Merge pull request #564 from satra/fix/testing

FIX: updated testing so that nipype.test(doctests=True) works fine

Author: satra

nipype/__init__.py

@@ -11,36 +11,40 @@
 from utils.logger import Logging
 logging = Logging(config)
 
-# We require numpy 1.2 for our test suite.  If Tester fails to import,
-# check the version of numpy the user has and inform them they need to
-# upgrade.
-import numpy as np
 from distutils.version import LooseVersion
-if LooseVersion(np.__version__) >= '1.2':
-    from numpy.testing import Tester
-else:
-    from testing.numpytesting import Tester
-
-
-class NipypeTester(Tester):
-    def test(self, label='fast', verbose=1, extra_argv=None,
-             doctests=False, coverage=False):
-        # setuptools does a chmod +x on ALL python modules when it
-        # installs.  By default, as a security measure, nose refuses to
-        # import executable files.  To forse nose to execute our tests, we
-        # must supply the '--exe' flag.  List thread on this:
-        # http://www.mail-archive.com/[email protected]/msg05009.html
-        if not extra_argv:
-            extra_argv = ['--exe']
-        else:
-            extra_argv.append('--exe')
-        super(NipypeTester, self).test(label, verbose, extra_argv,
-                                       doctests, coverage)
-    # Grab the docstring from numpy
-    #test.__doc__ = Tester.test.__doc__
-
-test = NipypeTester().test
-bench = NipypeTester().bench
+
+from .fixes.numpy.testing import nosetester
+
+class _NoseTester(nosetester.NoseTester):
+    """ Subclass numpy's NoseTester to add doctests by default
+    """
+
+    def _get_custom_doctester(self):
+        return None
+
+    def test(self, label='fast', verbose=1, extra_argv=['--exe'],
+             doctests=True, coverage=False):
+        """Run the full test suite
+
+        Examples
+        --------
+        This will run the test suite and stop at the first failing
+        example
+        >>> from nipype import test
+        >>> test(extra_argv=['--exe', '-sx']) #doctest: +SKIP
+        """
+        return super(_NoseTester, self).test(label=label,
+                                             verbose=verbose,
+                                             extra_argv=extra_argv,
+                                             doctests=doctests,
+                                             coverage=coverage)
+
+try:
+    test = _NoseTester(raise_warnings="release").test
+except TypeError:
+    # Older versions of numpy do not have a raise_warnings argument
+    test = _NoseTester().test
+del nosetester
 
 
 def _test_local_install():

nipype/interfaces/afni/preprocess.py

@@ -1126,7 +1126,7 @@ class Allineate(AFNICommand):
     >>> allineate = afni.Allineate()
     >>> allineate.inputs.in_file = 'functional.nii'
     >>> allineate.inputs.out_file= 'functional_allineate.nii'
-    >>> allineate.inputs.matrix= 'cmatrix.mat'
+    >>> allineate.inputs.in_matrix= 'cmatrix.mat'
     >>> res = allineate.run() # doctest: +SKIP
 
     """

nipype/interfaces/fsl/model.py

@@ -1472,12 +1472,9 @@ class Randomise(FSLCommand):
     Example
     -------
     >>> import nipype.interfaces.fsl as fsl
-    >>> rand = fsl.Randomise(in_file='allFA.nii', \
-    mask = 'mask.nii', \
-    tcon='design.con', \
-    design_mat='design.mat')
+    >>> rand = fsl.Randomise(in_file='allFA.nii', mask = 'mask.nii', tcon='design.con', design_mat='design.mat')
     >>> rand.cmdline
-    'randomise -i allFA.nii -o tbss_ -d design.mat -t design.con -m mask.nii'
+    'randomise -i allFA.nii -o "tbss_" -d design.mat -t design.con -m mask.nii'
 
     """
 
@@ -1536,20 +1533,25 @@ class GLMInputSpec(FSLCommandInputSpec):
     options = traits.String(
         argstr='%s',
         desc = 'fsl_glm options')
+
+
 class GLMOutputSpec(TraitedSpec):
     out_file = File(
         exists=True,
         desc = 'file or image output')
 
+
 class GLM(FSLCommand):
     """
     FSL GLM: 
 
     Example
     -------
     >>> import nipype.interfaces.fsl as fsl
-    >>> glm = fsl.GLM(in_file='functional.nii', design = 'maps.nii')
+    >>> glm = fsl.GLM(in_file='functional.nii', design='maps.nii')
     >>> glm.cmdline
+    'fsl_glm -d maps.nii -i functional.nii -o functional_glm.txt'
+
     """
     _cmd = 'fsl_glm'
     input_spec = GLMInputSpec
@@ -1560,17 +1562,12 @@ def _list_outputs(self):
         outputs['out_file'] = self.inputs.out_file
         # Generate an out_file if one is not provided
         if not isdefined(outputs['out_file']) and isdefined(self.inputs.in_file):
-            ext = Info.output_type_to_ext(self.inputs.output_type)
-            if split_filename(self.inputs.in_file)[-1] in Info.ftypes.values():
-                ext = '.txt'
-            outputs['out_file'] = self._gen_fname(self.inputs.in_file,
-                                                  suffix='_glm',
-                                                  ext=ext)
-
+            outputs['out_file'] = os.path.abspath(self._gen_filename('out_file'))
         return outputs
 
     def _gen_filename(self, name):
         if name in ('out_file'):
-            return self._list_outputs()[name]
-        else:
-            return None
+            from nipype.utils.filemanip import fname_presuffix
+            return fname_presuffix(self.inputs.in_file,
+                                   suffix='_glm.txt', use_ext=False)
+        return None

nipype/testing/__init__.py

@@ -12,15 +12,6 @@
    for running the algorithms in the NIPY library.  This file should
    import without nose being present on the python path.
 
-Examples
---------
-
->>> from nipy.testing import funcfile
->>> from nipy.io.api import load_image
->>> img = load_image(funcfile)
->>> img.shape
-(17, 21, 3, 20)
-
 """
 
 import os
@@ -37,11 +28,6 @@
 from nose.tools import *
 from numpy.testing import *
 
-# Overwrites numpy.testing.Tester
-from .nosetester import NipyNoseTester as Tester
-test = Tester().test
-bench = Tester().bench
-
 from . import decorators as dec
 from .utils import skip_if_no_package, package_check
 
@@ -58,10 +44,3 @@ def example_data(infile='functional.nii'):
         raise IOError('%s empty data file does NOT exist'%(outfile))
 
     return outfile
-
-# Allow failed import of nose if not now running tests
-try:
-    from nose.tools import assert_true, assert_false
-    from lightunit import ParametricTestCase, parametric
-except ImportError:
-    pass