Merge pull request #99 from templateflow/fix/bids-dotfolders

FIX: Preempt ``BIDSLayout`` from indexing dot-folders

Author: oesteban

docs/environment.yml

@@ -203,5 +203,5 @@ dependencies:
     - formulaic==0.3.4
     - nibabel==3.2.2
     - pandas==1.4.2
-    - pybids==0.15.1
+    - pybids==0.15.2
     - sqlalchemy==1.3.24

requirements.txt

@@ -1,4 +1,4 @@
-pybids>=0.12.1
+pybids>=0.15.2
 requests
 tqdm
 pytest

setup.cfg

@@ -30,7 +30,7 @@ setup_requires =
     setuptools_scm >= 6.2
     wheel
 install_requires =
-    pybids >= 0.12.1
+    pybids >= 0.15.2
     requests
     tqdm
 test_requires =

templateflow/conf/__init__.py

@@ -1,5 +1,6 @@
 """Configuration and settings."""
 from os import getenv
+import re
 from warnings import warn
 from pathlib import Path
 from contextlib import suppress
@@ -151,12 +152,9 @@ def init_layout():
         indexer=BIDSLayoutIndexer(
             validate=False,
             ignore=(
-                ".git",
-                ".datalad",
-                ".gitannex",
-                ".gitattributes",
-                ".github",
-                "scripts",
+                re.compile(r"scripts/"),
+                re.compile(r"/\."),
+                re.compile(r"^\."),
             ),
         ),
     )