relax SVN archive

Fix for testing of pA in lib function, when pA is just float.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

Removed the multi dimensional structure of pA.

pA is not multi-dimensional, and can just be multiplied with numpy arrays.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

Merged revisions 23784-23785 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r23784 | tlinnet | 2014-06-10 11:49:00 +0200 (Tue, 10 Jun 2014) | 7 lines

Lowered chi2 value test in system test Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster_NS_STAR.

This is due to the data produced on 32 bit machine, and tested on 64 bit machines.
The error was:
AssertionError: 2.4659455670347743e-05 != 0.0 within 7 places

The reason for this is due to truncation artifacts.
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r23785 | tlinnet | 2014-06-10 12:23:01 +0200 (Tue, 10 Jun 2014) | 5 lines

Fix for wrong path testing of Python.h.

Python.h would be in PYTHON_PREFIX/include/pythonX.Y/Python.h
and not in:
PYTHON_PREFIX/include/Python.h
........

Yet another small improvement for the profiling script.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

Implemented a masked array search for where "missing" array is equal 1.

This makes it possible to replace all values with this mask, from the value array.

This eliminates the last loops over the missing values.

It took over 4 hours to figure out, that the mask should be called with mask.mask,
to return the same fulls structure,

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

Removed line "# -*- coding: utf-8 -*-" which was automatically inserted by new python code editor.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

Merged revisions 23774,23779-23781,23784-23785 via svnmerge from
svn+ssh://tlinnet@.../svn/relax/trunk

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r23774 | bugman | 2014-06-10 09:40:22 +0200 (Tue, 10 Jun 2014) | 6 lines

The lib.compat.norm() replacement function for numpy.linalg.norm() now handles no axis argument.

This is to allow the function to be used in all cases where numpy.linalg.norm() is used, while
providing compatibility with the axis argument and all numpy versions.
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r23779 | bugman | 2014-06-10 10:07:22 +0200 (Tue, 10 Jun 2014) | 6 lines

Fix for the scons target for compiling the relax manual when using a repository checkout copy.

The method for compiling the relax manual was calling the version.revision() function, however this
has been replaced a while ago by the version.repo_revision variable.
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r23780 | bugman | 2014-06-10 10:08:33 +0200 (Tue, 10 Jun 2014) | 6 lines

Created two unit tests for the lib.io.file_root() function.

The second of the tests demonstrate a failure of the function if multiple file extensions are
present.
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r23781 | bugman | 2014-06-10 10:13:29 +0200 (Tue, 10 Jun 2014) | 5 lines

Bug fix for the lib.io.file_root() function for multiple file extensions.

The function will now strip off all file extensions.
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r23784 | tlinnet | 2014-06-10 11:49:00 +0200 (Tue, 10 Jun 2014) | 7 lines

Lowered chi2 value test in system test Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster_NS_STAR.

This is due to the data produced on 32 bit machine, and tested on 64 bit machines.
The error was:
AssertionError: 2.4659455670347743e-05 != 0.0 within 7 places

The reason for this is due to truncation artifacts.
........
r23785 | tlinnet | 2014-06-10 12:23:01 +0200 (Tue, 10 Jun 2014) | 5 lines

Fix for wrong path testing of Python.h.

Python.h would be in PYTHON_PREFIX/include/pythonX.Y/Python.h
and not in:
PYTHON_PREFIX/include/Python.h
........

Fix for wrong path testing of Python.h.

Python.h would be in PYTHON_PREFIX/include/pythonX.Y/Python.h
and not in:
PYTHON_PREFIX/include/Python.h

Lowered chi2 value test in system test Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster_NS_STAR.

This is due to the data produced on 32 bit machine, and tested on 64 bit machines.
The error was:
AssertionError: 2.4659455670347743e-05 != 0.0 within 7 places

The reason for this is due to truncation artifacts.

Modified the pymol.cone_pdb and pymol.frame_order user functions to use PyMOL IDs.

The PyMOL IDs are used to select individual objects in PyMOL rather than all objects so that the
subsequent PyMOL commands will only be applied to that object. This allows for multiple objects to
be handled simultaneously.