Author: bugman Date: Mon Jan 10 18:30:58 2011 New Revision: 12192 URL: http://svn.gna.org/viewcvs/relax?rev=12192&view=rev Log: Merged revisions 12087-12090,12092-12155,12167-12168,12172-12179,12187 via svnmerge from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3 ........ r12087 | bugman | 2011-01-03 10:26:24 +0100 (Mon, 03 Jan 2011) | 3 lines Shifted the location of the truncated PSE-4 data for the relax 1.2 results reading system test. ........ r12088 | bugman | 2011-01-03 10:29:31 +0100 (Mon, 03 Jan 2011) | 5 lines Added a system test for reading the final results file from TEM-1. This file is severely truncated, and is just to trigger a bug. ........ r12089 | bugman | 2011-01-03 10:39:15 +0100 (Mon, 03 Jan 2011) | 7 lines Fix for bug #17417 (https://gna.org/bugs/?17417). The model_free _model_setup() method should handle no model-free model being set when reading relax 1.2 results files. The problem was a check for the local_tm parameter in the parameter array, as this was also set to None. ........ r12090 | bugman | 2011-01-03 11:10:21 +0100 (Mon, 03 Jan 2011) | 3 lines The Mf.test_read_results_1_2_tem1 system test is now checking all of the model-free data correctly. ........ r12092 | bugman | 2011-01-03 19:25:44 +0100 (Mon, 03 Jan 2011) | 3 lines Removed old commented out code. ........ r12093 | bugman | 2011-01-03 19:44:32 +0100 (Mon, 03 Jan 2011) | 3 lines Big clean up of cruft from the Test_finder.scan_paths() method. ........ r12094 | bugman | 2011-01-03 19:48:40 +0100 (Mon, 03 Jan 2011) | 3 lines Removed the PY_UNIT_TEST_PATTERN constant as it is in the Unit_test_runner.test_case_patterns list. ........ r12095 | bugman | 2011-01-03 20:18:18 +0100 (Mon, 03 Jan 2011) | 3 lines Big clean up of the load_test_case() unit test function. ........ r12096 | bugman | 2011-01-03 20:23:55 +0100 (Mon, 03 Jan 2011) | 5 lines Fix for load_test_case() for a bug introduced in r12095. The import errro test case was not handled correctly. ........ r12097 | bugman | 2011-01-03 20:25:32 +0100 (Mon, 03 Jan 2011) | 3 lines The "testing units..." text is only printed if verbosity is set. ........ r12098 | bugman | 2011-01-03 20:32:13 +0100 (Mon, 03 Jan 2011) | 3 lines Clean up of the unit test runner code for command line usage. ........ r12099 | bugman | 2011-01-03 20:34:42 +0100 (Mon, 03 Jan 2011) | 3 lines Deleted the ExtendedException class as it was doing nothing. ........ r12100 | bugman | 2011-01-03 21:01:25 +0100 (Mon, 03 Jan 2011) | 3 lines Big code clean up in the Unit_test_runner class. ........ r12101 | bugman | 2011-01-03 21:19:24 +0100 (Mon, 03 Jan 2011) | 7 lines Shifted the global relax debug flag from __main__.debug to the relax status singleton. This allows the flag to be defined even when imported from outside of relax. Also the pedantic flag is now being directly passed into the relax warning system and hence has been shifted out of __main__. ........ r12102 | bugman | 2011-01-03 21:22:05 +0100 (Mon, 03 Jan 2011) | 3 lines Removed the status singleton from the main relax class namespace. ........ r12103 | bugman | 2011-01-04 08:48:52 +0100 (Tue, 04 Jan 2011) | 3 lines Made the N_state_model.test_pcs_fit_zero_pos system test less stringent so it passes on 32-bit Linux. ........ r12104 | bugman | 2011-01-04 08:53:38 +0100 (Tue, 04 Jan 2011) | 5 lines Added another set of valid optimisation values to Mf.test_opt_constr_newton_gmw_mt_S2_0_970_te_2048_Rex_0_149. This is a second set different numbers for 32-bit Linux! The result is the same though. ........ r12105 | bugman | 2011-01-04 08:58:39 +0100 (Tue, 04 Jan 2011) | 5 lines Shifted the relax installation path variable from __main__ into the status singleton object. This allows relax modules to be imported outside of relax. ........ r12106 | bugman | 2011-01-04 09:15:20 +0100 (Tue, 04 Jan 2011) | 7 lines Changed how the status singleton object is setup - it does it itself! The status object now sets up itself so that a call to setup() is no longer necessary. setup() is now private, and relax just overrides the default variables to set the debugging flag or installation path. ........ r12107 | bugman | 2011-01-04 09:16:01 +0100 (Tue, 04 Jan 2011) | 3 lines Shifted the status object instantiation to the import level. ........ r12108 | bugman | 2011-01-04 09:31:02 +0100 (Tue, 04 Jan 2011) | 5 lines Shifted the status singleton instantiation to the import level in all modules. This should save execution time. ........ r12109 | bugman | 2011-01-04 09:36:28 +0100 (Tue, 04 Jan 2011) | 5 lines Shifted the status singleton instantiation to the import level in all modules. This should save execution time. The last commit omitted the main relax directories. ........ r12110 | bugman | 2011-01-04 09:44:05 +0100 (Tue, 04 Jan 2011) | 5 lines Updated 3 optimisation system tests to pass under 32-bit Linux. Why these optimisation stats are now slightly different must be due to software differences. ........ r12111 | bugman | 2011-01-04 10:27:27 +0100 (Tue, 04 Jan 2011) | 3 lines Updated the copyright statement. ........ r12112 | bugman | 2011-01-04 10:28:06 +0100 (Tue, 04 Jan 2011) | 3 lines Updated the introductory copyright notice. ........ r12113 | bugman | 2011-01-04 10:45:41 +0100 (Tue, 04 Jan 2011) | 7 lines The RelaxTestLoader has been added as a replacement for unittest.TestLoader. This empty class will in the end handle the skipping of tests when Python packages optional for relax are not installed. The unit_test_runner uses this class if it can import it, otherwise it falls back to unittest.TestLoader to allow for non-relax usage. ........ r12114 | bugman | 2011-01-04 11:00:32 +0100 (Tue, 04 Jan 2011) | 3 lines Fixed the import of the RelaxTestLoader. ........ r12115 | bugman | 2011-01-04 11:01:17 +0100 (Tue, 04 Jan 2011) | 5 lines Added a replacment loadTestsFromTestCase() method to RelaxTestLoader. This method will later be modified to skip certain tests. ........ r12116 | bugman | 2011-01-04 11:01:29 +0100 (Tue, 04 Jan 2011) | 3 lines Fix for the copyright notice. ........ r12117 | bugman | 2011-01-04 11:18:08 +0100 (Tue, 04 Jan 2011) | 3 lines Added an empty list to the relax status object to store info about skipped system and unit tests. ........ r12118 | bugman | 2011-01-04 11:21:07 +0100 (Tue, 04 Jan 2011) | 3 lines System and unit tests can be skipped is the skip flag is set inside the TestCase class. ........ r12119 | bugman | 2011-01-04 11:30:38 +0100 (Tue, 04 Jan 2011) | 5 lines The RelaxTestLoader now skips tests if the are in the status.skipped_test list. This is instead of the skip flag being set or not. ........ r12120 | bugman | 2011-01-04 11:33:58 +0100 (Tue, 04 Jan 2011) | 6 lines Added __init__() to Test_scientific to skip all tests of this class if the module is not installed. The method adds the tests to the status.skipped_tests list and executes the base class __init__() method. ........ r12121 | bugman | 2011-01-04 11:35:12 +0100 (Tue, 04 Jan 2011) | 3 lines Updated the copyright. ........ r12122 | bugman | 2011-01-04 11:36:54 +0100 (Tue, 04 Jan 2011) | 3 lines Docstring fix for the __init__() method. ........ r12123 | bugman | 2011-01-04 11:37:16 +0100 (Tue, 04 Jan 2011) | 3 lines Another docstring fix. ........ r12124 | bugman | 2011-01-04 11:40:14 +0100 (Tue, 04 Jan 2011) | 3 lines The Test_api_base tests requiring Scientific python are now skipped if not installed. ........ r12125 | bugman | 2011-01-04 11:44:15 +0100 (Tue, 04 Jan 2011) | 3 lines The test suite summary is printed out even if not all of the test suite is run. ........ r12126 | bugman | 2011-01-04 11:49:13 +0100 (Tue, 04 Jan 2011) | 3 lines Improvements to the formatting.summary_line() function, and the removal of the indentation. ........ r12127 | bugman | 2011-01-04 12:10:35 +0100 (Tue, 04 Jan 2011) | 3 lines Shortened the test suite formatting.summary_line() default length. ........ r12128 | bugman | 2011-01-04 12:13:16 +0100 (Tue, 04 Jan 2011) | 3 lines The relax test suite now prints out a table of skipped tests. ........ r12129 | bugman | 2011-01-04 12:31:09 +0100 (Tue, 04 Jan 2011) | 3 lines Renamed the relax test suite formatting.heading() function to title() and simplified it. ........ r12130 | bugman | 2011-01-04 12:32:35 +0100 (Tue, 04 Jan 2011) | 3 lines Added a relax test suite formatting.subtitle() function for printing out subtitles. ........ r12131 | bugman | 2011-01-04 12:34:21 +0100 (Tue, 04 Jan 2011) | 3 lines Modified the test suite printout to use the formatting subtitle() and title() functions. ........ r12132 | bugman | 2011-01-04 12:35:14 +0100 (Tue, 04 Jan 2011) | 3 lines Fix for the subtitle() function, the width was too small. ........ r12133 | bugman | 2011-01-04 12:37:44 +0100 (Tue, 04 Jan 2011) | 3 lines Removed the top spacing from the subtitle() function. ........ r12134 | bugman | 2011-01-04 12:40:54 +0100 (Tue, 04 Jan 2011) | 3 lines Alphabetical ordering of functions, and comment updates. ........ r12135 | bugman | 2011-01-04 12:41:34 +0100 (Tue, 04 Jan 2011) | 3 lines Only print out the part of the optional module table when those tests are run. ........ r12136 | bugman | 2011-01-04 12:42:27 +0100 (Tue, 04 Jan 2011) | 3 lines Changed the text of the missing module test suite table print out. ........ r12137 | bugman | 2011-01-04 14:04:32 +0100 (Tue, 04 Jan 2011) | 3 lines The structure system tests involving scientific python are now skipped if the module is not installed. ........ r12138 | bugman | 2011-01-04 14:07:46 +0100 (Tue, 04 Jan 2011) | 3 lines The test suite summary is not longer printed for each category when all tests are run. ........ r12139 | bugman | 2011-01-04 14:19:29 +0100 (Tue, 04 Jan 2011) | 3 lines The unit vector system tests using scientific python are now being skipped if the module is not installed. ........ r12140 | bugman | 2011-01-04 14:21:12 +0100 (Tue, 04 Jan 2011) | 3 lines Missing import. ........ r12141 | bugman | 2011-01-04 14:22:27 +0100 (Tue, 04 Jan 2011) | 3 lines Fix for the system test Unit_vectors.__init__() method - the wrong base class __init__() was being called. ........ r12142 | bugman | 2011-01-04 14:24:43 +0100 (Tue, 04 Jan 2011) | 3 lines The system tests now use the RelaxTestLoader to allow tests to be skipped. ........ r12143 | bugman | 2011-01-04 14:29:41 +0100 (Tue, 04 Jan 2011) | 3 lines Removed a newline in the skipped test table. ........ r12144 | bugman | 2011-01-04 14:33:08 +0100 (Tue, 04 Jan 2011) | 3 lines Added scipy to the relax dependency checking module. ........ r12145 | bugman | 2011-01-04 14:35:29 +0100 (Tue, 04 Jan 2011) | 3 lines relax will now run without the scipy module installed, however the frame order analysis is not usable. ........ r12146 | bugman | 2011-01-04 14:43:57 +0100 (Tue, 04 Jan 2011) | 3 lines The data pipe generic code now uses dep_check to see if the relaxation curve fitting is available. ........ r12147 | bugman | 2011-01-04 14:45:49 +0100 (Tue, 04 Jan 2011) | 3 lines The frame order analysis is disabled if scipy is not installed. ........ r12148 | bugman | 2011-01-04 14:49:06 +0100 (Tue, 04 Jan 2011) | 3 lines The frame order system tests are being skipped if scipy is not installed. ........ r12149 | bugman | 2011-01-04 14:49:57 +0100 (Tue, 04 Jan 2011) | 3 lines Fix for the Frame_order.__init__() system test method - the wrong base class was being called. ........ r12150 | bugman | 2011-01-04 14:57:54 +0100 (Tue, 04 Jan 2011) | 3 lines Updated the copyright. ........ r12151 | bugman | 2011-01-04 14:58:19 +0100 (Tue, 04 Jan 2011) | 3 lines The frame order unit tests are now skipped if scipy is not installed. ........ r12152 | bugman | 2011-01-04 15:04:12 +0100 (Tue, 04 Jan 2011) | 3 lines Missing import. ........ r12153 | bugman | 2011-01-04 15:07:32 +0100 (Tue, 04 Jan 2011) | 3 lines The alignment tensor system test now uses the N-state model rather than frame order so it is always tested. ........ r12154 | bugman | 2011-01-04 16:01:15 +0100 (Tue, 04 Jan 2011) | 3 lines Updated the test suite table print outs to say both packages and modules. ........ r12155 | bugman | 2011-01-04 16:06:42 +0100 (Tue, 04 Jan 2011) | 5 lines The data pipe system test is avoiding the frame order data pipe. This allows the test to pass without scipy installed. ........ r12167 | bugman | 2011-01-05 10:41:39 +0100 (Wed, 05 Jan 2011) | 3 lines Renamed the full_analysis.py sample script to dauvergne_protocol.py to make it more obvious what it is. ........ r12168 | bugman | 2011-01-05 10:43:04 +0100 (Wed, 05 Jan 2011) | 3 lines Added the file sample_scripts/full_analysis.py with a single line pointing to dauvergne_protocol.py. ........ r12172 | bugman | 2011-01-10 12:16:09 +0100 (Mon, 10 Jan 2011) | 9 lines Added a new system test for the prolate diffusion tensor, this time checking the diffusion type. A spherical tensor is sent in, triggering the bug found by Vitaly Vostri <vvostri att gmail dott com> (Message-id: <AANLkTinRO3ZCNwL6GeqWdx0uBvv=PQ=zw6vpdQQeruBW@xxxxxxxxxxxxxx> https://mail.gna.org/public/relax-users/2010-12/msg00014.html). The problem is that the prolate tensor is changed to an oblate one!?! ........ r12173 | bugman | 2011-01-10 13:44:58 +0100 (Mon, 10 Jan 2011) | 3 lines The type of spheroid is now being checked in all of the oblate and prolate system tests. ........ r12174 | bugman | 2011-01-10 14:45:04 +0100 (Mon, 10 Jan 2011) | 12 lines The diffusion tensor spheroid_type variable is now only updated if it is never explicitly set. This is to fix the diffusion tensor setting bug found by Vitaly Vostri <vvostri att gmail dott com> (Message-id: <AANLkTinRO3ZCNwL6GeqWdx0uBvv=PQ=zw6vpdQQeruBW@xxxxxxxxxxxxxx> https://mail.gna.org/public/relax-users/2010-12/msg00014.html). The result of this bug is that initialising a prolate diffusion tensor with Da set to zero caused the spheroid_type to be automatically set to 'oblate'. This bug was introduced at exactly r11678, and was part of changes for better BMRB support. This affects relax version 1.3.6 and the 1.3 repository line from r11678 to 12174. ........ r12175 | bugman | 2011-01-10 15:07:29 +0100 (Mon, 10 Jan 2011) | 7 lines Implemented a system test to catch a bug in the use of volumes for relaxation curve-fitting. This bug was identified by Maddy Strickland <M.Strickland att bristol dott ac dot uk> in the post Message-id: <55870.137.222.43.71.1294412799.squirrel@xxxxxxxxxxxxxxxxxx> https://mail.gna.org/public/relax-users/2011-01/msg00007.html. ........ r12176 | bugman | 2011-01-10 15:11:10 +0100 (Mon, 10 Jan 2011) | 7 lines The peak volume errors are now calculated for replicated spectra in the relaxation curve-fitting. This bug was identified by Maddy Strickland <M.Strickland att bristol dott ac dot uk> in the post Message-id: <55870.137.222.43.71.1294412799.squirrel@xxxxxxxxxxxxxxxxxx> https://mail.gna.org/public/relax-users/2011-01/msg00007.html. ........ r12177 | bugman | 2011-01-10 15:12:21 +0100 (Mon, 10 Jan 2011) | 3 lines Fix for the new test_curve_fitting_volume() system test - the intensity type is volume, not height! ........ r12178 | bugman | 2011-01-10 15:38:25 +0100 (Mon, 10 Jan 2011) | 3 lines Decreased the number of simulations to speed up this system test script by a ~ 1/4. ........ r12179 | bugman | 2011-01-10 15:40:34 +0100 (Mon, 10 Jan 2011) | 6 lines Added a check for the peak intensity errors. This is part of the bug fix for bug r17457 (https://gna.org/bugs/index.php?17457) reported by Maddy Strickland <M.Strickland att bristol dott ac dot uk>. ........ r12187 | bugman | 2011-01-10 18:14:50 +0100 (Mon, 10 Jan 2011) | 6 lines Merged the relax version 1.3.7 CHANGES file into the main line. The command used was: svn merge -r12180:12181 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/1.3.7 . ........ Added: branches/relax_disp/sample_scripts/dauvergne_protocol.py - copied unchanged from r12187, 1.3/sample_scripts/dauvergne_protocol.py branches/relax_disp/sample_scripts/full_analysis.py - copied unchanged from r12187, 1.3/sample_scripts/full_analysis.py branches/relax_disp/test_suite/relax_test_loader.py - copied unchanged from r12187, 1.3/test_suite/relax_test_loader.py branches/relax_disp/test_suite/shared_data/model_free/pse4_trunc.bz2 - copied unchanged from r12187, 1.3/test_suite/shared_data/model_free/pse4_trunc.bz2 branches/relax_disp/test_suite/shared_data/model_free/tem1_trunc.bz2 - copied unchanged from r12187, 1.3/test_suite/shared_data/model_free/tem1_trunc.bz2 Removed: branches/relax_disp/test_suite/shared_data/results_files/pse_trunc.bz2 Modified: branches/relax_disp/ (props changed) branches/relax_disp/auto_analyses/dauvergne_protocol.py branches/relax_disp/auto_analyses/noe.py branches/relax_disp/auto_analyses/relax_fit.py branches/relax_disp/auto_analyses/stereochem_analysis.py branches/relax_disp/data/diff_tensor.py branches/relax_disp/dep_check.py branches/relax_disp/docs/CHANGES branches/relax_disp/generic_fns/minimise.py branches/relax_disp/generic_fns/pipes.py branches/relax_disp/generic_fns/spectrum.py branches/relax_disp/info.py branches/relax_disp/maths_fns/frame_order_matrix_ops.py branches/relax_disp/prompt/interpreter.py branches/relax_disp/relax branches/relax_disp/relax_errors.py branches/relax_disp/relax_warnings.py branches/relax_disp/specific_fns/model_free/main.py branches/relax_disp/status.py branches/relax_disp/test_suite/formatting.py branches/relax_disp/test_suite/relax_test_runner.py branches/relax_disp/test_suite/shared_data/align_data/CaM/generate_data.py branches/relax_disp/test_suite/shared_data/align_data/CaM/pre_bleach.py branches/relax_disp/test_suite/shared_data/align_data/missing_data/generate_missing.py branches/relax_disp/test_suite/shared_data/align_data/population_model/generate.py branches/relax_disp/test_suite/shared_data/pcs_data/generate_model.py branches/relax_disp/test_suite/shared_data/saved_states/create_peak_heights_T2_ncyc1.py branches/relax_disp/test_suite/system_tests/__init__.py branches/relax_disp/test_suite/system_tests/align_tensor.py branches/relax_disp/test_suite/system_tests/angles.py branches/relax_disp/test_suite/system_tests/consistency_tests.py branches/relax_disp/test_suite/system_tests/dasha.py branches/relax_disp/test_suite/system_tests/diffusion_tensor.py branches/relax_disp/test_suite/system_tests/frame_order.py branches/relax_disp/test_suite/system_tests/generic.py branches/relax_disp/test_suite/system_tests/jw_mapping.py branches/relax_disp/test_suite/system_tests/load_spins.py branches/relax_disp/test_suite/system_tests/model_elimination.py branches/relax_disp/test_suite/system_tests/model_free.py branches/relax_disp/test_suite/system_tests/model_selection.py branches/relax_disp/test_suite/system_tests/n_state_model.py branches/relax_disp/test_suite/system_tests/noe.py branches/relax_disp/test_suite/system_tests/noe_restraints.py branches/relax_disp/test_suite/system_tests/palmer.py branches/relax_disp/test_suite/system_tests/peak_lists.py branches/relax_disp/test_suite/system_tests/relax_fit.py branches/relax_disp/test_suite/system_tests/results.py [... 416 lines stripped ...]