Hi, I agree with you that optional programs may not cause failure, but I think they should be listed for users to know which one they actually have that are recognised for direct use with relax.
Regards, Séb Edward d'Auvergne wrote: > That is the idea, to have a print out very similar to yours. Though I > was thinking of the divisions being more like: > > Python modules ........................ [ OK ] > Optional modules ...................... [ Failed ] > Optional external programs ........ [ Failed ] > System/functional tests ............. [ OK ] > Unit tests ................................ [ OK ] > Synopsis ................................. [ OK ] > > I like the idea of listing all python modules and external programs > too. Note that in this mock-up, the synopsis is a pass even though > not all optional modules or external programs are installed. For > example many of the optional programs may not run on all operating > systems. So on Windows this would mean that passing the relax test > suite would not be possible. > > Regards, > > Edward > > > On Tue, Jul 29, 2008 at 3:43 PM, Sébastien Morin > <[EMAIL PROTECTED]> wrote: > >> Hi, >> >> This is a good idea. These tests could be separate from other ones and >> only informative for non essential dependencies such as ModelFree4. >> >> The output of the test-suite could be something like : >> >> >> >> ========== >> ################################### >> # Summary of the relax test suite # >> ################################### >> >> Required dependencies .............................. [ OK ] >> minfx .............................. ( ok ) >> python ............................. ( ok ) >> etc. >> Optional dependencies .............................. [ OK ] >> dasha .............................. ( ok ) >> modelfree4 ......................... ( ok ) >> etc. >> System/functional tests ............................ [ OK ] >> Unit tests ......................................... [ OK ] >> Synopsis ........................................... [ OK ] >> ========== >> >> >> >> instead of the actual : >> >> ========== >> ################################### >> # Summary of the relax test suite # >> ################################### >> >> System/functional tests ............................ [ OK ] >> Unit tests ......................................... [ OK ] >> Synopsis ........................................... [ OK ] >> ========== >> >> >> >> I think this would be really informative to the user which would see all >> required and optional programs at once. >> >> Regards, >> >> >> Séb >> >> >> >> >> Edward d'Auvergne wrote: >> >>> 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 >>> <[EMAIL PROTECTED]> 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 >>>>> <[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
