mailRe: r25011 - /branches/R1_fitting/test_suite/system_tests/relax_disp.py


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Posted by Troels Emtekær Linnet on August 19, 2014 - 10:42:
Hi Edward.

I deleted it, since I thought it was a clumsy ugly test.

It only tests:
-        
self.assert_(access(result_dir_name+sep+'resultsR1'+sep+'final'+sep+'phi_ex.out',
F_OK))
-        
self.assert_(access(result_dir_name+sep+'resultsR1'+sep+'final'+sep+'kex.out',
F_OK))
-        
self.assert_(access(result_dir_name+sep+'resultsR1'+sep+'final'+sep+'theta.out',
F_OK))

Which can be tested in the other tests.

Best
Troels

2014-08-19 10:37 GMT+02:00 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:

Hi Troels,

Why was this test not necessary?  Are all parts already tested in
another test?  It's always better to have too much test coverage than
to have small gaps in the coverage.  For the test suite, complete
coverage of code paths is always preferable to the total speed of the
test suite.  Hence why the test suite takes so long to complete.  But
this is why relax is incredibly stable and relatively bug-free.

Cheers,

Edward



On 13 August 2014 21:29,  <tlinnet@xxxxxxxxxxxxx> wrote:

Author: tlinnet
Date: Wed Aug 13 21:29:57 2014
New Revision: 25011

URL: http://svn.gna.org/viewcvs/relax?rev=25011&view=rev
Log:
Deleted systemtest test_r1rho_kjaergaard_man, since it was no necessary.

sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation 
rate for the off-resonance R1rho relaxation dispersion models.

Modified:
    branches/R1_fitting/test_suite/system_tests/relax_disp.py

Modified: branches/R1_fitting/test_suite/system_tests/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/R1_fitting/test_suite/system_tests/relax_disp.py?rev=25011&r1=25010&r2=25011&view=diff
==============================================================================
--- branches/R1_fitting/test_suite/system_tests/relax_disp.py   (original)
+++ branches/R1_fitting/test_suite/system_tests/relax_disp.py   Wed Aug 13 
21:29:57 2014
@@ -5100,199 +5100,6 @@
                                 self.assertAlmostEqual(float(y_prod), 
float(y_comp))


