relax SVN archive

Python 3 fixes for the newly included Geometry.Transformation ScientificPython module.

The command used was:
2to3 -w \
-f buffer \
-f idioms \
-f set_literal \
-f ws_comma \
-x except \
-x import \
-x imports \
-x long \
-x numliterals \
-x xrange \
/data/relax/relax-trunk/extern/scientific_python/Geometry/Transformation.py

Merged revisions 18343 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r18343 | bugman | 2013-02-01 12:37:16 +0100 (Fri, 01 Feb 2013) | 7 lines

Fix for bug #20469 (https://gna.org/bugs/?20469).

This is the Failure in reading X-ray PDB files using the ScientificPython parser. The
ScientificPython Geometry.Transformation module is now distributed with relax. Some linear algebra
imports in the Geometry.TensorModule in newly used code paths have been fixed as well.
........

Fix for bug #20469 (https://gna.org/bugs/?20469).

This is the Failure in reading X-ray PDB files using the ScientificPython parser. The
ScientificPython Geometry.Transformation module is now distributed with relax. Some linear algebra
imports in the Geometry.TensorModule in newly used code paths have been fixed as well.

Merged revisions 18341 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r18341 | bugman | 2013-02-01 11:56:06 +0100 (Fri, 01 Feb 2013) | 5 lines

Created the Structure.test_bug_20469_scientific_parser_xray_records system test.

This is to catch bug #20469 (https://gna.org/bugs/?20469).
........

Created the Structure.test_bug_20469_scientific_parser_xray_records system test.

This is to catch bug #20469 (https://gna.org/bugs/?20469).

Merged revisions 18338-18339 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r18338 | bugman | 2013-02-01 11:48:46 +0100 (Fri, 01 Feb 2013) | 5 lines

Fix for the bug reported as the support request #2998 (https://gna.org/support/?2998).

CONECT records pointing to non-existent atoms can now be handled.
........
r18339 | bugman | 2013-02-01 11:49:53 +0100 (Fri, 01 Feb 2013) | 3 lines

Copyright update.
........

Copyright update.

Fix for the bug reported as the support request #2998 (https://gna.org/support/?2998).

CONECT records pointing to non-existent atoms can now be handled.

Merged revisions 18335 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r18335 | bugman | 2013-02-01 11:43:26 +0100 (Fri, 01 Feb 2013) | 6 lines

Created the Structure.test_bug_sr_2998_broken_conect_records system test.

This is to catch the bug reported as service request #2998 (https://gna.org/support/?2998) and is
for corrupted PDB files with broken CONECT records.
........

Merged revisions 18333-18334 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r18333 | bugman | 2013-02-01 11:37:12 +0100 (Fri, 01 Feb 2013) | 70 lines

Fix for the N_state_model.test_monte_carlo_sims system test.

On certain systems, the chi2 check is too stringent giving the error message:

Traceback (most recent call last):
File "test_suite/system_tests/n_state_model.py", line 697, in test_monte_carlo_sims
self.assertAlmostEqual(cdp.chi2 / 1e6, 1745860.0485368515 / 1e6)
AssertionError: 1.7458601287217688 != 1.7458600485368516 within 7 places

This has now been relaxed a little. The system information for the computer where this failed is:

Hardware information:
Machine: i686
Processor: i686
Endianness: little
Total RAM size: 8054 Mb
Total swap size: 3999 Mb

Operating system information:
System: Linux
Release: 2.6.35.14-106.fc14.i686.PAE
Version: #1 SMP Wed Nov 23 13:39:51 UTC 2011
GNU/Linux version: Fedora 14 Laughlin
Distribution: fedora 14 Laughlin
Full platform string: Linux-2.6.35.14-106.fc14.i686.PAE-i686-with-fedora-14-Laughlin

Python information:
Architecture: 32bit ELF
Python version: 2.7.0
Python branch: tags/r27
Python build: r27:82500, Sep 16 2010 18:03:06
Python compiler: GCC 4.5.1 20100907 (Red Hat 4.5.1-3)
Libc version: glibc 2.0
Python implementation: CPython
Python revision: 82500
Python executable: /usr/bin/python
Python flags: sys.flags(debug=0, py3k_warning=0, division_warning=0, division_new=0, inspect=0, interactive=0, optimize=0, dont_write_bytecode=0, no_user_site=0, no_site=0, ignore_environment=0, tabcheck=0, verbose=0, unicode=0, bytes_warning=0)
Python float info: sys.float_info(max=1.7976931348623157e+308, max_exp=1024, max_10_exp=308, min=2.2250738585072014e-308, min_exp=-1021, min_10_exp=-307, dig=15, mant_dig=53, epsilon=2.220446049250313e-16, radix=2, rounds=1)
Python module path: ['', '/home/test/relax-trunk', '/usr/lib/python27.zip', '/usr/lib/python2.7', '/usr/lib/python2.7/plat-linux2', '/usr/lib/python2.7/lib-tk', '/usr/lib/python2.7/lib-old', '/usr/lib/python2.7/lib-dynload', '/usr/lib/python2.7/site-packages', '/usr/lib/python2.7/site-packages/Numeric', '/usr/lib/python2.7/site-packages/gst-0.10', '/usr/lib/python2.7/site-packages/gtk-2.0', '/usr/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg-info', '/usr/lib/python2.7/site-packages/webkit-1.0', '/usr/lib/python2.7/site-packages/wx-2.8-gtk2-unicode', '/home/test/relax-trunk/extern/scientific_python/linux2']

Python packages and modules (most are optional):

Name Installed Version Path
minfx True Unknown /home/test/relax-trunk/minfx
bmrblib True Unknown /home/test/relax-trunk/bmrblib
numpy True 1.4.1 /usr/lib/python2.7/site-packages/numpy
scipy True 0.7.2 /usr/lib/python2.7/site-packages/scipy
wxPython True 2.8.12.0 (gtk2-unicode) /usr/lib/python2.7/site-packages/wx-2.8-gtk2-unicode/wx
mpi4py False
epydoc False
optparse True 1.5.3 /usr/lib/python2.7/optparse.pyc
readline True /usr/lib/python2.7/lib-dynload/readline.so
profile True /usr/lib/python2.7/profile.pyc
bz2 True /usr/lib/python2.7/lib-dynload/bz2.so
gzip True /usr/lib/python2.7/gzip.pyc
io True /usr/lib/python2.7/io.pyc
os.devnull True /usr/lib/python2.7/os.pyc
xml True 0.8.4 (PyXML) /usr/lib/python2.7/site-packages/_xmlplus/__init__.pyc
xml.dom.minidom True /usr/lib/python2.7/site-packages/_xmlplus/dom/minidom.pyc

relax information:
Version: repository checkout r18327 http://svn.gna.org/svn/relax/trunk
Processor fabric: Uni-processor.

relax C modules:

Module Compiled File type Path
maths_fns.relax_fit False
........
r18334 | bugman | 2013-02-01 11:38:37 +0100 (Fri, 01 Feb 2013) | 6 lines

Reverted -r18325 as this change breaks the GUI tests.

The command used was:
svn merge -r18325:r18324 .
........