Merge remote-tracking branch 'upstream/master' into nipypeclick

* upstream/master:
  undo matplotlib change.
  move badge to codecov
  disable matplotlib extension to test doc building.
  merge upstream master
  fix: retroicor - cleaned up interface, vim presets

Author: satra

doc/_templates/indexsidebar.html

@@ -6,7 +6,7 @@ <h3>{{ _('Links') }}</h3>
     <li>Code: <a href="http://github.com/nipy/nipype">Github</a> · <a href="http://github.com/nipy/nipype/issues">Bugs-Requests</a></li>
     <li>Forum: <a href="http://neurostars.org/t/nipype">User</a> · <a href="http://projects.scipy.org/mailman/listinfo/nipy-devel">Developer</a></li>
     <li><a href="about.html#funding">Funding</a> · <a href="http://nipy.org/software/license/index.html"><img src="https://img.shields.io/pypi/l/nipype.svg" alt="License"></a></li>
-    <li><a href="https://travis-ci.org/nipy/nipype"><img src="https://travis-ci.org/nipy/nipype.png?branch=master" alt="travis"></a> · <a href='https://coveralls.io/r/nipy/nipype'><img src='https://coveralls.io/repos/nipy/nipype/badge.png' alt='Coverage Status' /></a></li>
+    <li><a href="https://travis-ci.org/nipy/nipype"><img src="https://travis-ci.org/nipy/nipype.png?branch=master" alt="travis"></a> · <a href='https://codecov.io/gh/nipy/nipype'><img src='https://codecov.io/gh/nipy/nipype/branch/master/graph/badge.svg' alt='Coverage Status' /></a></li>
     <a href='https://pypi.python.org/pypi/nipype/'><img src='https://img.shields.io/pypi/pyversions/nipype.svg' alt='Python Versions' /></a></li>
 </ul>
 

nipype/algorithms/tests/test_auto_FramewiseDisplacement.py

@@ -11,7 +11,8 @@ def test_FramewiseDisplacement_inputs():
     ignore_exception=dict(nohash=True,
     usedefault=True,
     ),
-    in_plots=dict(),
+    in_plots=dict(mandatory=True,
+    ),
     normalize=dict(usedefault=True,
     ),
     out_figure=dict(usedefault=True,

nipype/algorithms/tests/test_auto_TSNR.py

@@ -1,6 +1,6 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
 from ...testing import assert_equal
-from ..misc import TSNR
+from ..confounds import TSNR
 
 
 def test_TSNR_inputs():

nipype/interfaces/afni/preprocess.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
-# vi: set ft = python sts = 4 ts = 4 sw = 4 et:
+# vi: set ft=python sts=4 ts=4 sw=4 et:
 """Afni preprocessing interfaces
 
     Change directory to provide relative paths for doctests
@@ -2384,7 +2384,9 @@ class RetroicorInputSpec(AFNICommandInputSpec):
                    mandatory=True,
                    exists=True,
                    copyfile=False)
-    out_file = File(desc='output image file name', argstr='-prefix %s', mandatory=True, position=1)
+    out_file = File(name_template='%s_retroicor', name_source=['in_file'],
+                    desc='output image file name',
+                    argstr='-prefix %s', position=1)
     card = File(desc='1D cardiac data file for cardiac correction',
                 argstr='-card %s',
                 position=-2,
@@ -2438,6 +2440,7 @@ class Retroicor(AFNICommand):
     >>> ret.inputs.in_file = 'functional.nii'
     >>> ret.inputs.card = 'mask.1D'
     >>> ret.inputs.resp = 'resp.1D'
+    >>> ret.inputs.outputtype = 'NIFTI'
     >>> res = ret.run()   # doctest: +SKIP
     """
 
@@ -2446,6 +2449,13 @@ class Retroicor(AFNICommand):
     output_spec = AFNICommandOutputSpec
 
 
+    def _format_arg(self, name, trait_spec, value):
+        if name == 'in_file':
+            if not isdefined(self.inputs.card) and not isdefined(self.inputs.resp):
+                return None
+        return super(Retroicor, self)._format_arg(name, trait_spec, value)
+
+
 class AFNItoNIFTIInputSpec(AFNICommandInputSpec):
     in_file = File(desc='input file to 3dAFNItoNIFTI',
                    argstr='%s',

nipype/interfaces/afni/tests/test_auto_Retroicor.py

@@ -28,7 +28,8 @@ def test_Retroicor_inputs():
     position=-5,
     ),
     out_file=dict(argstr='-prefix %s',
-    mandatory=True,
+    name_source=[u'in_file'],
+    name_template='%s_retroicor',
     position=1,
     ),
     outputtype=dict(),