-    def test_r1rho_kjaergaard_man(self):
-        """Optimisation of the Kjaergaard et al., 2013 Off-resonance 
R1rho relaxation dispersion experiments using the 'DPL' model.
-
-        This uses the data from Kjaergaard's paper at U{DOI: 
10.1021/bi4001062<http://dx.doi.org/10.1021/bi4001062>}.
-
-        This uses the manual analysis.
-
-        """
-
-        # Cluster residues
-        cluster_ids = [
-        ":13@N",
-        ":15@N",
-        ":16@N",
-        ":25@N",
-        ":26@N",
-        ":28@N",
-        ":39@N",
-        ":40@N",
-        ":41@N",
-        ":43@N",
-        ":44@N",
-        ":45@N",
-        ":49@N",
-        ":52@N",
-        ":53@N"]
-
-
-        # Load the data.
-        self.setup_r1rho_kjaergaard(cluster_ids=cluster_ids)
-
-        # The grid search size (the number of increments per dimension).
-        GRID_INC = 4
-
-        # The number of Monte Carlo simulations to be used for error 
analysis at the end of the analysis.
-        MC_NUM = 3
-
-        # Execute the auto-analysis (fast).
-        # Standard parameters are: func_tol = 1e-25, grad_tol = None, 
max_iter = 10000000,
-        OPT_FUNC_TOL = 1e-1
-        OPT_MAX_ITERATIONS = 1000
-
-        result_dir_name = ds.tmpdir
-
-        # Make all spins free, and select a subset.
-        for curspin in cluster_ids:
-            self.interpreter.relax_disp.cluster('free spins', curspin)
-            # Shut them down
-            self.interpreter.deselect.spin(spin_id=curspin, 
change_all=False)
-
-        self.interpreter.select.spin(spin_id=':52@N', change_all=False)
-        #self.interpreter.relax_disp.cluster('model_cluster', ':52@N')
-
-        # Do the analysis manual
-        self.interpreter.spectrum.error_analysis(subset=['46_0_35_0', 
'48_0_35_4', '47_0_35_10', '49_0_35_20', '36_0_39_0', '39_0_39_4', 
'37_0_39_10', '40_0_39_20', '38_0_39_40', '41_0_41_0', '44_0_41_4', 
'42_0_41_10', '45_0_41_20', '43_0_41_40', '31_0_43_0', '34_0_43_4', 
'32_0_43_10', '35_0_43_20', '33_0_43_40', '1_0_46_0', '4_0_46_4', 
'2_0_46_10', '5_0_46_20', '3_0_46_40', '60_0_48_0', '63_0_48_4', 
'61_0_48_10', '62_0_48_14', '64_0_48_20', '11_500_46_0', '14_500_46_4', 
'12_500_46_10', '15_500_46_20', '13_500_46_40', '50_1000_41_0', 
'53_1000_41_4', '51_1000_41_10', '54_1000_41_20', '52_1000_41_40', 
'21_1000_46_0', '24_1000_46_4', '22_1000_46_10', '25_1000_46_20', 
'23_1000_46_40', '65_1000_48_0', '68_1000_48_4', '66_1000_48_10', 
'67_1000_48_14', '69_1000_48_20', '55_2000_41_0', '58_2000_41_4', 
'56_2000_41_10', '59_2000_41_20', '57_2000_41_40', '6_2000_46_0', 
'9_2000_46_4', '7_2000_46_10', '10_2000_46_20', '8_2000_46_40', 
'16_5000_46_0', '19_5000_46_4', '17_5000_46_10', '20_5000_46_20', 
'18_5000_46_40', '26_10000_46_0', '29_10000_46_4', '27_10000_46_10', 
'30_10000_46_20', '28_10000_46_40'])
-
-        ##- The 'R2eff' model -
-        self.interpreter.pipe.copy(pipe_from='base pipe', pipe_to='R2eff 
- relax_disp', bundle_to='relax_disp')
-        self.interpreter.pipe.switch(pipe_name='R2eff - relax_disp')
-        self.interpreter.relax_disp.select_model(model='R2eff')
-        self.interpreter.minimise.grid_search(lower=None, upper=None, 
inc=GRID_INC, constraints=True, verbosity=1)
-
-        self.interpreter.minimise.execute(min_algor='simplex', 
line_search=None, hessian_mod=None, hessian_type=None, 
func_tol=OPT_FUNC_TOL, grad_tol=None, max_iter=OPT_MAX_ITERATIONS, 
constraints=True, scaling=True, verbosity=1)
-        self.interpreter.eliminate(function=None, args=None)
-        self.interpreter.monte_carlo.setup(number=MC_NUM)
-        self.interpreter.monte_carlo.create_data(method='back_calc')
-        self.interpreter.monte_carlo.initial_values()
-
