Author: semor
Date: Tue Dec 18 15:42:51 2007
New Revision: 4205
URL: http://svn.gna.org/viewcvs/relax?rev=4205&view=rev
Log:
Merging of the 'consistency-tests' branch in the main 1.2 line (take 2).
The commands used were:
svn merge -r3320:4200
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/consistency_tests_1.2/
svn resolved .
This is the second time the merge of the branch is done. The first attempt
was erroneous and caused
by a beginner mistake by Sebastien Morin pointed out in the post by Edward
d'Auvergne:
https://mail.gna.org/public/relax-devel/2007-12/msg00015.html (Message-id:
<7f080ed10712171508w44f86ee9s813793c246832aeb@xxxxxxxxxxxxxx>
The main 1.2 line now contains all the code for consistency testing.
Added:
1.2/maths_fns/consistency_tests.py
- copied unchanged from r4200,
branches/consistency_tests_1.2/maths_fns/consistency_tests.py
1.2/prompt/consistency_tests.py
- copied unchanged from r4200,
branches/consistency_tests_1.2/prompt/consistency_tests.py
1.2/sample_scripts/consistency_tests.py
- copied unchanged from r4200,
branches/consistency_tests_1.2/sample_scripts/consistency_tests.py
1.2/specific_fns/consistency_tests.py
- copied unchanged from r4200,
branches/consistency_tests_1.2/specific_fns/consistency_tests.py
1.2/test_suite/consistency_tests.py
- copied unchanged from r4200,
branches/consistency_tests_1.2/test_suite/consistency_tests.py
Modified:
1.2/generic_fns/runs.py
1.2/prompt/__init__.py
1.2/prompt/grace.py
1.2/prompt/interpreter.py
1.2/prompt/molmol.py
1.2/prompt/run.py
1.2/prompt/value.py
1.2/specific_fns/__init__.py
1.2/specific_fns/main.py
1.2/specific_fns/specific_setup.py
1.2/test_suite/__init__.py
1.2/test_suite/test_suite.py
Modified: 1.2/generic_fns/runs.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/generic_fns/runs.py?rev=4205&r1=4204&r2=4205&view=diff
==============================================================================
--- 1.2/generic_fns/runs.py (original)
+++ 1.2/generic_fns/runs.py Tue Dec 18 15:42:51 2007
@@ -38,7 +38,7 @@
raise RelaxRunError, run
# List of valid run types.
- valid = ['jw', 'mf', 'noe', 'relax_fit', 'srls']
+ valid = ['ct', 'jw', 'mf', 'noe', 'relax_fit', 'srls']
# Test if run_type is valid.
if not run_type in valid:
Modified: 1.2/prompt/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/prompt/__init__.py?rev=4205&r1=4204&r2=4205&view=diff
==============================================================================
--- 1.2/prompt/__init__.py (original)
+++ 1.2/prompt/__init__.py Tue Dec 18 15:42:51 2007
@@ -22,6 +22,7 @@
__all__ = ['angles',
+ 'consistency_tests',
'command',
'dasha',
'diffusion_tensor',
Modified: 1.2/prompt/grace.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/prompt/grace.py?rev=4205&r1=4204&r2=4205&view=diff
==============================================================================
--- 1.2/prompt/grace.py (original)
+++ 1.2/prompt/grace.py Tue Dec 18 15:42:51 2007
@@ -25,6 +25,7 @@
from doc_string import regexp_doc
import help
from generic_fns.minimise import Minimise
+from specific_fns.consistency_tests import Consistency_tests
from specific_fns.model_free import Model_free
from specific_fns.jw_mapping import Jw_mapping
from specific_fns.noe import Noe
@@ -258,6 +259,7 @@
# Write function.
write.__doc__ = write.__doc__ + "\n\n" + regexp_doc() + "\n"
+ write.__doc__ = write.__doc__ +
Consistency_tests.return_data_name.__doc__ + "\n\n"
write.__doc__ = write.__doc__ + Minimise.return_data_name.__doc__ +
"\n\n"
write.__doc__ = write.__doc__ + Noe.return_data_name.__doc__ + "\n"
write.__doc__ = write.__doc__ + Relax_fit.return_data_name.__doc__ + "\n"
Modified: 1.2/prompt/interpreter.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/prompt/interpreter.py?rev=4205&r1=4204&r2=4205&view=diff
==============================================================================
--- 1.2/prompt/interpreter.py (original)
+++ 1.2/prompt/interpreter.py Tue Dec 18 15:42:51 2007
@@ -50,6 +50,7 @@
from pdb import PDB
# User classes.
+from consistency_tests import Consistency_tests
from dasha import Dasha
from diffusion_tensor import Diffusion_tensor
from grace import Grace
@@ -106,6 +107,7 @@
self._system = system
# Place the user classes into the interpreter class namespace.
+ self._Consistency_tests = Consistency_tests(relax)
self._Dasha = Dasha(relax)
self._Diffusion_tensor = Diffusion_tensor(relax)
self._OpenDX = OpenDX(relax)
@@ -163,6 +165,7 @@
pdb = self._PDB.pdb
# Place the user classes in the local namespace.
+ consistency_tests = self._Consistency_tests
dasha = self._Dasha
diffusion_tensor = self._Diffusion_tensor
dx = self._OpenDX
Modified: 1.2/prompt/molmol.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/prompt/molmol.py?rev=4205&r1=4204&r2=4205&view=diff
==============================================================================
--- 1.2/prompt/molmol.py (original)
+++ 1.2/prompt/molmol.py Tue Dec 18 15:42:51 2007
@@ -26,6 +26,7 @@
from doc_string import regexp_doc
import help
from generic_fns.minimise import Minimise
+from specific_fns.consistency_tests import Consistency_tests
from specific_fns.model_free import Molmol
from specific_fns.jw_mapping import Jw_mapping
from specific_fns.noe import Noe
Modified: 1.2/prompt/run.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/prompt/run.py?rev=4205&r1=4204&r2=4205&view=diff
==============================================================================
--- 1.2/prompt/run.py (original)
+++ 1.2/prompt/run.py Tue Dec 18 15:42:51 2007
@@ -54,6 +54,7 @@
The run name can be any string however the run type can only be one
of the following
+ 'ct': Consistency tests.
'jw': Reduced spectral density mapping,
'mf': Model-free analysis,
'noe': Steady state NOE calculation,
Modified: 1.2/prompt/value.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/prompt/value.py?rev=4205&r1=4204&r2=4205&view=diff
==============================================================================
--- 1.2/prompt/value.py (original)
+++ 1.2/prompt/value.py Tue Dec 18 15:42:51 2007
@@ -25,6 +25,7 @@
from doc_string import regexp_doc
import help
from generic_fns.diffusion_tensor import Diffusion_tensor
+from specific_fns.consistency_tests import Consistency_tests
from specific_fns.model_free import Model_free
from specific_fns.jw_mapping import Jw_mapping
from specific_fns.relax_fit import Relax_fit
@@ -510,6 +511,8 @@
# Copy function.
copy.__doc__ = copy.__doc__ + "\n\n" + regexp_doc() + "\n"
+ copy.__doc__ = copy.__doc__ + Consistency_tests.set.__doc__ + "\n"
+ copy.__doc__ = copy.__doc__ + Consistency_tests.return_data_name.__doc__
+ "\n"
copy.__doc__ = copy.__doc__ + Model_free.set_doc.__doc__ + "\n\n"
copy.__doc__ = copy.__doc__ + Model_free.return_data_name.__doc__ + "\n"
copy.__doc__ = copy.__doc__ + Jw_mapping.set.__doc__ + "\n"
@@ -519,12 +522,15 @@
# Display function.
display.__doc__ = display.__doc__ + "\n\n" + regexp_doc() + "\n"
+ display.__doc__ = display.__doc__ +
Consistency_tests.return_data_name.__doc__ + "\n"
display.__doc__ = display.__doc__ + Model_free.return_data_name.__doc__
+ "\n\n"
display.__doc__ = display.__doc__ + Jw_mapping.return_data_name.__doc__
+ "\n"
display.__doc__ = display.__doc__ + Relax_fit.return_data_name.__doc__ +
"\n"
# Read function.
read.__doc__ = read.__doc__ + "\n\n" + regexp_doc() + "\n"
+ read.__doc__ = read.__doc__ + Consistency_tests.set.__doc__ + "\n"
+ read.__doc__ = read.__doc__ + Consistency_tests.return_data_name.__doc__
+ "\n"
read.__doc__ = read.__doc__ + Model_free.set_doc.__doc__ + "\n\n"
read.__doc__ = read.__doc__ + Model_free.return_data_name.__doc__ + "\n"
read.__doc__ = read.__doc__ + Jw_mapping.set.__doc__ + "\n"
