DOCTEST: De-indent or remove testsetup blocks

Author: effigies

nipype/interfaces/base/core.py

@@ -692,14 +692,6 @@ class SimpleInterface(BaseInterface):
     Examples
     --------
 
-    .. testsetup::
-
-    >>> from .specs import TraitedSpec
-    >>> tmp = getfixture('tmpdir')
-    >>> old = tmp.chdir() # changing to a temporary directory
-
-    .. doctest::
-
     >>> def double(x):
     ...    return 2 * x
     ...
@@ -721,11 +713,6 @@ class SimpleInterface(BaseInterface):
     >>> dbl.inputs.x = 2
     >>> dbl.run().outputs.doubled
     4.0
-
-    .. testsetup::
-
-    >>> os.chdir(old.strpath)
-
     """
 
     def __init__(self, from_file=None, resource_monitor=None, **inputs):

nipype/interfaces/dcm2nii.py

@@ -106,26 +106,14 @@ class Dcm2nii(CommandLine):
     Examples
     ========
 
-    .. testsetup::
-
-    >>> tmp = getfixture('tmpdir')
-    >>> old = tmp.chdir() # changing to a temporary directory
-
-    .. doctest::
-
     >>> from nipype.interfaces.dcm2nii import Dcm2nii
     >>> converter = Dcm2nii()
-    >>> converter.inputs.source_names = [os.path.join(datadir, 'functional_1.dcm'), os.path.join(datadir, 'functional_2.dcm')]
+    >>> converter.inputs.source_names = ['functional_1.dcm', 'functional_2.dcm']
     >>> converter.inputs.gzip_output = True
     >>> converter.inputs.output_dir = '.'
-    >>> converter.cmdline #doctest: +ELLIPSIS
-    'dcm2nii -a y -c y -b config.ini -v y -d y -e y -g y -i n -n y -o . -p y -x n -f n ...functional_1.dcm'
-
-    .. testsetup::
-
-    >>> os.chdir(old.strpath)
-
-    """
+    >>> converter.cmdline  # doctest: +ELLIPSIS
+    'dcm2nii -a y -c y -b config.ini -v y -d y -e y -g y -i n -n y -o . -p y -x n -f n functional_1.dcm'
+"""
 
     input_spec = Dcm2niiInputSpec
     output_spec = Dcm2niiOutputSpec

nipype/interfaces/image.py

@@ -32,65 +32,63 @@ class ReorientOutputSpec(TraitedSpec):
 class Reorient(SimpleInterface):
     """Conform an image to a given orientation
 
-    Flips and reorder the image data array so that the axes match the
-    directions indicated in ``orientation``.
-    The default ``RAS`` orientation corresponds to the first axis being ordered
-    from left to right, the second axis from posterior to anterior, and the
-    third axis from inferior to superior.
+Flips and reorder the image data array so that the axes match the
+directions indicated in ``orientation``.
+The default ``RAS`` orientation corresponds to the first axis being ordered
+from left to right, the second axis from posterior to anterior, and the
+third axis from inferior to superior.
 
-    For oblique images, the original orientation is considered to be the
-    closest plumb orientation.
+For oblique images, the original orientation is considered to be the
+closest plumb orientation.
 
-    No resampling is performed, and thus the output image is not de-obliqued
-    or registered to any other image or template.
+No resampling is performed, and thus the output image is not de-obliqued
+or registered to any other image or template.
 
-    The effective transform is calculated from the original affine matrix to
-    the reoriented affine matrix.
+The effective transform is calculated from the original affine matrix to
+the reoriented affine matrix.
 