-        self.interpreter.minimise.execute(min_algor='simplex', 
line_search=None, hessian_mod=None, hessian_type=None, 
func_tol=OPT_FUNC_TOL, grad_tol=None, max_iter=OPT_MAX_ITERATIONS, 
constraints=True, scaling=True, verbosity=1)
-        self.interpreter.eliminate(function=None, args=None)
-        self.interpreter.monte_carlo.error_analysis()
-
-        # Write results
-        
#self.interpreter.relax_disp.plot_exp_curves(file='intensities.agr', 
dir=result_dir_name+sep+'resultsR1'+sep+'R2eff', force=True, norm=False)
-        
#self.interpreter.relax_disp.plot_exp_curves(file='intensities_norm.agr', 
dir=result_dir_name+sep+'resultsR1'+sep+'R2eff', force=True, norm=True)
-        
#self.interpreter.relax_disp.plot_disp_curves(dir=result_dir_name+sep+'resultsR1'+sep+'R2eff',
 num_points=1000, extend=500.0, force=True)
-        
#self.interpreter.relax_disp.write_disp_curves(dir=result_dir_name+sep+'resultsR1'+sep+'R2eff',
 force=True)
-        #self.interpreter.value.write(param='r2eff', file='r2eff.out', 
dir=result_dir_name+sep+'resultsR1'+sep+'R2eff', scaling=1.0, 
comment=None, bc=False, force=True)
-        #self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='r2eff', spin_id=None, plot_data='value', file='r2eff.agr', 
dir=result_dir_name+sep+'resultsR1'+sep+'R2eff', force=True, norm=False)
-        #self.interpreter.value.write(param='i0', file='i0.out', 
dir=result_dir_name+sep+'resultsR1'+sep+'R2eff', scaling=1.0, 
comment=None, bc=False, force=True)
-        #self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='i0', spin_id=None, plot_data='value', file='i0.agr', 
dir=result_dir_name+sep+'resultsR1'+sep+'R2eff', force=True, norm=False)
-        #self.interpreter.value.write(param='chi2', file='chi2.out', 
dir=result_dir_name+sep+'resultsR1'+sep+'R2eff', scaling=1.0, 
comment=None, bc=False, force=True)
-        #self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='chi2', spin_id=None, plot_data='value', file='chi2.agr', 
dir=result_dir_name+sep+'resultsR1'+sep+'R2eff', force=True, norm=False)
-
-        ## Save results as state
-        #self.interpreter.results.write(file='results', 
dir=result_dir_name+sep+'resultsR1'+sep+'R2eff', compress_type=1, 
force=True)
-
-        ##- The 'No Rex' model -
-        self.interpreter.pipe.copy(pipe_from='base pipe', pipe_to='No Rex 
- relax_disp', bundle_to='relax_disp')
-        self.interpreter.pipe.switch(pipe_name='No Rex - relax_disp')
-        self.interpreter.relax_disp.select_model(model='No Rex')
-        self.interpreter.value.copy(pipe_from='R2eff - relax_disp', 
pipe_to='No Rex - relax_disp', param='r2eff')
-        self.interpreter.minimise.grid_search(lower=None, upper=None, 
inc=GRID_INC, constraints=True, verbosity=1)
-
-        self.interpreter.minimise.execute(min_algor='simplex', 
line_search=None, hessian_mod=None, hessian_type=None, 
func_tol=OPT_FUNC_TOL, grad_tol=None, max_iter=OPT_MAX_ITERATIONS, 
constraints=True, scaling=True, verbosity=1)
-        self.interpreter.eliminate(function=None, args=None)
-
-        ## Write results
-        
#self.interpreter.relax_disp.plot_disp_curves(dir=result_dir_name+sep+'resultsR1'+sep+'No
 Rex', num_points=1000, extend=500.0, force=True)
-        
#self.interpreter.relax_disp.write_disp_curves(dir=result_dir_name+sep+'resultsR1'+sep+'No
 Rex', force=True)
-        #self.interpreter.value.write(param='chi2', file='chi2.out', 
dir=result_dir_name+sep+'resultsR1'+sep+'No Rex', scaling=1.0, 
comment=None, bc=False, force=True)
-        #self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='chi2', spin_id=None, plot_data='value', file='chi2.agr', 
dir=result_dir_name+sep+'resultsR1'+sep+'No Rex', force=True, norm=False)
