Accept external atlases by searching BIDS-Atlas datasets

[tsalo]

Closes #1226.

Allow users to provide paths to BIDS-Atlas datasets via the --datasets (renamed from --derivatives) parameter, as well as names of atlases in those datasets via the --atlases parameter.

Atlases need to be in fsLR-32k space (for CIFTI processing) or MNIInfant/MNI152NLin6Asym/MNI152NLin2009cAsym space (for NIfTI processing). This space/resolution limitation is hopefully only temporary, since I ultimately want to accept almost any input space. See #1076.

Changes to inputs

• No changes to inputs

Changes to outputs

• Output atlas sidecar files (i.e., JSONs in the atlases dataset) now share all of the same entities as the image file. Before they only had the atlas entity.

Internal changes

• Reorganize internal atlases into a BIDS-Atlas dataset. The 4S atlases from AtlasPack are in a BIDS-Atlas dataset now as well (from xcpd_build).

[codecov]

Codecov Report

Attention: Patch coverage is 91.42857% with 15 lines in your changes missing coverage. Please review.

Project coverage is 78.80%. Comparing base (68caadf) to head (dc18585).
Report is 42 commits behind head on main.

Files with missing lines	Patch %	Lines
xcp_d/utils/atlas.py	88.46%	3 Missing and 3 partials ⚠️
xcp_d/utils/utils.py	89.28%	0 Missing and 3 partials ⚠️
xcp_d/interfaces/connectivity.py	66.66%	2 Missing ⚠️
xcp_d/cli/combineqc.py	0.00%	1 Missing ⚠️
xcp_d/cli/parser.py	85.71%	0 Missing and 1 partial ⚠️
xcp_d/workflows/anatomical/parcellation.py	95.65%	0 Missing and 1 partial ⚠️
xcp_d/workflows/bold/cifti.py	50.00%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1265      +/-   ##
==========================================
+ Coverage   78.63%   78.80%   +0.16%     
==========================================
  Files          59       59              
  Lines        7308     7360      +52     
  Branches     1106     1136      +30     
==========================================
+ Hits         5747     5800      +53     
+ Misses       1273     1267       -6     
- Partials      288      293       +5     

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[tsalo]

Tests are passing, coverage is up, and the new behavior is documented, so I think we're good to go!