-    Examples
-    --------
+Examples
+--------
 
-    .. testsetup::
+If an image is not reoriented, the original file is not modified
+
+.. testsetup::
 
     >>> def print_affine(matrix):
     ...     print(str(matrix).replace(']', ' ').replace('[', ' '))
 
-    .. doctest::
-
-    If an image is not reoriented, the original file is not modified
-
-    >>> import numpy as np
-    >>> from nipype.interfaces.image import Reorient
-    >>> reorient = Reorient(orientation='LPS')
-    >>> reorient.inputs.in_file = 'segmentation0.nii.gz'
-    >>> res = reorient.run()
-    >>> res.outputs.out_file
-    'segmentation0.nii.gz'
-
-    >>> print_affine(np.loadtxt(res.outputs.transform))
-    1.  0.  0.  0.
-    0.  1.  0.  0.
-    0.  0.  1.  0.
-    0.  0.  0.  1.
-
-    >>> reorient.inputs.orientation = 'RAS'
-    >>> res = reorient.run()
-    >>> res.outputs.out_file  # doctest: +ELLIPSIS
-    '.../segmentation0_ras.nii.gz'
-
-    >>> print_affine(np.loadtxt(res.outputs.transform))
-    -1.   0.   0.  60.
-     0.  -1.   0.  72.
-     0.   0.   1.   0.
-     0.   0.   0.   1.
-
-    .. testcleanup::
-
-        >>> import os
-        >>> os.unlink(res.outputs.out_file)
-        >>> os.unlink(res.outputs.transform)
-
-    """
+>>> import numpy as np
+>>> from nipype.interfaces.image import Reorient
+>>> reorient = Reorient(orientation='LPS')
+>>> reorient.inputs.in_file = 'segmentation0.nii.gz'
+>>> res = reorient.run()
+>>> res.outputs.out_file
+'segmentation0.nii.gz'
+
+>>> print_affine(np.loadtxt(res.outputs.transform))
+1.  0.  0.  0.
+0.  1.  0.  0.
+0.  0.  1.  0.
+0.  0.  0.  1.
+
+>>> reorient.inputs.orientation = 'RAS'
+>>> res = reorient.run()
+>>> res.outputs.out_file  # doctest: +ELLIPSIS
+'.../segmentation0_ras.nii.gz'
+
+>>> print_affine(np.loadtxt(res.outputs.transform))
+-1.   0.   0.  60.
+ 0.  -1.   0.  72.
+ 0.   0.   1.   0.
+ 0.   0.   0.   1.
+
+.. testcleanup::
+
+    >>> import os
+    >>> os.unlink(res.outputs.out_file)
+    >>> os.unlink(res.outputs.transform)
+
+"""
     input_spec = ReorientInputSpec
     output_spec = ReorientOutputSpec
 

nipype/interfaces/io.py

@@ -2585,13 +2585,6 @@ class JSONFileGrabber(IOBase):
     Example
     -------
 
-    .. testsetup::
-
-    >>> tmp = getfixture('tmpdir')
-    >>> old = tmp.chdir() # changing to a temporary directory
-
-    .. doctest::
-
     >>> import pprint
     >>> from nipype.interfaces.io import JSONFileGrabber
     >>> jsonSource = JSONFileGrabber()
@@ -2603,11 +2596,6 @@ class JSONFileGrabber(IOBase):
     >>> res = jsonSource.run()
     >>> pprint.pprint(res.outputs.get())  # doctest:, +ELLIPSIS
     {'param1': 'exampleStr', 'param2': 4, 'param3': 1.0}
-
-    .. testsetup::
-
-    >>> os.chdir(old.strpath)
-
     """
     input_spec = JSONFileGrabberInputSpec
     output_spec = DynamicTraitedSpec

nipype/interfaces/niftyreg/regutils.py

@@ -450,13 +450,6 @@ class RegAverage(NiftyRegCommand):
     Examples
     --------
 
-    .. testsetup::
-
-    >>> tmp = getfixture('tmpdir')
-    >>> old = tmp.chdir() # changing to temporary file
-
-    .. doctest::
-
     >>> from nipype.interfaces import niftyreg
     >>> node = niftyreg.RegAverage()
     >>> one_file = 'im1.nii'
@@ -465,11 +458,6 @@ class RegAverage(NiftyRegCommand):
     >>> node.inputs.avg_files = [one_file, two_file, three_file]
     >>> node.cmdline  # doctest: +ELLIPSIS
     'reg_average --cmd_file .../reg_average_cmd'
-
-    .. testsetup::
-
-    >>> os.chdir(old.strpath)
-
     """
     _cmd = get_custom_path('reg_average')
     input_spec = RegAverageInputSpec