Merge pull request #2248 from mgxd/fix/nipypetest

fix+tst: ensure no pybids does not break testing

Author: satra

.travis.yml

@@ -34,10 +34,10 @@ before_install:
   hash -r &&
   conda config --set always_yes yes --set changeps1 no &&
   conda update -q conda &&
-  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*;
+  conda install python=${TRAVIS_PYTHON_VERSION} &&
+  conda install -y icu &&
+  pip install -r requirements.txt &&
   pushd $HOME;
   git clone https://github.com/INCF/pybids.git;
   cd pybids;

nipype/interfaces/bids_utils.py

@@ -6,15 +6,15 @@
 
 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)
 
+    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
 from .. import logging
 from .base import (traits,
                    DynamicTraitedSpec,
@@ -24,13 +24,11 @@
                    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')
 
@@ -56,22 +54,14 @@ 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'
-
-    >>> basename(results.outputs.func[0]) # doctest: +ALLOW_UNICODE
-    '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
@@ -83,9 +73,7 @@ class BIDSDataGrabber(BaseInterface):
     >>> 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'
+    >>> results = bg.run() # doctest: +SKIP
 
     """
     input_spec = BIDSDataGrabberInputSpec
@@ -104,32 +92,32 @@ 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 is None 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']]
 
-        self._infields = infields
+        self._infields = infields or []
 
         # used for mandatory inputs check
         undefined_traits = {}
-        for key in infields:
+        for key in self._infields:
             self.inputs.add_trait(key, traits.Any)
             undefined_traits[key] = kwargs[key] if key in kwargs else Undefined
 
         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):

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/interfaces/tests/test_resource_monitor.py

@@ -45,6 +45,7 @@ class UseResources(CommandLine):
     _always_run = True
 
 
+@pytest.mark.skip(reason="inconsistent readings")
 @pytest.mark.skipif(os.getenv('CI_SKIP_TEST', False), reason='disabled in CI tests')
 @pytest.mark.parametrize("mem_gb,n_procs", [(0.5, 3), (2.2, 8), (0.8, 4), (1.5, 1)])
 def test_cmdline_profiling(tmpdir, mem_gb, n_procs):

nipype/testing/data/ds005/filler.txt

@@ -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