ref+tst: allow bidsgrabber to initialize without pybids, grab dependencies from requirements.txt

Author: mgxd

.travis.yml

@@ -36,8 +36,8 @@ before_install:
   conda update -q conda &&
   conda config --add channels conda-forge &&
   conda install python=${TRAVIS_PYTHON_VERSION} &&
-  conda install -y nipype icu &&
-  rm -r ${CONDA_HOME}/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype*; }
+  conda install -y icu &&
+  pip install -r requirements.txt &&; }
 #  Add install of vtk and mayavi to test mesh (disabled): conda install -y vtk mayavi
 - travis_retry apt_inst
 - travis_retry conda_inst

nipype/interfaces/bids_utils.py

@@ -6,6 +6,12 @@
 
 BIDSDataGrabber: Query data from BIDS dataset using pybids grabbids.
 
+
+    Change directory to provide relative paths for doctests
+    >>> import os
+    >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
+    >>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data'))
+    >>> os.chdir(datadir)
 """
 from os.path import join, dirname
 import json
@@ -52,36 +58,29 @@ class BIDSDataGrabber(BaseInterface):
     from a project, and makes BIDS entities (e.g. subject) available for
     filtering outputs.
 
-    >>> bg = BIDSDataGrabber() # doctest: +SKIP
+    >>> bg = BIDSDataGrabber()
     >>> bg.inputs.base_dir = 'ds005/'
     >>> bg.inputs.subject = '01'
-    >>> results = bg.run() # doctest
-    >>> basename(results.outputs.anat[0])
-    'sub-01_T1w.nii.gz'
-
-    >>> basename(results.outputs.func[0])
-    'sub-01_task-mixedgamblestask_run-01_bold.nii.gz'
+    >>> results = bg.run() # doctest: +SKIP
 
 
     Dynamically created, user-defined output fields can also be defined to
     return different types of outputs from the same project. All outputs
     are filtered on common entities, which can be explicitly defined as
     infields.
 
-    >>> bg = BIDSDataGrabber(infields = ['subject'], outfields = ['dwi']) # doctest: +SKIP
+    >>> bg = BIDSDataGrabber(infields = ['subject'], outfields = ['dwi'])
     >>> bg.inputs.base_dir = 'ds005/'
     >>> bg.inputs.subject = '01'
     >>> bg.inputs.output_query['dwi'] = dict(modality='dwi')
-    >>> results = bg.run()
-    >>> basename(results.outputs.dwi[0])
-    'sub-01_dwi.nii.gz'
+    >>> results = bg.run() # doctest: +SKIP
 
     """
     input_spec = BIDSDataGrabberInputSpec
     output_spec = DynamicTraitedSpec
     _always_run = True
 
-    def __init__(self, infields=None, **kwargs):
+    def __init__(self, infields=[], **kwargs):
         """
         Parameters
         ----------
@@ -93,17 +92,13 @@ def __init__(self, infields=None, **kwargs):
             If no matching items, returns Undefined.
         """
         super(BIDSDataGrabber, self).__init__(**kwargs)
-        if not have_pybids:
-            raise ImportError(
-                "The BIDSEventsGrabber interface requires pybids."
-                " Please make sure it is installed.")
 
         if not isdefined(self.inputs.output_query):
             self.inputs.output_query = {"func": {"modality": "func"},
                                         "anat": {"modality": "anat"}}
 
-        # If infields is None, use all BIDS entities
-        if infields is None:
+        # If infields is empty, use all BIDS entities
+        if not infields and have_pybids:
             bids_config = join(dirname(gb.__file__), 'config', 'bids.json')
             bids_config = json.load(open(bids_config, 'r'))
             infields = [i['name'] for i in bids_config['entities']]
@@ -119,6 +114,10 @@ def __init__(self, infields=None, **kwargs):
         self.inputs.trait_set(trait_change_notify=False, **undefined_traits)
 
     def _run_interface(self, runtime):
+        if not have_pybids:
+            raise ImportError(
+                "The BIDSEventsGrabber interface requires pybids."
+                " Please make sure it is installed.")
         return runtime
 
     def _list_outputs(self):