Author: bugman
Date: Wed Oct 8 08:39:48 2014
New Revision: 26202
URL: http://svn.gna.org/viewcvs/relax?rev=26202&view=rev
Log:
Merged revisions 26189-26196 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r26189 | tlinnet | 2014-10-07 15:45:35 +0200 (Tue, 07 Oct 2014) | 3 lines
Added some test pymol script, to create dx maps and chi2 surface plot.
These will go to the wiki: http://wiki.nmr-relax.com/Chi2_surface_plot
........
r26190 | bugman | 2014-10-07 16:11:38 +0200 (Tue, 07 Oct 2014) | 10 lines
Big improvement for running the relax unit tests via the relax command line
options.
The unit test module path is now accepted as a command line option. This
brings more capabilities
of Gary Thompson's test_suite/unit_tests/unit_test_runner.py script into
the relax command line.
The _pipe_control/test_value unit test module path can be specified as, for
example, one of
'test_suite.unit_tests._pipe_control.test_value',
'test_suite/unit_tests/_pipe_control/test_value',
'_pipe_control.test_value', '_pipe_control/test_value'. This allows
individual modules of tests to
be run, rather than having to execute all unit tests, which is very useful
for debugging.
........
r26191 | bugman | 2014-10-07 16:21:30 +0200 (Tue, 07 Oct 2014) | 8 lines
Modified the printouts for the unit tests when running with the --time
command line option.
The test name is now being processed. The leading 'test_suite.unit_tests.'
text is now stripped
out. And the remaining text is split into the module name and the test
name. This is to allow the
unit test module name to be more easily identifiable, so it can then be
used as a command line
option to allow only a subset of tests to be performed.
........
r26192 | bugman | 2014-10-07 16:31:49 +0200 (Tue, 07 Oct 2014) | 6 lines
Modified the help strings for the test suite options shown when 'relax -h'
is run.
The ability to specify individual tests (or modules of tests for the unit
tests) is now documented.
The '--time' option help string has also been edited.
........
r26193 | bugman | 2014-10-07 16:44:32 +0200 (Tue, 07 Oct 2014) | 7 lines
Fix for the Bmrb.test_bug_22704_corrupted_state_file GUI test.
This was failing because the setUp() method in the inherited Bmrb system
test module was being
overwritten by the default Unittest.setUp() method. Therefore the system
test setUp() method has
been copied into the GUI test class.
........
r26194 | bugman | 2014-10-07 17:45:07 +0200 (Tue, 07 Oct 2014) | 9 lines
Fix for the Test_value.test_value_set_r1_rit test of the
_pipe_control.test_value unit test module.
This is a general fix for all unit test modules which use the
test_suite.unit_tests.value_testing_base.Value_testing_base base class.
After the molecules,
residues and spins are manually created, the
pipe_control.mol_res_spin.metadata_update() function is
called to make sure that all of the private and volatile metadata have been
correctly created, so
that the other pipe_control.mol_res_spin module functions can operate
correctly.
........
r26195 | bugman | 2014-10-07 17:47:01 +0200 (Tue, 07 Oct 2014) | 6 lines
Removal of repetitive code in the relaxation dispersion model_loop() API
method.
The spin loop does not need to be called twice, instead the if statements
have been modified to
better direct the code execution.
........
r26196 | tlinnet | 2014-10-07 18:43:52 +0200 (Tue, 07 Oct 2014) | 26 lines
Added script to simulate dispersion profiles at different settings.
This shows that something is wrong.
The back-calculated values in the graphs are not equal to the interpolated
values.
There must be something wrong somewhere.
This list shows the chi2 values, and judging from the dispersion graphs,
this simply cannot be True.
10.405 2.414 6722.833
9.900 1.000 6722.159
9.900 2.333 6722.159
9.900 3.667 6722.159
9.900 5.000 6722.159
10.300 1.000 6722.156
10.300 2.333 6722.156
10.300 3.667 6722.156
10.300 5.000 6722.156
10.700 1.000 6726.040
10.700 2.333 6726.040
10.700 3.667 6726.040
10.700 5.000 6726.040
11.100 1.000 6732.256
11.100 2.333 6732.256
11.100 3.667 6732.256
11.100 5.000 6732.256
........
