Moving source code url to the format use in nitfyseg

Author: byvernault

nipype/interfaces/niftyfit/asl.py

@@ -7,7 +7,8 @@
 Change directory to provide relative paths for doctests
     >>> import os
     >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
-    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
+    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/\
+data'))
     >>> os.chdir(datadir)
 """
 
@@ -139,7 +140,7 @@ class FitAsl(NiftyFitCommand):
     ASL fitting routines (following EU Cost Action White Paper recommendations)
     Fits Cerebral Blood Flow maps in the first instance.
 
-    For source code, see https://cmiclab.cs.ucl.ac.uk/CMIC/NiftyFit-Release
+    `Source code <https://cmiclab.cs.ucl.ac.uk/CMIC/NiftyFit-Release>`_
 
     Examples
     --------

nipype/interfaces/niftyfit/dwi.py

@@ -7,7 +7,8 @@
 Change directory to provide relative paths for doctests
     >>> import os
     >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
-    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
+    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/\
+data'))
     >>> os.chdir(datadir)
 """
 
@@ -236,7 +237,7 @@ class FitDwi(NiftyFitCommand):
     Diffusion-weighted MR Fitting.
     Fits DWI parameter maps to multi-shell, multi-directional data.
 
-    For source code, see https://cmiclab.cs.ucl.ac.uk/CMIC/NiftyFit-Release
+    `Source code <https://cmiclab.cs.ucl.ac.uk/CMIC/NiftyFit-Release>`_
 
     Examples
     --------
@@ -413,6 +414,8 @@ class DwiTool(NiftyFitCommand):
     Predicts DWI from previously fitted models and calculates model derived
     maps.
 
+    `Source code <https://cmiclab.cs.ucl.ac.uk/CMIC/NiftyFit-Release>`_
+
     Examples
     --------
 

nipype/interfaces/niftyfit/qt1.py

@@ -8,7 +8,8 @@
 Change directory to provide relative paths for doctests
     >>> import os
     >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
-    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
+    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/\
+data'))
     >>> os.chdir(datadir)
 """
 
@@ -156,7 +157,7 @@ class FitQt1(NiftyFitCommand):
     T1 Fitting Routine (To inversion recovery or spgr data).
     Fits single component T1 maps in the first instance.
 
-    For source code, see https://cmiclab.cs.ucl.ac.uk/CMIC/NiftyFit-Release
+    `Source code <https://cmiclab.cs.ucl.ac.uk/CMIC/NiftyFit-Release>`_
 
     Examples
     --------

nipype/interfaces/niftyreg/reg.py

@@ -11,7 +11,8 @@
 Change directory to provide relative paths for doctests
     >>> import os
     >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
-    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
+    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/\
+data'))
     >>> os.chdir(datadir)
 """
 
@@ -145,7 +146,7 @@ class RegAladin(NiftyRegCommand):
     asymmetric block-matching approach"
     J. Med. Img. 1(2) 024003, 2014, doi: 10.1117/1.JMI.1.2.024003
 
-    For source code, see https://cmiclab.cs.ucl.ac.uk/mmodat/niftyreg
+    `Source code <https://cmiclab.cs.ucl.ac.uk/mmodat/niftyreg>`_
 
     Examples
     --------
@@ -356,7 +357,7 @@ class RegF3D(NiftyRegCommand):
     Initially based on Modat et al., "Fast Free-Form Deformation using
     graphics processing units", CMPB, 2010
 
-    For source code, see https://cmiclab.cs.ucl.ac.uk/mmodat/niftyreg
+    `Source code <https://cmiclab.cs.ucl.ac.uk/mmodat/niftyreg>`_
 
     Examples
     --------

nipype/interfaces/niftyreg/regutils.py

@@ -10,7 +10,8 @@
 Change directory to provide relative paths for doctests
     >>> import os
     >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
-    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
+    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/\
+data'))
     >>> os.chdir(datadir)
 """
 
@@ -94,8 +95,7 @@ class RegResample(NiftyRegCommand):
     given a transformation parametrisation generated by reg_aladin, reg_f3d or
     reg_transform
 
-    For complete documentation, see https://cmiclab.cs.ucl.ac.uk/mmodat/\
-    niftyreg
+    `Source code <https://cmiclab.cs.ucl.ac.uk/mmodat/niftyreg>`_
 
     Examples
     --------
@@ -164,7 +164,7 @@ class RegJacobian(NiftyRegCommand):
     Tool to generate Jacobian determinant maps from transformation
     parametrisation generated by reg_f3d
 
-    For source code, see https://cmiclab.cs.ucl.ac.uk/mmodat/niftyreg
+    `Source code <https://cmiclab.cs.ucl.ac.uk/mmodat/niftyreg>`_
 
     Examples
     --------
@@ -280,7 +280,7 @@ class RegTools(NiftyRegCommand):
     resampling the input image to a chosen resolution or remove the nan and
     inf in the input image by a specified value.
 
-    For source code, see https://cmiclab.cs.ucl.ac.uk/mmodat/niftyreg
+    `Source code <https://cmiclab.cs.ucl.ac.uk/mmodat/niftyreg>`_
 
     Examples
     --------
@@ -387,7 +387,7 @@ class RegAverage(NiftyRegCommand):
     This interface is different than the others in the way that the options
     will be written in a command file that is given as a parameter.
 
-    For source code, see https://cmiclab.cs.ucl.ac.uk/mmodat/niftyreg
+    `Source code <https://cmiclab.cs.ucl.ac.uk/mmodat/niftyreg>`_
 
     Examples
     --------
@@ -584,7 +584,7 @@ class RegTransform(NiftyRegCommand):
     Tools to convert transformation parametrisation from one type to another
     as well as to compose, inverse or half transformations.
 
-    For source code, see https://cmiclab.cs.ucl.ac.uk/mmodat/niftyreg
+    `Source code <https://cmiclab.cs.ucl.ac.uk/mmodat/niftyreg>`_
 
     Examples
     --------
@@ -694,7 +694,7 @@ class RegMeasure(NiftyRegCommand):
 
     Given two input images, compute the specified measure(s) of similarity
 
-    For source code, see https://cmiclab.cs.ucl.ac.uk/mmodat/niftyreg
+    `Source code <https://cmiclab.cs.ucl.ac.uk/mmodat/niftyreg>`_
 
     Examples
     --------