[bug #25084] Running Model_Free on multi processors Fedora 20 complications

[Edward d Auvergne]

Follow-up Comment #9, bug #25084 (project relax):

I've attached a source code patch that implements MPI vendor information for
the relax information printout.  This relies on the new
mpi4py.MPI.get_vendor() function though, and it does not give information
about the MPI installation path.

(file #28805)
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Additional Item Attachment:

File name: mpi4py_info.patch  Size:1 KB


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[bug #25084] Running Model_Free on multi processors Fedora 20 complications

[Edward d Auvergne]

Follow-up Comment #8, bug #25084 (project relax):

Hmmm, mpi4py.MPI.get_vendor() is only present in later mpi4py versions.

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[bug #25084] Running Model_Free on multi processors Fedora 20 complications

[Edward d Auvergne]

Follow-up Comment #7, bug #25084 (project relax):

Maybe see mpi4py.MPI.get_vendor().  That will get you the exact MPI version
that mpi4py is compiled against (though not its path).  This might be worth
adding to the relax information printout.

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[bug #25133] Error using Dimer pdb files for model free

[Edward d Auvergne]

Update of bug #25133 (project relax):

  Status:None => Works For Me   
 Assigned to:None => bugman 
 Open/Closed:Open => Closed 
Operating System:64-bit GNU/Linux => All systems

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Follow-up Comment #2:

As in the mailing list discussions - this is simply a problem of loading one
molecule of the dimer.

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[bug #25133] Error using Dimer pdb files for model free

[Edward d Auvergne]

Follow-up Comment #1, bug #25133 (project relax):

For discussions, see:

https://mail.gna.org/public/relax-users/2016-09/msg00048.html
https://mail.gna.org/public/relax-users/2016-09/msg00054.html

and the subsequent thread.

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[bug #25084] Running Model_Free on multi processors Fedora 20 complications

[Edward d Auvergne]

Follow-up Comment #5, bug #25084 (project relax):

A correctly configured MPI system should result in relax printing out the
introductory text within seconds.  The problem is not from relax.

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[bug #24962] six System / functional tests faiiures against numpy 1.11.1 and scipy 0.18.0

[Edward d Auvergne]

Follow-up Comment #4, bug #24962 (project relax):

Let's see how long it takes them to release 0.18.1.  This bug is rather major
and anyone using 0.18.0 should really update once it is fixed.  In relax
however it is only used in the frame order analysis, so it is not a major
issue.

The nquad() fix seems like an ugly hack, as scipy.integrate quad(), dblquad()
and tplquad() are all used in the same code paths in relax, and converting
only one of these three to nquad() would be confusing.  It would be better to
convert all to nquad().  I'm wondering if we could just blacklist these system
tests for scipy 0.18.0.

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[bug #24962] six System / functional tests faiiures against numpy 1.11.1 and scipy 0.18.0

[Edward d Auvergne]

Update of bug #24962 (project relax):

Operating System:Mac OS X => All systems

___

Follow-up Comment #2:

Hmmm, it looks like SciPy broke backwards compatibility with the
scipy.integrate.dblquad() function.  I don't see anything mentioned on the
0.18.0 release notes . 
Maybe this should be reported as an upstream bug in SciPy?

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[bug #24675] Superfluous dispersion curves for missing data.

[Edward d Auvergne]

Update of bug #24675 (project relax):

  Status: In Progress => Wont Fix   
 Open/Closed:Open => Closed 
 Summary: superfluous dispersion curves for missing data =>
Superfluous dispersion curves for missing data.

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Follow-up Comment #3:

For discussions, see the mailing list thread at: 
http://thread.gmane.org/gmane.science.nmr.relax.user/1886/focus=1890.  This is
actually a deliberate feature to help understand why the data might be
missing.

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[bug #24675] superfluous dispersion curves for missing data

[Edward d Auvergne]

Follow-up Comment #2, bug #24675 (project relax):

Attaching a PDF file showing the dispersion curves for the CR72 model for
residue 134.

(file #27466)
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File name: disp_CKIRD_134_N.pdf   Size:24 KB


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[sr #3345] Inversion recovery curve fitting - incorrect equation.

[Edward d Auvergne]

Update of sr #3345 (project relax):

  Status:None => Done   
 Open/Closed:Open => Closed 

___

Follow-up Comment #2:

For discussions, see the mailing list thread: 
http://thread.gmane.org/gmane.science.nmr.relax.devel/7740.  This has been
treated as a bug report.  The bug has now been fixed, and this report will be
closed.

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[sr #3345] Inversion recovery curve fitting - incorrect equation.

[Edward d Auvergne]

Update of sr #3345 (project relax):

 Assigned to:None => bugman 
Operating System:   GNU/Linux => All systems
 Summary: Inversion recovery curve fitting => Inversion
recovery curve fitting - incorrect equation.


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[sr #3349] Relax GUI installation problem

[Edward d Auvergne]

Follow-up Comment #1, sr #3349 (project relax):

Hi Sam,

The problem is with the version of wxPython on your system.  The "phoenix"
versions are very, very new and are neither stable nor complete.  This is a
complete rewrite that is not compatible with older wxPython versions.  I have
not ported the relax GUI to wxPython-phoenix yet, as there are too many
features still missing, and the relax GUI will not run.  Do you have other,
older wxPython packages available on your system that you can install?

Regards,
Edward

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[bug #24723] The mean RMSD from the structure.rmsd user function is incorrectly calculated - it should be a quadratic mean.

[Edward d Auvergne]

Update of bug #24723 (project relax):

  Status:None => Fixed  
 Open/Closed:Open => Closed 


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[bug #24723] The mean RMSD from the structure.rmsd user function is incorrectly calculated - it should be a quadratic mean.

[Edward d Auvergne]

URL:
  

 Summary: The mean RMSD from the structure.rmsd user function
is incorrectly calculated - it should be a quadratic mean.
 Project: relax
Submitted by: bugman
Submitted on: Thu 02 Jun 2016 03:16:10 PM UTC
Category: relax's source code
Specific analysis category: All analyses
Priority: 7 - High
Severity: 4 - Important
  Status: None
 Assigned to: bugman
 Originator Name: 
Originator Email: 
 Open/Closed: Open
 Release: 4.0.2
 Discussion Lock: Any
Operating System: All systems

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Details:

The subject says it all ;)




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[bug #24601] R2eff dispersion model - missing data problem

[Edward d Auvergne]

Update of bug #24601 (project relax):

  Status:   Confirmed => Fixed  
 Open/Closed:Open => Closed 


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[bug #24601] R2eff dispersion model - missing data problem

[Edward d Auvergne]

Update of bug #24601 (project relax):

Operating System:*BSD => All systems
 Summary:missing data problem => R2eff dispersion model -
missing data problem

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Follow-up Comment #2:

This bug is easy enough to solve, however it is taking longer than normal as
there are a lot of downstream user functions (error analysis, plotting, data
output, etc.) which all need to be updated.

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[bug #24601] missing data problem

[Edward d Auvergne]

Update of bug #24601 (project relax):

  Status:None => Confirmed  


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[bug #24601] missing data problem

[Edward d Auvergne]

Update of bug #24601 (project relax):

 Assigned to:None => bugman 


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[bug #24300] Failure of the structure.read_pdb user function with merge=True and multiple structures and multiple models.

[Edward d Auvergne]

URL:
  

 Summary: Failure of the structure.read_pdb user function with
merge=True and multiple structures and multiple models.
 Project: relax
Submitted by: bugman
Submitted on: Mon 11 Jan 2016 08:36:23 AM UTC
Category: relax's source code
Specific analysis category: All analyses
Priority: 3 - Low
Severity: 2 - Minor
  Status: In Progress
 Assigned to: bugman
 Originator Name: 
Originator Email: 
 Open/Closed: Open
 Release: 4.0.1
 Discussion Lock: Any
Operating System: All systems

___

Details:

The error is:

relax> structure.read_pdb(file='C-dom.pdb', dir=None, read_mol=None,
set_mol_name=['CaM A', 'CaM B', 'CaM C'], read_model=None, set_model_num=None,
alt_loc=None, verbosity=1, merge=True)

Internal relax PDB parser.
Opening the file 'C-dom.pdb' for reading.
Merging with molecule 'CaM A' of model 1 (from the original molecule number 1
of model 1).
Merging with molecule 'CaM B' of model 1 (from the original molecule number 2
of model 1).
Merging with molecule 'CaM C' of model 1 (from the original molecule number 3
of model 1).
Merging with molecule 'CaM A' of model 2 (from the original molecule number 1
of model 2).
RelaxError: The new molecule name of 'CaM A' in model 2 does not match the
corresponding molecule's name of 'CaM C' in model 1.





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[bug #24300] Failure of the structure.read_pdb user function with merge=True and multiple structures and multiple models.

[Edward d Auvergne]

Update of bug #24300 (project relax):

  Status: In Progress => Fixed  
 Open/Closed:Open => Closed 


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[bug #24218] The alignment lables printed out by the align_tensor.matrix_angles user function are incorrect.

