: desktop-entry-lacks-keywords-entry
usr/share/applications/pymol.desktop
   W: pymol: command-in-menu-file-and-desktop-file pymol
usr/share/menu/pymol:7

I install examples/ to /usr/share/pymol (as a part of pymol-data package),
because when pymol is installed from sourceforge sources, this directory is
installed to the same place where scripts/ and data/ are installed. Some
scripts from examples/ use files from test/data/, I also install these
files. I also added patch to make these scripts callable from different
directory to allow save results to current directory and not to lose
test/data/ files (if they are used) at the same time.

Tanya.

2016-08-01 18:47 GMT+03:00 Andreas Tille <tille at debian.org>:

> Hi,
>
> just to let you know:  I have moved pymol to
>
>    https://anonscm.debian.org/git/debichem/packages/pymol.git
>
> and I can care for stripping jquery.js later today.
>
> Kind regards
>
>       Andreas.
>
> On Thu, Jul 28, 2016 at 09:54:15AM +0200, Andreas Tille wrote:
> > Hi once again,
> >
> > it seems the upstream source needs to be repackaged due to the
> > compressed copy of jquery (modules/web/examples/sample13/jquery.js).
> > The fact that a source tarball needs to be repackaged is IMHO a good
> > reason for moving the packaging to Git to make sure that all developers
> > are working on a md5sum identical orig.tar.xz.  I'd volunteer to do
> > the migration if nobody insists.
> >
> > Kind regards
> >
> >        Andreas.
> >
> > On Wed, Jul 27, 2016 at 10:42:05PM +0200, Andreas Tille wrote:
> > > Hi again,
> > >
> > > I commited two changes to SVN (fix changelog, remove strange file
> > > monkeypatch_distutils.pyc no idea how to do this better).  When trying
> > > to build in pbuilder this (expectedly) failed due to the pinning to a
> > > certain libpng12-0 version which does not exist in debian unstable.  I
> > > stumbled upon this after sending my previous mail and now I'm wondering
> > > what might have been your motivation for this.
> > >
> > > Kind regards
> > >
> > >       Andreas.
> > >
> > > On Wed, Jul 27, 2016 at 09:57:29PM +0200, Andreas Tille wrote:
> > > > Hi Tanya,
> > > >
> > > > I noticed you have created changelog entries for 1.8.2.1 so you seem
> to
> > > > have managed to update the patches and build the new version, right?
> > > >
> > > > Could you please merge both entries for 1.8.2.1-1 (UNRELEASED) and
> > > > 1.8.2.1-2?
> > > >
> > > > 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
> > > >
> > > >       Andreas.
> > > >
> > > > --
> > > > http://fam-tille.de
> > > >
> > > >
> > >
> > > --
> > > http://fam-tille.de
> > >
> > >
> >
> > --
> > http://fam-tille.de
> >
> > _______________________________________________
> > Debichem-devel mailing list
> > Debichem-devel at lists.alioth.debian.org
> > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debichem-devel
> >
>
> --
> http://fam-tille.de
>

-- 
Best wishes,
Tanya.
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