Merge pull request #896 from satra/fix/docbuild

Fix/docbuild

Author: satra

doc/_templates/indexsidebar.html

@@ -7,7 +7,7 @@ <h3>{{ _('Links') }}</h3>
     <li>Forum: <a href="http://groups.google.com/group/nipy-user">User</a> · <a href="http://projects.scipy.org/mailman/listinfo/nipy-devel">Developer</a></li>
     <li><a href="http://nipy.org/software/license/index.html"><img src="https://pypip.in/license/nipype/badge.png" alt="License"></a> · <a href="http://nipy.org/about/funding.html">Funding</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://pypi.python.org/pypi/nipype/"><img src="https://pypip.in/download/nipype/badge.png" alt="Downloads"></a> · <a href='https://pypi.python.org/pypi/nipype/'><img src='https://pypip.in/py_versions/nipype/badge.pngg' alt='Python Versions' /></a></li>
+    <li><a href="https://pypi.python.org/pypi/nipype/"><img src="https://pypip.in/download/nipype/badge.png" alt="Downloads"></a> · <a href='https://pypi.python.org/pypi/nipype/'><img src='https://pypip.in/py_versions/nipype/badge.png' alt='Python Versions' /></a></li>
 </ul>
 
 {% endblock %}

nipype/algorithms/misc.py

@@ -959,7 +959,7 @@ def calc_moments(timeseries_file, moment):
 class NormalizeProbabilityMapSetInputSpec(TraitedSpec):
     in_files = InputMultiPath(File(exists=True, mandatory=True,
                     desc='The tpms to be normalized') )
-    in_mask = File(exists=True, mandatory=False,
+    in_mask = File(exists=True,
                     desc='Masked voxels must sum up 1.0, 0.0 otherwise.')
 
 class NormalizeProbabilityMapSetOutputSpec(TraitedSpec):

nipype/algorithms/tests/test_auto_NormalizeProbabilityMapSet.py

@@ -4,8 +4,7 @@
 
 def test_NormalizeProbabilityMapSet_inputs():
     input_map = dict(in_files=dict(),
-    in_mask=dict(mandatory=False,
-    ),
+    in_mask=dict(),
     )
     inputs = NormalizeProbabilityMapSet.input_spec()
 

nipype/interfaces/elastix/base.py

@@ -16,13 +16,13 @@
 """
 
 from ..base import (CommandLine, CommandLineInputSpec, isdefined,
-                    TraitedSpec, File, traits, InputMultiPath)
+                    TraitedSpec, File, Directory, traits, InputMultiPath)
 from ... import logging
 logger = logging.getLogger('interface')
 
 
 class ElastixBaseInputSpec(CommandLineInputSpec):
-    output_path = traits.Directory('./', exists=True, mandatory=True, usedefault=True,
-                              argstr='-out %s', desc='output directory')
+    output_path = Directory('./', exists=True, mandatory=True, usedefault=True,
+                            argstr='-out %s', desc='output directory')
     num_threads = traits.Int(1, argstr='-threads %01d',
                              desc='set the maximum number of threads of elastix')

nipype/interfaces/elastix/tests/test_auto_EditTransform.py

@@ -14,8 +14,7 @@ def test_EditTransform_inputs():
     ),
     output_type=dict(argstr='ResultImagePixelType',
     ),
-    reference_image=dict(mandatory=False,
-    ),
+    reference_image=dict(),
     transform_file=dict(mandatory=True,
     ),
     )

nipype/interfaces/elastix/utils.py

@@ -27,8 +27,9 @@
 class EditTransformInputSpec(BaseInterfaceInputSpec):
     transform_file = File(exists=True, mandatory=True,
                           desc='transform-parameter file, only 1')
-    reference_image = File(exists=True, mandatory=False,
-                           desc='set a new reference image to change the target coordinate system.')
+    reference_image = File(exists=True,
+                           desc=('set a new reference image to change the '
+                                 'target coordinate system.'))
     interpolation = traits.Enum('cubic','linear','nearest', usedefault=True,
                                 argstr='FinalBSplineInterpolationOrder',
                                 desc='set a new interpolator for transformation')

nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py

@@ -20,6 +20,8 @@ def test_ConvertWarp_inputs():
     ),
     jacobian_min=dict(argstr='--jmin=%f',
     ),
+    midmat=dict(argstr='--midmat=%s',
+    ),
     out_abswarp=dict(argstr='--absout',
     xor=['out_relwarp'],
     ),

nipype/interfaces/io.py

@@ -1548,12 +1548,9 @@ def _list_outputs(self):
         return None
 
 class SSHDataGrabberInputSpec(DataGrabberInputSpec):
-    hostname = traits.Str(mandatory=True,
-                               desc='Server hostname.')
-    username = traits.Str(mandatory=False,
-                                desc='Server username.')
-    password = traits.Password(mandatory=False,
-                                desc='Server password.')
+    hostname = traits.Str(mandatory=True, desc='Server hostname.')
+    username = traits.Str(desc='Server username.')
+    password = traits.Password(desc='Server password.')
     download_files = traits.Bool(True, usedefault=True,
                                     desc='If false it will return the file names without downloading them')
     base_directory = traits.Str(mandatory=True,

nipype/interfaces/tests/test_auto_SSHDataGrabber.py

@@ -12,8 +12,7 @@ def test_SSHDataGrabber_inputs():
     ignore_exception=dict(nohash=True,
     usedefault=True,
     ),
-    password=dict(mandatory=False,
-    ),
+    password=dict(),
     raise_on_empty=dict(usedefault=True,
     ),
     sort_filelist=dict(mandatory=True,
@@ -25,8 +24,7 @@ def test_SSHDataGrabber_inputs():
     template_args=dict(),
     template_expression=dict(usedefault=True,
     ),
-    username=dict(mandatory=False,
-    ),
+    username=dict(),
     )
     inputs = SSHDataGrabber.input_spec()