Refactor CuBIDS to support file collections

tsalo commented 8 months ago

Closes .

Changes proposed in this pull request

Add file collection entities (echo, mt, flip, part, and inv) to NON_KEY_ENTITIES.
Replace "modality" with "datatype" when applicable.
Draft function to resolve BIDS URIs in IntendedFor definitions (resolve_bids_uri).
Use BIDSLayout when possible, instead of string manipulation and globbing.

Documentation that should be reviewed

-

codecov-commenter commented 8 months ago

Codecov Report

Attention: 48 lines in your changes are missing coverage. Please review.

Comparison is base (39770dc) 62.13% compared to head (c81bd2e) 59.65%. Report is 2 commits behind head on main.

Files	Patch %	Lines
cubids/cubids.py	79.11%	33 Missing :warning:
cubids/utils.py	6.66%	14 Missing :warning:
cubids/workflows.py	0.00%	1 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #308 +/- ## ========================================== - Coverage 62.13% 59.65% -2.48% ========================================== Files 9 9 Lines 1582 1527 -55 ========================================== - Hits 983 911 -72 - Misses 599 616 +17 ```

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tsalo commented 8 months ago

The BOLD filenames seem to be working correctly, but the associated files, including fmaps, aren't being updated.

PennLINC / CuBIDS