Hi Troels, For this change, it is clear that the file history is that test_suite/unit_tests/_lib/_dispersion/test_dpl94.py is a copy of test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_expanded.py. But this history is not preserved in the repository. For these copy operations, git-svn just cannot do it. According to the documentation at http://git-scm.com/docs/git-svn:
""" MERGE TRACKING While git svn can track copy history (including branches and tags) for repositories adopting a standard layout, it cannot yet represent merge history that happened inside git back upstream to SVN users. Therefore it is advised that users keep history as linear as possible inside Git to ease compatibility with SVN (see the CAVEATS section below). """ Therefore instead you need to have a subversion copy of the 'disp_speed' branch and then run the commands: $ cd test_suite/unit_tests/_lib/_dispersion/ $ svn cp test_ns_cpmg_2site_expanded.py test_dpl94.py $ svn ci This is how file copies must be performed in a subversion repository. Until git-svn acquires the ability to do this too, this is how one needs to make file copies. Cheers, Edward On 22 May 2014 16:56, <[email protected]> wrote: > Author: tlinnet > Date: Thu May 22 16:56:32 2014 > New Revision: 23338 > > URL: http://svn.gna.org/viewcvs/relax?rev=23338&view=rev > Log: > Added 7 unit tests demonstrating edge case 'no Rex' failures of the model > 'DPL94'. > > This follows from the ideas in the post > http://article.gmane.org/gmane.science.nmr.relax.devel/5858. > This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of > dispersion models. > > This is to implement catching of math domain errors, before they occur. > > These tests cover all parameter value combinations which result in no > exchange: > > - dw = 0.0, > - pA = 1.0, > - kex = 0.0, > - dw = 0.0 and pA = 1.0, > - dw = 0.0 and kex = 0.0, > - pA = 1.0 and kex = 0.0, > - dw = 0.0, pA = 1.0, and kex = 0.0. > > Added: > branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_dpl94.py > Modified: > branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/__init__.py > > Modified: > branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/__init__.py > URL: > http://svn.gna.org/viewcvs/relax/branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/__init__.py?rev=23338&r1=23337&r2=23338&view=diff > ============================================================================== > --- branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/__init__.py > (original) > +++ branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/__init__.py > Thu May 22 16:56:32 2014 > @@ -22,5 +22,6 @@ > > __all__ = [ > 'test___init__', > + 'test_ns_dpl94', > 'test_ns_cpmg_2site_expanded' > ] > > Added: > branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_dpl94.py > URL: > http://svn.gna.org/viewcvs/relax/branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_dpl94.py?rev=23338&view=auto > ============================================================================== > --- branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_dpl94.py > (added) > +++ branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_dpl94.py > Thu May 22 16:56:32 2014 > @@ -0,0 +1,180 @@ > +############################################################################### > +# > # > +# Copyright (C) 2014 Edward d'Auvergne > # > +# Copyright (C) 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 numpy import array, float64, int16, pi, zeros > +from unittest import TestCase > + > +# relax module imports. > +from lib.dispersion.dpl94 import r1rho_DPL94 > + > + > +class Test_dpl94(TestCase): > + """Unit tests for the lib.dispersion.dpl94 relax module.""" > + > + def setUp(self): > + """Set up for all unit tests.""" > + > + # Default parameter values. > + > + > + # The R1rho_prime parameter value (R1rho with no exchange). > + self.r1rho_prime = 2.5 > + # Population of ground state. > + self.pA = 0.9 > + # The chemical exchange difference between states A and B in ppm. > + self.dw = 0.5 > + self.kex = 1000.0 > + # The R1 relaxation rates. > + self.r1 = 1.0 > + # The spin-lock field strengths in Hertz. > + self.spin_lock_nu1 = array([ 1000., 1500., 2000., 2500., 3000., > 3500., 4000., 