Author: bugman
Date: Thu Sep 18 15:39:25 2014
New Revision: 25899
URL: http://svn.gna.org/viewcvs/relax?rev=25899&view=rev
Log:
Merged revisions 25846-25861,25897-25898 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
Added:
branches/frame_order_cleanup/extern/numdifftools/
- copied from r25898, trunk/extern/numdifftools/
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/auto_analyses/relax_disp_repeat_cpmg.py
branches/frame_order_cleanup/specific_analyses/relax_disp/optimisation.py
branches/frame_order_cleanup/test_suite/system_tests/dasha.py
branches/frame_order_cleanup/test_suite/system_tests/palmer.py
branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py
branches/frame_order_cleanup/test_suite/test_suite_runner.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/frame_order_cleanup/auto_analyses/relax_disp_repeat_cpmg.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/auto_analyses/relax_disp_repeat_cpmg.py?rev=25899&r1=25898&r2=25899&view=diff
Modified:
branches/frame_order_cleanup/specific_analyses/relax_disp/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_disp/optimisation.py?rev=25899&r1=25898&r2=25899&view=diff
Modified: branches/frame_order_cleanup/test_suite/system_tests/dasha.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/dasha.py?rev=25899&r1=25898&r2=25899&view=diff
Modified: branches/frame_order_cleanup/test_suite/system_tests/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/palmer.py?rev=25899&r1=25898&r2=25899&view=diff
Modified: branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py?rev=25899&r1=25898&r2=25899&view=diff
Modified: branches/frame_order_cleanup/test_suite/test_suite_runner.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/test_suite_runner.py?rev=25899&r1=25898&r2=25899&view=diff
r25899 - in /branches/frame_order_cleanup: ./ auto_analyses/ extern/numdifftools/ specific_analyses/relax_disp/ test_suite/ ...