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 > <[EMAIL PROTECTED]> 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 >> >> >> >> [EMAIL PROTECTED] 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. >>> >>> >>> _______________________________________________ >>> relax (http://nmr-relax.com) >>> >>> This is the relax-commits mailing list >>> [EMAIL PROTECTED] >>> >>> To unsubscribe from this list, get a password >>> reminder, or change your subscription options, >>> visit the list information page at >>> https://mail.gna.org/listinfo/relax-commits >>> >>> >>> >>> >> _______________________________________________ >> relax (http://nmr-relax.com) >> >> This is the relax-devel mailing list >> [email protected] >> >> To unsubscribe from this list, get a password >> reminder, or change your subscription options, >> visit the list information page at >> https://mail.gna.org/listinfo/relax-devel >> >> > > _______________________________________________ relax (http://nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
