@@ -89,8 +89,8 @@ before_install:
 fi;
 
 - travis_retry pip install -r requirements.txt
-- travis_retry pip install grabbit==0.1.2
-- travis_retry git clone -b 0.6.5 https://.com/INCF/pybids.git ${HOME}/pybids && pip install -e ${HOME}/pybids
+- travis_retry pip install grabbit==0.2.6
+- travis_retry pip install -e git+https://.com/bids-standard/pybids.git@0.7.0#egg=pybids
 
 install:
 - travis_retry pip install $EXTRA_PIP_FLAGS -e .[$NIPYPE_EXTRAS]

@@ -107,7 +107,7 @@ function generate_main_dockerfile() {
 --user neuro \
 --miniconda use_env=neuro \
 pip_opts="-e" \
-pip_install="/src/nipype[all]" \
+pip_install="/src/nipype[all] https://.com/bids-standard/pybids/tarball/0.7.0" \
 --workdir /work \
 --label org.label-schema.build-date='$BUILD_DATE' \
 org.label-schema.name="NIPYPE" \

@@ -172,7 +172,7 @@ def get_nipype_gitversion():
 'profiler': ['psutil>=5.0'],
 'duecredit': ['duecredit'],
 'xvfbwrapper': ['xvfbwrapper'],
-'pybids': ['pybids==0.6.5'],
+'pybids': ['pybids>=0.7.0'],
 'ssh': ['paramiko'],
 # 'mesh': ['mayavi'] # Enable when it works
 }

@@ -0,0 +1,65 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..epi import EddyQuad
+
+
+def test_EddyQuad_inputs():
+input_map = dict(
+args=dict(argstr='%s', ),
+base_name=dict(
+argstr='%s',
+position=0,
+usedefault=True,
+),
+bval_file=dict(
+argstr='--bvals=%s',
+mandatory=True,
+),
+bvec_file=dict(argstr='--bvecs=%s', ),
+environ=dict(
+nohash=True,
+usedefault=True,
+),
+field=dict(argstr='--field=%s', ),
+idx_file=dict(
+argstr='--eddyIdx=%s',
+mandatory=True,
+),
+mask_file=dict(
+argstr='--mask=%s',
+mandatory=True,
+),
+output_dir=dict(
+argstr='--output-dir=%s',
+name_source=['base_name'],
+name_template='%s.qc',
+),
+output_type=dict(),
+param_file=dict(
+argstr='--eddyParams=%s',
+mandatory=True,
+),
+slice_spec=dict(argstr='--slspec=%s', ),
+verbose=dict(argstr='--verbose', ),
+)
+inputs = EddyQuad.input_spec()
+
+for key, metadata in list(input_map.items()):
+for metakey, value in list(metadata.items()):
+assert getattr(inputs.traits()[key], metakey) == value
+def test_EddyQuad_outputs():
+output_map = dict(
+avg_b0_pe_png=dict(),
+avg_b_png=dict(),
+clean_volumes=dict(),
+cnr_png=dict(),
+qc_json=dict(),
+qc_pdf=dict(),
+residuals=dict(),
+vdm_png=dict(),
+)
+outputs = EddyQuad.output_spec()
+
+for key, metadata in list(output_map.items()):
+for metakey, value in list(metadata.items()):
+assert getattr(outputs.traits()[key], metakey) == value

@@ -2721,18 +2721,23 @@ def _list_outputs(self):
 
 
 class BIDSDataGrabberInputSpec(DynamicTraitedSpec):
-base_dir = Directory(exists=True,
-desc='Path to BIDS Directory.',
-mandatory=True)
-output_query = traits.Dict(key_trait=Str,
-value_trait=traits.Dict,
-desc='Queries for outfield outputs')
-raise_on_empty = traits.Bool(True, usedefault=True,
-desc='Generate exception if list is empty '
-'for a given field')
-return_type = traits.Enum('file', 'namedtuple', usedefault=True)
-strict = traits.Bool(desc='Return only BIDS "proper" files (e.g., '
-'ignore derivatives/, sourcedata/, etc.)')
+base_dir = Directory(
+exists=True,
+desc='Path to BIDS Directory.',
+mandatory=True)
+output_query = traits.Dict(
+key_trait=Str,
+value_trait=traits.Dict,
+desc='Queries for outfield outputs')
+raise_on_empty = traits.Bool(
+True, usedefault=True,
+desc='Generate exception if list is empty for a given field')
+index_derivatives = traits.Bool(
+False, mandatory=True, usedefault=True,
+desc='Index derivatives/ sub-directory')
+extra_derivatives = traits.List(
+Directory(exists=True),
+desc='Additional derivative directories to index')
 
 
 class BIDSDataGrabber(LibraryBaseInterface, IOBase):
@@ -2758,10 +2763,10 @@ class BIDSDataGrabber(LibraryBaseInterface, IOBase):
 are filtered on common entities, which can be explicitly defined as
 infields.
 
