relax SVN archive

Merged revisions 19612-19615 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r19612 | bugman | 2013-05-02 12:05:15 +0200 (Thu, 02 May 2013) | 3 lines

Removed the numpy dependence from the manual C module compilation script.
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r19613 | bugman | 2013-05-02 12:15:04 +0200 (Thu, 02 May 2013) | 5 lines

Created the lib.mathematics relax library module.

This currently contains two functions, order_of_magnitude() and round_to_next_order().
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r19614 | bugman | 2013-05-02 12:40:14 +0200 (Thu, 02 May 2013) | 3 lines

Added unit tests for the lib.mathematics module.
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r19615 | bugman | 2013-05-02 12:40:30 +0200 (Thu, 02 May 2013) | 3 lines

Bug fixes for the lib.mathematics module as found by the unit tests.
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Bug fixes for the lib.mathematics module as found by the unit tests.

Added unit tests for the lib.mathematics module.

Created the lib.mathematics relax library module.

This currently contains two functions, order_of_magnitude() and round_to_next_order().

Removed the numpy dependence from the manual C module compilation script.

Redesign of the relaxation dispersion models in the relax_disp.select_model user function front-end.

The models have been renamed and better defined based on the experiment type (CPMG or R1rho).

Merged revisions 19609 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r19609 | bugman | 2013-04-29 12:01:20 +0200 (Mon, 29 Apr 2013) | 3 lines

Added a developer script for testing of memory leaks in the relax_fit C modules.
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Added a developer script for testing of memory leaks in the relax_fit C modules.

Merged revisions 19595-19607 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r19595 | bugman | 2013-04-29 09:47:39 +0200 (Mon, 29 Apr 2013) | 3 lines

Clean up of unused headers and declarations in the exponential curve C module.
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r19596 | bugman | 2013-04-29 09:54:20 +0200 (Mon, 29 Apr 2013) | 5 lines

The relax_fit C module setup() function now uses the Py_RETURN_NONE macro to terminate.

This macro does exactly what the old code does anyway.
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r19597 | bugman | 2013-04-29 09:56:54 +0200 (Mon, 29 Apr 2013) | 3 lines

Removed an unused declaration in the relax_fit C module setup() function.
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r19598 | bugman | 2013-04-29 09:58:26 +0200 (Mon, 29 Apr 2013) | 3 lines

Increased the maximum number of relaxation times for the relax_fit C module to 50.
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r19599 | bugman | 2013-04-29 10:04:56 +0200 (Mon, 29 Apr 2013) | 8 lines

Shifted the C array creation to the relax_fit C module header.

The params, values, sd, relax_times, and scaling_matrix C arrays are now declared and allocated in
the header file rather than using malloc() calls in the setup() function. This is to attempt to
remove a memory leak. The arrays are now of fixed length and reused for each setup() call. These,
as well as the other variables declared in the header are no longer declared in the functions.
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r19600 | bugman | 2013-04-29 10:22:41 +0200 (Mon, 29 Apr 2013) | 3 lines

Improved the Python and C documentation of the functions of the relax_fit C module.
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r19601 | bugman | 2013-04-29 10:31:46 +0200 (Mon, 29 Apr 2013) | 5 lines

Converted the Py_BuildValue() calls to PyFloat_FromDouble() in the relax_fit C module.

This doesn't change much.
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r19602 | bugman | 2013-04-29 10:35:15 +0200 (Mon, 29 Apr 2013) | 3 lines

Documentation improvements for the back_calc_I() function of the relax_fit C module.
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r19603 | bugman | 2013-04-29 10:36:42 +0200 (Mon, 29 Apr 2013) | 3 lines

Spacing fixes.
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r19604 | bugman | 2013-04-29 11:11:06 +0200 (Mon, 29 Apr 2013) | 5 lines

The exponential C file now uses the exp() function from math.h rather than Python.h.

This file is independent from Python.
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r19605 | bugman | 2013-04-29 11:15:16 +0200 (Mon, 29 Apr 2013) | 6 lines

The numpy include is no longer used for the compilation of the C modules.

Numpy is not used at all in the C modules, so this just adds an annoying dependency for those who
need to compile the module themselves.
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r19606 | bugman | 2013-04-29 11:27:57 +0200 (Mon, 29 Apr 2013) | 7 lines

Removed some bad calls to status.exec_lock.release().

This commit may have to be reverted in the future. The problem is that the execution lock is not
being held when these calls are made. The calls were added as a kludge to handle certain situations
where the execution lock was not released. There may be cases were this behaviour is still needed.
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r19607 | bugman | 2013-04-29 11:37:47 +0200 (Mon, 29 Apr 2013) | 8 lines

Big bug fix for a memory leak in the relaxation curve-fitting C module.

Proper reference counting is used for the temporary 'element' Python objects used in the conversion
between Python and C objects. The use of the Py_CLEAR() macro removes the memory leak. However the
number of references as seen by sys.gettotalrefcount() in a debugging Python version keeps rising
and might be a problem in the future.
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Big bug fix for a memory leak in the relaxation curve-fitting C module.

Proper reference counting is used for the temporary 'element' Python objects used in the conversion
between Python and C objects. The use of the Py_CLEAR() macro removes the memory leak. However the
number of references as seen by sys.gettotalrefcount() in a debugging Python version keeps rising
and might be a problem in the future.