relax SVN archive

Merged revisions 25900,25902-25904,25906 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r25900 | tlinnet | 2014-09-18 17:46:44 +0200 (Thu, 18 Sep 2014) | 3 lines

Reordered functions in repeated analysis protocol.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25902 | tlinnet | 2014-09-18 18:04:46 +0200 (Thu, 18 Sep 2014) | 5 lines

Added more check of methods to the systemtest Relax_disp.test_repeat_cpmg().

This actually shows, that user function relax_disp.r20_from_min_r2eff maybe is broken.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25903 | tlinnet | 2014-09-18 19:00:17 +0200 (Thu, 18 Sep 2014) | 3 lines

Fix for the testing of method is finished when called.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25904 | tlinnet | 2014-09-18 19:00:19 +0200 (Thu, 18 Sep 2014) | 3 lines

Turned on minimisation in systemtest Relax_disp.test_repeat_cpmg().

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25906 | bugman | 2014-09-19 09:13:03 +0200 (Fri, 19 Sep 2014) | 9 lines

The lib.spectrum.nmrpipe has been made independent of the relax source code.

This was discussed at http://thread.gmane.org/gmane.science.nmr.relax.scm/23357/focus=7103.

The change allows the software verification tests pass. The dep_check module cannot be used in the
relax lib package. Only modules from within lib are allowed to be imported into modules of lib.
The fix now allows the full test suite to pass and hence new relax releases are once again possible.
........

The lib.spectrum.nmrpipe has been made independent of the relax source code.

This was discussed at http://thread.gmane.org/gmane.science.nmr.relax.scm/23357/focus=7103.

The change allows the software verification tests pass. The dep_check module cannot be used in the
relax lib package. Only modules from within lib are allowed to be imported into modules of lib.
The fix now allows the full test suite to pass and hence new relax releases are once again possible.

The starting time of the axis permutation model optimisations is now output.

This is in the frame order auto-analysis. This call to the time user function occurred for the
normal models, so extending it to the permuted axes models makes the output more consistent.

Turned on minimisation in systemtest Relax_disp.test_repeat_cpmg().

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.

Fix for the testing of method is finished when called.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.

Added more check of methods to the systemtest Relax_disp.test_repeat_cpmg().

This actually shows, that user function relax_disp.r20_from_min_r2eff maybe is broken.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.

Fix for the frame order system test optimisation printouts.

The cdp.num_int_pts variable is now called cdp.sobol_max_points.

Reordered functions in repeated analysis protocol.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.

Merged revisions 25846-25861,25897-25898 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r25846 | bugman | 2014-09-15 16:27:17 +0200 (Mon, 15 Sep 2014) | 5 lines

Added the Relax_disp.test_show_apod_rmsd_dir_to_files system test to the blacklist.

This is if the showApod program is not installed on the machine and allows the test suite to pass.
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r25847 | bugman | 2014-09-15 16:49:17 +0200 (Mon, 15 Sep 2014) | 6 lines

Extended the printout for the skipped tests in the test suite.

As tests using the NMRPipe showApod software are skipped and listed in this table, the text now
includes 'software' in the list.
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r25848 | bugman | 2014-09-15 17:00:53 +0200 (Mon, 15 Sep 2014) | 7 lines

Shifted the checks for the Dasha and Modelfree4 software into the system test __init__() method.

This is to bring this into the same design as the relaxation dispersion tests which require the
NMRPipe showApod software. Now the test suite will list either Dasha or Modelfree4 in the skipped
test table if they are not installed.
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r25849 | tlinnet | 2014-09-15 23:04:25 +0200 (Mon, 15 Sep 2014) | 3 lines

Adding another statistic method to plot for multi-data sets.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25850 | tlinnet | 2014-09-16 01:20:45 +0200 (Tue, 16 Sep 2014) | 3 lines

More adding of matplotlib snippets for plotting intermediate data.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25851 | tlinnet | 2014-09-16 01:48:57 +0200 (Tue, 16 Sep 2014) | 3 lines