[Edward d Auvergne]

URL:
  

 Summary: The alignment lables printed out by the
align_tensor.matrix_angles user function are incorrect.
 Project: relax
Submitted by: bugman
Submitted on: Mon 21 Dec 2015 10:04:21 AM UTC
Category: relax's source code
Specific analysis category: N-state model (ensemble analysis)
Priority: 5 - Normal
Severity: 3 - Normal
  Status: None
 Assigned to: bugman
 Originator Name: 
Originator Email: 
 Open/Closed: Open
 Release: 4.0.1
 Discussion Lock: Any
Operating System: All systems

___

Details:

For example, the following commands:

pipe.create('test', 'N-state')
align_tensor.init(tensor='A', align_id='A', params=(1, 1, 1, 1, 1))
align_tensor.init(tensor='B', align_id='A', params=(1, 1, 1, 1, 1))
align_tensor.init(tensor='C', align_id='A', params=(1, 1, 1, 1, 1))
align_tensor.matrix_angles(tensors=['B', 'C'])

Produce:

relax> align_tensor.matrix_angles(basis_set='matrix', tensors=['B', 'C'],
angle_units='deg', precision=1)
Standard inter-tensor matrix angles in degrees using the Euclidean inner
product divided by the Frobenius norms (theta =
arccos(/(||A1||.||A2||))):

 A   B   
A 0.0 0.0
B 0.0 0.0




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[bug #24218] The alignment lables printed out by the align_tensor.matrix_angles user function are incorrect.

[Edward d Auvergne]

Update of bug #24218 (project relax):

  Status:None => Fixed  
 Open/Closed:Open => Closed 


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[bug #24131] BMRB export fails with 'SpinContainer' object has no attribute 's2'.

[Edward d Auvergne]

Follow-up Comment #8, bug #24131 (project relax):

Try running 'svn up' again.  After creating the system test and making it
pass, I found other system tests failing and fixed those (see comment #5
below).  The behaviour should now be quite different, but I don't know if
everything is fixed, so more system tests might be necessary.

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[bug #24131] BMRB export fails with 'SpinContainer' object has no attribute 's2'.

[Edward d Auvergne]

Update of bug #24131 (project relax):

  Status:   Fixed => In Progress
 Open/Closed:  Closed => Open   


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[bug #24131] BMRB export fails with 'SpinContainer' object has no attribute 's2'.

[Edward d Auvergne]

Follow-up Comment #12, bug #24131 (project relax):

Ok, a new fix has been committed (see comment #11 below).  Could you please
check again?  Note that the RelaxError from the fails_duplicate_interaction.py
script should be there, as the interatomic N-H interaction is already defined.

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[bug #24131] BMRB export fails with 'SpinContainer' object has no attribute 's2'.

[Edward d Auvergne]

Update of bug #24131 (project relax):

  Status: In Progress => Fixed  
 Open/Closed:Open => Closed 

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Follow-up Comment #14:

No problems - this was quite an easy and quick one to solve with the data and
scripts you attached.  Cheers!

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[bug #23644] monte_carlo.error_analysis() does not update the mean value/expectation value from simulations

[Edward d Auvergne]

Update of bug #23644 (project relax):

Category:None => relax's source code
Specific analysis category:None => All analyses   
  Status:None => Invalid
 Assigned to:None => tlinnet
 Open/Closed:Open => Closed 

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Follow-up Comment #3:

I guess this bug should be classified as 'invalid'?

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[sr #3303] Automatic back-calculation of spin relaxation data.

[Edward d Auvergne]

Update of sr #3303 (project relax):

  Status: In Progress => Done   
 Open/Closed:Open => Closed 

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Follow-up Comment #2:

For discussions, see: 
http://thread.gmane.org/gmane.science.nmr.relax.devel/7681

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[bug #24131] BMRB export fails with 'SpinContainer' object has no attribute 's2'.

[Edward d Auvergne]

Update of bug #24131 (project relax):

  Status:   Need Info => Fixed  
 Open/Closed:Open => Closed 


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[bug #23389] GUI tests segfaults in 3.3.7

[Edward d Auvergne]

Update of bug #23389 (project relax):

  Status:None => Postponed  


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[bug #22557] Monte-Carlo simulations for R1rho dispersion analysis, does not include randomization of R1.

[Edward d Auvergne]

Update of bug #22557 (project relax):

  Status:None => Postponed  


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[bug #22542] NS R1rho 2-site seems to be wrong implemented.

[Edward d Auvergne]

Update of bug #22542 (project relax):

  Status:None => Postponed  


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[bug #24131] BMRB export fails with 'SpinContainer' object has no attribute 's2'.

[Edward d Auvergne]

Follow-up Comment #3, bug #24131 (project relax):

I would have guessed this to be the problem, but I need to check why it is not
skipped.  The system test is important to check if the bug is fixed, and that
it never returns.  Cheers!

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[bug #24131] BMRB export fails with 'SpinContainer' object has no attribute 's2'.

[Edward d Auvergne]

Update of bug #24131 (project relax):

Specific analysis category:None => Model-free analysis
  Status:None => Need Info  
 Assigned to:None => bugman 
Operating System:Mac OS X (Intel) => All systems
 Summary: BMRB export fails with 'SpinContainer' object has no
attribute 's2' => BMRB export fails with 'SpinContainer' object has no
attribute 's2'.

___

Follow-up Comment #1:

I would suggest using the residue.delete user function in a few tests to
narrow this down to one or two spins, then save a new results file.  Using
ranges such as ":1-100" to delete residues 1 to 100 will make this a quick
process.

You could then slightly randomise the data, change the molecule name, etc. all
within the XML file using a text editor.  Note, the number is really stored as
the  value, but you can delete this tag if you are
careful.  Or you can edit the values directly as:

cdp.mol[0].res[0].spin[0].s2
cdp.mol[0].res[0].spin[0].relax_data['R1_600']

If you could attach such a truncated and obfuscated results file, I can then
add the file to relax and create a new system test based on the current
'relax_output.txt' file to catch the bug.  Cheers!

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[sr #3303] Automatic back-calculation of spin relaxation data.

[Edward d Auvergne]

Update of sr #3303 (project relax):

  Status:None => In Progress
 Assigned to:None => bugman 
Operating System:   GNU/Linux => All systems
 Summary: Automatic back-calculation of spin relaxation data
=> Automatic back-calculation of spin relaxation data.


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[bug #23933] 'RelaxWarning: comparison to `None` will result in an elementwise object comparison in the future' in modelfree

[Edward d Auvergne]

Update of bug #23933 (project relax):

 Assigned to:None => bugman 
Operating System:   64-bit MS Windows => All systems


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[bug #23933] 'RelaxWarning: comparison to `None` will result in an elementwise object comparison in the future' in modelfree

[Edward d Auvergne]

Update of bug #23933 (project relax):

Category: GUI => relax's source code
  Status:None => Fixed  
 Open/Closed:Open => Closed 

___

Follow-up Comment #3:

This bug report consists of two issues:  1. The comparison to 'None' warning; 
2. The 'NameError: global name 'ids' is not defined' error.

=== Comparison to 'None' ===

Modified from
http://thread.gmane.org/gmane.science.nmr.relax.user/1839/focus=1842 :

This warning is due to something called a FutureWarning which was introduced
into numpy >= 1.9.  It looks like the numpy would like to change how '=='
operates on their numpy arrays.  So the previous relax code was of the form:

if vector == None:

This used to work and was good for checking if we had set a value.  However
the numpy people would like us to now instead use:

if vector is None:

To fix this, the suite was run with Python 3.5 and numpy 1.9.2, using:

$ python3.5 relax -x -d --tee test_suite.log --traceback

All these FutureWarnings were found and '==' and '=!' was replaced with 'is'
and 'is not' to silence them all.  This was also fixed in minfx
 and bmrblib
.


=== 'ids' is missing ===

The Mf.test_bug_23933_relax_data_read_ids system test was created based on the
attached data files, truncated to residues 329, 330, and 331.  It catches the
error:

relax> relax_data.read(ri_id='R1_600', ri_type='R1', frq=600402816.0,
file='r1_600.txt',
dir='/data/relax/relax-trunk/test_suite/shared_data/model_free/bug_23933_relax_data_read_ids',
spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=None,
spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None,
spin_id=None)
Opening the file
'/data/relax/relax-trunk/test_suite/shared_data/model_free/bug_23933_relax_data_read_ids/r1_600.txt'
for reading.
Traceback (most recent call last):
  File "/data/relax/relax-trunk/test_suite/system_tests/model_free.py", line
499, in test_bug_23933_relax_data_read_ids
self.interpreter.relax_data.read(ri_id='R1_600', ri_type='R1',
frq=600402816.0, file='r1_600.txt', dir=path, res_num_col=1, data_col=2,
error_col=3)
  File "/data/relax/relax-trunk/prompt/uf_objects.py", line 225, in __call__
self._backend(*new_args, **uf_kargs)
  File "/data/relax/relax-trunk/pipe_control/relax_data.py", line 920, in
read
pack_data(ri_id, ri_type, frq, values, errors, mol_names=mol_names,
res_nums=res_nums, res_names=res_names, spin_nums=spin_nums,
spin_names=spin_names, spin_id=spin_id)
  File "/data/relax/relax-trunk/pipe_control/relax_data.py", line 767, in
pack_data
if ids:
NameError: global name 'ids' is not defined


The problem was missing code that was planned to be added to relax, but never
was.  Now the correct behaviour occurs and the error is now seen correctly:

relax> relax_data.read(ri_id='R1_600', ri_type='R1', frq=600402816.0,
file='r1_600.txt',
dir='/data/relax/relax-trunk/test_suite/shared_data/model_free/bug_23933_relax_data_read_ids',
spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=None,
spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None,
spin_id=None)
Opening the file
'/data/relax/relax-trunk/test_suite/shared_data/model_free/bug_23933_relax_data_read_ids/r1_600.txt'
for reading.
Traceback (most recent call last):
  File "/data/relax/relax-trunk/test_suite/system_tests/model_free.py", line
499, in test_bug_23933_relax_data_read_ids
self.interpreter.relax_data.read(ri_id='R1_600', ri_type='R1',
frq=600402816.0, file='r1_600.txt', dir=path, res_num_col=1, data_col=2,
error_col=3)
  File "/data/relax/relax-trunk/prompt/uf_objects.py", line 225, in __call__
self._backend(*new_args, **uf_kargs)
  File "/data/relax/relax-trunk/pipe_control/relax_data.py", line 925, in
read
pack_data(ri_id, ri_type, frq, values, errors, mol_names=mol_names,
res_nums=res_nums, res_names=res_names, spin_nums=spin_nums,
spin_names=spin_names, spin_id=spin_id)
  File "/data/relax/relax-trunk/pipe_control/relax_data.py", line 773, in
pack_data
raise RelaxMultiSpinIDError(spin_ids[i], new_ids)
RelaxMultiSpinIDError: RelaxError: The spin ID
'#LARA_N_term_no_helixFH_reg_mol24:331' corresponds to multiple spins,
including '#LARA_N_term_no_helixFH_reg_mol24:331@N' and
'#LARA_N_term_no_helixFH_reg_mol24:331@H'.

