Merge pull request #1997 from satra/fix/niftydocs

doc: fix rst formatting

Author: satra

doc/devel/testing_nipype.rst

@@ -89,7 +89,7 @@ To enable the tests depending on these data, just unpack the targz file and set
 variable to point to that folder.
 
 Xfail tests
-~~~~~~~~~~
+~~~~~~~~~~~
 
 Some tests are expect to fail until the code will be changed or for other reasons.
 

nipype/interfaces/base.py

@@ -390,10 +390,6 @@ def _generate_handlers(self):
         xors = self.trait_names(**has_xor)
         for elem in xors:
             self.on_trait_change(self._xor_warn, elem)
-        has_requires = dict(requires=lambda t: t is not None)
-        requires = self.trait_names(**has_requires)
-        for elem in requires:
-            self.on_trait_change(self._requires_warn, elem)
         has_deprecation = dict(deprecated=lambda t: t is not None)
         deprecated = self.trait_names(**has_deprecation)
         for elem in deprecated:

nipype/interfaces/mipav/developer.py

@@ -658,7 +658,7 @@ class MedicAlgorithmSPECTRE2010(SEMLikeCommandLine):
 category: Developer Tools
 
 description: Simple Paradigm for Extra-Cranial Tissue REmoval
-################################################
+
 Algorithm Version: 1.6
 GUI Version: 1.10
 

nipype/interfaces/niftyseg/em.py

@@ -117,9 +117,8 @@ class EM(NiftySegCommand):
     it's simplest form, it takes in one 2D or 3D image and segments it in n
     classes.
 
-    For source code, see http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg
-    For Documentation, see:
-        http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation
+    `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
     --------
@@ -128,8 +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 \
--out im1_em.nii.gz -out_outlier im1_outlier_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'
 
     """
     _cmd = get_custom_path('seg_EM', env_dir='NIFTYSEGDIR')

nipype/interfaces/niftyseg/label_fusion.py

@@ -133,9 +133,8 @@ class LabelFusion(NiftySegCommand):
     FusedSegmentation.nii -STEPS 2 15 TargetImage.nii \
     4D_Propagated_Intensities.nii
 
-    For source code, see http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg
-    For Documentation, see:
-        http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation
+    `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
     --------
@@ -148,8 +147,7 @@ class LabelFusion(NiftySegCommand):
     >>> node.inputs.template_num = 2
     >>> node.inputs.classifier_type = 'STEPS'
     >>> node.cmdline  # doctest: +ALLOW_UNICODE
-    'seg_LabFusion -in im1.nii -STEPS 2.000000 2 im2.nii im3.nii -out \
-im1_steps.nii'
+    'seg_LabFusion -in im1.nii -STEPS 2.000000 2 im2.nii im3.nii -out im1_steps.nii'
 
     """
     _cmd = get_custom_path('seg_LabFusion', env_dir='NIFTYSEGDIR')
@@ -280,7 +278,6 @@ class CalcTopNCCInputSpec(CommandLineInputSpec):
 
     mask_file = File(argstr='-mask %s',
                      exists=True,
-                     mandatory=False,
                      desc='Filename of the ROI for label fusion')
 
 

nipype/interfaces/niftyseg/lesions.py

@@ -99,9 +99,8 @@ class FillLesions(NiftySegCommand):
 
     Fill all the masked lesions with WM intensity average.
 
-    For source code, see http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg
-    For Documentation, see:
-        http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation
+    `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
     --------

nipype/interfaces/niftyseg/maths.py

@@ -102,7 +102,8 @@ class UnaryMaths(MathsCommand):
     """Interface for executable seg_maths from NiftySeg platform.
 
     Interface to use any unary mathematical operations that can be performed
-    with the seg_maths command-line program. See below for those operations:
+    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.
@@ -133,9 +134,8 @@ class UnaryMaths(MathsCommand):
         -4to5           Flip the 4th and 5th dimension.
         -range          Reset the image range to the min max
 
-    For source code, see http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg
-    For Documentation, see:
-        http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation
+    `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
     --------
@@ -216,7 +216,8 @@ class BinaryMaths(MathsCommand):
     """Interface for executable seg_maths from NiftySeg platform.
 
     Interface to use any binary mathematical operations that can be performed
-    with the seg_maths command-line program. See below for those operations:
+    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.
@@ -248,9 +249,8 @@ class BinaryMaths(MathsCommand):
         -splitinter <x/y/z>     Split interleaved slices in direction <x/y/z>
                                 into separate time points
 
-    For source code, see http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg
-    For Documentation, see:
-        http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation
+    `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
     --------
@@ -348,8 +348,9 @@ class BinaryMathsInteger(MathsCommand):
     """Interface for executable seg_maths from NiftySeg platform.
 
     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)
+    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).
         -ero    <int>       Erode the image <int> times (in voxels).
@@ -358,9 +359,8 @@ class BinaryMathsInteger(MathsCommand):
         -pad    <int>       Pad <int> voxels with NaN value around each 3D
                             volume.
 
-    For source code, see http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg
-    For Documentation, see:
-        http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation
+    `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
     --------
@@ -436,17 +436,17 @@ class TupleMaths(MathsCommand):
     """Interface for executable seg_maths from NiftySeg platform.
 
     Interface to use any tuple mathematical operations that can be performed
-    with the seg_maths command-line program. See below for those operations:
+    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
 
-    For source code, see http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg
-    For Documentation, see:
-        http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation
+    `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
     --------
@@ -504,13 +504,13 @@ class Merge(MathsCommand):
     """Interface for executable seg_maths from NiftySeg platform.
 
     Interface to use the merge operation that can be performed
-    with the seg_maths command-line program. See below for this option:
+    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
 
-    For source code, see http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg
-    For Documentation, see:
-        http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation
+    `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
     --------

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):
@@ -96,9 +91,8 @@ class PatchMatch(NiftySegCommand):
     volumes than the input image allowing to propagate multiple labels
     in the same execution.
 
-    For source code, see http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg
-    For Documentation, see:
-        http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation
+    `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
     --------

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)
 
@@ -103,7 +101,8 @@ class UnaryStats(StatsCommand):
     Interface for executable seg_stats from NiftySeg platform.
 
     Interface to use any unary statistical operations that can be performed
-    with the seg_stats command-line program. See below for those operations:
+    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
@@ -130,9 +129,8 @@ class UnaryStats(StatsCommand):
         -xdim       | Output the voxel dimention in the x direction.
                     | Replace x with y/z for other directions.
 
-    For source code, see http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg
-    For Documentation, see:
-        http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation
+    `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
     --------
@@ -191,7 +189,8 @@ class BinaryStats(StatsCommand):
     Interface for executable seg_stats from NiftySeg platform.
 
     Interface to use any binary statistical operations that can be performed
-    with the seg_stats command-line program. See below for those operations:
+    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
@@ -206,9 +205,8 @@ 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.
 
-    For source code, see http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg
-    For Documentation, see:
-        http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation
+    `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
     --------

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',

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,

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,

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',