FIX: Filtering in BIDSLayoutIndexer

[alperkent]

Resolves (partially) #1062.

[codecov]

Codecov Report

❌ Patch coverage is 33.33333% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 89.74%. Comparing base (20007e5) to head (9b9c74e).
⚠️ Report is 344 commits behind head on main.

Files with missing lines	Patch %	Lines
bids/layout/index.py	33.33%	1 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1063      +/-   ##
==========================================
- Coverage   89.80%   89.74%   -0.06%     
==========================================
  Files          63       63              
  Lines        7177     7179       +2     
  Branches     1374     1375       +1     
==========================================
- Hits         6445     6443       -2     
- Misses        532      535       +3     
- Partials      200      201       +1     

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[effigies]

I'm realizing that the **filters argument only says it applies to filtering files opened during get_metadata(). It was not intended to filter files.

That said, I can't think of a good reason to filter metadata but not files. @adelavega Do you remember the reasoning here?

[effigies]

This is the equivalent of

Suggested change

	# Skip entities that don't match the filter
	if self.filters and e.name and e.name in self.filters and m and m not in self.filters[e.name]:
	continue
	if m is not None:
	if m is not None and (e.name not in self.filters or m in listify(self.filters[e.name])):

[adelavega]

I'm not sure tbh.

I traced this back to; #560

Then Yarkoni moved it around.

Looks like we thought at the time that meta-data indexing was the most time consuming step, and implemented a way to skip meta-data indexing for a subset of files, rather then excluding them from being indexed altogether.