The problem here is that the relaxation data needs to be loaded for either the
'N' or 'H' spins - the user function call is ambiguous and relax cannot work
out for which spin the data is for.


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[sr #3256] Using .rate Files for Relaxation Dispersion

[Edward d Auvergne]

Update of sr #3256 (project relax):

Operating System:  Mac OS = All systems

___

Follow-up Comment #1:

Try having a look at the relax_disp.r2eff_read and relax_disp.r2eff_read_spin
user funtions.  This might be what you are after.  This is not so well tested
in the GUI as it is designed around the processing of peak intensities, but it
might work.  It has been discussed before:

* Re: R1rho RD analysis
http://thread.gmane.org/gmane.science.nmr.relax.user/1666/focus=1672

I would recommend sending any detailed discussions to the relax-users att
gna.org mailing list instead of here.  Or to the relax-devel mailing list for
any development suggestions.

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[sr #3219] Help for inputting CPMG dispersion data from heigh list

[Edward d Auvergne]

Follow-up Comment #1, sr #3219 (project relax):

I've just tested this out, and for the sequence.read user function it looks
like the sep argument set to the comma ',' does not work.  I'll create a bug
report for this and fix it (by creating a system test using part of the data
attached here).

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[bug #23372] Comma separated files cannot be handled by the relax sequence.read user function.

[Edward d Auvergne]

URL:
  http://gna.org/bugs/?23372

 Summary: Comma separated files cannot be handled by the relax
sequence.read user function.
 Project: relax
Submitted by: bugman
Submitted on: Tue 10 Mar 2015 08:10:48 AM UTC
Category: relax's source code
Specific analysis category: All analyses
Priority: 5 - Normal
Severity: 3 - Normal
  Status: None
 Assigned to: bugman
 Originator Name: 
Originator Email: 
 Open/Closed: Open
 Release: 3.3.6
 Discussion Lock: Any
Operating System: All systems

___

Details:

If a CSV file is used for relax input, the sequence.read user function fails
with the repeated warning:

RelaxWarning: ror: The sequence data in the line
['338,43670116,25946892,25320942,26354478,26269982,26755484,21052750,27046646,25959150,26320168,25146354,26695994,25734376,27137566,24501030,24206178,22368290,23439314,25883196,26154024']
is invalid, the residue number data
'338,43670116,25946892,25320942,26354478,26269982,26755484,21052750,27046646,25959150,26320168,25146354,26695994,25734376,27137566,24501030,24206178,22368290,23439314,25883196,26154024'
is invalid.


An example input file which fails is attached to sr #3219
(https://gna.org/support/?3219).




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[bug #23372] Comma separated files cannot be handled by the relax sequence.read user function.

[Edward d Auvergne]

Update of bug #23372 (project relax):

  Status:None = Fixed  
 Open/Closed:Open = Closed 


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[sr #3219] Help for inputting CPMG dispersion data from heigh list

[Edward d Auvergne]

Follow-up Comment #5, sr #3219 (project relax):

The problem of not handling commas was reported in bug #23372
(https://gna.org/bugs/?23372), the sequence.read failure with CSV files.  I
implemented the Sequence.test_bug_23372_read_csv system test to catch the
problem using your Sam.csv file attached here (which you can now see at
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/peak_lists/).

If you have subversion installed on your system, you could use the source
version of relax
http://www.nmr-relax.com/download.html#Source_code_repository.  You should
now be able to read this file into relax for both sequence data and peak
heights.  Otherwise you will need to wait until I can find the time to release
a new version of relax.

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[sr #3219] Help for inputting CPMG dispersion data from height list.

[Edward d Auvergne]

Update of sr #3219 (project relax):

Operating System:   Microsoft Windows = All systems


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[sr #3219] Help for inputting CPMG dispersion data from height list.

[Edward d Auvergne]

Update of sr #3219 (project relax):

  Status:None = Done   
 Open/Closed:Open = Closed 
 Summary: Help for inputting CPMG dispersion data from heigh
list = Help for inputting CPMG dispersion data from height list.

___

Follow-up Comment #6:

The following pseudo-script will read the data out of the attached Sam.csv
file:


# Create the data pipe.
pipe.create(pipe_name='test', pipe_type='relax_disp')

# Load the sequence.
sequence.read('Sam.csv', dir='.', res_num_col=1, sep=',')

# Name the spins so they can be matched to the assignments, and the isotope
for field strength scaling.
spin.name(name='N')
spin.isotope(isotope='15N')

# Load the peak intensities.
spectrum.read_intensities('Sam.csv', dir='.', spectrum_id='test',
int_method='height', int_col=2, res_num_col=1, sep=',')


This is just a demonstration.  If using the GUI, just use the settings as
above.

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[bug #23295] PDB secondary structure HELIX and SHEET records not updated when merging molecules.

[Edward d Auvergne]

URL:
  http://gna.org/bugs/?23295

 Summary: PDB secondary structure HELIX and SHEET records not
updated when merging molecules.
 Project: relax
Submitted by: bugman
Submitted on: Fri 20 Feb 2015 10:37:26 AM UTC
Category: relax's source code
Specific analysis category: All analyses
Priority: 3 - Low
Severity: 2 - Minor
  Status: None
 Assigned to: bugman
 Originator Name: 
Originator Email: 
 Open/Closed: Open
 Release: 3.3.6
 Discussion Lock: Any
Operating System: All systems

___

Details:

The structure.read_pdb user function
http://www.nmr-relax.com/manual/structure_read_pdb.html fails to correctly
update HELIX and SHEET secondary structure metadata in a PDB file when
molecules are merged.  The attached '2BE6_secondary_structure.pdb' file which
contains the HELIX and SHEET records from the 2BE6 PDB file, as well as a few
atoms from each of the 6 molecules, together with the attached 'test.py' relax
script demonstrate the problem.  For example the input HELIX record:

HELIX9   9 VAL D 1615  GLY D 1638  1  24

should be converted to:

HELIX9   9 VAL A 1615  GLY A 1638  1  24

as the molecule with the 'D' chain ID is merged into the molecule with the 'A'
chain ID.  However the merger does not modify the HELIX record.



___

File Attachments:


---
Date: Fri 20 Feb 2015 10:37:26 AM UTC  Name: 2BE6_secondary_structure.pdb 
Size: 5kB   By: bugman

http://gna.org/bugs/download.php?file_id=23876
---
Date: Fri 20 Feb 2015 10:37:26 AM UTC  Name: test.py  Size: 388B   By: bugman

http://gna.org/bugs/download.php?file_id=23877

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[bug #23294] Automatic merging of PDB molecules results in an IndexError.

[Edward d Auvergne]

URL:
  http://gna.org/bugs/?23294

 Summary: Automatic merging of PDB molecules results in an
IndexError.
 Project: relax
Submitted by: bugman
Submitted on: Fri 20 Feb 2015 08:21:01 AM UTC
Category: relax's source code
Specific analysis category: All analyses
Priority: 3 - Low
Severity: 2 - Minor
  Status: None
 Assigned to: bugman
 Originator Name: 
Originator Email: 
 Open/Closed: Open
 Release: 3.3.6
 Discussion Lock: Any
Operating System: All systems

___

Details:

When reading a PDB file using the structure.read_pdb user function
http://www.nmr-relax.com/manual/structure_read_pdb.html and multiple
molecules are present (i.e. multiple chain IDs) and only one molecule name is
given, the following error is seen:

Internal relax PDB parser.
Opening the file 'in.pdb' for reading.
Traceback (most recent call last):
  File /data/relax/relax-trunk/multi/processor.py, line 494, in run
self.callback.init_master(self)
  File /data/relax/relax-trunk/multi/__init__.py, line 318, in
default_init_master
self.master.run()
  File /data/relax/relax-trunk/relax.py, line 199, in run
self.interpreter.run(self.script_file)
  File /data/relax/relax-trunk/prompt/interpreter.py, line 279, in run
return run_script(intro=self.__intro_string, local=locals(),
script_file=script_file, show_script=self.__show_script,
raise_relax_error=self.__raise_relax_error)
  File /data/relax/relax-trunk/prompt/interpreter.py, line 585, in
run_script
return console.interact(intro, local, script_file,
show_script=show_script, raise_relax_error=raise_relax_error)
  File /data/relax/relax-trunk/prompt/interpreter.py, line 484, in
interact_script
exec_script(script_file, local)
  File /data/relax/relax-trunk/prompt/interpreter.py, line 363, in
exec_script
runpy.run_module(module, globals)
  File /usr/lib64/python2.7/runpy.py, line 180, in run_module
fname, loader, pkg_name)
  File /usr/lib64/python2.7/runpy.py, line 72, in _run_code
exec code in run_globals
  File /data/relax/debugging/bug_x_multi_mol_automerge/test.py, line 3, in
module
structure.read_pdb('in.pdb', read_model=1, set_mol_name='merged mol')
  File /data/relax/relax-trunk/prompt/uf_objects.py, line 225, in __call__
self._backend(*new_args, **uf_kargs)
  File /data/relax/relax-trunk/pipe_control/structure/main.py, line 1099, in
read_pdb
cdp.structure.load_pdb(file_path, read_mol=read_mol,
set_mol_name=set_mol_name, read_model=read_model, set_model_num=set_model_num,
alt_loc=alt_loc, verbosity=verbosity, merge=merge)
  File /data/relax/relax-trunk/lib/structure/internal/object.py, line 2085,
in load_pdb
new_mol_name.append(set_mol_name[mol_index])
IndexError: list index out of range


This should not happen!  Instead either a RelaxError should be raised to point
out the problem, or the molecules should be automatically merged.  The
attached minimal 'in.pdb' structure and 'test.py' relax script demonstrate
this problem.



