relax SVN archive

Merged revisions 23373-23374 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r23373 | bugman | 2014-05-23 11:25:34 +0200 (Fri, 23 May 2014) | 7 lines

Speed up for the version module when using a repository copy of the code.

The repository revision and URL and now stored as module variables, so that the 'svn info' and
'git svn info' commands are only run twice, once for the revision() function and once for the url()
function.
........
r23374 | bugman | 2014-05-23 12:11:36 +0200 (Fri, 23 May 2014) | 15 lines

Large speed up for the relax start up times for svn and git-svn copies of the relax repository.

The 'svn info' and 'git svn info' commands are now only executed once when the version module is
first imported. The revision() and url() functions have been merged into the repo_info() function
and this is called when the module is imported. This repo_info() function stores the repository
revision and URL as the version.repo_revision and version.repo_url module variables. It also
catches if these variables are already set, so that multiple imports of the module do not cause the
repository information to be looked up each time.

Previously the revision() and url() functions where called every time a relax state or result file
was created, hence for repository copies the 'svn info' or 'git svn info' commands were being called
each time. The functions were also called for each interpreter object instantiated, and for each
import of the version module.
........

Large speed up for the relax start up times for svn and git-svn copies of the relax repository.

The 'svn info' and 'git svn info' commands are now only executed once when the version module is
first imported. The revision() and url() functions have been merged into the repo_info() function
and this is called when the module is imported. This repo_info() function stores the repository
revision and URL as the version.repo_revision and version.repo_url module variables. It also
catches if these variables are already set, so that multiple imports of the module do not cause the
repository information to be looked up each time.

Previously the revision() and url() functions where called every time a relax state or result file
was created, hence for repository copies the 'svn info' or 'git svn info' commands were being called
each time. The functions were also called for each interpreter object instantiated, and for each
import of the version module.

Speed up for the version module when using a repository copy of the code.

The repository revision and URL and now stored as module variables, so that the 'svn info' and
'git svn info' commands are only run twice, once for the revision() function and once for the url()
function.

Merged revisions 23365-23366,23368-23369 via svnmerge from
svn+ssh://tlinnet@.../svn/relax/trunk

........
r23365 | bugman | 2014-05-23 09:03:27 +0200 (Fri, 23 May 2014) | 7 lines

Attempt at fixing bug #22071, the relax unit test and system test not functioning.

This is reported at https://gna.org/bugs/?22071.

The fix here is that the git commands to show the current subversion revision number only works when
run from the relax base directory, or one of the subdirectories. This should now be fixed, as the
pipe running the command will first 'cd' to the relax base directory.
........
r23366 | bugman | 2014-05-23 09:18:34 +0200 (Fri, 23 May 2014) | 6 lines

Another attempt at fixing bug #22071, the relax unit test and system test not functioning.

This is reported at https://gna.org/bugs/?22071.

This time the complicated shell command "cd %s; git svn find-rev $(git rev-parse HEAD)" has been
replaced with "cd %s; git svn info".
........
r23368 | bugman | 2014-05-23 10:06:32 +0200 (Fri, 23 May 2014) | 11 lines

Changed most default dispersion parameter values to avoid edge cases where there is no exchange.

The dw parameters were all 0.0 and kex 1e5, both of which result in no exchange. If this is ever
used for an optimisation starting point - which it never should, apart from development, test suite,
and debugging purposes - then the optimisation algorithm will have a very hard time recovering. The
pA parameter has been changed to 0.90 to set it to a reasonable value while still staying far away
from the no exchange condition of pA = 1.0.

This follows from http://article.gmane.org/gmane.science.nmr.relax.devel/5917.
........
r23369 | bugman | 2014-05-23 10:10:46 +0200 (Fri, 23 May 2014) | 10 lines

Fixes for 3 dispersion system tests for the change in default parameter values.

The default values are used in the auto-analysis in the test suite to avoid the grid search. The
changed values affected the optimisation of two spins from Flemming Hansen's data located at
test_suite/shared_data/dispersion/Hansen/, residue 4 used as an example of no exchange and residue
70 used as an example where data is only available at one field. The system test
Relax_disp.test_set_grid_r20_from_min_r2eff_cpmg was also modified as it was directly checking these
default values.
........

Merged revisions 23368-23370 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r23368 | bugman | 2014-05-23 10:06:32 +0200 (Fri, 23 May 2014) | 11 lines

Changed most default dispersion parameter values to avoid edge cases where there is no exchange.

