Merge pull request #2679 from effigies/fix/pybids_refactor

FIX: Read BIDS config.json under grabbids or layout

Author: effigies

nipype/interfaces/io.py

@@ -42,10 +42,16 @@
 
 have_pybids = True
 try:
-    from bids import grabbids as gb
+    import bids
 except ImportError:
     have_pybids = False
 
+if have_pybids:
+    try:
+        from bids import layout as bidslayout
+    except ImportError:
+        from bids import grabbids as bidslayout
+
 try:
     import pyxnat
 except:
@@ -2810,7 +2816,7 @@ def __init__(self, infields=None, **kwargs):
 
         # If infields is empty, use all BIDS entities
         if infields is None and have_pybids:
-            bids_config = join(dirname(gb.__file__), 'config', 'bids.json')
+            bids_config = join(dirname(bidslayout.__file__), 'config', 'bids.json')
             bids_config = json.load(open(bids_config, 'r'))
             infields = [i['name'] for i in bids_config['entities']]
 
@@ -2835,7 +2841,7 @@ def _list_outputs(self):
         exclude = None
         if self.inputs.strict:
             exclude = ['derivatives/', 'code/', 'sourcedata/']
-        layout = gb.BIDSLayout(self.inputs.base_dir, exclude=exclude)
+        layout = bidslayout.BIDSLayout(self.inputs.base_dir, exclude=exclude)
 
         # If infield is not given nm input value, silently ignore
         filters = {}

nipype/interfaces/tests/test_io.py

@@ -77,7 +77,6 @@
 have_pybids = True
 try:
     import bids
-    from bids import grabbids as gb
     filepath = os.path.realpath(os.path.dirname(bids.__file__))
     datadir = os.path.realpath(os.path.join(filepath, 'tests/data/'))
 except ImportError: