Re: r6993 - in /1.3/test_suite/system_tests: __init__.py palmer.py scripts/palmer.py -- July 29, 2008

Hi,

There could still be a better way of doing this, although I'm not sure
how it could be implemented.  The problem is that all may seem fine to
the user (or to me) but due to the improper set up of the modelfree4
program, the test passes but is silent.  Maybe a way that this could
be done to properly inform the person running the test-suite would be
to add another category of test (on top of the system/functional test
framework and the unit test framework) which would check for both for
python dependencies and for the presence (and maybe proper execution)
of external programs.  I'll have to think about this one for a while.

Regards,

Edward


On Tue, Jul 29, 2008 at 3:00 PM, Sébastien Morin
<sebastien.morin.1@xxxxxxxxx> wrote:

Hi Ed,

I agree with what you propose here. It is important that installation of
ModelFree4 stays a possibility, not an obligation, while, for those with
an installed program, the tools in relax should be tested to see if they
work.

I think your approach in r7017
(http://svn.gna.org/viewcvs/relax?rev=7017&view=rev) is really perfect
for this purpose and has the advantage of leaving complete flexibility
for the user.

Regards,


Séb




Edward d'Auvergne wrote:

Hi,

This is a difficult question.  At the moment, I think the simplest
solution would be to use the relax_io.test_binary() function to see if
these binaries are located in the system path and are executable and
if not skip the test (essentially just return without executing the
main part of the test, hence the test counts as a pass).  I'll add
this to your new Modelfree4 system test to see if it works.  Ideally
though, the system tests should report that this test could not be run
as the binary could not be found, but still the system tests should
pass.  Otherwise the failing system test will make users think that
they need to install Modelfree4, which is not possible on all
platforms.

Additionally in this test, a temporary directory should be given to
Modelfree4 to dump it's output into.  This directory would then be
destroyed by the tearDown() method, no matter what happens in the
test.

Regards,

Edward


On Mon, Jul 28, 2008 at 10:06 PM, Sébastien Morin
<sebastien.morin.1@xxxxxxxxx> wrote:

Hi Ed (and others)

I don't know what you think about this... as some people might not have
ModelFree4 installed and could not be interested in the features related
to it... On the other hand, we most have system tests for interaction
with ModelFree4 stuff...

The same applies for Dasha...

What do you think ?

Regards,


Séb



sebastien.morin.1@xxxxxxxxx wrote:

Author: semor
Date: Mon Jul 28 21:36:19 2008
New Revision: 6993

URL: http://svn.gna.org/viewcvs/relax?rev=6993&view=rev
Log:
Started to add system tests for model-free analysis using Modelfree4.


Added:
    1.3/test_suite/system_tests/palmer.py
    1.3/test_suite/system_tests/scripts/palmer.py
Modified:
    1.3/test_suite/system_tests/__init__.py

Modified: 1.3/test_suite/system_tests/__init__.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/__init__.py?rev=6993&r1=6992&r2=6993&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/__init__.py (original)
+++ 1.3/test_suite/system_tests/__init__.py Mon Jul 28 21:36:19 2008
@@ -41,6 +41,7 @@
 from model_selection import Modsel
 from n_state_model import N_state_model
 from nmrview import NMRView
+from palmer import Palmer
 from pipe_create import Pipe_create
 from relax_fit import Relax_fit
 from results import Results
@@ -57,6 +58,7 @@
            'model_selection',
            'n_state_model',
            'nmrview',
+           'palmer',
            'pipe_create',
            'relax_fit',
            'results',
@@ -89,6 +91,7 @@
         
suite_array.append(TestLoader().loadTestsFromTestCase(Load_spins))
         suite_array.append(TestLoader().loadTestsFromTestCase(Mf))
         suite_array.append(TestLoader().loadTestsFromTestCase(Modsel))
+        suite_array.append(TestLoader().loadTestsFromTestCase(Palmer))
         
suite_array.append(TestLoader().loadTestsFromTestCase(Relax_fit))
         suite_array.append(TestLoader().loadTestsFromTestCase(Results))
         suite_array.append(TestLoader().loadTestsFromTestCase(Sequence))

Added: 1.3/test_suite/system_tests/palmer.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/palmer.py?rev=6993&view=auto
==============================================================================
--- 1.3/test_suite/system_tests/palmer.py (added)
+++ 1.3/test_suite/system_tests/palmer.py Mon Jul 28 21:36:19 2008
@@ -1,0 +1,39 @@
+###############################################################################
+#                                                                       
      #
+# Copyright (C) 2008 Sebastien Morin                                    
      #
+#                                                                       
      #
+# This file is part of the program relax.                               
      #
+#                                                                       
      #
+# relax is free software; you can redistribute it and/or modify         
      #
+# it under the terms of the GNU General Public License as published by  
      #
+# the Free Software Foundation; either version 2 of the License, or     
      #
+# (at your option) any later version.                                   
      #
+#                                                                       
      #
+# relax is distributed in the hope that it will be useful,              
      #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of        
      #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         
      #
+# GNU General Public License for more details.                          
      #
+#                                                                       
      #
+# You should have received a copy of the GNU General Public License     
      #
+# along with relax; if not, write to the Free Software                  
      #
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  
USA   #
+#                                                                       
      #
+###############################################################################
+
+# Python module imports.
+import sys
+from unittest import TestCase
+
+
+class Palmer(TestCase):
+    """Class for testing various aspects specific to model-free 
analysis using the program
+    'Modelfree4'.
+    """
+
+    def test_palmer_stage_1(self):
+        """Test a complete model-free analysis using the program 
'Modelfree4'."""
+
+        # Execute the script.
+        self.relax.interpreter.run(script_file=sys.path[-1] + 
'/test_suite/system_tests/scripts/palmer.py')
+
+

Added: 1.3/test_suite/system_tests/scripts/palmer.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/palmer.py?rev=6993&view=auto
==============================================================================
--- 1.3/test_suite/system_tests/scripts/palmer.py (added)
+++ 1.3/test_suite/system_tests/scripts/palmer.py Mon Jul 28 21:36:19 
2008
@@ -1,0 +1,136 @@
+# Script for model-free analysis using the program 'Modelfree4'.
+
+# Python module imports.
+import sys
+
+# The RelaxError system.
+from relax_errors import RelaxError
+
+# Set the stage of analysis.
+#
+# The three stages in this script are:
+#   Stage 1:  Initial model-free minimisation.
+#   Stage 2:  Model-free model selection.
+#   Stage 3:  Final optimisation of diffusion tensor parameters 
together with model-free parameters.
+
+
+# Functions.
+
+def exec_stage_1(runs):
+    """Stage 1 function.
+
+    Initial model-free minimisation.
+    """
+
+    # Loop over the runs.
+    for name in runs:
+        # Create the run.
+        print "\n\n# " + name + " #"
+        pipe.create(name, 'mf')
+
+        # Load the sequence.
+        sequence.read(sys.path[-1] + 
'/test_suite/system_tests/data/jw_mapping/noe.dat')
+
+        # PDB.
+        #structure.read_pdb(name, 'Ap4Aase_new_3.pdb')
+
+        # Load the relaxation data.
+        relax_data.read('R1', '600', 600.0 * 1e6, sys.path[-1] + 
'/test_suite/system_tests/data/jw_mapping/R1.dat')
+        relax_data.read('R2', '600', 600.0 * 1e6, sys.path[-1] + 
'/test_suite/system_tests/data/jw_mapping/R2.dat')
+        relax_data.read('NOE', '600', 600.0 * 1e6, sys.path[-1] + 
'/test_suite/system_tests/data/jw_mapping/noe.dat')
+
+        # Setup other values.
+        diffusion_tensor.init(1e-8)
+        value.set(NUCLEI, 'heteronucleus')
+        value.set(1.02 * 1e-10, 'bond_length')
+        value.set(-172 * 1e-6, 'csa')
+
+        # Select the model-free model.
+        model_free.select_model(model=name)
+
+        # Create the Modelfree4 files.
+        palmer.create(force=True, sims=0)
+
+        # Run Modelfree4.
+        palmer.execute(force=True)
+
+    # Save the program state.
+    state.save('stage1.save', force=True)
+
+
+def exec_stage_2(runs):
+    """Stage 2 function.
+
+    Model-free model selection.
+    """
+
+    # Load the saved state from stage 1.
+    state.load('stage1.save')
+
+    # Print out.
+    print "\n\nLoading all the Modelfree 4 data."
+
+    # Extract the Modelfree4 data from the 'mfout' files.
+    for name in runs:
+        palmer.extract()
+
+    # Print out.
+    print "\n\nModel selection."
+
+    # Create the model selection run.
+    name = 'aic'
+    pipe.create(name, 'mf')
+
+    # Model selection.
+    model_selection(method='AIC', modsel_run=name)
+
+    # Write the results.
+    results.write(file='results', force=True)
+
+    # Save the program state.
+    state.save('stage2.save', force=True)
+
+
+def exec_stage_3():
+    """Stage 3 function.
+
+    Final optimisation of diffusion tensor parameters together with 
model-free parameters.
+    """
+
+    # Load the saved state from stage 2.
+    state.load('stage2.save')
+
+    # Set the run name.
+    name = 'aic'
+
+    # Let the diffusion tensor parameters be optimised.
+    fix(name, 'diff', 0)
+
+    # Create the Modelfree4 files (change sims as needed, see below).
+    palmer.create(dir='final', force=True, sims=0)
+
+    # Run Modelfree4.
+    palmer.execute(dir='final', force=True)
+
+    # Extract the Modelfree4 data from the 'mfout' file.
+    palmer.extract(dir='final')
+
+    # Save the program state.
+    state.save('stage3.save', force=True)
+
+
+# Main section of the script.
+#############################
+
+# Nuclei type.
+NUCLEI = '15N'
+
+# Set the run name (also the name of a preset model-free model).
+runs = ['m1', 'm2', 'm3']
+
+# Run the stages.
+exec_stage_1(runs)
+exec_stage_2(runs)
+exec_stage_3()
+
+# Either repeat all the above with the optimised diffusion tensor or 
run Monte Carlo simulations on the final results.


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Re: r6993 - in /1.3/test_suite/system_tests: init.py palmer.py scripts/palmer.py

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