sty+tst: fix doc styles and tests

satra · satra · commit cb69df58536b · 2017-05-05T14:59:58.000-04:00
diff --git a/doc/documentation.rst b/doc/documentation.rst
@@ -29,7 +29,7 @@ Previous versions:  `0.12.0 <http://nipype.readthedocs.io/en/0.12.0/>`_ `0.11.0
             :maxdepth: 2
 
             users/index
-            
+
          .. toctree::
             :maxdepth: 1
 
diff --git a/doc/users/config_file.rst b/doc/users/config_file.rst
@@ -145,7 +145,7 @@ Execution
     crashfiles allow interactive debugging and rerunning of nodes, while text
     crashfiles allow portability across machines and shorter load time.
     (possible values: ``pklz`` and ``txt``; default value: ``pklz``)
-    
+
 Example
 ~~~~~~~
 
diff --git a/nipype/interfaces/afni/preprocess.py b/nipype/interfaces/afni/preprocess.py
@@ -2417,7 +2417,7 @@ class QwarpPlusMinusOutputSpec(TraitedSpec):
 
 
 class QwarpPlusMinus(CommandLine):
-    """A version of 3dQwarp for performing field susceptibility correction 
+    """A version of 3dQwarp for performing field susceptibility correction
     using two images with opposing phase encoding directions.
 
     For complete details, see the `3dQwarp Documentation.
@@ -2434,7 +2434,7 @@ class QwarpPlusMinus(CommandLine):
     >>> qwarp.cmdline  # doctest: +ALLOW_UNICODE
     '3dQwarp -prefix Qwarp.nii.gz -plusminus -base sub-01_dir-RL_epi.nii.gz -nopadWARP -source sub-01_dir-LR_epi.nii.gz'
     >>> res = warp.run()  # doctest: +SKIP
-    
+
     """
     _cmd = '3dQwarp -prefix Qwarp.nii.gz -plusminus'
     input_spec = QwarpPlusMinusInputSpec
diff --git a/nipype/interfaces/afni/utils.py b/nipype/interfaces/afni/utils.py
@@ -695,7 +695,7 @@ class FWHMx(AFNICommandBase):
     _cmd = '3dFWHMx'
     input_spec = FWHMxInputSpec
     output_spec = FWHMxOutputSpec
-    
+
     references_ = [{'entry': BibTeX('@article{CoxReynoldsTaylor2016,'
                                     'author={R.W. Cox, R.C. Reynolds, and P.A. Taylor},'
                                     'title={AFNI and clustering: false positive rates redux},'
diff --git a/nipype/interfaces/base.py b/nipype/interfaces/base.py
@@ -386,6 +386,10 @@ def _generate_handlers(self):
         """Find all traits with the 'xor' metadata and attach an event
         handler to them.
         """
+        has_xor = dict(xor=lambda t: t is not None)
+        xors = self.trait_names(**has_xor)
+        for elem in xors:
+            self.on_trait_change(self._xor_warn, elem)
         has_deprecation = dict(deprecated=lambda t: t is not None)
         deprecated = self.trait_names(**has_deprecation)
         for elem in deprecated:
diff --git a/nipype/interfaces/fsl/utils.py b/nipype/interfaces/fsl/utils.py
@@ -73,7 +73,7 @@ class RobustFOVInputSpec(FSLCommandInputSpec):
     brainsize = traits.Int(desc=('size of brain in z-dimension (default '
                                  '170mm/150mm)'),
                            argstr='-b %d')
-    out_transform = File(desc=("Transformation matrix in_file to out_roi "  
+    out_transform = File(desc=("Transformation matrix in_file to out_roi "
                                "output name"),
                          argstr="-m %s",
                          name_source=['in_file'], hash_files=False,
@@ -83,17 +83,17 @@ class RobustFOVInputSpec(FSLCommandInputSpec):
 class RobustFOVOutputSpec(TraitedSpec):
     out_roi = File(exists=True, desc="ROI volume output name")
     out_transform = File(exists=True,
-                         desc=("Transformation matrix in_file to out_roi " 
+                         desc=("Transformation matrix in_file to out_roi "
                                "output name"))
 
 
 class RobustFOV(FSLCommand):
     """Automatically crops an image removing lower head and neck.
-    
-    Interface is stable 5.0.0 to 5.0.9, but default brainsize changed from 
+
+    Interface is stable 5.0.0 to 5.0.9, but default brainsize changed from
     150mm to 170mm.
     """
-    
+
     _cmd = 'robustfov'
     input_spec = RobustFOVInputSpec
     output_spec = RobustFOVOutputSpec
diff --git a/nipype/interfaces/niftyseg/em.py b/nipype/interfaces/niftyseg/em.py
@@ -117,7 +117,7 @@ class EM(NiftySegCommand):
     it's simplest form, it takes in one 2D or 3D image and segments it in n
     classes.
