TEST: Parallelize pytest

nipype/__init__.py

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

nipype/algorithms/confounds.py

@@ -3,13 +3,6 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 '''
 Algorithms to compute confounds in :abbr:`fMRI (functional MRI)`
-
-    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'))
-    >>> os.chdir(datadir)
-
 '''
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/algorithms/mesh.py

@@ -3,14 +3,6 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """
 Miscellaneous algorithms for 2D contours and 3D triangularized meshes handling
-
-  .. testsetup::
-    # 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'))
-    >>> os.chdir(datadir)
-
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/algorithms/metrics.py

@@ -4,13 +4,6 @@
 '''
 Image assessment algorithms. Typical overlap and error computation
 measures to evaluate results from other processing units.
-
-    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'))
-    >>> os.chdir(datadir)
-
 '''
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/algorithms/misc.py

@@ -3,13 +3,6 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 '''
 Miscellaneous algorithms
-
-    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'))
-    >>> os.chdir(datadir)
-
 '''
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/algorithms/modelgen.py

@@ -10,13 +10,6 @@
 These functions include:
 
   * SpecifyModel: allows specification of sparse and non-sparse models
-
-   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'))
-   >>> os.chdir(datadir)
-
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/algorithms/rapidart.py

@@ -11,12 +11,6 @@
 
   * StimulusCorrelation: determines correlation between stimuli
     schedule and movement/intensity parameters
-
-   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'))
-   >>> os.chdir(datadir)
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/caching/memory.py

@@ -2,12 +2,6 @@
 """
 Using nipype with persistence and lazy recomputation but without explicit
 name-steps pipeline: getting back scope in command-line based programming.
-
-   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'))
-   >>> os.chdir(datadir)
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/conftest.py

@@ -2,12 +2,20 @@
 import numpy
 import os
 
+DATADIR = os.path.realpath(
+    os.path.join(os.path.dirname(__file__), 'testing/data'))
+
 
 @pytest.fixture(autouse=True)
 def add_np(doctest_namespace):
     doctest_namespace['np'] = numpy
     doctest_namespace['os'] = os
 
-    filepath = os.path.dirname(os.path.realpath(__file__))
-    datadir = os.path.realpath(os.path.join(filepath, 'testing/data'))
-    doctest_namespace["datadir"] = datadir
+    doctest_namespace["datadir"] = DATADIR
+
+
+@pytest.fixture(autouse=True)
+def in_testing(request):
+    # This seems to be a reliable way to distinguish tests from doctests
+    if request.function is None:
+        os.chdir(DATADIR)

nipype/info.py

@@ -153,7 +153,7 @@ def get_nipype_gitversion():
 if sys.version_info <= (3, 4):
     REQUIRES.append('configparser')
 
-TESTS_REQUIRES = ['pytest-cov', 'codecov']
+TESTS_REQUIRES = ['pytest-cov', 'codecov', 'pytest-xdist', 'pytest-env']
 
 EXTRA_REQUIRES = {
     'doc': ['Sphinx>=1.4', 'numpydoc', 'matplotlib', 'pydotplus', 'pydot>=1.2.3'],

nipype/interfaces/afni/model.py

@@ -6,11 +6,6 @@
 Examples
 --------
 See the docstrings of the individual classes for examples.
-  .. testsetup::
-    # Change directory to provide relative paths for doctests
-    >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
-    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
-    >>> os.chdir(datadir)
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/interfaces/afni/preprocess.py

@@ -2,12 +2,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """AFNI preprocessing interfaces
-
-    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'))
-    >>> os.chdir(datadir)
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/interfaces/afni/svm.py

@@ -2,12 +2,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft = python sts = 4 ts = 4 sw = 4 et:
 """Afni svm interfaces
-
-    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'))
-    >>> os.chdir(datadir)
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/interfaces/afni/utils.py

@@ -6,11 +6,6 @@
 Examples
 --------
 See the docstrings of the individual classes for examples.
-  .. testsetup::
-    # Change directory to provide relative paths for doctests
-    >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
-    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
-    >>> os.chdir(datadir)
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/interfaces/ants/legacy.py

@@ -4,12 +4,6 @@
 #        of the antsApplyTransform program.  This implementation is here
 #        for backwards compatibility.
 """ANTS Apply Transforms interface
-
-   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'))
-   >>> os.chdir(datadir)
 """
 
 from builtins import range

nipype/interfaces/ants/registration.py

@@ -1,12 +1,6 @@
 # -*- coding: utf-8 -*-
 """The ants module provides basic functions for interfacing with ants
    functions.
-
-   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'))
-   >>> os.chdir(datadir)
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/interfaces/ants/resampling.py

@@ -1,11 +1,5 @@
 # -*- coding: utf-8 -*-
 """ANTS Apply Transforms interface
-
-   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'))
-   >>> os.chdir(datadir)
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/interfaces/ants/segmentation.py

@@ -1,12 +1,5 @@
 # -*- coding: utf-8 -*-
 """The ants module provides basic functions for interfacing with ants functions.
-
-   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'))
-   >>> os.chdir(datadir)
-
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/interfaces/ants/utils.py

@@ -1,11 +1,5 @@
 # -*- coding: utf-8 -*-
 """ANTS Apply Transforms interface
-
-   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'))
-   >>> os.chdir(datadir)
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/interfaces/ants/visualization.py

@@ -1,10 +1,5 @@
 # -*- coding: utf-8 -*-
 """The ants visualisation module provides basic functions based on ITK.
-   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'))
-   >>> os.chdir(datadir)
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/interfaces/bru2nii.py

@@ -1,11 +1,5 @@
 # -*- coding: utf-8 -*-
 """The bru2nii module provides basic functions for dicom conversion
-
-    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'))
-    >>> os.chdir(datadir)
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/interfaces/c3.py

@@ -1,12 +1,6 @@
 # -*- coding: utf-8 -*-
 """The ants module provides basic functions for interfacing with ants
    functions.
-
-   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'))
-   >>> os.chdir(datadir)
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)

nipype/interfaces/camino/calib.py

@@ -1,12 +1,4 @@
 # -*- coding: utf-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'))
-    >>> os.chdir(datadir)
-
-"""
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)
 

nipype/interfaces/camino/connectivity.py

@@ -1,12 +1,4 @@
 # -*- coding: utf-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'))
-    >>> os.chdir(datadir)
-
-"""
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)
 import os

nipype/interfaces/camino/convert.py

@@ -1,12 +1,4 @@
 # -*- coding: utf-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'))
-    >>> os.chdir(datadir)
-
-"""
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)
 

nipype/interfaces/camino/dti.py

@@ -1,12 +1,4 @@
 # -*- coding: utf-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'))
-    >>> os.chdir(datadir)
-
-"""
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)
 

nipype/interfaces/camino/odf.py

@@ -1,12 +1,4 @@
 # -*- coding: utf-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'))
-    >>> os.chdir(datadir)
-
-"""
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)
 

nipype/interfaces/camino/utils.py

@@ -1,12 +1,4 @@
 # -*- coding: utf-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'))
-    >>> os.chdir(datadir)
-
-"""
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)
 import os

nipype/interfaces/camino2trackvis/convert.py

@@ -1,13 +1,6 @@
 # -*- coding: utf-8 -*-
 """
 Provides interfaces to various commands provided by Camino-Trackvis
-
-    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'))
-    >>> os.chdir(datadir)
-
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)