svn+ssh://bugman@.../svn/relax/trunk
........
r17693 | bugman | 2012-10-03 22:46:34 +0200 (Wed, 03 Oct 2012) | 6 lines
Fix to the DummyFileObject to allow Python 2.5 and lower to run relax.
The byte arrays are now placed in eval() statements to allow the 2.5 and lower interpreters to parse
the code.
........
r17697 | bugman | 2012-10-04 18:20:51 +0200 (Thu, 04 Oct 2012) | 7 lines
Added the Mf.test_bug_20213_asn_sidechain() system test to catch bug #20213.
The data and script comes from the files 'sh3-47.2.zip' and 'run.py' attached to the bug report
https://gna.org/bugs/?20213. The PDB now only contains Asp47, the optimisation parameters have been
made almost insignificant, and all models but 'tm0' have been removed from the analysis.
........
r17698 | bugman | 2012-10-04 18:23:16 +0200 (Thu, 04 Oct 2012) | 3 lines
The Mf.test_bug_20213_asn_sidechain() system test now uses a temporary directory for output.
........
r17699 | bugman | 2012-10-04 18:37:56 +0200 (Thu, 04 Oct 2012) | 5 lines
Created the simple Sequence.test_sequence_copy() system test to catch bug #20213.
https://gna.org/bugs/?20213.
........
r17700 | bugman | 2012-10-04 19:02:08 +0200 (Thu, 04 Oct 2012) | 8 lines
Fix for bug #20213 (https://gna.org/bugs/?20213).
The problem was that the generic_fns.sequence.generate() function was searching for a spin based on
its spin ID generated from the spin name and not spin number. Hence two spins with the same name
but different numbers were treated as the same spin, and only data from one was being generated via
the copy() function.
........
r17701 | bugman | 2012-10-05 18:42:15 +0200 (Fri, 05 Oct 2012) | 8 lines
Created the relax_io.readlines method for handling the bz2 and gzip module byte strings in Python 3.
The bz2.BZ2File and gzip.GzipFile classes now return lists of bytes strings from their readlines()
methods in Python 3. This causes failures all over relax. This behaviour is probably a bug in
these classes. The relax_io.readlines method is a workaround for this problem, to have a list of
standard strings returned.
........
r17702 | bugman | 2012-10-05 18:43:11 +0200 (Fri, 05 Oct 2012) | 3 lines
Python 3 bug fix for the internal PDB and XYZ 3D structure readers by using relax_io.readlines().
........
r17703 | bugman | 2012-10-05 19:39:17 +0200 (Fri, 05 Oct 2012) | 3 lines
First attempt at making the relaxation curve-fitting C module Python 3 compatible.
........
r17704 | bugman | 2012-10-05 19:45:46 +0200 (Fri, 05 Oct 2012) | 3 lines
The relaxation curve-fitting C module now supports compilation on both Python 2 and 3.
........
r17705 | bugman | 2012-10-05 19:48:03 +0200 (Fri, 05 Oct 2012) | 6 lines
The relax_fit specific analysis module now supports both Python 2 and 3.
The command used was:
2to3 -w specific_fns/relax_fit.py
........
r17706 | bugman | 2012-10-07 15:00:19 +0200 (Sun, 07 Oct 2012) | 3 lines
Added a script for testing out the C module compilation on multiple python targets.
........
r17707 | bugman | 2012-10-07 15:13:52 +0200 (Sun, 07 Oct 2012) | 3 lines
Finished off the C module compilation testing script.
........
r17708 | bugman | 2012-10-07 15:16:28 +0200 (Sun, 07 Oct 2012) | 3 lines
Renamed the 'scripts' directory to 'devel_scripts' so that users are less likely to ask about the scripts.
........
r17709 | bugman | 2012-10-07 15:26:15 +0200 (Sun, 07 Oct 2012) | 3 lines
The manual C module compilation script is now executable.