___

File Attachments:


---
Date: Fri 20 Feb 2015 08:21:01 AM UTC  Name: in.pdb  Size: 652B   By: bugman

http://gna.org/bugs/download.php?file_id=23873
---
Date: Fri 20 Feb 2015 08:21:01 AM UTC  Name: test.py  Size: 172B   By: bugman

http://gna.org/bugs/download.php?file_id=23874

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[bug #23294] Automatic merging of PDB molecules results in an IndexError.

[Edward d Auvergne]

Update of bug #23294 (project relax):

  Status:None = Fixed  
 Open/Closed:Open = Closed 


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[bug #23295] PDB secondary structure HELIX and SHEET records not updated when merging molecules.

[Edward d Auvergne]

Update of bug #23295 (project relax):

  Status:None = Fixed  
 Open/Closed:Open = Closed 


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[bug #23293] PDB HETATM loading error - the last HETATM record is sometimes not read from the PDB file.

[Edward d Auvergne]

Update of bug #23293 (project relax):

  Status:None = Fixed  
 Open/Closed:Open = Closed 


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[bug #23293] PDB HETATM loading error - the last HETATM record is sometimes not read from the PDB file.

[Edward d Auvergne]

URL:
  http://gna.org/bugs/?23293

 Summary: PDB HETATM loading error - the last HETATM record is
sometimes not read from the PDB file.
 Project: relax
Submitted by: bugman
Submitted on: Thu 19 Feb 2015 01:17:04 PM UTC
Category: relax's source code
Specific analysis category: All analyses
Priority: 5 - Normal
Severity: 2 - Minor
  Status: None
 Assigned to: bugman
 Originator Name: 
Originator Email: 
 Open/Closed: Open
 Release: 3.3.6
 Discussion Lock: Any
Operating System: All systems

___

Details:

The last HETATM record of a molecule, when multiple molecules are present in
the PDB file, will not be read.  This does not affect the last molecule.

The following files are attached:

- A test PDB file 'in.pdb'.
- A simple relax script 'test.py' which creates a data pipe, loads
'in.pdb' and creates the output 'out.pdb' file.
- The resultant corrupted 'out.pdb' file.



___

File Attachments:


---
Date: Thu 19 Feb 2015 01:17:05 PM UTC  Name: out.pdb  Size: 2kB   By: bugman

http://gna.org/bugs/download.php?file_id=23868
---
Date: Thu 19 Feb 2015 01:17:05 PM UTC  Name: test.py  Size: 108B   By: bugman

http://gna.org/bugs/download.php?file_id=23869
---
Date: Thu 19 Feb 2015 01:17:04 PM UTC  Name: in.pdb  Size: 2kB   By: bugman

http://gna.org/bugs/download.php?file_id=23867

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[bug #23288] Failure of the structure.read_pdb user function when simultaneously merging multiple molecules from one file.

[Edward d Auvergne]

Update of bug #23288 (project relax):

  Status:None = Fixed  
 Open/Closed:Open = Closed 


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[bug #23288] Failure of the structure.read_pdb user function when simultaneously merging multiple molecules from one file.

[Edward d Auvergne]

URL:
  http://gna.org/bugs/?23288

 Summary: Failure of the structure.read_pdb user function when
simultaneously merging multiple molecules from one file.
 Project: relax
Submitted by: bugman
Submitted on: Tue 17 Feb 2015 08:43:02 AM UTC
Category: relax's source code
Specific analysis category: All analyses
Priority: 3 - Low
Severity: 2 - Minor
  Status: None
 Assigned to: bugman
 Originator Name: 
Originator Email: 
 Open/Closed: Open
 Release: 3.3.6
 Discussion Lock: Any
Operating System: All systems

___

Details:

The following two user function calls are sufficient to trigger this bug when
running relax from the relax base directory:

pipe.create(pipe_name='merge test', pipe_type='N-state')
structure.read_pdb(file='2BE6_core_I_IV.pdb',
dir='test_suite/shared_data/structures', read_mol=[1, 3], set_mol_name='CaM
A', merge=True)


This results in the error:

Internal relax PDB parser.
Opening the file 'test_suite/shared_data/structures/2BE6_core_I_IV.pdb' for
reading.
Traceback (most recent call last):
  File console, line 1, in module
  File /data/relax/relax-trunk/prompt/uf_objects.py, line 225, in __call__
self._backend(*new_args, **uf_kargs)
  File /data/relax/relax-trunk/pipe_control/structure/main.py, line 1099, in
read_pdb
cdp.structure.load_pdb(file_path, read_mol=read_mol,
set_mol_name=set_mol_name, read_model=read_model, set_model_num=set_model_num,
alt_loc=alt_loc, verbosity=verbosity, merge=merge)
  File /data/relax/relax-trunk/lib/structure/internal/object.py, line 2084,
in load_pdb
new_mol_name.append(set_mol_name[mol_index])
IndexError: list index out of range




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[bug #23265] Failure of the edit buttons in the user function GUI windows.

[Edward d Auvergne]

URL:
  http://gna.org/bugs/?23265

 Summary: Failure of the edit buttons in the user function GUI
windows.
 Project: relax
Submitted by: bugman
Submitted on: Thu 12 Feb 2015 05:33:39 PM UTC
Category: GUI
Specific analysis category: All analyses
Priority: 7 - High
Severity: 5 - Blocker
  Status: None
 Assigned to: bugman
 Originator Name: 
Originator Email: 
 Open/Closed: Open
 Release: 3.3.6
 Discussion Lock: Any
Operating System: All systems

___

Details:

Certain buttons for editing list values in the GUI user function windows fail.
 For example, open the relax GUI and select the menu item 'User
functions-structure-superimpose'.  Then click on the edit button for the
molecule list or model list.  The relax controller will appear with the
following message:


Traceback (most recent call last):
  File /data/relax/relax-trunk/gui/input_elements/sequence_2D.py, line 112,
in open_dialog
self.selection_win_show()
  File /data/relax/relax-trunk/gui/input_elements/sequence_2D.py, line 131,
in selection_win_show
self.sel_win = Sequence_window_2D(name=self.name, seq_type=self.seq_type,
value_type=self.value_type, titles=self.titles, dim=self.dim)
  File /data/relax/relax-trunk/gui/input_elements/sequence_2D.py, line 164,
in __init__
self.titles = [wx.EmptyString] * dim[1]
TypeError: 'NoneType' object has no attribute '__getitem__'





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[bug #23259] Broken user functions in the prompt UI - RelaxError: The user function 'X' has been renamed to 'Y'.

[Edward d Auvergne]

URL:
  http://gna.org/bugs/?23259

 Summary: Broken user functions in the prompt UI - RelaxError:
The user function 'X' has been renamed to 'Y'.
 Project: relax
Submitted by: bugman
Submitted on: Mon 09 Feb 2015 09:44:35 AM UTC
Category: relax's source code
Specific analysis category: All analyses
Priority: 5 - Normal
Severity: 3 - Normal
  Status: None
 Assigned to: bugman
 Originator Name: 
Originator Email: 
 Open/Closed: Open
 Release: 3.3.5
 Discussion Lock: Any
Operating System: All systems

___

Details:

When running certain user functions from the prompt user interface (UI), a
RelaxError is incorrectly raised saying that the user function has been
renamed.  For example, start relax in the prompt mode and type:

relax minimise.execute()
RelaxError: The user function 'minimise' has been renamed to
'minimise.execute'.

This appears to only affect the minimise.calculate, minimise.execute,
minimise.grid_search and minimise.grid_zoom user functions.




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[bug #23259] Broken user functions in the prompt UI - RelaxError: The user function 'X' has been renamed to 'Y'.

[Edward d Auvergne]

Update of bug #23259 (project relax):

  Status:None = Fixed  
 Open/Closed:Open = Closed 
 Release:   3.3.5 = 3.3.6  


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[sr #3211] Provide veusz plots as an alternative to grace

[Edward d Auvergne]

Follow-up Comment #1, sr #3211 (project relax):

For discussions about this subject, see the thread at
http://thread.gmane.org/gmane.science.nmr.relax.devel/7532.

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[sr #3210] relaxation experimental data and fitting curve plot

[Edward d Auvergne]

Follow-up Comment #3, sr #3210 (project relax):

An example of the plots produced by the relax_disp.plot_disp_curve user
function is in the relax file
test_suite/shared_data/dispersion/Korzhnev_et_al_2005/relax_results/1H_SQ_CPMG/disp_9_N.agr.

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[sr #3210] relaxation experimental data and fitting curve plot

[Edward d Auvergne]

Update of sr #3210 (project relax):

Operating System:  Mac OS = None   


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[sr #3210] relaxation experimental data and fitting curve plot

[Edward d Auvergne]

Follow-up Comment #2, sr #3210 (project relax):

One option might be to create something similar to the
relax_disp.plot_disp_curve user function
(http://www.nmr-relax.com/manual/relax_disp_plot_disp_curves.html).  The
grace.plot_curve user function could be implemented taking ideas from
relax_disp.plot_disp_curve.  This would then create one plot per spin system
analysed.

