Author: bugman
Date: Tue Oct 16 11:15:45 2012
New Revision: 17846
URL: http://svn.gna.org/viewcvs/relax?rev=17846&view=rev
Log:
Merged revisions 17780-17806 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r17780 | bugman | 2012-10-09 10:26:13 +0200 (Tue, 09 Oct 2012) | 3 lines
Python 3 fix for the model-free BMRB export - many string module methods no
longer exist.
........
r17781 | bugman | 2012-10-09 10:29:53 +0200 (Tue, 09 Oct 2012) | 3 lines
More Python 3 fixes for the use of now non-existent string module functions.
........
r17782 | bugman | 2012-10-09 11:53:02 +0200 (Tue, 09 Oct 2012) | 6 lines
All system and GUI tests reliant on the relax-fit C modules are deactivated
if import fails.
This removes a pile of useless error messages from the test, and presents a
table of skipped tests
at the end.
........
r17783 | bugman | 2012-10-09 12:03:29 +0200 (Tue, 09 Oct 2012) | 6 lines
Python 2.5 and lower fix for the test_write_protein_sequence() unit test.
The byte array is wrapped in an eval() statement to allow Python 2.5 and
lower to parse the code
without failing, and the byte array comparison is now only used for Python
3+.
........
r17784 | bugman | 2012-10-09 12:09:45 +0200 (Tue, 09 Oct 2012) | 5 lines
The Results system tests are no longer dependent on the relaxation
curve-fitting C modules.
This allows these tests to run when the module cannot be imported.
........
r17785 | bugman | 2012-10-09 12:50:29 +0200 (Tue, 09 Oct 2012) | 6 lines
Created a special script for testing out relax with Python versions 1.0 all
the way to 3.3.
This builds the C modules for each Python version in ~/bin and then runs
the test suite, outputting
everything to log files.
........
r17786 | bugman | 2012-10-09 12:52:34 +0200 (Tue, 09 Oct 2012) | 6 lines
Python 2.4 fixes - the ctypes module does not exist in Python versions 2.4
and lower.
This is only used for some non-essential functionality on MS Windows, so
now it is deactivated if
not present.
........
r17787 | bugman | 2012-10-09 12:59:11 +0200 (Tue, 09 Oct 2012) | 6 lines
Python 2.4 and lower fix for the pipe_loop() generator method.
In these Python versions, a 'try' block with a 'finally' statement cannot
contain 'yield'
statements! This work around should be compatible with all Python versions.
........
r17788 | bugman | 2012-10-09 13:36:46 +0200 (Tue, 09 Oct 2012) | 3 lines
Fix for the test_write_protein_sequence() unit test for a recently
introduced bug.
........
r17789 | bugman | 2012-10-09 14:28:30 +0200 (Tue, 09 Oct 2012) | 6 lines
Reactivated support for Python 2.3.
This mainly skips the missing 'subprocess' module. This however decreases
relax's functionality a
little.
........
r17790 | bugman | 2012-10-09 14:35:38 +0200 (Tue, 09 Oct 2012) | 3 lines
Small improvements to the multiple python version test suite testing script.
........
r17791 | bugman | 2012-10-09 15:59:34 +0200 (Tue, 09 Oct 2012) | 6 lines
Fix for the Mf.test_write_results() system test for Python 3.1.
The XML version in Python 3.1 is the old style! Therefore the old results
file is being used to
check this Python 3.1 result.
........
r17792 | bugman | 2012-10-09 20:47:25 +0200 (Tue, 09 Oct 2012) | 7 lines
Better Python 2.3 support.
The compat module is now imported at the very start to allow the builtins
to be set before any other
imports. The sorted() builtin method is now mimicked and the os.devnull
string set for Python 2.3
and earlier.
........
r17793 | bugman | 2012-10-09 20:59:17 +0200 (Tue, 09 Oct 2012) | 3 lines
Python 2.4 fix - the unit test runner no longer uses the builtin set()
method.
