fix+tst: ensure no pybids does not break testing

Author: mgxd

.travis.yml

@@ -37,12 +37,7 @@ before_install:
   conda install python=${TRAVIS_PYTHON_VERSION} &&
   conda config --add channels conda-forge &&
   conda install -y nipype icu &&
-  rm -r ${CONDA_HOME}/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype*;
-  pushd $HOME;
-  git clone https://github.com/INCF/pybids.git;
-  cd pybids;
-  pip install -e .;
-  popd; }
+  rm -r ${CONDA_HOME}/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype*; }
 #  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

@@ -6,15 +6,9 @@
 
 BIDSDataGrabber: Query data from BIDS dataset using pybids grabbids.
 
-Change directory to provide relative paths for doctests
->>> import os
->>> import bids
->>> filepath = os.path.realpath(os.path.dirname(bids.__file__))
->>> datadir = os.path.realpath(os.path.join(filepath, 'grabbids/tests/data/'))
->>> os.chdir(datadir)
-
 """
 from os.path import join, dirname
+import json
 from .. import logging
 from .base import (traits,
                    DynamicTraitedSpec,
@@ -24,13 +18,11 @@
                    Str,
                    Undefined)
 
+have_pybids = True
 try:
     from bids import grabbids as gb
-    import json
 except ImportError:
     have_pybids = False
-else:
-    have_pybids = True
 
 LOGGER = logging.getLogger('workflows')
 
@@ -56,36 +48,33 @@ class BIDSDataGrabber(BaseInterface):
     Examples
     --------
 
-    >>> from nipype.interfaces.bids_utils import BIDSDataGrabber
-    >>> from os.path import basename
-
     By default, the BIDSDataGrabber fetches anatomical and functional images
     from a project, and makes BIDS entities (e.g. subject) available for
     filtering outputs.
 
-    >>> bg = BIDSDataGrabber()
-    >>> bg.inputs.base_dir = 'ds005/'
-    >>> bg.inputs.subject = '01'
-    >>> results = bg.run()
-    >>> basename(results.outputs.anat[0]) # doctest: +ALLOW_UNICODE
-    'sub-01_T1w.nii.gz'
+    >>> bg = BIDSDataGrabber() # doctest: +SKIP
+    >>> bg.inputs.base_dir = 'ds005/' # doctest: +SKIP
+    >>> bg.inputs.subject = '01' # doctest: +SKIP
+    >>> results = bg.run() # doctest # doctest: +SKIP
+    >>> basename(results.outputs.anat[0]) # doctest: +SKIP
+    'sub-01_T1w.nii.gz' # doctest: +SKIP
 
-    >>> basename(results.outputs.func[0]) # doctest: +ALLOW_UNICODE
-    'sub-01_task-mixedgamblestask_run-01_bold.nii.gz'
+    >>> basename(results.outputs.func[0]) # doctest: +SKIP
+    'sub-01_task-mixedgamblestask_run-01_bold.nii.gz' # 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'])
-    >>> 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]) # doctest: +ALLOW_UNICODE
-    'sub-01_dwi.nii.gz'
+    >>> bg = BIDSDataGrabber(infields = ['subject'], outfields = ['dwi']) # doctest: +SKIP
+    >>> bg.inputs.base_dir = 'ds005/' # doctest: +SKIP
+    >>> bg.inputs.subject = '01' # doctest: +SKIP
+    >>> bg.inputs.output_query['dwi'] = dict(modality='dwi') # doctest: +SKIP
+    >>> results = bg.run() # doctest: +SKIP
+    >>> basename(results.outputs.dwi[0]) # doctest: +SKIP
+    'sub-01_dwi.nii.gz' # doctest: +SKIP
 
     """
     input_spec = BIDSDataGrabberInputSpec

nipype/interfaces/tests/test_bids.py

@@ -0,0 +1,50 @@
+import os
+import json
+import sys
+
+import pytest
+from nipype.interfaces.bids_utils import BIDSDataGrabber
+from nipype.utils.filemanip import dist_is_editable
+
+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, 'grabbids/tests/data/'))
+except ImportError:
+    have_pybids = False
+
+
+# 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):
+    tmpdir.chdir()
+    bg = BIDSDataGrabber()
+    bg.inputs.base_dir = os.path.join(datadir, 'ds005')
+    bg.inputs.subject = '01'
+    results = bg.run()
+    assert os.path.basename(results.outputs.anat[0]) == 'sub-01_T1w.nii.gz'
+    assert os.path.basename(results.outputs.func[0]) == (
+           'sub-01_task-mixedgamblestask_run-01_bold.nii.gz')
+
+
+@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 = 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')
+    results = bg.run()
+    assert os.path.basename(results.outputs.dwi[0]) == 'sub-01_dwi.nii.gz'

nipype/utils/filemanip.py

@@ -646,3 +646,20 @@ def write_rst_dict(info, prefix=''):
     for key, value in sorted(info.items()):
         out.append('{}* {} : {}'.format(prefix, key, str(value)))
     return '\n'.join(out) + '\n\n'
+
+
+def dist_is_editable(dist):
+    """Is distribution an editable install?
+
+    Parameters
+    ----------
+    dist : string
+        Package name
+
+    # Borrowed from `pip`'s' API
+    """
+    for path_item in sys.path:
+        egg_link = os.path.join(path_item, dist + '.egg-link')
+        if os.path.isfile(egg_link):
+            return True
+    return False