->>> bg = BIDSDataGrabber(infields = ['subject'], outfields = ['dwi'])
+>>> bg = BIDSDataGrabber(infields = ['subject'])
 >>> bg.inputs.base_dir = 'ds005/'
 >>> bg.inputs.subject = '01'
->>> bg.inputs.output_query['dwi'] = dict(modality='dwi')
+>>> bg.inputs.output_query['dwi'] = dict(datatype='dwi')
 >>> results = bg.run() # doctest: +SKIP
 
 """
@@ -2781,18 +2786,17 @@ def __init__(self, infields=None, **kwargs):
 
 if not isdefined(self.inputs.output_query):
 self.inputs.output_query = {
-"func": {"modality": "func", 'extensions': ['nii', '.nii.gz']},
-"anat": {"modality": "anat", 'extensions': ['nii', '.nii.gz']},
+"bold": {"datatype": "func", "suffix": "bold",
+"extensions": ["nii", ".nii.gz"]},
+"T1w": {"datatype": "anat", "suffix": "T1w",
+"extensions": ["nii", ".nii.gz"]},
 }
 
 # If infields is empty, use all BIDS entities
 if infields is None:
-# Version resilience
-try:
-from bids import layout as bidslayout
-except ImportError:
-from bids import grabbids as bidslayout
-bids_config = join(dirname(bidslayout.__file__), 'config', 'bids.json')
+from bids import layout as bidslayout
+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']]
 
@@ -2807,15 +2811,12 @@ def __init__(self, infields=None, **kwargs):
 self.inputs.trait_set(trait_change_notify=False, **undefined_traits)
 
 def _list_outputs(self):
-# Version resilience
-try:
-from bids import BIDSLayout
-except ImportError:
-from bids.grabbids import BIDSLayout
-exclude = None
-if self.inputs.strict:
-exclude = ['derivatives/', 'code/', 'sourcedata/']
-layout = BIDSLayout(self.inputs.base_dir, exclude=exclude)
+from bids import BIDSLayout
+layout = BIDSLayout(self.inputs.base_dir,
+derivatives=self.inputs.index_derivatives)
+
+if isdefined(self.inputs.extra_derivatives):
+layout.add_derivatives(self.inputs.extra_derivatives)
 
 # If infield is not given nm input value, silently ignore
 filters = {}
@@ -2828,7 +2829,7 @@ def _list_outputs(self):
 for key, query in self.inputs.output_query.items():
 args = query.copy()
 args.update(filters)
-filelist = layout.get(return_type=self.inputs.return_type, **args)
+filelist = layout.get(return_type='file', **args)
 if len(filelist) == 0:
 msg = 'Output key: %s returned no files' % key
 if self.inputs.raise_on_empty:

@@ -6,10 +6,13 @@
 def test_BIDSDataGrabber_inputs():
 input_map = dict(
 base_dir=dict(mandatory=True, ),
+extra_derivatives=dict(),
+index_derivatives=dict(
+mandatory=True,
+usedefault=True,
+),
 output_query=dict(),
 raise_on_empty=dict(usedefault=True, ),
-return_type=dict(usedefault=True, ),
-strict=dict(),
 )
 inputs = BIDSDataGrabber.input_spec()
 

@@ -581,8 +581,6 @@ def test_jsonsink(tmpdir, inputs_attributes):
 # There are three reasons these tests will be skipped:
 @pytest.mark.skipif(not have_pybids,
 reason="Pybids is not installed")
-@pytest.mark.skipif(sys.version_info < (3, 0),
-reason="Pybids no longer supports Python 2")
 @pytest.mark.skipif(not dist_is_editable('pybids'),
 reason="Pybids is not installed in editable mode")
 def test_bids_grabber(tmpdir):
@@ -591,31 +589,27 @@ def test_bids_grabber(tmpdir):
 bg.inputs.base_dir = os.path.join(datadir, 'ds005')
 bg.inputs.subject = '01'
 results = bg.run()
-assert 'sub-01_T1w.nii.gz' in map(os.path.basename, results.outputs.anat)
+assert 'sub-01_T1w.nii.gz' in map(os.path.basename, results.outputs.T1w)
 assert 'sub-01_task-mixedgamblestask_run-01_bold.nii.gz' in \
-map(os.path.basename, results.outputs.func)
+map(os.path.basename, results.outputs.bold)
 
 
 @pytest.mark.skipif(not have_pybids,
 reason="Pybids is not installed")
-@pytest.mark.skipif(sys.version_info < (3, 0),
-reason="Pybids no longer supports Python 2")
 @pytest.mark.skipif(not dist_is_editable('pybids'),
 reason="Pybids is not installed in editable mode")
 def test_bids_fields(tmpdir):
 tmpdir.chdir()
 bg = nio.BIDSDataGrabber(infields = ['subject'], outfields = ['dwi'])
 bg.inputs.base_dir = os.path.join(datadir, 'ds005')
 bg.inputs.subject = '01'
-bg.inputs.output_query['dwi'] = dict(modality='dwi')
+bg.inputs.output_query['dwi'] = dict(datatype='dwi')
 results = bg.run()
 assert 'sub-01_dwi.nii.gz' in map(os.path.basename, results.outputs.dwi)
 
 
 @pytest.mark.skipif(not have_pybids,
 reason="Pybids is not installed")
-@pytest.mark.skipif(sys.version_info < (3, 0),
-reason="Pybids no longer supports Python 2")
 @pytest.mark.skipif(not dist_is_editable('pybids'),
 reason="Pybids is not installed in editable mode")
 def test_bids_infields_outfields(tmpdir):
@@ -633,9 +627,9 @@ def test_bids_infields_outfields(tmpdir):
 for outfield in outfields:
 assert(outfield in bg._outputs().traits())
 
-# now try without defining outfields, we should get anat and func for free
+# now try without defining outfields
 bg = nio.BIDSDataGrabber()
-for outfield in ['anat', 'func']:
+for outfield in ['T1w', 'bold']:
 assert outfield in bg._outputs().traits()