Some small edits to the intro chapter of the relax user manual.
Fix for the relax version file for the relax user manual construction.

This was causing 'scons user_manual_pdf' and related targets to fail when a local git repository is
used (via git-svn).
Many improvements to the indexing in the relax user manual.
Bug fix for the page numbers in the index - these were often out by a few pages.

The makeindex command was being run too early in the repetitive LaTeX compilation chain, causing the
page numbers to be incorrect.  It is now run twice to fix the problem.
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>
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>
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>
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>
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>
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.
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>
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>
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>
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@nmr-relax.com>
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@nmr-relax.com>
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@nmr-relax.com>
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@nmr-relax.com>
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@nmr-relax.com>
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@nmr-relax.com>
Fix for the spectrum.read_intensities user function in the GUI.

The menu string was truncated to spectrum.read.