relax SVN archive

Merged revisions 10330 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

........
r10330 | bugman | 2010-01-25 21:01:23 +0100 (Mon, 25 Jan 2010) | 3 lines

As a precaution, the spins will always be named in the automatic model-free protocol.
........

As a precaution, the spins will always be named in the automatic model-free protocol.

Merged revisions 10178-10188,10197,10204-10205,10240,10242-10245,10267,10296-10302,10304-10326 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

........
r10178 | bugman | 2010-01-12 13:20:36 +0100 (Tue, 12 Jan 2010) | 3 lines

Modified the import of euler_zyz_to_R to allow easy switching later on to a different notation.
........
r10179 | bugman | 2010-01-12 13:21:01 +0100 (Tue, 12 Jan 2010) | 3 lines

Copyright notice update.
........
r10180 | bugman | 2010-01-12 13:32:12 +0100 (Tue, 12 Jan 2010) | 3 lines

Renamed all euler_ijk_to_R() functions to euler_to_R_ijk().
........
r10181 | bugman | 2010-01-12 13:35:04 +0100 (Tue, 12 Jan 2010) | 3 lines

Ordered the euler angle conversion functions.
........
r10182 | bugman | 2010-01-12 13:40:33 +0100 (Tue, 12 Jan 2010) | 3 lines

Fixes for all the euler angle to rotation matrix unit tests.
........
r10183 | bugman | 2010-01-12 13:42:00 +0100 (Tue, 12 Jan 2010) | 3 lines

Fix for reverse_euler_zyz() due to the function renaming.
........
r10184 | bugman | 2010-01-12 14:22:09 +0100 (Tue, 12 Jan 2010) | 3 lines

Created a unit test to check all hard-coded conversion functions for all 12 static axis rotations.
........
r10185 | bugman | 2010-01-12 14:22:52 +0100 (Tue, 12 Jan 2010) | 3 lines

Fix for the euler_to_axis_angle_xzx() function.
........
r10186 | bugman | 2010-01-12 15:10:54 +0100 (Tue, 12 Jan 2010) | 5 lines

Improvements to the test_euler_cycle_1() unit test.

This includes verbose printing of data structures and checking of the rotation matrix at each cycle.
........
r10187 | bugman | 2010-01-12 15:36:01 +0100 (Tue, 12 Jan 2010) | 5 lines

Added 12 unit tests for all notations of R -> Euler -> R.

This uses a random rotation matrix and sees if the matrix is returned.
........
r10188 | bugman | 2010-01-12 15:39:31 +0100 (Tue, 12 Jan 2010) | 6 lines

Important bug fix for the R_to_euler() function.

The special angle wrapping when beta was negative is only for the ijk Euler notation when i == k!
When i != k, another type of wrapping will be required.
........
r10197 | bugman | 2010-01-13 15:15:37 +0100 (Wed, 13 Jan 2010) | 3 lines

Removed the alpha Euler angle from the isotropic code frame order model.
........
r10204 | bugman | 2010-01-13 17:33:24 +0100 (Wed, 13 Jan 2010) | 5 lines

Bug fix for the frame order isotropic cone target function.

The optimised rotation matrix for the alignment tensor orientations was being applied in reverse!!!
........
r10205 | bugman | 2010-01-13 19:21:19 +0100 (Wed, 13 Jan 2010) | 6 lines

Reverted r10204 as this was a not a bug and the revision introduced a bug!!!

The command used was:
svn merge -r10204:10203 .
........
r10240 | bugman | 2010-01-15 15:35:22 +0100 (Fri, 15 Jan 2010) | 5 lines

Bug fixes for the code validator script.

The 4 character spacing check was faulty.
........
r10242 | bugman | 2010-01-18 17:15:33 +0100 (Mon, 18 Jan 2010) | 5 lines

Shifted the target function initialisation into _target_fn_setup().

This will be shared by the calculate() method.
........
r10243 | bugman | 2010-01-18 17:20:45 +0100 (Mon, 18 Jan 2010) | 3 lines

The calculate() method now uses _target_fn_setup() and stores the chi2 in the cdp.
........
r10244 | bugman | 2010-01-18 17:34:19 +0100 (Mon, 18 Jan 2010) | 3 lines

The number of elements in the atomic position arg is now checked to be 3.
........
r10245 | bugman | 2010-01-18 18:07:36 +0100 (Mon, 18 Jan 2010) | 5 lines

Removed the print out from _overfit_deselect_dummy().

