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List: relax-commits
Subject: r19253 - in /branches/relax_disp: specific_analyses/ test_suite/system_tests/ test_suite/system_test
From: edward () nmr-relax ! com
Date: 2013-03-27 14:53:01
Message-ID: E1UKrin-0001FR-Iw () subversion ! gna ! org
[Download RAW message or body]
Author: bugman
Date: Wed Mar 27 15:53:01 2013
New Revision: 19253
URL: http://svn.gna.org/viewcvs/relax?rev=19253&view=rev
Log:
Ported r11698 from the old relax_disp branch into the new branch.
The commands used were:
svn merge -r11697:11698 \
svn+ssh://bugman@svn.gna.org/svn/relax/branches/relax_disp/specific_fns/@r18123 \
specific_analyses svn merge -r11697:11698 \
svn+ssh://bugman@svn.gna.org/svn/relax/branches/relax_disp/test_suite/@r18123 \
test_suite
.....
r11698 | bugman | 2010-11-23 14:02:38 +0100 (Tue, 23 Nov 2010) | 6 lines
Changed paths:
M /branches/relax_disp/dep_check.py
M /branches/relax_disp/prompt/relax_disp.py
M /branches/relax_disp/specific_fns/relax_disp.py
M /branches/relax_disp/specific_fns/relax_fit.py
M /branches/relax_disp/test_suite/system_tests/relax_disp.py
M /branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_fast.py
M /branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_slow.py
M /branches/relax_disp/test_suite/unit_tests/_prompt/test_relax_disp.py
Brought the relaxation dispersion branch into sync with the 1.3 line.
There were many design changes within the 1.3 line that required that the old \
relaxation dispersion code be updated.
.....
Modified:
branches/relax_disp/specific_analyses/relax_disp.py
branches/relax_disp/test_suite/system_tests/relax_disp.py
branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_fast.py
branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_slow.py
branches/relax_disp/test_suite/unit_tests/_prompt/test_relax_disp.py
Modified: branches/relax_disp/specific_analyses/relax_disp.py
URL: http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp.py?rev=19253&r1=19252&r2=19253&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp.py Wed Mar 27 15:53:01 2013
@@ -1,6 +1,6 @@
###############################################################################
# #
-# Copyright (C) 2004-2008 Edward d'Auvergne #
+# Copyright (C) 2004-2010 Edward d'Auvergne #
# Copyright (C) 2009 Sebastien Morin #
# #
# This file is part of the program relax. #
@@ -31,7 +31,8 @@
# relax module imports.
from dep_check import C_module_exp_fn
-from base_class import Common_functions
+from api_base import API_base
+from api_common import API_common
from generic_fns import pipes
from generic_fns.mol_res_spin import exists_mol_res_spin_data, generate_spin_id, \
return_spin, spin_loop from minfx.generic import generic_minimise
@@ -42,7 +43,7 @@
from maths_fns.relax_disp import setup, func, dfunc, d2func, back_calc_I
-class Relax_disp(Common_functions):
+class Relax_disp(API_base, API_common):
"""Class containing functions for relaxation dispersion curve fitting."""
def assemble_param_vector(self, spin=None, sim_index=None):
Modified: branches/relax_disp/test_suite/system_tests/relax_disp.py
URL: http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/relax_disp.py?rev=19253&r1=19252&r2=19253&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/relax_disp.py (original)
+++ branches/relax_disp/test_suite/system_tests/relax_disp.py Wed Mar 27 15:53:01 \
2013 @@ -22,27 +22,24 @@
###############################################################################
# Python module imports.
+import __main__
from os import sep
from shutil import rmtree
-from string import split
-import sys
from tempfile import mkdtemp
-from unittest import TestCase
# relax module imports.
+from base_classes import SystemTestCase
from data import Relax_data_store; ds = Relax_data_store()
-from generic_fns.mol_res_spin import spin_index_loop
-from generic_fns import pipes
-class Relax_disp(TestCase):
+class Relax_disp(SystemTestCase):
"""Class for testing various aspects specific to relaxation dispersion \
curve-fitting."""
def setUp(self):
"""Set up for all the functional tests."""
# Create the data pipe.
- self.relax.interpreter._Pipe.create('relax_disp', 'relax_disp')
+ self.interpreter.pipe.create('relax_disp', 'relax_disp')
# Create a temporary directory for dumping files.
ds.tmpdir = mkdtemp()
@@ -64,7 +61,7 @@
fast-exchange limit."""
# Execute the script.
- self.relax.interpreter.run(script_file=sys.path[-1] + \
'/test_suite/system_tests/scripts/relax_disp_cpmg_fast.py') + \
self.interpreter.run(script_file=__main__.install_path + \
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp_cpmg_fast.py')
def test_curve_fitting_cpmg_slow(self):
@@ -72,22 +69,19 @@
slow-exchange limit."""
# Execute the script.
- self.relax.interpreter.run(script_file=sys.path[-1] + \
'/test_suite/system_tests/scripts/relax_disp_cpmg_slow.py') + \
self.interpreter.run(script_file=__main__.install_path + \
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp_cpmg_slow.py')
def test_read_r2eff(self):
"""Test the reading of a file containing r2eff values."""