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[bug #23244] Missing one fitting parameter in relaxation curve fitting report.

[Edward d Auvergne]

Update of bug #23244 (project relax):

  Status:   Confirmed = Fixed  
 Assigned to:None = bugman 
 Open/Closed:Open = Closed 

___

Follow-up Comment #5:

This has now been fixed:

http://article.gmane.org/gmane.science.nmr.relax.scm/25270

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[sr #3210] relaxation experimental data and fitting curve plot

[Edward d Auvergne]

Follow-up Comment #1, sr #3210 (project relax):

Could you confirm that this is similar to the currently generated
'intensities.agr' file, except that the plotted curve is that of the fitted
curve?

This is complicated as the grace.write infrastructure does not currently
support this.  From the attached plot, this consists of two data plots - a
graph of the measured values and a graph of the intepolated values
back-calculated from the fitted parameters.  The main issue is that the
'intensities.agr' file contains one graph per spin.  Can you see how you would
generate these plots in Grace?

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[bug #23244] Missing one fitting parameter in relaxation curve fitting report.

[Edward d Auvergne]

Update of bug #23244 (project relax):

  Status:   Need Info = Confirmed  


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[bug #23244] Missing one fitting parameter in relaxation curve fitting report.

[Edward d Auvergne]

Update of bug #23244 (project relax):

Specific analysis category:None = Relaxation
curve-fitting
  Status:None = Need Info  
Operating System:None = All systems
 Summary: missing one fitting parameter in relaxation curve
fitting report = Missing one fitting parameter in relaxation curve fitting
report.

___

Follow-up Comment #1:

Would it be possible for you to attach a set of test peak lists to the bug
report (http://gna.org/bugs/?23244)?  The best would be to delete almost all
data so that only a single peak is in the files.  You could randomise the peak
heights slightly and change the assignment if you wish to keep the data
confidential.  In addition, a log file of the output of running a quick
analysis on the truncated data set (either running relax with the --log or
--tee options, or copying and pasting the contents of the relax controller
window) would be very useful for me to reproduce the problem.  I could then
take the peak lists and the relax user functions from the log file and create
what is know as a system test.  If I can create a system test that reproduces
the issue, then it normally takes 5-10 minutes to fix.  Cheers!

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[bug #23232] FAIL: test_create_diff_tensor_pdb_oblate (test_suite.system_tests.structure.Structure)

[Edward d Auvergne]

Update of bug #23232 (project relax):

  Status:None = Confirmed  
 Assigned to:None = bugman 


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[bug #23232] FAIL: test_create_diff_tensor_pdb_oblate (test_suite.system_tests.structure.Structure)

[Edward d Auvergne]

Update of bug #23232 (project relax):

  Status:   Confirmed = Fixed  
 Open/Closed:Open = Closed 

___

Follow-up Comment #2:

This is only a test suite bug due to machine precision differences on
different operating systems and has no effect on the operation of relax.  The
test has been redesigned to be an exact solution rather than an approximate
solution of fitting an oblate diffusion tensor to prolate diffusion relaxation
data.

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[bug #23189] Failure of the relax GUI tests with a segmentation fault - a wxPython 2.8 bug.

[Edward d Auvergne]

URL:
  http://gna.org/bugs/?23189

 Summary: Failure of the relax GUI tests with a segmentation
fault - a wxPython 2.8 bug.
 Project: relax
Submitted by: bugman
Submitted on: Thu 15 Jan 2015 02:04:19 PM UTC
Category: Test suite
Specific analysis category: All analyses
Priority: 1 - Later
Severity: 2 - Minor
  Status: None
 Assigned to: None
 Originator Name: 
Originator Email: 
 Open/Closed: Open
 Release: 3.3.4
 Discussion Lock: Any
Operating System: All systems

___

Details:

Due to a bug in wxPython 2.8, triggered by code for the spin viewer GUI
window, the GUI tests will sometimes terminate with a 'Segmentation fault'. 
This only happens when using wxPython 2.8, using 2.9 or higher does not result
in segfaults.  The following bash command will show the problem:

$ rm -f gui_tests.log; for i in {1..10}; do echo Round $i; relax --gui-tests
--time -d  gui_tests.log 21 || echo -e \n\nCrash with $? \n\n\n 
gui_tests.log; done

With wxPython 2.9, I see:

Round 1
Round 2
Round 3
Round 4
Round 5
Round 6
Round 7
Round 8
Round 9
Round 10


With wxPython 2.8, I see:

Round 1
Round 2
Segmentation fault
Round 3
Round 4
Segmentation fault
Round 5
Segmentation fault
Round 6
Round 7
Segmentation fault
Round 8
Segmentation fault
Round 9
Segmentation fault
Round 10


This can be isolated to a few GUI tests with:

$ rm -f gui_tests.log; for i in {1..10}; do echo Round $i; ./relax --gui-tests
--time -d General Noe  gui_tests.log 21 || echo -e \n\nCrash with $?
\n\n\n  gui_tests.log; done
Round 1
Segmentation fault
Round 2
Segmentation fault
Round 3
Segmentation fault
Round 4
Segmentation fault
Round 5
Segmentation fault
Round 6
Segmentation fault
Round 7
Segmentation fault
Round 8
Segmentation fault
Round 9
Round 10
Segmentation fault


After deleting the contents of the update() method in
gui/spin_viewer/tree.py:

$ rm -f gui_tests.log; for i in {1..10}; do echo Round $i; ./relax --gui-tests
--time -d General Noe  gui_tests.log 21 || echo -e \n\nCrash with $?
\n\n\n  gui_tests.log; done
Round 1
Round 2
Round 3
Round 4
Round 5
Round 6
Round 7
Round 8
Round 9
Round 10




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[bug #23187] Deleting residue in GUI, and then open spin viewer crashes relax.

[Edward d Auvergne]

Follow-up Comment #7, bug #23187 (project relax):

Ok, I've fixed the GUI code:

http://article.gmane.org/gmane.science.nmr.relax.scm/24915

Now to work out how the error can be caught in the test!

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[bug #23186] Error calculation of individual parameter dw from Monte-Carlo, is based on first spin.

[Edward d Auvergne]

Follow-up Comment #6, bug #23186 (project relax):

I would suggest the following (which would require a lot of testing and
checking, as it may kill the R2eff model):

$ svn diff specific_analyses/relax_disp/api.py
Index: specific_analyses/relax_disp/api.py
===
--- specific_analyses/relax_disp/api.py (revision 27163)
+++ specific_analyses/relax_disp/api.py (working copy)
@@ -1485,8 +1485,10 @@
 # Convert the parameter index.
 if model_param:
 param_name, si, mi = param_index_to_param_info(index=index,
spins=spins)
-if not param_name in ['r2eff', 'i0']:
+if param_name in ['r2eff', 'i0']:
 si = 0
+elif si == None:
+si = 0
 else:
 param_name = aux_params[index - total_param_num]
 si = 0

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[bug #23187] Deleting residue in GUI, and then open spin viewer crashes relax.

[Edward d Auvergne]

Follow-up Comment #9, bug #23187 (project relax):

Unfortunately I don't think that this bug can be caught in the relax test
suite as the wxPython RuntimeError handler seems to be completely incompatible
with the Python unittest framework.

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[bug #23187] Opening the spin viewer GUI window, deleting a residue, and then reopening the spin viewer crashes relax.

[Edward d Auvergne]

Update of bug #23187 (project relax):

  Status:None = Fixed  
 Assigned to:None = bugman 
 Open/Closed:Open = Closed 
 Summary: Deleting residue in GUI, and then open spin viewer
crashes relax. = Opening the spin viewer GUI window, deleting a residue, and
then reopening the spin viewer crashes relax.


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[task #7873] Write wrapper function to nmrglue, to read .ft2 files and process them.

[Edward d Auvergne]

Follow-up Comment #94, task #7873 (project relax):

When I run the Nmrglue system tests in Python 2, they pass.  However in Python
3 I see:

$ python3 ./relax -s --time Nmrglue
Echoing of user function calls has been enabled.


=
= System / functional tests =
=

. 0.00 s for Nmrglue.test_nmrglue_read
. 0.00 s for Nmrglue.test_nmrglue_read_several
. 0.16 s for Nmrglue.test_plot_contour
. 0.10 s for Nmrglue.test_plot_contour_cpmg
. 0.12 s for Nmrglue.test_plot_correlation
. 2.90 s for Nmrglue.test_plot_hist_cpmg
. 3.44 s for Nmrglue.test_plot_hist_cpmg_several
E 0.00 s for Nmrglue.test_save_state
. 0.00 s for Nmrglue.test_version

