Collect associated files at beginning of workflow

[tsalo]

Closes #237.

Changes proposed in this pull request

• Create new function, collect_run_data to collect M0 file, M0 metadata, SBRef, and ASLContext file, as available.
  • Feed these files/metadata into the appropriate interfaces in the CBF workflows, rather than trying to get those files with simple string manipulation within the interfaces.
• Move BIDSDataGrabber interface from niworkflows to main BIDS module.
  • Drop "func" from the search.
• Streamline M0 extraction.
  • I still want to consolidate the GE and non-GE M0 extraction code, since it's mostly the same. The only difficulty is that non-GE M0 extraction has a mask, while GE M0 extraction will use the M0 map to make the mask later.

Documentation that should be reviewed

[codecov-commenter]

Codecov Report

Patch coverage: 51.25% and project coverage change: +0.12 🎉

Comparison is base (075038d) 45.63% compared to head (ca7cd03) 45.76%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #246      +/-   ##
==========================================
+ Coverage   45.63%   45.76%   +0.12%     
==========================================
  Files         132      132              
  Lines       12483    12508      +25     
==========================================
+ Hits         5697     5724      +27     
+ Misses       6786     6784       -2     

Impacted Files	Coverage Δ
aslprep/utils/misc.py	68.19% <ø> (+1.92%)	⬆️
aslprep/workflows/asl/ge_utils.py	18.75% <ø> (-0.55%)	⬇️
aslprep/interfaces/ge.py	25.33% <7.27%> (+0.97%)	⬆️
aslprep/workflows/asl/gecbf.py	14.78% <11.11%> (+0.12%)	⬆️
aslprep/interfaces/cbf_computation.py	69.30% <54.54%> (+0.51%)	⬆️
aslprep/utils/bids.py	54.36% <68.42%> (+3.68%)	⬆️
aslprep/interfaces/bids.py	96.42% <94.44%> (-3.58%)	⬇️
aslprep/workflows/asl/base.py	79.48% <100.00%> (+1.86%)	⬆️
aslprep/workflows/asl/cbf.py	59.52% <100.00%> (+0.35%)	⬆️
aslprep/workflows/base.py	88.75% <100.00%> (+0.14%)	⬆️

... and 1 file with indirect coverage changes

Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here.

☔ View full report in Codecov by Sentry.
📢 Do you have feedback about the report comment? Let us know in this issue.