 
-    `Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ | 
+    `Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ |
     `Documentation <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation>`_
 
     Examples
@@ -127,7 +127,7 @@ class EM(NiftySegCommand):
     >>> node.inputs.in_file = 'im1.nii'
     >>> node.inputs.no_prior = 4
     >>> node.cmdline  # doctest: +ALLOW_UNICODE
-    'seg_EM -in im1.nii -nopriors 4 -bc_out im1_bc_em.nii.gz 
+    'seg_EM -in im1.nii -nopriors 4 -bc_out im1_bc_em.nii.gz
     -out im1_em.nii.gz -out_outlier im1_outlier_em.nii.gz'
 
     """
diff --git a/nipype/interfaces/niftyseg/label_fusion.py b/nipype/interfaces/niftyseg/label_fusion.py
@@ -133,7 +133,7 @@ class LabelFusion(NiftySegCommand):
     FusedSegmentation.nii -STEPS 2 15 TargetImage.nii \
     4D_Propagated_Intensities.nii
 
-    `Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ | 
+    `Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ |
     `Documentation <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation>`_
 
     Examples
@@ -278,7 +278,6 @@ class CalcTopNCCInputSpec(CommandLineInputSpec):
 
     mask_file = File(argstr='-mask %s',
                      exists=True,
-                     mandatory=False,
                      desc='Filename of the ROI for label fusion')
 
 
diff --git a/nipype/interfaces/niftyseg/lesions.py b/nipype/interfaces/niftyseg/lesions.py
@@ -99,7 +99,7 @@ class FillLesions(NiftySegCommand):
 
     Fill all the masked lesions with WM intensity average.
 
-    `Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ | 
+    `Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ |
     `Documentation <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation>`_
 
     Examples
diff --git a/nipype/interfaces/niftyseg/maths.py b/nipype/interfaces/niftyseg/maths.py
@@ -103,7 +103,7 @@ class UnaryMaths(MathsCommand):
 
     Interface to use any unary mathematical operations that can be performed
     with the seg_maths command-line program. See below for those operations::
-    
+
         -sqrt           Square root of the image.
         -exp            Exponential root of the image.
         -log            Log of the image.
@@ -134,7 +134,7 @@ class UnaryMaths(MathsCommand):
         -4to5           Flip the 4th and 5th dimension.
         -range          Reset the image range to the min max
 
-    `Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ | 
+    `Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ |
     `Documentation <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation>`_
 
     Examples
@@ -217,7 +217,7 @@ class BinaryMaths(MathsCommand):
 
     Interface to use any binary mathematical operations that can be performed
     with the seg_maths command-line program. See below for those operations::
-    
+
         -mul    <float/file>    Multiply image <float> value or by other image.
         -div    <float/file>    Divide image by <float> or by other image.
         -add    <float/file>    Add image by <float> or by other image.
@@ -249,7 +249,7 @@ class BinaryMaths(MathsCommand):
         -splitinter <x/y/z>     Split interleaved slices in direction <x/y/z>
                                 into separate time points
 
-    `Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ | 
+    `Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ |
     `Documentation <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation>`_
 
     Examples
@@ -349,7 +349,7 @@ class BinaryMathsInteger(MathsCommand):
 
     Interface to use any integer mathematical operations that can be performed
     with the seg_maths command-line program. See below for those operations::
-    
+
         (requiring integer values)
         -equal  <int>       Get voxels equal to <int>
         -dil    <int>       Dilate the image <int> times (in voxels).
@@ -359,7 +359,7 @@ class BinaryMathsInteger(MathsCommand):
         -pad    <int>       Pad <int> voxels with NaN value around each 3D
                             volume.
 
-    `Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ | 
+    `Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ |
     `Documentation <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation>`_
 
     Examples
@@ -437,15 +437,15 @@ class TupleMaths(MathsCommand):
 
     Interface to use any tuple mathematical operations that can be performed
     with the seg_maths command-line program. See below for those operations::
-    
+
         -lncc      <file> <std>    Local CC between current img and <file>
                                 on a kernel with <std>
         -lssd      <file> <std>    Local SSD between current img and <file>
                                 on a kernel with <std>
         -lltsnorm  <file_norm> <float>   Linear LTS normalisation assuming
                                          <float> percent outliers
 
-    `Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ | 
+    `Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ |
     `Documentation <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation>`_
 
     Examples
@@ -505,11 +505,11 @@ class Merge(MathsCommand):
 
     Interface to use the merge operation that can be performed
     with the seg_maths command-line program. See below for this option::
-    
+
         -merge  <i> <d> <files>   Merge <i> images and the working image in the
                                   <d> dimension
 
-    `Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ | 
+    `Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ |
     `Documentation <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation>`_
 
     Examples
diff --git a/nipype/interfaces/niftyseg/patchmatch.py b/nipype/interfaces/niftyseg/patchmatch.py
@@ -53,27 +53,22 @@ class PatchMatchInputSpec(CommandLineInputSpec):
 
     # Optional arguments
     patch_size = traits.Int(desc="Patch size, #voxels",
-                            argstr='-size %i',
-                            mandatory=False)
+                            argstr='-size %i')
 
     desc = "Constrained search area size, number of times bigger than the \
 patchsize"
     cs_size = traits.Int(desc=desc,
-                         argstr='-cs %i',
-                         mandatory=False)
+                         argstr='-cs %i')
 
     match_num = traits.Int(desc="Number of better matching",
-                           argstr='-match %i',
-                           mandatory=False)
+                           argstr='-match %i')
 
     pm_num = traits.Int(desc="Number of patchmatch executions",
-                        argstr='-pm %i',
-                        mandatory=False)
+                        argstr='-pm %i')
 
     desc = "Number of iterations for the patchmatch algorithm"
     it_num = traits.Int(desc=desc,
-                        argstr='-it %i',
-                        mandatory=False)
+                        argstr='-it %i')
 
 
 class PatchMatchOutputSpec(TraitedSpec):
@@ -96,7 +91,7 @@ class PatchMatch(NiftySegCommand):
     volumes than the input image allowing to propagate multiple labels
     in the same execution.