==
ERROR: test_save_state (test_suite.system_tests.nmrglue.Nmrglue)
Test saving a state with numpy arrays, reset relax, and read the state again.
--

relax pipe.create(pipe_name='mf', pipe_type='mf', bundle=None)

relax spectrum.nmrglue_read(file='128_0_FT.ft2',
dir='/data/relax/branches/nmrglue/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data',
nmrglue_id='test')
Filesize of .ft2 file is: 527360
Type of encoding is: class 'numpy.ndarray'
Storing numpy array to: /tmp/tmpl4p2zk/data.npy
Filesize of .npy file is: 525392
Shape of data is 256x513
dtype of data is float32
Type of data[0][0]:  class 'numpy.float32'

relax state.save(state='state', dir='/tmp/tmpl4p2zk', compress_type=1,
force=True)
Opening the file '/tmp/tmpl4p2zk/state.bz2' for writing.
Traceback (most recent call last):
  File /data/relax/branches/nmrglue/test_suite/system_tests/nmrglue.py, line
569, in test_save_state
self.interpreter.state.save('state', dir=dirpath, compress_type=1,
force=True)
  File /data/relax/branches/nmrglue/prompt/uf_objects.py, line 225, in
__call__
self._backend(*new_args, **uf_kargs)
  File /data/relax/branches/nmrglue/pipe_control/state.py, line 128, in
save_state
ds.to_xml(file)
  File /data/relax/branches/nmrglue/data_store/__init__.py, line 643, in
to_xml
self[pipe].to_xml(xmldoc, pipe_element, pipe_type=self[pipe].pipe_type)
  File /data/relax/branches/nmrglue/data_store/pipe_container.py, line 335,
in to_xml
self.nmrglue.to_xml(doc, element)
  File /data/relax/branches/nmrglue/data_store/data_classes.py, line 244, in
to_xml
self[key].to_xml(doc, dict_item_element)
  File /data/relax/branches/nmrglue/data_store/nmrglue.py, line 138, in
to_xml
string = b64encode(self.data)
  File /usr/lib64/python3.3/base64.py, line 58, in b64encode
raise TypeError(expected bytes, not %s % s.__class__.__name__)
TypeError: expected bytes, not ndarray

--
Ran 9 tests in 6.725s

FAILED (errors=1)

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[bug #23187] Deleting residue in GUI, and then open spin viewer crashes relax.

[Edward d Auvergne]

Follow-up Comment #1, bug #23187 (project relax):

I cannot reproduce the bug with the following steps:

1)  Start relax in GUI mode.

2)  Open the prompt window.

3)  Type:

pipe.create('test', 'mf')
residue.create(res_num=1)
residue.create(res_num=2)
residue.delete(':2')

4)  Close the prompt window.

5)  Open the spin viewer window.


This is on a 64-bit GNU/Linux system with wxPython 2.8.12.1 (gtk2-unicode). 
Maybe it is operating system dependent, wxPython version dependent, or there
is something strange with the data.  A system test which triggers the bug will
be able to isolate the issue.

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[bug #23187] Deleting residue in GUI, and then open spin viewer crashes relax.

[Edward d Auvergne]

Follow-up Comment #2, bug #23187 (project relax):

I also have no problem on 64-bit Linux with wxPython 2.9.4.1 gtk2 (classic).

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[bug #23017] Multidimensional numpy arrays are not being stored as IEEE 754 arrays in the XML state and results files.

[Edward d Auvergne]

URL:
  http://gna.org/bugs/?23017

 Summary: Multidimensional numpy arrays are not being stored
as IEEE 754 arrays in the XML state and results files.
 Project: relax
Submitted by: bugman
Submitted on: Tue 02 Dec 2014 07:52:23 PM UTC
Category: relax's source code
Specific analysis category: All analyses
Priority: 5 - Normal
Severity: 3 - Normal
  Status: None
 Assigned to: bugman
 Originator Name: 
Originator Email: 
 Open/Closed: Open
 Release: 3.3.3
 Discussion Lock: Any
Operating System: All systems

___

Details:

The following relax code demonstrates the problem:

from numpy import array

pipe.create('test', 'mf')
cdp.test = array([1, 2, 3.])
cdp.test2 = array([[1, 2, 3.], [4, 5, 6]])
state.save('test', force=True)

Opening the test.bz2 file, the XML for the numpy arrays is:

test type=dtype('float64')
value
array([ 1.,  2.,  3.])
/value
ieee_754_byte_array
[[0, 0, 0, 0, 0, 0, 240, 63], [0, 0, 0, 0, 0, 0, 0, 64],
[0, 0, 0, 0, 0, 0, 8, 64]]
/ieee_754_byte_array
/test
test2 type=dtype('float64')
value
array([[ 1.,  2.,  3.],
   [ 4.,  5.,  6.]])
/value
/test2

The test2 tag should also be represented with the non-truncating
ieee_754_byte_array tag.




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[task #7415] Implement support for inversion-recovery R1 curve fitting

[Edward d Auvergne]

Update of task #7415 (project relax):

  Status:   Postponed = Completed  
Percent Complete: 50% = 100%   
 Open/Closed:Open = Closed 

___

Follow-up Comment #9:

This is now fully implemented in the relax trunk.  The system test
Relax_fit.test_inversion_recovery, based on the original inversion-recovery
branch and the relax_fit_exp_3param_inv_neg.py system test script, now passes.
 This demonstrates that the inversion recovery R1 curve-fitting is fully
functional.

The C code from the original branch was not used, as it was simpler to
duplicate the target_functions/exponential.c file to exponential_inv.c and
update function, gradient, and Hessian functions for the different curve type.
 The original code did not have gradient or Hessians implemented, as this is
relatively new for the curve-fitting analysis.

In addition, the saturation recovery model type has also been fully
implemented and a system test based on the attached files passes.

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[task #4124] Update the Mail Archive (http://mail-archive.com/) to include all of the mailing list messages.

[Edward d Auvergne]

Update of task #4124 (project relax):

  Status:None = Completed  
 Open/Closed:Open = Closed 


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[task #7415] Implement support for inversion-recovery R1 curve fitting

[Edward d Auvergne]

Follow-up Comment #8, task #7415 (project relax):

For more discussions about this task, see the thread at
http://thread.gmane.org/gmane.science.nmr.relax.devel/3693.

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[task #7415] Implement support for inversion-recovery R1 curve fitting

[Edward d Auvergne]

Update of task #7415 (project relax):

   Should be Finished on: Fri 15 Jul 2011 04:00:00 AM UTC = Thu 01 Jan 2015
12:00:00 AM UTC
Category:None = relax's source code


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[sr #3195] Fitting of saturation recovery experiment.

[Edward d Auvergne]

Update of sr #3195 (project relax):

  Status:None = Duplicate  
 Assigned to:None = bugman 
 Open/Closed:Open = Closed 
Operating System:  Mac OS = None   
 Summary: Fitting of saturation recovery experiment = Fitting
of saturation recovery experiment.

___

Follow-up Comment #1:

This has been a relax task for quite a while now (https://gna.org/task/?7415).
 This was started back in 2011 by Sébastien Morin as the 'inversion-recovery'
branch (http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/). 
However it was put on hold due to requiring a developer with better C code
knowledge for switching between different target functions.  I have never
completed the branch, but it remains for the next person interested in
reviving it.  Note that as this is a duplicate of the task tracker at
https://gna.org/task/?7415, which should be used instead, this is being
closed.

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[task #7415] Implement support for inversion-recovery R1 curve fitting

[Edward d Auvergne]

Update of task #7415 (project relax):

Percent Complete:  0% = 50%

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Follow-up Comment #1:

A better formatted thread of the old discussions is
http://thread.gmane.org/gmane.science.nmr.relax.devel/3221.

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[task #7415] Implement support for inversion-recovery R1 curve fitting

[Edward d Auvergne]

Follow-up Comment #2, task #7415 (project relax):

This was asked for as a support request at https://gna.org/support/?3195.

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[task #7415] Implement support for inversion-recovery R1 curve fitting

[Edward d Auvergne]

Follow-up Comment #3, task #7415 (project relax):

The original discussion thread in the original submission can be better read
from http://thread.gmane.org/gmane.science.nmr.relax.devel/3217.

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[task #7415] Implement support for inversion-recovery R1 curve fitting

[Edward d Auvergne]

Follow-up Comment #4, task #7415 (project relax):

Note that the inversion-recovery branch is now too old - it was branched from
r13061 of relax 1.3.  As the relax source code has changed and been rearranged
hugely since then, to resurrect the branch will require creating a new branch
(maybe 'inversion-recovery-new') and manually porting the desired patches from
the original branch.  For example the target function code
maths_fns/relax_fit.c is now called target_functions/relax_fit.c.

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[task #7415] Implement support for inversion-recovery R1 curve fitting

[Edward d Auvergne]

Follow-up Comment #5, task #7415 (project relax):

Note that any developments here will also affect the relaxation dispersion
analysis in relax.

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[task #7415] Implement support for inversion-recovery R1 curve fitting

[Edward d Auvergne]

Follow-up Comment #6, task #7415 (project relax):

Note that for development in the inversion-recovery branch, that there should
be a slightly different design of the target function for simplifying this.

There should be one target function in target_functions/relax_fit.c per
function type, and that the correct one is selected by the wrapper code in
specific_analyses/relax_fit/optimisation.py.  This could be simplified by
shifting all the *func_wrapper() functions into a new target function class in
say target_functions/relax_fit_wrapper.py and having the target function
selection performed there just like in the other analysis types.

This would avoid requiring any switching in the C code during optimisation,
hence it would be much faster.  And the problem which killed the original
branch would then not be an issue.  The new code could then just mimic the
current code, as a duplication and modification, as the functions are very
simple but could not use shared functions.  Then no new C concepts would be
needed.

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[task #7415] Implement support for inversion-recovery R1 curve fitting

[Edward d Auvergne]

Follow-up Comment #7, task #7415 (project relax):

The hardest part of this task would be to create synthetic data for the 8
different exponential curves identified and implemented by Séb, or at least a
subset of these.  And then to create 8 separate system tests to check that the
implementation is as expected.  This would be the first step required for
reviving the branch.

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[bug #22963] Using '@N*' to define the interatomic interactions for a model-free analysis fails when using non-backbone 15N spins.

