TST: adapt nipy doctests to numpy 1.14

matthew-brett · matthew-brett · commit 2cfb95e08b5e · 2018-01-15T09:38:50.000Z
Numpy 1.14 has new printing output.  Use a version of Chris M's nibabel
fix to revert printing output to 1.13 style.
diff --git a/nipy/algorithms/registration/affine.py b/nipy/algorithms/registration/affine.py
@@ -9,6 +9,9 @@
 from ...externals.transforms3d.quaternions import mat2quat, quat2axangle
 from .transform import Transform
 
+# Legacy repr printing from numpy.
+from nipy.testing import legacy_printing as setup_module  # noqa
+
 # Globals
 RADIUS = 100
 MAX_ANGLE = 1e10 * 2 * np.pi
diff --git a/nipy/algorithms/slicetiming/timefuncs.py b/nipy/algorithms/slicetiming/timefuncs.py
@@ -30,6 +30,9 @@
 
 import numpy as np
 
+# Legacy repr printing from numpy.
+from nipy.testing import legacy_printing as setup_module  # noqa
+
 # Dictionary (key, value) == (name, function) for slice timing functions
 SLICETIME_FUNCTIONS = {}
 
diff --git a/nipy/algorithms/statistics/formula/formulae.py b/nipy/algorithms/statistics/formula/formulae.py
@@ -128,6 +128,10 @@
 
 from nipy.algorithms.utils.matrices import matrix_rank, full_rank
 
+# Legacy repr printing from numpy.
+from nipy.testing import legacy_printing as setup_module  # noqa
+
+
 @np.deprecate(message = "Please use sympy.Dummy instead of this function")
 def make_dummy(name):
     """ Make dummy variable of given name
diff --git a/nipy/algorithms/statistics/models/regression.py b/nipy/algorithms/statistics/models/regression.py
@@ -36,6 +36,9 @@
 
 from .model import LikelihoodModel, LikelihoodModelResults
 
+# Legacy repr printing from numpy.
+from nipy.testing import legacy_printing as setup_module  # noqa
+
 
 class OLSModel(LikelihoodModel):
     """ A simple ordinary least squares model.
@@ -342,9 +345,9 @@ class ARModel(OLSModel):
     AR coefficients: [-0.7220361  -1.05365352]
     AR coefficients: [-0.72229201 -1.05408193]
     AR coefficients: [-0.722278   -1.05405838]
-    >>> results.theta #doctest: +FP_6DP
+    >>> results.theta #doctest: +NP_ALLCLOSE
     array([ 1.59564228, -0.58562172])
-    >>> results.t() #doctest: +FP_6DP
+    >>> results.t() #doctest: +NP_ALLCLOSE
     array([ 38.0890515 ,  -3.45429252])
     >>> print(results.Tcontrast([0,1]))  #doctest: +FP_6DP
     <T contrast: effect=-0.58562172384377043, sd=0.16953449108110835,
diff --git a/nipy/algorithms/statistics/models/utils.py b/nipy/algorithms/statistics/models/utils.py
@@ -4,11 +4,11 @@
 from __future__ import print_function
 from __future__ import absolute_import
 
+__docformat__ = 'restructuredtext'
+
 import numpy as np
 import scipy.interpolate
 
-__docformat__ = 'restructuredtext'
-
 
 def mad(a, c=0.6745, axis=0):
     """
@@ -24,22 +24,24 @@ def mad(a, c=0.6745, axis=0):
 
 
 class StepFunction(object):
-    """
-    A basic step function: values at the ends are handled in the simplest
-    way possible: everything to the left of x[0] is set to ival; everything
-    to the right of x[-1] is set to y[-1].
+    """ A basic step function
+
+    Values at the ends are handled in the simplest way possible: everything to
+    the left of ``x[0]`` is set to `ival`; everything to the right of ``x[-1]``
+    is set to ``y[-1]``.
 
     Examples
     --------
     >>> x = np.arange(20)
     >>> y = np.arange(20)
     >>> f = StepFunction(x, y)
     >>>
-    >>> print(f(3.2))
+    >>> f(3.2)
     3.0
-    >>> print(f([[3.2,4.5],[24,-3.1]]))
-    [[  3.   4.]
-     [ 19.   0.]]
+    >>> res = f([[3.2, 4.5],[24, -3.1]])
+    >>> np.all(res == [[ 3, 4],
+    ...                [19, 0]])
+    True
     """
 
     def __init__(self, x, y, ival=0., sorted=False):
diff --git a/nipy/algorithms/statistics/rft.py b/nipy/algorithms/statistics/rft.py
@@ -17,12 +17,16 @@
 from __future__ import absolute_import
 
 import numpy as np
-from numpy.linalg import pinv    
+from numpy.linalg import pinv
 
 from scipy import stats
 from scipy.misc import factorial
 from scipy.special import gamma, gammaln, beta, hermitenorm
 
+# Legacy repr printing from numpy.
+from nipy.testing import legacy_printing as setup_module  # noqa
+
+
 def binomial(n, k):
     """ Binomial coefficient
 
diff --git a/nipy/core/image/image.py b/nipy/core/image/image.py
@@ -27,6 +27,9 @@
                                        input_axis_index)
 from ..reference.array_coords import ArrayCoordMap
 
+# Legacy repr printing from numpy.
+from nipy.testing import legacy_printing as setup_module  # noqa
+
 
 class Image(object):
     """ The `Image` class provides the core object type used in nipy.
diff --git a/nipy/core/image/image_spaces.py b/nipy/core/image/image_spaces.py
@@ -80,6 +80,9 @@
 from ..reference import spaces as rsp
 from ..reference.coordinate_map import AffineTransform
 
