Feature/surface feature

[frheault]

Quick description

Getting ready for the next DIPY release including the StatefulSurface.
A lot of the changed files were about warning from DIPY about keyword arguments needing to be name (instead of being used like positional)

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Type of change

Check the relevant options.

• 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

Provide data, screenshots, command line to test (if relevant)

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Checklist

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

[frheault]

@arnaudbore This was old, but it was waiting on 1.12 !

[codecov]

Codecov Report

❌ Patch coverage is 59.21053% with 93 lines in your changes missing coverage. Please review.
✅ Project coverage is 72.26%. Comparing base (7de90f3) to head (e04883d).

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1195      +/-   ##
==========================================
- Coverage   72.53%   72.26%   -0.27%     
==========================================
  Files         297      300       +3     
  Lines       25885    26060     +175     
  Branches     3644     3668      +24     
==========================================
+ Hits        18775    18833      +58     
- Misses       5580     5689     +109     
- Partials     1530     1538       +8     

Flag	Coverage Δ
smoketests	69.46% <58.77%> (-0.25%)	⬇️
unittests	14.00% <5.26%> (-0.08%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Components	Coverage Δ
Scripts	74.85% <55.92%> (-0.23%)	⬇️
Library	69.15% <65.78%> (-0.33%)	⬇️

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[ThoumyreStanislas]

For the most part I have nothing to say about it, I'm not sure I understood all the subtleties in the entirety of the changes but the code works for all the modified scripts. There might be a little lack of description for the custom color scripts but otherwise everything seems good. Well done!

[arnaudbore]

Some comments but we are getting there. Can you check codecoverage and don't hesitate if you need more data, I can quickly fix this.