BUG: symlink dirs treated as files during indexing

[cookpa]

Fixes #1086

[effigies]

Thanks. We have a bids_examples fixture:

pybids/bids/conftest.py

Lines 41 to 52 in 95c7aa9

	def bids_examples():
	examples_dir = Path(os.getenv(
	"BIDS_EXAMPLES",
	Path(__file__).absolute().parent.parent / "bids-examples"
	))
	if not Path.is_dir(examples_dir / "ds001"):
	pytest.skip(
	f"BIDS examples missing from {examples_dir}. "
	"Override default location with BIDS_EXAMPLES environment variable."
	)
	return examples_dir

I think you should be able to create a test using one of the example datasets (https://github.com/bids-standard/bids-examples) that demonstrates this error?

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 89.77%. Comparing base (95c7aa9) to head (6ecffc7).
Report is 3 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1087      +/-   ##
==========================================
+ Coverage   89.75%   89.77%   +0.02%     
==========================================
  Files          63       63              
  Lines        7123     7141      +18     
  Branches     1364     1367       +3     
==========================================
+ Hits         6393     6411      +18     
  Misses        531      531              
  Partials      199      199              

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[effigies]

Thanks!

[effigies]

@cookpa Would you like to be listed as a contributor in releases? https://github.com/bids-standard/pybids/blob/master/.zenodo.json

[cookpa]

Sure, thanks! I'll edit the file

[effigies]

Feel free to just paste your snippet here and I'll include it in the release process. (A PR is also fine if you're already in the middle of it.)