Author: bugman
Date: Mon Jan 10 18:25:09 2011
New Revision: 12188
URL: http://svn.gna.org/viewcvs/relax?rev=12188&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/bieri_gui/sample_scripts/dauvergne_protocol.py
- copied unchanged from r12187, 1.3/sample_scripts/dauvergne_protocol.py
branches/bieri_gui/sample_scripts/full_analysis.py
- copied unchanged from r12187, 1.3/sample_scripts/full_analysis.py
branches/bieri_gui/test_suite/relax_test_loader.py
- copied unchanged from r12187, 1.3/test_suite/relax_test_loader.py
branches/bieri_gui/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/bieri_gui/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/bieri_gui/test_suite/shared_data/results_files/pse_trunc.bz2
Modified:
branches/bieri_gui/ (props changed)
branches/bieri_gui/auto_analyses/dauvergne_protocol.py
branches/bieri_gui/auto_analyses/noe.py
branches/bieri_gui/auto_analyses/relax_fit.py
branches/bieri_gui/auto_analyses/stereochem_analysis.py
branches/bieri_gui/data/diff_tensor.py
branches/bieri_gui/dep_check.py
branches/bieri_gui/docs/CHANGES
branches/bieri_gui/generic_fns/minimise.py
branches/bieri_gui/generic_fns/pipes.py
branches/bieri_gui/generic_fns/spectrum.py
branches/bieri_gui/info.py
branches/bieri_gui/maths_fns/frame_order_matrix_ops.py
branches/bieri_gui/prompt/interpreter.py
branches/bieri_gui/relax
branches/bieri_gui/relax_errors.py
branches/bieri_gui/relax_warnings.py
branches/bieri_gui/specific_fns/model_free/main.py
branches/bieri_gui/status.py
branches/bieri_gui/test_suite/formatting.py
branches/bieri_gui/test_suite/relax_test_runner.py
branches/bieri_gui/test_suite/shared_data/align_data/CaM/generate_data.py
branches/bieri_gui/test_suite/shared_data/align_data/CaM/pre_bleach.py
branches/bieri_gui/test_suite/shared_data/align_data/missing_data/generate_missing.py
branches/bieri_gui/test_suite/shared_data/align_data/population_model/generate.py
branches/bieri_gui/test_suite/shared_data/pcs_data/generate_model.py
branches/bieri_gui/test_suite/shared_data/saved_states/create_peak_heights_T2_ncyc1.py
branches/bieri_gui/test_suite/system_tests/__init__.py
branches/bieri_gui/test_suite/system_tests/align_tensor.py
branches/bieri_gui/test_suite/system_tests/angles.py
branches/bieri_gui/test_suite/system_tests/consistency_tests.py
branches/bieri_gui/test_suite/system_tests/dasha.py
branches/bieri_gui/test_suite/system_tests/diffusion_tensor.py
branches/bieri_gui/test_suite/system_tests/frame_order.py
branches/bieri_gui/test_suite/system_tests/generic.py
branches/bieri_gui/test_suite/system_tests/jw_mapping.py
branches/bieri_gui/test_suite/system_tests/load_spins.py
branches/bieri_gui/test_suite/system_tests/model_elimination.py
branches/bieri_gui/test_suite/system_tests/model_free.py
branches/bieri_gui/test_suite/system_tests/model_selection.py
branches/bieri_gui/test_suite/system_tests/n_state_model.py
branches/bieri_gui/test_suite/system_tests/noe.py
branches/bieri_gui/test_suite/system_tests/noe_restraints.py
branches/bieri_gui/test_suite/system_tests/palmer.py
branches/bieri_gui/test_suite/system_tests/peak_lists.py
branches/bieri_gui/test_suite/system_tests/relax_fit.py
branches/bieri_gui/test_suite/system_tests/results.py
[... 416 lines stripped ...]
r12188 - in /branches/bieri_gui: ./ auto_analyses/ data/ docs/ generic_fns/ maths_fns/ prompt/ sample_scripts/ specific_fns/...