........
r17794 | bugman | 2012-10-09 21:06:42 +0200 (Tue, 09 Oct 2012) | 5 lines
Python 2.4 and earlier fix for the GUI.
Try-except-finally statement blocks are not supported, so these have to
nested in two try statements.
........
r17795 | bugman | 2012-10-10 16:37:34 +0200 (Wed, 10 Oct 2012) | 6 lines
Fix for the Mf.test_write_results() system test for the Python 3 versions.
The logic for determining Python 3 versions was broken and the incorrect
files was used for Python
3.1.
........
r17796 | bugman | 2012-10-10 16:44:00 +0200 (Wed, 10 Oct 2012) | 6 lines
Fix for the Mf.test_read_results_1_3_v2_broken() system test for Python 3.2.
The object comparison method no longer converts dictionaries to strings for
the comparison, as the
string version is different in different Python versions.
........
r17797 | bugman | 2012-10-11 10:53:47 +0200 (Thu, 11 Oct 2012) | 5 lines
Disabled the initial relax intro print out from the GUI when running the
test suite.
This prevents the intro text from appearing in the first failed test.
........
r17798 | bugman | 2012-10-12 11:48:22 +0200 (Fri, 12 Oct 2012) | 10 lines
Redesigned the reset user function backend.
This now no only clears out the relax data store, but it also resets the
GUI if present. Some of
the reset code comes from the tearDown() method of the GUI tests. All
windows but the main GUI
window are closed and the relax controller gauges are set to zero and the
log window text cleared.
These changes should allow GUI tests after an error or failure to pass,
something which is currently
problematic.
........
r17799 | bugman | 2012-10-15 10:21:37 +0200 (Mon, 15 Oct 2012) | 6 lines
Python 3 fix for the ScientificPython PDB reader unit tests.
The order of the keys returned by a dictionary's keys() method changes
randomly in Python 3, so now
they are sorted prior to comparison.
........
r17800 | bugman | 2012-10-15 10:31:28 +0200 (Mon, 15 Oct 2012) | 3 lines
Python 2.3 fix - eliminated the superfluous operator.itemgetter() call in
the diffusion tensor code.
........
r17801 | bugman | 2012-10-15 10:39:20 +0200 (Mon, 15 Oct 2012) | 5 lines
Python 2.3 and earlier fix - the subprocess module is only imported when
present.
This is for the stereochem_analysis auto-analysis, but the import kills all
of the auto-analyses.
........
r17802 | bugman | 2012-10-15 10:42:56 +0200 (Mon, 15 Oct 2012) | 5 lines
Python 2.3 and earlier fix for the Test_relax_re.test_search() unit test.
The unittest assertTrue() and assertFalse() methods do not exist, so
assertEqual() is used instead.
........
r17803 | bugman | 2012-10-15 10:48:09 +0200 (Mon, 15 Oct 2012) | 3 lines
Python 2.3- fixes - the Modelfree4 and Dasha system tests are now skipped
if the subprocess module is missing.
........
r17804 | bugman | 2012-10-15 13:50:51 +0200 (Mon, 15 Oct 2012) | 7 lines
Test suite bug fix - the GUI tests now cleanly terminate the interpreter
thread.
This allows the test suite to terminate normally. With different Python
versions on different
operating systems, this could sometimes cause the test suite to freeze at
the end, the final
printout to be missing, or other strange behaviour.
........
r17805 | bugman | 2012-10-15 14:24:14 +0200 (Mon, 15 Oct 2012) | 3 lines
Removed an unused import of the Queue module from the multi-processor.
........
r17806 | bugman | 2012-10-15 14:25:51 +0200 (Mon, 15 Oct 2012) | 7 lines
Python 2.4 and earlier fixes for the Queuing module.
The TaskQueue class from http://code.activestate.com/recipes/475160/ which
was added to Python 2.5+
has been added to the compat module. This module is now used for all
imports of the Queue class for
all Python versions.
........