Added:
branches/frame_order_cleanup/test_suite/shared_data/dispersion/KTeilum_FMPoulsen_MAkke_2006/surface_chi2_clustered_fitting/
- copied from r26196,
trunk/test_suite/shared_data/dispersion/KTeilum_FMPoulsen_MAkke_2006/surface_chi2_clustered_fitting/
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/relax.py
branches/frame_order_cleanup/specific_analyses/relax_disp/api.py
branches/frame_order_cleanup/test_suite/gui_tests/bmrb.py
branches/frame_order_cleanup/test_suite/relax_test_runner.py
branches/frame_order_cleanup/test_suite/test_suite_runner.py
branches/frame_order_cleanup/test_suite/unit_tests/unit_test_runner.py
branches/frame_order_cleanup/test_suite/unit_tests/value_testing_base.py
Propchange: branches/frame_order_cleanup/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Wed Oct 8 08:39:48 2014
@@ -1 +1 @@
-/trunk:1-26139,26142-26176,26188
+/trunk:1-26139,26142-26176,26188-26196
Modified: branches/frame_order_cleanup/relax.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/relax.py?rev=26202&r1=26201&r2=26202&view=diff
==============================================================================
--- branches/frame_order_cleanup/relax.py (original)
+++ branches/frame_order_cleanup/relax.py Wed Oct 8 08:39:48 2014
@@ -312,11 +312,11 @@
# Recognised command line options for the test suite.
group = OptionGroup(parser, 'Test suite options')
group.add_option('-x', '--test-suite', action='store_true',
dest='test_suite', default=0, help='execute the full relax test suite')
- group.add_option('-s', '--system-tests', action='store_true',
dest='system_tests', default=0, help='execute the system/functional tests')
- group.add_option('-u', '--unit-tests', action='store_true',
dest='unit_tests', default=0, help='execute the unit tests')
- group.add_option('--gui-tests', action='store_true',
dest='gui_tests', default=0, help='execute the GUI tests')
- group.add_option('--verification-tests', action='store_true',
dest='verification_tests', default=0, help='execute the software verification
tests')
- group.add_option('--time', action='store_true', dest='tt',
default=0, help='enable the timing of individual tests in the test suite')
+ group.add_option('-s', '--system-tests', action='store_true',
dest='system_tests', default=0, help='execute the system/functional tests.
Test names, revealed with the --time option, can be supplied to perform a
subset of all tests.')
+ group.add_option('-u', '--unit-tests', action='store_true',
dest='unit_tests', default=0, help='execute the unit tests. Module names,
revealed with the --time option, can be supplied to perform a subset of all
tests.')
+ group.add_option('--gui-tests', action='store_true',
dest='gui_tests', default=0, help='execute the GUI tests. Test names,
revealed with the --time option, can be supplied to perform a subset of all
tests.')
+ group.add_option('--verification-tests', action='store_true',
dest='verification_tests', default=0, help='execute the software verification
tests. Test names, revealed with the --time option, can be supplied to
perform a subset of all tests.')
+ group.add_option('--time', action='store_true', dest='tt',
default=0, help='print out the timings of individual tests in the test suite')
group.add_option('--no-skip', action='store_true', dest='no_skip',
default=0, help='a debugging option for relax developers to turn on all
blacklisted tests, even those that will fail')
parser.add_option_group(group)
Modified: branches/frame_order_cleanup/specific_analyses/relax_disp/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_disp/api.py?rev=26202&r1=26201&r2=26202&view=diff
==============================================================================
--- branches/frame_order_cleanup/specific_analyses/relax_disp/api.py
(original)
+++ branches/frame_order_cleanup/specific_analyses/relax_disp/api.py Wed
Oct 8 08:39:48 2014
@@ -846,24 +846,7 @@
"""
# Loop over individual spins for the R2eff model.
- if hasattr(cdp, 'model_type'):
- if cdp.model_type == MODEL_R2EFF:
- # The spin loop.