[Edward d Auvergne]

URL:
  http://gna.org/bugs/?22963

 Summary: Using '@N*' to define the interatomic interactions
for a model-free analysis fails when using non-backbone 15N spins.
 Project: relax
Submitted by: bugman
Submitted on: Mon 17 Nov 2014 10:08:56 AM UTC
Category: relax's source code
Specific analysis category: Model-free analysis
Priority: 5 - Normal
Severity: 3 - Normal
  Status: None
 Assigned to: bugman
 Originator Name: 
Originator Email: 
 Open/Closed: Open
 Release: 3.3.2
 Discussion Lock: Any
Operating System: All systems

___

Details:

During the dauvergne_protocol model-free auto-analysis, the error seen is:


Traceback (most recent call last):
  File /data/relax/relax-trunk/test_suite/system_tests/model_free.py, line
810, in test_dauvergne_protocol_sphere
dAuvergne_protocol(pipe_name='sphere test', pipe_bundle='sphere test',
results_dir=ds.tmpdir, diff_model=['local_tm', 'sphere'], mf_models=['m1',
'm2'], local_tm_models=['tm0', 'tm1'], grid_inc=3,
diff_tensor_grid_inc={'sphere': 5, 'prolate': 5, 'oblate': 5, 'ellipsoid': 3},
min_algor='newton', mc_sim_num=2, max_iter=1, conv_loop=True)
  File /data/relax/relax-trunk/auto_analyses/dauvergne_protocol.py, line
246, in __init__
self.execute()
  File /data/relax/relax-trunk/auto_analyses/dauvergne_protocol.py, line
600, in execute
self.multi_model(local_tm=True)
  File /data/relax/relax-trunk/auto_analyses/dauvergne_protocol.py, line
888, in multi_model
self.interpreter.minimise.grid_search(inc=self.grid_inc)
  File /data/relax/relax-trunk/prompt/uf_objects.py, line 225, in __call__
self._backend(*new_args, **uf_kargs)
  File /data/relax/relax-trunk/pipe_control/minimise.py, line 213, in
grid_search
api.grid_search(lower=model_lower, upper=model_upper, inc=model_inc,
scaling_matrix=scaling_matrix, constraints=constraints, verbosity=verbosity)
  File /data/relax/relax-trunk/specific_analyses/model_free/api.py, line
1028, in grid_search
self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc,
scaling_matrix=scaling_matrix, constraints=constraints, verbosity=verbosity,
sim_index=sim_index)
  File /data/relax/relax-trunk/specific_analyses/model_free/api.py, line
1233, in minimise
raise RelaxError(The spin '%s' has %s dipolar relaxation interactions
defined, but only a maximum of one is currently supported. % (spin_id,
count))
RelaxError: RelaxError: The spin '#sphere_mol1:9@NE1' has 10 dipolar
relaxation interactions defined, but only a maximum of one is currently
supported.



The problem occurred earlier during the set up stage when defining the
interatomic interactions:


relax interatom.define(spin_id1='@N*', spin_id2='@H*', direct_bond=True,
spin_selection=True, pipe=None)
Interatomic interactions are now defined for the following spins:

# Spin_ID_1 Spin_ID_2   
'#sphere_mol1:9@NE1''#sphere_mol1:1@H'  
'#sphere_mol1:9@NE1''#sphere_mol1:2@H'  
'#sphere_mol1:9@NE1''#sphere_mol1:3@H'  
'#sphere_mol1:9@NE1''#sphere_mol1:4@H'  
'#sphere_mol1:9@NE1''#sphere_mol1:5@H'  
'#sphere_mol1:9@NE1''#sphere_mol1:6@H'  
'#sphere_mol1:9@NE1''#sphere_mol1:7@H'  
'#sphere_mol1:9@NE1''#sphere_mol1:8@H'  
'#sphere_mol1:9@NE1''#sphere_mol1:9@H'  
'#sphere_mol1:9@NE1''#sphere_mol1:9@HE1'


Obviously the NE1 Trp indole spin of residue 9 should not be defined to have a
dipole-dipole interaction with all protons in the system, as is happening
here.




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[bug #22961] Loading of relaxation data fails with IndexError: list index out of range.

[Edward d Auvergne]

URL:
  http://gna.org/bugs/?22961

 Summary: Loading of relaxation data fails with IndexError:
list index out of range.
 Project: relax
Submitted by: bugman
Submitted on: Mon 17 Nov 2014 07:55:51 AM UTC
Category: relax's source code
Specific analysis category: Model-free analysis
Priority: 5 - Normal
Severity: 3 - Normal
  Status: None
 Assigned to: bugman
 Originator Name: 
Originator Email: 
 Open/Closed: Open
 Release: 3.3.2
 Discussion Lock: Any
Operating System: All systems

___

Details:

The loading of relaxation data, in some rare cases, fails with and IndexError.
 This is now caught by the Mf.test_data_loading_failures system test:

==
ERROR: test_data_loading_failures (test_suite.system_tests.model_free.Mf)
Catch a failure when loading relaxation data.
--

relax pipe.create(pipe_name='mf', pipe_type='mf', bundle=None)

relax sequence.read(file='noe.500.out',
dir='/data/relax/relax-trunk/test_suite/shared_data/model_free/sphere',
spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3,
spin_num_col=4, spin_name_col=5, sep=None, spin_id=None)
Opening the file
'/data/relax/relax-trunk/test_suite/shared_data/model_free/sphere/noe.500.out'
for reading.
# mol_name res_numres_namespin_numspin_name
sphere_mol11  GLY 1   N
sphere_mol11  GLY 2   H
sphere_mol12  GLY 3   N
sphere_mol12  GLY 4   H
sphere_mol13  GLY 5   N
sphere_mol13  GLY 6   H
sphere_mol14  GLY 7   N
sphere_mol14  GLY 8   H
sphere_mol15  GLY 9   N
sphere_mol15  GLY 10  H
sphere_mol16  GLY 11  N
sphere_mol16  GLY 12  H
sphere_mol17  GLY 13  N
sphere_mol17  GLY 14  H
sphere_mol18  GLY 15  N
sphere_mol18  GLY 16  H
sphere_mol19  GLY 17  N
sphere_mol19  GLY 18  H
sphere_mol19  GLY 19  NE1  
sphere_mol19  GLY 20  HE1  
  
  
 
relax relax_data.read(ri_id='noe500', ri_type='NOE', frq=5.0,
file='noe.500.out',
dir='/data/relax/relax-trunk/test_suite/shared_data/model_free/sphere',
spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3,
spin_num_col=4, spin_name_col=5, data_col=6, error_col=7, sep=None,
spin_id='@N') 
   
RelaxWarning: The precise spectrometer frequency should be supplied, a value
such as 5 or 5e8 for a 500 MHz machine is not acceptable.  Please see
the 'sfrq' parameter in the Varian procpar file or the 'SFO1' parameter in the
Bruker acqus file.
  
  
Opening the file
'/data/relax/relax-trunk/test_suite/shared_data/model_free/sphere/noe.500.out'
for reading.  

RelaxWarning: The precise spectrometer frequency should be supplied, a value
such as 5 or 5e8 for a 500 MHz machine is not acceptable.  Please see
the 'sfrq' parameter in the Varian procpar file or the 'SFO1' parameter in the
Bruker acqus file.
  
  
Traceback (most recent call last):
  
 
  File /data/relax/relax-trunk/test_suite/system_tests/model_free.py, line
503, in test_data_loading_failures
 

[bug #22801] Failure of the relax test suite on Python 2.5.

[Edward d Auvergne]

Update of bug #22801 (project relax):

  Status: In Progress = Fixed  
 Open/Closed:Open = Closed 


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[bug #22730] Model-free auto-analysis - relax stops and quits at the polate step.

[Edward d Auvergne]

Update of bug #22730 (project relax):

  Status:   Need Info = Works For Me   
 Open/Closed:Open = Closed 

___

Follow-up Comment #21:

Closing this bug as the original problem of relax terminating prior to the end
of the analysis cannot be reproduced.

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[bug #22540] The Relax Controller does not follow output when doing Monte-Carlo simulations.

[Edward d Auvergne]

Update of bug #22540 (project relax):

  Status:None = Fixed  
 Assigned to:None = bugman 
 Open/Closed:Open = Closed 

___

Follow-up Comment #2:

Closing this bug as the relax controller should now be fixed.

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[bug #21599] allow import of nmr data from ccpn projects (optionally also export)

[Edward d Auvergne]

Update of bug #21599 (project relax):

  Status:None = Postponed  

___

Follow-up Comment #2:

This task, rather than bug, has been postponed until a future date (see the
mention of v3 of CCPN at
http://thread.gmane.org/gmane.science.nmr.relax.devel/4957/focus=5139).

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[bug #22937] Failure of the Relax_disp.test_estimate_r2eff_err_auto system test on Python 2.5.