This was totally unnecessary!
........
r10267 | bugman | 2010-01-20 12:01:00 +0100 (Wed, 20 Jan 2010) | 3 lines

Removed the beta angle folding from the frame order module as it was failing.
........
r10296 | bugman | 2010-01-25 11:13:06 +0100 (Mon, 25 Jan 2010) | 14 lines

Spun out the automatic model-free protocol code from the full_analysis.py script.

This is discussed in the post https://mail.gna.org/public/relax-devel/2010-01/msg00075.html.

The aim is to have a single code base for the automatic protocols for all UI designs (prompt,
script, GUI, web interface, etc.). The API interface will be via class initialisations. The
automatic model-free protocol has been placed into the dAuvergne_protocol class.

Future aims of this code is to have the UI fill a single data pipe with all the data required for
the analysis, and then to pass in this pipe into the protocol. Then the auto-analysis will copy
this info into any other data pipes it requires. This will allow for better GUI interaction, data
display, etc.
........
r10297 | bugman | 2010-01-25 11:33:22 +0100 (Mon, 25 Jan 2010) | 3 lines

Removed all the now unused imports and a useless comment.
........
r10298 | bugman | 2010-01-25 11:34:54 +0100 (Mon, 25 Jan 2010) | 3 lines

Updated the copyright notice.
........
r10299 | bugman | 2010-01-25 11:37:25 +0100 (Mon, 25 Jan 2010) | 3 lines

Fixed the import of the dAuvergne_protocol class.
........
r10300 | bugman | 2010-01-25 12:13:59 +0100 (Mon, 25 Jan 2010) | 3 lines

Modifications to the phthalic_acid_noes.py system test script to allow for standalone operation.
........
r10301 | bugman | 2010-01-25 12:40:54 +0100 (Mon, 25 Jan 2010) | 5 lines

Fixes for the N-state model for when only NOEs are present.

This fixes a bug introduced at r10243.
........
r10302 | bugman | 2010-01-25 12:54:34 +0100 (Mon, 25 Jan 2010) | 5 lines

Bug fix for the bug fix of r10301!

The bug fix actually introduced a bug, and this commit fixes that!
........
r10304 | bugman | 2010-01-25 14:25:32 +0100 (Mon, 25 Jan 2010) | 11 lines

Redesign of the setup of the names spaces for the user functions.

All the user functions and other objects located in the run() method namespace have been shifted
into the interpreter self._locals dictionary. These are then placed into the run() method namespace
by looping over the keys and using the 'locals()[key] = object' syntax. There may be better ways to
do this.

This has no visible effect on the prompt or script based interfaces. It will change how this is
seen by other modules though, and will allow the namespace to be more easily accessed.
........
r10305 | bugman | 2010-01-25 14:26:57 +0100 (Mon, 25 Jan 2010) | 3 lines

Removed some unused and commented out code.
........
r10306 | bugman | 2010-01-25 14:31:09 +0100 (Mon, 25 Jan 2010) | 5 lines

Eliminated the dummy mode.

This is only used by the fetch_docstrings script and will soon not be necessary.
........
r10307 | bugman | 2010-01-25 15:55:49 +0100 (Mon, 25 Jan 2010) | 7 lines

The relax base object is no longer passed into the class namespace of the user functions.

This was only being used for access to the intro flag (a few other cases exist, but these should be
fixed). Now a new container object with this flag is being passed in. This significantly
simplifies the code paths and removes the need for the test suite to create 'fake' relax instances.
........
r10308 | bugman | 2010-01-25 16:08:41 +0100 (Mon, 25 Jan 2010) | 7 lines

Modified how the Exec_info data container is handled.

The class was shifted from prompt.interpreter to prompt.base_class. In addition if not container
is passed into the user function classes, then one is created with the intro flag set to a default
of True.
........
r10309 | bugman | 2010-01-25 16:34:44 +0100 (Mon, 25 Jan 2010) | 8 lines

The prompt info has been shifted into the execution info container.

The sys.ps1, sys.ps2, and sys.ps3 prompts are still set, but these strings are hardcoded into the
execution info container. This allows the user functions to be imported and operate outside of the
prompt/scripting based interface, as the no longer require sys.ps3 to be set or the relax main
instance passed into them.
........
r10310 | bugman | 2010-01-25 16:39:34 +0100 (Mon, 25 Jan 2010) | 5 lines

Eliminated the fake_relax instance dependence.