- # Get the current data pipe.
- cdp = pipes.get_pipe()
-
# Create the sequence data, and name the spins.
- self.relax.interpreter._Residue.create(1, 'Gly')
- self.relax.interpreter._Residue.create(2, 'Gly')
- self.relax.interpreter._Residue.create(3, 'Gly')
+ self.interpreter.residue.create(1, 'Gly')
+ self.interpreter.residue.create(2, 'Gly')
+ self.interpreter.residue.create(3, 'Gly')
# Read the file.
- self.relax.interpreter._Relax_data.read('R2eff', '600', 600 * 1e6, \
'r2eff.out', dir=sys.path[-1] + "/test_suite/shared_data/curve_fitting_disp/r2eff") + \
self.interpreter.relax_data.read('R2eff', '600', 600 * 1e6, 'r2eff.out', \
dir=__main__.install_path + \
sep+'test_suite'+sep+'shared_data'+sep+'curve_fitting_disp'+sep+'r2eff')
# Test the data.
Modified: branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_fast.py
URL: http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_fast.py?rev=19253&r1=19252&r2=19253&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_fast.py \
(original)
+++ branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_fast.py Wed \
Mar 27 15:53:01 2013 @@ -1,17 +1,19 @@
# Script for CPMG relaxation dispersion curve fitting in the fast-exchange limit.
-import sys
+# Python module imports.
+import __main__
+from os import sep
# Create the data pipe.
pipe.create('rex', 'relax_disp')
# The path to the data files.
-data_path_1 = sys.path[-1] + \
'/test_suite/shared_data/curve_fitting_disp/Hansen/500_MHz'
-data_path_2 = sys.path[-1] + \
'/test_suite/shared_data/curve_fitting_disp/Hansen/800_MHz' +data_path1 = \
__main__.install_path + \
sep+'test_suite'+sep+'shared_data'+sep+'curve_fitting_disp'+sep+'Hansen'+sep+'500_MHz'
+data_path2 = __main__.install_path + \
sep+'test_suite'+sep+'shared_data'+sep+'curve_fitting_disp'+sep+'Hansen'+sep+'800_MHz'
# Load the sequence.
-sequence.read('fake_sequence.in', dir=sys.path[-1] + \
'/test_suite/shared_data/curve_fitting_disp/Hansen') \
+sequence.read('fake_sequence.in', dir=__main__.install_path + \
sep+'test_suite'+sep+'shared_data'+sep+'curve_fitting_disp'+sep+'Hansen', \
res_num_col=1, res_name_col=2)
# Name the spins so they can be matched to the assignments.
spin.name(name='N')
Modified: branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_slow.py
URL: http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_slow.py?rev=19253&r1=19252&r2=19253&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_slow.py \
(original)
+++ branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_slow.py Wed \
Mar 27 15:53:01 2013 @@ -1,16 +1,18 @@
# Script for CPMG relaxation dispersion curve fitting in the slow-exchange limit.
-import sys
+# Python module imports.
+import __main__
+from os import sep
# Create the data pipe.
pipe.create('rex', 'relax_disp')
# The path to the data files.
-data_path = sys.path[-1] + \
'/test_suite/shared_data/curve_fitting_disp/Hansen/500_MHz' +data_path = \
__main__.install_path + \
sep+'test_suite'+sep+'shared_data'+sep+'curve_fitting_disp'+sep+'Hansen'+sep+'500_MHz'
# Load the sequence.
-sequence.read('fake_sequence.in', dir=sys.path[-1] + \
'/test_suite/shared_data/curve_fitting_disp/Hansen') \
+sequence.read('fake_sequence.in', dir=__main__.install_path + \
sep+'test_suite'+sep+'shared_data'+sep+'curve_fitting_disp'+sep+'Hansen', \
res_num_col=1, res_name_col=2)
# Name the spins so they can be matched to the assignments.
spin.name(name='N')
Modified: branches/relax_disp/test_suite/unit_tests/_prompt/test_relax_disp.py
URL: http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/unit_tests/_prompt/test_relax_disp.py?rev=19253&r1=19252&r2=19253&view=diff
==============================================================================
--- branches/relax_disp/test_suite/unit_tests/_prompt/test_relax_disp.py (original)
+++ branches/relax_disp/test_suite/unit_tests/_prompt/test_relax_disp.py Wed Mar 27 \
15:53:01 2013 @@ -1,6 +1,6 @@
###############################################################################
# #
-# Copyright (C) 2008 Edward d'Auvergne #
+# Copyright (C) 2008-2010 Edward d'Auvergne #
# Copyright (C) 2009 Sebastien Morin #
# #
# This file is part of the program relax. #
@@ -30,14 +30,13 @@
# Unit test imports.
from data_types import DATA_TYPES
-import fake_relax
class Test_relax_disp(TestCase):
"""Unit tests for the functions of the 'prompt.relax_disp' module."""
# Instantiate the user function class.
- relax_disp_fns = Relax_disp(fake_relax.fake_instance())
+ relax_disp_fns = Relax_disp()
def test_relax_calc_r2eff_argfail_exp_type(self):
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