-
-        ## Save results as state
-        self.interpreter.results.write(file='results', 
dir=result_dir_name+sep+'resultsR1'+sep+'No Rex', compress_type=1, 
force=True)
-
-        ##- The 'DPL94' model -
-        self.interpreter.pipe.copy(pipe_from='base pipe', pipe_to='DPL94 
- relax_disp', bundle_to='relax_disp')
-        self.interpreter.pipe.switch(pipe_name='DPL94 - relax_disp')
-        self.interpreter.relax_disp.select_model(model='DPL94')
-        self.interpreter.value.copy(pipe_from='R2eff - relax_disp', 
pipe_to='DPL94 - relax_disp', param='r2eff')
-        self.interpreter.relax_disp.insignificance(level=1.0)
-        self.interpreter.minimise.grid_search(lower=None, upper=None, 
inc=GRID_INC, constraints=True, verbosity=1)
-
-        self.interpreter.minimise.execute(min_algor='simplex', 
line_search=None, hessian_mod=None, hessian_type=None, 
func_tol=OPT_FUNC_TOL, grad_tol=None, max_iter=OPT_MAX_ITERATIONS, 
constraints=True, scaling=True, verbosity=1)
-        self.interpreter.eliminate(function=None, args=None)
-
-        ## Write results
-        
#self.interpreter.relax_disp.plot_disp_curves(dir=result_dir_name+sep+'resultsR1'+sep+'DPL94',
 num_points=1000, extend=500.0, force=True)
-        
#self.interpreter.relax_disp.write_disp_curves(dir=result_dir_name+sep+'resultsR1'+sep+'DPL94',
 force=True)
-        #self.interpreter.value.write(param='phi_ex', file='phi_ex.out', 
dir=result_dir_name+sep+'resultsR1'+sep+'DPL94', scaling=1.0, 
comment=None, bc=False, force=True)
-        #self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='phi_ex', spin_id=None, plot_data='value', file='phi_ex.agr', 
dir=result_dir_name+sep+'resultsR1'+sep+'DPL94', force=True, norm=False)
-        #self.interpreter.value.write(param='k_AB', file='k_AB.out', 
dir=result_dir_name+sep+'resultsR1'+sep+'DPL94', scaling=1.0, 
comment=None, bc=False, force=True)
-        #self.interpreter.value.write(param='kex', file='kex.out', 
dir=result_dir_name+sep+'resultsR1'+sep+'DPL94', scaling=1.0, 
comment=None, bc=False, force=True)
-        #self.interpreter.value.write(param='tex', file='tex.out', 
dir=result_dir_name+sep+'resultsR1'+sep+'DPL94', scaling=1.0, 
comment=None, bc=False, force=True)
-        #self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='k_AB', spin_id=None, plot_data='value', file='k_AB.agr', 
dir=result_dir_name+sep+'resultsR1'+sep+'DPL94', force=True, norm=False)
-        #self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='kex', spin_id=None, plot_data='value', file='kex.agr', 
dir=result_dir_name+sep+'resultsR1'+sep+'DPL94', force=True, norm=False)
-        #self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='tex', spin_id=None, plot_data='value', file='tex.agr', 
dir=result_dir_name+sep+'resultsR1'+sep+'DPL94', force=True, norm=False)
-        #self.interpreter.value.write(param='chi2', file='chi2.out', 
dir=result_dir_name+sep+'resultsR1'+sep+'DPL94', scaling=1.0, 
comment=None, bc=False, force=True)
-        #self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='chi2', spin_id=None, plot_data='value', file='chi2.agr', 
dir=result_dir_name+sep+'resultsR1'+sep+'DPL94', force=True, norm=False)
-
-        ## Save results as state
-        #self.interpreter.results.write(file='results', 
dir=result_dir_name+sep+'resultsR1'+sep+'DPL94', compress_type=1, 
force=True)
-
-        ##- The 'final' model -
-        self.interpreter.model_selection(method='AIC', modsel_pipe='final 
- relax_disp', bundle='relax_disp', pipes=['No Rex - relax_disp', 'DPL94 - 
relax_disp'])
-        self.interpreter.monte_carlo.setup(number=MC_NUM)
-        self.interpreter.monte_carlo.create_data(method='back_calc')