This is no longer necessary as the user functions can be initialised without relax.
........
r10311 | bugman | 2010-01-25 16:53:14 +0100 (Mon, 25 Jan 2010) | 3 lines

Created the populate_self() method to place all user functions into the interpreter namespace.
........
r10312 | bugman | 2010-01-25 16:58:57 +0100 (Mon, 25 Jan 2010) | 5 lines

The relax main instance is no longer passed into the test suite.

This can be done as the prompt/script interface has been detached from relax.
........
r10313 | bugman | 2010-01-25 17:00:12 +0100 (Mon, 25 Jan 2010) | 5 lines

The relax main instance is no longer passed into the prompt/script interface.

This can be done as the prompt/script interface has been detached from relax.
........
r10314 | bugman | 2010-01-25 17:06:28 +0100 (Mon, 25 Jan 2010) | 3 lines

The relax main instance is no longer handled by the system test initialisation code.
........
r10315 | bugman | 2010-01-25 18:04:17 +0100 (Mon, 25 Jan 2010) | 5 lines

Created the SystemTestCase base class for all the system tests to use.

This base class initialises the relax interpreter within the TestCase class instances.
........
r10316 | bugman | 2010-01-25 18:13:12 +0100 (Mon, 25 Jan 2010) | 3 lines

The interpreter _on() method does not need to be called as user fn intros are turned on by default.
........
r10317 | bugman | 2010-01-25 18:52:04 +0100 (Mon, 25 Jan 2010) | 5 lines

Fixed all the calls to the user functions located in the interpreter class.

self.relax is no longer referenced and the user functions are now directly called.
........
r10318 | bugman | 2010-01-25 18:52:38 +0100 (Mon, 25 Jan 2010) | 3 lines

Fixed the script user function.
........
r10319 | bugman | 2010-01-25 18:54:20 +0100 (Mon, 25 Jan 2010) | 3 lines

Removed redundant and now non-functional code from interact_script().
........
r10320 | bugman | 2010-01-25 19:04:45 +0100 (Mon, 25 Jan 2010) | 3 lines

Comment fix.
........
r10321 | bugman | 2010-01-25 19:11:25 +0100 (Mon, 25 Jan 2010) | 6 lines

Update the user function print out functions.

_off() and _on() are no longer private, and accept the verbose keyword arg to allow the print out to
be suppressed.
........
r10322 | bugman | 2010-01-25 19:11:59 +0100 (Mon, 25 Jan 2010) | 3 lines

Alphabetical ordering of methods.
........
r10323 | bugman | 2010-01-25 19:21:05 +0100 (Mon, 25 Jan 2010) | 3 lines

The dAuvergne_protocol class now calls the user functions from the self.interpreter instance directly.
........
r10324 | bugman | 2010-01-25 19:26:36 +0100 (Mon, 25 Jan 2010) | 5 lines

Fix for the automatic model-free protocol in dAuvergne_protocol.

The sequence.read() and relax_data.read() user functions args are now sent in as keywords.
........
r10325 | bugman | 2010-01-25 20:31:25 +0100 (Mon, 25 Jan 2010) | 3 lines

Created the RelaxFileEmptyWarning class.
........
r10326 | bugman | 2010-01-25 20:36:30 +0100 (Mon, 25 Jan 2010) | 3 lines

Modified read_spin_data() to throw a warning rather than error when an empty file is encountered.
........

Merged revisions 10117,10157,10178-10188,10197,10204-10205,10240,10242-10245,10267,10296-10302,10304-10326 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

........
r10117 | bugman | 2010-01-06 18:57:55 +0100 (Wed, 06 Jan 2010) | 6 lines

Modified the IO redirection methods.

The original IO streams are stored and then restore instead of sys.__stdout__ and sys.__stderr__.
This might help in the multi-processor branch where IO redirection has gone haywire.
........
r10157 | bugman | 2010-01-08 10:57:41 +0100 (Fri, 08 Jan 2010) | 6 lines

Big bug fix for the model-free grid search!!!