........
r17710 | bugman | 2012-10-07 15:37:52 +0200 (Sun, 07 Oct 2012) | 3 lines
Added the IO module to the relax information print out and dependency checks.
........
r17711 | bugman | 2012-10-07 15:40:50 +0200 (Sun, 07 Oct 2012) | 7 lines
The relax_io.open_read_file() now supports all Python versions over 2.4.
This required some really nasty hacks for Python 3.0, 3.1 and 3.2 with the Bzip2Fixed and GzipFixed
classes overriding the incomplete and buggy bz2.BZ2File and gzip.GzipFile modules, and being wrapped
around io.TextIOWrapper().
........
r17712 | bugman | 2012-10-07 15:50:10 +0200 (Sun, 07 Oct 2012) | 11 lines
Reverted revisions r17702, r17701, r17693, r17687, r17685, r17684, and r17669.
The command used were:
svn merge -r17702:17669 relax_io.py
svn merge -r17702:r17701 /data/relax/relax-trunk/generic_fns/structure/internal.py
The relax_io module should now handle all files as text, independent of compression. These reverted
revisions were attempts at fixing the buggy behaviour of Python 3.0, 3.1 and 3.2. But now the
io.TextIOWrapper() class is being used to eliminate the byte streams, which should be text streams.
........
r17713 | bugman | 2012-10-07 15:56:44 +0200 (Sun, 07 Oct 2012) | 3 lines
The C module compilation testing script now accepts the Python version as a first argument.
........
r17714 | bugman | 2012-10-07 16:15:02 +0200 (Sun, 07 Oct 2012) | 6 lines
Reverted r17681 as file objects in relax are now always treated as text, so byte streams are not needed.
The command used was:
svn merge -r17681:r17680 .
........
r17715 | bugman | 2012-10-07 16:29:56 +0200 (Sun, 07 Oct 2012) | 5 lines
Python 3 fix for the Pipes.test_pipe_bundle() system test.
The order of bundle names returned by generic_fns.pipes.bundle_names() is not guaranteed in Python 3.
........
r17716 | bugman | 2012-10-07 16:38:01 +0200 (Sun, 07 Oct 2012) | 5 lines
For consistency between Python 2 and 3, the grace.write user function outputs to 15 decimal places.
This increased precision will only be of use in the relax test suite.
........
r17717 | bugman | 2012-10-07 16:38:43 +0200 (Sun, 07 Oct 2012) | 3 lines
Python 3 fix for the Noe.test_noe_analysis() system test for the grace.write precision changes.
........
r17718 | bugman | 2012-10-07 18:12:33 +0200 (Sun, 07 Oct 2012) | 8 lines
Python 3 fix for the relax_io.open_write_file() function.
This now matches the behaviour of open_read_file() in that there are three different behaviours for
opening bz2 and gz files for writing to for the different Python versions (one for Python 2, one for
Python 3.0 to 3.2, and one for Python 3.3+). All byte streams have been eliminated as
open_write_file() is for creating text files.
........
r17719 | bugman | 2012-10-07 18:45:38 +0200 (Sun, 07 Oct 2012) | 3 lines
Fix for the Relax_fit.test_bug_12670_12679() system test for the changes to Grace files at r17716.
........
r17720 | bugman | 2012-10-07 18:53:30 +0200 (Sun, 07 Oct 2012) | 3 lines
Python 3 fix - removed the use of the string module from generic_fns.spectrum.
........
r17721 | bugman | 2012-10-07 18:59:12 +0200 (Sun, 07 Oct 2012) | 6 lines
Removed the ability to save and restore states using the pickle module.
A pickled state is of no use to relax anymore. It's removal is needed for Python 3 support. So now
everything defaults to the XML formatted output.
........
r17722 | bugman | 2012-10-07 18:59:43 +0200 (Sun, 07 Oct 2012) | 3 lines
Eliminated the State.test_state_pickle() system test as pickled states are no longer supported.