- for spin, spin_id in spin_loop(return_id=True):
- # Skip deselected spins
- if not spin.select:
- continue
-
- # Yield the spin ID as a list.
- yield [spin_id]
-
- # The cluster loop.
- else:
- for spin_ids in loop_cluster(skip_desel=False):
- yield spin_ids
-
- # If no model is present, then set the values.
- else:
+ if not hasattr(cdp, 'model_type') or cdp.model_type == MODEL_R2EFF:
# The spin loop.
for spin, spin_id in spin_loop(return_id=True):
# Skip deselected spins
@@ -872,6 +855,11 @@
# Yield the spin ID as a list.
yield [spin_id]
+
+ # The cluster loop.
+ else:
+ for spin_ids in loop_cluster(skip_desel=False):
+ yield spin_ids
def model_statistics(self, model_info=None, spin_id=None,
global_stats=None):
Modified: branches/frame_order_cleanup/test_suite/gui_tests/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/gui_tests/bmrb.py?rev=26202&r1=26201&r2=26202&view=diff
==============================================================================
--- branches/frame_order_cleanup/test_suite/gui_tests/bmrb.py (original)
+++ branches/frame_order_cleanup/test_suite/gui_tests/bmrb.py Wed Oct 8
08:39:48 2014
@@ -22,7 +22,11 @@
# Module docstring.
"""GUI tests for the BMRB related activities."""
+# Python module imports.
+from tempfile import mkdtemp, mktemp
+
# relax module imports.
+from data_store import Relax_data_store; ds = Relax_data_store()
from test_suite.gui_tests.base_classes import GuiTestCase
from test_suite import system_tests
@@ -35,3 +39,13 @@
# Force execution of the GuiTestCase __init__ method.
GuiTestCase.__init__(self, methodName)
+
+
+ def setUp(self):
+ """Common set up for these GUI tests."""
+
+ # Create a temporary file name.
+ ds.tmpfile = mktemp()
+
+ # Create a temporary directory for dumping files.
+ self.tmpdir = mkdtemp()
Modified: branches/frame_order_cleanup/test_suite/relax_test_runner.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/relax_test_runner.py?rev=26202&r1=26201&r2=26202&view=diff
==============================================================================
--- branches/frame_order_cleanup/test_suite/relax_test_runner.py
(original)
+++ branches/frame_order_cleanup/test_suite/relax_test_runner.py Wed
Oct 8 08:39:48 2014
@@ -21,6 +21,7 @@
# Python module imports.
import dep_check
+from re import split
import sys
from time import time
from unittest import TextTestRunner
@@ -166,10 +167,21 @@
# Subtract the end time from the start time.
self.time -= time()
- # Change the test name.
+ # Change the test name for all but unit tests.
if self.category != 'unit':
test_name = test_name.split('.')
test_name = "%s.%s" % (test_name[-2], test_name[-1])
+
+ # Modify the unit test name printout.
+ else:
+ # Strip out the leading 'test_suite.unit_tests.' text.
+ test_name = test_name.replace('test_suite.unit_tests.', '')
+
+ # Split out the module name from the test name.
+ module_name, test_name = split('.Test_', test_name)
+
+ # Rebuild the test name.
+ test_name = "module %s, test Test_%s" % (module_name, test_name)
# The printout.
self.stream.write(' %7.2f s for %s\n' % (-self.time, test_name))
Modified: branches/frame_order_cleanup/test_suite/test_suite_runner.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/test_suite_runner.py?rev=26202&r1=26201&r2=26202&view=diff
==============================================================================
--- branches/frame_order_cleanup/test_suite/test_suite_runner.py
(original)