The lower and upper bounds were being scaled iteratively for each spin causing the values to be
ridiculously bigger and bigger. This caused a total failure of the grid search.
........
r10178 | bugman | 2010-01-12 13:20:36 +0100 (Tue, 12 Jan 2010) | 3 lines

Modified the import of euler_zyz_to_R to allow easy switching later on to a different notation.
........
r10179 | bugman | 2010-01-12 13:21:01 +0100 (Tue, 12 Jan 2010) | 3 lines

Copyright notice update.
........
r10180 | bugman | 2010-01-12 13:32:12 +0100 (Tue, 12 Jan 2010) | 3 lines

Renamed all euler_ijk_to_R() functions to euler_to_R_ijk().
........
r10181 | bugman | 2010-01-12 13:35:04 +0100 (Tue, 12 Jan 2010) | 3 lines

Ordered the euler angle conversion functions.
........
r10182 | bugman | 2010-01-12 13:40:33 +0100 (Tue, 12 Jan 2010) | 3 lines

Fixes for all the euler angle to rotation matrix unit tests.
........
r10183 | bugman | 2010-01-12 13:42:00 +0100 (Tue, 12 Jan 2010) | 3 lines

Fix for reverse_euler_zyz() due to the function renaming.
........
r10184 | bugman | 2010-01-12 14:22:09 +0100 (Tue, 12 Jan 2010) | 3 lines

Created a unit test to check all hard-coded conversion functions for all 12 static axis rotations.
........
r10185 | bugman | 2010-01-12 14:22:52 +0100 (Tue, 12 Jan 2010) | 3 lines

Fix for the euler_to_axis_angle_xzx() function.
........
r10186 | bugman | 2010-01-12 15:10:54 +0100 (Tue, 12 Jan 2010) | 5 lines

Improvements to the test_euler_cycle_1() unit test.

This includes verbose printing of data structures and checking of the rotation matrix at each cycle.
........
r10187 | bugman | 2010-01-12 15:36:01 +0100 (Tue, 12 Jan 2010) | 5 lines

Added 12 unit tests for all notations of R -> Euler -> R.

This uses a random rotation matrix and sees if the matrix is returned.
........
r10188 | bugman | 2010-01-12 15:39:31 +0100 (Tue, 12 Jan 2010) | 6 lines

Important bug fix for the R_to_euler() function.

The special angle wrapping when beta was negative is only for the ijk Euler notation when i == k!
When i != k, another type of wrapping will be required.
........
r10197 | bugman | 2010-01-13 15:15:37 +0100 (Wed, 13 Jan 2010) | 3 lines

Removed the alpha Euler angle from the isotropic code frame order model.
........
r10204 | bugman | 2010-01-13 17:33:24 +0100 (Wed, 13 Jan 2010) | 5 lines

Bug fix for the frame order isotropic cone target function.

The optimised rotation matrix for the alignment tensor orientations was being applied in reverse!!!
........
r10205 | bugman | 2010-01-13 19:21:19 +0100 (Wed, 13 Jan 2010) | 6 lines

Reverted r10204 as this was a not a bug and the revision introduced a bug!!!

The command used was:
svn merge -r10204:10203 .
........
r10240 | bugman | 2010-01-15 15:35:22 +0100 (Fri, 15 Jan 2010) | 5 lines

Bug fixes for the code validator script.

The 4 character spacing check was faulty.
........
r10242 | bugman | 2010-01-18 17:15:33 +0100 (Mon, 18 Jan 2010) | 5 lines

Shifted the target function initialisation into _target_fn_setup().

This will be shared by the calculate() method.
........
r10243 | bugman | 2010-01-18 17:20:45 +0100 (Mon, 18 Jan 2010) | 3 lines

The calculate() method now uses _target_fn_setup() and stores the chi2 in the cdp.
........
r10244 | bugman | 2010-01-18 17:34:19 +0100 (Mon, 18 Jan 2010) | 3 lines

The number of elements in the atomic position arg is now checked to be 3.
........
r10245 | bugman | 2010-01-18 18:07:36 +0100 (Mon, 18 Jan 2010) | 5 lines

Removed the print out from _overfit_deselect_dummy().

This was totally unnecessary!
........
r10267 | bugman | 2010-01-20 12:01:00 +0100 (Wed, 20 Jan 2010) | 3 lines

Removed the beta angle folding from the frame order module as it was failing.
........
r10296 | bugman | 2010-01-25 11:13:06 +0100 (Mon, 25 Jan 2010) | 14 lines

Spun out the automatic model-free protocol code from the full_analysis.py script.

This is discussed in the post https://mail.gna.org/public/relax-devel/2010-01/msg00075.html.

