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List:       relax-devel
Subject:    Re: [bug #11483] Parsing problem in ModelFree4 gets relax crash when using "palmer.py"
From:       "Edward d'Auvergne" <edward () domain ! hid>
Date:       2008-04-16 19:11:04
Message-ID: 7f080ed10804161211o1813ec6r7b70e4075234690d () domain ! hid
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Hi,

This bug is now truely fixed.  I simply forgot to use svnmerge.py
(http://www.orcaware.com/svn/wiki/Svnmerge.py) to merge the fixes from
the 1.3 line back to 1.2.  I've tested it out, and the Modelfree mfout
bug is now properly handled in relax's mfout parsing code.

Cheers,

Edward


On Sun, Apr 13, 2008 at 11:46 PM, Edward d'Auvergne
<edward@domain.hid> wrote:
> Hi,
>
>  I've committed a fix to this problem.  Because I can't check if this
>  code functions myself, there are likely to be a few other bugs lying
>  in there.
>
>
>  Cheers,
>
>  Edward
>
>
>  On Sun, Apr 13, 2008 at 11:16 PM, Sébastien Morin
>  <NO-REPLY.INVALID-ADDRESS@gna.org> wrote:
>  >
>
>
> >  Follow-up Comment #4, bug #11483 (project relax):
>  >
>  >  Hi,
>  >
>  >  I tested if the bug was still present.
>  >
>  >  However, I can't tell if the bug is fixed, since there is a new problem
>  >  caused by the fix...
>  >
>  >  For any model (I tested with all 5 model : m1, m2, m3, m4, m5), I get the
>  >  following :
>  >
>  >  ============================================
>  >  relax> palmer.extract(run='m1', dir=None)
>  >
>  > Traceback (most recent call last):
>  >   File "/home/semor/pse-4/collaborations/relax/relax-1.2/relax", line 454, in
>  >  ?
>  >     Relax()
>  >   File "/home/semor/pse-4/collaborations/relax/relax-1.2/relax", line 166, in
>  >
>  > __init__
>  >     self.interpreter.run()
>  >   File
>  >  "/home/semor/pse-4/collaborations/relax/relax-1.2/prompt/interpreter.py",
>  >
>  > line 216, in run
>  >     run_script(intro=self.relax.intro_string, local=self.local,
>  >  script_file=self.relax.script_file, quit=1)
>  >   File
>  >  "/home/semor/pse-4/collaborations/relax/relax-1.2/prompt/interpreter.py",
>  >
>  > line 391, in run_script
>  >     console.interact(intro, local, script_file, quit)
>  >   File
>  >  "/home/semor/pse-4/collaborations/relax/relax-1.2/prompt/interpreter.py",
>  >
>  > line 343, in interact_script
>  >     execfile(script_file, local)
>  >   File "./palmer__stage_2.py", line 142, in ?
>  >     exec_stage_2(runs)
>  >   File "./palmer__stage_2.py", line 76, in exec_stage_2
>  >     palmer.extract(run=name)
>  >   File "/home/semor/pse-4/collaborations/relax/relax-1.2/prompt/palmer.py",
>  >
>  > line 263, in extract
>  >     self.__relax__.generic.palmer.extract(run=run, dir=dir)
>  >   File
>  >  "/home/semor/pse-4/collaborations/relax/relax-1.2/generic_fns/palmer.py",
>  >  line 543, in extract
>  >     data.s2, data.s2_err = self.get_mf_data(self.mfout_S2_pos + pos)
>  >   File
>  >  "/home/semor/pse-4/collaborations/relax/relax-1.2/generic_fns/palmer.py",
>  >  line 614, in get_mf_data
>  >     if search('*', val) or search('*', err):
>  >   File "/usr/lib/python2.4/sre.py", line 134, in search
>  >     return _compile(pattern, flags).search(string)
>  >   File "/usr/lib/python2.4/sre.py", line 227, in _compile
>  >     raise error, v # invalid expression
>  >  sre_constants.error: nothing to repeat
>  >  ============================================
>  >
>  >  This problem is new and apparently caused by the fix proposed.
>  >
>  >  If I comment out lines 613 to 621 in "generic_fns/palmer.py", everything
>  >  passes, so the fix for this bug is fine, and the fix for the "*" character
>  >  bug makes relax crash.
>  >
>  >
>  >
>  >     _______________________________________________________
>  >
>  >  Reply to this item at:
>  >
>  >   <http://gna.org/bugs/?11483>
>  >
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>  >   http://gna.org/
>  >
>  >
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