........
r17723 | bugman | 2012-10-07 19:12:26 +0200 (Sun, 07 Oct 2012) | 3 lines
Removed the pickle format information and arguments from the state user function definitions.
........
r17724 | bugman | 2012-10-07 19:21:06 +0200 (Sun, 07 Oct 2012) | 6 lines
Python 3 support for Modelfree4 and Dasha.
The subprocess.Popen class works with byte arrays rather than strings in Python 3+. The Python
objects are now interconverted when the Python 3 encode() and decode() methods are detected.
........
r17725 | bugman | 2012-10-07 19:22:04 +0200 (Sun, 07 Oct 2012) | 3 lines
Small comment edit.
........
r17726 | bugman | 2012-10-07 20:56:21 +0200 (Sun, 07 Oct 2012) | 6 lines
Python 3 fix for the Mf.test_latex_table system test.
The latex_mf_table.py model-free system test script docstring contains backslashes, so the raw
string format r"""Text""" is now used.
........
r17727 | bugman | 2012-10-07 20:59:22 +0200 (Sun, 07 Oct 2012) | 3 lines
The OMP model-free results file generation script now outputs for any relax version.
........
r17728 | bugman | 2012-10-07 21:54:24 +0200 (Sun, 07 Oct 2012) | 6 lines
Removed the Python 3 byte array hack which should have been removed earlier.
This code is from r17669 which should have been removed at r17712 but was accidentally left out.
Instead of reverting, the code has been deleted as r17669 contained another useful change.
........
r17729 | bugman | 2012-10-07 21:58:58 +0200 (Sun, 07 Oct 2012) | 5 lines
Added a Python 3 version of the truncated OMP model-free results file.
This was created with trunk which is during the 2.1 relax releases.
........
r17730 | bugman | 2012-10-07 22:06:49 +0200 (Sun, 07 Oct 2012) | 6 lines
The messsage about skipping the GUI tests due to wxPython being missing is now more specific.
This was being shown for all runs of the test suite when it only needs to appear if GUI tests have
been run.
........
r17731 | bugman | 2012-10-07 22:11:43 +0200 (Sun, 07 Oct 2012) | 6 lines
The relaxation curve-fitting system tests are now skipped if the module is missing or broken.
This improves the printouts from the test suite and shows a summary of skipped tests rather than a
pile of traceback messages and errors.
........
r17732 | bugman | 2012-10-08 00:11:32 +0200 (Mon, 08 Oct 2012) | 7 lines
Python 3 fix for the model-free results file reading tests.
The ordering of dictionaries is different in Python 3, so now these are properly converted from
strings to dictionaries before comparison. This was not happening because of the XML changes from
Python 2.7.3 onwards.
........
r17733 | bugman | 2012-10-08 00:34:46 +0200 (Mon, 08 Oct 2012) | 5 lines
Python 3 fix for the setting of diffusion and alignment tensor simulation values.
The previous code somehow worked in Python 2 but was not formally correct and broke in Python 3.
........
r17734 | bugman | 2012-10-08 00:41:24 +0200 (Mon, 08 Oct 2012) | 5 lines
The fix of r17733 actually broke Python 2.
The list.__setattr__() method is fundamentally different between Python 2 and 3!
........
r17735 | bugman | 2012-10-08 00:47:19 +0200 (Mon, 08 Oct 2012) | 3 lines
Removed some debugging printouts accidentally committed in r17734.
........
r17736 | bugman | 2012-10-08 00:48:50 +0200 (Mon, 08 Oct 2012) | 5 lines
Fix for the fix of r17734 which attempted to fix r17733.
The Python version is now being detected.
........
r17737 | bugman | 2012-10-08 11:04:32 +0200 (Mon, 08 Oct 2012) | 6 lines
Updated the relax version numbers and 'trunk' used relax user manual.
For example the information about checking out the main development line was still talking about 1.3
rather than the trunk.
........
