Author: bugman
Date: Fri Nov 21 09:49:29 2008
New Revision: 7997
URL: http://svn.gna.org/viewcvs/relax?rev=7997&view=rev
Log:
Merged revisions 7991-7992,7996 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r7991 | bugman | 2008-11-20 22:53:30 +0100 (Thu, 20 Nov 2008) | 5 lines
Added a catch for bug #12607 (https://gna.org/bugs/?12607) to the
bugs_12582_12591.py script.
This bug was reported by Chris Brosey (chris dot a dot brosey att
vanderbilt dot edu).
........
r7992 | bugman | 2008-11-20 23:23:56 +0100 (Thu, 20 Nov 2008) | 8 lines
Fix for bug #12607 (https://gna.org/bugs/?12607).
This bug was reported by Chris Brosey (chris dot a dot brosey att
vanderbilt dot edu).
The problem was that the fixed flag was being checked for all spins.
However deselected spins
should be ignored.
........
r7996 | bugman | 2008-11-21 09:45:57 +0100 (Fri, 21 Nov 2008) | 3 lines
Renamed the bugs_12582_12591.py system test script to include bug #12607.
........
Added:
branches/spectral_errors/test_suite/system_tests/scripts/bugs_12582_12591_12607.py
- copied unchanged from r7996,
1.3/test_suite/system_tests/scripts/bugs_12582_12591_12607.py
Removed:
branches/spectral_errors/test_suite/system_tests/scripts/bugs_12582_12591.py
Modified:
branches/spectral_errors/ (props changed)
branches/spectral_errors/specific_fns/model_free/main.py
branches/spectral_errors/test_suite/system_tests/model_free.py
Propchange: branches/spectral_errors/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Fri Nov 21 09:49:29 2008
@@ -1,1 +1,1 @@
-/1.3:1-7983
+/1.3:1-7996
Modified: branches/spectral_errors/specific_fns/model_free/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spectral_errors/specific_fns/model_free/main.py?rev=7997&r1=7996&r2=7997&view=diff
==============================================================================
--- branches/spectral_errors/specific_fns/model_free/main.py (original)
+++ branches/spectral_errors/specific_fns/model_free/main.py Fri Nov 21
09:49:29 2008
@@ -952,6 +952,10 @@
# Check if any model-free parameters are allowed to vary.
mf_all_fixed = True
for spin in spin_loop():
+ # Skip deselected spins.
+ if not spin.select:
+ continue
+
# Test the fixed flag.
if not hasattr(spin, 'fixed'):
mf_all_fixed = False
Modified: branches/spectral_errors/test_suite/system_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spectral_errors/test_suite/system_tests/model_free.py?rev=7997&r1=7996&r2=7997&view=diff
==============================================================================
--- branches/spectral_errors/test_suite/system_tests/model_free.py (original)
+++ branches/spectral_errors/test_suite/system_tests/model_free.py Fri Nov 21
09:49:29 2008
@@ -143,11 +143,17 @@
self.assertEqual(str(sub_obj1), str(sub_obj2))
- def test_bugs_12582_12591(self):
- """Test catching bugs #12582 and #12591 as submitted by Chris
Brosey."""
+ def test_bugs_12582_12591_12607(self):
+ """Test catching bugs #12582, #12591 and #12607 as submitted by
Chris Brosey."""
# Execute the script.
- self.relax.interpreter.run(script_file=sys.path[-1] +
'/test_suite/system_tests/scripts/bugs_12582_12591.py')
+ self.relax.interpreter.run(script_file=sys.path[-1] +
'/test_suite/system_tests/scripts/bugs_12582_12591_12607.py')
+
+ # Alias the current data pipe.
+ cdp = pipes.get_pipe()
+
+ # Test for bug #12607 (S2 changes because it is in the grid search
when it should not be).
+ self.assertNotEqual(cdp.mol[0].res[1].spin[0].s2, 1.0)
def test_create_m4(self):
Removed:
branches/spectral_errors/test_suite/system_tests/scripts/bugs_12582_12591.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spectral_errors/test_suite/system_tests/scripts/bugs_12582_12591.py?rev=7996&view=auto
==============================================================================
---
branches/spectral_errors/test_suite/system_tests/scripts/bugs_12582_12591.py
(original)
+++
branches/spectral_errors/test_suite/system_tests/scripts/bugs_12582_12591.py
(removed)
@@ -1,39 +1,0 @@
-"""This system test catches 2 bugs submitted by Chris Brosey.
-
-The bugs include:
- - Bug #12582 (https://gna.org/bugs/index.php?12582).
- - Bug #12591 (https://gna.org/bugs/index.php?12591).
-"""
-
-# Python module imports.
-import sys
-
-
-# Path of the files.
-path = sys.path[-1] +
'/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149'
-
-# Loop over the models.
-for name in ['tm0', 'tm1']:
- # Setup.
- pipe.create(pipe_name=name, pipe_type='mf')
- sequence.read(file='noe.500.out', dir=path, mol_name_col=None,
res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None,
sep=None)
- relax_data.read(ri_label='R1', frq_label='500', frq=500208000.0,
file='r1.500.out', dir=path, mol_name_col=None, res_num_col=0,
res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2,
error_col=3, sep=None)
- relax_data.read(ri_label='R2', frq_label='500', frq=500208000.0,
file='r2.500.out', dir=path, mol_name_col=None, res_num_col=0,
res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2,
error_col=3, sep=None)
- relax_data.read(ri_label='NOE', frq_label='500', frq=500208000.0,
file='noe.500.out', dir=path, mol_name_col=None, res_num_col=0,
res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2,
error_col=3, sep=None)
- value.set(val=1.0200000000000001e-10, param='bond_length', spin_id=None)
- value.set(val=-0.00017199999999999998, param='csa', spin_id=None)
- value.set(val='15N', param='heteronucleus', spin_id=None)
- value.set(val='1H', param='proton', spin_id=None)
- model_free.select_model(model=name, spin_id=None)
-
- # Optimisation.
- grid_search(lower=None, upper=None, inc=11, constraints=True,
verbosity=1)
- minimise('newton', func_tol=1e-25, max_iterations=10000000,
constraints=True, scaling=True, verbosity=1)
-
- # Results writing.
- results.write(file='devnull', force=True, compress_type=1)
-
-# Model selection.
-sequence.display()
-eliminate(function=None, args=None)
-model_selection(method='AIC', modsel_pipe='aic', pipes=['tm0', 'tm1'])
r7997 - in /branches/spectral_errors: ./ specific_fns/model_free/ test_suite/system_tests/ test_suite/system_tests/scripts/