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[r20531] by bugman

Added some hyphenation rules for better formatting in the user manual.

For this, the external hyphenation.tex has been created.

2013-08-04 20:43:00 Tree
[r20530] by bugman

Added extensive cross-referencing to the index of the relax user manual.

2013-08-04 20:11:28 Tree
[r20529] by bugman

Added subsubindexing for the optimisation algorithm index entries.

2013-08-04 19:45:06 Tree
[r20528] by bugman

Fix for the spectrum.read_intensities user function docstring.

Grammatically, the text "spectrum ID's" should be "spectrum IDs". The problem though was that this
text was strangely causing the user manual compilation to fail.

2013-08-04 19:37:50 Tree
[r20527] by bugman

Changed the chapter layout of the relax user manual.

The development chapter has been moved forwards.

2013-08-04 18:07:44 Tree
[r20526] by bugman

Creation of the optimisation chapter of the relax user manual.

The main text of this chapter originates as part of the model-free chapter. As this most of this
text was not model-free specific, it has been spun out as its own chapter. Text has also been taken
from the "Optimisation of relaxation data – values, gradients, and Hessians" chapter.

The indexing for the optimisation topics has also been improved.

2013-08-04 18:06:05 Tree
[r20525] by bugman

The relax user manual is now broken into parts.

The higher level LaTeX part command is now used to group related chapters. This should make it
easier for users to navigate this huge thing.

2013-08-04 12:34:35 Tree
[r20524] by bugman

Added the tp02 module to the lib.dispersion package __all__ list.

2013-08-03 13:24:39 Tree
[r20523] by bugman

Merged revisions 20501-20522 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r20501 | bugman | 2013-08-02 13:39:53 +0200 (Fri, 02 Aug 2013) | 7 lines

Removed the flag for single_spectrum.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinnet _aaattt_ gmail_dot_com

Signed-off-by: Edward d'Auvergne <edward _att_ nmr-relax _dott_ com>
........
r20502 | bugman | 2013-08-02 13:40:28 +0200 (Fri, 02 Aug 2013) | 7 lines

Fixed wrong reference to Sparky format.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinset _aaattt_ gmail_dot_com

Signed-off-by: Edward d'Auvergne <edward _att_ nmr-relax _dott_ com>
........
r20503 | bugman | 2013-08-02 13:51:50 +0200 (Fri, 02 Aug 2013) | 7 lines

Modfied the intensity list to handle intensities for all spectra per spin.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinset _aaattt_ gmail_dot_com

Signed-off-by: Edward d'Auvergne <edward _att_ nmr-relax _dott_ com>
........
r20504 | bugman | 2013-08-02 13:52:16 +0200 (Fri, 02 Aug 2013) | 7 lines

Fixed the extraction of NMRPipe seriestab data in pipe_control.spectrum.read().

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinset _aaattt_ gmail_dot_com

Signed-off-by: Edward d'Auvergne <edward _att_ nmr-relax _dott_ com>
........
r20505 | bugman | 2013-08-02 13:53:52 +0200 (Fri, 02 Aug 2013) | 7 lines

Fix for handling reading spin of type heteronuc='NE1' and proton='HE1'.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinset _aaattt_ gmail_dot_com

Signed-off-by: Edward d'Auvergne <edward _att_ nmr-relax _dott_ com>
........
r20506 | bugman | 2013-08-02 14:00:20 +0200 (Fri, 02 Aug 2013) | 9 lines

Adding NMR seriesTab data file for a multiple column / multiple spectrum formatted file.

This file is from https://gna.org/support/download.php?file_id=18618 attached to the support request
https://gna.org/support/?3043 by Troels Linnet.

This is if the command:
seriesTab -in ../../peaks.dat -out seriesTab_multi.ser -list nmrfiles.list -sum -dx 1 -dy 1

where nmrfiles.list contains file reference to 10 .ft2 files.
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r20507 | bugman | 2013-08-02 17:35:01 +0200 (Fri, 02 Aug 2013) | 7 lines

Fix for unit test of nmrpipe.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinset _aaattt_ gmail_dot_com

Signed-off-by: Edward d'Auvergne <edward _att_ nmr-relax _dott_ com>
........
r20508 | bugman | 2013-08-02 17:35:57 +0200 (Fri, 02 Aug 2013) | 7 lines

Replacing a pointer-reference structure to an empty creation of list of lists.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinset _aaattt_ gmail_dot_com

Signed-off-by: Edward d'Auvergne <edward _att_ nmr-relax _dott_ com>
........
r20509 | bugman | 2013-08-02 17:55:23 +0200 (Fri, 02 Aug 2013) | 7 lines

The ID of spins in seriesTab_multi.ser was not formatted correctly to SPARKY format.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinset _aaattt_ gmail_dot_com

Signed-off-by: Edward d'Auvergne <edward _att_ nmr-relax _dott_ com>
........
r20510 | bugman | 2013-08-02 20:56:54 +0200 (Fri, 02 Aug 2013) | 14 lines

Added system test for reading of a multi column formatted NMRPipe seriesTab file.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Generated the reference data in Excell, for the system test.
The spectrum ID's are auto generated by supplying the keyword spectrum_id='auto'.
The first few tests was matched against integers rather than floats. Adding '.0' to the end of each number.