+# Legacy repr printing from numpy.
+from nipy.testing import legacy_printing as setup_module  # noqa
+
 
 def xyz_affine(img, name2xyz=None):
     """ Return xyz affine from image `img` if possible, or raise error
diff --git a/nipy/core/reference/array_coords.py b/nipy/core/reference/array_coords.py
@@ -24,6 +24,9 @@
 from .coordinate_map import shifted_range_origin
 from .coordinate_system import CoordinateSystem
 
+# Legacy repr printing from numpy.
+from nipy.testing import legacy_printing as setup_module  # noqa
+
 
 class ArrayCoordMap(object):
     """ Class combining coordinate map and array shape
@@ -187,6 +190,7 @@ def __repr__(self):
         return "ArrayCoordMap(\n  coordmap=" + \
             '\n  '.join(repr(self.coordmap).split('\n')) + ',\n  shape=%s' % repr(self.shape) + '\n)'
 
+
 def _slice(coordmap, shape, *slices):
     """
     Slice a 'voxel' CoordinateMap's function_domain with slices. A
@@ -264,7 +268,6 @@ def _slice(coordmap, shape, *slices):
     A = A.astype(function_domain.coord_dtype)
     slice_cmap = AffineTransform(function_domain, coordmap.function_domain, A)
     return ArrayCoordMap(compose(coordmap, slice_cmap), tuple(newshape))
-                   
 
 
 class Grid(object):
diff --git a/nipy/core/reference/coordinate_map.py b/nipy/core/reference/coordinate_map.py
@@ -76,6 +76,9 @@
                                product as coordsys_product
                                )
 
+# Legacy repr printing from numpy.
+from nipy.testing import legacy_printing as setup_module  # noqa
+
 # shorthand
 CS = CoordinateSystem
 
diff --git a/nipy/core/reference/spaces.py b/nipy/core/reference/spaces.py
@@ -13,6 +13,10 @@
 
 from ...externals.six import string_types
 
+# Legacy repr printing from numpy.
+from nipy.testing import legacy_printing as setup_module  # noqa
+
+
 class XYZSpace(object):
     """ Class contains logic for spaces with XYZ coordinate systems
 
diff --git a/nipy/core/reference/tests/test_coordinate_map.py b/nipy/core/reference/tests/test_coordinate_map.py
@@ -24,6 +24,8 @@
 
 from numpy.testing import (assert_array_equal, assert_almost_equal, dec)
 
+# Legacy repr printing from numpy.
+from nipy.testing import legacy_printing
 
 # Dtypes for testing coordinate map creation / processing
 _SYMPY_SAFE_DTYPES = (np.sctypes['int'] + np.sctypes['uint'] +
@@ -61,6 +63,7 @@ def g(x):
                                               [ 8,  9, 10, 11],
                                               [ 8,  9, 10, 11],
                                               [ 0,  0,  0,  1]]))
+    legacy_printing()
 
 
 def test_shift_origin():
diff --git a/nipy/core/utils/generators.py b/nipy/core/utils/generators.py
@@ -23,6 +23,9 @@
 
 from nipy.utils import seq_prod
 
+# Legacy repr printing from numpy.
+from nipy.testing import legacy_printing as setup_module  # noqa
+
 
 def parcels(data, labels=None, exclude=()):
     """ Return a generator for ``[data == label for label in labels]``
diff --git a/nipy/externals/transforms3d/quaternions.py b/nipy/externals/transforms3d/quaternions.py
@@ -18,8 +18,12 @@
 from __future__ import absolute_import
 
 import math
+
 import numpy as np
 
+# Legacy repr printing from numpy.
+from nipy.testing import legacy_printing as setup_module  # noqa
+
 _MAX_FLOAT = np.maximum_sctype(np.float)
 _FLOAT_EPS = np.finfo(np.float).eps
 
diff --git a/nipy/modalities/fmri/utils.py b/nipy/modalities/fmri/utils.py
@@ -31,6 +31,9 @@
 
 from nipy.algorithms.statistics.formula.formulae import Term, Formula
 
+# Legacy repr printing from numpy.
+from nipy.testing import legacy_printing as setup_module  # noqa
+
 T = Term('t')
 
 
diff --git a/nipy/testing/__init__.py b/nipy/testing/__init__.py
@@ -26,7 +26,7 @@
 
 import os
 
-#__all__ = ['funcfile', 'anatfile']
+import numpy as np
 
 # Discover directory path
 filepath = os.path.abspath(__file__)
@@ -48,3 +48,13 @@
     from nose.tools import assert_true, assert_false
 except ImportError:
     pass
+
+
+def legacy_printing():
+    """ Set numpy print options to "legacy" for new versions of numpy
+
+    If imported into a file, nosetest will run this before any doctests.
+    """
+    from distutils.version import LooseVersion
+    if LooseVersion(np.__version__) >= LooseVersion('1.14'):
+        np.set_printoptions(legacy="1.13")

Original file line number	Diff line number	Diff line change
`@@ -76,6 +76,9 @@`
`76`	`76`	`product as coordsys_product`
`77`	`77`	`)`
`78`	`78`
	`79`	`+# Legacy repr printing from numpy.`
	`80`	`+from nipy.testing import legacy_printing as setup_module # noqa`
	`81`	`+`
`79`	`82`	`# shorthand`
`80`	`83`	`CS = CoordinateSystem`
`81`	`84`