-        self.interpreter.monte_carlo.initial_values()
-
-        self.interpreter.minimise.execute(min_algor='simplex', 
line_search=None, hessian_mod=None, hessian_type=None, 
func_tol=OPT_FUNC_TOL, grad_tol=None, max_iter=OPT_MAX_ITERATIONS, 
constraints=True, scaling=True, verbosity=1)
-        self.interpreter.eliminate(function=None, args=None)
-        self.interpreter.monte_carlo.error_analysis()
-
-        ## Write results
-        
#self.interpreter.relax_disp.plot_disp_curves(dir=result_dir_name+sep+'resultsR1'+sep+'final',
 num_points=1000, extend=500.0, force=True)
-        
#self.interpreter.relax_disp.write_disp_curves(dir=result_dir_name+sep+'resultsR1'+sep+'final',
 force=True)
-        #self.interpreter.value.write(param='model', file='model.out', 
dir=result_dir_name+sep+'resultsR1'+sep+'final', scaling=1.0, 
comment=None, bc=False, force=True)
-        #self.interpreter.value.write(param='pA', file='pA.out', 
dir=result_dir_name+sep+'resultsR1'+sep+'final', scaling=1.0, 
comment=None, bc=False, force=True)
-        #self.interpreter.value.write(param='pB', file='pB.out', 
dir=result_dir_name+sep+'resultsR1'+sep+'final', scaling=1.0, 
comment=None, bc=False, force=True)
-        #self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='pA', spin_id=None, plot_data='value', file='pA.agr', 
dir=result_dir_name+sep+'resultsR1'+sep+'final', force=True, norm=False)
-        #self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='pB', spin_id=None, plot_data='value', file='pB.agr', 
dir=result_dir_name+sep+'resultsR1'+sep+'final', force=True, norm=False)
-        self.interpreter.value.write(param='phi_ex', file='phi_ex.out', 
dir=result_dir_name+sep+'resultsR1'+sep+'final', scaling=1.0, 
comment=None, bc=False, force=True)
-        #self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='phi_ex', spin_id=None, plot_data='value', file='phi_ex.agr', 
dir=result_dir_name+sep+'resultsR1'+sep+'final', force=True, norm=False)
-        #self.interpreter.value.write(param='phi_ex_B', 
file='phi_ex_B.out', dir=result_dir_name+sep+'resultsR1'+sep+'final', 
scaling=1.0, comment=None, bc=False, force=True)
-        #self.interpreter.value.write(param='phi_ex_C', 
file='phi_ex_C.out', dir=result_dir_name+sep+'resultsR1'+sep+'final', 
scaling=1.0, comment=None, bc=False, force=True)
-        #self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='phi_ex_B', spin_id=None, plot_data='value', 
file='phi_ex_B.agr', dir=result_dir_name+sep+'resultsR1'+sep+'final', 
force=True, norm=False)
-        #self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='phi_ex_C', spin_id=None, plot_data='value', 
file='phi_ex_C.agr', dir=result_dir_name+sep+'resultsR1'+sep+'final', 
force=True, norm=False)
-        #self.interpreter.value.write(param='dw', file='dw.out', 
dir=result_dir_name+sep+'resultsR1'+sep+'final', scaling=1.0, 
comment=None, bc=False, force=True)
-        #self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='dw', spin_id=None, plot_data='value', file='dw.agr', 
dir=result_dir_name+sep+'resultsR1'+sep+'final', force=True, norm=False)
-        #self.interpreter.value.write(param='dwH', file='dwH.out', 
dir=result_dir_name+sep+'resultsR1'+sep+'final', scaling=1.0, 
comment=None, bc=False, force=True)
-        #self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='dwH', spin_id=None, plot_data='value', file='dwH.agr', 
dir=result_dir_name+sep+'resultsR1'+sep+'final', force=True, norm=False)
-        #self.interpreter.value.write(param='k_AB', file='k_AB.out', 
dir=result_dir_name+sep+'resultsR1'+sep+'final', scaling=1.0, 
comment=None, bc=False, force=True)
-        self.interpreter.value.write(param='kex', file='kex.out', 
