Run make check-before-commit.

Author: tsalo

doc/devel/testing_nipype.rst

@@ -39,7 +39,7 @@ dependencies. Installing software dependencies and downloading the necessary dat
 will reduce the number of skip tests.
 
 Some tests in Nipype make use of some images distributed within the `FSL course data
-<http://fsl.fmrib.ox.ac.uk/fslcourse/>`_. This reduced version of the package can be downloaded `here 
+<http://fsl.fmrib.ox.ac.uk/fslcourse/>`_. This reduced version of the package can be downloaded `here
 <https://3552243d5be815c1b09152da6525cb8fe7b900a6.googledrive.com/host/0BxI12kyv2olZVUswazA3NkFvOXM/nipype-fsl_course_data.tar.gz>`_.
 To enable the tests depending on these data, just unpack the targz file and set the :code:`FSL_COURSE_DATA` environment
 variable to point to that folder.

nipype/algorithms/tests/test_auto_ErrorMap.py

@@ -1,42 +1,39 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
 from ...testing import assert_equal
-from ..misc import TSNR
+from ..confounds import TCompCor
 
 
-def test_TSNR_inputs():
-    input_map = dict(detrended_file=dict(hash_files=False,
+def test_TCompCor_inputs():
+    input_map = dict(components_file=dict(mandatory=False,
     usedefault=True,
     ),
     ignore_exception=dict(nohash=True,
     usedefault=True,
     ),
-    in_file=dict(mandatory=True,
+    mask_file=dict(mandatory=False,
     ),
-    mean_file=dict(hash_files=False,
-    usedefault=True,
+    num_components=dict(usedefault=True,
     ),
-    regress_poly=dict(),
-    stddev_file=dict(hash_files=False,
-    usedefault=True,
+    percentile_threshold=dict(usedefault=True,
     ),
-    tsnr_file=dict(hash_files=False,
-    usedefault=True,
+    realigned_file=dict(mandatory=True,
+    ),
+    regress_poly_degree=dict(usedefault=True,
+    ),
+    use_regress_poly=dict(usedefault=True,
     ),
     )
-    inputs = TSNR.input_spec()
+    inputs = TCompCor.input_spec()
 
     for key, metadata in list(input_map.items()):
         for metakey, value in list(metadata.items()):
             yield assert_equal, getattr(inputs.traits()[key], metakey), value
 
 
-def test_TSNR_outputs():
-    output_map = dict(detrended_file=dict(),
-    mean_file=dict(),
-    stddev_file=dict(),
-    tsnr_file=dict(),
+def test_TCompCor_outputs():
+    output_map = dict(components_file=dict(),
     )
-    outputs = TSNR.output_spec()
+    outputs = TCompCor.output_spec()
 
     for key, metadata in list(output_map.items()):
         for metakey, value in list(metadata.items()):

nipype/algorithms/tests/test_auto_Overlap.py

@@ -15,5 +15,5 @@
                          Fim, BlurInMask, Autobox, TCorrMap, Bandpass, Retroicor,
                          TCorrelate, TCorr1D, BrickStat, ROIStats, AutoTcorrelate,
                          AFNItoNIFTI, Eval, Means, Hist, FWHMx, OutlierCount,
-                         QualityIndex)
+                         QualityIndex, Notes)
 from .svm import (SVMTest, SVMTrain)

nipype/algorithms/tests/test_auto_TSNR.py renamed to nipype/algorithms/tests/test_auto_TCompCor.py

@@ -3058,7 +3058,7 @@ class Notes(CommandLine):
     _cmd = '3dNotes'
     input_spec = NotesInputSpec
     output_spec = AFNICommandOutputSpec
-    
+
     def _list_outputs(self):
         outputs = self.output_spec().get()
         outputs["out_file"] = os.path.abspath(self.inputs.in_file)

nipype/interfaces/afni/__init__.py

@@ -0,0 +1,52 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ....testing import assert_equal
+from ..preprocess import Notes
+
+
+def test_Notes_inputs():
+    input_map = dict(add=dict(argstr="-a '%s'",
+    ),
+    add_history=dict(argstr="-h '%s'",
+    xor=[u'rep_history'],
+    ),
+    args=dict(argstr='%s',
+    ),
+    delete=dict(argstr='-d %d',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(argstr='%s',
+    copyfile=False,
+    mandatory=True,
+    position=-1,
+    ),
+    out_file=dict(argstr='%s',
+    ),
+    outputtype=dict(),
+    rep_history=dict(argstr="-HH '%s'",
+    xor=[u'add_history'],
+    ),
+    ses=dict(argstr='-ses',
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    )
+    inputs = Notes.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+
+
+def test_Notes_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = Notes.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value

nipype/interfaces/afni/preprocess.py

@@ -22,7 +22,7 @@
 
 Examples
 --------
-See the docstrings of the individual classes for examples.  
+See the docstrings of the individual classes for examples.
 
 """
 from __future__ import print_function, division, unicode_literals, absolute_import