Author: tlinnet
Date: Tue May 20 17:40:12 2014
New Revision: 23261
URL: http://svn.gna.org/viewcvs/relax?rev=23261&view=rev
Log:
Merged revisions 23254,23260 via svnmerge from
svn+ssh://tlinnet@xxxxxxxxxxx/svn/relax/trunk
........
r23254 | bugman | 2014-05-20 13:37:32 +0200 (Tue, 20 May 2014) | 12 lines
Fix for the chain-reaction failures in the test suite.
This fixes bug #22055 (https://gna.org/bugs/?22055), the
processor.run_queue() not cleaning up in
uni_processor - chain-reaction failures in the test suite.
The fix was insanely simple, just implementing what was mentioned Gary's
FIXME comment in the
run_queue() method of the uni-processor object. The queue execution code
has been placed inside a
'try' statement and the queue cleaning up code in a 'finally' statement.
This closes a painfully difficult to find bug that has been in relax since
2006.
........
r23260 | bugman | 2014-05-20 16:19:30 +0200 (Tue, 20 May 2014) | 6 lines
Converted the Mf.test_opendx_s2_te_rex system test into a GUI test.
This is to demonstrate bug #22035 (https://gna.org/bugs/?22035), the dx.map
user function being
broken in the GUI.
........
Modified:
branches/disp_speed/ (props changed)
branches/disp_speed/multi/uni_processor.py
branches/disp_speed/test_suite/gui_tests/model_free.py
branches/disp_speed/test_suite/system_tests/scripts/model_free/opendx_s2_te_rex.py
Propchange: branches/disp_speed/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Tue May 20 17:40:12 2014
@@ -1 +1 @@
-/trunk:1-23237
+/trunk:1-23260
Modified: branches/disp_speed/multi/uni_processor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/multi/uni_processor.py?rev=23261&r1=23260&r2=23261&view=diff
==============================================================================
--- branches/disp_speed/multi/uni_processor.py (original)
+++ branches/disp_speed/multi/uni_processor.py Tue May 20 17:40:12 2014
@@ -175,15 +175,18 @@
def run_queue(self):
- #FIXME: need a finally here to cleanup exceptions states for windows
etc
+ """Safely run each command in the queue, cleaning up after
failures."""
- last_command = len(self.command_queue)-1
- for i, command in enumerate(self.command_queue):
- completed = (i == last_command)
+ # Run each command in the queue.
+ try:
+ last_command = len(self.command_queue)-1
+ for i, command in enumerate(self.command_queue):
+ completed = (i == last_command)
- command.run(self, completed)
+ command.run(self, completed)
- #self.run_command_queue()
- #TODO: add cheques for empty queues and maps if now warn
- del self.command_queue[:]
- self.memo_map.clear()
+ # Clear the queue, even if a failure occurs.
+ finally:
+ #TODO: add cheques for empty queues and maps if now warn
+ del self.command_queue[:]
+ self.memo_map.clear()
Modified: branches/disp_speed/test_suite/gui_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/test_suite/gui_tests/model_free.py?rev=23261&r1=23260&r2=23261&view=diff
==============================================================================
--- branches/disp_speed/test_suite/gui_tests/model_free.py (original)
+++ branches/disp_speed/test_suite/gui_tests/model_free.py Tue May 20
17:40:12 2014
@@ -518,6 +518,16 @@
self.assertAlmostEqual(interatom.r, 1.02 * 1e-10)
+ def test_opendx_s2_te_rex(self):
+ """Mapping the {S2, te, Rex} chi2 space through the OpenDX user
function dx.map().
+
+ This is to catch U{bug #22035<https://gna.org/bugs/?22035>}, the
dx.map user function being broken in the GUI.
+ """
+
+ # Execute the script.
+ self.script_exec(status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opendx_s2_te_rex.py')
+
+
class Fake_right_click:
"""Simulate a grid_cell_right_click event ."""
Modified:
branches/disp_speed/test_suite/system_tests/scripts/model_free/opendx_s2_te_rex.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/test_suite/system_tests/scripts/model_free/opendx_s2_te_rex.py?rev=23261&r1=23260&r2=23261&view=diff
==============================================================================
---
branches/disp_speed/test_suite/system_tests/scripts/model_free/opendx_s2_te_rex.py
(original)
+++
branches/disp_speed/test_suite/system_tests/scripts/model_free/opendx_s2_te_rex.py
Tue May 20 17:40:12 2014
@@ -12,34 +12,34 @@
path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'S2_0.970_te_2048_Rex_0.149'
# Set up the 15N spins.
-sequence.read(file='noe.500.out', dir=path, res_num_col=1, res_name_col=2)
-spin.name('N')
-spin.element('N')
-spin.isotope('15N', spin_id='@N')
+self._execute_uf(uf_name='sequence.read', file='noe.500.out', dir=path,
res_num_col=1, res_name_col=2)
+self._execute_uf(uf_name='spin.name', name='N')
+self._execute_uf(uf_name='spin.element', element='N')
+self._execute_uf(uf_name='spin.isotope', isotope='15N', spin_id='@N')
