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Commit Date  
[r18341] by bugman

Created the Structure.test_bug_20469_scientific_parser_xray_records system test.

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

 2013-02-01 10:56:06 Tree
[r18340] by bugman

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.
........

 2013-02-01 10:55:37 Tree
[r18339] by bugman

Copyright update.

 2013-02-01 10:49:53 Tree
[r18338] by bugman

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.

 2013-02-01 10:48:46 Tree
[r18337] by bugman

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.
........

 2013-02-01 10:46:17 Tree
[r18336] by bugman

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 .
........

 2013-02-01 10:44:56 Tree
[r18335] by bugman

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.

 2013-02-01 10:43:26 Tree
[r18334] by bugman

Reverted -r18325 as this change breaks the GUI tests.

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

 2013-02-01 10:38:37 Tree
[r18333] by bugman

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

 2013-02-01 10:37:12 Tree
[r18332] by bugman

Merged revisions 18331 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r18331 | bugman | 2013-02-01 11:28:43 +0100 (Fri, 01 Feb 2013) | 6 lines

Clean up of the Mf.test_bug_20464_missing_ri_data system test.

The directories and files created are now placed in a temporary directory to be removed by the
tearDown() method, and the optimisation is now much faster.
........

 2013-02-01 10:30:39 Tree
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