Merge branch 'master' into fix/CircleTests

Author: oesteban

README.rst

@@ -78,8 +78,8 @@ Support and Communication
 -------------------------
 
 If you have a problem or would like to ask a question about how to do something in Nipype please open an issue to
-`NeuroStars.org <http://neurostars.org>`_ with a *nipype* tag. `NeuroStars.org <http://neurostars.org>`_  is a 
-platform similar to StackOverflow but dedicated to neuroinformatics. 
+`NeuroStars.org <http://neurostars.org>`_ with a *nipype* tag. `NeuroStars.org <http://neurostars.org>`_  is a
+platform similar to StackOverflow but dedicated to neuroinformatics.
 
 To participate in the Nipype development related discussions please use the following mailing list::
 

nipype/algorithms/tests/test_auto_CompCor.py

@@ -17,6 +17,8 @@ def test_ComputeDVARS_inputs():
     ),
     in_mask=dict(mandatory=True,
     ),
+    intensity_normalization=dict(usedefault=True,
+    ),
     remove_zerovariance=dict(usedefault=True,
     ),
     save_all=dict(usedefault=True,

nipype/algorithms/tests/test_auto_ComputeDVARS.py

@@ -19,6 +19,8 @@ def test_FramewiseDisplacement_inputs():
     ),
     out_file=dict(usedefault=True,
     ),
+    parameter_source=dict(mandatory=True,
+    ),
     radius=dict(usedefault=True,
     ),
     save_plot=dict(usedefault=True,

nipype/algorithms/tests/test_auto_FramewiseDisplacement.py

@@ -1,34 +1,26 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
 from __future__ import unicode_literals
-from ..metrics import ErrorMap
+from ..confounds import NonSteadyStateDetector
 
 
-def test_ErrorMap_inputs():
+def test_NonSteadyStateDetector_inputs():
     input_map = dict(ignore_exception=dict(nohash=True,
     usedefault=True,
     ),
-    in_ref=dict(mandatory=True,
+    in_file=dict(mandatory=True,
     ),
-    in_tst=dict(mandatory=True,
-    ),
-    mask=dict(),
-    metric=dict(mandatory=True,
-    usedefault=True,
-    ),
-    out_map=dict(),
     )
-    inputs = ErrorMap.input_spec()
+    inputs = NonSteadyStateDetector.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_ErrorMap_outputs():
-    output_map = dict(distance=dict(),
-    out_map=dict(),
+def test_NonSteadyStateDetector_outputs():
+    output_map = dict(n_volumes_to_discard=dict(),
     )
-    outputs = ErrorMap.output_spec()
+    outputs = NonSteadyStateDetector.output_spec()
 
     for key, metadata in list(output_map.items()):
         for metakey, value in list(metadata.items()):

nipype/algorithms/tests/test_auto_ErrorMap.py renamed to nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py

@@ -67,6 +67,7 @@ def test_dvars(tmpdir):
     assert (np.abs(dv1[:, 2] - ground_truth[:, 2]).sum() / len(dv1)) < 0.05
 
 def test_outliers(tmpdir):
+    np.random.seed(0)
     in_data = np.random.randn(100)
     in_data[0] += 10
 

nipype/algorithms/tests/test_auto_Overlap.py

@@ -11,7 +11,6 @@ def test_CreateJacobianDeterminantImage_inputs():
     position=1,
     ),
     doLogJacobian=dict(argstr='%d',
-    mandatory=False,
     position=3,
     ),
     environ=dict(nohash=True,
@@ -35,7 +34,6 @@ def test_CreateJacobianDeterminantImage_inputs():
     terminal_output=dict(nohash=True,
     ),
     useGeometric=dict(argstr='%d',
-    mandatory=False,
     position=4,
     ),
     )

nipype/algorithms/tests/test_auto_TSNR.py

@@ -145,9 +145,9 @@ class CreateJacobianDeterminantImageInputSpec(ANTSCommandInputSpec):
     outputImage = File(argstr='%s', mandatory=True,
                          position=2,
                          desc='output filename')
-    doLogJacobian = traits.Enum(0, 1, argstr='%d', mandatory=False, position=3,
+    doLogJacobian = traits.Enum(0, 1, argstr='%d', position=3,
                           desc='return the log jacobian')
-    useGeometric = traits.Enum(0, 1, argstr='%d', mandatory=False, position=4,
+    useGeometric = traits.Enum(0, 1, argstr='%d', position=4,
                           desc='return the geometric jacobian')
 
 class CreateJacobianDeterminantImageOutputSpec(TraitedSpec):