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Merge pull request #2469 from effigies/ci/parallel_pytest
TEST: Parallelize pytest
2 parents 41a5583 + 6d2c325 commit bc6df5b

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‎nipype/__init__.py

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@@ -25,19 +25,19 @@
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class NipypeTester(object):
28-
def __call__(self, doctests=True):
28+
def __call__(self, doctests=True, parallel=True):
2929
try:
3030
import pytest
3131
except:
3232
raise RuntimeError(
3333
'py.test not installed, run: pip install pytest')
34-
params = {'args': []}
35-
if doctests:
36-
params['args'].append('--doctest-modules')
37-
nipype_path = os.path.dirname(__file__)
38-
params['args'].extend(
39-
['-x', '--ignore={}/external'.format(nipype_path), nipype_path])
40-
pytest.main(**params)
34+
args = []
35+
if not doctests:
36+
args.extend(['-p', 'no:doctest'])
37+
if not parallel:
38+
args.append('-n0')
39+
args.append(os.path.dirname(__file__))
40+
pytest.main(args=args)
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test = NipypeTester()

‎nipype/algorithms/confounds.py

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# vi: set ft=python sts=4 ts=4 sw=4 et:
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'''
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Algorithms to compute confounds in :abbr:`fMRI (functional MRI)`
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Change directory to provide relative paths for doctests
8-
>>> import os
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>>> filepath = os.path.dirname(os.path.realpath(__file__))
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>>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data'))
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>>> os.chdir(datadir)
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'''
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from __future__ import (print_function, division, unicode_literals,
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absolute_import)

‎nipype/algorithms/mesh.py

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# vi: set ft=python sts=4 ts=4 sw=4 et:
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"""
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Miscellaneous algorithms for 2D contours and 3D triangularized meshes handling
6-
7-
.. testsetup::
8-
# Change directory to provide relative paths for doctests
9-
>>> import os
10-
>>> filepath = os.path.dirname(os.path.realpath( __file__ ))
11-
>>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data'))
12-
>>> os.chdir(datadir)
13-
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"""
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from __future__ import (print_function, division, unicode_literals,
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absolute_import)

‎nipype/algorithms/metrics.py

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'''
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Image assessment algorithms. Typical overlap and error computation
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measures to evaluate results from other processing units.
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Change directory to provide relative paths for doctests
9-
>>> import os
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>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
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>>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data'))
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>>> os.chdir(datadir)
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'''
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from __future__ import (print_function, division, unicode_literals,
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absolute_import)

‎nipype/algorithms/misc.py

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# vi: set ft=python sts=4 ts=4 sw=4 et:
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'''
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Miscellaneous algorithms
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Change directory to provide relative paths for doctests
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>>> import os
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>>> filepath = os.path.dirname(os.path.realpath(__file__))
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>>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data'))
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>>> os.chdir(datadir)
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'''
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from __future__ import (print_function, division, unicode_literals,
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absolute_import)

‎nipype/algorithms/modelgen.py

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These functions include:
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* SpecifyModel: allows specification of sparse and non-sparse models
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Change directory to provide relative paths for doctests
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>>> import os
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>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
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>>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data'))
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>>> os.chdir(datadir)
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2013
"""
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from __future__ import (print_function, division, unicode_literals,
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absolute_import)

‎nipype/algorithms/rapidart.py

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* StimulusCorrelation: determines correlation between stimuli
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schedule and movement/intensity parameters
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Change directory to provide relative paths for doctests
16-
>>> import os
17-
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
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>>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data'))
19-
>>> os.chdir(datadir)
2014
"""
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from __future__ import (print_function, division, unicode_literals,
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absolute_import)

‎nipype/caching/memory.py

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"""
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Using nipype with persistence and lazy recomputation but without explicit
44
name-steps pipeline: getting back scope in command-line based programming.
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Change directory to provide relative paths for doctests
7-
>>> import os
8-
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
9-
>>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data'))
10-
>>> os.chdir(datadir)
115
"""
126
from __future__ import (print_function, division, unicode_literals,
137
absolute_import)

