Tractogram scripts parts2

[EmmaRenauld]

Quick description

• Using the hdf5 methods from part 1 in scripts where I found hdf5 usage.
• scil_tractogram_commit: clarifying. Adding test coverage.
• scil_tractogram_compress: ok!
• scil_tractogram_compute_density_map: ok!
• scil_tractogram_compute_TODI: clarifying. After discussion with @frheault , moving option --normalize out of the if.
• scil_tractogram_convert: ok!
• scil_tractogram_convert_hdf5_to_trk: Clarifying help. More checks. --labels_list and --save_empty were both needed OR both not used. Merged the two args.

Type of change

Check the relevant options.

• [x] Bug fix (non-breaking change which fixes an issue)
• [ ] New feature (non-breaking change which adds functionality)
• [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
• [ ] This change requires a documentation update

Checklist

• [x] My code follows the style guidelines of this project (run autopep8)
• [x] I added relevant citations to scripts, modules and functions docstrings and descriptions
• [x] I have performed a self-review of my code
• [x] I have commented my code, particularly in hard-to-understand areas
• [x] I have made corresponding changes to the documentation
• [x] My changes generate no new warnings
• [x] I moved all functions from the script file (except the argparser and main) to scilpy modules
• [x] I have added tests that prove my fix is effective or that my feature works
• [x] New and existing unit tests pass locally with my changes

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 66.87117% with 54 lines in your changes are missing coverage. Please review.

Project coverage is 68.05%. Comparing base (377bed3) to head (bc1c8f7). Report is 18 commits behind head on master.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #954 +/- ## ========================================== + Coverage 66.98% 68.05% +1.06% ========================================== Files 396 397 +1 Lines 21411 21372 -39 Branches 3253 3234 -19 ========================================== + Hits 14343 14545 +202 + Misses 5752 5515 -237 + Partials 1316 1312 -4 ``` | [Components](https://app.codecov.io/gh/scilus/scilpy/pull/954/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/954/components?src=pr&el=component&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scilus) | `69.07% <68.49%> (+0.99%)` | :arrow_up: | | [Library](https://app.codecov.io/gh/scilus/scilpy/pull/954/components?src=pr&el=component&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scilus) | `66.51% <52.94%> (+1.20%)` | :arrow_up: |

[EmmaRenauld]

Thanks, @AlexVCaron, it seems to have worked!