[Debian-med-packaging] Bug#855494: PMV in Debian: oldnumeric is no more

[Andreas Tille]

Hi,

$ runPmv
Run PMV from  /usr/lib/python2.7/dist-packages/Pmv
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/Pmv/__init__.py", line 378, in runPmv
    from Pmv.moleculeViewer import MoleculeViewer
  File "/usr/lib/python2.7/dist-packages/Pmv/moleculeViewer.py", line 16, in <module>
    from MolKit.molecule import Atom, AtomSet, BondSet, Molecule , MoleculeSet
  File "/usr/lib/python2.7/dist-packages/MolKit/molecule.py", line 26, in <module>
    from numpy.oldnumeric import sum, array, less_equal, take, nonzero, argsort
ImportError: No module named oldnumeric
hit enter to continue
$ apt-cache policy mgltools-pmv
mgltools-pmv:
  Installiert:           1.5.7-1
  Installationskandidat: 1.5.7-1
  Versionstabelle:
 *** 1.5.7-1 100
         50 http://ftp.de.debian.org/debian unstable/non-free amd64 Packages
        100 /var/lib/dpkg/status


So the problem persists.  Please, pretty please fix it.  Otherwise it
needs to be removed from the archive.

Kind regards

      Andreas.

On Thu, Sep 28, 2017 at 11:39:44AM +0200, Steffen Möller wrote:
> Hello,
> 
> Michel may have spotted this nicely. I have just tested 1.5.7-2 (the
> version currently in unstable) and this works - both autodocktools and
> runPmv are starting up just fine. Could you please confirm so on your
> site, Andreas?
> 
> Concerning the official download point, Andreas is right. While had
> acquired some routine with your CVS repository, those skills are slowly
> fading away :) An official tarball like there is one visibly announced
> for 1.5.6 would be nice.
> 
> Should Andreas confirm that this bug report is mute, then this was just
> some horrible noise that prevented the new version to migrate to
> testing. Yeah.
> 
> Cheers,
> 
> Steffen
> 
> 
> On 28.09.17 08:21, Andreas Tille wrote:
> > [Put publicly archived bug page in CC to have a record of the discussion]
> >
> > Hi Michel,
> >
> > I'm not involved in MGLTools packaging but out of curiosity:  Where can
> > I download MGLTools 1.5.7.  The page
> >
> >     http://mgltools.scripps.edu/downloads/
> >
> > only lists 1.5.6.
> >
> > Kind regards
> >
> >        Andreas.
> >
> > On Wed, Sep 27, 2017 at 04:46:47PM -0700, Michel Sanner wrote:
> >> Hallo Steffen
> >>
> >> I am not sure what this bug is about but MGLTools 1.5.7 does not use
> >> oldnumeric at all
> >>
> >> the bug mentions version 1.5.7-1 which I am not sure if it a debian release
> >> numbering thing or whether this refers to 1.5.7rc1 which pre-dates 1.5.7
> >> (final)
> >>
> >> So this might be a non-issue in the end
> >>
> >> -Michel
> >>
> >> On 09/20/2017 02:53 PM, Steffen Möller wrote:
> >>> Dear all,
> >>>
> >>> It is quite some time that we had been in touch and I hope you are doing
> >>> just fine.
> >>>
> >>> I am very bad myself at skimming through our bug reports and was only
> >>> now pointed by Andreas (CCed) to a report from February that with the
> >>> advent of numpy 1.9.1 the oldnumeric is gone. The report is at
> >>> https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=855494
> >>>
> >>> ...
> 

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