Hi,
I have now fixed the bug. Carl, would you be able to test the fixes?
I unfortunately cannot replicate the bug as the relaxation data you
use is not available (however if absolutely necessary I could extract
it from the saved file). To check it you need the program Subversion
installed and then either type:
svn co svn://svn.gna.org/svn/relax/1.2 relax-1.2
or:
svn co http://svn.gna.org/svn/relax/1.2 relax-1.2
The resultant code in the 'relax-1.2' directory can then be directly
run using the script. I'll attempt a fix for your other bug report
and then maybe release relax-1.2.11.
Cheers,
Edward
On 5/7/07, Edward d'Auvergne <edward.dauvergne@xxxxxxxxx> wrote:
> Hi Carl,
>
> I'm sorry about the delayed response. I have just moved from
> Australia to Germany to start a postdoc and have been too busy to
> reply to any email until now. Thank you for the bug report. I've
> tried replicating the bug you have identified using your attached
> files but unfortunately I have recently upgraded my system and
> realised that relax doesn't function using Python 2.5. The relax
> error system is completely broken. I'll fix that then try to fix your
> problem.
>
> Cheers,
>
> Edward
>
>
>
> On 4/25/07, anonymous <NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
> >
> > URL:
> > <http://gna.org/bugs/?8996>
> >
> > Summary: Bugs in palmer.py
> > Project: relax
> > Submitted by: None
> > Submitted on: Wednesday 04/25/2007 at 12:32 CEST
> > Category: relax's source code
> > Severity: 3 - Normal
> > Priority: 5 - Normal
> > Status: None
> > Privacy: Public
> > Assigned to: None
> > Originator Name: Carl Diehl
> > Originator Email: carl.diehl@xxxxxxxxx
> > Open/Closed: Open
> > Discussion Lock: Any
> > Release: 1.2.10
> > Operating System: GNU/Linux
> >
> > _______________________________________________________
> >
> > Details:
> >
> > The following bug were encountered while running the palmer.py script with
> > stage=2, stage=1 worked fine with the original data.
> >
> >
> > relax> run.create(run='aic', run_type='mf')
> >
> > relax> model_selection(method='AIC', modsel_run='aic', runs=None)
> > AIC model selection.
> >
> > Instance 0.
> >
> > Run Num_params_(k) Num_data_sets_(n) Chi2
> > Criterion
> >
> > The model from the run None has been selected.
> >
> > Instance 1.
> >
> > Run Num_params_(k) Num_data_sets_(n) Chi2
> > Criterion
> > m1 1 6 4.17590
> > 6.17590
> > m2 2 6 3.77440
> > 7.77440
> > m3 2 6 4.17590
> > 8.17590
> > m4 3 6 3.77440
> > 9.77440
> > m5 3 6 6.09960
> > 12.09960
> >
> > The model from the run 'm1' has been selected.
> >
> > relax> results.write(run='aic', file='results', dir='aic', force=1,
> > format='columnar', compress_type=1)
> > Opening the file 'aic/results.bz2' for writing.
> > Traceback (most recent call last):
> > File "/home/matsl/carl/apps/relax-1.2.10/relax", line 454, in ?
> > Relax()
> > File "/home/matsl/carl/apps/relax-1.2.10/relax", line 166, in __init__
> > self.interpreter.run()
> > File "/home/matsl/carl/apps/relax-1.2.10/prompt/interpreter.py", line
213,
> > in run
> > run_script(intro=self.relax.intro_string, local=self.local,
> > script_file=self.relax.script_file, quit=1)
> > File "/home/matsl/carl/apps/relax-1.2.10/prompt/interpreter.py", line
388,
> > in run_script
> > console.interact(intro, local, script_file, quit)
> > File "/home/matsl/carl/apps/relax-1.2.10/prompt/interpreter.py", line
340,
> > in interact_script
> > execfile(script_file, local)
> > File "palmer.py", line 132, in ?
> > exec_stage_2(runs)
> > File "palmer.py", line 85, in exec_stage_2
> > results.write(run=name, file='results', force=1)
> > File "/home/matsl/carl/apps/relax-1.2.10/prompt/results.py", line 201,
in
> > write
> > self.__relax__.generic.results.write(run=run, file=file,
directory=dir,
> > force=force, format=format, compress_type=compress_type)
> > File "/home/matsl/carl/apps/relax-1.2.10/generic_fns/results.py", line
166,
> > in write
> > self.write_function(results_file, run)
> > File "/home/matsl/carl/apps/relax-1.2.10/specific_fns/model_free.py",
line
> > 4980, in write_columnar_results
> > self.write_columnar_line(file=file, num=data.num, name=data.name,
> > select=data.select, data_set='error', nucleus=nucleus, model=model,
> > equation=equation, params=params, param_set=self.param_set, s2=s2,
s2f=s2f,
> > s2s=s2s, local_tm=local_tm, te=te, tf=tf, ts=ts, rex=rex, r=r, csa=csa,
> > diff_type=diff_type, diff_params=diff_params, pdb=pdb,
pdb_model=pdb_model,
> > pdb_heteronuc=data.heteronuc, pdb_proton=data.proton, xh_vect=xh_vect,
> > ri_labels=ri_labels, remap_table=remap_table, frq_labels=frq_labels,
frq=frq,
> > ri=ri, ri_error=ri_error)
> > AttributeError: Element instance has no attribute 'heteronuc'
> >
> >
> >
> >
> > _______________________________________________________
> >
> > File Attachments:
> >
> >
> > -------------------------------------------------------
> > Date: Wednesday 04/25/2007 at 12:32 CEST Name: palmer.py Size: 4kB By:
> > None
> >
> > <http://gna.org/bugs/download.php?file_id=2268>
> > -------------------------------------------------------
> > Date: Wednesday 04/25/2007 at 12:32 CEST Name: stage1.save.bz2 Size: 3kB
> > By: None
> >
> > <http://gna.org/bugs/download.php?file_id=2269>
> >
> > _______________________________________________________
> >
> > Reply to this item at:
> >
> > <http://gna.org/bugs/?8996>
> >
> > _______________________________________________
> > Message sent via/by Gna!
> > http://gna.org/
> >
> >
> > _______________________________________________
> > relax (http://nmr-relax.com)
> >
> > This is the relax-devel mailing list
> > relax-devel@xxxxxxx
> >
> > To unsubscribe from this list, get a password
> > reminder, or change your subscription options,
> > visit the list information page at
> > https://mail.gna.org/listinfo/relax-devel
> >
>
Re: [bug #8996] Bugs in palmer.py