Spaces added after the commas in the self.assertAlmostEqual() calls.
The 2to3 conversion program (for Python 2 to Python 3 conversion) highlights this issue.

Troels E. Linnet provided this patch. Commit by: tlinset _aaattt_ gmail_dot_com

Signed-off-by: Edward d'Auvergne <edward@...>
........
r20511 | bugman | 2013-08-02 20:58:55 +0200 (Fri, 02 Aug 2013) | 7 lines

Added check for number of supplied spectra ID's and the number of returned intensity columns.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinset _aaattt_ gmail_dot_com

Signed-off-by: Edward d'Auvergne <edward@...>
........
r20512 | bugman | 2013-08-02 20:58:57 +0200 (Fri, 02 Aug 2013) | 7 lines

Made it possible to autogenerate spectrum ID's, if spectrum_id='auto'.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinset _aaattt_ gmail_dot_com

Signed-off-by: Edward d'Auvergne <edward@...>
........
r20513 | bugman | 2013-08-02 20:58:59 +0200 (Fri, 02 Aug 2013) | 7 lines

Remove from datalist where empty list starts. These are created where spins are skipped for ID = '?-?'.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinset _aaattt_ gmail_dot_com

Signed-off-by: Edward d'Auvergne <edward@...>
........
r20514 | bugman | 2013-08-02 20:59:00 +0200 (Fri, 02 Aug 2013) | 7 lines

Moved checks for matching length of spectrum IDs and intensities columns.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinset _aaattt_ gmail_dot_com

Signed-off-by: Edward d'Auvergne <edward@...>
........
r20515 | bugman | 2013-08-02 20:59:02 +0200 (Fri, 02 Aug 2013) | 8 lines

Moved the adding function of adding the spectrum id (and ncproc) to the relax data store.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Shifting it to later will prevent the cdp.spectrum_ids list to be populated after the user calls the user function incorrectly.
Troels E. Linnet provided this patch. Commit by: tlinnet _aaattt_ gmail_dot_com

Signed-off-by: Edward d'Auvergne <edward@...>
........
r20516 | bugman | 2013-08-02 21:29:16 +0200 (Fri, 02 Aug 2013) | 3 lines

Fix for the spectrum.read_intensities user function in the GUI.

The menu string was truncated to spectrum.read.
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r20517 | bugman | 2013-08-02 22:07:49 +0200 (Fri, 02 Aug 2013) | 7 lines

Added epydoc documentation in pipe_control\spectrum.py .read() when supplying keyword 'auto'.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinnet _aaattt_ gmail_dot_com

Signed-off-by: Edward d'Auvergne <edward@...>
........
r20518 | bugman | 2013-08-02 22:07:51 +0200 (Fri, 02 Aug 2013) | 7 lines

Added GUI description for when supplying 'auto' to the spectrum_id.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinnet _aaattt_ gmail_dot_com

Signed-off-by: Edward d'Auvergne <edward@...>
........
r20519 | bugman | 2013-08-02 22:07:52 +0200 (Fri, 02 Aug 2013) | 7 lines

Added a stub GUI describtion in the File formats, for NMRPipe seriesTab.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinnet _aaattt_ gmail_dot_com

Signed-off-by: Edward d'Auvergne <edward@...>
........
r20520 | bugman | 2013-08-03 00:08:24 +0200 (Sat, 03 Aug 2013) | 8 lines

Fix for two spaces are used after a period in documentation.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

relax uses the double space for easier for the eyes to pick up the sentence structure.
Troels E. Linnet provided this patch. Commit by: tlinnet _aaattt_ gmail_dot_com

Signed-off-by: Edward d'Auvergne <edward@...>
........
r20521 | bugman | 2013-08-03 00:08:26 +0200 (Sat, 03 Aug 2013) | 8 lines

Fix for two spaces are used after a period in documentation.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

relax uses the double space for easier for the eyes to pick up the sentence structure.
Troels E. Linnet provided this patch. Commit by: tlinnet _aaattt_ gmail_dot_com

Signed-off-by: Edward d'Auvergne <edward@...>
........
r20522 | bugman | 2013-08-03 00:08:28 +0200 (Sat, 03 Aug 2013) | 8 lines

Fix for two spaces are used after a period in documentation.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

relax uses the double space for easier for the eyes to pick up the sentence structure.
Troels E. Linnet provided this patch. Commit by: tlinnet _aaattt_ gmail_dot_com

Signed-off-by: Edward d'Auvergne <edward@...>
........

2013-08-03 11:26:56 Tree
[r20522] by bugman

Fix for two spaces are used after a period in documentation.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

relax uses the double space for easier for the eyes to pick up the sentence structure.
Troels E. Linnet provided this patch. Commit by: tlinnet _aaattt_ gmail_dot_com

Signed-off-by: Edward d'Auvergne <edward@...>

2013-08-02 22:08:28 Tree
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