moving print to warning and editing docstring

Author: byvernault

nipype/interfaces/niftyreg/base.py

@@ -23,16 +23,12 @@
 from distutils.version import StrictVersion
 import os
 import subprocess
-import warnings
+from warnings import warn
 
 from ..base import CommandLine, isdefined, traits
 from ...utils.filemanip import split_filename
 
 
-warn = warnings.warn
-warnings.filterwarnings('always', category=UserWarning)
-
-
 def get_custom_path(command):
     try:
         specific_dir = os.environ['NIFTYREGDIR']
@@ -77,13 +73,13 @@ def __init__(self, required_version=None, **inputs):
         if _version:
             _version = _version.decode("utf-8")
             if StrictVersion(_version) < StrictVersion(self._min_version):
-                warn = 'A later version of Niftyreg is required (%s < %s)'
-                print(warn % (_version, self._min_version))
+                msg = 'A later version of Niftyreg is required (%s < %s)'
+                warn(msg % (_version, self._min_version))
             if required_version is not None:
                 if StrictVersion(_version) != StrictVersion(required_version):
-                    warn = 'The version of NiftyReg differs from the required'
-                    warn += '(%s != %s)'
-                    print(warn % (_version, required_version))
+                    msg = 'The version of NiftyReg differs from the required'
+                    msg += '(%s != %s)'
+                    warn(msg % (_version, self.required_version))
 
     def check_version(self):
         _version = self.get_version()

nipype/interfaces/niftyreg/reg.py

@@ -157,7 +157,7 @@ class RegAladin(NiftyRegCommand):
     >>> node.inputs.omp_core_val = 4
     >>> node.cmdline  # doctest: +ELLIPSIS +ALLOW_UNICODE
     'reg_aladin -aff .../im2_aff.txt -flo im2.nii -omp 4 -ref im1.nii \
--rmask mask.nii -res .../im2_res.nii.gz'
+-res .../im2_res.nii.gz -rmask mask.nii'
 
     """
     _cmd = get_custom_path('reg_aladin')
@@ -386,9 +386,8 @@ class RegF3D(NiftyRegCommand):
     >>> node.inputs.rmask_file = 'mask.nii'
     >>> node.inputs.omp_core_val = 4
     >>> node.cmdline  # doctest: +ELLIPSIS +ALLOW_UNICODE
-    'reg_f3d -be 0.100000 -cpp .../im2_cpp.nii.gz -flo im2.nii -le \
-0.100000 -omp 4 -ref im1.nii -res .../flo_res.nii.gz -rmask mask.nii \
--vel'
+    'reg_f3d -cpp .../im2_cpp.nii.gz -flo im2.nii -omp 4 -ref im1.nii \
+-res .../flo_res.nii.gz -rmask mask.nii'
 
     """
     _cmd = get_custom_path('reg_f3d')

nipype/interfaces/niftyreg/regutils.py

@@ -110,7 +110,7 @@ class RegResample(NiftyRegCommand):
     >>> node.inputs.inter_val = 'LIN'
     >>> node.inputs.omp_core_val = 4
     >>> node.cmdline  # doctest: +ELLIPSIS +ALLOW_UNICODE
-    'reg_resample -flo im2.nii.gz -inter 1 -omp 4 -ref im1.nii -trans \
+    'reg_resample -flo im2.nii -inter 1 -omp 4 -ref im1.nii -trans \
 warpfield.nii -res .../im2_res.nii.gz'
 
     """
@@ -409,8 +409,8 @@ class RegAverage(NiftyRegCommand):
     >>> two_file = 'im2.nii'
     >>> three_file = 'im3.nii'
     >>> node.inputs.avg_files = [one_file, two_file, three_file]
-    >>> node.cmdline  # doctest: +ALLOW_UNICODE
-    'reg_average --cmd_file reg_average_cmd'
+    >>> node.cmdline  # doctest: +ELLIPSIS +ALLOW_UNICODE
+    'reg_average --cmd_file .../reg_average_cmd'
 
     """
     _cmd = get_custom_path('reg_average')