dir=result_dir_name+sep+'resultsR1'+sep+'final', scaling=1.0, 
comment=None, bc=False, force=True)
-        #self.interpreter.value.write(param='tex', file='tex.out', 
dir=result_dir_name+sep+'resultsR1'+sep+'final', scaling=1.0, 
comment=None, bc=False, force=True)
-        #self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='k_AB', spin_id=None, plot_data='value', file='k_AB.agr', 
dir=result_dir_name+sep+'resultsR1'+sep+'final', force=True, norm=False)
-        #self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='kex', spin_id=None, plot_data='value', file='kex.agr', 
dir=result_dir_name+sep+'resultsR1'+sep+'final', force=True, norm=False)
-        #self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='tex', spin_id=None, plot_data='value', file='tex.agr', 
dir=result_dir_name+sep+'resultsR1'+sep+'final', force=True, norm=False)
-        #self.interpreter.value.write(param='k_AB', file='k_AB.out', 
dir=result_dir_name+sep+'resultsR1'+sep+'final', scaling=1.0, 
comment=None, bc=False, force=True)
-        #self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='k_AB', spin_id=None, plot_data='value', file='k_AB.agr', 
dir=result_dir_name+sep+'resultsR1'+sep+'final', force=True, norm=False)
-        #self.interpreter.value.write(param='kB', file='kB.out', 
dir=result_dir_name+sep+'resultsR1'+sep+'final', scaling=1.0, 
comment=None, bc=False, force=True)
-        #self.interpreter.value.write(param='kC', file='kC.out', 
dir=result_dir_name+sep+'resultsR1'+sep+'final', scaling=1.0, 
comment=None, bc=False, force=True)
-        #self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='kB', spin_id=None, plot_data='value', file='kB.agr', 
dir=result_dir_name+sep+'resultsR1'+sep+'final', force=True, norm=False)
-        #self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='kC', spin_id=None, plot_data='value', file='kC.agr', 
dir=result_dir_name+sep+'resultsR1'+sep+'final', force=True, norm=False)
-        #self.interpreter.value.write(param='chi2', file='chi2.out', 
dir=result_dir_name+sep+'resultsR1'+sep+'final', scaling=1.0, 
comment=None, bc=False, force=True)
-        #self.interpreter.grace.write(x_data_type='res_num', 
y_data_type='chi2', spin_id=None, plot_data='value', file='chi2.agr', 
dir=result_dir_name+sep+'resultsR1'+sep+'final', force=True, norm=False)
-
-        # Test of new parameters to write out.
-        self.interpreter.value.write(param='theta', file='theta.out', 
dir=result_dir_name+sep+'resultsR1'+sep+'final', scaling=1.0, 
comment=None, bc=False, force=True)
-        #self.interpreter.value.write(param='theta', file='theta.out', 
dir='~', scaling=1.0, comment=None, bc=False, force=True)
-        #self.assert_(hasattr(cdp.mol[0].res[7].spin[0], 'theta'))
-
-        ## Save results as state
-        #self.interpreter.results.write(file='results', 
dir=result_dir_name+sep+'resultsR1'+sep+'final', compress_type=1, 
force=True)
-        ## Save all results in all pipes in state
-        #self.interpreter.state.save(state='final_state', 
dir=result_dir_name+sep+'resultsR1', compress_type=1, force=True)
-
-        # Assert the file existence of the written value files
-        
self.assert_(access(result_dir_name+sep+'resultsR1'+sep+'final'+sep+'phi_ex.out',
 F_OK))
-        
self.assert_(access(result_dir_name+sep+'resultsR1'+sep+'final'+sep+'kex.out',
 F_OK))
-        
self.assert_(access(result_dir_name+sep+'resultsR1'+sep+'final'+sep+'theta.out',
 F_OK))
-
-
     def test_r1rho_kjaergaard_missing_r1(self):
         """Optimisation of the Kjaergaard et al., 2013 Off-resonance 
R1rho relaxation dispersion experiments using the 'DPL' model.



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