The aim is to have a single code base for the automatic protocols for all UI designs (prompt,
script, GUI, web interface, etc.). The API interface will be via class initialisations. The
automatic model-free protocol has been placed into the dAuvergne_protocol class.

Future aims of this code is to have the UI fill a single data pipe with all the data required for
the analysis, and then to pass in this pipe into the protocol. Then the auto-analysis will copy
this info into any other data pipes it requires. This will allow for better GUI interaction, data
display, etc.
........
r10297 | bugman | 2010-01-25 11:33:22 +0100 (Mon, 25 Jan 2010) | 3 lines

Removed all the now unused imports and a useless comment.
........
r10298 | bugman | 2010-01-25 11:34:54 +0100 (Mon, 25 Jan 2010) | 3 lines

Updated the copyright notice.
........
r10299 | bugman | 2010-01-25 11:37:25 +0100 (Mon, 25 Jan 2010) | 3 lines

Fixed the import of the dAuvergne_protocol class.
........
r10300 | bugman | 2010-01-25 12:13:59 +0100 (Mon, 25 Jan 2010) | 3 lines

Modifications to the phthalic_acid_noes.py system test script to allow for standalone operation.
........
r10301 | bugman | 2010-01-25 12:40:54 +0100 (Mon, 25 Jan 2010) | 5 lines

Fixes for the N-state model for when only NOEs are present.

This fixes a bug introduced at r10243.
........
r10302 | bugman | 2010-01-25 12:54:34 +0100 (Mon, 25 Jan 2010) | 5 lines

Bug fix for the bug fix of r10301!

The bug fix actually introduced a bug, and this commit fixes that!
........
r10304 | bugman | 2010-01-25 14:25:32 +0100 (Mon, 25 Jan 2010) | 11 lines

Redesign of the setup of the names spaces for the user functions.

All the user functions and other objects located in the run() method namespace have been shifted
into the interpreter self._locals dictionary. These are then placed into the run() method namespace
by looping over the keys and using the 'locals()[key] = object' syntax. There may be better ways to
do this.

This has no visible effect on the prompt or script based interfaces. It will change how this is
seen by other modules though, and will allow the namespace to be more easily accessed.
........
r10305 | bugman | 2010-01-25 14:26:57 +0100 (Mon, 25 Jan 2010) | 3 lines

Removed some unused and commented out code.
........
r10306 | bugman | 2010-01-25 14:31:09 +0100 (Mon, 25 Jan 2010) | 5 lines

Eliminated the dummy mode.

This is only used by the fetch_docstrings script and will soon not be necessary.
........
r10307 | bugman | 2010-01-25 15:55:49 +0100 (Mon, 25 Jan 2010) | 7 lines

The relax base object is no longer passed into the class namespace of the user functions.

This was only being used for access to the intro flag (a few other cases exist, but these should be
fixed). Now a new container object with this flag is being passed in. This significantly
simplifies the code paths and removes the need for the test suite to create 'fake' relax instances.
........
r10308 | bugman | 2010-01-25 16:08:41 +0100 (Mon, 25 Jan 2010) | 7 lines

Modified how the Exec_info data container is handled.

The class was shifted from prompt.interpreter to prompt.base_class. In addition if not container
is passed into the user function classes, then one is created with the intro flag set to a default
of True.
........
r10309 | bugman | 2010-01-25 16:34:44 +0100 (Mon, 25 Jan 2010) | 8 lines

The prompt info has been shifted into the execution info container.

The sys.ps1, sys.ps2, and sys.ps3 prompts are still set, but these strings are hardcoded into the
execution info container. This allows the user functions to be imported and operate outside of the
prompt/scripting based interface, as the no longer require sys.ps3 to be set or the relax main
instance passed into them.
........
r10310 | bugman | 2010-01-25 16:39:34 +0100 (Mon, 25 Jan 2010) | 5 lines

Eliminated the fake_relax instance dependence.

This is no longer necessary as the user functions can be initialised without relax.
........
r10311 | bugman | 2010-01-25 16:53:14 +0100 (Mon, 25 Jan 2010) | 3 lines

Created the populate_self() method to place all user functions into the interpreter namespace.
........
r10312 | bugman | 2010-01-25 16:58:57 +0100 (Mon, 25 Jan 2010) | 5 lines

The relax main instance is no longer passed into the test suite.

This can be done as the prompt/script interface has been detached from relax.
........
r10313 | bugman | 2010-01-25 17:00:12 +0100 (Mon, 25 Jan 2010) | 5 lines

The relax main instance is no longer passed into the prompt/script interface.

