Connectivity: compute_matrices script

[EmmaRenauld]

Refactored the scil_connectivity_compute_matrices.py script:

• Took out the main computation part and put it in connectivity.connectivity file
• (also renamed connectivity.connectivity_tools to connectivity.matrix_too0ls)
• Clarified the docstring
  • Note that I already mention the scil_connectivity_compute_simple_matrix.py, which does not exist, but in the end I think that this PR is big enough. Will add it soon in another PR.
  • Please help me describe the --similarity option better.
• Removed the --maps option, as discussed with François and Arnaud offline.
• Removed one buggy logging.info: the -len(label_list) could end up in a negative number of total_elem if some diagonal values were not found.

• Now all headers compatibility are done before loading (except for the --similarity folder)

In short, the code is simplified a lot, but the result should be exactly the same, if you want to test with some data!

[codecov]

Codecov Report

Attention: Patch coverage is 62.03704% with 82 lines in your changes missing coverage. Please review.

Project coverage is 68.84%. Comparing base (1d6f848) to head (8b80520).
Report is 31 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1031      +/-   ##
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+ Coverage   68.78%   68.84%   +0.06%     
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  Files         429      433       +4     
  Lines       22265    22460     +195     
  Branches     3324     3035     -289     
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+ Hits        15314    15462     +148     
- Misses       5665     5695      +30     
- Partials     1286     1303      +17     

Components	Coverage Δ
Scripts	69.89% <72.64%> (+0.24%)	⬆️
Library	67.37% <49.49%> (-0.17%)	⬇️