Add options to subset atlases

[tsalo]

Closes #995.

Changes proposed in this pull request

• Add two mutually exclusive command-line parameters, --skip-parcellation and --atlases, to control which atlases are used for parcellation.
  • --skip-parcellation will set the atlases parameter to an empty list ([]), so that no atlases are used for parcellation, and the parcellation workflow doesn't happen.
  • --atlases will set the atlases parameter. Users can provide a space-separated list of which atlases they actually want to use. The default is to use all of the atlases in XCP-D.

Documentation that should be reviewed

[mattcieslak]

This looks great. One question - is using atlases more intuitive for you than atlas_names? It's ultimately being used as an atlas ID

[tsalo]

This looks great. One question - is using atlases more intuitive for you than atlas_names? It's ultimately being used as an atlas ID

Thanks! I think atlases makes more sense as a command-line parameter, since it's shorter and equally clear. I used atlas_names in internal functions before because they weren't user-facing, but since now atlases will be what users see in the command line, I want to make the variable names consistent throughout the package.

[codecov]

Codecov Report

Attention: Patch coverage is 96.00000% with 6 lines in your changes missing coverage. Please review.

Project coverage is 82.51%. Comparing base (b93205e) to head (7a53363).
Report is 139 commits behind head on main.

Files with missing lines	Patch %	Lines
xcp_d/interfaces/connectivity.py	71.42%	1 Missing and 1 partial ⚠️
xcp_d/workflows/cifti.py	66.66%	0 Missing and 2 partials ⚠️
xcp_d/workflows/bold.py	83.33%	0 Missing and 1 partial ⚠️
xcp_d/workflows/concatenation.py	94.73%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff            @@
##           main    #1034       +/-   ##
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+ Coverage      0   82.51%   +82.51%     
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  Files         0       48       +48     
  Lines         0     5846     +5846     
  Branches      0      786      +786     
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+ Hits          0     4824     +4824     
- Misses        0      826      +826     
- Partials      0      196      +196     

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