This can be done as the prompt/script interface has been detached from relax.
........
r10314 | bugman | 2010-01-25 17:06:28 +0100 (Mon, 25 Jan 2010) | 3 lines

The relax main instance is no longer handled by the system test initialisation code.
........
r10315 | bugman | 2010-01-25 18:04:17 +0100 (Mon, 25 Jan 2010) | 5 lines

Created the SystemTestCase base class for all the system tests to use.

This base class initialises the relax interpreter within the TestCase class instances.
........
r10316 | bugman | 2010-01-25 18:13:12 +0100 (Mon, 25 Jan 2010) | 3 lines

The interpreter _on() method does not need to be called as user fn intros are turned on by default.
........
r10317 | bugman | 2010-01-25 18:52:04 +0100 (Mon, 25 Jan 2010) | 5 lines

Fixed all the calls to the user functions located in the interpreter class.

self.relax is no longer referenced and the user functions are now directly called.
........
r10318 | bugman | 2010-01-25 18:52:38 +0100 (Mon, 25 Jan 2010) | 3 lines

Fixed the script user function.
........
r10319 | bugman | 2010-01-25 18:54:20 +0100 (Mon, 25 Jan 2010) | 3 lines

Removed redundant and now non-functional code from interact_script().
........
r10320 | bugman | 2010-01-25 19:04:45 +0100 (Mon, 25 Jan 2010) | 3 lines

Comment fix.
........
r10321 | bugman | 2010-01-25 19:11:25 +0100 (Mon, 25 Jan 2010) | 6 lines

Update the user function print out functions.

_off() and _on() are no longer private, and accept the verbose keyword arg to allow the print out to
be suppressed.
........
r10322 | bugman | 2010-01-25 19:11:59 +0100 (Mon, 25 Jan 2010) | 3 lines

Alphabetical ordering of methods.
........
r10323 | bugman | 2010-01-25 19:21:05 +0100 (Mon, 25 Jan 2010) | 3 lines

The dAuvergne_protocol class now calls the user functions from the self.interpreter instance directly.
........
r10324 | bugman | 2010-01-25 19:26:36 +0100 (Mon, 25 Jan 2010) | 5 lines

Fix for the automatic model-free protocol in dAuvergne_protocol.

The sequence.read() and relax_data.read() user functions args are now sent in as keywords.
........
r10325 | bugman | 2010-01-25 20:31:25 +0100 (Mon, 25 Jan 2010) | 3 lines

Created the RelaxFileEmptyWarning class.
........
r10326 | bugman | 2010-01-25 20:36:30 +0100 (Mon, 25 Jan 2010) | 3 lines

Modified read_spin_data() to throw a warning rather than error when an empty file is encountered.
........

Merged revisions 10304-10326 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

........
r10304 | bugman | 2010-01-25 14:25:32 +0100 (Mon, 25 Jan 2010) | 11 lines

Redesign of the setup of the names spaces for the user functions.

All the user functions and other objects located in the run() method namespace have been shifted
into the interpreter self._locals dictionary. These are then placed into the run() method namespace
by looping over the keys and using the 'locals()[key] = object' syntax. There may be better ways to
do this.

This has no visible effect on the prompt or script based interfaces. It will change how this is
seen by other modules though, and will allow the namespace to be more easily accessed.
........
r10305 | bugman | 2010-01-25 14:26:57 +0100 (Mon, 25 Jan 2010) | 3 lines

Removed some unused and commented out code.
........
r10306 | bugman | 2010-01-25 14:31:09 +0100 (Mon, 25 Jan 2010) | 5 lines

Eliminated the dummy mode.

This is only used by the fetch_docstrings script and will soon not be necessary.
........
r10307 | bugman | 2010-01-25 15:55:49 +0100 (Mon, 25 Jan 2010) | 7 lines

The relax base object is no longer passed into the class namespace of the user functions.

This was only being used for access to the intro flag (a few other cases exist, but these should be
fixed). Now a new container object with this flag is being passed in. This significantly
simplifies the code paths and removes the need for the test suite to create 'fake' relax instances.
........
r10308 | bugman | 2010-01-25 16:08:41 +0100 (Mon, 25 Jan 2010) | 7 lines

Modified how the Exec_info data container is handled.

