Replace smriprep calls with dependency calls

[tsalo]

Closes None, but works toward #199.

Changes proposed in this pull request

• The classes and functions used directly in aslprep from smriprep are:
  • init_anat_preproc_wf
  • ReconAll
  • _bids_relative
  • collect_derivatives
• I tried copying the code from smriprep 0.6.1 into the aslprep folder to see what the diff was. There weren't any meaningful differences, except maybe the removal of surfaces from io_spec.json in the aslprep version.

[codecov-commenter]

Codecov Report

Base: 39.95% // Head: 39.64% // Decreases project coverage by -0.32% ⚠️

Coverage data is based on head (f890ebd) compared to base (92f2ede).
Patch coverage: 100.00% of modified lines in pull request are covered.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #217      +/-   ##
==========================================
- Coverage   39.95%   39.64%   -0.32%     
==========================================
  Files         192      176      -16     
  Lines       19940    18868    -1072     
==========================================
- Hits         7967     7480     -487     
+ Misses      11973    11388     -585     

Impacted Files	Coverage Δ
aslprep/interfaces/reports.py	91.30% <100.00%> (ø)
aslprep/niworkflows/viz/utils.py	55.78% <100.00%> (ø)
aslprep/workflows/asl/outputs.py	44.10% <100.00%> (ø)
aslprep/workflows/base.py	88.46% <100.00%> (ø)
aslprep/niworkflows/anat/__init__.py	0.00% <0.00%> (-100.00%)	⬇️
aslprep/niworkflows/interfaces/ants.py	0.00% <0.00%> (-57.82%)	⬇️
aslprep/niworkflows/interfaces/nitransforms.py	0.00% <0.00%> (-50.00%)	⬇️
aslprep/niworkflows/anat/skullstrip.py	0.00% <0.00%> (-30.00%)	⬇️
aslprep/niworkflows/anat/ants.py	0.00% <0.00%> (-12.36%)	⬇️
aslprep/niworkflows/interfaces/masks.py	46.74% <0.00%> (-11.84%)	⬇️
... and 3 more

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[mattcieslak]

Glad to be rid of aslprep.smriprep!