‎nipype/conftest.py

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Original file line numberDiff line numberDiff line change
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import numpy
33
import os
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5+
DATADIR = os.path.realpath(
6+
os.path.join(os.path.dirname(__file__), 'testing/data'))
7+
58

69
@pytest.fixture(autouse=True)
710
def add_np(doctest_namespace):
811
doctest_namespace['np'] = numpy
912
doctest_namespace['os'] = os
1013

11-
filepath = os.path.dirname(os.path.realpath(__file__))
12-
datadir = os.path.realpath(os.path.join(filepath, 'testing/data'))
13-
doctest_namespace["datadir"] = datadir
14+
doctest_namespace["datadir"] = DATADIR
15+
16+
17+
@pytest.fixture(autouse=True)
18+
def in_testing(request):
19+
# This seems to be a reliable way to distinguish tests from doctests
20+
if request.function is None:
21+
os.chdir(DATADIR)

‎nipype/info.py

Lines changed: 1 addition & 1 deletion
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@@ -153,7 +153,7 @@ def get_nipype_gitversion():
153153
if sys.version_info <= (3, 4):
154154
REQUIRES.append('configparser')
155155

156-
TESTS_REQUIRES = ['pytest-cov', 'codecov']
156+
TESTS_REQUIRES = ['pytest-cov', 'codecov', 'pytest-xdist', 'pytest-env']
157157

158158
EXTRA_REQUIRES = {
159159
'doc': ['Sphinx>=1.4', 'numpydoc', 'matplotlib', 'pydotplus', 'pydot>=1.2.3'],

‎nipype/interfaces/afni/model.py

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Examples
77
--------
88
See the docstrings of the individual classes for examples.
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.. testsetup::
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# Change directory to provide relative paths for doctests
11-
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
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>>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
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>>> os.chdir(datadir)
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"""
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from __future__ import (print_function, division, unicode_literals,
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absolute_import)

‎nipype/interfaces/afni/preprocess.py

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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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# vi: set ft=python sts=4 ts=4 sw=4 et:
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"""AFNI preprocessing interfaces
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Change directory to provide relative paths for doctests
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>>> import os
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>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
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>>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
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>>> os.chdir(datadir)
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"""
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from __future__ import (print_function, division, unicode_literals,
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absolute_import)

‎nipype/interfaces/afni/svm.py

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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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# vi: set ft = python sts = 4 ts = 4 sw = 4 et:
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"""Afni svm interfaces
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>>> import os
8-
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
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>>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
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>>> os.chdir(datadir)
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"""
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from __future__ import (print_function, division, unicode_literals,
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absolute_import)

‎nipype/interfaces/afni/utils.py

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Examples
77
--------
88
See the docstrings of the individual classes for examples.
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.. testsetup::
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# Change directory to provide relative paths for doctests
11-
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
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>>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
13-
>>> os.chdir(datadir)
149
"""
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from __future__ import (print_function, division, unicode_literals,
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absolute_import)

‎nipype/interfaces/ants/legacy.py

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# of the antsApplyTransform program. This implementation is here
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# for backwards compatibility.
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"""ANTS Apply Transforms interface
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Change directory to provide relative paths for doctests
9-
>>> import os
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>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
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>>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
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>>> os.chdir(datadir)
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"""
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from builtins import range

‎nipype/interfaces/ants/registration.py

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# -*- coding: utf-8 -*-
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"""The ants module provides basic functions for interfacing with ants
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functions.
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Change directory to provide relative paths for doctests
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>>> import os
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>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
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>>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
9-
>>> os.chdir(datadir)
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"""
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from __future__ import (print_function, division, unicode_literals,
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absolute_import)

‎nipype/interfaces/ants/resampling.py

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# -*- coding: utf-8 -*-
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"""ANTS Apply Transforms interface
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Change directory to provide relative paths for doctests
5-
>>> import os
6-
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
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>>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
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>>> os.chdir(datadir)
93
"""
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from __future__ import (print_function, division, unicode_literals,
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absolute_import)