The class was shifted from prompt.interpreter to prompt.base_class. In addition if not container
is passed into the user function classes, then one is created with the intro flag set to a default
of True.
........
r10309 | bugman | 2010-01-25 16:34:44 +0100 (Mon, 25 Jan 2010) | 8 lines

The prompt info has been shifted into the execution info container.

The sys.ps1, sys.ps2, and sys.ps3 prompts are still set, but these strings are hardcoded into the
execution info container. This allows the user functions to be imported and operate outside of the
prompt/scripting based interface, as the no longer require sys.ps3 to be set or the relax main
instance passed into them.
........
r10310 | bugman | 2010-01-25 16:39:34 +0100 (Mon, 25 Jan 2010) | 5 lines

Eliminated the fake_relax instance dependence.

This is no longer necessary as the user functions can be initialised without relax.
........
r10311 | bugman | 2010-01-25 16:53:14 +0100 (Mon, 25 Jan 2010) | 3 lines

Created the populate_self() method to place all user functions into the interpreter namespace.
........
r10312 | bugman | 2010-01-25 16:58:57 +0100 (Mon, 25 Jan 2010) | 5 lines

The relax main instance is no longer passed into the test suite.

This can be done as the prompt/script interface has been detached from relax.
........
r10313 | bugman | 2010-01-25 17:00:12 +0100 (Mon, 25 Jan 2010) | 5 lines

The relax main instance is no longer passed into the prompt/script interface.

This can be done as the prompt/script interface has been detached from relax.
........
r10314 | bugman | 2010-01-25 17:06:28 +0100 (Mon, 25 Jan 2010) | 3 lines

The relax main instance is no longer handled by the system test initialisation code.
........
r10315 | bugman | 2010-01-25 18:04:17 +0100 (Mon, 25 Jan 2010) | 5 lines

Created the SystemTestCase base class for all the system tests to use.

This base class initialises the relax interpreter within the TestCase class instances.
........
r10316 | bugman | 2010-01-25 18:13:12 +0100 (Mon, 25 Jan 2010) | 3 lines

The interpreter _on() method does not need to be called as user fn intros are turned on by default.
........
r10317 | bugman | 2010-01-25 18:52:04 +0100 (Mon, 25 Jan 2010) | 5 lines

Fixed all the calls to the user functions located in the interpreter class.

self.relax is no longer referenced and the user functions are now directly called.
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r10318 | bugman | 2010-01-25 18:52:38 +0100 (Mon, 25 Jan 2010) | 3 lines

Fixed the script user function.
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r10319 | bugman | 2010-01-25 18:54:20 +0100 (Mon, 25 Jan 2010) | 3 lines

Removed redundant and now non-functional code from interact_script().
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r10320 | bugman | 2010-01-25 19:04:45 +0100 (Mon, 25 Jan 2010) | 3 lines

Comment fix.
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r10321 | bugman | 2010-01-25 19:11:25 +0100 (Mon, 25 Jan 2010) | 6 lines

Update the user function print out functions.

_off() and _on() are no longer private, and accept the verbose keyword arg to allow the print out to
be suppressed.
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r10322 | bugman | 2010-01-25 19:11:59 +0100 (Mon, 25 Jan 2010) | 3 lines

Alphabetical ordering of methods.
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r10323 | bugman | 2010-01-25 19:21:05 +0100 (Mon, 25 Jan 2010) | 3 lines

The dAuvergne_protocol class now calls the user functions from the self.interpreter instance directly.
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r10324 | bugman | 2010-01-25 19:26:36 +0100 (Mon, 25 Jan 2010) | 5 lines

Fix for the automatic model-free protocol in dAuvergne_protocol.

The sequence.read() and relax_data.read() user functions args are now sent in as keywords.
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r10325 | bugman | 2010-01-25 20:31:25 +0100 (Mon, 25 Jan 2010) | 3 lines

Created the RelaxFileEmptyWarning class.
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r10326 | bugman | 2010-01-25 20:36:30 +0100 (Mon, 25 Jan 2010) | 3 lines

Modified read_spin_data() to throw a warning rather than error when an empty file is encountered.
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Modified read_spin_data() to throw a warning rather than error when an empty file is encountered.

Created the RelaxFileEmptyWarning class.

Fix for the automatic model-free protocol in dAuvergne_protocol.

The sequence.read() and relax_data.read() user functions args are now sent in as keywords.

The dAuvergne_protocol class now calls the user functions from the self.interpreter instance directly.

Alphabetical ordering of methods.