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[bot]]

Codecov Report

Attention: Patch coverage is 62.21198% with 82 lines in your changes missing coverage. Please review.

Project coverage is 68.99%. Comparing base (546f1a9) to head (ea79c39). Report is 209 commits behind head on master.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #1031 +/- ## ========================================== + Coverage 68.89% 68.99% +0.09% ========================================== Files 434 439 +5 Lines 22646 22895 +249 Branches 3078 3103 +25 ========================================== + Hits 15603 15796 +193 - Misses 5727 5778 +51 - Partials 1316 1321 +5 ``` | [Components](https://app.codecov.io/gh/scilus/scilpy/pull/1031/components?src=pr&el=components&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scilus) | Coverage Δ | | |---|---|---| | [Scripts](https://app.codecov.io/gh/scilus/scilpy/pull/1031/components?src=pr&el=component&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scilus) | `70.09% <72.64%> (+0.47%)` | :arrow_up: | | [Library](https://app.codecov.io/gh/scilus/scilpy/pull/1031/components?src=pr&el=component&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scilus) | `67.47% <50.00%> (-0.43%)` | :arrow_down: |

[EmmaRenauld]

I used the new script on older data to compare before vs after.

Could you please send me your data? Thanks!

[EmmaRenauld]

This is my error:

Sorry @frheault . Fixed!