Deep CNS scripts checking and example cleaning

[amjjbonvin]

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A careful check of all output files of the various examples revealed several small issues like duplication of some parameters, missing variables in some CNS scripts, inconsistencies between files (format mainly) and example config files.

This pull request resolves all those issues.

[codecov]

Codecov Report

Attention: 1 lines in your changes are missing coverage. Please review.

Comparison is base (18a5528) 72.54% compared to head (a0515fc) 72.55%.

Files	Patch %	Lines
src/haddock/libs/libparallel.py	83.33%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #763   +/-   ##
=======================================
  Coverage   72.54%   72.55%           
=======================================
  Files          80       80           
  Lines        7566     7571    +5     
=======================================
+ Hits         5489     5493    +4     
- Misses       2077     2078    +1     

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[amjjbonvin]

@rvhonorato - tests are failing on my mac because of a difference in the 15th digit in the contacts module test...
May-be an overkill? I did not touch that module. They do pass here however.

========================================================================================== FAILURES ==========================================================================================
______________________________________________________________________________ test_make_ideogram_arc_moduloAB _______________________________________________________________________________

    def test_make_ideogram_arc_moduloAB():
        """Test usage of moduloAB while providing outranged angle values."""
        nb_points = 2
        arc_positions = make_ideogram_arc(1.1, (1, -1), nb_points=nb_points)
        excpected_output = np.array([
            0.5943325364549538 + 0.9256180832886862j,
            0.5943325364549535 - 0.9256180832886863j,
            ])
        assert arc_positions.shape == excpected_output.shape
        for i in range(nb_points):
>           assert arc_positions[i] == excpected_output[i]
E           assert (0.5943325364549534-0.9256180832886863j) == (0.5943325364549535-0.9256180832886863j)

As for the alascan integration test, if might need to be revisited...

[rvhonorato]

This test is wrong, looks like we missed it during #731. It's comparing two arrays down to its numeric precision - should be using numpy.isclose.

git blame says @VGPReys added it, could you open another PR and change it?

[amjjbonvin]

While this pull request might appear rather large, the changes are somewhat limited:

• 54 of 98 files are cleaned config file examples (harmonisation and cleaning unneeded paramters/steps)

• 26 files are topo/param files, mainly with harmonised CNS verbosity settings.

• A few files from the toppar directory have large differences because their line endings were corrected from Windows to Linux. Their content is further the same.

• Most of the remaining files are CNS scripts with rather minor corrections to remove error messages (e.g. correcting a variable name). Some missing in a module were added.

[rvhonorato]

It's impossible for me to review 1.000+ lines, if you think its ok just go ahead and merge it!

[amjjbonvin]

It is possible :-) A lot of those 1000 lines are simply files in which I corrected Windows style line ending into Linux. All others have very similar changes.