relax SVN archive

More removal of run arguments.

These changes are part of the new design.

Added the temporary directory path to the state.save() function.

Completed the coding for the system tests temporary directory used by external programs.

This follows the thread started by Edward d'Auvergne at:
https://mail.gna.org/public/relax-devel/2008-07/msg00056.html (message ID:
7f080ed10807310053w4cf118bajab47aad7536db4dc@...).

Started to implement system tests for the use of the external program Dasha.

This code is mimicked on the palmer code for testing interaction with ModelFree4.

Removed many unused imports.

More conversions of 'relax.IO' to 'relax_io'.

Old instances are now completely converted.

Converted 'self.relax.IO' instances to 'relax_io' and added corresponding imports.

Added a missing import.

Added some basic BMRB file format displaying/reading/writing functions.

The STAR format parser and model-free specific code needs to be implemented before this code will
work.

Merged revisions 7022-7028,7030-7040 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

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r7022 | semor | 2008-07-29 22:38:16 +0200 (Tue, 29 Jul 2008) | 3 lines

Simplified the code by removing useless lines as well as converting one remaining flag to bool.
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r7023 | semor | 2008-07-29 22:44:42 +0200 (Tue, 29 Jul 2008) | 3 lines

Removed an unused import.
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r7024 | semor | 2008-07-29 23:01:07 +0200 (Tue, 29 Jul 2008) | 3 lines

Added the "dir" variable to the palmer commands.
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r7025 | semor | 2008-07-29 23:04:16 +0200 (Tue, 29 Jul 2008) | 3 lines

Uncommented a line as this was a temporary and local change which should not have been committed.
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r7026 | semor | 2008-07-29 23:15:27 +0200 (Tue, 29 Jul 2008) | 9 lines

A temporary directory is now created for ModelFree4 output.

This directory is only created and the function for deleting it still needs to be added.

This follows the proposal of Edward d'Auvergne at:
https://mail.gna.org/public/relax-devel/2008-07/msg00038.html (message ID:
7f080ed10807290219m18601df6nf2df7e91848a9680@...).
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r7027 | semor | 2008-07-29 23:20:16 +0200 (Tue, 29 Jul 2008) | 3 lines

Added the setUp() and tearDown() functions to the palmer system test code.
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r7028 | semor | 2008-07-29 23:40:09 +0200 (Tue, 29 Jul 2008) | 7 lines

Improved the tearDown() function so the temporary directory is deleted after the test.

This follows r7026 (http://svn.gna.org/viewcvs/relax?rev=7026&view=rev) and the proposal of Edward
d'Auvergne at: https://mail.gna.org/public/relax-devel/2008-07/msg00038.html (message ID:
7f080ed10807290219m18601df6nf2df7e91848a9680@...).
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r7030 | semor | 2008-07-30 18:13:00 +0200 (Wed, 30 Jul 2008) | 14 lines

Changed the location of the temporary directory creation command.

This change now avoids relax from crashing on Windows when the directory does not exist and follows
a post by Ed at: https://mail.gna.org/public/relax-devel/2008-07/msg00047.html (message ID:
7f080ed10807291455k1d11d51fpdb2382806e55efdb@...).

Note that the directory separators are fine in Windows using the current syntax ('/').

Also, note that this change is temporary as the temporary directory should be placed in an user
accessible location and created as proposed by Ed in a post at:
https://mail.gna.org/public/relax-devel/2008-07/msg00048.html (message ID:
7f080ed10807291507x5b6aab2fv820a6fc219fc7e2b@...).
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r7031 | semor | 2008-07-30 20:09:59 +0200 (Wed, 30 Jul 2008) | 3 lines

Removed a deprecated run argument.
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r7032 | semor | 2008-07-30 20:39:37 +0200 (Wed, 30 Jul 2008) | 3 lines

Converted run arguments to pipes.
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r7033 | semor | 2008-07-30 20:45:55 +0200 (Wed, 30 Jul 2008) | 3 lines

Removed run arguments.
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r7034 | semor | 2008-07-30 20:54:50 +0200 (Wed, 30 Jul 2008) | 3 lines

More conversions to the new design.
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r7035 | semor | 2008-07-30 21:00:30 +0200 (Wed, 30 Jul 2008) | 3 lines

More conversion to the new design.
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r7036 | semor | 2008-07-30 21:10:06 +0200 (Wed, 30 Jul 2008) | 5 lines

Other conversions to the new design.

Removal of run arguments and introduction of the exists_mol_res_spin_data() function.
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r7037 | semor | 2008-07-30 21:13:07 +0200 (Wed, 30 Jul 2008) | 3 lines

Still the same conversions to the desing concerning the check for the loading of the sequence.
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r7038 | semor | 2008-07-30 21:22:46 +0200 (Wed, 30 Jul 2008) | 3 lines

Corrected a comment to the new design.
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r7039 | semor | 2008-07-30 21:26:04 +0200 (Wed, 30 Jul 2008) | 3 lines

Conversion of a run argument to pipe, etc.
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r7040 | semor | 2008-07-30 22:37:09 +0200 (Wed, 30 Jul 2008) | 7 lines

Changed the temporary directory to the system's default location using 'tempfile.mkdtemp'.

This is in response to a post of Edward d'Auvergne at:
https://mail.gna.org/public/relax-devel/2008-07/msg00048.html (message ID:
7f080ed10807291507x5b6aab2fv820a6fc219fc7e2b@...).
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