4500., 5000., 5500., 6000.]) > + # The rotating frame tilt angles for each dispersion point. > + self.theta = array([1.5707963267948966, 1.5707963267948966, > 1.5707963267948966, 1.5707963267948966, 1.5707963267948966, > 1.5707963267948966, 1.5707963267948966, 1.5707963267948966, > 1.5707963267948966, 1.5707963267948966, 1.5707963267948966]) > + > + # The spin Larmor frequencies. > + self.sfrq = 599.8908617*1E6 > + > + # Required data structures. > + self.num_points = 11 > + > + > + def calc_r1rho(self): > + """Calculate and check the R1rho values.""" > + > + # Parameter conversions. > + phi_ex_scaled, spin_lock_omega1_squared = > self.param_conversion(pA=self.pA, dw=self.dw, sfrq=self.sfrq, > spin_lock_nu1=self.spin_lock_nu1) > + > + # Calculate the R1rho values. > + R1rho = r1rho_DPL94(r1rho_prime=self.r1rho_prime, > phi_ex=phi_ex_scaled, kex=self.kex, theta=self.theta, R1=self.r1, > spin_lock_fields2=spin_lock_omega1_squared, num_points=self.num_points) > + > + # Check all R1rho values. > + for i in range(self.num_points): > + self.assertAlmostEqual(R1rho[i], self.r1rho_prime) > + > + > + def param_conversion(self, pA=None, dw=None, sfrq=None, > spin_lock_nu1=None): > + """Convert the parameters. > + > + @keyword pA: The population of state A. > + @type pA: float > + @keyword dw: The chemical exchange difference between > states A and B in ppm. > + @type dw: float > + @keyword sfrq: The spin Larmor frequencies in Hz. > + @type sfrq: float > + @keyword spin_lock_nu1: The spin-lock field strengths in Hertz. > + @type spin_lock_nu1: float > + @return: The parameters {phi_ex_scaled, k_BA}. > + @rtype: tuple of float > + """ > + > + # Calculate pB. > + pB = 1.0 - pA > + > + # Calculate spin Larmor frequencies in 2pi. > + frqs = sfrq * 2 * pi > + > + # The phi_ex parameter value (pA * pB * delta_omega^2). > + phi_ex = pA * pB * dw**2 > + > + # Convert phi_ex from ppm^2 to (rad/s)^2. > + phi_ex_scaled = phi_ex * frqs**2 > + > + # The R1rho spin-lock field strengths squared (in rad^2.s^-2). > + spin_lock_omega1_squared = (2. * pi * spin_lock_nu1)**2 > + > + # Return all values. > + return phi_ex_scaled, spin_lock_omega1_squared > + > + > + def test_dpl94_no_rex1(self): > + """Test the r1rho_dpl94() function for no exchange when dw = 0.0.""" > + > + # Parameter reset. > + self.dw = 0.0 > + > + # Calculate and check the R1rho values. > + self.calc_r1rho() > + > + > + def test_dpl94_no_rex2(self): > + """Test the r1rho_dpl94() function for no exchange when pA = 1.0.""" > + > + # Parameter reset. > + self.pA = 1.0 > + > + # Calculate and check the R1rho values. > + self.calc_r1rho() > + > + > + def test_dpl94_no_rex3(self): > + """Test the r1rho_dpl94() function for no exchange when kex = 0.0.""" > + > + # Parameter reset. > + self.kex = 0.0 > + > + # Calculate and check the R1rho values. > + self.calc_r1rho() > + > + > + def test_dpl94_no_rex4(self): > + """Test the r1rho_dpl94() function for no exchange when dw = 0.0 and > pA = 1.0.""" > + > + # Parameter reset. > + self.pA = 1.0 > + self.dw = 0.0 > + > + # Calculate and check the R1rho values. > + self.calc_r1rho() > + > + > + def test_dpl94_no_rex5(self): > + """Test the r1rho_dpl94() function for no exchange when dw = 0.0 and > kex = 0.0.""" > + > + # Parameter reset. > + self.dw = 0.0 > + self.kex = 0.0 > + > + # Calculate and check the R1rho values. > + self.calc_r1rho() > + > + > + def test_dpl94_no_rex6(self): > + """Test the r1rho_dpl94() function for no exchange when pA = 1.0 and > kex = 0.0.""" > + > + # Parameter reset. > + self.pA = 1.0 > + self.kex = 0.0 > + > + # Calculate and check the R1rho values. > + self.calc_r1rho() > + > + > + def test_dpl94_no_rex7(self): > + """Test the r1rho_dpl94() function for no exchange when dw = 0.0, pA > = 1.0, and kex = 0.0.""" > + > + # Parameter reset. > + self.dw = 0.0 > + self.kex = 0.0 > + > + # Calculate and check the R1rho values. > + self.calc_r1rho() > > > _______________________________________________ > relax (http://www.nmr-relax.com) > > This is the relax-commits mailing list > [email protected] > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page at > https://mail.gna.org/listinfo/relax-commits _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