 
-    `Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ | 
+    `Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ |
     `Documentation <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation>`_
 
     Examples
diff --git a/nipype/interfaces/niftyseg/stats.py b/nipype/interfaces/niftyseg/stats.py
@@ -29,14 +29,12 @@ class StatsInput(CommandLineInputSpec):
 
     # Constrains
     mask_file = File(exists=True,
-                     mandatory=False,
                      position=-2,
                      argstr='-m %s',
                      desc='statistics within the masked area')
 
     desc = 'Only estimate statistics if voxel is larger than <float>'
     larger_voxel = traits.Float(argstr='-t %f',
-                                mandatory=False,
                                 position=-3,
                                 desc=desc)
 
@@ -104,7 +102,7 @@ class UnaryStats(StatsCommand):
 
     Interface to use any unary statistical operations that can be performed
     with the seg_stats command-line program. See below for those operations::
-    
+
         -r          | The range <min max> of all voxels.
         -R          | The robust range (assuming 2% outliers on both sides)
                     | of all voxels
@@ -131,7 +129,7 @@ class UnaryStats(StatsCommand):
         -xdim       | Output the voxel dimention in the x direction.
                     | Replace x with y/z for other directions.
 
-    `Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ | 
+    `Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ |
     `Documentation <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation>`_
 
     Examples
@@ -192,7 +190,7 @@ class BinaryStats(StatsCommand):
 
     Interface to use any binary statistical operations that can be performed
     with the seg_stats command-line program. See below for those operations::
-    
+
         -p <float>      | The <float>th percentile of all voxels intensity
                         | (float=[0,100])
         -sa  <ax>       | Average of all voxels
@@ -207,7 +205,7 @@ class BinaryStats(StatsCommand):
         -Vl <csv>       | Volume of each integer label <in>. Save to <csv>file.
         -Nl <csv>       | Count of each label <in>. Save to <csv> file.
 
-    `Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ | 
+    `Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ |
     `Documentation <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation>`_
 
     Examples
diff --git a/nipype/interfaces/niftyseg/tests/test_auto_BinaryStats.py b/nipype/interfaces/niftyseg/tests/test_auto_BinaryStats.py
@@ -17,11 +17,9 @@ def test_BinaryStats_inputs():
     position=2,
     ),
     larger_voxel=dict(argstr='-t %f',
-    mandatory=False,
     position=-3,
     ),
     mask_file=dict(argstr='-m %s',
-    mandatory=False,
     position=-2,
     ),
     operand_file=dict(argstr='%s',
diff --git a/nipype/interfaces/niftyseg/tests/test_auto_CalcTopNCC.py b/nipype/interfaces/niftyseg/tests/test_auto_CalcTopNCC.py
@@ -21,7 +21,6 @@ def test_CalcTopNCC_inputs():
     position=3,
     ),
     mask_file=dict(argstr='-mask %s',
-    mandatory=False,
     ),
     num_templates=dict(argstr='-templates %s',
     mandatory=True,
diff --git a/nipype/interfaces/niftyseg/tests/test_auto_StatsCommand.py b/nipype/interfaces/niftyseg/tests/test_auto_StatsCommand.py
@@ -17,11 +17,9 @@ def test_StatsCommand_inputs():
     position=2,
     ),
     larger_voxel=dict(argstr='-t %f',
-    mandatory=False,
     position=-3,
     ),
     mask_file=dict(argstr='-m %s',
-    mandatory=False,
     position=-2,
     ),
     terminal_output=dict(nohash=True,
diff --git a/nipype/interfaces/niftyseg/tests/test_auto_UnaryStats.py b/nipype/interfaces/niftyseg/tests/test_auto_UnaryStats.py
@@ -17,11 +17,9 @@ def test_UnaryStats_inputs():
     position=2,
     ),
     larger_voxel=dict(argstr='-t %f',
-    mandatory=False,
     position=-3,
     ),
     mask_file=dict(argstr='-m %s',
-    mandatory=False,
     position=-2,
     ),
     operation=dict(argstr='-%s',