‎nipype/interfaces/ants/segmentation.py

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# -*- coding: utf-8 -*-
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"""The ants module provides basic functions for interfacing with ants functions.
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Change directory to provide relative paths for doctests
5-
>>> import os
6-
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
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>>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
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>>> os.chdir(datadir)
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"""
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from __future__ import (print_function, division, unicode_literals,
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absolute_import)

‎nipype/interfaces/ants/utils.py

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# -*- coding: utf-8 -*-
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"""ANTS Apply Transforms interface
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Change directory to provide relative paths for doctests
5-
>>> import os
6-
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
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>>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
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>>> os.chdir(datadir)
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"""
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from __future__ import (print_function, division, unicode_literals,
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absolute_import)

‎nipype/interfaces/ants/visualization.py

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# -*- coding: utf-8 -*-
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"""The ants visualisation module provides basic functions based on ITK.
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Change directory to provide relative paths for doctests
4-
>>> import os
5-
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
6-
>>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
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>>> os.chdir(datadir)
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"""
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from __future__ import (print_function, division, unicode_literals,
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absolute_import)

‎nipype/interfaces/bru2nii.py

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# -*- coding: utf-8 -*-
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"""The bru2nii module provides basic functions for dicom conversion
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Change directory to provide relative paths for doctests
5-
>>> import os
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>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
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>>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data'))
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>>> os.chdir(datadir)
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"""
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from __future__ import (print_function, division, unicode_literals,
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absolute_import)

‎nipype/interfaces/c3.py

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# -*- coding: utf-8 -*-
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"""The ants module provides basic functions for interfacing with ants
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functions.
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Change directory to provide relative paths for doctests
6-
>>> import os
7-
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
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>>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data'))
9-
>>> os.chdir(datadir)
104
"""
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from __future__ import (print_function, division, unicode_literals,
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absolute_import)

‎nipype/interfaces/camino/calib.py

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# -*- coding: utf-8 -*-
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"""
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Change directory to provide relative paths for doctests
4-
>>> import os
5-
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
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>>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
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>>> os.chdir(datadir)
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"""
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from __future__ import (print_function, division, unicode_literals,
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absolute_import)
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‎nipype/interfaces/camino/connectivity.py

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# -*- coding: utf-8 -*-
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"""
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Change directory to provide relative paths for doctests
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>>> import os
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>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
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>>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
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>>> os.chdir(datadir)
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"""
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from __future__ import (print_function, division, unicode_literals,
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absolute_import)
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import os

‎nipype/interfaces/camino/convert.py

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# -*- coding: utf-8 -*-
2-
"""
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Change directory to provide relative paths for doctests
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>>> import os
5-
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
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>>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
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>>> os.chdir(datadir)
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"""
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from __future__ import (print_function, division, unicode_literals,
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absolute_import)
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‎nipype/interfaces/camino/dti.py

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# -*- coding: utf-8 -*-
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"""
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Change directory to provide relative paths for doctests
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>>> import os
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>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
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>>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
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>>> os.chdir(datadir)
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"""
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from __future__ import (print_function, division, unicode_literals,
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absolute_import)
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‎nipype/interfaces/camino/odf.py

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# -*- coding: utf-8 -*-
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"""
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Change directory to provide relative paths for doctests
4-
>>> import os
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>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
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>>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
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>>> os.chdir(datadir)
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"""
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from __future__ import (print_function, division, unicode_literals,
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absolute_import)
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‎nipype/interfaces/camino/utils.py

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# -*- coding: utf-8 -*-
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"""
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Change directory to provide relative paths for doctests
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>>> import os
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>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
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>>> os.chdir(datadir)
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9-
"""
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from __future__ import (print_function, division, unicode_literals,
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absolute_import)
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import os

‎nipype/interfaces/camino2trackvis/convert.py

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# -*- coding: utf-8 -*-
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"""
33
Provides interfaces to various commands provided by Camino-Trackvis
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Change directory to provide relative paths for doctests
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>>> import os
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>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
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>>> os.chdir(datadir)
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"""
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from __future__ import (print_function, division, unicode_literals,
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absolute_import)

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