# Read the relaxation data.
-relax_data.read(ri_id='R1_600', ri_type='R1', frq=600.0*1e6,
file='r1.600.out', dir=path, res_num_col=1, res_name_col=2, data_col=3,
error_col=4)
-relax_data.read(ri_id='R2_600', ri_type='R2', frq=600.0*1e6,
file='r2.600.out', dir=path, res_num_col=1, res_name_col=2, data_col=3,
error_col=4)
-relax_data.read(ri_id='NOE_600', ri_type='NOE', frq=600.0*1e6,
file='noe.600.out', dir=path, res_num_col=1, res_name_col=2, data_col=3,
error_col=4)
-relax_data.read(ri_id='R1_500', ri_type='R1', frq=500.0*1e6,
file='r1.500.out', dir=path, res_num_col=1, res_name_col=2, data_col=3,
error_col=4)
-relax_data.read(ri_id='R2_500', ri_type='R2', frq=500.0*1e6,
file='r2.500.out', dir=path, res_num_col=1, res_name_col=2, data_col=3,
error_col=4)
-relax_data.read(ri_id='NOE_500', ri_type='NOE', frq=500.0*1e6,
file='noe.500.out', dir=path, res_num_col=1, res_name_col=2, data_col=3,
error_col=4)
+self._execute_uf(uf_name='relax_data.read', ri_id='R1_600', ri_type='R1',
frq=600.0*1e6, file='r1.600.out', dir=path, res_num_col=1, res_name_col=2,
data_col=3, error_col=4)
+self._execute_uf(uf_name='relax_data.read', ri_id='R2_600', ri_type='R2',
frq=600.0*1e6, file='r2.600.out', dir=path, res_num_col=1, res_name_col=2,
data_col=3, error_col=4)
+self._execute_uf(uf_name='relax_data.read', ri_id='NOE_600', ri_type='NOE',
frq=600.0*1e6, file='noe.600.out', dir=path, res_num_col=1, res_name_col=2,
data_col=3, error_col=4)
+self._execute_uf(uf_name='relax_data.read', ri_id='R1_500', ri_type='R1',
frq=500.0*1e6, file='r1.500.out', dir=path, res_num_col=1, res_name_col=2,
data_col=3, error_col=4)
+self._execute_uf(uf_name='relax_data.read', ri_id='R2_500', ri_type='R2',
frq=500.0*1e6, file='r2.500.out', dir=path, res_num_col=1, res_name_col=2,
data_col=3, error_col=4)
+self._execute_uf(uf_name='relax_data.read', ri_id='NOE_500', ri_type='NOE',
frq=500.0*1e6, file='noe.500.out', dir=path, res_num_col=1, res_name_col=2,
data_col=3, error_col=4)
# Initialise the diffusion tensor.
-diffusion_tensor.init(1e-8, fixed=True)
+self._execute_uf(uf_name='diffusion_tensor.init', params=1e-8, fixed=True)
# Create all attached protons.
-sequence.attach_protons()
+self._execute_uf(uf_name='sequence.attach_protons')
# Define the magnetic dipole-dipole relaxation interaction.
-interatom.define(spin_id1='@N', spin_id2='@H', direct_bond=True)
-interatom.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.02 * 1e-10)
+self._execute_uf(uf_name='interatom.define', spin_id1='@N', spin_id2='@H',
direct_bond=True)
+self._execute_uf(uf_name='interatom.set_dist', spin_id1='@N', spin_id2='@H',
ave_dist=1.02 * 1e-10)
# Define the CSA relaxation interaction.
-value.set(N15_CSA, 'csa')
+self._execute_uf(uf_name='value.set', val=N15_CSA, param='csa')
# Select the model.
-model_free.select_model(model='m4')
+self._execute_uf(uf_name='model_free.select_model', model='m4')
# Map the space.
-dx.map(params=['s2', 'te', 'rex'], spin_id=':2@N', inc=2, lower=[0.0, 0, 0],
upper=[1.0, 10000e-12, 3.0 / (2.0 * pi * 600000000.0)**2], point=[0.970,
2048.0e-12, 0.149 / (2.0 * pi * 600000000.0)**2], file_prefix='devnull',
point_file='devnull')
+self._execute_uf(uf_name='dx.map', params=['s2', 'te', 'rex'],
spin_id=':2@N', inc=2, lower=[0.0, 0, 0], upper=[1.0, 10000e-12, 3.0 / (2.0 *
pi * 600000000.0)**2], point=[0.970, 2048.0e-12, 0.149 / (2.0 * pi *
600000000.0)**2], file_prefix='devnull', point_file='devnull')
r23261 - in /branches/disp_speed: ./ multi/ test_suite/gui_tests/ test_suite/system_tests/scripts/model_free/