@@ -534,6 +540,9 @@
# Set function.
set.__doc__ = set.__doc__ + "\n\n" + regexp_doc() + "\n"
+ set.__doc__ = set.__doc__ + Consistency_tests.set.__doc__ + "\n"
+ set.__doc__ = set.__doc__ + Consistency_tests.return_data_name.__doc__ +
"\n"
+ set.__doc__ = set.__doc__ + Consistency_tests.default_value.__doc__ +
"\n"
set.__doc__ = set.__doc__ + Model_free.set_doc.__doc__ + "\n"
set.__doc__ = set.__doc__ + Model_free.return_data_name.__doc__ + "\n"
set.__doc__ = set.__doc__ + Model_free.default_value.__doc__ + "\n\n"
@@ -549,6 +558,7 @@
# Write function.
write.__doc__ = write.__doc__ + "\n\n" + regexp_doc() + "\n"
+ write.__doc__ = write.__doc__ +
Consistency_tests.return_data_name.__doc__ + "\n\n"
write.__doc__ = write.__doc__ + Model_free.return_data_name.__doc__ +
"\n\n"
write.__doc__ = write.__doc__ + Jw_mapping.return_data_name.__doc__ +
"\n\n"
write.__doc__ = write.__doc__ + Noe.return_data_name.__doc__ + "\n"
Modified: 1.2/specific_fns/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/specific_fns/__init__.py?rev=4205&r1=4204&r2=4205&view=diff
==============================================================================
--- 1.2/specific_fns/__init__.py (original)
+++ 1.2/specific_fns/__init__.py Tue Dec 18 15:42:51 2007
@@ -21,7 +21,8 @@
###############################################################################
-__all__ = [ 'base_class',
+__all__ = [ 'consistency_tests',
+ 'base_class',
'hybrid',
'jw_mapping',
'main',
Modified: 1.2/specific_fns/main.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/specific_fns/main.py?rev=4205&r1=4204&r2=4205&view=diff
==============================================================================
--- 1.2/specific_fns/main.py (original)
+++ 1.2/specific_fns/main.py Tue Dec 18 15:42:51 2007
@@ -21,6 +21,7 @@
###############################################################################
+from consistency_tests import Consistency_tests
from hybrid import Hybrid
from jw_mapping import Jw_mapping
from model_free import Model_free
@@ -37,6 +38,7 @@
self.relax = relax
# Set up all the functions
+ self.consistency_tests = Consistency_tests(self.relax)
self.hybrid = Hybrid(self.relax)
self.jw_mapping = Jw_mapping(self.relax)
self.model_free = Model_free(self.relax)
Modified: 1.2/specific_fns/specific_setup.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/specific_fns/specific_setup.py?rev=4205&r1=4204&r2=4205&view=diff
==============================================================================
--- 1.2/specific_fns/specific_setup.py (original)
+++ 1.2/specific_fns/specific_setup.py Tue Dec 18 15:42:51 2007
@@ -37,6 +37,10 @@
# Initialise.
string = "this analysis"
+ # Consistency testing.
+ if function_type == 'ct':
+ string = "consistency testing"
+
# NOE calculation.
if function_type == 'noe':
string = "NOE calculations"
@@ -69,6 +73,10 @@
# Get the function.
try:
+ # Consistency testing.
+ if function_type == 'ct':
+ function = self.ct_funcs()
+
# NOE calculation.
if function_type == 'noe':
function = self.noe()
@@ -205,6 +213,86 @@
# Write results function (Columnar format).
if self.eqi == 'write_columnar_results':
return self.relax.specific.jw_mapping.write_columnar_results
+
+
+ def ct_funcs(self):
+ """Consistency testing functions."""
+
+ # Calculate function.
+ if self.eqi == 'calculate':
+ return self.relax.specific.consistency_tests.calculate
+
+ # Copy function.
+ if self.eqi == 'copy':
+ return self.relax.specific.consistency_tests.copy
+
+ # Create Monte Carlo data function (same as data returning function).
+ if self.eqi == 'create_mc_data':
+ return self.relax.specific.consistency_tests.return_data
+
+ # Number of instances.
+ if self.eqi == 'num_instances':
+ return self.relax.specific.consistency_tests.num_instances
+
+ # Overfit deselect.