Changing the range of plotting for statistics.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25852 | tlinnet | 2014-09-16 02:03:38 +0200 (Tue, 16 Sep 2014) | 3 lines

More changes to plotting for statistics.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25853 | tlinnet | 2014-09-16 02:25:02 +0200 (Tue, 16 Sep 2014) | 3 lines

Fix for axis limits when plotting stats.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25854 | tlinnet | 2014-09-16 02:44:55 +0200 (Tue, 16 Sep 2014) | 3 lines

Fix for globbing, to prevent incidentally taking wrong intensity file.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25855 | tlinnet | 2014-09-16 07:15:04 +0200 (Tue, 16 Sep 2014) | 3 lines

Correction to figure limits.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25856 | tlinnet | 2014-09-16 13:19:38 +0200 (Tue, 16 Sep 2014) | 3 lines

Implemented writing out of statistics to file.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25857 | tlinnet | 2014-09-16 13:42:13 +0200 (Tue, 16 Sep 2014) | 3 lines

Adding writing out of png files from matplotlib, when looking at statistics.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25858 | tlinnet | 2014-09-16 19:45:57 +0200 (Tue, 16 Sep 2014) | 5 lines

Another math domain checking, if ref intensity is set to 0.0, then points are skipped, rather than raising an Error.

This can happen for extremely bad dispersion data.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25859 | tlinnet | 2014-09-16 19:45:59 +0200 (Tue, 16 Sep 2014) | 5 lines

Trying implementing flexibility, when data expected data is missing.

This can be due failing of processing data, where a whole run of data is randomly skipped.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25860 | tlinnet | 2014-09-16 19:52:12 +0200 (Tue, 16 Sep 2014) | 3 lines

Better check for math domain error in intensity propertionality.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25861 | tlinnet | 2014-09-16 19:52:13 +0200 (Tue, 16 Sep 2014) | 3 lines

Removeal of initialised of dictionary, before data existence have been checked.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25897 | tlinnet | 2014-09-18 11:13:40 +0200 (Thu, 18 Sep 2014) | 3 lines

Small fix for correct check of missing of data.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r25898 | bugman | 2014-09-18 11:47:22 +0200 (Thu, 18 Sep 2014) | 17 lines

Imported the Numdifftools 0.6.0 package into the relax source tree.

This package is extremely useful for testing the implementation of gradients, Hessians, and
Jacobians for all relax target functions. The numerical values from numdifftools can be compared to
the directly calculated values. And for analysis types where the partial derivatives with respect
to each model parameter are too complicated to calculated, or the derivatives are very complicated
and hence slow, numdifftools can be used to provide a numerical estimate for direct use in the
optimisation.

The Numdifftools package is from https://pypi.python.org/pypi/Numdifftools and
https://code.google.com/p/numdifftools/. The current version 0.6.0 has been placed into
extern/numdifftools. This is only the numdifftools package within the official distribution files
and the Python package setup.py file and associated files and directories have not been included.
The package uses the New BSD licence (the revised licence with no advertising clause) which is
compatible with the GPL v3 licence.
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Imported the Numdifftools 0.6.0 package into the relax source tree.

This package is extremely useful for testing the implementation of gradients, Hessians, and
Jacobians for all relax target functions. The numerical values from numdifftools can be compared to
the directly calculated values. And for analysis types where the partial derivatives with respect
to each model parameter are too complicated to calculated, or the derivatives are very complicated
and hence slow, numdifftools can be used to provide a numerical estimate for direct use in the
optimisation.

The Numdifftools package is from https://pypi.python.org/pypi/Numdifftools and
https://code.google.com/p/numdifftools/. The current version 0.6.0 has been placed into
extern/numdifftools. This is only the numdifftools package within the official distribution files
and the Python package setup.py file and associated files and directories have not been included.
The package uses the New BSD licence (the revised licence with no advertising clause) which is
compatible with the GPL v3 licence.