[Edward d Auvergne]

URL:
  http://gna.org/bugs/?22937

 Summary: Failure of the
Relax_disp.test_estimate_r2eff_err_auto system test on Python 2.5.
 Project: relax
Submitted by: bugman
Submitted on: Mon 10 Nov 2014 05:18:21 PM UTC
Category: Test suite
Specific analysis category: None
Priority: 5 - Normal
Severity: 3 - Normal
  Status: None
 Assigned to: bugman
 Originator Name: 
Originator Email: 
 Open/Closed: Open
 Release: 3.3.1
 Discussion Lock: Any
Operating System: All systems

___

Details:

Due to a missing newline character at the end of the
test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/1_setup_r1rho_GUI.py
script, the test fails with:


==
ERROR: Test the user function for estimating R2eff errors from exponential
curve fitting, via the auto_analyses menu.
--

relax pipe.create(pipe_name='relax_disp', pipe_type='relax_disp',
bundle=None)

relax pipe.create(pipe_name='base pipe', pipe_type='relax_disp',
bundle='relax_disp')

relax
script(file='/data/relax/relax-trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/1_setup_r1rho_GUI.py',
dir=None)
script =
'/data/relax/relax-trunk/test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/1_setup_r1rho_GUI.py'

###
#
#
# Copyright (C) 2013-2014 Troels E. Linnet   
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com). 
#
#
#
# This program is free software: you can redistribute it and/or modify   
#
# it under the terms of the GNU General Public License as published by   
#
# the Free Software Foundation, either version 3 of the License, or  
#
# (at your option) any later version.
#
#
#
# This program is distributed in the hope that it will be useful,
#
# but WITHOUT ANY WARRANTY; without even the implied warranty of 
#
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the  
#
# GNU General Public License for more details.   
#
#
#
# You should have received a copy of the GNU General Public License  
#
# along with this program.  If not, see http://www.gnu.org/licenses/.  
#
#
#
###

# Python module imports.
from os import getcwd, sep

# relax module imports.
from status import Status; status = Status()

#data_path = getcwd()
data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Kjaergaard_et_al_2013'

# Read the spins.
spectrum.read_spins(file='1_0_46_0_max_standard.ser',
dir=data_path+sep+'peak_lists')

# Name the isotope for field strength scaling.
spin.isotope(isotope='15N')

# Load the experiments settings file.
expfile = open(data_path+sep+'exp_parameters_sort.txt', 'r')
expfileslines = expfile.readlines()
expfile.close()

# In MHz
yOBS = 81.050
# In ppm
yCAR = 118.078
centerPPM_N15 = yCAR

## Read the chemical shift data.
chemical_shift.read(file='1_0_46_0_max_standard.ser',
dir=data_path+sep+'peak_lists')

## The lock power to field, has been found in an calibration experiment.
spin_lock_field_strengths_Hz = {'35': 431.0, '39': 651.2, '41': 800.5, '43':
984.0, '46': 1341.11, '48': 1648.5}

## Apply spectra settings.
for i in range(len(expfileslines)):
line = expfileslines[i]
if line[0] == #:
continue
else:
# DIRN I deltadof2 dpwr2slock ncyc trim ss sfrq
DIRN = line.split()[0]
I = int(line.split()[1])
deltadof2 = line.split()[2]
dpwr2slock = line.split()[3]
ncyc = int(line.split()[4])
trim = float(line.split()[5])
ss = int(line.split()[6])
set_sfrq = float(line.split()[7])
apod_rmsd = float(line.split()[8])
spin_lock_field_strength = spin_lock_field_strengths_Hz[dpwr2slock]

# Calculate spin_lock time
time_sl = 2*ncyc*trim

# Define file name for peak list.
FNAME = %s_%s_%s_%s_max_standard.ser%(I, 

[bug #22937] Failure of the Relax_disp.test_estimate_r2eff_err_auto system test on Python 2.5.

[Edward d Auvergne]

Update of bug #22937 (project relax):

  Status:None = Fixed  
 Open/Closed:Open = Closed 


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[bug #22938] Failure of the test suite in the relax GUI.

[Edward d Auvergne]

URL:
  http://gna.org/bugs/?22938

 Summary: Failure of the test suite in the relax GUI.
 Project: relax
Submitted by: bugman
Submitted on: Mon 10 Nov 2014 05:48:53 PM UTC
Category: GUI
Specific analysis category: None
Priority: 7 - High
Severity: 4 - Important
  Status: None
 Assigned to: bugman
 Originator Name: 
Originator Email: 
 Open/Closed: Open
 Release: 3.3.1
 Discussion Lock: Any
Operating System: All systems

___

Details:

Executing the test suite via the GUI results in the following error:


Traceback (most recent call last):
  File /data/relax/relax-trunk/gui/relax_gui.py, line 602, in
run_test_suite_gui
self.run_test_suite(event, categories=['gui'])
  File /data/relax/relax-trunk/gui/relax_gui.py, line 573, in
run_test_suite
runner.run_all_tests()
  File /data/relax/relax-trunk/test_suite/test_suite_runner.py, line 113, in
run_all_tests
status = self.run_gui_tests(summary=False)
  File /data/relax/relax-trunk/test_suite/test_suite_runner.py, line 156, in
run_gui_tests
self.gui_result = gui_runner.run(self.tests, runner=self.runner)
  File /data/relax/relax-trunk/test_suite/gui_tests/__init__.py, line 118,
in run
suite_array.append(TestLoader().loadTestsFromTestCase(Bmrb))
  File /data/relax/relax-trunk/test_suite/relax_test_loader.py, line 59, in
loadTestsFromTestCase
if status.skip_blacklisted_tests and status.skipped_tests and
testCaseNames[i] in list(zip(*status.skipped_tests))[0]:
AttributeError: 'Status' object has no attribute 'skip_blacklisted_tests'





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[bug #22938] Failure of the test suite in the relax GUI.

[Edward d Auvergne]

Follow-up Comment #1, bug #22938 (project relax):

For the system test part of the test suite, the error is:

Traceback (most recent call last):
  File /data/relax/relax-trunk/gui/relax_gui.py, line 573, in
run_test_suite
runner.run_all_tests()
  File /data/relax/relax-trunk/test_suite/test_suite_runner.py, line 101, in
run_all_tests
status = self.run_system_tests(summary=False)
  File /data/relax/relax-trunk/test_suite/test_suite_runner.py, line 202, in
run_system_tests
self.system_result = system_runner.run(self.tests, runner=self.runner)
  File /data/relax/relax-trunk/test_suite/system_tests/__init__.py, line
162, in run
suite_array.append(TestLoader().loadTestsFromTestCase(Align_tensor))
  File /data/relax/relax-trunk/test_suite/relax_test_loader.py, line 59, in
loadTestsFromTestCase
if status.skip_blacklisted_tests and status.skipped_tests and
testCaseNames[i] in list(zip(*status.skipped_tests))[0]:
AttributeError: 'Status' object has no attribute 'skip_blacklisted_tests'

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[bug #22938] Failure of the test suite in the relax GUI.

[Edward d Auvergne]

Update of bug #22938 (project relax):

  Status:None = Fixed  
 Open/Closed:Open = Closed 


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[bug #22939] Failure of the test suite in the relax GUI with ImportError: No module named backend_wxagg.

[Edward d Auvergne]

URL:
  http://gna.org/bugs/?22939

 Summary: Failure of the test suite in the relax GUI with
ImportError: No module named backend_wxagg.
 Project: relax
Submitted by: bugman
Submitted on: Mon 10 Nov 2014 05:59:56 PM UTC
Category: GUI
Specific analysis category: None
Priority: 7 - High
Severity: 4 - Important
  Status: None
 Assigned to: bugman
 Originator Name: 
Originator Email: 
 Open/Closed: Open
 Release: 3.3.1
 Discussion Lock: Any
Operating System: All systems

___

Details:

Running the test suite in the GUI with certain Python/maplotlib versions
results in the following error:


Traceback (most recent call last):
  File /data/relax/relax-trunk/gui/relax_gui.py, line 571, in
run_test_suite
import test_suite.test_suite_runner
  File /data/relax/relax-trunk/test_suite/test_suite_runner.py, line 37, in
module
from test_suite.gui_tests import GUI_test_runner
  File /data/relax/relax-trunk/test_suite/gui_tests/__init__.py, line 34, in
module
from test_suite.gui_tests.bmrb import Bmrb
  File /data/relax/relax-trunk/test_suite/gui_tests/bmrb.py, line 31, in
module
from test_suite import system_tests
  File /data/relax/relax-trunk/test_suite/system_tests/__init__.py, line 61,
in module
from test_suite.system_tests.relax_disp import Relax_disp
  File /data/relax/relax-trunk/test_suite/system_tests/relax_disp.py, line
36, in module
from auto_analyses.relax_disp_repeat_cpmg import DIC_KEY_FORMAT,
Relax_disp_rep
  File /data/relax/relax-trunk/auto_analyses/relax_disp_repeat_cpmg.py, line
55, in module
import pylab as plt
  File /usr/lib64/python2.7/site-packages/pylab.py, line 1, in module
from matplotlib.pylab import *
  File /usr/lib64/python2.7/site-packages/matplotlib/pylab.py, line 269, in
module
from matplotlib.pyplot import *
  File /usr/lib64/python2.7/site-packages/matplotlib/pyplot.py, line 98, in
module
_backend_mod, new_figure_manager, draw_if_interactive, _show =
pylab_setup()
  File /usr/lib64/python2.7/site-packages/matplotlib/backends/__init__.py,
line 25, in pylab_setup
globals(),locals(),[backend_name])
ImportError: No module named backend_wxagg





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[bug #22939] Failure of the test suite in the relax GUI with ImportError: No module named backend_wxagg.

[Edward d Auvergne]

Follow-up Comment #1, bug #22939 (project relax):

This issue can be reproduced as follows:

1)  Start the relax GUI.
2)  Open the relax prompt window (using View-relax prompt for example).
3)  Type import pylab as plt

This will result in:

relax import pylab as plt
Traceback (most recent call last):
  File input, line 1, in module
  File /usr/lib64/python2.7/site-packages/pylab.py, line 1, in module
from matplotlib.pylab import *
  File /usr/lib64/python2.7/site-packages/matplotlib/pylab.py, line 269, in
module
from matplotlib.pyplot import *
  File /usr/lib64/python2.7/site-packages/matplotlib/pyplot.py, line 98, in
module
_backend_mod, new_figure_manager, draw_if_interactive, _show =
pylab_setup()
  File /usr/lib64/python2.7/site-packages/matplotlib/backends/__init__.py,
line 25, in pylab_setup
globals(),locals(),[backend_name])
ImportError: No module named backend_wxagg


When running relax in the prompt UI mode however, this matplotlib import works
successfully.

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