+ if self.eqi == 'overfit_deselect':
+ return self.relax.specific.consistency_tests.overfit_deselect
+
+ # Pack Monte Carlo simulation data function.
+ if self.eqi == 'pack_sim_data':
+ return self.relax.specific.consistency_tests.sim_pack_data
+
+ # Data returning function.
+ if self.eqi == 'return_data':
+ return self.relax.specific.consistency_tests.return_data
+
+ # Data or parameter name returning function.
+ if self.eqi == 'return_data_name':
+ return self.relax.specific.consistency_tests.return_data_name
+
+ # Factor of conversion between different parameter units returning
function.
+ if self.eqi == 'return_conversion_factor':
+ return
self.relax.specific.consistency_tests.return_conversion_factor
+
+ # Data error returning function.
+ if self.eqi == 'return_error':
+ return self.relax.specific.consistency_tests.return_error
+
+ # Grace string returning function.
+ if self.eqi == 'return_grace_string':
+ return self.relax.specific.consistency_tests.return_grace_string
+
+ # Simulation parameter array returning function.
+ if self.eqi == 'return_sim_param':
+ return self.relax.specific.consistency_tests.sim_return_param
+
+ # Simulation parameter array returning function.
+ if self.eqi == 'return_selected_sim':
+ return self.relax.specific.consistency_tests.sim_return_selected
+
+ # String of the external parameter units returning function.
+ if self.eqi == 'return_units':
+ return self.relax.specific.consistency_tests.return_units
+
+ # Value and error returning function.
+ if self.eqi == 'return_value':
+ return self.relax.specific.consistency_tests.return_value
+
+ # Set function.
+ if self.eqi == 'set':
+ return self.relax.specific.consistency_tests.set
+
+ # Set error function.
+ if self.eqi == 'set_error':
+ return self.relax.specific.consistency_tests.set_error
+
+ # Set error function.
+ if self.eqi == 'set_selected_sim':
+ return self.relax.specific.consistency_tests.set_selected_sim
+
+ # Write results function (Columnar format).
+ if self.eqi == 'write_columnar_results':
+ return
self.relax.specific.consistency_tests.write_columnar_results
def mf_funcs(self):
Modified: 1.2/test_suite/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/test_suite/__init__.py?rev=4205&r1=4204&r2=4205&view=diff
==============================================================================
--- 1.2/test_suite/__init__.py (original)
+++ 1.2/test_suite/__init__.py Tue Dec 18 15:42:51 2007
@@ -22,6 +22,7 @@
__all__ = ['test_suite',
+ 'consistency_tests',
'diffusion_tensor',
'generic.py',
'jw_mapping',
Modified: 1.2/test_suite/test_suite.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/test_suite/test_suite.py?rev=4205&r1=4204&r2=4205&view=diff
==============================================================================
--- 1.2/test_suite/test_suite.py (original)
+++ 1.2/test_suite/test_suite.py Tue Dec 18 15:42:51 2007
@@ -27,6 +27,7 @@
# Import the tests.
from angles import Angles
+from consistency_tests import Consistent
from diffusion_tensor import Diffusion_tensor
from generic import Generic
from jw_mapping import Jw
@@ -192,6 +193,23 @@
self.exec_tests(self.jw_test_array)
+ # Consistency tests tests.
+ ##########################
+
+ # Heading
+ self.heading("The consistency tests tests")
+
+ # Initialise the array containing each test element.
+ self.consistent_test_array = []
+
+ # User function value.set() test.
+ self.consistent_test_array.append(Consistent(self.relax, 'set'))
+ self.consistent_test_array.append(Consistent(self.relax, 'calc'))
+
+ # Execute the tests.
+ self.exec_tests(self.consistent_test_array)
+
+
# Model selection tests.
########################
@@ -404,6 +422,21 @@
self.summary_line(test)
+ # Consistentcy tests test.
+ ##########################
+
+ # Heading.
+ sys.stdout.write("\nThe consistency tests tests:\n")
+
+ # Loop over the tests.
+ for test in self.consistent_test_array:
+ # Synopsis.
+ global_pass = global_pass and test.passed
+
+ # Print the summary line.
+ self.summary_line(test)
+
+
# Model selection tests.
########################
r4205 - in /1.2: generic_fns/ maths_fns/ prompt/ sample_scripts/ specific_fns/ test_suite/