Added:
branches/frame_order_testing/devel_scripts/python_multiversion_test_suite.py
- copied unchanged from r17806,
trunk/devel_scripts/python_multiversion_test_suite.py
Modified:
branches/frame_order_testing/ (props changed)
branches/frame_order_testing/ansi.py
branches/frame_order_testing/auto_analyses/stereochem_analysis.py
branches/frame_order_testing/compat.py
branches/frame_order_testing/dep_check.py
branches/frame_order_testing/generic_fns/dasha.py
branches/frame_order_testing/generic_fns/diffusion_tensor.py
branches/frame_order_testing/generic_fns/molmol.py
branches/frame_order_testing/generic_fns/palmer.py
branches/frame_order_testing/generic_fns/pipes.py
branches/frame_order_testing/generic_fns/pymol_control.py
branches/frame_order_testing/generic_fns/relax_data.py
branches/frame_order_testing/generic_fns/reset.py
branches/frame_order_testing/gui/controller.py
branches/frame_order_testing/gui/interpreter.py
branches/frame_order_testing/gui/relax_gui.py
branches/frame_order_testing/info.py
branches/frame_order_testing/multi/multi_processor_base.py
branches/frame_order_testing/relax.py
branches/frame_order_testing/relax_io.py
branches/frame_order_testing/specific_fns/model_free/bmrb.py
branches/frame_order_testing/status.py
branches/frame_order_testing/test_suite/gui_tests/__init__.py
branches/frame_order_testing/test_suite/gui_tests/base_classes.py
branches/frame_order_testing/test_suite/gui_tests/rx.py
branches/frame_order_testing/test_suite/shared_data/results_files/empty.bz2
branches/frame_order_testing/test_suite/system_tests/dasha.py
branches/frame_order_testing/test_suite/system_tests/model_free.py
branches/frame_order_testing/test_suite/system_tests/palmer.py
branches/frame_order_testing/test_suite/system_tests/peak_lists.py
branches/frame_order_testing/test_suite/system_tests/relax_fit.py
branches/frame_order_testing/test_suite/system_tests/results.py
branches/frame_order_testing/test_suite/system_tests/state.py
branches/frame_order_testing/test_suite/unit_tests/_generic_fns/_structure/test_scientific.py
branches/frame_order_testing/test_suite/unit_tests/_generic_fns/test_relax_re.py
branches/frame_order_testing/test_suite/unit_tests/sequence_testing_base.py
branches/frame_order_testing/test_suite/unit_tests/unit_test_runner.py
branches/frame_order_testing/version.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/frame_order_testing/ansi.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/ansi.py?rev=17846&r1=17845&r2=17846&view=diff
Modified: branches/frame_order_testing/auto_analyses/stereochem_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/auto_analyses/stereochem_analysis.py?rev=17846&r1=17845&r2=17846&view=diff
Modified: branches/frame_order_testing/compat.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/compat.py?rev=17846&r1=17845&r2=17846&view=diff
Modified: branches/frame_order_testing/dep_check.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/dep_check.py?rev=17846&r1=17845&r2=17846&view=diff
Modified: branches/frame_order_testing/generic_fns/dasha.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/dasha.py?rev=17846&r1=17845&r2=17846&view=diff
Modified: branches/frame_order_testing/generic_fns/diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/diffusion_tensor.py?rev=17846&r1=17845&r2=17846&view=diff
Modified: branches/frame_order_testing/generic_fns/molmol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/molmol.py?rev=17846&r1=17845&r2=17846&view=diff
Modified: branches/frame_order_testing/generic_fns/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/palmer.py?rev=17846&r1=17845&r2=17846&view=diff
Modified: branches/frame_order_testing/generic_fns/pipes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/pipes.py?rev=17846&r1=17845&r2=17846&view=diff
Modified: branches/frame_order_testing/generic_fns/pymol_control.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/pymol_control.py?rev=17846&r1=17845&r2=17846&view=diff
Modified: branches/frame_order_testing/generic_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/relax_data.py?rev=17846&r1=17845&r2=17846&view=diff
Modified: branches/frame_order_testing/generic_fns/reset.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/reset.py?rev=17846&r1=17845&r2=17846&view=diff
Modified: branches/frame_order_testing/gui/controller.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/gui/controller.py?rev=17846&r1=17845&r2=17846&view=diff
