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[Savannah-register-public] [task #14528] Submission of relax
From: |
Edward d'Auvergne |
Subject: |
[Savannah-register-public] [task #14528] Submission of relax |
Date: |
Thu, 31 Aug 2017 05:44:55 -0400 (EDT) |
User-agent: |
Mozilla/5.0 (X11; Linux x86_64; rv:52.0) Gecko/20100101 Firefox/52.0 |
Follow-up Comment #8, task #14528 (project administration):
> Thank you, great work!
>
> Unfortunately, some issues still need resolving.
>
> Licensing of some files in extern/ is not very clear,
> for example, extern/sobol/sobol_lib.py has no copyright notices,
> and it could have more unambiguous license notice;
> extern/sobol/test.py has no notices at all.
The Sobol package is fixed
<https://sourceforge.net/p/nmr-relax/code/ci/21dc63c15832fb521cc833c7efeb0700254be7b7/>
and a numdifftools README added
<https://sourceforge.net/p/nmr-relax/code/ci/887528de2c741c63ba3bd99896901c56a32f6501/>.
> Images like graphics/screenshots/dispersion_analysis/disp_64_N.eps.gz
> and docs/latex/images/pec_diag.eps suggest they were exported from GIMP
> or created with gnuplot, so your users would have to provide
> the source code for those files.
These are mostly found in the _test_suite/shared_data_ directories, and
pointed to in the manual as these are used for student tutorials. For example
_disp_64_N.eps.gz_ is used at:
http://www.nmr-relax.com/manual/Dispersion_GUI_mode_inspection_of_the_results.html
This is a section from:
http://www.nmr-relax.com/manual/The_relaxation_dispersion_auto_analysis_in_the_GUI.html
And the data, distributed with relax, to load and auto-generate this graph is
referenced at:
http://www.nmr-relax.com/manual/Dispersion_GUI_mode_loading_the_data.html
where it says _"In this tutorial, the Sparky formatted peak lists in the
test_suite/shared_data/dispersion/Hansen/500_MHz and
test_suite/shared_data/dispersion/Hansen/800_MHz directories will be
loaded."_ This is the base data for relax for generating the plots.
The _docs/latex/images/pec_diag.eps_ diagram is different in that it was
plotted in Mathematica. The base data generation was considered so trivial
that the ~5 line script and 1-2 line Mathematica notebook was not kept. I
have recreated a small relax script to quickly regenerate the data
<https://sourceforge.net/p/nmr-relax/code/ci/master/tree/docs/latex/images/pec_diag.py>.
> Likewise, graphics/screenshots/noe_analysis/grace.svg seems generated
> from a different source.
Such plots should have had the base plotting files added. I'm not sure why
some were missed. This example is now included
<https://sourceforge.net/p/nmr-relax/code/ci/master/tree/graphics/screenshots/noe_analysis/grace.agr>.
In addition, the Xmgrace plot file for
_graphics/screenshots/xmgrace_peak_intensities.agr_ has been added as well
<https://sourceforge.net/p/nmr-relax/code/ci/99721d296ff41d132086b0346c5182288060bd4f/>.
As far as I can tell, everything else is either in _test_suite/shared_data/_
or the original sources are there. Since the start of the project, we have
made a lot of effort to obtain all original sources to include within the
relax distribution. Any discrepancies are by accident.
> Then, the documentation has some terminological inconsistencies:
> in files like docs/latex/develop.tex the operating system sometimes is
> called "Linux" rather than "GNU/Linux"; also, some
TeX files speak
> about "open source"; Savannah supports
> free software.
Our intent was to use "GNU/Linux", and most references use this.
This is now updated
<https://sourceforge.net/p/nmr-relax/code/ci/22032805a5405a799a8fa27dcebca6ff32eb5e30/>.
All other references are either non-mutable quotes, old commit messages, or
the index reference back to "GNU/Linux".
We have also switched all "open source" references, excluding the
non-mutable ones, with "free sofware"
<https://sourceforge.net/p/nmr-relax/code/ci/81e854e6402697907374cc1355f1bfb4ac03f5af/>.
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