+++ branches/frame_order_cleanup/test_suite/test_suite_runner.py Wed
Oct 8 08:39:48 2014
@@ -231,7 +231,7 @@
# Run the tests.
unit_runner =
Unit_test_runner(root_path=status.install_path+os.sep+'test_suite'+os.sep+'unit_tests')
self.runner.category = 'unit'
- self.unit_result = unit_runner.run(runner=self.runner)
+ self.unit_result = unit_runner.run(self.tests,
runner=self.runner)
# Print out a summary of the test suite.
if summary:
Modified:
branches/frame_order_cleanup/test_suite/unit_tests/unit_test_runner.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/unit_tests/unit_test_runner.py?rev=26202&r1=26201&r2=26202&view=diff
==============================================================================
--- branches/frame_order_cleanup/test_suite/unit_tests/unit_test_runner.py
(original)
+++ branches/frame_order_cleanup/test_suite/unit_tests/unit_test_runner.py
Wed Oct 8 08:39:48 2014
@@ -5,7 +5,7 @@
# (see https://gna.org/users/varioustoxins
#
# for contact details)
#
#
#
-# Copyright (C) 2007-2013 Edward d'Auvergne
#
+# Copyright (C) 2007-2014 Edward d'Auvergne
#
#
#
#
#
# This file is part of the program relax.
#
@@ -577,9 +577,11 @@
return result
- def run(self, runner=None):
+ def run(self, tests=None, runner=None):
"""Run a unit test or set of unit tests.
+ @keyword tests: The list of system tests to perform.
+ @type tests: list of str
@keyword runner: A unit test runner such as TextTestRunner. None
indicates use of the default unit test runner. For an example of how to
write a test runner see the python documentation for TextTestRunner in the
python source.
@type runner: Unit test runner instance (TextTestRunner,
BaseGUITestRunner subclass, etc.)
@return: A string indicating success or failure of the
unit tests run.
@@ -598,7 +600,27 @@
print('----------------')
print('')
- module_paths = self.paths_from_test_module(self.test_module)
+ # The test module path for individual tests.
+ if tests:
+ # Initialise the list of paths.
+ module_paths = []
+
+ # Loop over each test.
+ for test in tests:
+ # Strip out the leading 'test_suite.unit_tests.' if present.
+ test = test.replace('test_suite.unit_tests.', '')
+ test = test.replace('test_suite%sunit_tests%s' % (os.sep,
os.sep), '')
+
+ # Replace the Python '.' separator with the system's path
separator.
+ test = test.replace('.', os.sep)
+
+ # Append to the module path list.
+ module_paths +=
self.paths_from_test_module(self.test_module+os.sep+test)
+
+ # The test module path for all tests.
+ else:
+ module_paths = self.paths_from_test_module(self.test_module)
+
if self.verbose:
print("%-22s %s" % ('Test module:', self.test_module))
print("%-22s %s" % ('Root path', self.root_path))
Modified:
branches/frame_order_cleanup/test_suite/unit_tests/value_testing_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/unit_tests/value_testing_base.py?rev=26202&r1=26201&r2=26202&view=diff
==============================================================================
--- branches/frame_order_cleanup/test_suite/unit_tests/value_testing_base.py
(original)
+++ branches/frame_order_cleanup/test_suite/unit_tests/value_testing_base.py
Wed Oct 8 08:39:48 2014
@@ -25,7 +25,7 @@
# relax module imports.
from data_store import Relax_data_store; ds = Relax_data_store()
-from pipe_control import diffusion_tensor, pipes
+from pipe_control import diffusion_tensor, pipes, mol_res_spin
from lib.errors import RelaxError, RelaxParamSetError,
RelaxUnknownParamCombError
from test_suite.unit_tests.base_classes import UnitTestCase
@@ -98,6 +98,9 @@
pipe.mol[0].res[1].spin[0].num = 112
pipe.mol[0].res[1].spin[0].name = 'NH'
+ # Update the metadata so that the other pipe_control.mol_res_spin
module functions can operate correctly.
+ mol_res_spin.metadata_update(pipe=pipe_name)
+
r26202 - in /branches/frame_order_cleanup: ./ specific_analyses/relax_disp/ test_suite/ test_suite/gui_tests/ test_suite/sha...