Modified: branches/frame_order_testing/gui/interpreter.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/gui/interpreter.py?rev=17846&r1=17845&r2=17846&view=diff
Modified: branches/frame_order_testing/gui/relax_gui.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/gui/relax_gui.py?rev=17846&r1=17845&r2=17846&view=diff
Modified: branches/frame_order_testing/info.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/info.py?rev=17846&r1=17845&r2=17846&view=diff
Modified: branches/frame_order_testing/multi/multi_processor_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/multi/multi_processor_base.py?rev=17846&r1=17845&r2=17846&view=diff
Modified: branches/frame_order_testing/relax.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/relax.py?rev=17846&r1=17845&r2=17846&view=diff
Modified: branches/frame_order_testing/relax_io.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/relax_io.py?rev=17846&r1=17845&r2=17846&view=diff
Modified: branches/frame_order_testing/specific_fns/model_free/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/specific_fns/model_free/bmrb.py?rev=17846&r1=17845&r2=17846&view=diff
Modified: branches/frame_order_testing/status.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/status.py?rev=17846&r1=17845&r2=17846&view=diff
Modified: branches/frame_order_testing/test_suite/gui_tests/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/gui_tests/__init__.py?rev=17846&r1=17845&r2=17846&view=diff
Modified: branches/frame_order_testing/test_suite/gui_tests/base_classes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/gui_tests/base_classes.py?rev=17846&r1=17845&r2=17846&view=diff
Modified: branches/frame_order_testing/test_suite/gui_tests/rx.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/gui_tests/rx.py?rev=17846&r1=17845&r2=17846&view=diff
Modified:
branches/frame_order_testing/test_suite/shared_data/results_files/empty.bz2
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/shared_data/results_files/empty.bz2?rev=17846&r1=17845&r2=17846&view=diff
Modified: branches/frame_order_testing/test_suite/system_tests/dasha.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/dasha.py?rev=17846&r1=17845&r2=17846&view=diff
Modified: branches/frame_order_testing/test_suite/system_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/model_free.py?rev=17846&r1=17845&r2=17846&view=diff
Modified: branches/frame_order_testing/test_suite/system_tests/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/palmer.py?rev=17846&r1=17845&r2=17846&view=diff
Modified: branches/frame_order_testing/test_suite/system_tests/peak_lists.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/peak_lists.py?rev=17846&r1=17845&r2=17846&view=diff
Modified: branches/frame_order_testing/test_suite/system_tests/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/relax_fit.py?rev=17846&r1=17845&r2=17846&view=diff
Modified: branches/frame_order_testing/test_suite/system_tests/results.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/results.py?rev=17846&r1=17845&r2=17846&view=diff
Modified: branches/frame_order_testing/test_suite/system_tests/state.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/state.py?rev=17846&r1=17845&r2=17846&view=diff
Modified:
branches/frame_order_testing/test_suite/unit_tests/_generic_fns/_structure/test_scientific.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/unit_tests/_generic_fns/_structure/test_scientific.py?rev=17846&r1=17845&r2=17846&view=diff
Modified:
branches/frame_order_testing/test_suite/unit_tests/_generic_fns/test_relax_re.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/unit_tests/_generic_fns/test_relax_re.py?rev=17846&r1=17845&r2=17846&view=diff
Modified:
branches/frame_order_testing/test_suite/unit_tests/sequence_testing_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/unit_tests/sequence_testing_base.py?rev=17846&r1=17845&r2=17846&view=diff
Modified:
branches/frame_order_testing/test_suite/unit_tests/unit_test_runner.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/unit_tests/unit_test_runner.py?rev=17846&r1=17845&r2=17846&view=diff
Modified: branches/frame_order_testing/version.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/version.py?rev=17846&r1=17845&r2=17846&view=diff
r17846 - in /branches/frame_order_testing: ./ auto_analyses/ devel_scripts/ generic_fns/ gui/ multi/ specific_fns/model_free...