The dw parameters were all 0.0 and kex 1e5, both of which result in no exchange. If this is ever
used for an optimisation starting point - which it never should, apart from development, test suite,
and debugging purposes - then the optimisation algorithm will have a very hard time recovering. The
pA parameter has been changed to 0.90 to set it to a reasonable value while still staying far away
from the no exchange condition of pA = 1.0.

This follows from http://article.gmane.org/gmane.science.nmr.relax.devel/5917.
........
r23369 | bugman | 2014-05-23 10:10:46 +0200 (Fri, 23 May 2014) | 10 lines

Fixes for 3 dispersion system tests for the change in default parameter values.

The default values are used in the auto-analysis in the test suite to avoid the grid search. The
changed values affected the optimisation of two spins from Flemming Hansen's data located at
test_suite/shared_data/dispersion/Hansen/, residue 4 used as an example of no exchange and residue
70 used as an example where data is only available at one field. The system test
Relax_disp.test_set_grid_r20_from_min_r2eff_cpmg was also modified as it was directly checking these
default values.
........
r23370 | bugman | 2014-05-23 10:18:37 +0200 (Fri, 23 May 2014) | 7 lines

Fix for the Relax_disp.test_cpmg_synthetic_dx_map_points system test.

This uses the default parameter values to start the optimisation, therefore the recent change away
from edge case 'no Rex' values allows the parameter values stored in ds.dx_clust_val to be correctly
optimised.
........

Fix for the Relax_disp.test_cpmg_synthetic_dx_map_points system test.

This uses the default parameter values to start the optimisation, therefore the recent change away
from edge case 'no Rex' values allows the parameter values stored in ds.dx_clust_val to be correctly
optimised.

Fixes for 3 dispersion system tests for the change in default parameter values.

The default values are used in the auto-analysis in the test suite to avoid the grid search. The
changed values affected the optimisation of two spins from Flemming Hansen's data located at
test_suite/shared_data/dispersion/Hansen/, residue 4 used as an example of no exchange and residue
70 used as an example where data is only available at one field. The system test
Relax_disp.test_set_grid_r20_from_min_r2eff_cpmg was also modified as it was directly checking these
default values.

Changed most default dispersion parameter values to avoid edge cases where there is no exchange.

The dw parameters were all 0.0 and kex 1e5, both of which result in no exchange. If this is ever
used for an optimisation starting point - which it never should, apart from development, test suite,
and debugging purposes - then the optimisation algorithm will have a very hard time recovering. The
pA parameter has been changed to 0.90 to set it to a reasonable value while still staying far away
from the no exchange condition of pA = 1.0.

This follows from http://article.gmane.org/gmane.science.nmr.relax.devel/5917.

Merged revisions 23362,23365-23366 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r23362 | bugman | 2014-05-22 19:55:47 +0200 (Thu, 22 May 2014) | 9 lines

Created the test_ns_cpmg_2site_expanded_no_rex8() relaxation dispersion unit test.

This is a demonstration commit, showing the 'NS CPMG 2-site expanded' model with no exchange when
kex = 1e5. I.e. when the motion is too fast for exchange to be observed. This test should be used
for all dispersion models to make sure that they model this edge case correctly as well.

This follows from http://article.gmane.org/gmane.science.nmr.relax.devel/5906.
........
r23365 | bugman | 2014-05-23 09:03:27 +0200 (Fri, 23 May 2014) | 7 lines

Attempt at fixing bug #22071, the relax unit test and system test not functioning.

This is reported at https://gna.org/bugs/?22071.

The fix here is that the git commands to show the current subversion revision number only works when
run from the relax base directory, or one of the subdirectories. This should now be fixed, as the
pipe running the command will first 'cd' to the relax base directory.
........
r23366 | bugman | 2014-05-23 09:18:34 +0200 (Fri, 23 May 2014) | 6 lines

Another attempt at fixing bug #22071, the relax unit test and system test not functioning.

This is reported at https://gna.org/bugs/?22071.

This time the complicated shell command "cd %s; git svn find-rev $(git rev-parse HEAD)" has been
replaced with "cd %s; git svn info".
........

Another attempt at fixing bug #22071, the relax unit test and system test not functioning.

This is reported at https://gna.org/bugs/?22071.

This time the complicated shell command "cd %s; git svn find-rev $(git rev-parse HEAD)" has been
replaced with "cd %s; git svn info".