DOCTEST: De-indent docstrings with testsetup/cleanup blocks

effigies · effigies · commit 152a44484478 · 2018-06-05T08:51:51.000-04:00
diff --git a/nipype/interfaces/base/core.py b/nipype/interfaces/base/core.py
@@ -680,26 +680,24 @@ def _post_run_hook(self, runtime):
 
 class SimpleInterface(BaseInterface):
     """ An interface pattern that allows outputs to be set in a dictionary
-    called ``_results`` that is automatically interpreted by
-    ``_list_outputs()`` to find the outputs.
+called ``_results`` that is automatically interpreted by
+``_list_outputs()`` to find the outputs.
 
-    When implementing ``_run_interface``, set outputs with::
+When implementing ``_run_interface``, set outputs with::
 
-        self._results[out_name] = out_value
+    self._results[out_name] = out_value
 
-    This can be a way to upgrade a ``Function`` interface to do type checking.
+This can be a way to upgrade a ``Function`` interface to do type checking.
 
-    Examples
-    --------
+Examples
+--------
 
-    .. testsetup::
+.. testsetup::
 
     >>> from .specs import TraitedSpec
     >>> tmp = getfixture('tmpdir')
     >>> old = tmp.chdir() # changing to a temporary directory
 
-    .. doctest::
-
     >>> def double(x):
     ...    return 2 * x
     ...
@@ -722,11 +720,10 @@ class SimpleInterface(BaseInterface):
     >>> dbl.run().outputs.doubled
     4.0
 
-    .. testsetup::
+.. testcleanup::
 
     >>> os.chdir(old.strpath)
-
-    """
+"""
 
     def __init__(self, from_file=None, resource_monitor=None, **inputs):
         super(SimpleInterface, self).__init__(
diff --git a/nipype/interfaces/dcm2nii.py b/nipype/interfaces/dcm2nii.py
@@ -103,29 +103,26 @@ class Dcm2niiOutputSpec(TraitedSpec):
 class Dcm2nii(CommandLine):
     """Uses MRIcron's dcm2nii to convert dicom files
 
-    Examples
-    ========
+Examples
+========
 
-    .. testsetup::
+.. 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.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'
+>>> 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.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::
+.. testcleanup::
 
     >>> os.chdir(old.strpath)
-
-    """
+"""
 
     input_spec = Dcm2niiInputSpec
     output_spec = Dcm2niiOutputSpec
diff --git a/nipype/interfaces/image.py b/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
 
diff --git a/nipype/interfaces/io.py b/nipype/interfaces/io.py
@@ -2579,36 +2579,33 @@ class JSONFileGrabberInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
 
 class JSONFileGrabber(IOBase):
     """
-    Datagrabber interface that loads a json file and generates an output for
-    every first-level object
+Datagrabber interface that loads a json file and generates an output for
+every first-level object
 
-    Example
-    -------
+Example
+-------
 
-    .. testsetup::
+.. testsetup::
 
     >>> tmp = getfixture('tmpdir')
     >>> old = tmp.chdir() # changing to a temporary directory
 
-    .. doctest::
+>>> import pprint
+>>> from nipype.interfaces.io import JSONFileGrabber
+>>> jsonSource = JSONFileGrabber()
+>>> jsonSource.inputs.defaults = {'param1': 'overrideMe', 'param3': 1.0}
+>>> res = jsonSource.run()
+>>> pprint.pprint(res.outputs.get())
+{'param1': 'overrideMe', 'param3': 1.0}
+>>> jsonSource.inputs.in_file = os.path.join(datadir, 'jsongrabber.txt')
+>>> res = jsonSource.run()
+>>> pprint.pprint(res.outputs.get())  # doctest:, +ELLIPSIS
+{'param1': 'exampleStr', 'param2': 4, 'param3': 1.0}
 
-    >>> import pprint
-    >>> from nipype.interfaces.io import JSONFileGrabber
-    >>> jsonSource = JSONFileGrabber()
-    >>> jsonSource.inputs.defaults = {'param1': 'overrideMe', 'param3': 1.0}
-    >>> res = jsonSource.run()
-    >>> pprint.pprint(res.outputs.get())
-    {'param1': 'overrideMe', 'param3': 1.0}
-    >>> jsonSource.inputs.in_file = os.path.join(datadir, 'jsongrabber.txt')
-    >>> res = jsonSource.run()
-    >>> pprint.pprint(res.outputs.get())  # doctest:, +ELLIPSIS
-    {'param1': 'exampleStr', 'param2': 4, 'param3': 1.0}
-
-    .. testsetup::
+.. testcleanup::
 
     >>> os.chdir(old.strpath)
-
-    """
+"""
     input_spec = JSONFileGrabberInputSpec
     output_spec = DynamicTraitedSpec
     _always_run = True
diff --git a/nipype/interfaces/niftyreg/regutils.py b/nipype/interfaces/niftyreg/regutils.py
@@ -437,40 +437,37 @@ class RegAverageOutputSpec(TraitedSpec):
 class RegAverage(NiftyRegCommand):
     """Interface for executable reg_average from NiftyReg platform.
 
-    Compute average matrix or image from a list of matrices or image.
-    The tool can be use to resample images given input transformation
-    parametrisation as well as to demean transformations in Euclidean or
-    log-Euclidean space.
+Compute average matrix or image from a list of matrices or image.
+The tool can be use to resample images given input transformation
+parametrisation as well as to demean transformations in Euclidean or
+log-Euclidean space.
 
-    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.
+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.
 
-    `Source code <https://cmiclab.cs.ucl.ac.uk/mmodat/niftyreg>`_
+`Source code <https://cmiclab.cs.ucl.ac.uk/mmodat/niftyreg>`_
 
-    Examples
-    --------
+Examples
+--------
 
-    .. testsetup::
+.. testsetup::
 
     >>> tmp = getfixture('tmpdir')
     >>> old = tmp.chdir() # changing to temporary file
 
-    .. doctest::
+>>> from nipype.interfaces import niftyreg
+>>> node = niftyreg.RegAverage()
+>>> one_file = 'im1.nii'
+>>> two_file = 'im2.nii'
+>>> three_file = 'im3.nii'
+>>> node.inputs.avg_files = [one_file, two_file, three_file]
+>>> node.cmdline  # doctest: +ELLIPSIS
+'reg_average --cmd_file .../reg_average_cmd'
 
-    >>> from nipype.interfaces import niftyreg
-    >>> node = niftyreg.RegAverage()
-    >>> one_file = 'im1.nii'
-    >>> two_file = 'im2.nii'
-    >>> three_file = 'im3.nii'
-    >>> node.inputs.avg_files = [one_file, two_file, three_file]
-    >>> node.cmdline  # doctest: +ELLIPSIS
-    'reg_average --cmd_file .../reg_average_cmd'
-
-    .. testsetup::
+.. testcleanup::
 
     >>> os.chdir(old.strpath)
-
-    """
+"""
     _cmd = get_custom_path('reg_average')
     input_spec = RegAverageInputSpec
     output_spec = RegAverageOutputSpec
